Anti-defense system polypeptides and uses thereof

Abstract

Provided are anti defense proteins, viruses comprising same as well as methods of producing and using such proteins and viruses. Also provided are methods of identifying putative anti-defense system polypeptides.

Description

[0001] ANTI-DEFENSE SYSTEM POLYPEPTIDES AND USES THEREOF

[0002] RELATED APPLICATION / S

[0003] This application claims the benefit of priority of U.S. Provisional Patent Application No. 63 / 575,883 filed on 8 April 2024 and Israel Patent Application No. 317215 filed 24 November 2024, the contents of which are incorporated herein by reference in their entirety.

[0004] SEQUENCE LISTING STATEMENT

[0005] The XML file, entitled 103239 Sequence Listing.XML, created on 3 April 2025, comprising 13,152,256 bytes, submitted concurrently with the filing of this application is incorporated herein by reference.

[0006] FIELD AND BACKGROUND OF THE INVENTION

[0007] The present invention, in some embodiments thereof, relates to anti-defense system polypeptides and uses thereof.

[0008] The ongoing arms race between prokaryotes and the viruses that infect them, bacteriophages (phages), has led to the continuous and intensive evolution of efficient resistance systems to protect prokaryotes from phage infection. Bacteria employ a highly diverse set of defense systems to resist phage infections1 5, some of which are the ancestors of innate immune pathways in animals and plants6 1 1. Phages, in return, evolved diverse anti-defense proteins to overcome bacterial defenses12 l4. Phage proteins were demonstrated to inhibit immunity by binding immune complexes15 20, by sequestering or cleaving immune signaling molecules21 26, by enzymatically modifying immune proteins27 29, and via additional mechanisms13,14.

[0009] Harnessing phages and their defense mechanisms as anti-bacterial agents for therapeutic uses has gained much interest over the last decade, especially in light of the substantial rise in the prevalence of bacterial antibiotic resistance, coupled with an inadequate number of new antibiotics (see e.g. Gibb et al. Pharmaceuticals 2021, 14, 634).

[0010] Nonetheless, current phage sequence databases contain millions of phage genomes, and in most of these sequenced genomes, the majority of genes are of unknown function30 32. Even in model phages such as T4, T5 and T7, that have been extensively studied for many decades, the functions of 30-60 % of the genes remain obscure33 35. It was recently estimated that many of these genes may serve to inhibit bacterial defenses1,13,36, but there is currently no robust screening methodology for prediction anti defense phage genes inhibits and their cognate bacterial system. Additional background art includes International Application Publication Nos. WO20 15 / 059690, WO2018142416, WO2018 / 220616, W02023 / 100189 and W02023 / 209708.

[0011] SUMMARY OF THE INVENTION

[0012] According to an aspect of some embodiments of the present invention there is provided avirus comprising an exogenous polynucleotide encoding an anti-defense system polypeptide, wherein the anti-defense system polypeptide is selected from the group consisting of:

[0013] (i) a Tad3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594-11520 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594- 11520, wherein the Tad3 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;

[0014] (ii) a Tad4 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766, wherein the Tad4 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;

[0015] (iii) a Tad5 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849, wherein the Tad5 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;

[0016] (iv) a Tad6 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888, wherein the Tad7 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;

[0017] (v) a Tad7 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918, wherein the Tad7 polypeptide binds the defense system polypeptide ThsB of a Type II Thoeris set forth in SEQ ID NO: 228;

[0018] (vi) a Tad8 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290, wherein the Tad8 polypeptide binds the defense system polypeptide ThsA of a Type II Thoeris set forth in SEQ ID NO: 227; and

[0019] (vii) an Acb3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593, wherein the Acb3 polypeptide binds the bacterial defense system polypeptide cGAS of a CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233.

[0020] According to some embodiments of the invention, the virus having an increased infectivity to at least one cell as compared to a virus of the same species not comprising the exogenous polynucleotide.

[0021] According to an aspect of some embodiments of the present invention there is provided a cell comprising an exogenous anti-defense system polypeptide or a polynucleotide encoding same, wherein the anti-defense system polypeptide is selected from the group consisting of:

[0022] (i) a Tad3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594-11520 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594- 11520, wherein the Tad3 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;

[0023] (ii) a Tad4 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766, wherein the Tad4 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;

[0024] (iii) a Tad5 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849, wherein the Tad5 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;

[0025] (iv) a Tad6 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888, wherein the Tad7 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;

[0026] (v) a Tad7 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918, wherein the Tad7 polypeptide binds the defense system polypeptide ThsB of a Type II Thoeris set forth in SEQ ID NO: 228;

[0027] (vi) a Tad8 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290, wherein the Tad8 polypeptide binds the defense system polypeptide ThsA of a Type II Thoeris set forth in SEQ ID NO: 227; and

[0028] (vii) an Acb3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593, wherein the Acb3 polypeptide binds the bacterial defense system polypeptide cGAS of CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233.

[0029] According to an aspect of some embodiments of the present invention there is provided a nucleic acid construct comprising a polynucleotide encoding an anti-defense polypeptide selected from the group consisting of:

[0030] (i) a Tad3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594-11520 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594- 11520, wherein the Tad3 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;

[0031] (ii) a Tad4 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766, wherein the Tad4 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;

[0032] (iii) a Tad5 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849, wherein the Tad5 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10; (iv) a Tad6 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888, wherein the Tad7 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;

[0033] (v) a Tad7 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918, wherein the Tad7 polypeptide binds the defense system polypeptide ThsB of a Type II Thoeris set forth in SEQ ID NO: 228;

[0034] (vi) a Tad8 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290, wherein the Tad8 polypeptide binds the defense system polypeptide ThsA of a Type II Thoeris set forth in SEQ ID NO: 227; and

[0035] (vii) an Acb3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593, wherein the Acb3 polypeptide binds the bacterial defense system polypeptide cGAS of a CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233; and a nucleic acid sequence heterologous to the polynucleotide which facilitates expression of the polynucleotide in a cell, integration of the polynucleotide in a genome of a virus or a cell, and / or selection or detection.

[0036] According to some embodiments of the invention, the nucleic acid sequence heterologous to the polynucleotide is selected from the group consisting of: a promoter, a recombination element, an element for expression of multiple polynucleotides from a single construct, a transmissible element and a selectable marker.

[0037] According to an aspect of some embodiments of the present invention there is provided a method of producing the virus, the method comprising introducing into a virus the exogenous polynucleotide encoding the anti-defense system polypeptide, thereby producing the virus.

[0038] According to some embodiments of the invention, the method comprises introducing into the virus the nucleic acid construct, under conditions which allow integration of the polynucleotide in a genome of the virus.

[0039] According to some embodiments of the invention, the virus does not endogenously comprise the polynucleotide encoding the anti-defense system polypeptide.

[0040] According to an aspect of some embodiments of the present invention there is provided a method of infecting a cell, the method comprising contacting the cell with the virus.

[0041] According to an aspect of some embodiments of the present invention there is provided a method of producing the cell, the method comprising introducing into a cell the anti-defense system polypeptide or the polynucleotide encoding same, thereby producing the cell.

[0042] According to an aspect of some embodiments of the present invention there is provided a method of impairing ability of a cell to respond to stress, the method comprising introducing into the cell an anti-defense system polypeptide or a polynucleotide encoding same, wherein the antidefense system polypeptide is selected from the group consisting of:

[0043] (i) a Tad3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594-11520 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594- 11520, wherein the Tad3 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;

[0044] (ii) a Tad4 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766, wherein the Tad4 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10; (iii) a Tad5 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849, wherein the Tad5 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;

[0045] (iv) a Tad6 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888, wherein the Tad7 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;

[0046] (v) a Tad7 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918, wherein the Tad7 polypeptide binds the defense system polypeptide ThsB of a Type II Thoeris set forth in SEQ ID NO: 228;

[0047] (vi) a Tad8 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290, wherein the Tad8 polypeptide binds the defense system polypeptide ThsA of a Type II Thoeris set forth in SEQ ID NO: 227; and

[0048] (vii) an Acb3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593, wherein the Acb3 polypeptide binds the bacterial defense system polypeptide cGAS of a CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233, thereby impairing ability of a cell to respond to stress.

[0049] According to some embodiments of the invention, the stress comprises a viral infection.

[0050] According to some embodiments of the invention, the method comprises introducing into the cell the nucleic acid construct, under conditions which allow expression of the anti-defense polypeptide in the cell.

[0051] According to some embodiments of the invention, the cell is a prokaryotic cell.

[0052] According to some embodiments of the invention, the virus is a phage.

[0053] According to some embodiments of the invention, the cell is a eukaryotic cell.

[0054] According to some embodiments of the invention, the eukaryotic cell is a plant cell.

[0055] According to some embodiments of the invention, the eukaryotic cell is a human cell.

[0056] According to some embodiments of the invention, the cell expresses the defense system polypeptide or a homolog thereof.

[0057] According to some embodiments of the invention, the cell further comprises an exogenous polynucleotide of interest.

[0058] According to some embodiments of the invention, the method further comprising introducing into the cell an exogenous polynucleotide of interest.

[0059] According to some embodiments of the invention, the method being effected in-vitro or ex-vivo.

[0060] According to some embodiments of the invention, the method being effected in-vivo.

[0061] According to an aspect of some embodiments of the present invention there is provided a method of treating a bacterial infection in a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of the phage comprising the exogenous polynucleotide encoding the anti-defense system polypeptide, thereby treating the bacterial infection in the subject.

[0062] According to some embodiments of the invention, the method comprising administering to the subject a therapeutically effective amount of an antibiotic.

[0063] According to an aspect of some embodiments of the present invention there is provided an article of manufacture comprising as active ingredients the phage comprising the exogenous polynucleotide encoding the anti-defense system polypeptide; and an antibiotic.

[0064] According to an aspect of some embodiments of the present invention there is provided a method of improving resistance of a plant to biotic stress, the method comprising introducing into the plant an anti-defense system polypeptide or a polynucleotide encoding same, wherein the anti-defense system polypeptide is selected from the group consisting of:

[0065] (i) a Tad3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594-11520 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594- 11520, wherein the Tad3 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 endogenously expressed in the plant;

[0066] (ii) a Tad4 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766, wherein the Tad4 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 endogenously expressed in the plant;

[0067] (iii) a Tad5 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849, wherein the Tad5 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 endogenously expressed in the plant;

[0068] (iv) a Tad6 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888, wherein the Tad7 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 endogenously expressed in the plant;

[0069] (v) a Tad7 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918, wherein the Tad7 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 228 endogenously expressed in the plant;

[0070] (vi) a Tad8 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290, wherein the Tad8 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 227 endogenously expressed in the plant; and

[0071] (vii) an Acb3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593, wherein the Acb3 polypeptide binds a homolog of the bacterial defense system polypeptide cGAS of a CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233 endogenously expressed in the plant, thereby improving resistance of the plant to biotic stress.

[0072] According to an aspect of some embodiments of the present invention there is provided a method of treating a disease that can benefit from inhibiting a defense system polypeptide in a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of an anti-defense system polypeptide or a polynucleotide encoding same, wherein: when the defense system polypeptide is a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 endogenously expressed in the subject, the anti-defense system polypeptide is a Tad3 polypeptide, a Tad4 polypeptide, a Tad5 polypeptide and / or a Tad6 polypeptide which binds the homolog of SEQ ID NO: 10; when the defense system polypeptide is a homolog of the defense system polypeptide ThsB of a Type II Thoeris set forth in SEQ ID NO: 228 endogenously expressed in the subject, the anti-defense system polypeptide is a Tad7 polypeptide which binds the homolog of SEQ ID NO: 228; when the defense system polypeptide is a homolog of the defense system polypeptide

[0073] ThsA of a Type II Thoeris set forth in SEQ ID NO: 227 endogenously expressed in the subject, the anti-defense system polypeptide is a Tad8 polypeptide which binds the homolog of SEQ ID

[0074] NO: 227; and / or when the defense system polypeptide is a homolog of the defense system polypeptide cGAS of CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233 endogenously expressed in the subject, the anti-defense system polypeptide is an Acb3 polypeptide which binds the homolog of amino acid sequence selected from the group consisting of SEQ ID NO: 229-231 and 233; wherein:

[0075] (i) the Tad3 polypeptide has a sequence similarity defined by an e- value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594-11520 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594- 11520;

[0076] (ii) the Tad4 polypeptide has a sequence similarity defined by an e- value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766;

[0077] (iii) the Tad5 polypeptide has a sequence similarity defined by an e- value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849;

[0078] (iv) the Tad6 polypeptide has a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888;

[0079] (v) the Tad7 polypeptide has a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918;

[0080] (vi) the Tad8 polypeptide has a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290; and

[0081] (vii) the Acb3 polypeptide has a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593, thereby treating the disease in the subject.

[0082] According to some embodiments of the invention, the disease is selected from the group consisting of autoimmune disease, interferonopathy and a disease associated with neuronal degeneration.

[0083] According to some embodiments of the invention, the Tad3 polypeptide, Tad4 polypeptide, Tad5 polypeptide, Tad6 polypeptide, Tad7 polypeptide, Tad8 polypeptide and / or Acb3 polypeptide inhibits activity of the defense system polypeptide.

[0084] According to some embodiments of the invention, the Tad3 polypeptide and / or Tad8 polypeptide is capable of forming a homodimer.

[0085] According to some embodiments of the invention, the Tad3 polypeptide and / or Tad8 polypeptide binds as a homodimer two monomers of the defense system polypeptide.

[0086] According to some embodiments of the invention, expression of the Tad3 polypeptide, Tad4 polypeptide, Tad5 polypeptide and / or Tad6 polypeptide in a B. subtilis BEST7003 comprising SEQ ID NO: 1 increases sensitivity of the B. subtilis BEST7003 to infection by a B. subtilis phage SBSphiJ.

[0087] According to some embodiments of the invention, expression of the Tad7 polypeptide and / or Tad8 polypeptide in a B. subtilis BEST7003 comprising SEQ ID NO: 2 increases sensitivity of the B. subtilis BEST7003 to infection by a B. subtilis phage SBSphiJ. According to some embodiments of the invention, expression of the Acb3 polypeptide in a E. coil MG1655 comprising SEQ ID NO: 4 increases sensitivity of the E. coll MG1655 to infection by an E. coll phage BAS 18.

[0088] According to some embodiments of the invention, expression of the Acb3 polypeptide in a B. subtilis BEST7003 comprising SEQ ID NO: 3 increases sensitivity of the B. subtilis BEST7003 to infection by a B. subtilis phage SBSphiC.

[0089] According to some embodiments of the invention, the Tad4 polypeptide binds and / or inhibits activity of plant Brachypodium distachyon (BdTIR) set forth SEQ ID NO: 8.

[0090] According to some embodiments of the invention, the Tad3 polypeptide and / or Tad4 polypeptide binds and / or inhibits activity of SARM1TIR set forth SEQ ID NO: 6.

[0091] According to some embodiments of the invention, the Acb3 polypeptide binds and / or inhibits activity of human cGAS of a CBASS set forth SEQ ID NO: 12291.

[0092] According to some embodiments of the invention, the anti-defense polypeptide comprises the SEQ ID NO.

[0093] According to some embodiments of the invention, the amino acid sequence of the Tad3 polypeptide comprises the SEQ ID NO: 58; the amino acid sequence of the Tad4 polypeptide comprises the SEQ ID NO: 66; the amino acid sequence of the Tad5 polypeptide comprises the SEQ ID NO: 59; the amino acid sequence of the Tad6 polypeptide comprises the SEQ ID NO: 65; the amino acid sequence of the Tad7 polypeptide comprises the SEQ ID NO: 239; the amino acid sequence of the Tad8 polypeptide comprises the SEQ ID NO: 240; and / or the amino acid sequence of the Acb3 polypeptide comprises the SEQ ID NO: 244.

[0094] According to an aspect of some embodiments of the present invention there is provided a method of identifying a putative anti-defense system polypeptide, the method comprising:

[0095] (i) clustering a dataset comprising more than 1000 viral proteins based on sequence and / or structural similarity, to thereby obtain multiple clusters;

[0096] (ii) in-silico modeling an interaction between a single viral protein of a cluster of the multiple clusters and the defense system polypeptide, to thereby select a viral protein having a predicted co-folding confidence score with the defense system polypeptide above a predetermined threshold;

[0097] (iii) in-silico modeling an interaction between at least one additional viral protein of the cluster of the selected protein having the predicted co-folding confidence score above the predetermined threshold, to thereby select a cluster having a predetermined number of viral proteins having predicted co-folding confidence scores with the defense system polypeptide above the predetermined threshold, wherein a protein of the selected cluster having the viral proteins having the predicted cofolding confidence scores above the predetermined threshold being putative anti-defense system polypeptide.

[0098] According to some embodiments of the invention, the method comprises in-silico modelling a three dimensional structure of the single viral protein of the cluster prior to the (ii), and proceeding to step (ii) with a viral protein having a predicted structural confidence score above a predetermined threshold.

[0099] According to some embodiments of the invention, when the viral protein is predicted to be a homodimer in the three dimensional structure modelling, the (ii) is effected on a homodimer conformation.

[0100] According to some embodiments of the invention, the method comprising selecting only viral proteins with an unknown function prior to the (iii).

[0101] According to some embodiments of the invention, the method comprising selecting only viral proteins having a length ≤200 amino acids prior to the (iii).

[0102] According to some embodiments of the invention, the method comprising determining an amount of amino acid residues in the selected viral protein having the predicted co-folding confidence score above the predetermined threshold interacting with the defense system polypeptide, to thereby select a viral protein having at least 20 interacting residues with the defense system polypeptide.

[0103] According to some embodiments of the invention, the method further comprising in-vitro or in-vivo determining a functional activity of the putative anti-defense system polypeptide following the (iii).

[0104] According to some embodiments of the invention, the sequence similarity is defined by an e-value ≤ 0.05.

[0105] According to some embodiments of the invention, the e-value ≤ 0.01.

[0106] According to some embodiments of the invention, the e-value ≤0.001.

[0107] According to some embodiments of the invention, the wherein sequence similarity is defined by an alignment length covering at least 80 % of the aligned viral proteins sequences.

[0108] According to some embodiments of the invention, the structural similarity is defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms.

[0109] According to some embodiments of the invention, the defense system is a prokaryotic defense system.

[0110] According to some embodiments of the invention, the defense system is a eukaryotic defense system. According to some embodiments of the invention, the viral proteins are phage proteins.

[0111] Unless otherwise defined, all technical and / or scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the invention, exemplary methods and / or materials are described below. In case of conflict, the patent specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be necessarily limiting.

[0112] BRIEF DESCRIPTION OF THE DRAWINGS

[0113] Some embodiments of the invention are herein described, by way of example only, with reference to the accompanying drawings. With specific reference now to the drawings in detail, it is stressed that the particulars shown are by way of example and for purposes of illustrative discussion of embodiments of the invention. In this regard, the description taken with the drawings makes apparent to those skilled in the art how embodiments of the invention may be practiced.

[0114] In the drawings:

[0115] FIGs. 1A-F show structure-guided discovery of protein inhibitors of type I Thoeris. Figure 1A is a schematic representation of clustering the phage protein space and establishing a database of phage clusters representing short proteins of unknown function. Figure IB is a schematic representation of an iterative pipeline for the prediction of interactions between a bacterial immune protein and phage proteins. High-scoring interactions based on a single AlphaFold2-Multimer model are further examined via multiple models. Figure 1C is a graph demonstrating the anti-defense activity of the indicated anti-Thoeris candidates. Data represent plaque-forming units per milliliter (PFU / ml) of phage SBSphiJ infecting control cells (no system), cells expressing the Thoeris system (Thoeris) and cells co-expressing the Thoeris system and each of the anti-Thoeris candidates. Shown is the average of three replicates, with individual data points overlaid. Figure ID is a schematic representation of the mechanism of the Thoeris defense system. Figure IE is a graph demonstrating that the anti-defense proteins referred to herein as “Tad3”, “Tad4”, “Tad5” and “Tad6” inhibit ThsB. Cells expressing ThsB, coexpressing ThsB and each of the anti-Thoeris proteins, or control cells that do not express ThsB, were infected with phage SBSphiJ at a multiplicity of infection (MOI) of 10. Lysates from infected cells were extracted and filtered, and NADase activity of purified ThsA incubated with filtered lysates was measured using a nicotinamide l,N6-ethenoadenine dinucleotide (sNAD) cleavage fluorescence assay. Bars represent the mean of three experiments, with individual data points overlaid. Figure IF is an SDS-PAGE image demonstrating that the Tad3, Tad4, Tad5 and Tad6 anti-defense proteins bind ThsB. Pulldown of a 6xHis-SUMO2-tagged ThsB protein coexpressed with Tad3, Tad4 Tad5 or Tad6 retrieves the respective anti-Thoeris protein.

[0116] FIGs. 2A-B demonstrate that the Tad3, Tad4, Tad5 and Tad6 anti-defense proteins bind ThsB. Figure 2A is a graph demonstrating that knock-in of Tad.3 in phage SBSphiJ renders the phage resistant to Thoeris type I. Data represent plaque-forming units per milliliter (PFU / ml) of phages infecting control cells (no defense system) and cells expressing the Thoeris defense system. Shown is the average of three replicates, with individual data points overlaid. Figure 2B shows the predicted complex structures of ThsB bound to each one of the anti-Thoeris proteins Tad3, Tad4, Tad5 and Tad6. ThsB is presented in the same orientation, with the active site frontfacing, in all cases.

[0117] FIGs. 3A-C shows comparison between in-vitro verified inhibitors to non-verified candidates. Figure 3A shows that homologs of in-vitro verified Thoeris inhibitors are also predicted to bind ThsB when analyzed via AlphaFold2-Multimer, but homologs of most of the in-vitro non-verified candidates are not. For each of the 16 proteins tested as candidate anti- Thoeris inhibitors, 10 homologs ranging in sequence identity between 25 % and 95 % were analyzed by AlphaFold2-Multimer. Presented are the AlphaFold2-Multimer model confidence scores for protein-protein interactions of each homolog when co-folded with the respective immune protein. Scores are the averages of 25 co-folding predictions. Sequence homology between each candidate and its 10 homologs is presented in a white to blue scale. Figures 3B-C show depiction of ThsB surfaces predicted to interact with each of the anti-Thoeris proteins (Figure 3B) or with a false-positive candidate anti-Thoeris proteins that did not inhibit Thoeris when tested experimentally (Figure 3C). Surface on ThsB predicted to interact with the respected anti-defense protein is marked in green. Structure of ThsB differs between models, as binding of the anti-Thoeris protein sometimes affects the predicted ThsB structure.

[0118] FIGs. 4A-I show an improved computational pipeline for predicting phage-encoded inhibitors of bacterial immune proteins. Figure 4 A is a schematic representation of the modified computational pipeline which takes into account co-folding of protein homologs. Figure 4B is a graph demonstrating the anti-defense activity of the anti-Thoeris type II candidates referred to herein as “Tad7” and “Tad8”. Data represent plaque-forming units per milliliter (PFU / ml) of phage SBSphiJ infecting control cells (no defense system), cells expressing type II Thoeris system and cells co-expressing type II Thoeris and each of the indicated anti-Thoeris candidates. Figure 4C shows the structure of the AlphaFold2-Multimer predicted complex formed between Tad7 (red) and ThsB (dark green). Figure 4D is a zoom in on the Tad7-ThsB complex, showing a detailed view of how the active site of ThsB is blocked by a loop of Tad7. E99 is the catalytic residue of the type II ThsB. Figure 4E shows the structure of the AlphaFold2-Multimer predicted complex formed by a Tad8 homodimer (shades of red) binding to ThsA (dark green). Figure 4F shows a detailed view of the Macro domain pocket of ThsA blocked by Tad8. Residues in the Macro domain that also interact with His-ADPR are indicated. Figure 4G shows a detailed view of the Macro domain pocket in complex with the His-ADPR immune signal40, showing that His-ADPR occupies the same pocket that is blocked by Tad8. Figure 4H is a graph demonstrating the anti-defense activity of the anti-CBASS type III candidate referred to herein as “Acb3”. Data represent plaque-forming units per milliliter (PFU / ml) of phage Bas 18 infecting control cells (no defense system), cells expressing the type III CBASS system from E. coli KTE188, and cells co-expressing type III CBASS and Acb3. Figure 41 shows the structure of the AlphaFold2-Multimer predicted complex formed between Acb3 (red) and the CD-NTase enzyme of the E. coli KTE188 CBASS (green). D73 and D75 are two catalytic residues required for 2'3'-cGAMP production41. Bar graph data shown in Figure 4B and 4H are the average of three replicates, with individual data points overlaid.

[0119] FIGs. 5A-E demonstrate that phage-derived anti-defense proteins bind and inhibit human and plant immune proteins. Figure 5A is an SDS-PAGE image showing pulldown of a 6xHis- SUMO2-tagged BdTIR co-expressed with Tad4, demonstrating that these proteins co-elute together. Figure 5B is a graph demonstrating NADase activity of purified ThsA incubated with filtered lysates derived from cells expressing BdTIR alone, BdTIR together with Tad4, or control cells that do not express BdTIR. NADase activity was measured using a nicotinamide 1,N6- ethenoadenine dinucleotide (sNAD) cleavage fluorescence assay. Bars represent the mean of five experiments, with individual data points overlaid. Figure 5C is an SDS-PAGE image showing pulldown of a His-tagged TIR domain of the human SARM1 protein (SARMITIR) that was co-expressed with Tad4, demonstrating physical interactions. Figure 5D is a graph demonstrating NAD+levels in filtered lysates derived from cells expressing IISARMITIR, cells co-expressing IISARMITIR and Tad4, or control cells that do not express IISARMITIR. Bars represent the mean of five experiments, with individual data points overlaid. Figure 5E is a graph demonstrating that co-expression of Acb3 with the human cGAS prevents 2'3'-cGAMP production. Lysates were analyzed by LC-MS. The y axis represents the area under the curve (AUC) of 2'3'-cGAMP ions detected in MS analysis. FIG. 6 shows multiple sequence alignment of Tad3 anti-Thoeris proteins. Alignment was generated using 10 randomly selected homologous sequences of each anti-Thoeris protein. Conserved residues are colored in purple. Red boxes indicate residues that comprise a loop that blocks the ThsB pocket. Positions in the alignments not occupied in the verified anti-Thoeris protein sequences are not shown.

[0120] FIGs. 7A-B show multiple sequence alignment of anti-Thoeris proteinsTad4 (Figure 7 A) and Tad6 (Figure 7B). Alignment was generated using 10 randomly selected homologous sequences of each anti-Thoeris protein. Conserved residues are colored in purple. Red boxes indicate residues that comprise a loop that blocks the ThsB pocket. Positions in the alignments not occupied in the verified anti-Thoeris protein sequences are not shown.

