A novel system for producing recombinant proteins

Abstract

The present invention relates to a novel system for producing recombinant proteins in Streptomyces host strains, including vectors and novel recombinant host strains, in particular for the production of Actinoallomurus endopeptidase.

Description

[Technical field]

[0001] The present invention relates to a novel system for producing recombinant proteins in Streptomyces host strains.

[0002] The novel system includes, inter alia, vectors and novel recombinant host strains for the production of Actinoallomurus endopeptidase. [Background technology]

[0003] Recombinant DNA (rDNA) technology offers a very powerful set of technological platforms for the controlled and scalable production of polypeptides of interest in a relatively inexpensive procedure. Recombinant proteins are usually obtained by recombinant DNA technology in E. coli, Saccharomyces cerevisiae, insect, hamster and mammalian cells. However, there is a demand for improved mass production of recombinant proteins. Furthermore, there are very stringent requirements to be met if proteins are produced for human use (e.g., for use as food supplements and / or as pharmaceuticals in the prevention and / or treatment of human diseases). Actinomycetes are considered as a safe source of protein for human consumption. Two examples of food enzymes from the Streptomyces genus are glucose isomerase, used in the production of fructose syrup (Non-Patent Document 1), and the widely utilized transglutaminase from S. mobaraensis, which is used in the food industry for its properties that improve the texture and overall quality of the final food, such as processed meat and fish products, as well as household and baked goods (Non-Patent Document 2).

[0004] S. lividans cells are known to be efficient host cells for producing recombinant proteins because recombinant proteins expressed in the cells can be directly secreted and released into the medium. However, various proteins are obtained in S. lividans in very different yields, and the results are unpredictable (Non-Patent Document 1).

[0005] To improve the yield of heterologous proteins, a collection of derivative strains of S. lividans TK24 (TK24 taxonomy ID: 457428) was constructed by sequentially deleting known potentially interfering secondary metabolite gene clusters. Non-Patent Document 3 discloses that this optimized strain collection is used to efficiently produce mithramycin A with a yield approaching 3 g / L. Nevertheless, reproducibility of high yields is not guaranteed, regardless of the polynucleotide encoding any polypeptide. In addition, there is still room for further improvement in providing a recombinant protein production system.

[0006] The present invention aims to provide an improved system for the efficient production of recombinant proteins in a Streptomyces, preferably a Streptomyces lividans host strain.

[0007] In particular, the system of the present invention has been found to be particularly useful for the mass production of recombinant endopeptidase (endopeptidase 40 or E40) of Actinoallomurus strains.

[0008] The E40 native protein consists of 398 amino acid residues (see SEQ ID NO:3), an N-terminal signal peptide has been identified between positions 1 and 27, and the mature form of the protein (E40mat) is predicted to be a 32.5 kDa polypeptide of the sequence of SEQ ID NO:1 beginning at position 74 of the native protein (see Figure 1).

[0009] In the following, "E40prepro" is used to specify the native preproendopeptidase with its native signal peptide consisting of the sequence of SEQ ID NO:3 or a derivative thereof (for example, tagged E40prepro having the sequence of SEQ ID NO:4 (his-tagged E40prepro). In the following, "E40pre" is used to specify the E40 proenzyme without the signal peptide consisting of the amino acid sequence of SEQ ID NO:9. In the following, "E40mat" is used to specify the mature endopeptidase with the amino acid sequence consisting of SEQ ID NO:1 or a derivative thereof (for example, tagged E40mat (E40Hismat) having the amino acid sequence of SEQ ID NO:2).

[0010] The endopeptidase was first disclosed in US Pat. No. 5,399,633 and has been shown to degrade gluten peptides very quickly and efficiently into non-toxic peptides, to be active over the entire pH range of the gastric and intestinal environment (enzyme activity is shown in the pH range 3-6 with an optimum at pH 5), and to be resistant to degradation by endogenous gastrointestinal enzymes. This makes the Actinoallomurus endopeptidase highly suitable for use in the treatment and / or prevention of celiac disease (CD) and CD-related disorders. There is therefore strong interest in developing an efficient and inexpensive method for the production of the Actinoallomurus endopeptidase.

[0011] WO 02 / 06333 discloses a method for producing recombinant Actinoallomurus endopeptidase in S. lividans host cells, where expression of E40 is preferably carried out in S. lividans TK24 strain by a high copy replicative expression vector (pIJ86, SEQ ID NO: 7).