[0121] FIG. 8 is a graph demonstrating that substitutions in the loops predicted to block the ThsB pocket impact anti-Thoeris function. Data represents plaque-forming units per ml (PFU / ml) of phage SBSphiJ infecting cells co-expressing the Thoeris system and a WT or mutated anti-Thoeris protein (SEQ ID NOs: 58, 12292 and 12293 for WT and mutated Tad3, SEQ ID NOs: 66, 12294 and 12295 for WT and mutated Tad4 and SEQ ID NOs: 65, 12296 and 12297 for WT and mutated Tad6), as well as control cells expressing no defense system and cells expressing the Thoeris system alone (“type I Thoeris”). Shown is the average of three replicates, with individual datapoints overlaid. Data for type I Thoeris and the WT anti-defense proteins are the same as those presented in Figure 1C.

[0122] FIG. 9 shows a structural comparison between the ThsB proteins of type I and of type II Thoeris systems.

[0123] FIG. 10 demonstrates that Type I Thoeris inhibitors Tad3, Tad4 and Tad6 do not inhibit type II Thoeris. Data represents plaque-forming units per ml (PFU / ml) of phage SBSphiJ infecting cells co-expressing the type II Thoeris system and a type I Thoeris inhibitor, as well as control cells expressing no defense system and cells expressing the type II Thoeris system alone (“type II Thoeris”). Shown is the average of three replicates, with individual data points overlaid.

[0124] FIGs. 11A-B show that Acb3 is predicted to bind diverse CD-NTase enzymes. Figure 11A is an overview of the predicted complex between Acb3 and the CD-NTase of the E. coli KTE188 CBASS (SEQ ID NO: 229). Acb3 surface electrostatics are shown to highlight the hydrophobic patch that covers the CD-NTase ligand binding groove. Figure 11B shows that predicted complexes formed between Acb3 (red) and four bacterial CD-NTase enzymes (green, SEQ ID NOs: 230, 231, 234 and 233). AlphaFold2-Multimer model co-folding confidence scores are indicated above the models. FIG. 12 demonstrates that Acb3 inhibits type I CBASS from B. cereus VD146. Data represent plaque-forming units per ml (PFU / ml) of phage SBSphiC infecting cells co-expressing the type I CBASS system and Acb3, as well as control cells expressing no defense system and cells expressing the type I CBASS system alone (“type I CBASS”). Shown is the average of three replicates, with individual datapoints overlaid.

[0125] FIGs. 13A-D demonstrate that phage-derived anti-defense proteins (red / orange) are predicted to bind eukaryotic immune proteins (green). Predicted complexes formed between BdTIR and Tad4 (Figure 13 A), the TIR domain of SARM1 and Tad3 (Figure 13B), the TIR domain of SARM1 and Tad4 (Figure 13C), and cGAS and Acb3 (Figure 13D). AlphaFold2- Multimer model co-folding confidence scores are indicated above the models.

[0126] DESCRIPTION OF SPECIFIC EMBODIMENTS OF THE INVENTION

[0127] The present invention, in some embodiments thereof, relates to anti-defense system polypeptides and uses thereof.

[0128] Before explaining at least one embodiment of the invention in detail, it is to be understood that the invention is not necessarily limited in its application to the details set forth in the following description or exemplified by the Examples. The invention is capable of other embodiments or of being practiced or carried out in various ways.

[0129] Viruses encode numerous proteins that inhibit host defenses (e.g. anti-phage bacterial defense systems). Properly formulated and applied viruses (e.g. phages) or their defense mechanisms have vast scientific, biotechnological and clinical potential. Nonetheless, current viral sequence databases contain millions of viral genomes wherein the vast majority of the viral protein universe comprises proteins of unknown function. Thus, sifting through the millions of the available viral proteins for anti-defense system proteins was so far impractical.

[0130] Whilst conceiving embodiments of the invention, the present inventors have now developed a computational pipeline that makes use of structural physical interactions predictions to identify anti-defense system proteins within large viral protein databases.

[0131] Specifically, as is illustrated hereinunder and in the examples section which follows, the present inventors developed an iterative process that utilizes AlphaFold2 -Multimer, a software that predicts physical interactions between input proteins37, combined with a dimension-reduction process and a set of reliability measures aimed to reduce computation loads to thereby systematically screen phage-encoded proteins for inhibitors that physically bind and antagonize bacterial defense system proteins (Examples 1-5 of the Examples section which follows). While AlphaFold2-Multimer notoriously yields false positive predictions, the present inventors showed that false positive rates can be substantially reduced by co-folding sets of protein homologs with the target defense system protein. Focusing on Thoeris and CBASS, two previously described bacterial defense systems that are the ancestors of eukaryotic TIR- and cGAS-mediated immunity, the present inventors discovered six families of Thoeris inhibitors (referred to herein as “Tad3”, “Tad4”, “Tad5”, “Tad6”, “Tad7” and “Tad8”) and one family of CBASS inhibitors (referred to herein as “Acb3”), encompassing thousands of genes widespread in phages. Verified inhibitors exhibit extensive physical interactions with the respective immune protein counterpart and inhibit its activity, with all inhibitors predicted to block the active site of the immune protein. Further, by cloning such inhibitors into bacterial cells that express Thoeris or CBASS bacterial defense system, or alternatively by engineering the inhibitor into the genome of a phage normally blocked by Thoeris or CBASS bacterial defense system, the present inventors show that they efficiently cancel the respective defensive activity. In addition, the inventors showed that phage- encoded inhibitors of bacterial Thoeris proteins can also bind and inhibit distantly related human and plant immune TIRs, and that the phage-derived inhibitor of bacterial CBASS can inhibit the activity of human cGAS as well (Example 6 of the Examples section which follows). These results demonstrate that phage genomes are a reservoir for immune modulatory proteins capable of inhibiting prokaryotic and eukaryotic defense systems.

[0132] Consequently, specific embodiments of the present teachings suggest methods for the discovery of viral proteins that inhibit a defense system of interest, that can further be used for various research, biotechnological, agricultural and clinical applications.

[0133] Thus, according to an aspect of the present invention, there is provided a method of identifying a putative anti-defense system polypeptide, the method comprising:

[0134] (i) clustering a dataset comprising more than 1000 viral proteins based on sequence and / or structural similarity, to thereby obtain multiple clusters;

[0135] (ii) in-silico modeling an interaction between a single viral protein of a cluster of said multiple clusters and the defense system polypeptide, to thereby select a viral protein having a predicted co-folding confidence score with said defense system polypeptide above a predetermined threshold;

[0136] (iii) in-silico modeling an interaction between at least one additional viral protein of the cluster of said selected protein having said predicted co-folding confidence score above said predetermined threshold, to thereby select a cluster having a predetermined number of viral proteins having predicted co-folding confidence scores with said defense system polypeptide above said predetermined threshold, wherein a protein of said selected cluster having said viral proteins having said predicted co-folding confidence scores above said predetermined threshold being putative anti-defense system polypeptide.

[0137] As used herein, the term “defense system” refers to a polypeptide or polypeptides expressed in a cell and having a role in a cell’s autonomous mechanism (i.e. independent of other cells e.g. immune cells) for responding to stress.

[0138] As used herein, the term “stress” refers to any condition or agent, whether physical, chemical, or biological, that challenges the optimal functioning of the cell and adversely affects the metabolism, growth, development, propagation, and / or survival of a cell.

[0139] According to specific embodiments, the stress is an abiotic stress, including but not limited to, cell damage due to injury or trauma, toxic chemical agent, lack of nutrients, extreme temperature, osmotic pressure, oxidative stress etc.

[0140] According to specific embodiments, the stress is a biotic stress, including but not limited to, viral, bacterial or fungi infection, pest infestation etc.

[0141] According to specific embodiments, the stress comprises a viral infection.

[0142] Numerous such defense systems are known in the art, and are described for example in Wein T and Sorek R. Nat Rev Immunol. (2022) Oct;22(10):629-638; Hampton, H.G. et al. Nature (2022) 577, 327-336; Doron, S. Et al. Science (2018) 359, eaar4120. 10.1126 / science.aar4120; Gao, L. Et al. Science (2020) 369, 1077-1084; Millman, A. Et al. Cell Host Microbe (2022) 30, 1556-1569.e5; Tai, N., and Sorek, R. Cell (2022) 185, 578-578.el; Morehouse, B.R. et al. Nature (2022) 586, 429-433; Ofir, G. et al. Nature (2021) 600, 116-120; Bernheim, A. Et al. Nature (2021) 589, 120-124; Johnson, A.G. et al. Science (2022) 375, 221-225; and Rousset, F. Et al. Cell (2023) 186, 3619-363 l.el3, the contents of which are fully incorporated herein by reference.

[0143] According to specific embodiments, the defense system is a eukaryotic defense system. Numerous eukaryotic defense systems are known in the art, including, but not limited to TIR, cGAS-STING, SAMHD1, Viperin, Argonaute and Gasdermin.

[0144] According to specific embodiments, the defense system is a prokaryotic defense system.

[0145] According to specific embodiments, the defense system is a bacterial defense system.

[0146] According to specific embodiments, the defense system is an anti-phage bacterial system. Numerous anti-phage bacterial defense systems are known in the art, including, but not limited to Thoeris, CBASS, Hachiman, Gabija, DSR2, Septu, Lamassu, BREX, DISARM, CRISPR-Cas, a restriction modification and toxin anti-toxin systems (see e.g. Labrie et al. Nature Reviews Microbiology 8, 317-327 (2010); Bernheim, A. & Sorek, R. Nat. Rev. Microbiol. 18, 113-119 (2020); Goldfarb et al. EMBO J. (2015) 34, 169—83; Doron, S. et al. Science 359, eaar4120 (2018);

[0147] Bernheim, A. et al. Nature 589, 120-124 (2021); Milman A et al. Cell (2020) 183(6): 1551- 1561.E12; Johnson A.G. et al. Science (2022) 375 (6577): 221-225; Tai N et al. nature Microbiology 7, 1200-1209 (2022); Tai N et al. Cell (2021) 184 (23): 5728-2739.E16; and International Application Publication Nos. WO2015 / 059690, WO2018142416, WO20I8 / 220616 and W02023 / 100189, the contents of which are fully incorporated herein by reference).

[0148] According to specific embodiments, the anti-phage bacterial defense system is not CRISPR-Cas, not a restriction modification system and / or not a toxin anti-toxin system.

[0149] According to specific embodiments, the defense system is Thoeris.

[0150] Thoeris is a prokaryotic defense system described in details in Doron, S. et al. Science 359, eaar4120 (2018); and International Application Publication Nos. WO2018 / 220616 and W02023 / 209708, the contents of which are fully incorporated herein by reference.

[0151] This system comprises two core proteins, one of which (named “ThsB”) has a Toll / interleukin-1 receptor (TIR) domain and serves as the sensor for phage infection. Recognition of phage triggers the ThsB TIR domain to produce a signaling molecule that activated a second Thoeris protein, Ths A. In some embodiments, Ths A depletes the cell of nicotinamide adenine dinucleotide (NAD+) when active, thus leading to premature cell death and abortive infection. In other embodiments, Ths A is a membrane- spanning effector that depolarizes the membrane when it becomes active. According to specific embodiments, the Thoeris is a Type I Thoeris.

[0152] In the type I Thoeris defense system (e.g. from Bacillus cereus MSX-D12, SEQ ID NOs: 10 and 9), ThsB senses phage infection and then produces l''-3' gcADPR as the signaling molecule that activates ThsA. Additional description on type I Thoeris system can be found in e.g. Leavitt A et al. (2022). Nature 611, 326-331, the contents of which are fully incorporated herein by reference.

[0153] According to specific embodiments, the Thoeris is a Type II Thoeris.

[0154] In the type II Thoeris system (e.g. from Bacillus amyloliquefaciens XI, SEQ ID NOs: 228 and 227) ThsB senses phage infection and then generates a histidine conjugated to ADPR (His-ADPR) as the signaling molecule that activated the ThsA. The ThsA effector protein of type II Thoeris encodes a Macro domain capable of binding His-ADPR, and a transmembranespanning domain that likely impairs membrane integrity once activated by the signaling molecule. Additional description on type II Thoeris system can be found in e.g. Sabonis D et al. (2024). Preprint at bioRxiv. 10.1101 / 2024.01.03.573942, the contents of which are fully incorporated herein by reference.

[0155] The Toll / interleukin-1 receptor (TIR) domain is known as a signal transducing module in immune receptors that recognize pathogen invasion in the immune systems of plants and animals as well, and thus Eukaryotic homologs of the prokaryotic Thoeris have been described in the art e.g. Wein T and Sorek R. (2022) Nat Rev Immunol. 22(10): 629-638. doi: 10.1038 / s41577-022- 00705-4, the contents of which are fully incorporated herein by reference. Non-limiting examples of such homologs include the plant Brachypodium distachyon (BdTIR, e.g. SEQ ID NO: 8 as a homolog of the bacterial ThsB) and human SARM1TIR (e.g. SEQ ID NO: 6 as a homolog of the bacterial ThsB).

[0156] According to specific embodiments, the defense system is cyclic-oligonucleotide-based anti-phage signaling system (CBASS).

[0157] CBASS is a prokaryotic defense system described in details in Cohen, D. Et al. (2019) Nature 574, 691-695; and Millman, A. et al. (2020) Nat. Microbiol. 5, 1608-1615, the contents of which are fully incorporated herein by reference.

[0158] This system comprises a Cyclic GMP-AMP synthase (cGAS)-like enzyme named cGAS / DncV-like nucleotidyltransferases (CD-NTases). During phage infection, these enzymes are activated and produce cyclic oligonucleotides that bind to and activate a downstream effector protein. The activated effector proteins are proposed to induce premature cell death through various mechanisms, including membrane impairment, DNA degradation, NAD+ depletion, etc.

[0159] CBASS operons are classified on the basis of their architecture, with type I CBASS encoding only a CD-NTase and an effector protein, and a non-Type I CBASS (e.g. types II, III and IV) encoding additional proteins with proposed regulatory roles.

[0160] According to specific embodiments, the CBASS is a non-Type I CBASS.

[0161] Non-limiting examples of non-Type I CBASS include those of Escherichia coli KTE188 (SEQ ID NO: 229), mycobacterium absessus ATCC 19977 (SEQ ID NO: 230), Escherichia coli ECOR31 (SEQ ID NO: 231) and Escherichia coli MOD1-EX1698 (SEQ ID NO: 233).

[0162] According to specific embodiments, the CBASS is a Type III CBASS. A non-limiting example of a Type III CBASS includes the one of Escherichia coli KTE188 (SEQ ID NO: 229).

[0163] According to specific embodiments, the CBASS is a Type I CBASS.

[0164] A non-limiting example of Type I includes the one of B. cereus VD146 (SEQ ID NO: 234).

[0165] Eukaryotic homologs of the prokaryotic CBASS have been described in the art, e.g. Wein T and Sorek R. (2022) Nat Rev Immunol. 22(10): 629-638. doi: 10.1038 / s41577-022-00705-4, the contents of which are fully incorporated herein by reference. For example, in mammalian cells, Cyclic GMP-AMP synthase (cGAS) binds viral DNA and is activated to produce 2’, 3’- cyclic GMP-AMP (2’,3’-cGAMP) dinucleotides, which activate the STING (stimulator of interferon genes) effector protein to initiate a potent interferon response

[0166] A non-limiting example of such homologs includes the human cGAS (e.g. SEQ ID NO: 12291).

[0167] As used herein, “anti-defense system polypeptide” refers to a polypeptide which expression in a cell disables a defense system polypeptide expressed in the cell, thereby impairing ability of the cell to respond to stress.

[0168] As used herein, the phrase “impairing an ability to respond to stress” or “impaired ability to respond to stress” refers to a significant decrease in the ability of the cell to autonomously respond to stress, as compared to a control cell of the same species not expressing the antidefense system polypeptide and under the same conditions, as may be manifested by the cell phenotype e.g. in growth arrest, death (e.g., apoptotic, necrotic), change in gene expression (secretion of cytokines etc.), sensitivity to infection by a pathogen e.g. a virus. According to specific embodiments, the decrease is by at least 5 %, at least 10%, 20 %, 30 %, 40 % or even higher say, 50 %, 60 %, 70 %, 80 %, 90 % or more than 99 %. According to specific embodiments the decrease is by at least 1.5 fold, at least 2 fold, at least 3 fold, at least 5 fold, at least 10 fold, or at least 20 fold.

[0169] According to specific embodiments, the impaired ability to respond to stress is manifested by increased sensitivity of the cell to infection by at least one virus.

[0170] As used herein, “increasing sensitivity” or “increased infectivity” refers to a significant increase in the cell susceptibility towards a virus, as compared to a cell of the same species not expressing the anti-defense system polypeptide, as may be manifested e.g. in growth arrest, death, integration of the viral nucleic acid sequence into the cell genome, prevention of lysogeny and / or viral genomic replication. According to specific embodiments, the increase is in at least 5 %, at least 10%, 20 %, 30 %, 40 % or even higher say, 50 %, 60 %, 70 %, 80 %, 90 % or more than 100 %. According to specific embodiments the increase is at least 1.5 fold, at least 2 fold, at least 3 fold, at least 5 fold, at least 10 fold, or at least 20 fold.

[0171] Assays for testing sensitivity or infectivity are well known in the art, and are also described in the Examples section which follows. Thus, for example, the lysogenic activity of a virus can be assessed by PCR or DNA sequencing. The DNA replication activity of a virus can be assessed e.g. by DNA sequencing or southern blot analysis. The lytic activity of a virus can be assessed e.g. by optical density, plaque assay or living dye indicators. For example, the lytic activity of a phage can be measured indirectly by following the decrease in optical density of the bacterial cultures owing to lysis. This method involves introduction of phage into a fluid bacterial culture medium. After a period of incubation, the phage lyses the bacteria in the broth culture resulting in clearing of the fluid medium resulting in decrease in optical density. Although less common, optical density assays can be adapted for use with eukaryotic cells. For example, methods that include redox chemistry, employing cell respiration as a universal reporter. During active growth of cells, cellular respiration reduces a dye (e.g., tetrazolium dye) leading to a color change that can be measured automatically. When a virus successfully infects its host cell and replicates, it often disrupts normal cellular processes, including growth and respiration. This viral activity results in reduced cellular respiration, which is reflected by a corresponding decrease in the intensity of the color change. Such colorimetric assays include for example the MTT assay or WST-1 assay that involves the reduction of a tetrazolium salt to a colored formazan product by metabolically active cells. The amount of color produced, which can be measured by optical density, correlates with the number of viable cells in the sample.

[0172] Another exemplary method, known as the plaque assay, in which cultured cells are infected with a diluted virus sample. After incubation, the virus causes localized cell death, resulting in clear zones called plaques. These plaques can be counted to determine the virus titer. Thus, for example, phages may be introduced into a few milliliters of soft agar along with some bacterial host cells. This soft agar mixture is laid over a hard agar base (seeded-agar overlay). The phage adsorbs onto the host bacterial cells, infect and lyse the cells, and then begin the process anew with other bacterial cells in the vicinity. After 6 - 24 hours, plaques are observable within the lawn of bacterial growth on the plate. Each plaque represents a single infective phage particle in the original sample.

[0173] Yet another exemplary method is the one-step viral (e.g. phage) growth curve which allows determining the production of progeny virions by cells as a function of time after infection. The assay is based on the fact that cells in the culture are infected simultaneously with a low number of viruses so that no cell can be infected with more than one virus. At various time intervals, samples are removed for a plaque assay allowing quantitative determination of the number of phages present in the medium.

[0174] According to specific embodiments, the cell is a bacterial cell and the defense system is an anti-phage bacterial defense system. Thus, according to specific embodiments, the anti-defense system polypeptide is a polypeptide which expression in an infected bacteria disables an anti-phage bacterial defense system, thereby increasing sensitivity of the bacteria to a phage.

[0175] According to specific embodiments, the anti-defense system polypeptide directly binds the defense system polypeptide.

[0176] Assays for testing binding include both in-silico and experimental methods (e.g. flow cytometry, western blow, immunoprecipitation, surface plasmon resonance (e.g. Biacore), biolayer interferometry Blitz® assay, HPLC and functional assays depending on the polypeptide of interest). Such methods are well known in the art, and exemplary assays for specific defense system polypeptides are also described infra and in the Examples section which follows.

[0177] According to specific embodiments, the anti-defense system polypeptide inhibits activity of the defense system polypeptide.

[0178] As used herein the term “inhibit activity” refers to a significant decrease in activity of the defense system polypeptide in the presence of the anti-defense system polypeptide, as compared to the activity in the absence of the anti-defense system polypeptide. Methods of determining activity of a target defense system polypeptide are well known in the art and depend on the specific function of the target polypeptide. Such methods include for example enzymatic assays (e.g. kinase, hydrolase, deaminase, oxidase, transferase, ligase, protease, isomerase assays etc.), expression of downstream molecules involved in the signaling cascade using e.g. PCR, Western blot, immunoprecipitation, immunohistochemistry etc.; and functional assays such as viability, proliferation, apoptosis etc. in a cell expressing the target polypeptide, expression of signaling. Exemplary assays for specific defense system polypeptides are also described infra and in the Examples section which follows. According to specific embodiments, the decrease is by at least 5 %, at least 10%, 20 %, 30 %, 40 % or even higher say, 50 %, 60 %, 70 %, 80 %, 90 % or more than 99 %. According to specific embodiments the decrease is by at least 1.5 fold, at least 2 fold, at least 3 fold, at least 5 fold, at least 10 fold, or at least 20 fold.

[0179] As noted above, viruses encode numerous proteins that inhibit defense system polypeptides. Nonetheless, current viral sequence databases contain millions of viral genomes, the vast majority of them are of unknown function. The present inventors have now developed a computational pipeline to identify such anti-defense system polypeptide within large viral protein databases.

[0180] According to specific embodiments, the method comprises clustering a dataset of viral proteins based on sequence, structure similarity or a combination of both. Any viral protein dataset known in the art can be used with specific embodiments of the invention. Non-limiting examples include the IMG / VR v3 database, the NCBI viral database (https: / / www(dot)ncbi(dot)nlm(dot)nih(dot)gov / labs / virus / vssi / # / ), the INPHARED (database of sequenced phages, https: / / pubmed(dot)ncbi(dot)nlm.nih.gov / 36159887 / ), the viral zone (https: / / viralzone(dot)expasy(dot)org / ), MGV (metagenomic gut viruses, https: / / www(dot)nature(dot)com / articles / s41564-021-00928-6) etc.

[0181] According to specific embodiments, the viral proteins are phage proteins.

[0182] According to specific embodiments, the dataset comprises more than 1000 viral proteins.

[0183] According to specific embodiments, the dataset comprises more than 5000, more than 104, more than 5xl04, more than 105, more than 5xl05, or more than 106viral proteins.

[0184] As used herein, the term “clustering” refers to the process of grouping a set of viral proteins such that the proteins within the same cluster, exhibit greater similarity in sequence and / or structure to each other than to proteins in other groups (clusters). Sequence similarity and structure similarity can be determined by methods which are well known in the art as further described herein. Clustering is a general analytical task rather than a specific algorithm, and it can be accomplished through various algorithms that differ in their definitions of what constitutes a cluster and in the methods they use to identify them. For instance, clustering can involve techniques that emphasize different aspects of similarity, such as sequence alignment or structural motifs. A non-limiting example of a clustering tool includes the one provided by MMseqs2. Specific embodiments suggest that clustering is effected based on sequence similarity, structure similarity or a combination of both.

[0185] According to specific embodiments, the clustering is based on sequence similarity.

[0186] According to specific embodiments, the sequence similarity is defined by percentage of sequence identity between the polypeptides or polynucleotides when aligned to each other. When percentage of sequence identity is used in reference to polypeptides it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g. charge or hydrophobicity) and therefore do not change the functional properties of the molecule. Where sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Means for making this adjustment are well-known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., according to the algorithm of Henikoff S and Henikoff JG. [Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U.S.A. 1992, 89(22): 10915-9].

[0187] Sequence identity can be determined using any protein or nucleic acid sequence alignment algorithm such as Mmseqs2, Blast, ClustalW, MUSCLE, HHpred and Needleman- Wunsch.

[0188] In some embodiments, the sequence alignment program is a basic local alignment program, e.g., BLAST.

[0189] According to some embodiments of the invention, the identity is a global identity, i.e., an identity over the entire sequences aligned and not over portions thereof.

[0190] According to specific embodiments, the sequence alignment program is Mmseqs2 (which can do both local alignment or global alignment).

[0191] According to specific embodiments, sequence similarity is defined by an alignment length covering at least 50 %, at least 60 %, at least 70 %, at least 80 % or at least 90 % of the aligned sequences.

[0192] According to specific embodiments, sequence similarity is defined by an alignment length covering at least 80 % of the aligned sequences.

[0193] According to specific embodiments, sequence similarity is defined by at least 20 % identity between the aligned sequences.

[0194] According to specific embodiments, the at least 20 % identity comprises at least 25 %, at least 30 %, at least 35%, at least 40 %, at least 45 %, at least 50 %, at least 60 %, at least 65 %, at least 70 %, at least 75 %, at least 80 %, at least 85 %, at least 90 %, at least 91 %, at least 92 %, at least 93 %, at least 94 %, at least 95 %, at least 96 %, at least 97 %, at least 98 %, or at least 99 % or 100 % identity.

[0195] According to specific embodiments, the sequence similarity is defined by an e- value.

[0196] As used herein, “e-value” refers to a parameter that describes the number of hits one can expect to see by chance in a sequence alignment search to the recited sequence using a database of a particular size. It decreases exponentially as the Score (S) of the match increases. Essentially, the e-value describes the random background noise. An e-value of 1 assigned to a hit can be interpreted as meaning that in a database of the current size one might expect to see 1 match with a similar score simply by chance.

[0197] According to specific embodiments, the e-value represents a statistically significant similarity between the sequences.

[0198] Thus, according to specific embodiments, the e-value is ≤ 0.05. According to specific embodiments, the e-value is ≤ 0.01, ≤ 0.001 or ≤ 0.0001.

[0199] According to specific embodiments, the clustering is based on structural similarity.

[0200] As used herein, “structural similarity” or “structure similarity” refers to the extent to which the three-dimensional (3D) shapes of two or more proteins resemble each other. This similarity can be assessed by comparing the spatial arrangement of the protein's secondary structure (such as alpha-helices, beta-sheets), the overall folding pattern (tertiary structure) and / or quaternary structure. According to specific embodiments, the structure similarity is determined using computational tools that align protein structures and calculate the degree of similarity, such as root-mean-square deviation (RMSD) of atomic positions or other structural alignment metrics. Commercial computations tools for computing RMSD are known in the art and include for example Dali, PDBeFOLD, PyMOL, FoldSeek.

[0201] Typically an RMSD >5 angstroms indicates a low structural similarity, 2 angstroms < RMSD < 2 angstroms indicates a moderate similarity, and RMSD ≤ 2.0 angstroms indicates high similarity.

[0202] According to specific embodiments, the structure similarity is defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms.

[0203] According to specific embodiments, the structure similarity is defined by a Root Mean Square Deviation (RMSD) ≤1.5 angstroms.

[0204] According to specific embodiments, the structure similarity is defined by a Root Mean Square Deviation (RMSD) ≤ 1 angstroms.

[0205] Once multiple clusters have been obtained, the method comprises in-silico modeling an interaction between a single viral protein of a cluster and the defense system polypeptide of interest.

[0206] Selection of the single viral protein of the cluster may be effected either randomly of systematically.

[0207] According to specific embodiments, the clustering is effected such that there is a representative sequence (“center” of the cluster) that is significantly similar in sequence and / or structure to each member in the cluster. In this case, according to specific embodiments, the selected viral protein is the one in the center of the cluster (in other words, the closes member to all the sequences in the cluster).

[0208] “Modeling of an interaction between a viral protein and a defense system polypeptide” refers to in-silico predicting formation of a protein complex comprising both the viral protein and the defense system polypeptide. Such prediction can be effected by any method known in the art, such as, but not limited to AlphaFold-Multimer. According to specific embodiments, the method comprises proceeding to the following step only with a viral protein having a predicted co-folding confidence score with the defense system polypeptide above a predetermined threshold.

[0209] As used herein, the phrase “predicted co-folding confidence score above a predetermined threshold” refers to a score that signifies a high level of confidence that the model’s predicted co-folding of the viral protein and the defense system closely represents a true complex formation. These scores, which vary depending on the computational model and prediction scale, are well-established in the field.

[0210] Thus, for example, according to specific embodiments, the predetermined threshold comprises a predicted co-folding confidence score > 0.5 in a confidence scale of 0 to 1.

[0211] Thus, for example, according to specific embodiments, the predetermined threshold comprises a predicted co-folding confidence score > 0.6, > 0.7, > 0.8 or > 0.9 in a confidence scale of 0 to 1.

[0212] According to specific embodiments, the predetermined threshold comprises a predicted co-folding confidence score > 0.8 in a confidence scale of 0 to 1.

[0213] According to specific embodiments, when the modelling algorithm comprises multiple rounds of prediction, the co-folding confidence score comprises the average co-folding scores of all rounds.

[0214] According to specific embodiments, when the modelling algorithm comprises multiple rounds of prediction, co-folding confidence scores above the predetermined threshold of at least 0.5, at least 0.55 or at least 0.6 of the scores obtained are considered a co-folding confidence score above the predetermined threshold.

[0215] The present inventors show in the Examples section which follows that modeling of an interaction between a single viral protein of a cluster and the defense system polypeptide yield false positive results, and that these rates are substantially reduced by modelling sets of homologs of the viral protein being members of the same cluster with the target immune protein.

[0216] Hence, once a viral protein having a predicted co-folding confidence score above a predetermined threshold has been selected, the method comprises in-silico modeling an interaction between at least one additional viral protein of the cluster of the selected protein.

[0217] In this manner only a cluster having a predetermined number of viral proteins having predicted co-folding confidence scores with the defense system polypeptide above the predetermined threshold is selected. A protein being part of the selected cluster is identified as a putative anti-defense system polypeptide. According to specific embodiments, the at least one additional viral protein comprises at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9 or at least 10 additional viral proteins.

[0218] According to specific embodiments, the method comprises in-silico modeling an interaction between at least 10 viral proteins of the cluster of the selected protein.

[0219] As used herein, the phrase “predetermined number of viral proteins having predicted cofolding confidence scores” refer to a number of viral proteins that signifies a high level of confidence that viral proteins of the selected cluster are indeed anti-defense system polypeptides.

[0220] Thus, for example, according to specific embodiments, the predetermined number comprises at least 50 %, at least 60 %, at least 70 %, at least 80 %, at least 90 % or more of the modelled viral proteins of the cluster.

[0221] According to specific embodiments, the predetermined number comprises the average co-folding score of all the modelled viral proteins of the cluster.

[0222] According to specific embodiments, the method further comprises in-silico modelling a three dimensional structure of the viral protein prior to modeling its interaction with the defense system polypeptide.

[0223] Methods of modelling a three dimensional structure are well known in the art. Nonlimiting Examples of commercial computations tools that can be used include AlphaFold and RoseTTAFold.

[0224] According to specific embodiments, the method comprises proceeding to the following step only with a viral protein having a predicted structural confidence score above a predetermined threshold.

[0225] According to specific embodiments, when the viral protein is predicted to be a homodimer modelling its interaction with the defense system polypeptide is effected on a homodimer conformation.

[0226] As used herein, the phrase “predicted structural confidence score above a predetermined threshold” refers to a score that signifies a high level of confidence that the model’s predicted structure closely represents the true structure. These scores, which vary depending on the computational model and prediction scale, are well-established in the field.

[0227] Thus, for example, according to specific embodiments, the predetermined threshold comprises a predicted structural confidence score > 50 in a confidence scale of 0 to 100.

[0228] Thus, for example, according to specific embodiments, the predetermined threshold comprises a predicted structural confidence score > 60, > 70, > 80 or > 90 in a confidence scale of 0 to 100. According to specific embodiments, the predetermined threshold comprises a predicted structural confidence score > 80 in a confidence scale of 0 to 100.

[0229] According to specific embodiments, the method described above can have additional steps imposing sequence, structure or function limitations aiming to reduce computational load and / or improve the method. According to specific embodiments, such steps can be inserted prior or following any of the recited steps hereinabove.

[0230] Thus, according to specific embodiments, the method comprises omitting identical viral proteins from the dataset.

[0231] According to specific embodiments, the method comprises selecting only a viral protein(s) with an unknown function. Such viral proteins do not have a previous annotation in publicly available databases.

[0232] According to specific embodiments, the method comprises filtering out proteins that are not biased towards viruses. In other words, proteins with a higher number of homologs detected in a general metagenomic database (e.g. MGnify database) than the viral protein database used may be considered as not biased towards viruses.

[0233] According to specific embodiments, the method comprises selecting only a viral protein(s) having a length ≤1000 amino acids, ≤800 amino acids, ≤600 amino acids, ≤500 amino acids, ≤400 amino acids, ≤300 amino acids, or ≤200 amino acids.

[0234] According to specific embodiments, the method comprises selecting only a viral protein(s) having a length ≤200 amino acids.

[0235] According to specific embodiments, the method comprises determining an amount of amino acid residues in said selected viral protein having said predicted co-folding confidence score above said predetermined threshold interacting with said defense system polypeptide system polypeptide.

[0236] Amino acid residues of the viral protein may form various interactions with the defense system polypeptides, including but not limited to hydrogen (H)-bonds, 7t-7t stacking, 7t-Cation interaction, ionic bonds (salt bridges), 7t-H Bonds, van der Waals and disulphide bonds. Methods of determining such bonds are known in the art such as, but not limited to the RING version 4 server and the Biopython PDBparser

[0237] According to specific embodiments, the method comprises selecting a viral protein having at least 20, at least 25, at least 30, at least 35 or at least 40 interacting residues with said defense system polypeptide

[0238] According to specific embodiments, the method comprises screening for additional proteins having sequence and / or structure similarity to the selected putative anti-defense system polypeptide (e.g. in other databases or with less constringent parameters), to thereby identify additional protein(s) being a putative anti-defense system polypeptide.

[0239] According to specific embodiments, the method comprises experimentally determining in-vitro, ex-vivo or in-vivo the functional activity of the putative anti-defense system polypeptide.

[0240] Thus, for example, the method may further comprises experimentally testing binding of the putative anti-defense system polypeptide to the defense system polypeptide or testing the inhibitory activity of the putative anti-defense system polypeptide on the defense system polypeptide. Such methods are well known in the art and depend on the specific function of the target defense system polypeptide. Exemplary non limiting assays for specific defense system polypeptides are also described hereinabove and below and in the Examples section which follows.

[0241] To this end, according to specific embodiments, the method further comprises synthesizing the proteins by any techniques known to those skilled in the art of peptide synthesis, for example but not limited to recombinant DNA techniques or solid phase peptide synthesis.

[0242] According to specific embodiments, the viral protein with the highest co-folding confidence score with the defense system polypeptide is the one selected (e.g. for experimental verification).

[0243] It is noted that the present inventors demonstrated that identified phage-encoded inhibitors of bacterial defense systems can also inhibit their eukaryotic homologs (Example 6 of the Examples section which follows). Hence, specific embodiments of the present invention contemplates that the selected anti-defense system polypeptide may be used to inhibit a homolog of the defense system polypeptide used in the identification method.

[0244] As used herein, the phrase “a homolog of a defense system” refers to a defense system protein(s) of a different species (orthologs, such as in prokaryotes and eukaryotes), of a different gene within the same organism (paralogs) or a synthetic version thereof that exhibits similarities in sequence, structure and / or function. The homolog may comprise a deletion, insertion, or substitution variant, including an amino acid substitution in the sequence of the defense system polypeptide.

[0245] Hence, anti-defense system polypeptides identified by the methods described herein may further be used, according to specific embodiments, in various research, biotechnological, agricultural and clinical applications associated with the defense system polypeptide or a homolog thereof. Using the method disclosed herein, the present inventors discovered several anti-defense system polypeptides. Specifically, six families of Thoeris inhibitors (referred to herein as “Tad3”, “Tad4”, “Tad5”, “Tad6”, “Tad7” and “Tad8”) and one family of CBASS inhibitors (referred to herein as “Acb3”).

[0246] According to specific embodiments, the anti-defense system polypeptide is a Tad3 polypeptide. A Tad3 polypeptide disables the anti -phage bacterial system Thoeris type I.

[0247] For the sake of simplicity, a “Tad3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594-11520 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67- 76, 245-5265 and 7594-11520, wherein the polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 and / or a homolog thereof’, is also referred to herein as a “Tad3 polypeptide”.

[0248] According to specific embodiments, the Tad3 polypeptide has an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594-11520, each possibility represents a separate embodiment of the claimed invention.

[0249] According to specific embodiments, the Tad3 polypeptide has a RMSD ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594-11520, each possibility represents a separate embodiment of the claimed invention.

[0250] The Tad3 polypeptide of some embodiments has a sequence similarity defined by an e- value ≤ 0.05 to SEQ ID NO: 58 and / or a structural similarity defined by a RMSD ≤ 2.0 angstroms to the structure of SEQ ID NO: 58.

[0251] According to specific embodiments, the Tad3 polypeptide comprises a serine residue at position 48 corresponding to SEQ ID NO: 58.

[0252] According to specific embodiments, the Tad3 polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594- 11520, each possibility represents a separate embodiment of the claimed invention.

[0253] According to specific embodiments, the Tad3 polypeptide comprises SEQ ID NO: 58.

[0254] According to specific embodiments, the Tad3 polypeptide consists of an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594- 11520, each possibility represents a separate embodiment of the claimed invention. According to specific embodiments, the Tad3 polypeptide consists of SEQ ID NO: 58.

[0255] According to specific embodiments, the Tad3 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10.

[0256] Determining binding to a defense system polypeptide (e.g. ThsB of a Type I Thoeris set forth in SEQ ID NO: 10) can be effected by any method known in the art. Non-limiting examples are described hereinabove and in the Examples section which follows, and include e.g. in-silico prediction interaction models, immunoprecipitation / pull-down followed by SDS-PAGE or SEC-MALS.

[0257] According to specific embodiments, the Tad3 polypeptide binds the active site of ThsB (and specifically forms a loop that penetrates the active site).

[0258] According to specific embodiments, the Tad3 polypeptide forms a hydrogen bond with the catalytic E85 residue of ThsB set forth in SEQ ID NO: 10.

[0259] According to specific embodiments, the Tad3 polypeptide is capable of forming a homodimer.

[0260] According to specific embodiments, the Tad3 polypeptide binds as a homodimer two monomers of ThsB.

[0261] Methods of determining dimerization are known in the art and are further described hereinabove and in the Examples section which follows.

[0262] According to specific embodiments, the Tad3 polypeptide inhibits activity of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10.

[0263] Determining inhibition of activity of a defense system polypeptide (e.g. ThsB set forth in SEQ ID NO: 10) can be effected by any method known in the art. Non-limiting examples are described hereinabove and in the Examples section which follows. For example, one can measure the ability of filtered cell lysates derived from Thoeris-infected cells to activate the Thoeris effector ThsA (e.g. the NADase activity of the Thoeris effector ThsA). Additionally or alternatively, one can measure phage infectivity of a bacteria expressing the defense system by e.g. a plaque assay or liquid culture infection. For example, inhibition can be determined by increased sensitivity of B. subtilis BEST7003 expressing an exogenous Thoeris type I and the anti-defense system polypeptide to infection by the SBSphiJ phage. Thus, according to specific embodiments, expression of the Tad3 polypeptide in a B. subtilis BEST7003 comprising SEQ ID NO: 1 increases sensitivity of B. subtilis BEST7003 to infection by a B. subtilis phage SBSphiJ. Alternatively or additionally, inhibition can be determined by increased sensitivity of B. subtilis BEST7003 expressing an exogenous Thoeris type I to infection by a SBSphiJ phage genetically modified to express the anti-defense system polypeptide. According to specific embodiments, the Tad3 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10.

[0264] According to specific embodiments, the Tad3 polypeptide inhibits activity of a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10.

[0265] Additional description on such homologs is provided hereinabove and below.

[0266] According to specific embodiments, the homolog is SARM1TIR set forth SEQ ID NO: 6. Methods of determining binding to and activity of SARM1TIR are known in the art and also described in the examples section which follows, and include e.g. computational modeling and experimental (e.g. immunoprecipitation, NADase activity, axonal cell death in response to neuronal injury etc.).

[0267] According to specific embodiments, the anti-defense system polypeptide is a Tad4 polypeptide. A Tad4 polypeptide disables the anti -phage bacterial system Thoeris type I.

[0268] For the sake of simplicity, a “Tad4 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77- 86, 5266-5865 and 11521-11766, wherein the polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 and / or a homolog thereof’ is also referred to herein as a “Tad4 polypeptide”.

[0269] According to specific embodiments, the Tad4 polypeptide has an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766, each possibility represents a separate embodiment of the claimed invention.

[0270] According to specific embodiments, the Tad4 polypeptide has a RMSD ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766, each possibility represents a separate embodiment of the claimed invention.

[0271] The Tad4 polypeptide of some embodiments has a sequence similarity defined by an e- value ≤ 0.05 to SEQ ID NO: 66 and / or a structural similarity defined by a RMSD ≤ 2.0 angstroms to the structure of SEQ ID NO: 66.

[0272] According to specific embodiments, the Tad4 polypeptide comprises a threonine residue at position 69 corresponding to SEQ ID NO: 66. According to specific embodiments, the Tad4 polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521- 11766, each possibility represents a separate embodiment of the claimed invention.

[0273] According to specific embodiments, the Tad4 polypeptide comprises SEQ ID NO: 66.

[0274] According to specific embodiments, the Tad4 polypeptide consists of an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521- 11766, each possibility represents a separate embodiment of the claimed invention.

[0275] According to specific embodiments, the Tad4 polypeptide consists of SEQ ID NO: 66.

[0276] According to specific embodiments, the Tad4 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10.

[0277] According to specific embodiments, the Tad4 polypeptide binds the active site of ThsB (and specifically forms a loop that penetrates the active site).

[0278] According to specific embodiments, the Tad4 polypeptide forms a hydrogen bond with the catalytic E85 residue of ThsB set forth in SEQ ID NO: 10.

[0279] According to specific embodiments, the Tad4 polypeptide inhibits activity of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10.

[0280] Determining binding to a defense system polypeptide, and activity of a defense system polypeptide are known in the art and are further described hereinabove and in the Examples section which follows.

[0281] According to specific embodiments, expression of the Tad4 polypeptide in a B. subtilis BEST7003 comprising SEQ ID NO: 1 increases sensitivity of B. subtilis BEST7003 to infection by a B. subtilis phage SBSphiJ.

[0282] According to specific embodiments, the Tad4 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10.

[0283] According to specific embodiments, the Tad4 polypeptide inhibits activity of a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10.

[0284] Additional description on such homologs is provided hereinabove and below.

[0285] According to specific embodiments, the homolog is plant Brachypodium distachyon (BdTIR) set forth SEQ ID NO: 8. Methods of determining binding to and activity of BdTIR are known in the art and also described in the examples section which follows, and include e.g. computational modeling and experimental (e.g. immunoprecipitation, NADase activity).

[0286] According to specific embodiments, the homolog is SARM1TIR set forth SEQ ID NO: 6. Methods of determining binding to and activity of SARM1TIR are known in the art and also described hereinabove and in the examples section which follows. According to specific embodiments, the anti-defense system polypeptide is a Tad5 polypeptide. A Tad5 polypeptide disables the anti -phage bacterial system Thoeris type I.

[0287] For the sake of simplicity, a “Tad5 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87- 96, 5866-5961 and 11767-11849, wherein the polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 and / or a homolog thereof’, is also referred to herein as a “Tad5 polypeptide”.

[0288] According to specific embodiments, the Tad5 polypeptide has an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849, each possibility represents a separate embodiment of the claimed invention.

[0289] According to specific embodiments, the Tad5 polypeptide has a RMSD ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849, each possibility represents a separate embodiment of the claimed invention.

[0290] The Tad5 polypeptide of some embodiments has a sequence similarity defined by an e- value ≤ 0.05 to SEQ ID NO: 59 and / or a structural similarity defined by a RMSD ≤ 2.0 angstroms to the structure of SEQ ID NO: 59.

[0291] According to specific embodiments, the Tad5 polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767- 11849, each possibility represents a separate embodiment of the claimed invention.

[0292] According to specific embodiments, the Tad5 polypeptide comprises SEQ ID NO: 59.

[0293] According to specific embodiments, the Tad5 polypeptide consists of an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767- 11849, each possibility represents a separate embodiment of the claimed invention.

[0294] According to specific embodiments, the Tad5 polypeptide consists of SEQ ID NO: 59.

[0295] According to specific embodiments, the Tad5 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10.

[0296] According to specific embodiments, the Tad5 polypeptide binds the active site of ThsB (and specifically forms a loop that penetrates the active site). According to specific embodiments, the Tad5 polypeptide forms a hydrogen bond with the catalytic E85 residue of ThsB set forth in SEQ ID NO: 10.

[0297] According to specific embodiments, the Tad5 polypeptide inhibits activity of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10.

[0298] Determining binding to a defense system polypeptide, and activity of a defense system polypeptide are known in the art and are further described hereinabove and in the Examples section which follows.

[0299] According to specific embodiments, expression of the Tad5 polypeptide in a B. subtilis BEST7003 comprising SEQ ID NO: 1 increases sensitivity of B. subtilis BEST7003 to infection by a B. subtilis phage SBSphiJ.

[0300] According to specific embodiments, the anti-defense system polypeptide is a Tad6 polypeptide. A Tad6 polypeptide disables the anti -phage bacterial system Thoeris type I.

[0301] For the sake of simplicity, a “Tad6 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97- 106, 5962-6369 and 11850-11888, wherein the polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 and / or a homolog thereof’, is also referred to herein as a “Tad6 polypeptide”.

[0302] According to specific embodiments, the Tad6 polypeptide has an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888, each possibility represents a separate embodiment of the claimed invention.

[0303] According to specific embodiments, the Tad6 polypeptide has a RMSD ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888, each possibility represents a separate embodiment of the claimed invention.

[0304] The Tad6 polypeptide of some embodiments has a sequence similarity defined by an e- value ≤ 0.05 to SEQ ID NO: 65 and / or a structural similarity defined by a RMSD ≤ 2.0 angstroms to the structure of SEQ ID NO: 65.

[0305] According to specific embodiments, the Tad6 polypeptide comprises an arginine residue at position 92 corresponding to SEQ ID NO: 65. According to specific embodiments, the Tad6 polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850- 11888, each possibility represents a separate embodiment of the claimed invention.

[0306] According to specific embodiments, the Tad6 polypeptide comprises SEQ ID NO: 65.

[0307] According to specific embodiments, the Tad6 polypeptide consists of an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850- 11888, each possibility represents a separate embodiment of the claimed invention.

[0308] According to specific embodiments, the Tad6 polypeptide consists of SEQ ID NO: 65.

[0309] According to specific embodiments, the Tad6 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10.

[0310] According to specific embodiments, the Tad6 polypeptide binds the active site of ThsB (and specifically forms a loop that penetrates the active site).

[0311] According to specific embodiments, the Tad6 polypeptide forms a hydrogen bond with the catalytic E85 residue of ThsB set forth in SEQ ID NO: 10.

[0312] According to specific embodiments, the Tad6 polypeptide inhibits activity of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10.

[0313] Determining binding to a defense system polypeptide, and activity of a defense system polypeptide are known in the art and are further described hereinabove and in the Examples section which follows.

[0314] According to specific embodiments, expression of the Tad6 polypeptide in a B. subtilis BEST7003 comprising SEQ ID NO: 1 increases sensitivity of B. subtilis BEST7003 to infection by a B. subtilis phage SBSphiJ.

[0315] According to specific embodiments, the anti-defense system polypeptide is a Tad7 polypeptide. A Tad7 polypeptide disables the anti -phage bacterial system Thoeris type II.

[0316] For the sake of simplicity, a “Tad7 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370- 6461 and 11889-11918, wherein the polypeptide binds the defense system polypeptide ThsB of a Type II Thoeris set forth in SEQ ID NO: 228 and / or a homolog thereof, is also referred to herein as a “Tad7 polypeptide”.

[0317] According to specific embodiments, the Tad7 polypeptide has an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918, each possibility represents a separate embodiment of the claimed invention.

[0318] According to specific embodiments, the Tad7 polypeptide has a RMSD ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918, each possibility represents a separate embodiment of the claimed invention.

[0319] The Tad7 polypeptide of some embodiments has a sequence similarity defined by an e- value ≤ 0.05 to SEQ ID NO: 239 and / or a structural similarity defined by a RMSD ≤ 2.0 angstroms to the structure of SEQ ID NO: 239.

[0320] According to specific embodiments, the Tad7 polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918, each possibility represents a separate embodiment of the claimed invention.

[0321] According to specific embodiments, the Tad7 polypeptide comprises SEQ ID NO: 239.

[0322] According to specific embodiments, the Tad7 polypeptide consists of an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918, each possibility represents a separate embodiment of the claimed invention.

[0323] According to specific embodiments, the Tad7 polypeptide consists of SEQ ID NO: 239.

[0324] According to specific embodiments, the Tad7 polypeptide binds the defense system polypeptide ThsB of a Type II Thoeris set forth in SEQ ID NO: 228.

[0325] According to specific embodiments, the Tad7 polypeptide binds the active site of ThsB (and specifically forms a loop that penetrates the active site).

[0326] According to specific embodiments, the Tad7 polypeptide forms a bond with the catalytic E99 residue of ThsB set forth in SEQ ID NO: 228.

[0327] According to specific embodiments, the Tad7 polypeptide inhibits activity of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 228.

[0328] Determining binding to a defense system polypeptide, and activity of a defense system polypeptide are known in the art and are further described hereinabove and in the Examples section which follows.

[0329] According to specific embodiments, expression of the Tad7 polypeptide in a B. subtilis BEST7003 comprising SEQ ID NO: 2 increases sensitivity of said B. subtilis BEST7003 to infection by a B. subtilis phage SBSphiJ.

[0330] According to specific embodiments, the anti-defense system polypeptide is a Tad8 polypeptide. A Tad8 polypeptide disables the anti -phage bacterial system Thoeris type II. For the same of simplicity, a “Tad8 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462- 6616 and 11919-12290, wherein the polypeptide binds the defense system polypeptide ThsA of a Type II Thoeris set forth in SEQ ID NO: 227 and / or a homolog thereof, is also referred to herein as a “Tad8 polypeptide”.

[0331] According to specific embodiments, the Tad8 polypeptide has an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290, each possibility represents a separate embodiment of the claimed invention.

[0332] According to specific embodiments, the Tad8 polypeptide has a RMSD ≤ 2.0 angstroms toa structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290, each possibility represents a separate embodiment of the claimed invention.

[0333] The Tad8 polypeptide of some embodiments has a sequence similarity defined by an e- value ≤ 0.05 to SEQ ID NO: 240 and / or a structural similarity defined by a RMSD ≤ 2.0 angstroms to the structure of SEQ ID NO: 240.

[0334] According to specific embodiments, the Tad8 polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290, each possibility represents a separate embodiment of the claimed invention.

[0335] According to specific embodiments, the Tad8 polypeptide comprises SEQ ID NO: 240.

[0336] According to specific embodiments, the Tad8 polypeptide consists of an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290, each possibility represents a separate embodiment of the claimed invention.

[0337] According to specific embodiments, the Tad8 polypeptide consists of SEQ ID NO: 240.

[0338] According to specific embodiments, the Tad8 polypeptide binds the defense system polypeptide ThsA of a Type II Thoeris set forth in SEQ ID NO: 227.

[0339] According to specific embodiments, the Tad8 polypeptide binds the active site of ThsA (and specifically forms a loop that penetrates the Macro domain of ThsA).

[0340] According to specific embodiments, the Tad8 polypeptide forms a bond with a residue of the Macro domain pocked of ThsA selected from the group consisting of A202, R240, Q135 and Y277 of ThsA set forth in SEQ ID NO: 227. According to specific embodiments, the Tad8 polypeptide is capable of forming a homodimer.

[0341] According to specific embodiments, the Tad8 polypeptide binds as a homodimer two monomers of ThsA.

[0342] According to specific embodiments, the Tad8 polypeptide inhibits activity of the defense system polypeptide ThsA of a Type I Thoeris set forth in SEQ ID NO: 227.

[0343] Determining dimerization, binding to a defense system polypeptide, and activity of a defense system polypeptide are known in the art and are further described hereinabove and in the Examples section which follows.

[0344] According to specific embodiments, expression of the Tad8 polypeptide in a B. subtilis BEST7003 comprising SEQ ID NO: 2 increases sensitivity of said B. subtilis BEST7003 to infection by a B. subtilis phage SBSphiJ.

[0345] According to specific embodiments, the anti-defense system polypeptide is an Acb3 polypeptide. An Acb3 polypeptide disables the anti-phage bacterial system CBASS (e.g. CBASS Type III).