[0012] Several replicating plasmids, especially those with high copy numbers, have been successfully used for the overproduction of many biotechnologically relevant heterologous proteins in actinomycetes. However, replicating vectors have several drawbacks. For example, they can only be introduced into actinomycetes by laborious protoplast transformation, and their stable maintenance in actinomycetes requires permanent antibiotic selection.

[0013] Integration vectors containing DNA segments encoding binding / integration functions (Att / Int) for site-specific integration into specific sites of the Streptomyces genome (e.g., attB sites for specific integrases) have also been employed to express recombinant proteins in Streptomyces. Most of the site-specific integration systems are based on various actinomycete temperate bacteriophages (actinophages) identified in Streptomyces species. The temperate bacteriophages (and the integration vectors prepared with their functional elements) are integrated into the host chromosome at specific sites by a recombination process that requires specific binding sites, attP of the phage (or integration vector) and attB of the host chromosome.

[0014] Despite some advantages, these Att / Int systems also have some limitations, such as integrating the entire integrative plasmid with the E. coli replicon, integrase gene, and resistance marker gene. This can be a significant biotechnological obstacle since the stability of the construct may be affected. In fact, instability of some Att / Int systems has been reported in some Streptomyces strains (Non-Patent Document 4). Therefore, these integrative vector methods have been considered unsuitable for the construction of stable biotechnological production strains.

[0015] In addition, several other elements (eg, regulatory elements of the expression cassette cloned into the expression vector) also play a role in the efficiency of the recombinant protein production system.

[0016] Thus, in the field of recombinant protein production, achieving satisfactory protein yields and avoiding undesirable drawbacks is by no means an easy or clear-cut task.

[0017] The present invention provides a surprisingly improved system for producing recombinant proteins, preferably recombinant Actinoallomurus endopeptidase, in Streptomyces, preferably S. lividans host cells. [Prior art documents] [Patent documents]

[0018] [Patent Document 1] International Publication No. 2013 / 083338 [Patent Document 2] International Publication No. 2021 / 013553 [Non-patent literature]

[0019] [Non-Patent Document 1] Anne,et al.Molecular Cell Research,2014 [Non-Patent Document 2] Kieliszek,et al.Folia Microbiologica,2013 [Non-Patent Document 3] Novakova et al.(Applied Microbiology and Biotechnology,2018) [Non-Patent Document 4] Kormanec J.et al.,Applied Microbiology and Biotechnology 103:5463-5482,2019 Summary of the Invention

[0020] The system of the invention for the production of recombinant proteins in a Streptomyces host cell, preferably a S. lividans strain, is based on a strong promoter [the artificial kasO promoter of sequence SEQ ID NO: 10 (kasOp *The present invention also includes a novel recombinant vector having an expression cassette containing a polynucleotide encoding a recombinant protein of interest under the control of the PhiC31 capsid protein gene (Bai et al. 2015, Proc Natl Acad Sci USA 112, 12181-12186), and a regulatory element that is a synthetic variant SR40 ribosome binding site (RBS) of the sequence of SEQ ID NO: 11 based on the PhiC31 capsid protein gene (Bai et al. 2015, Proc Natl Acad Sci USA 112, 12181-12186). The recombinant vector of the present invention is a single-site integration vector based on the phage PhiBT1, and is preferably integrated into the attB site in the Streptomyces genome.

[0021] The polynucleotide encoding the recombinant protein of interest encodes a recombinant preprotein comprising a signal peptide. In a preferred embodiment, said signal peptide is a heterologous signal peptide, more preferably the signal peptide vsi of the subtilisin inhibitor of Streptomyces venezuelae having the sequence of SEQ ID NO: 12 (Lammertyn et al. 1997 Appl Environ Microbiol 63, 1808-1813).

[0022] Preferably, the recombinant protein of interest is an Actinoallomurus endopeptidase, preferably Actinoallomurus endopeptidase 40 (E40), a biologically active fragment, variant, or derivative thereof.

[0023] The system of the present invention also includes novel recombinant host strains comprising the novel vectors. The present invention also relates to the use of the novel system of the present invention for the production of recombinant proteins by their secretion in the culture medium of the host cells, in particular for the production of Actinoallomurus endopeptidase, and to a method for the production of recombinant proteins by the novel system of the present invention.