[0346] For the sake of simplicity, a “Acb3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593, wherein the polypeptide binds the bacterial defense system polypeptide cGAS of a CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233 and / or a homolog thereof’, is also referred to herein as a “Acb3 polypeptide”.

[0347] According to specific embodiments, the Acb3 polypeptide has an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593, each possibility represents a separate embodiment of the claimed invention.

[0348] According to specific embodiments, the Acb3 polypeptide has a RMSD ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593, each possibility represents a separate embodiment of the claimed invention.

[0349] The Acb3 polypeptide of some embodiments has a sequence similarity defined by an e- value ≤ 0.05 to SEQ ID NO: 244 and / or a structural similarity defined by a RMSD ≤ 2.0 angstroms to the structure of SEQ ID NO: 244. According to specific embodiments, the Acb3 polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593, each possibility represents a separate embodiment of the claimed invention.

[0350] According to specific embodiments, the Acb3 polypeptide comprises SEQ ID NO: 244.

[0351] According to specific embodiments, the Acb3 polypeptide consists of an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593, each possibility represents a separate embodiment of the claimed invention.

[0352] According to specific embodiments, the Acb3 polypeptide consists of SEQ ID NO: 244.

[0353] According to specific embodiments, the Acb3 polypeptide binds the bacterial defense system polypeptide cGAS of CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NO: 229-231 and 233.

[0354] According to specific embodiments, the Acb3 polypeptide binds the active site of cGAS.

[0355] According to specific embodiments, the Acb3 polypeptide forms a bond with the nucleotidyltransferase active site and / or the putative ligand binding domain that is required for CD-NTase activation.

[0356] According to specific embodiments, the Acb3 polypeptide inhibits activity of the defense system polypeptide cGAS of a CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233.

[0357] Determining binding to a defense system polypeptide, and activity of a defense system polypeptide are known in the art and are further described hereinabove and below and in the Examples section which follows.

[0358] For example, one can measure the ability of filtered cell lysates derived from CBASS- infected cells to produce 2'3'-cGAMP. Additionally or alternatively, one can measure phage infectivity of a bacteria expressing the defense system by e.g. a plaque assay or liquid culture infection.

[0359] According to specific embodiments, expression of the Acb3 polypeptide in a E. coil MG1655 comprising SEQ ID NO: 4 increases sensitivity of the E. coll MG 1655 to infection by an E. coli phage BAS 18.

[0360] According to specific embodiments, expression of the Acb3 polypeptide in a B. subtilis BEST7003 comprising SEQ ID NO: 3 increases sensitivity of the B. subtilis BEST7003 to infection by a B. subtilis phage SBSphiC.

[0361] According to specific embodiments, the Acb3 polypeptide binds a homolog of the defense system polypeptide cGAS of a CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233. According to specific embodiments, the Acb3 polypeptide inhibits activity of a homolog of the defense system polypeptide cGAS of CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233.

[0362] Additional description on such homologs is provided hereinabove and below.

[0363] According to specific embodiments, the homolog is cGAS of a Type I CBASS set forth SEQ ID NO: 234.

[0364] According to specific embodiments, the homolog is human cGAS of a CBASS set forth SEQ ID NO: 12291.

[0365] To render explicit, the “Tad3 polypeptide”, “Tad4 polypeptide”, “Tad5 polypeptide”, “Tad6 polypeptide”, “Tad7 polypeptide”, “Tad8 polypeptide” and / or “Acb3 polypeptide” of some embodiments of the invention may comprise a homolog, an ortholog, a deletion, insertion, or substitution variant, including an amino acid substitution of the recited amino acid sequence.

[0366] According to a specific embodiment, the “Tad3 polypeptide”, “Tad4 polypeptide”, “Tad5 polypeptide”, “Tad6 polypeptide”, “Tad7 polypeptide”, “Tad8 polypeptide” and / or “Acb3 polypeptide” comprises the recited amino acid sequence.

[0367] According to a specific embodiment, the “Tad3 polypeptide”, “Tad4 polypeptide”, “Tad5 polypeptide”, “Tad6 polypeptide”, “Tad7 polypeptide”, “Tad8 polypeptide” and / or “Acb3 polypeptide” consists of the recited amino acid sequence.

[0368] According to specific embodiments, the terms “Tad3 polypeptide”, “Tad4 polypeptide”, “Tad5 polypeptide”, “Tad6 polypeptide”, “Tad7 polypeptide”, “Tad8 polypeptide” and / or “Acb3 polypeptide” refer to a fragment of the amino acid sequence of “Tad3 polypeptide”, “Tad4 polypeptide”, “Tad5 polypeptide”, “Tad6 polypeptide”, “Tad7 polypeptide”, “Tad8 polypeptide” and / or “Acb3 polypeptide”, respectively, provided herein, which maintains the activity as described herein.

[0369] According to specific embodiments, “Tad3 polypeptide”, “Tad4 polypeptide”, “Tad5 polypeptide”, “Tad6 polypeptide”, “Tad7 polypeptide”, “Tad8 polypeptide” and / or “Acb3 polypeptide” is up to 800, up to 700, up to 600, up to 500, up to 400, up to 300 or up to 200 amino acids long.

[0370] According to specific embodiments, “Tad3 polypeptide”, “Tad4 polypeptide”, “Tad5 polypeptide”, “Tad6 polypeptide”, “Tad7 polypeptide”, “Tad8 polypeptide” and / or “Acb3 polypeptide” is at least 50, at least 100, at least 150, at least 200, at least 250 amino acids long.

[0371] As the Tad3, Tad4, Tad5, Tad6, Tad7, Tad8 and Acb3 polypeptides have a detrimental effect on the bacterial Thoeris and CBASS anti-phage defense systems and homologs thereof as described herein, embodiments of the present invention also contemplate viruses genetically modified to express these polypeptide, cells comprising these polypeptides, methods of producing same and methods of use thereof.

[0372] Thus, according to an aspect of the present invention there is provided a virus comprising an exogenous polynucleotide encoding an anti-defense system polypeptide, wherein said antidefense system polypeptide is selected from the group consisting of:

[0373] (i) a Tad3 polypeptide;

[0374] (ii) a Tad4 polypeptide;

[0375] (iii) a Tad5 polypeptide;

[0376] (iv) a Tad6 polypeptide;

[0377] (v) a Tad7 polypeptide;

[0378] (vi) a Tad8 polypeptide; and

[0379] (vii) an Acb3 polypeptide.

[0380] Thus, according to an aspect of the present invention, there is provided a genetically modified virus comprising a polynucleotide encoding an anti-defense system polypeptide as described herein.

[0381] Typically, a virus will be characterized by: 1) the nature of the nucleic acids that make up its genome, e.g., DNA, RNA, single-stranded or double- stranded; 2) the nature of its infectivity, e.g., lytic or temperate; and 3) the particular cell species that it infects (and in certain instances the particular subspecies or strain). This is known as “host range”.

[0382] According to specific embodiments, the viral genome can be ssDNA or dsDNA.

[0383] According to specific embodiments, the viral genome can be ssRNA or dsRNA.

[0384] According to some embodiments, the virus is a lytic virus.

[0385] The term “lytic virus” refers to a virus that infects a host cell and causes that host cell to lyse without incorporating the virus nucleic acids into the host genome. A lytic virus is typically not capable of reproducing using the lysogenic cycle.

[0386] According to other embodiments, the virus is temperate (also referred to as lysogenic).

[0387] The term “temperate virus” refers to a virus that is capable of reproducing using both the lysogenic cycle and the lytic cycle. Lysogeny is characterized by integration of the virus nucleic acid into the host cell’s genome or formation of a circular replicon in the cytoplasm.

[0388] According to specific embodiments, the virus infects eukaryotic cells.

[0389] Non-limiting examples of such viruses that can be used with specific embodiments of the invention include retroviruses, circoviruses, parvoviruses, papovaviruses, adenoviruses, adeno- associated virus, herpesviruses, iridoviruses, poxviruses, hepadnaviruses, picomaviruses, caliciviruses, togaviruses, flaviviruses, reoviruses, orthomyxoviruses, paramyxoviruses, rhabdoviruses, bunyaviruses, coronaviruses, arenaviruses, filoviruses, lentivirus, baculovirus, vesicular stomatitis virus. Specific non-limiting examples of viruses encompassed by the present invention include human immunodeficiency virus (HlV)-induced acquired immunodeficiency syndrome (AIDS), influenza, rhinoviral infection, viral meningitis, Epstein-Barr virus (EBV) infection, hepatitis A, B or C virus infection, measles, papilloma virus infection / warts, cytomegalovirus (CMV) infection, Herpes simplex virus infection, yellow fever, Ebola virus infection, rabies, etc.

[0390] According to specific embodiments, the virus infects prokaryotic cells.

[0391] Thus, according to specific embodiments, the virus is a phage.

[0392] As used herein, the term "phage" or “bacteriophage” refers to a virus that selectively infects one or more bacterial species. Many phages are specific to a particular genus or species or strain of bacteria.

[0393] According to specific embodiments, phages that infect bacteria that are pathogenic to plants and / or animals (including humans) find particular use.

[0394] Exemplary phages which fall under the scope of some embodiments of the invention include, but are not limited to, phages that belong to any of the following virus families: Corticoviridae, Cystoviridae, Inoviridae, Leviviridae, Microviridae, Myoviridae, Podoviridae, Siphoviridae, or Tectiviridae.

[0395] According to specific embodiments, the phage is isolated and / or developed to target a specific bacteria. Isolation and characterization of such phages can be done, for example, as described in Hayman Pharmaceuticals (Basel) (2019) 12(1): 35, DOI: 10.3390 / phl2010035 and https: / / doi(dot)org / 10.1016 / j. cels.2015.08.013, the contents of which are fully incorporated herein by reference.

[0396] According to specific embodiments, the phage infects a pathogenic bacteria (i.e. a bacteria that can cause or be associated with a disease in humans, livestock, crops, or other living organism).

[0397] According to specific embodiments, the virus (e.g. phage) is a clinically approved phage.

[0398] According to specific embodiments, the virus is FDA approved for clinical use. Thus, for example, according to specific embodiments, the phage is FDA approved for treatment of an infectious bacterium.

[0399] The phages of some embodiments of the invention comprise an exogenous or a heterologous polynucleotide encoding an anti-defense system polypeptide.

[0400] As used herein the term “polynucleotide” or “nucleic acid sequence”, which are interchangeably used herein, refers to a single or double stranded nucleic acid sequence provided e.g., in the form of an RNA sequence, a DNA and / or a composite polynucleotide sequences (e.g., a combination of the above).

[0401] A non-limiting example of a polynucleotide encoding Tad3 is provided in SEQ ID NO:

[0402] 42.

[0403] A non-limiting example of a polynucleotide encoding Tad4 is provided in SEQ ID NO: 50.

[0404] A non-limiting example of a polynucleotide encoding Tad5 is provided in SEQ ID NO:

[0405] 43.

[0406] A non-limiting example of a polynucleotide encoding Tad6 is provided in SEQ ID NO: 49.

[0407] A non-limiting example of a polynucleotide encoding Tad7 is provided in SEQ ID NO:

[0408] 235.

[0409] A non-limiting example of a polynucleotide encoding Tad8 is provided in SEQ ID NO:

[0410] 236.

[0411] A non-limiting example of a polynucleotide encoding Acb3 is provided in SEQ ID NO: 243.

[0412] According to specific embodiments, the polynucleotide encoding the “Tad3 polypeptide”, “Tad4 polypeptide”, “Tad5 polypeptide”, “Tad6 polypeptide”, “Tad7 polypeptide”, “Tad8 polypeptide” or “Acb3 polypeptide” is at least 70 %, at least 75 %, at least 80 %, at least 81 %, at least 82 %, at least 83 %, at least 84 %, at least 85 %, at least 86 %, at least 87 %, at least 88 %, at least 89 %, at least 90 %, at least 91 %, at least 92 %, at least 93 %, at least 94 %, at least 95 %, at least 96 %, at least 97 %, at least 98 %, at least 99 % or 100 % identical or homologous to the SEQ ID NOs: 42, 50, 43, 49, 235, 236 or 243, respectively.

[0413] It should be appreciated that the nucleic acid sequences encoding of the polypeptides of some embodiments of the invention may be optimized for expression in a specific organism.

[0414] According to specific embodiments, the polynucleotide of the present invention encodes no more than 20, no more than 15, no more than 10 genes expression products.

[0415] According to specific embodiments, the polynucleotide encodes one of the anti-defense polypeptides (i)-(vii) described herein.

[0416] According to specific embodiments, the polynucleotide comprises a nucleic acid sequence encoding one of the anti-defense polypeptides (i)-(vii) described herein, whereby a plurality of polynucleotides can be used to assemble several anti-defense polypeptides, as described below.

[0417] According to other specific embodiments, a single polynucleotide encodes at least two, at least three, at least four, at least five or six of the anti-defense polypeptides (i)-(vii) described herein. Further description on expression of multiple polypeptides from a single polynucleotide is provided hereinbelow.

[0418] The term “heterologous” or “exogenous” means the sequence (polynucleotide or polypeptide) is not natively expressed in at least localization (e.g. genomic, cellular compartment and / or cell type) or level / amount or is completely absent from the native counterpart.

[0419] In comparison, the term “endogenous” means expression of the native sequence (polynucleotide or polypeptide) in its natural location and expression level.

[0420] According to other specific embodiments, the virus is devoid of an endogenous polynucleotide encoding the anti-defense polypeptide.

[0421] In essence, the virus of some embodiments of the invention is genetically modified to express the anti-defense system polypeptide.

[0422] As used herein, “expressing” or “expression” refers to expression at the nucleic acid and / or protein level. Expression can be determined using methods known in the art e.g. but not limited to selectable marker gene, Northern blot analysis, PCR analysis, DNA sequencing, RNA sequencing, Western blot analysis, and Immunohistochemistry.

[0423] Methods of genetically modifying a virus (e.g. phage) are well known in the art and described in e.g. Gibb et al. (2021) Pharmaceuticals, 14, 634; Chen et al. (2019) Front. Microbiol. 10:954; and Rustad, et al. (2018) Synthetic Biology, 3(1) ysy002, doidotorg / 10.1093 / synbio / ysy002, the contents of which are fully incorporated herein by reference, and are further described hereinbelow and in the Examples section which follows. Non-limiting Examples include, homologous recombination, bacteriophage recombineering of electroporated DNA (BRED), CRISPR-Cas-based engineering and rebooting viruses using assembled vims genomic DNA.

[0424] One Exemplary' method of obtaining the genetically modified virus is by recombination- mediated genetic exchange between at least 2 distinct viruses, as described for example in International Patent Application Publication No. W02023 / 100189, the contents of which are fully incorporated herein by reference.

[0425] Thus, according to specific embodiments, the vims (e.g. phage) comprises genomic segments of a distinct virus (e.g. phage) integrated in a genome of said vims (e.g. phage).

[0426] According to specific embodiments, these segments are about 1000 - 60,000, 2000 - 50,000 or 10,000 - 30, 000 long.

[0427] According to specific embodiments, these segments constitute about 0.5 - 50 % of the viral genome. According to specific embodiments, these segments constitute less than 40 %, less than 30 %, less than 20 %, less than 10 % of the viral genome.

[0428] According to specific embodiments, these segments constitute more than 1%, more than 5 %, more than 10 %, more than 20 % of the viral genome.

[0429] According to specific embodiments, these segments constitute less than 1% of the viral genome.

[0430] The virus may also be genetically engineered to change its host range, convert a temperate phage to a lytic phage, encode an anti-defense system polypeptide and the like.

[0431] Non-limiting Examples of modifications that can be introduced to a virus include genetic engineering of host-range-determining regions (HRDRs) in the tail fiber protein [see e.g. Yehl et al. Cell (2019) 179(2):459-469.e9 doi: 10.1016 / j.cell.2019.09.015, the contents of which are fully incorporated herein by reference] or receptor-binding proteins [see e.g. Lenneman et al. Curr Opin Biotechnol (2021) 68: 151-159 doi: 10.1016 / j.copbio.2020.11.003, the contents of which are fully incorporated herein by reference].

[0432] According to specific embodiments, the vims disclosed herein has an increased infectivity to at least one cell as compared to a virus of the same species not comprising said exogenous polynucleotide.

[0433] Specifically, according to specific embodiments, the phage disclosed herein has an increased infectivity to at least one bacteria as compared to a phage of the same species or strain not comprising said exogenous polynucleotide.

[0434] Various modalities may be used to introduce or express an exogenous or heterologous polynucleotide encoding the anti-defense polypeptide in the virus, as further described hereinabove and below.

[0435] Thus, according to an aspect of the present invention there is provided a method of producing a virus, the method comprising introducing into a virus an exogenous polynucleotide encoding the anti-defense system polypeptide, thereby producing the virus.

[0436] According to specific embodiments, the method comprises introducing the polynucleotide into the virus, under conditions which allow integration of the polynucleotide in a genome of the virus.

[0437] Various methods known within the art can be used to introduce the polynucleotides into a virus or a cell, typically involving contacting (e.g. the virus with the polynucleotide, the cell with the polynucleotide, the cell with the virus etc.) such as by way of genetic engineering. Such methods are described for example in Gibb et al. (2021) Pharmaceuticals, 14, 634; Chen et al. (2019) Front. Microbiol. 10:954; and Rustad, et al. (2018) Synthetic Biology, 3(1) ysy002, doi(dot)org / 10.1093 / synbio / ysy002, the contents of which are fully incorporated herein by reference.

[0438] According to specific embodiments, in order to allow expression of the polypeptides described herein in an infected host cell, the polynucleotides described herein are part of a nucleic acid construct (also referred to herein as an "expression vector" or a “vector”) which facilitates expression of the polynucleotide in a cell, integration of the polynucleotide in a genome of a virus or a cell, and / or selection or detection. Additional description on nucleic acid constructs is provided hereinbelow.

[0439] The present invention also contemplates cells comprising the anti-defense system polypeptide described herein.

[0440] Thus, according to an aspect of the present invention there is provided a cell comprising an exogenous anti-defense system polypeptide or a polynucleotide encoding same, wherein said anti-defense system polypeptide is selected from the group consisting of:

[0441] (i) a Tad3 polypeptide;

[0442] (ii) a Tad4 polypeptide;

[0443] (iii) a Tad5 polypeptide;

[0444] (iv) a Tad6 polypeptide;

[0445] (v) a Tad7 polypeptide;

[0446] (vi) a Tad8 polypeptide; and

[0447] (vii) an Acb3 polypeptide.

[0448] As used herein, the term “cell” refers to a prokaryotic or a eukaryotic cell. Non-limiting examples of cells that can be used in some embodiments of the present invention include, but are not limited to, bacteria, yeast, plant cell or an animal cell.

[0449] According to specific embodiments, the cell is a prokaryotic cell.

[0450] According to specific embodiments, the cell is a bacteria.

[0451] According to specific embodiments, the cell is an eukaryotic cell.

[0452] According to specific embodiments, the cell is a plant cell.

[0453] According to specific embodiments, the cell is an animal cell.

[0454] According to specific embodiments, the cell is a mammalian cell.

[0455] According to specific embodiments, the cell is a human cell.

[0456] According to specific embodiments, the cell is a differentiated cell.

[0457] According to specific embodiments, the cell is a stem or progenitor cell.

[0458] According to another specific embodiment, the cell is a primary cell.

[0459] According to a specific embodiment, the cell is a cell line. Non-limiting examples of such cell lines include a Chinese Hamster Ovary (CHO), HEK293, PER.C6, HT1080, NSO, Sp2 / 0, BHK, Namalwa, COS, HeLa and Vero cell.

[0460] The cell may be derived from a suitable tissue including but not limited to blood, muscle, nerve, brain, heart, lung, liver, pancreas, spleen, thymus, esophagus, stomach, intestine, kidney, testis, ovary, hair, skin, bone, breast, uterus, bladder, spinal cord, or various kinds of body fluids.

[0461] According to specific embodiments, the cell expresses the defense system polypeptide or a homolog thereof.

[0462] According to specific embodiments, the cell comprises one of the anti-defense polypeptides (i)-(vii) described herein or polynucleotides encoding same.

[0463] According to specific embodiments, the cell comprises at least two, at least three, at least four, at least five or six of the anti-defense polypeptides (i)-(vii) described herein or polynucleotide encoding same.

[0464] According to specific embodiments, the cell has increased sensitivity to infection by at least one virus as compared to a cell of the same species not comprising the exogenous antidefense system polypeptide or polynucleotide encoding same.

[0465] According to specific embodiments, the cell has an impaired ability to respond to stress as compared to a cell of the same species not comprising the exogenous anti-defense system polypeptide or polynucleotide encoding same.

[0466] Thus, according to an aspect of the present invention there is provided a method of impairing ability of a cell to respond to stress, the method comprising introducing into the cell an anti-defense system polypeptide or a polynucleotide encoding same, wherein said anti-defense system polypeptide is selected from the group consisting of:

[0467] (i) a Tad3 polypeptide;

[0468] (ii) a Tad4 polypeptide;

[0469] (iii) a Tad5 polypeptide;

[0470] (iv) a Tad6 polypeptide;

[0471] (v) a Tad7 polypeptide;

[0472] (vi) a Tad8 polypeptide; and

[0473] (vii) an Acb3 polypeptide, thereby impairing ability of a cell to respond to stress.

[0474] Various modalities may be used to introduce or express an exogenous anti-defense polypeptide or a polynucleotide encoding same in the cell, as further described hereinabove and below. It will be appreciated that the cell may be comprised inside a particular organism, for example inside a mammalian body or inside a plant.

[0475] Thus, according to other specific embodiments, the introducing or the contacting is effected in-vivo.

[0476] According to other specific embodiments, the introducing or the contacting is effected in- vitro or ex- vivo.

[0477] Thus, according to an aspect of the present invention there is provided a method of producing a cell, the method comprising introducing into a cell the anti-defense system polypeptide or the polynucleotide encoding same, thereby producing the cell.

[0478] According to specific embodiments, the method comprises introducing into the cell the anti-defense system polypeptide.

[0479] As used herein, the terms "peptide" and “polypeptide”, which are interchangeably used, encompass native peptides (either degradation products, synthetically synthesized peptides or recombinant peptides) and peptidomimetics (typically, synthetically synthesized peptides), as well as peptoids and semipeptoids which are peptide analogs, which may have, for example, modifications rendering the peptides more stable while in a body or more capable of penetrating into cells. Such modifications include, but are not limited to N terminus modification, C terminus modification, peptide bond modification, backbone modifications, and residue modification. Methods for preparing peptidomimetic compounds are well known in the art and are specified, for example, in Quantitative Drug Design, C.A. Ramsden Gd., Chapter 17.2, F. Choplin Pergamon Press (1992), which is incorporated by reference as if fully set forth herein. Further details in this respect are provided hereinunder.

[0480] Peptide bonds (-CO-NH-) within the peptide may be substituted, for example, by N- methylated amide bonds (-N(CH3)-C0-), ester bonds (-C(=O)-O-), ketomethylene bonds (-CO- CH2-), sulfinylmethylene bonds (-S(=O)-CH2-), a-aza bonds (-NH-N(R)-CO-), wherein R is any alkyl (e.g., methyl), amine bonds (-CH2-NH-), sulfide bonds (-CH2-S-), ethylene bonds (- CH2-CH2-), hydroxyethylene bonds (-CH(0H)-CH2-), thioamide bonds (-CS-NH-), olefinic double bonds (-CH=CH-), fluorinated olefinic double bonds (-CF=CH-), retro amide bonds (- NH-CO-), peptide derivatives (-N(R)-CH2-C0-), wherein R is the "normal" side chain, naturally present on the carbon atom.

[0481] These modifications can occur at any of the bonds along the peptide chain and even at several (2-3) bonds at the same time. Natural aromatic amino acids, Trp, Tyr and Phe, may be substituted by non-natural aromatic amino acids such as l,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (Tic), naphthylalanine, ring-methylated derivatives of Phe, halogenated derivatives of Phe or O- methyl-Tyr.

[0482] The peptides of some embodiments of the invention may also include one or more modified amino acids or one or more non-amino acid monomers (e.g. fatty acids, complex carbohydrates etc).

[0483] The term "amino acid" or "amino acids" is understood to include the 20 naturally occurring amino acids; those amino acids often modified post-translationally in vivo, including, for example, hydroxyproline, phosphoserine and phospho threonine; and other unusual amino acids including, but not limited to, 2-aminoadipic acid, hydroxylysine, isodesmosine, nor-valine, nor-leucine and ornithine. Furthermore, the term "amino acid" includes both D- and L-amino acids.

[0484] The amino acids of the peptides disclosed herein may be substituted either conservatively or non-conservatively.

[0485] The term “conservative substitution” as used herein, refers to the replacement of an amino acid present in the native sequence in the peptide with a naturally or non-naturally occurring amino or a peptidomimetics having similar steric properties. Where the side-chain of the native amino acid to be replaced is either polar or hydrophobic, the conservative substitution should be with a naturally occurring amino acid, a non-naturally occurring amino acid or with a peptidomimetic moiety which is also polar or hydrophobic (in addition to having the same steric properties as the side-chain of the replaced amino acid).

[0486] As naturally occurring amino acids are typically grouped according to their properties, conservative substitutions by naturally occurring amino acids can be easily determined bearing in mind the fact that in accordance with the invention replacement of charged amino acids by sterically similar non-charged amino acids are considered as conservative substitutions.

[0487] For producing conservative substitutions by non-naturally occurring amino acids it is also possible to use amino acid analogs (synthetic amino acids) well known in the art. A peptidomimetic of the naturally occurring amino acid is well documented in the literature known to the skilled practitioner.

[0488] When affecting conservative substitutions the substituting amino acid should have the same or a similar functional group in the side chain as the original amino acid.

[0489] The phrase "non-conservative substitutions" as used herein refers to replacement of the amino acid as present in the parent sequence by another naturally or non-naturally occurring amino acid, having different electrochemical and / or steric properties. Thus, the side chain of the substituting amino acid can be significantly larger (or smaller) than the side chain of the native amino acid being substituted and / or can have functional groups with significantly different electronic properties than the amino acid being substituted. Examples of non-conservative substitutions of this type include the substitution of phenylalanine or cycohexylmethyl glycine for alanine, isoleucine for glycine, or -NH-CH [(-CH2)5-COOH] -CO- for aspartic acid. Those non-conservative substitutions which fall under the scope of the present invention are those which still constitute a peptide having anti-bacterial properties.

[0490] The N and C termini of the peptides of the present invention may be protected by function groups. Suitable functional groups are described in Green and Wuts, "Protecting Groups in Organic Synthesis", John Wiley and Sons, Chapters 5 and 7, 1991, the teachings of which are incorporated herein by reference. Preferred protecting groups are those that facilitate transport of the compound attached thereto into a cell, for example, by reducing the hydrophilicity and increasing the lipophilicity of the compounds.

[0491] Various methods known within the art can be used to introduce a polypeptide into a cell, typically involving contacting (e.g. the cell with the polypeptide or composition comprising same).

[0492] According to specific embodiments, the peptides of the present invention may be attached (either covalently or non-covalently) to- or encapsulated by- a cell penetrating moiety.

[0493] As used herein the phrase "cell penetrating moiety" refers to a heterologous moiety which enhances translocation of the polypeptide across a cell membrane. Non-limiting examples of cell penetrating moieties include cell penetrating peptides and lipid particles.

[0494] For example, the polypeptide may be incorporated into a particulated delivery vehicle, e.g., a liposome, or a nano- or microparticle, by any of the methods known in the art [e.g. Liposome Technology, Vol. II, Incorporation of Drugs, Proteins, and Genetic Material, CRC Press; Monkkonen, J. et al., 1994, J. Drug Target, 2:299-308; Monkkonen, J. et al., 1993, Calcif. Tissue Int., 53: 139-145; Lasic D D., Liposomes Technology Inc., Elsevier, 1993, 63-105. (Chapter 3); Winterhalter M, Lasic D D, Chem Phys Lipids, 1993 September;64(l-3):35-43; Ramishetti et al. Adv Mater. 2020 Jan 30:e 1906128, International Patent Application Publication Nos. WG2018 / 015881 and WO2018087753, WO2017194454 and US Patent Application Publication no. US20130245107, the contents of which are fully incorporated herein by reference]. Liposomes include any synthetic (i.e., not naturally occurring) structure composed of lipid bilayers, which enclose a volume. Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. Liposomes can be of different sizes, may contain a low or a high pH and may be of different charge.

[0495] According to specific embodiments, the cell penetrating moiety is a cell penetrating peptide.

[0496] Typically, peptide penetrating agents have an amino acid composition containing either a high relative abundance of positively charged amino acids such as lysine or arginine, or have sequences that contain an alternating pattern of polar / charged amino acids and non-polar, hydrophobic amino acids. Non-limiting examples of CPPs that can penetrate cells in a non-toxic and efficient manner and may be suitable for use in accordance with some embodiments of the invention include TAT (transcription activator from HIV-1), pAntp (also named penetratin, Drosophila antennapedia homeodomain transcription factor) and VP22 (from Herpes Simplex virus). Protocols for producing CPPs-cargos conjugates and for infecting cells with such conjugates can be found, for example L Theodore et al. [The Journal of Neuroscience, (1995) 15(11): 7158- 7167], Fawell S, et al. [Proc Natl Acad Sci USA, (1994) 91:664-668], and Jing Bian et al. [Circulation Research. (2007) 100: 1626-1633].

[0497] The peptides of the present invention may also comprise non-amino acid moieties, such as for example, hydrophobic moieties (various linear, branched, cyclic, polycyclic or hetrocyclic hydrocarbons and hydrocarbon derivatives) attached to the peptides; non-peptide penetrating agents; various protecting groups, especially where the compound is linear, which are attached to the compound’s terminals to decrease degradation. Chemical (non-amino acid) groups present in the compound may be included in order to improve various physiological properties such; decreased degradation or clearance; decreased repulsion by various cellular pumps, improve immunogenic activities, improve various modes of administration (such as attachment of various sequences which allow penetration through various barriers, through the gut, etc.); increased specificity, increased affinity, decreased toxicity and the like.

[0498] Attaching the amino acid sequence component of the peptides of the invention to other non- amino acid agents may be by covalent linking, by non-covalent complexion, for example, by complexion to a hydrophobic polymer, which can be degraded or cleaved producing a compound capable of sustained release; by entrapping the amino acid part of the peptide in liposomes or micelles to produce the final peptide of the invention. The association may be by the entrapment of the amino acid sequence within the other component (liposome, micelle) or the impregnation of the amino acid sequence within a polymer to produce the final peptide of the invention.

[0499] The polypeptides of some embodiments of the invention may be synthesized and purified by any techniques known to those skilled in the art of peptide synthesis, such as, but not limited to, solid phase techniques and recombinant techniques such as further described herein.

[0500] According to specific embodiments, the method comprises introducing into the cell a polynucleotide encoding the anti-defense system polypeptide, under conditions which allow expression of the anti-defense polypeptide in the cell.

[0501] According to specific embodiments, in order to allow expression of the polypeptides described herein in an infected host cell, the polynucleotides described herein are part of a nucleic acid construct (also referred to herein as an "expression vector" or a “vector”) which facilitates expression of the polynucleotide in a cell, integration of the polynucleotide in a genome of a virus or a cell, and / or selection or detection.

[0502] As used herein, the terms “nucleic acid construct” and “expression vector” refer to a nucleic acid vector designed to introduce specific expression products of interest (i.e. polynucleotides) in a virus or a cell. The expression can be transient or consistent, episomal or integrated into the chromosome. According to specific embodiments, the expression is on a transmissible genetic element such as a plasmid.

[0503] Hence, the nucleic acid construct of some embodiments of the invention includes additional sequences which render this vector suitable for replication and integration in prokaryotes, eukaryotes, or preferably both (e.g., shuttle vectors). In addition, a typical cloning vector may contain regulatory elements e.g. promoters, enhancers, transcription and translation initiation sequence, transcription and translation terminator, polyadenylation signal transcription termination signals, a multiple cloning site (MCS) etc.

[0504] Hence, according to an aspect of the present invention, there is provided a nucleic acid construct comprising a polynucleotide encoding an anti-defense polypeptide selected from the group consisting of:

[0505] (i) a Tad3 polypeptide;

[0506] (ii) a Tad4 polypeptide;

[0507] (iii) a Tad5 polypeptide;

[0508] (iv) a Tad6 polypeptide;

[0509] (v) a Tad7 polypeptide;

[0510] (vi) a Tad8 polypeptide; and

[0511] (vii) an Acb3 polypeptide; and a nucleic acid sequence heterologous to said polynucleotide which facilitates expression of said polynucleotide in a cell, integration of said polynucleotide in a genome of a virus or a cell, and / or selection or detection.

[0512] According to specific embodiments, the nucleic acid sequence heterologous to the polynucleotide encoding the anti-defense polypeptide is a cis-acting regulatory element for directing expression of the polynucleotide in a cell.

[0513] Cis-acting regulatory sequences include those that direct constitutive expression of a nucleotide sequence as well as those that direct inducible expression of the polynucleotide only under certain conditions. Thus, for example, a promoter sequence for directing transcription of the polynucleotide sequence in the cell in a constitutive or inducible manner is included in the nucleic acid construct.

[0514] According to specific embodiments the promoter is active in a specific cell population transformed.

[0515] Eukaryotic promoters typically contain two types of recognition sequences, the TATA box and upstream promoter elements. The TATA box, located 25-30 base pairs upstream of the transcription initiation site, is thought to be involved in directing RNA polymerase to begin RNA synthesis. The other upstream promoter elements determine the rate at which transcription is initiated.

[0516] Enhancer elements can stimulate transcription up to 1,000 fold from linked homologous or heterologous promoters. Enhancers are active when placed downstream or upstream from the transcription initiation site. Many enhancer elements derived from viruses have a broad host range and are active in a variety of tissues. For example, the SV40 early gene enhancer is suitable for many cell types. Other enhancer / promoter combinations that are suitable for some embodiments of the invention include those derived from polyoma virus, human or murine cytomegalovirus (CMV), the long term repeat from various retroviruses such as murine leukemia virus, murine or Rous sarcoma virus and HIV. See, Enhancers and Eukaryotic Expression, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. 1983, which is incorporated herein by reference.

[0517] Constitutive promoters suitable for use with some embodiments of the invention are promoter sequences which are active under most environmental conditions and most types of cells such as the cytomegalovirus (CMV) and Rous sarcoma virus (RSV).

[0518] Other non-limiting examples of constitutive promoters suitable for use with some embodiments of the invention include T7, Sp6 and T3.

[0519] Non-limiting Examples of inducible promoters suitable for use with some embodiments of the invention include the tetracycline-inducible promoter (Zabala M, et al., Cancer Res. 2004, 64(8): 2799-804), the arabinose metabolic operon promoter (araBAD) or pathogen-inducible promoters. Such promoters include those from pathogenesis-related proteins (PR proteins), which are induced following infection by a pathogen.

[0520] According to specific embodiments the promoter is a bacterial promoter.

[0521] A bacterial promoter is any DNA sequence capable of binding bacterial RNA polymerase and initiating the downstream (3') transcription of a coding sequence into mRNA. A promoter can have a transcription initiation region, which is usually placed proximal to the 5' end of the coding sequence. This transcription initiation region typically includes an RNA polymerase binding site and a transcription initiation site. A bacterial promoter can also have a second domain called an operator, which can overlap an adjacent RNA polymerase binding site at which RNA synthesis begins. The operator permits negative regulated (inducible) transcription, as a gene repressor protein can bind the operator and thereby inhibit transcription of a specific gene. Constitutive expression can occur in the absence of negative regulatory elements, such as the operator. In addition, positive regulation can be achieved by a gene activator protein binding sequence, which, if present is usually proximal (5') to the RNA polymerase binding sequence.

[0522] An example of a gene activator protein is the catabolite activator protein (CAP), which helps initiate transcription of the lac operon in Escherichia coli (Raibaud et al. (1984) Annu. Rev. Genet. 18: 173). Regulated expression can therefore be either positive or negative, thereby either enhancing or reducing transcription. Other examples of positive and negative regulatory elements are well known in the art. Various promoters that can be included in the protein expression system include, but are not limited to, a T7 / LacO hybrid promoter, a trp promoter, a T7 promoter, a lac promoter, and a bacteriophage lambda promoter.

[0523] Sequences encoding metabolic pathway enzymes provide particularly useful promoter sequences. Examples include promoter sequences derived from sugar metabolizing enzymes, such as galactose, lactose (lac) (Chang et al. (1987) Nature 198: 1056), and maltose. Additional examples include promoter sequences derived from biosynthetic enzymes such as tryptophan (trp) (Goeddel et al. (1980) Nucleic Acids Res. 8:4057; Yelverton et al. (1981) Nucleic Acids Res. 9:731; U.S. Pat. No. 4,738,921; EPO Publication Nos. 36,776 and 121,775). The betalactamase (bla) promoter system (Weissmann, (1981) "The Cloning of Interferon and Other Mistakes," in Interferon 3 (ed. I. Gresser); bacteriophage lambda PL (Shimatake et al. (1981) Nature 292: 128); the arabinose-inducible araB promoter (U.S. Pat. No. 5,028,530); and T5 (U.S. Pat. No. 4,689,406) promoter systems also provide useful promoter sequences. See also Baibas (2001) Mol. Biotech. 19:251-267, where E. coli expression systems are discussed. In addition, synthetic promoters that do not occur in nature also function as bacterial promoters. For example, transcription activation sequences of one bacterial or phage promoter can be joined with the operon sequences of another bacterial or phage promoter, creating a synthetic hybrid promoter (U.S. Pat. No. 4,551,433). For example, the tac (Amann et al. (1983) Gene 25: 167; de Boer et al. (1983) Proc. Natl. Acad. Sci. 80:21) and trc (Brosius et al. (1985) J. Biol. Chem. 260:3539-3541) promoters are hybrid trp-lac promoters comprised of both trp promoter and lac operon sequences that are regulated by the lac repressor. The tac promoter has the additional feature of being an inducible regulatory sequence. Thus, for example, expression of a coding sequence operably linked to the tac promoter can be induced in a cell culture by adding isopropyl- l-thio-.beta.-D-galactoside (IPTG). Furthermore, a bacterial promoter can include naturally occurring promoters of non-bacterial origin that have the ability to bind bacterial RNA polymerase and initiate transcription. A naturally occurring promoter of non- bacterial origin can also be coupled with a compatible RNA polymerase to produce high levels of expression of some genes in prokaryotes. The phage T7 RNA polymerase / promoter system is an example of a coupled promoter system (Studier et al. (1986) J. Mol. Biol. 189: 113; Tabor et al. (1985) Proc. Natl. Acad. Sci. 82: 1074). In addition, a hybrid promoter can also be comprised of a phage promoter and an E. coli operator region (EPO Publication No. 267,851).

[0524] In the construction of the construct, the promoter is preferably positioned approximately the same distance from the heterologous transcription start site as it is from the transcription start site in its natural setting. As is known in the art, however, some variation in this distance can be accommodated without loss of promoter function.

[0525] Alternatively or additionally, the nucleic acid construct is designed to allow integration of the polynucleotide in a location enabling expression of the polynucleotide from a native promoter.

[0526] Hence, according to specific embodiments, the nucleic acid construct is devoid of a promoter.

[0527] According to specific embodiments, in order to avoid negatively affecting virus infectivity and specificity, the polynucleotide sequence is typically not inserted inside an existing viral open reading frame.

[0528] The nucleic acid construct can additionally contain a nucleic acid sequence encoding the repressor (or inducer) for the promoter. For example, an inducible construct of the present invention can regulate transcription from the Lac operator (LacO) by expressing the nucleotide sequence encoding the LacI repressor protein. Other examples include the use of the lexA gene to regulate expression of pRecA, and the use of trpO to regulate ptrp. Alleles of such genes that increase the extent of repression (e.g., laclq) or that modify the manner of induction (e.g., lambda CI857, rendering lambda pL thermo-inducible, or lambda CI+, rendering lambda pL chemo-inducible) can be employed.

[0529] Various construct schemes can be utilized to express few genes from a single nucleic acid construct. According to specific embodiments, the construct encodes a polycistronic mRNA comprising the polynucleotides of the present invention; that is the polynucleotides can be cotranscribed as a polycistronic message from a single promoter sequence of the nucleic acid construct. To enable co-translation of all the genes from a single polycistronic message, the different polynucleotide segments can be transcriptionally fused via a linker sequence including an internal ribosome entry site (IRES) sequence which enables the translation of the polynucleotide segment downstream of the IRES sequence. In this case, a transcribed polycistronic RNA molecule including the coding sequences of different combinations of the polynucleotides of the present invention will be translated from both the capped 5' end and the internal IRES sequence of the polycistronic RNA molecule. According to specific embodiments, the construct has an operon structure. Alternatively, each two nucleic acid sequence segments can be translationally fused via a protease recognition site cleavable by a protease expressed by the cell to be transformed with the nucleic acid construct. In this case, a chimeric polypeptide translated will be cleaved by the cell expressed protease. Still alternatively, the nucleic acid construct of some embodiments of the invention can include at least two Cis acting regulatory elements (e.g. promoter) each being for separately expressing a distinct polynucleotide. These at least two Cis acting regulatory elements can be identical or distinct.

[0530] Hence, according to specific embodiments, the nucleic acid sequence heterologous to the polynucleotide encoding the anti-defense system polypeptide is an element for expression of multiple polynucleotides from a single construct.

[0531] The nucleic acid construct of some embodiments of the invention includes additional sequences which render this construct suitable for replication and integration in prokaryotes, eukaryotes, or preferably both (e.g., shuttle vectors).

[0532] According to specific embodiments, the nucleic acid sequence heterologous to the polynucleotide encoding the anti-defense system polypeptide is a transmissible genetic element.

[0533] In other words, according to specific embodiments, the polynucleotide is on a transmissible genetic element, hence specific embodiments of the invention contemplate a transmissible element comprising a polynucleotide encoding the anti-defense system polypeptide. As used herein the term “transmissible element” or “transmissible genetic element”, which are interchangeably used, refers to a nucleic acid sequence that allows the transfer of the polynucleotide from one cell to another, e.g. a plasmid.

[0534] According to specific embodiments, the construct comprises a recombination element for integrating the polynucleotide into a genome of a virus or a cell transfected with the construct.

[0535] According to specific embodiments, the nucleic acid sequence heterologous to the polynucleotide encoding the anti-defense system polypeptide is a recombination element.

[0536] 1. According to a specific embodiment, the nucleic acid construct comprises a plurality of cloning sites for ligating a nucleic acid sequence of the invention such that it is under transcriptional regulation of the regulatory elements.

[0537] In addition to the elements already described, the expression vector of some embodiments of the invention may typically contain other specialized elements intended to increase the level of expression of cloned nucleic acids or to facilitate the identification of cells that carry the recombinant DNA. For example, a number of animal viruses contain DNA sequences that promote the extra chromosomal replication of the viral genome in permissive cell types. Plasmids bearing these viral replicons are replicated episomally as long as the appropriate factors are provided by genes either carried on the plasmid or with the genome of the host cell.

[0538] The vector may or may not include a eukaryotic replicon. If a eukaryotic replicon is present, then the vector is amplifiable in eukaryotic cells using the appropriate selectable marker. If the vector does not comprise a eukaryotic replicon, no episomal amplification is possible. Instead, the recombinant DNA integrates into the genome of the engineered cell, where the promoter directs expression of the desired nucleic acid.

[0539] 2. Selectable marker genes that ensure maintenance of the construct in the virus or cell can also be included in the construct.

[0540] 3. According to specific embodiments, the nucleic acid sequence heterologous to the polynucleotide encoding the anti-defense system polypeptide is a selectable marker.

[0541] 4. Preferred selectable markers include those which confer resistance to drugs such as ampicillin, chloramphenicol, erythromycin, kanamycin (neomycin), and tetracycline (Davies et al. (1978) Annu. Rev. Microbiol. 32:469). Selectable markers can also allow a cell to grow on minimal medium, or in the presence of toxic metabolite and can include biosynthetic genes, such as those in the histidine, tryptophan, and leucine biosynthetic pathways.

[0542] Other than containing the necessary elements for the transcription and translation of the inserted coding sequence, the expression construct of some embodiments of the invention can also include sequences engineered to enhance stability, production, purification, yield or toxicity of the expressed polypeptide.

[0543] Where appropriate, the nucleic acid sequences may be optimized for increased expression in the transformed organism. For example, the nucleic acid sequences can be synthesized using preferred codons for improved expression.

[0544] When needed, recovery of the recombinant polypeptide is effected following an appropriate time in culture.

[0545] Examples for mammalian expression vectors include, but are not limited to, pcDNA3, pcDNA3.1(+ / -), pGL3, pZeoSV2(+ / -), pSecTag2, pDisplay, pEF / myc / cyto, pCMV / myc / cyto, pCR3.1, pSinRep5, DH26S, DHBB, pNMTl, pNMT41, pNMT81, which are available from Invitrogen, pCI which is available from Promega, pMbac, pPbac, pBK-RSV and pBK-CMV which are available from Strategene, pTRES which is available from Clontech, and their derivatives.

[0546] Examples of bacterial constructs include the pET series of E. coli expression vectors [Studier et al. (1990) Methods in Enzymol. 185:60-89).

[0547] In yeast, a number of vectors containing constitutive or inducible promoters can be used, as disclosed in U.S. Pat. Application No: 5,932,447. Alternatively, vectors can be used which promote integration of foreign DNA sequences into the yeast chromosome.

[0548] In cases where plant expression vectors are used, the expression of the coding sequence can be driven by a number of promoters. For example, viral promoters such as the 35S RNA and 19S RNA promoters of CaMV [Brisson et al. (1984) Nature 310:511-514], or the coat protein promoter to TMV [Takamatsu et al. (1987) EMBO J. 6:307-311] can be used. Alternatively, plant promoters such as the small subunit of RUBISCO [Coruzzi et al. (1984) EMBO J. 3: 1671- 1680 and Brogli et al., (1984) Science 224:838-843] or heat shock promoters, e.g., soybean hspl7.5-E or hspl7.3-B [Gurley et al. (1986) Mol. Cell. Biol. 6:559-565] can be used. These constructs can be introduced into plant cells using Ti plasmid, Ri plasmid, plant viral vectors, direct DNA transformation, microinjection, electroporation and other techniques well known to the skilled artisan. See, for example, Weissbach & Weissbach, 1988, Methods for Plant Molecular Biology, Academic Press, NY, Section VIII, pp 421-463.

[0549] Other expression systems such as insects and mammalian host cell systems which are well known in the art can also be used by some embodiments of the invention.

[0550] Expression vectors containing regulatory elements from eukaryotic viruses such as retroviruses can be also used. SV40 vectors include pSVT7 and pMT2. Vectors derived from bovine papilloma virus include pBV-lMTHA, and vectors derived from Epstein Bar virus include pHEBO, and p2O5. Other exemplary vectors include pMSG, pAV009 / A+, pMTO10 / A+, pMAMneo-5, baculovirus pDSVE, and any other vector allowing expression of proteins under the direction of the SV-40 early promoter, SV-40 later promoter, metallo thionein promoter, murine mammary tumor virus promoter, Rous sarcoma virus promoter, polyhedrin promoter, or other promoters shown effective for expression in eukaryotic cells.

[0551] The type of vector used by some embodiments of the invention will depend on the cell type transformed. The ability to select suitable vectors according to the virus or cell type transformed is well within the capabilities of the ordinary skilled artisan and as such no general description of selection consideration is provided herein.

[0552] Various methods can be used to introduce the polynucleotides and expression vectors of some embodiments of the invention into cells. Such methods are generally described in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Springs Harbor Laboratory, New York (1989, 1992), in Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1989), Chang et al., Somatic Gene Therapy, CRC Press, Ann Arbor, Mich. (1995), Vega et al., Gene Targeting, CRC Press, Ann Arbor Mich. (1995), Vectors: A Survey of Molecular Cloning Vectors and Their Uses, Butterworths, Boston Mass. (1988) and Gilboa et at. [Biotechniques 4 (6): 504-512, 1986] and include, for example, stable or transient transfection, lipofection, electroporation and infection with recombinant viral vectors. In addition, see U.S. Pat. Nos. 5,464,764 and 5,487,992 for positive-negative selection methods.

[0553] Introduction of nucleic acids by viral infection offers several advantages over other methods such as lipofection and electroporation, since higher transfection efficiency can be obtained due to the infectious nature of viruses.

[0554] Currently preferred in vivo nucleic acid transfer techniques include transfection with viral or non-viral constructs, such as adenovirus, lentivirus, Herpes simplex I virus, or adeno- associated virus (AAV) and lipid-based systems. Useful lipids for lipid-mediated transfer of the gene are, for example, DOTMA, DOPE, and DC-Chol [Tonkinson et al., Cancer Investigation, 14(1): 54-65 (1996)]. The most preferred constructs for use in gene therapy are viruses, most preferably adenoviruses, AAV, lentiviruses, or retroviruses. A viral construct such as a retroviral construct includes at least one transcriptional promoter / enhancer or locus-defining element(s), or other elements that control gene expression by other means such as alternate splicing, nuclear RNA export, or post-translational modification of messenger. Such vector constructs also include a packaging signal, long terminal repeats (LTRs) or portions thereof, and positive and negative strand primer binding sites appropriate to the virus used, unless it is already present in the viral construct. Other vectors can be used that are non-viral, such as cationic lipids, polylysine, and dendrimers.

[0555] According to specific embodiments, introducing the polynucleotides or constructs into a cell is effected by contacting the cell with the genetically modified virus disclosed herein.

[0556] Thus, according to an aspect of the present invention, there is provided a method of infecting a cell, the method comprising contacting the cell with the virus of some embodiments of the invention.

[0557] According to specific embodiments, the cell further comprises an exogenous polynucleotide of interest.

[0558] Thus, according to specific embodiments, the method disclosed herein further comprises introducing into the cell an exogenous polynucleotide of interest.

[0559] The present invention also contemplates uses of the viruses and cells disclosed herein.

[0560] Hence, the phages of some embodiments of the invention comprising the polynucleotide encoding an anti-defense system polypeptide can be used for infecting a bacteria and / or treating a bacterial infection.

[0561] Thus, according to an aspect of the present invention there is provided a method of infecting a bacteria, the method comprising contacting the bacteria with the phage comprising the exogenous polynucleotide encoding the anti-defense system polypeptide disclosed herein, thereby infecting the bacteria.

[0562] According to an additional or an alternative aspect of the present invention there is provided a method of treating a bacterial infection in a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of the phage comprising the exogenous polynucleotide encoding the anti-defense system polypeptide disclosed herein, thereby treating the bacterial infection in the subject.

[0563] According to an additional or an alternative aspect of the present invention there is provided the phage comprising the exogenous polynucleotide encoding the anti-defense system polypeptide disclosed herein, for use in treating a bacterial infection in the subject in need thereof.

[0564] The term “treating” refers to inhibiting or arresting the development of a pathology (disease, disorder or condition) and / or causing the reduction, remission, or regression of a pathology. Those of skill in the art will understand that various methodologies and assays can be used to assess the development of a pathology, and similarly, various methodologies and assays may be used to assess the reduction, remission or regression of a pathology. Thus, for example, bacterial infection may be assessed by, but not limited to, clinical evaluation, urine dipstick tests, throat culture, sputum tests, histology, indirect non-culture-based tests, including C-reactive protein and procalcitonin tests, serological tests and / or nucleic acid amplification tests.

[0565] As used herein, the phrase “subject in need thereof’ includes mammals, preferably human beings of any gender and at any age which suffer from the pathology.

[0566] According to specific embodiments, the bacteria is of a Gram-negative bacteria or Negativicutes that stain negative in Gram stain.

[0567] Non-limiting examples of Gram-negative bacteria include Acinetobacter calcoaceticus, Actinobacillus actinomycetemcomitans, Aeromonas hydrophila, Alcaligenes xylosoxidans, Bacteroides, Bacteroides fragilis, Bartonella bacilliformis, Bordetella spp., Borrelia burgdorferi, Branhamella catarrhalis, Brucella spp., Campylobacter spp., Chalmydia pneumoniae, Chlamydia psittaci, Chlamydia trachomatis, Chromobacterium violaceum, Citrobacter spp., Eikenella corrodens, Enterobacter aerogenes, Escherichia coli, Flavobacterium meningosepticum, Fusobacterium spp., Haemophilus influenzae, Haemophilus spp., Helicobacter pylori, Klebsiella spp., Eegionella spp., Eeptospira spp., Moraxella catarrhalis, Morganella morganii, Mycoplasma pneumoniae, Neisseria gonorrhoeae, Neisseria meningitidis, Pasteurella multocida, Plesiomonas shigelloides, Prevotella spp., Proteus spp., Providencia rettgeri, Pseudomonas aeruginosa, Pseudomonas spp., Rickettsia prowazekii, Rickettsia rickettsii, Rochalimaea spp., Salmonella spp., Salmonella typhi, Serratia marcescens, Shigella spp., Treponema carateum, Treponema pallidum, Treponema pallidum endemicum, Treponema pertenue, Veillonella spp., Vibrio cholerae, Vibrio vulnificus, Yersinia enterocolitica, Yersinia pestis.