[0024] Surprisingly, despite the use of a single copy vector, the system of the present invention provides stable and abundant expression of recombinant proteins. [Brief description of the drawings]

[0025] [Figure 1] Sequence of the native E40 preproenzyme (E40prepro), whose signal peptide is shown in bold and the mature enzyme is underlined. [Diagram 2] Scheme of prior art recombinant vector pIJ86 / e40, containing the e40 gene (with and without 6xHis tag) encoding E40pre endopeptidase inserted between the BamHI and HindIII sites of the cloning vector pIJ86. The sequences of the ermEp* promoter region (SEQ ID NO:30), including the -10 and -35 regions of the promoter (bold and underlined), the TSS (bold, underlined and highlighted), and the BamHI / BclI fusion with e40, are shown below the plasmid scheme. The amino acids of E40 are in the second position of each codon. [Diagram 3] Scheme of the expression vector pMU1s-kasOpSR40vsi3mRFPA. Below the plasmid scheme is the sequence of the vsi-mRFP fusion with the restriction sites (bold and underlined) inserted. The amino acids of the Vsi signal peptide (bold) and mRFP (red) are in the second position of each codon. [Figure 4] 13.5% SDS-PAGE of 20 μl media samples after mRFP secretion in S. lividans TK24 harboring pMU1s-kasOpSR40vsi3mRFPA grown to various time points in TSB medium (two individual clones). Lanes: 1 = LMW standard; 2-5 = TK24 pMU1s-kasOpSR40vsi3mRFPA grown for 24, 48, 72, and 146 h, respectively; 10 = TK24 grown for 48 h. [Diagram 5] Scheme of the cloning vector pLit-kasOpSR40vsi3mRFP, which contains the strong kasOp* promoter, an optimized strong SR40 RBS, and a single NdeI site inserted at the ATG codon of the vsi-mRFP reporter fusion gene. [Figure 6]Schemes of recombinant plasmids pLit-e40 and pLit-e40His containing the entire e40 gene with the original signal peptide sequence (6xHis tagged and untagged, respectively) inserted between the NdeI and AvrII sites of the cloning vector pLit kasOpSR40vsi3mRFP. The sequence of the kasOp* promoter, including the -10 and -35 regions of the promoter (bold and underlined), its TSS (bold, underlined and highlighted), RBS (bold and underlined), and the NdeI fusion with e40, are shown below the plasmid scheme. The amino acids of E40 are in the second position of each codon. [Figure 7] Scheme of the cloning expression vector pMU1s-kasOpSR40gusA containing the strong kasOp* promoter, the optimized strong SR40 RBS, and a single NdeI site inserted at the ATG codon of the gusA reporter gene. The sequence of this promoter and RBS region, including the -10 and -35 regions of the promoter (bold and underlined), its TSS (bold, underlined and highlighted), and the RBS (bold and underlined), are shown below the plasmid scheme. [Figure 8] Scheme of recombinant plasmids pLit-vsie40pre, pLit-e40Hispre, pLitvsie40HQHispre, pLit-vsie40mat, pLit-vsie40Hismat containing the vsi-e40pre gene fusion of Vsi to proenzyme E40pre and the vsi-e40mat gene fusion of Vsi to mature enzyme E40mat (with and without 6xHis tag, respectively) inserted between the NheI and HindIII sites of the cloning vector pLit-kasOpSR40vsi3mRFP. The sequence of the kasOp* promoter including the -10 and -35 regions of the promoter (bold and underlined), its TSS (bold, underlined and highlighted), RBS (bold and underlined), and the vsi-E40 fusion sites NdeI and NheI are shown below the plasmid scheme. [Figure 9]Scheme of recombinant plasmids pMU1s-e40, pMU1s-e40His, pMU1svsie40pre, pMU1s-vsie40Hispre, pMU1s-vsie40HQHispre, pMU1s vsie40mat, pMU1s-vsie40Hismat containing all forms of e40 gene fusions as KpnI EcoRV DNA fragments from pLit plasmids (see Figures 6, 8) inserted between the KpnI and EcoRV sites of the cloning vector pMU1s-kasOpSR40gusA (Figure 7). [Figure 10] Scheme of recombinant plasmids pIJ86-kasOpe40, pIJ86-kasOpe40His, pIJ86-vsie40pre, pIJ86-vsie40Hispre, pIJ86-vsie40HQHispre, pIJ86-vsie40mat, pIJ86-vsie40Hismat containing all forms of e40 gene