[0568] According to specific embodiments, the bacteria is a gammaproteobacteria (e.g. Escherichia coli, pseudomonas, vibrio and klebsiellA' ) or a Firmicutes (belonging to class Negativicutes that stain negative in Gram stain).

[0569] According to specific embodiments, the bacteria is a Gram-positive bacteria.

[0570] Non-limiting examples of Gram-positive bacteria include, but are not limited to, Actinomyces spp., Bacillus anthracis, Bifidobacterium spp., Clostridium botulinum, Clostridium perfringens, Clostridium spp., Clostridium tetani, Corynebacterium diphtheriae, Corynebacterium jeikeium, Enterococcus faecalis, Enterococcus faecium, Erysipelothrix rhusiopathiae, Eubacterium spp., Gardnerella vaginalis, Gemella morbillorum, Leuconostoc spp., Mycobacterium abcessus, Mycobacterium avium complex, Mycobacterium chelonae, Mycobacterium fortuitum, Mycobacterium haemophilium, Mycobacterium kansasii, Mycobacterium leprae, Mycobacterium marinum, Mycobacterium scrofulaceum, Mycobacterium smegmatis, Mycobacterium terrae, Mycobacterium tuberculosis, Mycobacterium ulcerans, Nocardia spp., Peptococcus niger, Peptostreptococcus spp., Proprionibacterium spp., Staphylococcus aureus, Staphylococcus auricularis, Staphylococcus capitis, Staphylococcus cohnii, Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus lugdanensis, Staphylococcus saccharolyticus, Staphylococcus saprophyticus, Staphylococcus schleiferi, Staphylococcus similans, Staphylococcus warneri, Staphylococcus xylosus, Streptococcus agalactiae (group B streptococcus), Streptococcus anginosus, Streptococcus bovis, Streptococcus canis, Streptococcus equi, Streptococcus milleri, Streptococcus mitior, Streptococcus mutans, Streptococcus pneumoniae, Streptococcus pyogenes (group A streptococcus), Streptococcus salivarius, Streptococcus sanguis.

[0571] According to specific embodiments the bacteria is a species selected from the group consisting of Escherichia, Shigella, Salmonella, Erwinia, Yersinia, Bacillus, Vibrio, Legionella, Pseudomonas, Neisseria, Bordetella, Helicobacter, Listeria, Agrobacterium, Staphylococcus, Streptococcus, Enterococcus, Clostridium, Corynebacterium, Mycobacterium, Treponema, Borrelia, Francisella, Brucella, Campylobacter, Klebsiella, Frankia, Bartonella, Rickettsia, Shewanella, Serratia, Enterobacter, Proteus, Providencia, Brochothrix, and Brevibacterium.

[0572] According to specific embodiments, the bacteria is selected from the group consisting of Escherichia coli, Klebsiella pneumoniae, Clostridium difficile and Pseudomonas aeruginosa.

[0573] According to specific embodiments, the bacterium expresses the bacterial defense system the anti-defense system polypeptide is directed against e.g. Thoeris and / or CBASS.

[0574] According to specific embodiments, the method comprises determining expression of the bacterial defense system in the bacteria prior to the introducing, the contacting or the treating. Methods of determining expression are well known in the art and include e.g. sequencing, PCR, Western blot etc.

[0575] The phage therapy of some embodiments of the invention may be combined with one or more non-phage therapeutic and / or prophylactic agents, useful for the treatment and / or prevention of bacterial infections, as described herein and / or known in the art (e.g. one or more traditional antibiotic agents). Other therapeutic and / or prophylactic agents that may be used in combination with the phage(s) of some embodiments of the invention include, but are not limited to, antibiotic agents, anti-inflammatory agents, antiviral agents, antifungal agents, or local anesthetic agents.

[0576] Thus, according to specific embodiments, the methods of the present invention further comprise administering to the subject a therapeutically effective amount of an antibiotic or contacting the bacteria with an antibiotic. According to specific embodiments, the uses of the present invention further comprise an antibiotic.

[0577] Exemplary antibiotics include, but are not limited to aminoglycoside antibiotics, cephalosporins, quinolone antibiotics, macrolide antibiotics, penicillins, sulfonamides, tetracyclines and carbapenems.

[0578] Standard or traditional antibiotic agents that can be administered with the phages described herein include, but are not limited to, amikacin, gentamicin, kanamycin, neomycin, netilmicin, paromomycin, rhodostreptomycin, streptomycin, tobramycin, apramycin, rifamycin, naphthomycin, mupirocin, geldanamycin, ansamitocin, carbacephems, imipenem, meropenem, ertapenem, faropenem, doripenem, panipenem / betamipron, biapenem, PZ-601, cephalosporins, cefacetrile, cefadroxil, cefalexin, cefaloglycin, cefalonium, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazaflur, cefazedone, cefazolin, cefradine, cefroxadine, ceftezole, cefaclor, cefonicid, cefprozil, cefuroxime, cefuzonam, cefmetazole, cefotetan, cefoxitin, cefcapene, cefdaloxime, cefdinir, cefditoren, cefetamet, cefixime, cefmenoxime, cefteram, ceftibuten, ceftiofur, ceftiolene, ceftizoxime, ceftriaxone, cefoperazone, ceftazidime latamoxef, cefclidine, cefepime, cefluprenam, cefoselis, cefozopran, cefpirome, cefquinome, flomoxef. ceftobiprole, azithromycin, clarithromycin, dirithromycin, erythromycin, roxithromycin, aztreonam, pencillin and penicillin derivatives, actinomycin, bacitracin, colistin, polymyxin B, cinoxacin, flumequine, nalidixic acid, oxolinic acid, piromidic acid, pipemidic acid, rosoxacin, ciprofloxacin, enoxacin, fleroxacin, lomefloxacin, nadifloxacin, norfloxacin, ofloxacin, pefloxacin, rufloxacin, balofloxacin, gatifloxacin, grepafloxacin, levofloxacin, moxifloxacin, pazufloxacin, sparfloxacin, temafloxacin, tosufloxacin, clinafloxacin, garenoxacin, gemifloxacin, stifloxacin, trovalfloxacin, prulifloxacin, acetazolamide, benzolamide, bumetanide, celecoxib, chlorthalidone, clopamide, dichlorphenamide, dorzolamide, ethoxyzolamide, furosemide, hydrochlorothiazide, indapamide, mafendide, mefruside, metolazone, probenecid, sulfacetamide, sulfadimethoxine, sulfadoxine, sulfanilamides, sulfamethoxazole, sulfasalazine, sultiame, sumatriptan, xipamide, tetracycline, chlortetracycline, oxytetracycline, doxycycline, lymecycline, meclocycline, methacycline, minocycline, rolitetracycline, methicillin, nafcillin, oxacilin, cioxacillin, vancomycin, teicoplanin, clindamycin, co-trimoxazole, flucloxacillin, dicloxacillin, ampicillin, amoxicillin and any combination thereof.

[0579] According to another aspect there is provided an article of manufacture or a kit comprising as active ingredients the phage comprising the exogenous polynucleotide encoding the anti-defense system polypeptide disclosed herein; and an antibiotic. According to specific embodiments, the article of manufacture is identified for treating a bacterial infection.

[0580] According to specific embodiments, the phage and the antibiotic are in separate formulations.

[0581] Thus, according to specific embodiments, the phage and the antibiotic are packaged in separate containers.

[0582] According to yet other specific embodiments the phage and the antibiotic are in a coformulation.

[0583] According to other specific embodiments, the phage therapy is the only active agent administered to the subject, e.g. in the absence of a standard or traditional effective antibiotic agent.

[0584] The examples section which follows demonstrate that phage-encoded inhibitors of bacterial defense systems can also inhibit their eukaryotic plant and human homologs (Example 6 of the Examples section which follows). Hence, specific embodiments of the present invention contemplate they can be used to improve resistance of a plant to biotic stress and to treat diseases that can benefit from inhibiting the defense system homologs.

[0585] Thus, according to an aspect of the present invention, there is provided a method of improving resistance of a plant to biotic stress, the method comprising introducing into the plant an anti-defense system polypeptide or a polynucleotide encoding same, wherein said anti-defense system polypeptide is selected from the group consisting of:

[0586] (i) a Tad3 polypeptide, wherein said Tad3 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 endogenously expressed in said plant;

[0587] (ii) a Tad4 polypeptide, wherein said Tad4 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 endogenously expressed in said plant;

[0588] (iii) a Tad5 polypeptide, wherein said Tad5 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 endogenously expressed in said plant;

[0589] (iv) a Tad6 polypeptide, wherein said Tad7 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 endogenously expressed in said plant; (v) a Tad7 polypeptide, wherein said Tad7 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 228 endogenously expressed in said plant;

[0590] (vi) a Tad8 polypeptide, wherein said Tad8 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 227 endogenously expressed in said plant; and

[0591] (vii) an Acb3 polypeptide, wherein said Acb3 polypeptide binds a homolog of the bacterial defense system polypeptide cGAS of a CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233 endogenously expressed in said plant, thereby improving resistance of the plant to biotic stress.

[0592] According to an additional or an alternative aspect of the present invention there is provided a method of treating a disease that can benefit from inhibiting a defense system polypeptide in a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of an anti-defense system polypeptide or a polynucleotide encoding same, wherein: when said defense system polypeptide is a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 endogenously expressed in said subject, the anti-defense system polypeptide is a Tad3 polypeptide, a Tad4 polypeptide, a Tad5 polypeptide and / or a Tad6 polypeptide which binds said homolog of SEQ ID NO: 10; when said defense system polypeptide is a homolog of the defense system polypeptide ThsB of a Type II Thoeris set forth in SEQ ID NO: 228 endogenously expressed in said subject, the anti-defense system polypeptide is a Tad7 polypeptide which binds said homolog of SEQ ID NO: 228; when said defense system polypeptide is a homolog of the defense system polypeptide ThsA of a Type II Thoeris set forth in SEQ ID NO: 227 endogenously expressed in said subject, the anti-defense system polypeptide is a Tad8 polypeptide which binds said homolog of SEQ ID NO: 227; and / or when said defense system polypeptide is a homolog of the defense system polypeptide cGAS of a CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233 endogenously expressed in said subject, the anti-defense system polypeptide is an Acb3 polypeptide which binds said homolog of amino acid sequence selected from the group consisting of SEQ ID NO: 229-231 and 233, thereby treating the disease in the subject. According to an additional or an alternative aspect of the present invention there is provided the anti-defense system polypeptide or a polynucleotide encoding same for use in treating a disease that can benefit from inhibiting a defense system polypeptide in a subject in need thereof, wherein: when said defense system polypeptide is a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 endogenously expressed in said subject, the anti-defense system polypeptide is a Tad3 polypeptide, a Tad4 polypeptide, a Tad5 polypeptide and / or a Tad6 polypeptide which binds said homolog of SEQ ID NO: 10; when said defense system polypeptide is a homolog of the defense system polypeptide ThsB of a Type II Thoeris set forth in SEQ ID NO: 228 endogenously expressed in said subject, the anti-defense system polypeptide is a Tad7 polypeptide which binds said homolog of SEQ ID NO: 228; when said defense system polypeptide is a homolog of the defense system polypeptide ThsA of a Type II Thoeris set forth in SEQ ID NO: 227 endogenously expressed in said subject, the anti-defense system polypeptide is a Tad8 polypeptide which binds said homolog of SEQ ID NO: 227; and / or when said defense system polypeptide is a homolog of the defense system polypeptide cGAS of a CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233 endogenously expressed in said subject, the anti-defense system polypeptide is an Acb3 polypeptide which binds said homolog of SEQ ID NO. selected from the group consisting of 229-231 and 233.

[0593] According to specific embodiments, the disease is selected from the group consisting of autoimmune disease, interferonopathy and a disease associated with neuronal degeneration.

[0594] According to specific embodiments, the disease is an autoimmune disease. Exemplary autoimmune diseases include, but are not limited to, rheumatoid arthritis (RA), lupus (SLE), atherosclerosis, multiple sclerosis (MS), hashimoto disease, type I diabetes, autoimmune pancreatitis, graft-versus-host disease (GVHD), sepsis, Ebola, avian influenza, smallpox, systemic inflammatory response syndrome (SIRS), hemophagocytic lymphohistiocytosis, Crohn’s and ulcerative colitis, familial Mediterranean fever (FMF), TNF receptor-associated periodic syndrome (TRAPS), hyperimmunoglobulinemia D with periodic fever syndrome (HIDS), familial cold autoinflammatory syndrome (FCAS), the Muckle-Wells syndrome (MWS), neonatal-onset multisystem inflammatory disease (NOMID), deficiency of ADA2 (DADA2), NLRC4 inflammasomopathies, X-linked lymphoproliferative type 2 disorder (XLP), the Takenouchi-Kosaki syndrome, and the Wiskott-Aldrich syndrome (WAS). According to specific embodiments, the disease is associated with neuronal degeneration. The injury may be brought about by a disease e.g. a neurodegenerative disease, stroke or by an injury per se, such as a traumatic brain injury, a spinal cord injury, a peripheral nerve injury or an eye injury. Exemplary neurodegenerative diseases include, but are not limited to Amyotrophic Lateral Sclerosis (ALS), Parkinson's disease, Multiple System Atrophy (MSA), Huntington's disease, Alzheimer's disease, Rett Syndrome and Multiple Sclerosis (MS).

[0595] The therapeutic agent described herein may be used per se or as part of a pharmaceutical composition, where it is mixed with suitable carriers or excipients.

[0596] As used herein a "pharmaceutical composition" refers to a preparation of one or more of the active ingredients described herein with other chemical components such as physiologically suitable carriers and excipients. The purpose of a pharmaceutical composition is to facilitate administration of a compound to an organism.

[0597] Hereinafter, the phrases "physiologically acceptable carrier" and "pharmaceutically acceptable carrier" which may be interchangeably used refer to a carrier or a diluent that does not cause significant irritation to an organism and does not abrogate the biological activity and properties of the administered compound. An adjuvant is included under these phrases.

[0598] Herein the term "excipient" refers to an inert substance added to a pharmaceutical composition to further facilitate administration of an active ingredient. Examples, without limitation, of excipients include calcium carbonate, calcium phosphate, various sugars and types of starch, cellulose derivatives, gelatin, vegetable oils and polyethylene glycols.

[0599] Techniques for formulation and administration of drugs may be found in “Remington’s Pharmaceutical Sciences,” Mack Publishing Co., Easton, PA, latest edition, which is incorporated herein by reference.

[0600] Suitable routes of administration may, for example, include topical, oral, rectal, transmucosal, especially transnasal, intestinal or parenteral delivery, including intramuscular, subcutaneous and intramedullary injections as well as intrathecal, direct intraventricular, intracardiac, e.g., into the right or left ventricular cavity, into the common coronary artery, intravenous, intraperitoneal, intranasal, or intraocular injections.

[0601] Alternately, one may administer the pharmaceutical composition in a local rather than systemic manner, for example, via injection of the pharmaceutical composition directly into a tissue region of a patient. In one embodiment, the phage may be administered directly into an infected area or tissue of the subject.

[0602] Pharmaceutical compositions of some embodiments of the invention may be manufactured by processes well known in the art, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping, spray drying, coating or lyophilizing processes.

[0603] Pharmaceutical compositions for use in accordance with some embodiments of the invention thus may be formulated in conventional manner using one or more physiologically acceptable carriers comprising excipients and auxiliaries, which facilitate processing of the active ingredients into preparations which, can be used pharmaceutically. Proper formulation is dependent upon the route of administration chosen.

[0604] For injection, the active ingredients of the pharmaceutical composition may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hank’s solution, Ringer’s solution, or physiological salt buffer. For transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.

[0605] For oral administration, the pharmaceutical composition can be formulated readily by combining the active compounds with pharmaceutically acceptable carriers well known in the art. Such carriers enable the pharmaceutical composition to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions, and the like, for oral ingestion by a patient. Pharmacological preparations for oral use can be made using a solid excipient, optionally grinding the resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries if desired, to obtain tablets or dragee cores. Suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carbomethylcellulose; and / or physiologically acceptable polymers such as polyvinylpyrrolidone (PVP). If desired, disintegrating agents may be added, such as cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.

[0606] Dragee cores are provided with suitable coatings. For this purpose, concentrated sugar solutions may be used which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, titanium dioxide, lacquer solutions and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.

[0607] Pharmaceutical compositions which can be used orally, include push-fit capsules made of gelatin as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. The push-fit capsules may contain the active ingredients in admixture with filler such as lactose, binders such as starches, lubricants such as talc or magnesium stearate and, optionally, stabilizers. In soft capsules, the active ingredients may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols. In addition, stabilizers may be added. All formulations for oral administration should be in dosages suitable for the chosen route of administration.

[0608] For buccal administration, the compositions may take the form of tablets or lozenges formulated in conventional manner.

[0609] For administration by nasal inhalation, the active ingredients for use according to some embodiments of the invention are conveniently delivered in the form of an aerosol spray presentation from a pressurized pack or a nebulizer with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichloro-tetrafluoroethane or carbon dioxide. In the case of a pressurized aerosol, the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, e.g., gelatin for use in a dispenser may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.

[0610] The pharmaceutical composition described herein may be formulated for parenteral administration, e.g., by bolus injection or continues infusion. Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multidose containers with optionally, an added preservative. The compositions may be suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and / or dispersing agents.

[0611] Pharmaceutical compositions for parenteral administration include aqueous solutions of the active preparation in water-soluble form. Additionally, suspensions of the active ingredients may be prepared as appropriate oily or water based injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acids esters such as ethyl oleate, triglycerides or liposomes. Aqueous injection suspensions may contain substances, which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol or dextran. Optionally, the suspension may also contain suitable stabilizers or agents which increase the solubility of the active ingredients to allow for the preparation of highly concentrated solutions.

[0612] Alternatively, the active ingredient may be in powder form for constitution with a suitable vehicle, e.g., sterile, pyrogen-free water based solution, before use.

[0613] The pharmaceutical composition of some embodiments of the invention may also be formulated in rectal compositions such as suppositories or retention enemas, using, e.g., conventional suppository bases such as cocoa butter or other glycerides. Pharmaceutical compositions suitable for use in context of some embodiments of the invention include compositions wherein the active ingredients are contained in an amount effective to achieve the intended purpose. More specifically, a therapeutically effective amount means an amount of active ingredients (e.g. phage, antibiotic) effective to prevent, alleviate or ameliorate symptoms of a disorder (e.g. bacterial infection) or prolong the survival of the subject being treated.

[0614] Determination of a therapeutically effective amount is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein.

[0615] For any preparation used in the methods of the invention, the therapeutically effective amount or dose can be estimated initially from in vitro and cell culture assays. For example, a dose can be formulated in animal models to achieve a desired concentration or titer. Such information can be used to more accurately determine useful doses in humans.

[0616] In some embodiments, the pharmaceutical composition is delivered to a subject in need thereof so as to provide one or more phages in an amount corresponding to a multiplicity of infection (MOI) of about 0.001 to about 10. MOI is determined by assessing the approximate bacterial load, or using an estimate for a given type of infection; and then providing phage in an amount calculated to give the desired MOI.

[0617] According to a specific embodiment the composition comprises at least about 106PFU, 107PFU, 108PFU, 109PFU, or even IO10PFU or more of the phage disclosed herein.

[0618] In other embodiments, the amount of phage is provided so as to reduce the amount of bacteria by at least 10 %, 20 %, 30 %, 40 %, 50 %, 60 %, 70 %, 80 %, 90 % or even 100 %.

[0619] Toxicity and therapeutic efficacy of the active ingredients described herein can be determined by standard pharmaceutical procedures in vitro, in cell cultures or experimental animals. The data obtained from these in vitro and cell culture assays and animal studies can be used in formulating a range of dosage for use in human. The dosage may vary depending upon the dosage form employed and the route of administration utilized. The exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. (See e.g., Fingl, et al., 1975, in "The Pharmacological Basis of Therapeutics", Ch. 1 P-l).

[0620] Dosage amount and interval may be adjusted individually to provide levels of the active ingredient are sufficient to induce or suppress the biological effect (minimal effective concentration, MEC). The MEC will vary for each preparation, but can be estimated from in vitro data. Dosages necessary to achieve the MEC will depend on individual characteristics and route of administration. Detection assays can be used to determine plasma concentrations. Depending on the severity and responsiveness of the condition to be treated, dosing can be of a single or a plurality of administrations, with course of treatment lasting from several days to several weeks or until cure is effected or diminution of the disease state is achieved.

[0621] The amount of a composition to be administered will, of course, be dependent on the subject being treated, the severity of the affliction, the manner of administration, the judgment of the prescribing physician, etc.

[0622] It will be appreciated that since the phages of embodiments of this invention may enhance the anti-bacterial effect of an antibiotic, doses of the antibiotic may be lower (e.g. 20 % lower, 30 % lower, 40 % lower, 50 % lower, 60 % lower, 70 % lower, 80 % lower or even 90 % lower) than their gold standard dose or in a sub-efficacious dose when administered as a single agent.

[0623] Compositions of some embodiments described herein may comprise a single phage strain or a cocktail of multiple distinct phages wherein as least one of the phages is the phage disclosed herein.

[0624] According to specific embodiments, the compositions described herein comprise more than one phage strain. In one embodiment, the composition comprises 2 phage strains, 3 phage strains, 4 phage strains, 5 phage strains or more.

[0625] The phage cocktails of some embodiments comprise phages that target a single bacteria species or subspecies.

[0626] According to other specific embodiments, the phage cocktail comprises phages that target multiple bacteria species or subspecies, each phage with a distinct host range.

[0627] Compositions of some embodiments of the invention may, if desired, be presented in a pack or dispenser device, such as an FDA approved kit, which may contain one or more unit dosage forms containing the active ingredient. The pack may, for example, comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration. The pack or dispenser may also be accommodated by a notice associated with the container in a form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals, which notice is reflective of approval by the agency of the form of the compositions or human or veterinary administration. Such notice, for example, may be of labeling approved by the U.S. Food and Drug Administration for prescription drugs or of an approved product insert. Compositions comprising a preparation of the invention formulated in a compatible pharmaceutical carrier may also be prepared, placed in an appropriate container, and labeled for treatment of an indicated condition, as is further detailed above. The phages, phage cocktails and articles of manufacture of some embodiments of the invention can be also used in anti-infective compositions for controlling the growth of bacteria on a surface contacted therewith. Thus, the phages of some embodiments of the invention may be incorporated into compositions that are formulated for application to biological surfaces, such as the skin and mucus membranes, as well as for application to non-biological surfaces.

[0628] Anti-infective formulations for use on biological surfaces include, but are not limited to, gels, creams, ointments, sprays, and the like. In particular embodiments, the anti-infective formulation is used to sterilize a surgical field, or the hands and / or exposed skin of healthcare workers and / or patients.

[0629] Anti-infective formulations for use on non-biological surfaces include sprays, solutions, suspensions, wipes impregnated with a solution or suspension and the like. In particular embodiments, the anti-infective formulation is used on solid surfaces in hospitals, nursing homes, ambulances, etc., including, e.g., appliances, countertops, and medical devices, hospital equipment. In preferred embodiments, the non-biological surface is a surface of a hospital apparatus or piece of hospital equipment. In particularly preferred embodiments, the non- biological surface is a surgical apparatus or piece of surgical equipment.

[0630] As used herein the term “about” refers to ± 10 %

[0631] The terms "comprises", "comprising", "includes", "including", “having” and their conjugates mean "including but not limited to".

[0632] The term “consisting of’ means “including and limited to”.

[0633] The term "consisting essentially of" means that the composition, method or structure may include additional ingredients, steps and / or parts, but only if the additional ingredients, steps and / or parts do not materially alter the basic and novel characteristics of the claimed composition, method or structure.

[0634] As used herein, the singular form "a", "an" and "the" include plural references unless the context clearly dictates otherwise. For example, the term "a compound" or "at least one compound" may include a plurality of compounds, including mixtures thereof.

[0635] Throughout this application, various embodiments of this invention may be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 3, 4, 5, and 6. This applies regardless of the breadth of the range.

[0636] Whenever a numerical range is indicated herein, it is meant to include any cited numeral (fractional or integral) within the indicated range. The phrases “ranging / ranges between” a first indicate number and a second indicate number and “ranging / ranges from” a first indicate number “to” a second indicate number are used herein interchangeably and are meant to include the first and second indicated numbers and all the fractional and integral numerals therebetween.

[0637] As used herein the term "method" refers to manners, means, techniques and procedures for accomplishing a given task including, but not limited to, those manners, means, techniques and procedures either known to, or readily developed from known manners, means, techniques and procedures by practitioners of the chemical, pharmacological, biological, biochemical and medical arts.

[0638] When reference is made to particular sequence listings, such reference is to be understood to also encompass sequences that substantially correspond to its complementary sequence as including minor sequence variations, resulting from, e.g., sequencing errors, cloning errors, or other alterations resulting in base substitution, base deletion or base addition, provided that the frequency of such variations is less than 1 in 50 nucleotides, alternatively, less than 1 in 100 nucleotides, alternatively, less than 1 in 200 nucleotides, alternatively, less than 1 in 500 nucleotides, alternatively, less than 1 in 1000 nucleotides, alternatively, less than 1 in 5,000 nucleotides, alternatively, less than 1 in 10,000 nucleotides.

[0639] It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable subcombination or as suitable in any other described embodiment of the invention. Certain features described in the context of various embodiments are not to be considered essential features of those embodiments, unless the embodiment is inoperative without those elements.

[0640] Various embodiments and aspects of the present invention as delineated hereinabove and as claimed in the claims section below find experimental support in the following examples.

[0641] EXAMPLES

[0642] Reference is now made to the following examples, which together with the above descriptions illustrate some embodiments of the invention in a non limiting fashion. MATERIALS AND METHODS

[0643] A database of short phage proteins of unknown function - To construct a database of short phage proteins of unknown function, the IMG / VR v3 database38was downloaded. Identical protein sequences were removed, resulting in ~32 million non-identical protein sequences. Next, the 32 million proteins were clustered into groups of homologs via an iterative clustering process, to thereby reduce computational load. Clustering was based on sequence identity, wherein homologs were eventually defined as sequences having an e-value ≤0.001 when aligned to each other; and the clusters were defined as groups of homologs in which there is a representative sequence (“center” of the cluster) having an e-value ≤ 0.001 to each member in the cluster. To this end, the protein sequences were first clustered using the “cluster” option of MMseqs2 release 12-113e354with default parameters. Then, a representative sequence from each cluster was extracted using the “createsubdb” option of MMseqs2, and the representative sequences were aggregated into groups using the “cluster” option of MMseqs2 with the parameter “-c 0”. Next, the 2 sets of clusters were merged using the “mergeclusters” option of MMseqs2. Merged-clusters that include at least 40 members and at least one group of homologs from the first step of clustering with an MMseqs2-as signed representative sequence shorter than 200 amino acids were retained for downstream analysis. The MMseqs2-assigned sequence representing the largest number of proteins in the first step of clustering that is also shorter than 200 amino acids was selected as the representative sequence of each merged cluster. In the next step, the structure of the representative sequence was modeled using AlphaFold2 version 2.255with default parameters, with the addition of the IMG / VR v3 database to the default protein databases searched through the AlphaFold2 pipeline to collect homologous sequences. Proteins that were modeled with an average pLDDT score (a a confidence score provided by AlphaFold) lower than 80 were removed from the analysis. Additionally, proteins with a higher number of homologs detected in the MGnify database (a general metagenomic database)56than the IMG / VR v3 database (a database of phage proteins) were removed, as these proteins were considered as not primarily carried on phage genomes. The retaining proteins were searched against an annotated database of proteins constructed previously4using the “search” option of MMseqs2 with default parameters, and the top hit of each phage protein was extracted. Phage proteins similar to a protein with a known function were removed, resulting in a final database of -38,700 protein sequences, each representing a family of short phage proteins enriched for proteins with unknown functions. Each one of the -38,700 proteins was modeled as a homodimer using AlphaFold2-Multimer version 2.237, and predictions with an average PAE score lower than 5 were considered as homodimers for downstream analyses. Prediction of phage-encoded proteins that inhibit type I Thoeris - To discover phage proteins that bind the type I Thoeris system, each one of the -38,700 phage protein sequences was predicted as a protein complex with the ThsA and ThsB proteins of type I Thoeris in an iterative process using AlphaFold2-Multimer version 2.337. First, each one of the phage proteins was modeled together with each immune protein generating one predicted complex using the first model of AlphaFold2-Multimer ran with default parameters. Complexes that were generated with a co-folding model confidence score higher than 0.8 were collected for further analysis. Each of the collected interactions was predicted with AlphaFold2-Multimer again, this time generating five predictions based on the five different AlphaFold2-Multimer models. Predicted interactions with a co-folding model confidence score above 0.8 in at least three of the five predicted complexes were collected. Finally, the collected complexes were modeled again using AlphaFold2-Multimer, generating five predictions per each one of the five AlphaFold2-Multimer models, resulting in 25 predicted protein complexes for each pair of immune and phage proteins. Predicted interactions with a co-folding model confidence score above 0.8 in at least 15 of the 25 predicted complexes were defined as final candidate anti-defense proteins, and were taken for experimental verification. Notably, phage proteins that were predicted to form a homodimer were presented in two copies when modeled as a protein complex with an immune protein. Multiple sequence alignments presented in Figures 6 and 7A-B were computed with MAFFT version 7.49057and visualized using Jalview58.

[0644] Bacterial strains and growth conditions - E. coll and B. subtilis strains were grown in magnesium manganese broth (MMB; LB + O.l mM MnCh + 5 mM MgCh) at 37 °C while shaking at 200 RPM. Whenever applicable, the appropriate antibiotics were added at the following concentrations: For B. subtilis strains spectinomycin (100 pg ml-1) and chloramphenicol (5 pg mF1), and for E. coll strains ampicillin (100 pg ml”1) and kanamycin (50 pg ml”1). The type I and type II Thoeris systems, as well as the type I CBASS system, were cloned under their native promoters into the amyE locus of the B. subtilis BEST7003 genome, as described in2,41(SEQ ID NOs: 1-3, respectively). The type III CBASS system was synthetized and cloned with its native promoter into plasmid pSGl-CBASS, as described in11(SEQ ID NO: 4).

[0645] Phage strains - The B. subtilis phages SBSphiJ (GenBank: LT960608.1) and SBSphiC (GenBank: LT960610.1) were isolated as described in2. The E. coll phage BAS 18 from the BASEL phage collection was described in59. Phages were propagated on either E. coll MG1655 or B. subtilis BEST7003 by picking a single phage plaque into a liquid culture grown at 37 °C to an optical density at 600 nm (ODeoonm) of 0.3 in MMB broth until culture collapse (or 3 hours in the case of no lysis). The culture was then centrifuged for 10 minutes at 3,200 g and the supernatant was filtered through a 0.2-pm filter to get rid of remaining bacteria and bacterial debris.

[0646] Cloning of candidate anti-defense genes - Anti-defense genes were synthesized and cloned by Genscript Corp. The anti-defense candidates for type I and type II Thoeris and type I CBASS were cloned into the pSG-thrC-Phspank vector22and transformed into NEB 5-alpha competent cells. The cloned vector was subsequently transformed into B. subtilis BEST7003 cells containing the respective defense system integrated into the amyE locus2,41, resulting in cultures expressing both a defense system and the corresponding anti-defense gene candidate, integrated into the amyE and rArC loci, respectively. As a negative control, a transformant with an identical plasmid containing sl'GFP instead of the anti-defense gene was used. Transformation to B. subtilis was carried out using MC medium as previously described2and transformants were plated on LB agar plates supplemented with 5 pg ml”1chloramphenicol and incubated overnight at 30 °C. Whole-genome sequencing was then applied to all transformed B. subtilis strains, and Breseq (vO.34.1) analysis60was used to verify the integrity of the inserts and lack of mutations. Substitutions and indels in anti-defense proteins were made using the KLD Enzyme Mix (NEB) with the primers listed in Table 1 hereinbelow. The anti-defense candidate for type III CBASS was cloned into the pBbS8k vector (Addgene #35276) and subsequently transformed into NEB 5-alpha competent cells. The cloned vector was further transformed into E. coli MG1655 cells containing the pSGl-CBASS system11. As controls, transformants with an identical plasmid containing RFP instead of the anti-defense gene were used.

[0647] Plaque assays - Phage titer was determined using the small drop plaque assay method61. A 300 pl (E. coli) or 400 ul (B. subtilis) volume of overnight culture of bacteria was mixed with 0.5 % agar and 30 ml MMB and poured into a 10-cm square plate followed by incubation for 1 hour at room temperature. In cases of bacteria expressing anti-defense candidates, 1 mM IPTG (B. subtilis) or 0.2 % arabinose (E. coli) was added to the 30 ml MMB 0.5 % agar. Tenfold serial dilutions in MMB were carried out for each of the tested phages and 10-pl drops were put on the bacterial layer. After the drops had dried up, the plates were inverted and incubated at 25 °C overnight. Plaque-forming units (PFUs) were determined by counting the derived plaques after overnight incubation and lysate titer was determined by calculating PFUs per milliliter. When no individual plaques could be identified, a faint lysis zone across the drop area was considered to be 10 plaques. The efficiency of plating was measured by comparing plaque assay results for control bacteria and those for bacteria containing the defense system and / or a candidate anti-defense gene. Protein co-expression for biochemical assessment of metabolites - B. subtilis BEST7003 cultures, co-expressing a genomically-integrated B. cereus MSX-D12 Thoeris system (ThsANii2AB)7(SEQ ID NO: 12298, as sequence in which the effector of the defense system is mutated, so the Thoeris system produces the immune signal but does not lead to activation of the effector and cell death) under native promoter and either Tad3 (SEQ ID NO: 15), Tad4 (SEQ ID NO: 16), Tad5 (SEQ ID NO: 17, or Tad6 (SEQ ID NO: 18) under the Physpank promoter were grown in 50 ml MMB media supplemented with ImM IPTG. Cultures were grown for ~2 hours at 37 °C, 200 RPM, until reaching an ODeoo of 0.3. Cultures were then infected with phage SBSphiJ at MOI ~ 10. Cultures were collected 120 minutes following infection and centrifuged (3200 g) for 10 minutes at 4 °C. The pellet was flash-frozen and stored at -80 °C. Control cultures included B. subtilis BEST7003 expressing GFP without the Thoeris system, and B. subtilis BEST7003 co-expressing the Thoeris system (ThsB + T1ISANII2A) with GFP under the Physpank promoter. Human SARM1 TIR domain (position 561-724, NCBI Ref seq: NP_055892.2, SEQ ID NOs: 5-6) and BdTIR (Brachypodium distachyon TIR, NCBI ref seq: XP_003560074.3, SEQ ID NOs: 7-8) were co-expressed with Tad4 (SEQ ID NO: 16) in E. coli MG1655. Cultures were grown in 50 ml MMB media with ampicillin (100 pg ml1) and chloramphenicol (30 pg ml’1). Initially, cultures were grown for ~2 hours at 37°C, 200 RPM, until reaching an ODeoo of 0.3. This was followed by inducing expression of Tad4 with ImM IPTG and lowering growth temperature to 30 °C. After 30 minutes, 0.2 % arabinose was added to induce the expression of either the hSARMl TIR domain or BdTIR. Cells were harvested following 3 hours by centrifugation at 3200 g for 15 minutes at 4 °C followed by flash freezing the pellets and storing them in -80 °C. Control cultures included E. coli MG1655 co-expressing hSARMlyiR or BdTIR with RFP and a negative control expressing only RFP (Addgene #35290).

[0648] Preparation of filtered cell lysates - To extract cell metabolites from frozen pellets, 1 ml of 100 mM Na-phosphate buffer (pH 8.0) was added to each pellet. Tubes were then incubated for 10 minutes at 25 °C and returned to ice. Samples were transferred to FastPrep Lysing Matrix B in a 2 ml tube (MP Biomedicals, no. 116911100) and lysed at 4 °C using a FastPrep bead beater for 2 * 40 s at 6 m s-1. Tubes were then centrifuged at 4 °C for 10 minutes at 15,000 g. Supernatant was then transferred to an Amicon Ultra-0.5 Centrifugal Filter Unit 3 kDa (Merck Millipore, no. UFC500396) and centrifuged for 45 minutes at 4 °C, 12,000 g.

[0649] Enzymatic assays - The ThsA protein (SEQ ID NO: 7) was expressed and purified as described in12, and ThsA-based NADase activity assay for the detection gcADPR was carried out as described in12. The NAD / NADH-Glo (Promega) kit was used for directly measuring the NAD+levels in filtered cell lysates. The lysates were diluted 1 : 150 in 0.1 M Na-phosphate buffer, pH 8.0. Reactions were performed in a volume of 10 pl (5 pl of sample + 5 pl of reaction mixture) according to ratios recommended in the manufacturer’s instructions. Luciferin signal, proportional to the amount of NAD+, was detected using the kit luciferase enzyme. Tecan Infinite 200 PRO plate reader was used to monitor the developing luminescent signal. NAD+concentrations were calculated from the calibration curve using a set of NAD+standards with known concentrations.

[0650] Protein expression and purification - ThsB, BdTIR, and SARMITIR sequences were codon optimized for E. Coli (SEQ ID NOs: 11-13), synthesized (Integrated DNA Technologies), and cloned into a custom pET-based expression vector with an N-terminal 6xHis-SUMO2 tag. A spacer (AAAGAGGAGAAATTAACT, SEQ ID NO: 14) containing a second ribosome binding site was inserted directly downstream of ThsB, BdTIR, and SARMITIR, and codon- optimized sequences for Tad3-6 (SEQ ID NOs: 15-18) were cloned into the second open reading frame for co-expression studies. Expression plasmids were transformed into RIL cells (Agilent) and plated on MDG plates (1.5 % Bacto agar, 0.5 % glucose, 25 mM Na2HPO4, 25 mM KH2PO4, 50 mM NH4CI, 5 mM Na2SO4, 0.25 % aspartic acid, 2-50 pM trace metals, 100 pg ml-1ampicillin, 34 pg ml-1chloramphenicol). Colonies were picked into 30 ml MDG liquid media and grown overnight at 37 °C with shaking. Overnight cultures were diluted 1 : 100 into 2 L of M9ZB media (47.8 mM Na2HPO4, 22 mM KH2PO4, 18.7 mM NH4C1, 85.6 mM NaCl, 1 % casamino acids, 0.5 % glycerol, 2 mM MgSO4, 2-50 pM trace metals, 100 pg ml-1ampicillin, 34 pg ml-1chloramphenicol) and grown at 37 °C with shaking for 5-6 hours until OD = 1.5-2.0. Cultures were cooled on ice for 15 minutes before addition of IPTG to a final concentration of 500 pM. Induced cultures were then incubated at 16 °C with shaking for 16 hours before centrifugation (4000g for 20 minutes at 4 °C). Cell pellets were resuspended in 120 ml lysis buffer (20 mM HEPES-KOH pH 7.5, 400 mM NaCl, 10 % glycerol, 30 mM imidazole, 1 mM TCEP) and lysed by sonication using 10"on / 20"off pulses at 70 % power for a total sonication time of 5 minutes (Qsonica). Lysates were then centrifuged (50,000g for 30 minutes at 4 °C) and clarified supernatants were poured over 8 ml of Ni-NTA resin twice (Qiagen). Resin was then washed with 20 ml lysis buffer, 50 ml wash buffer (20 mM HEPES-KOH pH 7.5, 1 M NaCl, 10 % glycerol, 30 mM imidazole, 1 mM TCEP). Bound protein was eluted in 20 ml elution buffer (20 mM HEPES-KOH pH 7.5, 400 mM NaCl, 10% glycerol, 300 mM imidazole, 1 mM TCEP). Samples were dialysed overnight in dialysis tubing with a 20 kDa molecular weight cutoff (Ward’s Science), and SUMO2 tag cleavage was carried out with recombinant human SENP2 protease as described in50. Proteins were further purified by size-exclusion chromatography using a 16 / 600 Superdex 200 (Cytiva) and concentrated to a final concentration of >15 mg ml-1and aliquots were flash frozen in liquid nitrogen and stored at -80 °C.

[0651] SDS-PAGE analysis -_Protein purity and complex formation were assessed by SDS- PAGE by mixing 10 pl of protein (containing 1-10 pg of protein sample) with 4 pl of loading buffer. The samples were run on a 15 % gel for 45 minutes at 200 V. Proteins were stained using BrilliantBlue Coomassie stain (VWR) and visualized using a ChemiDoc MP Imaging system (BioRad).

[0652] Knock-in of Tad3 into phage SBSphiJ - The DNA sequence of Tad3 was amplified from the tad3- containing pSG-thrC-Phspank plasmid using KAPA HiFi HotStart ReadyMix (Roche, catalogue number KK2601) with the primer pair IO95Tad3_9F and IO96Tad3„9R (Table 1 hereinbelow). The backbone fragment with the upstream and downstream genomic arms (±1.2 kb) for the integration site of Tad3 was amplified from the plasmid used previously for knock-in of the Tadl gene22, with the primer pair IO34_JKIR2 and IO22_JKIF (Table 1 hereinbelow). Cloning was earned out using the NEBuilder HiFi DNA Assembly cloning kit (NEB, number E5520S) and the cloned vector was transformed into NEB 5-aIpha competent cells. The cloned vector was subsequently transformed into the thrC site of B. subtilis BEST7003. The TaJ3-containing B. subtilis BEST7003 strain was then infected with phage SBSphiJ with a multiplicity of infection (MOI) of 0.1 and cell lysate was collected. Tad3 lysate was used to infect a Thoeris-containing B. subtilis culture in two consecutive rounds with an MOI of 2 in each round at 30 °C. Several plaques were collected and screened using PCR for the desired insertion within the phage genome. Phages with Tad3 were purified three times on B. subtilis BEST7003. Purified phages were verified again for the presence of Tad3 using PCR amplifications.

[0653] Selection of homologs of anti-defense candidates for binding analysis -_Homologs of candidate anti-defense proteins were identified in the IMG / VR v3 database using the “search” option of MMseqs2 release 12-113e3 with the parameter “-c 0.8”. Then, the homologs of each candidate anti-defense protein were separated into 10 bins based on their sequence identity percentage to the query anti-defense candidate. A random sequence was selected from each bin and predicted as a complex with the relevant immune protein using AlphaFold2-Multimer version 2.3, generating five predictions per each one of the five AlphaFold2-Multimer models.

[0654] Prediction of phage encoded proteins that inhibit type II Thoeris or CBASS - Inhibitors of type II Thoeris and CBASS were predicted by analyzing the ThsB and ThsA proteins of type II Thoeris and the CD-NTase protein from E. coli KTE188 together with each of the phage proteins as described above, with the exception that two additional filtering steps were applied to the results. First, interactions that were predicted to have less than 25 residues of the immune protein interacting with the candidate inhibitor based on an analysis in the RING version 4 server66were removed. Additionally, 10 homologs of each predicted binder were selected and modeled as a complex with the immune protein using AlphaFold2-Multimer as described in the “Selection of homologs of anti-defense candidates for binding analysis” part hereinabove. Candidate inhibitors that did not have diverse homologs predicted to bind the immune protein with an average co-folding model confidence score higher than 0.75 were removed. For each of the retaining candidates, the homolog having the highest co-folding model confidence score was selected for experimental verification.

[0655] Distribution of anti-defense proteins in phage genomes - Homologs of anti-defense genes were identified in the IMG / VR v4 database30by conducting sequence-based and structurebased homology searches. To this end, ~5.5 million phage scaffolds labeled as “high-confidence virus” were downloaded from the IMG / VR v4 database. Sequence homology was defined by an e- value lower than 0.001 with the anti-defense protein, and an alignment length covering at least 80% of the anti-defense protein. Specifically, homologous sequences of the anti-defense proteins detected in this study were identified using the “search” option of MMseqs2 release 12- 113e3 with the parameters “-c 0.8 -cov-mode 2”. To identify structural homologs, the downloaded proteins from IMG / VR v4 were clustered using the “cluster” option of MMseqs2 with default parameters. Next, structure-based homologs were defined as sequences that have a predicted structure that is significantly similar (probability of 1.0 in foldseek, a program that aligns protein structures and provides homology probability scores) to the predicted structure of the anti-defense protein. Specifically, a representative sequence was extracted from each cluster containing at least 30 non-identical members, and its structure was predicted using AlphaFold2 version 2.3 with default parameters, resulting in 182,179 phage protein structures. Structures of the anti-defense proteins were searched against this set of 182,179 phage protein structures using foldseek release 5.53465f067with default parameters. Hits with probability of 1.0 were collected with all their cluster members as structural homologs of the anti-defense proteins. Finally, hits longer than 800 amino acids were discarded. Homologs of anti-defense proteins were detected in the Metagenomic Gut Virus (MGV) database32using the “search” option of MMseqs2 with the parameter “-c 0.8”, using all of the anti-defense homologs detected in IMG / VR v4 as queries.

[0656] LC-MS polar metabolite analysis - Samples were centrifuged twice (20,800g) and transferred to HPLC vials. Sample evaluation was conducted according to the method described by Zheng et al.68with minor modifications as described below. Briefly, analysis was performed using Acquity I class UPLC System combined with mass spectrometer Q Exactive Plus Orbitrap™ (Thermo Fisher Scientific), operated in a negative ionization mode with a scan range of 70 - 1050 m / z. The LC separation was done using the SeQuant Zic-pHilic (150 mm x 2.1 mm) with the SeQuant guard column (20 mm x 2.1 mm) (Merck). Mobile phase consisted of two different mobile phases: The first phase (A) consisting of acetonitrile, and the second phase

[0657] (B) consisting of 20 mM ammonium carbonate, 0.1 % ammonia hydroxide in DDW : acetonitrile (80 : 20, v / v). The chromatographic conditions were as described in Gnainsky el al69. Data processing was done using the TraceFinder version 5.1 (Thermo Fisher Scientific) software. Identification of 2'3'-cGAMP was done by MS-MS and retention time, and validated by the injection of a commercially available standard (Biolog).

[0658] Table 1: list of primers EXAMPLE 1

[0659] A COMPUTATIONAL PIPELINE FOR THE DISCOVERY OF ANTI-DEFENSE PROTEINS

[0660] To access the vast diversity of protein functions encoded by phages, -67 million phage proteins from -2 million phage genome scaffolds present in the IMG / VR v3 phage genome database38were analyzed. These proteins were clustered based on sequence homology and the resulting clusters were screened via several filtering steps (see the Materials and Methods for detailed description), requiring sufficient sequence coverage, no known functional annotation, and considering only clusters with proteins shorter than 200 amino acids (because most of the anti-defense proteins discovered to date are small14). Following, the three-dimensional structure of a representative sequence from each cluster was predicted, and only clusters generating structures with reliable folding prediction were retained. This analysis retrieved -38,700 clusters, each representing a phage protein family with at least 40 homologs (Figure 1 A).

[0661] To examine whether AlphaFold2-Multimer37could be used to discover phage proteins that inhibit bacterial immunity, the type I Thoeris defense system from Bacillus cereus MSX- D12, a two-gene system that protects against a broad array of phages and whose function is well understood7,22, was considered. The Thoeris system encodes ThsB, a TIR-domain protein that generates a signaling molecule once it detects phage infection, and ThsA, an effector NAD+- cleaving protein that is activated by the signaling molecule. A representative sequence from each of the -38,700 phage protein clusters was co-folded together with each of the two proteins of Thoeris (SEQ ID NOs: 9 and 10), using an iterative process aimed to reduce computation loads (Figure IB). Possible interactions between the Thoeris proteins and each phage protein were ranked based on the model confidence score of AlphaFold2-Multimer37, ultimately selecting phage proteins whose scores were consistently high across 25 co-folding predictions generated by AlphaFold2-Multimer (Figure IB).

[0662] EXAMPLE 2

[0663] PHAGE PROTEINS THAT INHIBIT TYPE I THOERIS

[0664] Sixteen phage proteins whose predicted co-folding scores with one of the Thoeris proteins passed the cutoff threshold were detected. Fifteen of these proteins were predicted to bind ThsB, the TIR-do main-containing protein responsible for sensing phage infection7,22, and one was predicted to bind the Thoeris immune effector ThsA (Table 2 hereinbelow). The DNA sequence for each of the candidate immune inhibitor proteins was synthesized together with an inducible promoter and integrated into the genome of a Bacillus subtilis strain also carrying the Thoeris system2. Using phage infection assays, it was found that four out of the sixteen tested phage proteins inhibited the activity of Thoeris, as phage infection was no longer blocked by Thoeris in the presence of the anti-defense proteins (Figure 1C). These four Thoeris Anti Defense proteins are referred to herein as “Tad3”, “Tad4”, “Tad5” and “Tad6”.

[0665] All four verified anti-Thoeris proteins were predicted to bind the TIR-domain protein ThsB. In the type I Thoeris defense system, ThsB senses phage infection and then produces the immune signaling molecule 1"— 3' gcADPR22. This molecule binds and activates the NADase activity of ThsA, which then depletes the cell of the essential molecule NAD+ 7’22’39(Figure ID). To test whether the anti-Thoeris proteins specifically inhibit ThsB as predicted, each of these proteins was expressed in cells expressing ThsB only, without an active ThsA protein, and these cells were infected with phage SBSphiJ. Following, the infected cells were lysed, filtered to include only small molecules, and incubated with a purified ThsA protein in vitro. The filtered lysates extracted from infected cells that expressed only ThsB were able to induce the NADase activity of ThsA, but lysates from cells also expressing Tad3, Tad4, Tad5 or Tad6 failed to activate ThsA (Figure IE). These results indicate that the four anti-Thoeris proteins inhibit the activity of ThsB, as predicted from the AlphaFold2-Multimer binding predictions.

[0666] To test whether Tad3, Tad4, Tad5 and Tad6 indeed directly bind ThsB, each of these proteins was co-expressed with a 6xHis-SUMO2-tagged ThsB and interaction was assessed in a pull-down assay. In all four cases, ThsB was co-purified with the respective anti-Thoeris protein (Figure IF). These results confirm that each of the anti-Thoeris proteins Tad3, Tad4, Tad5 and Tad6 forms a protein complex to directly inhibit ThsB.

[0667] To further interrogate whether the proteins detected represent bona fide phage inhibitors of Thoeris, the present inventors focused on one of the proteins, Tad3. Tad3 was engineered into the genome of SBSphiJ, a phage normally blocked by Thoeris, under the control of the native promoter of Tadl, a previously identified Thoeris inhibitor22. SBSphiJ knocked-in for Tad3 became fully resistant to Thoeris, showing that tad3 expression from the phage genome is sufficient for Thoeris inhibition (Figure 2A).

[0668] Examining the predicted structural models for the interactions between ThsB and the phage-derived binders, it was observed that Tad3, Tad4 and Tad6directly block the active site pocket of ThsB via a loop that interacts with the active site residues (Figure 2B). The amino acid residues that block the ThsB active site pocket are highly conserved among homologs of each of Tad3, Tad4 and Tad6, suggesting that blockage of the active site of ThsB is a conserved function of these anti-Thoeris proteins (Figures 6 and 7A-B). Tad5 is also predicted to interact with E85 and other active site residues in ThsB but does not completely block the active site pocket (Figure 2B).

[0669] Following, the loop residues in Tad3, Tad4 and Tad6 that are predicted to block the catalytic site of ThsB were mutated. Removal of the loop, or a point mutation in the respective Tad residue predicted to directly interact with the E85 active site of ThsB, impaired the function of Tad4 and Tad6 as anti-Thoeris proteins (Figure 8). Similar mutations in Tad3 were not sufficient to impair its anti-Thoeris activity (Figure 8).

[0670] Table 2: Anti-Thoeris Type I candidates

[0671] EXAMPLE 3

[0672] REFINEMENT OF THE COMPUTATIONAL PIPELINE

[0673] Examining viral protein homologs of each of the four verified inhibitors by AlphaFold2- Multimer modeling demonstrated that these homologs were also predicted to bind ThsB with high confidence (Figure 3A). Remarkably, when repeating this analysis for the 12 candidates that failed to inhibit Thoeris when tested experimentally, the present inventors noticed that in most cases homologs of the candidate phage protein were not predicted by AlphaFold2-Multimer to bind the immune protein (Figure 3A, Table 3 hereinbelow). In some cases, even close homologs with >80 % sequence identity when compared to the tested candidate showed poor binding predictions when analyzed by AlphaFold2-Multimer, suggesting that the original prediction for binding was spurious (Figure 3A). These results suggested that a computational analysis of homologs could be used to increase chances for the discovery of biologically meaningful protein-protein interactions via AlphaFold2-Multimer analyses.

[0674] In an additional attempt to better define parameters predictive of true positive hits, the predicted structures of the four verified inhibitors were compared to those of the 12 tested candidates that did not inhibit Thoeris when tested experimentally. While all verified inhibitors presented an ample binding surface with their ThsB binding partner, some of the non-verified candidates were predicted to bind only via a relatively small surface patch (Figures 3B-C, Table 4 hereinbelow). These observations additionally suggested that potential interactions involving large surface areas between the immune protein and the candidate phage protein may be a factor predictive of bona fide inhibitors.