fusion (shown in Figs. 6, 8) (with and without 6xHis tag, respectively) as KpnI-EcoRV DNA fragment from pLit plasmid (Figs. 6, 8) inserted between KpnI and HindIII sites of cloning vector pIJ86 (Fig. 2). [Figure 11] Scheme of recombinant plasmid pMU1s-ermEe40, containing the ermEp*-e40His fusion from plasmid pIJ86 / e40His, which contains the e40 gene with a 6xHis tag. [Figure 12] E40 activity in wild-type and mutant S. lividans RedStrep1.3 strains associated with prior art high-copy replicative plasmids. [Figure 13] E40 activity in wild-type and mutant S. lividans RedStrep strains bound to a single-site integration plasmid expressing native E40 under the ermEp* promoter. [Figure 14A] E40 activity in wild-type S. lividans strains conjugated with a single-site integration plasmid expressing native E40 under the kasOp* promoter and an optimized strong SR40 RBS according to the present invention. [Figure 14B]E40 activity in a wild-type S. lividans strain conjugated with a single-site integration plasmid expressing His-tagged E40 under the kasOp* promoter and an optimized strong SR40 RBS according to the present invention. [Figure 15A] E40 activity in a wild-type S. lividans strain coupled with a high-copy pIJ86 plasmid expressing E40 under the kasOp* promoter and an optimized strong SR40 RBS. [Figure 15B] E40 activity in a wild-type S. lividans strain coupled with a high-copy pIJ86 plasmid expressing an E40His tag under the kasOp* promoter and an optimized strong SR40 RBS. [Figure 16A] E40 activity in a wild-type S. lividans strain coupled with the high-copy pIJ86 plasmid pIJ86 containing vsi-e40pre under the kasOp* promoter and an optimized strong SR40 RBS. [Figure 16B] E40 activity in a wild-type S. lividans strain coupled with the high-copy pIJ86 plasmid pIJ86 containing His-tagged vsi-e40pre under the kasOp* promoter and an optimized strong SR40 RBS. [Figure 16C] E40 activity in a wild-type S. lividans strain coupled with the high-copy pIJ86 plasmid pIJ86 containing vsi-e40mat under the kasOp* promoter and an optimized strong SR40 RBS. [Figure 16D] E40 activity in wild-type S. lividans strains coupled with the high-copy pIJ86 plasmid pIJ86 containing a His-tagged vsi-e40mat fusion gene under the kasOp* promoter and an optimized strong SR40 RBS. [Figure 17A] E40 activity in a wild-type S. lividans strain conjugated with a single-site integration plasmid containing vsi-e40pre under the kasOp* promoter and an optimized strong SR40 RBS. [Figure 17B]E40 activity in a wild-type S. lividans strain coupled with a single-site integration plasmid containing His-tagged vsi-e40pre under the kasOp* promoter and an optimized strong SR40 RBS. [Figure 18A] E40 activity in wild-type or mutant S. lividans RedStrep strains coupled with a single-site integration plasmid expressing native E40 under the kasOp* promoter and an optimized strong SR40 RBS. [Figure 18B] E40 activity in wild-type or mutant S. lividans RedStrep strains coupled with a single-site integration plasmid expressing the native E40His tag under the kasOp* promoter and an optimized strong SR40 RBS. [Figure 19A] E40 activity in wild-type or mutant S. lividans RedStrep strains coupled with a single-site integration plasmid expressing vsi-e40pre under the kasOp* promoter and an optimized strong SR40 RBS. [Figure 19B] E40 activity in wild-type or mutant S. lividans RedStrep strains coupled with a single-site integration plasmid expressing His-tagged vsi-e40pre under the kasOp* promoter and an optimized strong SR40 RBS. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0026] Firstly, the present invention relates to a recombinant vector carrying an expression cassette for the heterologous expression of a recombinant protein in a Streptomyces host cell, said cassette comprising a promoter, a regulatory element downstream of said promoter, and a polynucleotide encoding a recombinant protein, downstream of and operably linked to said promoter and said regulatory element.

[0027] The terms "vector," "expression vector," and "plasmid" are used interchangeably herein.

[0028] The expression vector for heterologous expression of a recombinant protein in a Streptomyces host cell of the invention is a single-site integration vector comprising an attP site and an integrase gene from PhiBT1 phage, more preferably a vector having the sequence of SEQ ID NO: 13, which is integrated into the attB site of Streptomyces.

[0029] Examples of single-site integration vectors according to the present invention include those described in Kormanec J. et al., Applied Microbiology and Biotechnology (2019) 103:5463-5482.

[0030] In a preferred embodiment, the single-site integration vector is a vector having the backbone of the pMU1 vector (Craney et al. 2007, Nucleic Acids Res 35, e46).

[0031] The promoter of the expression cassette is the artificial kasO promoter (kasOp * ); the regulatory element of the expression cassette is a synthetic ribosome binding site (SR40 RBS) of sequence SEQ ID NO: 11; and the polynucleotide encoding the recombinant protein of interest is a polynucleotide encoding a recombinant protein including a signal peptide.

[0032] The expression cassette of the invention is particularly suitable for the heterologous expression of recombinant proteins in Streptomyces host cells. The recombinant protein is expressed by the host cells cultured in a medium under conditions suitable for the growth of the host cells and is secreted into said medium. The signal peptide facilitates the secretion of the protein into the medium.

[0033] Optionally, the signal peptide is a heterologous signal peptide, more preferably the Vsi signal peptide of the subtilisin inhibitor of Streptomyces venezuelae having the sequence of SEQ ID NO: 12. Surprisingly, the use according to the present invention of a heterologous signal peptide fused to a protein of interest provides for as good secretion of the recombinant protein as the native signal peptide of the protein.

[0034] In a preferred embodiment of the invention, the recombinant protein encoded by the polynucleotide of the expression cassette is a recombinant Actinoallomurus endopeptidase having glutenase activity. More preferably, said endopeptidase is endopeptidase 40 (E40) of a sequence comprising SEQ ID NO:1, a biologically active fragment of E40, a naturally occurring allelic variant of E40; or an endopeptidase of a sequence having at least 60%, 70%, 80%, 90% or 95% identity to SEQ ID NO:1.

[0035] SEQ ID NO:1 is the polypeptide sequence of the mature form of E40.

[0036] Thus, preferably, the expression cassette comprises a polynucleotide encoding endopeptidase E40 having a sequence comprising SEQ ID NO:1, a biologically active fragment of E40, a naturally occurring allelic variant of E40, or an endopeptidase having a sequence having at least 60%, 70%, 80%, 90% or 95% identity to SEQ ID NO:1.

[0037] The term "biologically active fragment" of E40 refers to a portion that maintains the specific glutenase activity of the endopeptidase. Polynucleotides encoding "biologically active fragments" of E40 can be identified as disclosed by WO2021 / 013553.

[0038] A polynucleotide encoding a recombinant protein of interest may have a sequence that differs from the annotated nucleic acid sequence due to the degeneracy of the genetic code, and therefore encodes the same protein as the protein encoded by the polynucleotide having the annotated nucleic acid sequence.

[0039] The terms "identity" or "homology" when referring to nucleotide or amino acid sequences are used interchangeably herein and refer to the degree to which two polynucleotide or polypeptide sequences are identical or homologous on a residue-by-residue basis over a particular region of comparison.Sequence and percent identity or homology can be determined using any suitable software program known in the art, such as those described in Current Protocols in Molecular Biology (Ausubel FM et al., "Commercially Available Software", Current Protocols in Molecular, 1987, Supplement 30, Section 7.7.18, Table 7.7.1). Preferred programs include the GCG Pileup program, FASTA (Pearson R. and Lipman DJ "Improved Tools for Biological Sequence Analysis" Proc. Natl., Acad. Sci. USA, 1988, 85, 2444-2448) and BLAST (Altschul SF, Gish W., Miller W., Myers EW, Lipman DJ "Basic local alignment search tool" J. Mol. Biol., 1990, 215, 403-410).

[0040] The term "allelic variant" refers to any of two or more alternative forms of a gene occupying the same chromosomal locus. Allelic variation arises naturally by mutation and can result in phenotypic polymorphism within a population. Genetic variations can be silent (no change in the encoded polypeptide) or can encode a polypeptide with an altered amino acid sequence. The term allelic variant also refers to a protein encoded by an allelic variant of a gene.

[0041] The polynucleotide encoding the recombinant protein of interest may encode a protein operably fused to another polypeptide, for example a tag, such as a histidine tag. For example, the polynucleotide may be a polynucleotide encoding a tagged protein, for example a tagged E40 with a sequence comprising or consisting of SEQ ID NO: 2. In a preferred embodiment, the polynucleotide encoding the protein of interest is a polynucleotide with a sequence comprising or consisting of SEQ ID NO: 5, 6, 15, 16, 17 or 18, and the expression cassette is of the sequence of SEQ ID NO: 20, 21, 22 or 23.