[0675] Table 3: Tads’ homologs analysis

[0676] Table 4: Tads binding residues

[0677] EXAMPLE 4 PHAGE PROTEINS THAT INHIBIT TYPE II THOERIS AND CBASS SYSTEM

[0678] Based on the above observations the computational pipeline was updated to consider the binding scores for homologs of each candidate, as well as the surface area of the interaction (Figure 4A). Within the updated pipeline, high-scoring phage proteins are tested experimentally as inhibitors only if co-folding of protein homologs with the target immune protein also results in high scores, and only if the phage protein co-folds with its counterpart via extensive surface interactions.

[0679] To test whether the updated pipeline can discover phage-derived immunity inhibitors with a higher rate of success, we applied it to the type II Thoeris system from Bacillus amyloliquefaciens Y2. This system employs a ThsB TIR-domain protein that generates a histidine conjugated to ADPR (His-ADPR) as an immune signaling molecule40. The Ths A effector protein of type II Thoeris encodes a Macro domain capable of binding His-ADPR, and a transmembrane- spanning domain that likely impairs membrane integrity once activated by the signaling molecule2,40. The ThsB TIR-domain protein of the type II Thoeris system (SEQ ID NO: 228) is substantially different to that of type I Thoeris (SEQ ID NO: 10), with no detectable sequence similarity between the two and only little structural similarity (Figure 9). As expected from the structural divergence between the TIR-domain proteins, AlphaFold2-Multimer did not predict high scoring interactions between ThsB of type II Thoeris and the anti type I proteins identified in this study, and, consistently, inhibitors of type I Thoeris did not inhibit type II Thoeris defense when tested experimentally (Figure 10).

[0680] Following, the present inventors ran the computational pipeline to predict inhibitors of type II Thoeris, attempting to co-fold each of the 38,700 phage proteins together with either ThsA or ThsB of this system (SEQ ID NOs: 227 and 228, respectively). This analysis retrieved three proteins predicted to bind ThsA and one predicted to bind ThsB (Table 5 hereinbelow). Of these, two were verified experimentally as bona fide inhibitors of type II Thoeris defense (Figure 4B), one of them predicted to bind ThsB (Figures 4C-D) and the other one predicted to bind ThsA (Figures 4E-G). These two proteins are referred to herein as “Tad7” and “Tad8”, respectively. Examining the predicted structural interactions between the verified inhibitors and the type II Thoeris proteins, it was found that similar to inhibitors of type I Thoeris, Tad7 binds the ThsB protein of type II Thoeris and inserts a loop into the active site pocket (Figures 4C-D). Tad8 is predicted to form a homodimer and insert loops into the Macro domain of ThsA. These loops occupy the same space that would be otherwise occupied by the His-ADPR immune signaling molecule (Figures 4E-G).

[0681] In the next step, the present inventors set out to detect phage proteins that inhibit the bacterial CBASS defense system41,42. To this end, the pipeline was applied on the cGAS-like protein (CD-NTase) from the type III CBASS of Escherichia coli KTE18811(SEQ ID NO: 229). The computational pipeline retrieved only one phage protein predicted to interact with the bacterial CD-NTase (Table 6 hereinbelow). When co-expressed with the E. coli KTE188 CBASS, the phage protein inhibited its ability to defend against phages, verifying the pipeline prediction (Figure 4H). This CBASS inhibitor referred to herein as “Acb3” (anti-CBASS 3).

[0682] Analysis of the predicted structure shows that Acb3 wraps around the CD-NTase and makes extensive contacts with both the nucleotidyltransferase active site and the putative ligand binding domain that is required for CD-NTase activation (Figure 41). Despite extensive efforts, the present inventors were unable to purify Acb3 to perform biochemical assays. This is possibly due to a large solvent exposed hydrophobic patch on Acb3 that likely decreases protein solubility and may further disrupt CD-NTase function (Figure 11 A). AlphaFold2-Multimer analysis showed that Acb3 is predicted to bind multiple CD- NTases from previously studied CBASS systems, despite substantial divergence in sequence between these CD-NTases (Figure 11B). To test whether Acb3 is indeed a broad-range inhibitor of CBASS, it was co-expressed in Bacillus subtilis together with the type I CBASS system from B. cereus VD146. Despite the low sequence similarity (21.7 %) between the B. cereus VD146 CD-NTase enzyme and the E. coli KTE188 one, Acb3 was capable of inhibiting both systems (Figures 4H and 12). These results demonstrate that Acb3 can inhibit diverse CBASS systems.

[0683] Table 5: Anti-Thoeris Type II candidates

[0684] Table 6: Anti-CBASS candidate EXAMPLE 5

[0685] DISTRIBUTION OF ANTI-THOERIS AND ANTI-CBASS PROTEINS IN PHAGE GENOMES

[0686] Sequence- and structure-based homology searches revealed over 7,000 homologs of the anti-defense proteins discovered in this study in the IMG / VR v4 database of viral proteins30. These proteins were derived from phages predicted to infect over 40 families of bacteria from a diverse set of taxonomic phyla including Firmicutes, Bacteroidota, Proteobacteria and Actinobacteriota (Table 7 hereinbelow). Tad3 was the most abundant anti-Thoeris protein family in this set, represented in more than 5,000 homologs; and the least abundant were the Tad5 and Tad7 protein families occurring in 96 and 92 homologs, respectively. About 1,000 homologs of Acb3 were detected in this set.

[0687] The MGV database32, an independent database containing -190,000 genome scaffolds representing sequenced and partially sequenced phage genomes, was also examined (Table 7 hereinbelow). The anti-Thoeris proteins detected in this study were found in 4,356 of these genome scaffolds (2.3% of the scaffolds), with Tad3 being the most abundant anti-Thoeris protein also in this set, occurring in 3,627 scaffolds. Acb3 was underrepresented in this set of phage genomes, detected in only 8 scaffolds.

[0688] Table 7: Homologs in the IMG / VR v4 and MGV databases EXAMPLE 6 PHAGE-ENCODED ANTI-DEFNESE PROTEINS BIND AND ANTAGONIZE EUKARYOTIC IMMUNE PROTEINS

[0689] Recent studies show that central components of the eukaryotic cell- autonomous innate immune system originated from bacterial defense systems6Specifically, ample evidence suggest that the human cGAS-STING pathway originated from the bacterial CBASS system, and it was shown that the human cGAS is structurally similar to its bacterial counterpart6,43. It was also shown that bacterial immune TIR domains are structurally and functionally similar to plant and human TIR domains that are involved in immunity and regulated cell death44,45. The structural and functional similarities between the bacterial immune proteins and their homologs in eukaryotes led the present inventors to hypothesize that some of the phage-encoded inhibitors discovered might also inhibit human and plant TIR and cGAS proteins.

[0690] To test this hypothesis, the present inventors first focused on the TIR domain protein from the plant Brachypodium distachyon (BdTIR), which is known to produce l''-2' gcADPR and l''-3' gcADPR molecules46. The interaction between each of the anti-TIR phage proteins discovered (Tad3-Tad7) and the BdTIR protein was modeled using AlphaFold2-Multimer and high- scoring predicted interactions were found between Tad4 and BdTIR, suggesting that Tad4 may bind BdTIR (Figure 13A). To test the predicted binding, Tad4 was co-expressed in cells also expressing a 6xHis-SUMO2-tagged BdTIR. Co-immunoprecipitation experiments demonstrated that Tad4 strongly binds BdTIR and stabilizes its expression (Figure 5A). BdTIR is known to constitutively produce l"-2' gcADPR and l"-3' gcADPR molecules when expressed in E. cold'(\ and indeed, filtered cell lysates derived from cells expressing BdTIR activated Ths A from type I Thoeris, a protein triggered by l"-3' gcADPR (Figure 5B). However, filtered lysates derived from cells in which BdTIR was co-expressed with Tad4 failed to activate ThsA in vitro, demonstrating that Tad4 inhibits the TIR-mediated enzymatic activity of BdTIR (Figure 5B).

[0691] Next, the present inventors considered the human Sterile alpha and TIR motif-containing 1 protein (SARM1). SARM1 is an essential protein within a pathway that leads to axonal death in response to neuronal injury, and it was shown that the SARM1 TIR domain degrades cellular NAD+when activated following neuron insult47,48. Co-folding the TIR domain of human SARM1 (SARMITIR) with either of Tad3, Tad4, Tad5, Tad6 and Tad7 using AlphaFold2- Multimer strongly predicted that Tad4, and to a lesser extent also Tad3, bind SARMITIR (Figures 13B-C). Co-expression and co-immunoprecipitation of a 6xHis-SUMO2-tagged SARMITIR with Tad4 demonstrated that Tad4 bind SARMITIR (Figure 5C). It was previously shown that SARMITIR is constitutively active as an NADase when expressed in bacterial cells, depleting NAD+in these cells49. To test whether the binding of Tad4 to SARMITIR inhibits its enzymatic function, the levels of NAD+were measured in lysates derived from cells in which SARMITIR was co-expressed with Tad4. It was found that Tad4 inhibited SARMITIR activity almost completely (Figure 5D). Taken together, these results demonstrate that the phage-derived anti- Thoeris protein Tad4 is also capable of binding and inhibiting the human SARM1 TIR domain.

[0692] Finally, possible interactions between Acb3 and the human cGAS (hcGAS, SEQ ID NO: 12291) were examined. AlphaFold2-Multimer analysis predicted interactions between Acb3 and hcGAS (Figure 13D), and hence these two proteins were co-expressed in bacterial cells. When expressed alone in bacteria, hcGAS constitutively produced 2'3'-cGAMP, as previously shown50(Figure 5E). In contrast, 2'3'-cGAMP could not detected in lysates derived from cells in which hcGAS was co-expressed with Acb3 (Figure 5E). These results demonstrate that conservation of immune proteins between prokaryotes and eukaryotes render the eukaryotic homologs susceptible to inhibition by viral proteins that primarily evolved to inhibit bacterial immunity.

[0693] Although the invention has been described in conjunction with specific embodiments thereof, it is evident that many alternatives, modifications and variations will be apparent to those skilled in the art. Accordingly, it is intended to embrace all such alternatives, modifications and variations that fall within the spirit and broad scope of the appended claims.

[0694] All publications, patents and patent applications mentioned in this specification are herein incorporated in their entirety by reference into the specification, to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated herein by reference. In addition, citation or identification of any reference in this application shall not be construed as an admission that such reference is available as prior art to the present invention. To the extent that section headings are used, they should not be construed as necessarily limiting. In addition, any priority document(s) of this application is / are hereby incorporated herein by reference in its / their entirety. REFERENCES

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Claims

WHAT IS CLAIMED IS:

1. A virus comprising an exogenous polynucleotide encoding an anti-defense system polypeptide, wherein said anti-defense system polypeptide is selected from the group consisting of:(i) a Tad3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594-11520 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594- 11520, wherein said Tad3 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;(ii) a Tad4 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766, wherein said Tad4 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;(iii) a Tad5 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849, wherein said Tad5 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;(iv) a Tad6 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888, wherein said Tad7 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;(v) a Tad7 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918, wherein said Tad7 polypeptide binds the defense system polypeptide ThsB of a Type II Thoeris set forth in SEQ ID NO: 228;(vi) a Tad8 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290, wherein said Tad8 polypeptide binds the defense system polypeptide ThsA of a Type II Thoeris set forth in SEQ ID NO: 227; and(vii) an Acb3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593, wherein said Acb3 polypeptide binds the bacterial defense system polypeptide cGAS of a CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233.

2. The virus of claim 1, having an increased infectivity to at least one cell as compared to a virus of the same species not comprising said exogenous polynucleotide.

3. A cell comprising an exogenous anti-defense system polypeptide or a polynucleotide encoding same, wherein said anti-defense system polypeptide is selected from the group consisting of:(i) a Tad3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594-11520 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594-11520, wherein said Tad3 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;(ii) a Tad4 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766, wherein said Tad4 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;(iii) a Tad5 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849, wherein said Tad5 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;(iv) a Tad6 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888, wherein said Tad7 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;(v) a Tad7 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918, wherein said Tad7 polypeptide binds the defense system polypeptide ThsB of a Type II Thoeris set forth in SEQ ID NO: 228;(vi) a Tad8 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acidsequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290, wherein said Tad8 polypeptide binds the defense system polypeptide ThsA of a Type II Thoeris set forth in SEQ ID NO: 227; and(vii) an Acb3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593, wherein said Acb3 polypeptide binds the bacterial defense system polypeptide cGAS of a CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233.

4. A nucleic acid construct comprising a polynucleotide encoding an anti-defense polypeptide selected from the group consisting of:(i) a Tad3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594-11520 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594- 11520, wherein said Tad3 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;(ii) a Tad4 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766, wherein said Tad4 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;(iii) a Tad5 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849, wherein said Tad5 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;(iv) a Tad6 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888, wherein said Tad7 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;(v) a Tad7 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918, wherein said Tad7 polypeptide binds the defense system polypeptide ThsB of a Type II Thoeris set forth in SEQ ID NO: 228;(vi) a Tad8 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290, wherein said Tad8 polypeptide binds the defense system polypeptide ThsA of a Type II Thoeris set forth in SEQ ID NO: 227; and(vii) an Acb3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593, wherein said Acb3 polypeptide binds the bacterial defense system polypeptide cGAS of a CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233; and a nucleic acid sequence heterologous to said polynucleotide which facilitates expression of said polynucleotide in a cell, integration of said polynucleotide in a genome of a virus or a cell, and / or selection or detection.

5. The nucleic acid construct of claim 4, wherein said nucleic acid sequence heterologous to said polynucleotide is selected from the group consisting of: a promoter, arecombination element, an element for expression of multiple polynucleotides from a single construct, a transmissible element and a selectable marker.

6. A method of producing the virus of any one of claims 1-2, the method comprising introducing into a virus said exogenous polynucleotide encoding said anti-defense system polypeptide, thereby producing the virus.

7. The method of claim 6, wherein said method comprises introducing into the virus the nucleic acid construct of any one of claims 4-5, under conditions which allow integration of said polynucleotide in a genome of said virus.

8. The virus of any one of claims 1-2 or the method of any one of claims 6-7, wherein said virus does not endogenously comprise said polynucleotide encoding said antidefense system polypeptide.

9. A method of infecting a cell, the method comprising contacting the cell with the virus of any one of claims 1-2 and 8.

10. A method of producing the cell of claim 3, the method comprising introducing into a cell said anti-defense system polypeptide or said polynucleotide encoding same, thereby producing the cell.

11. A method of impairing ability of a cell to respond to stress, the method comprising introducing into the cell an anti-defense system polypeptide or a polynucleotide encoding same, wherein said anti-defense system polypeptide is selected from the group consisting of:(i) a Tad3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594-11520 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594- 11520, wherein said Tad3 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;(ii) a Tad4 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQID NO: 66, 77-86, 5266-5865 and 11521-11766 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766, wherein said Tad4 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;(iii) a Tad5 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849, wherein said Tad5 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;(iv) a Tad6 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888, wherein said Tad7 polypeptide binds the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10;(v) a Tad7 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918, wherein said Tad7 polypeptide binds the defense system polypeptide ThsB of a Type II Thoeris set forth in SEQ ID NO: 228;(vi) a Tad8 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290, wherein said Tad8 polypeptide binds the defense system polypeptide ThsA of a Type II Thoeris set forth in SEQ ID NO: 227; and(vii) an Acb3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593, wherein said Acb3 polypeptide binds the bacterial defense system polypeptide cGAS of a CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233, thereby impairing ability of a cell to respond to stress.

12. The method of claim 11, wherein said stress comprises a viral infection.

13. The method of any one of claims 10-12, wherein said method comprises introducing into the cell the nucleic acid construct of any one of claims 4-5, under conditions which allow expression of said anti-defense polypeptide in said cell.

14. The cell, the nucleic acid construct or the method of any one of claims 3-5 and 9- 13, wherein said cell is a prokaryotic cell.

15. The virus, the nucleic acid construct or the method of any one of claims 1-2, 4-9 and 13-14, wherein said virus is a phage.

16. The cell, the nucleic acid construct or the method of any one of claims 3-5 and 9- 13, wherein said cell is a eukaryotic cell.

17. The cell, the nucleic acid construct or the method of claim 16, wherein said eukaryotic cell is a plant cell.

18. The cell, the nucleic acid construct or the method of claim 16, wherein said eukaryotic cell is a human cell.

19. The cell, the nucleic acid construct or the method of any one of claims 3-5 and 9- 18, wherein said cell expresses said defense system polypeptide or a homolog thereof.

20. The cell, the nucleic acid construct or the method of any one of claims 3-5 and 9- 19, wherein said cell further comprises an exogenous polynucleotide of interest.

21. The method of any one of claims 9-20, further comprising introducing into said cell an exogenous polynucleotide of interest.

22. The method of any one of claims 6-21, being effected in-vitro or ex- vivo.

23. The method of any one of claims 6-21, being effected in-vivo.

24. A method of treating a bacterial infection in a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of the phage comprising said exogenous polynucleotide encoding said anti-defense system polypeptide of claim 15, thereby treating the bacterial infection in the subject.

25. The method of claim 24, comprising administering to the subject a therapeutically effective amount of an antibiotic.

26. An article of manufacture comprising as active ingredients the phage comprising said exogenous polynucleotide encoding said anti-defense system polypeptide of claim 15; and an antibiotic.

27. A method of improving resistance of a plant to biotic stress, the method comprising introducing into the plant an anti-defense system polypeptide or a polynucleotide encoding same, wherein said anti-defense system polypeptide is selected from the group consisting of:(i) a Tad3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594-11520 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594- 11520, wherein said Tad3 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 endogenously expressed in said plant;(ii) a Tad4 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766, wherein said Tad4 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 endogenously expressed in said plant;(iii) a Tad5 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849, wherein said Tad5 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 endogenously expressed in said plant;(iv) a Tad6 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888, wherein said Tad7 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 endogenously expressed in said plant;(v) a Tad7 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918, wherein said Tad7 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 228 endogenously expressed in said plant;(vi) a Tad8 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290 and / or a structural similarity defined by a Root MeanSquare Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290, wherein said Tad8 polypeptide binds a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 227 endogenously expressed in said plant; and(vii) an Acb3 polypeptide having a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593, wherein said Acb3 polypeptide binds a homolog of the bacterial defense system polypeptide cGAS of a CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233 endogenously expressed in said plant, thereby improving resistance of the plant to biotic stress.

28. A method of treating a disease that can benefit from inhibiting a defense system polypeptide in a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of an anti-defense system polypeptide or a polynucleotide encoding same, wherein: when said defense system polypeptide is a homolog of the defense system polypeptide ThsB of a Type I Thoeris set forth in SEQ ID NO: 10 endogenously expressed in said subject, the anti-defense system polypeptide is a Tad3 polypeptide, a Tad4 polypeptide, a Tad5 polypeptide and / or a Tad6 polypeptide which binds said homolog of SEQ ID NO: 10; when said defense system polypeptide is a homolog of the defense system polypeptide ThsB of a Type II Thoeris set forth in SEQ ID NO: 228 endogenously expressed in said subject, the anti-defense system polypeptide is a Tad7 polypeptide which binds said homolog of SEQ ID NO: 228; when said defense system polypeptide is a homolog of the defense system polypeptide ThsA of a Type II Thoeris set forth in SEQ ID NO: 227 endogenously expressed in said subject, the anti-defense system polypeptide is a Tad8 polypeptide which binds said homolog of SEQ ID NO: 227; and / or when said defense system polypeptide is a homolog of the defense system polypeptide cGAS of a CBASS set forth in amino acid sequence selected from the group consisting of SEQ ID NOs: 229-231 and 233 endogenously expressed in said subject, the anti-defense systempolypeptide is an Acb3 polypeptide which binds said homolog of amino acid sequence selected from the group consisting of SEQ ID NO: 229-231 and 233; wherein:(i) said Tad3 polypeptide has a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594-11520 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 58, 67-76, 245-5265 and 7594- 11520;(ii) said Tad4 polypeptide has a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 66, 77-86, 5266-5865 and 11521-11766;(iii) said Tad5 polypeptide has a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 59, 87-96, 5866-5961 and 11767-11849;(iv) said Tad6 polypeptide has a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 65, 97-106, 5962-6369 and 11850-11888;(v) said Tad7 polypeptide has a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 239, 6370-6461 and 11889-11918;(vi) said Tad8 polypeptide has a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQID NO: 240, 6462-6616 and 11919-12290 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 240, 6462-6616 and 11919-12290; and(vii) said Acb3 polypeptide has a sequence similarity defined by an e-value ≤ 0.05 to a sequence of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593 and / or a structural similarity defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms to a structure of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 244 and 6617-7593, thereby treating the disease in the subject.

29. The method of claim 28, wherein said disease is selected from the group consisting of autoimmune disease, interferonopathy and a disease associated with neuronal degeneration.

30. The virus, the cell, the nucleic acid construct or the method of any one of claims 1-29, wherein said Tad3 polypeptide, Tad4 polypeptide, Tad5 polypeptide, Tad6 polypeptide, Tad7 polypeptide, Tad8 polypeptide and / or Acb3 polypeptide inhibits activity of said defense system polypeptide.

31. The virus, the cell, the nucleic acid construct or the method of any one of claims 1-30, wherein said Tad3 polypeptide and / or Tad8 polypeptide is capable of forming a homodimer.

32. The virus, the cell, the nucleic acid construct or the method of any one 1-31, wherein said Tad3 polypeptide and / or Tad8 polypeptide binds as a homodimer two monomers of said defense system polypeptide.

33. The virus, the cell, the nucleic acid construct or the method of any one 1-32, wherein expression of said Tad3 polypeptide, Tad4 polypeptide, Tad5 polypeptide and / or Tad6 polypeptide in a B. subtilis BEST7003 comprising SEQ ID NO: 1 increases sensitivity of said B. subtilis BEST7003 to infection by a B. subtilis phage SBSphiJ.

34. The virus, the cell, the nucleic acid construct or the method of any one of claims 1-33, wherein expression of said Tad7 polypeptide and / or Tad8 polypeptide in a B. subtilis BEST7003 comprising SEQ ID NO: 2 increases sensitivity of said B. subtilis BEST7003 to infection by a B. subtilis phage SBSphiJ.

35. The virus, the cell, the nucleic acid construct or the method of any one of claims 1-34, wherein expression of said Acb3 polypeptide in a E. coli MG 1655 comprising SEQ ID NO: 4 increases sensitivity of said E. coli MG1655 to infection by an E. coli phage BAS 18.

36. The virus, the cell, the nucleic acid construct or the method of any one of claims 1-35, wherein expression of said Acb3 polypeptide in a B. subtilis BEST7003 comprising SEQ ID NO: 3 increases sensitivity of said B. subtilis BEST7003 to infection by a B. subtilis phage SBSphiC.

37. The virus, the cell, the nucleic acid construct or the method of any one of claims 1-36, wherein said Tad4 polypeptide binds and / or inhibits activity of plant Brachypodium distachyon (BdTIR) set forth SEQ ID NO: 8.

38. The virus, the cell, the nucleic acid construct or the method of any one of claims 1-37, wherein said Tad3 polypeptide and / or Tad4 polypeptide binds and / or inhibits activity of SARM1TIR set forth SEQ ID NO: 6.

39. The virus, the cell, the nucleic acid construct or the method of any one of claims 1-38, wherein said Acb3 polypeptide binds and / or inhibits activity of human cGAS of a CBASS set forth SEQ ID NO: 12291.

40. The virus, the cell, the nucleic acid construct or the method of any one of claims 1-39, wherein said anti-defense polypeptide comprises said SEQ ID NO.

41. The virus, the cell, the nucleic acid construct or the method of any one of claims 1-40, wherein: said amino acid sequence of said Tad3 polypeptide comprises said SEQ ID NO: 58; said amino acid sequence of said Tad4 polypeptide comprises said SEQ ID NO: 66; said amino acid sequence of said Tad5 polypeptide comprises said SEQ ID NO: 59;said amino acid sequence of said Tad6 polypeptide comprises said SEQ ID NO: 65; said amino acid sequence of said Tad7 polypeptide comprises said SEQ ID NO: 239; said amino acid sequence of said Tad8 polypeptide comprises said SEQ ID NO: 240; and / or said amino acid sequence of said Acb3 polypeptide comprises said SEQ ID NO: 244.

42. A method of identifying a putative anti-defense system polypeptide, the method comprising:(i) clustering a dataset comprising more than 1000 viral proteins based on sequence and / or structural similarity, to thereby obtain multiple clusters;(ii) in-silico modeling an interaction between a single viral protein of a cluster of said multiple clusters and the defense system polypeptide, to thereby select a viral protein having a predicted co-folding confidence score with said defense system polypeptide above a predetermined threshold;(iii) in-silico modeling an interaction between at least one additional viral protein of the cluster of said selected protein having said predicted co-folding confidence score above said predetermined threshold, to thereby select a cluster having a predetermined number of viral proteins having predicted co-folding confidence scores with said defense system polypeptide above said predetermined threshold, wherein a protein of said selected cluster having said viral proteins having said predicted co-folding confidence scores above said predetermined threshold being putative anti-defense system polypeptide.

43. The method of claim 42, wherein said method comprises in-silico modelling a three dimensional structure of said single viral protein of said cluster prior to said (ii), and proceeding to step (ii) with a viral protein having a predicted structural confidence score above a predetermined threshold.

44. The method of any one of claims 42-43, comprising selecting only viral proteins with an unknown function prior to said (iii); and / or selecting only viral proteins having a length ≤200 amino acids prior to said (iii).

45. The method of any one of claims 42-44, comprising determining an amount of amino acid residues in said selected viral protein having said predicted co-folding confidencescore above said predetermined threshold interacting with said defense system polypeptide, to thereby select a viral protein having at least 20 interacting residues with said defense system polypeptide.

46. The method of any one of claims 42-45, further comprising in-vitro or in-vivo determining a functional activity of said putative anti-defense system polypeptide following said (iii).

47. The method of any one of claims 42-46, wherein said sequence similarity is defined by an e-value ≤ 0.05; and / or wherein said structural similarity is defined by a Root Mean Square Deviation (RMSD) ≤ 2.0 angstroms.

48. The virus, the cell, the nucleic acid construct or the method of any one of claims 1-41 or the method of claim 47, wherein said e-value ≤ 0.01.

49. The virus, the cell, the nucleic acid construct or the method of any one of claims 1-41 or the method of claim 47, wherein said e-value ≤ 0.001.

50. The virus, the cell, the nucleic acid construct or the method of any one of claims 1-49, wherein sequence similarity is defined by an alignment length covering at least 80 % of the aligned viral proteins sequences.

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