[0042] Thus, in a preferred embodiment, the present invention relates to a single-site integration vector, more preferably an Actinoallomurus endopeptidase, preferably Actinoallomurus endopeptidase 40 (E40), a biologically active fragment, variant or derivative thereof, expressed under the artificial kasO promoter (kasOp) of sequence SEQ ID NO: 10 in a Streptomyces host cell, preferably a S. lividans strain. * ) and an expression cassette for expression under the control of a ribosome binding site (RBS) of sequence SEQ ID NO: 11 (SR40 RBS), for integration into the attB site for the PhiBT1 phage of Streptomyces. Optionally, the recombinant protein is Actinoallomurus endopeptidase, the signal peptide of which has been replaced by the Vsi signal peptide.

[0043] More preferably, the single-site integration vector carrying an expression cassette for the expression of Actinoallomurus endopeptidase 40 (E40) is the pMU1 vector of sequence SEQ ID NO: 25, 26, 27 or 28.

[0044] The present invention also relates to a host cell, preferably a recombinant Streptomyces host cell, more preferably a S. lividans host cell, for heterologous expression of a recombinant protein comprising an expression vector according to the invention. The host cell may be a wild-type S. lividans host cell or a mutant S. lividans host cell, for example an S. lividans host cell of the strain S. lividans RedStrep1.3 (Δact, Δred, Δcda), the strain S. lividans RedStrep1.6 (Δact, Δred, Δcda, Δmel) or the strain S. lividans RedStrep1.9 (Δact, Δred, Δcda, Δmel, ΔmatAB) (Novakova et al., 2018).

[0045] Preferably, the host cell is a cell of strain DSM 33930 (S. lividans 1.3 combined with pMU1s-e40His) or strain DSM 33931 (S. lividans 1.9 combined with pMU1s-e40His) deposited under the provisions of the Budapest Treaty at the Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7B 38124 Braunschweig - GERMANY on June 24, 2021.

[0046] The present invention then also relates to the use of a recombinant vector or a host cell of the invention for the production of a recombinant protein which is secreted into the host cell medium.

[0047] Advantageously, the system of the present invention provides for stable, high-yield production of a protein of interest, which can be easily recovered from the host cell medium into which it is secreted.

[0048] Indeed, the system of the present invention also relates to a method for producing a recombinant protein in a Streptomyces host cell, comprising the successive steps of: culturing a recombinant Streptomyces host cell, preferably a S. lividans host cell, more preferably a host cell of the TK24 strain, in a medium under fermentation conditions; said recombinant host cell comprising a recombinant expression vector according to the present invention; recovering the supernatant of the medium, and purifying a preparation comprising the recombinant protein from said supernatant.

[0049] "Fermentation conditions" refers to the culture conditions (media composition, agitation parameters, aeration and temperature) of the host cell strain suitable for the host cell strain to grow and produce the compound of interest (recombinant endopeptidase). Suitable fermentation conditions may be, for example, those described in WO 2021 / 013553 or those described in the Examples below.

[0050] It is to be understood that all possible combinations of the preferred aspects of the invention are described and therefore similarly preferred.

[0051] Examples of embodiments of the present invention are set forth below, which are provided for illustrative and non-limiting purposes. EXAMPLES

[0052] Plasmids The plasmids prepared in the following Examples 1 to 6 are summarized in Table 1. For each plasmid, the promoter, RBS, signal peptide, gene and vector backbone are reported.

[0053] [Table 1]

[0054] host cell S. lividans wild-type strain TK24 (Taxonomy ID: 457428) and S. lividans mutant strains RedStrep1.3, 1.6, and 1.9 (Novakova et al. 2018) were employed in Examples 7–14 to test the production of recombinant proteins using various plasmids.

[0055] Example 1 pIJ86 / e40 and pIJ86 / e40His (Figure 2) are the pIJ86 high copy replicative plasmids of the prior art (see WO 2021 / 013553) and the ermEp * Promoters (relatively weak ermEp2 and relatively strong mutant ermEp1 * These were obtained from the Fondazione Istituto Insubrico di Ricerche per la Vita (FIIRV).

[0056] Example 2 pMU1s-kasOpSR40gusA (Figure 7) is a PhiBT1-based integrative vector pMU1s (Craney et al. 2007, Nucleic Acids Res 35, e46) that expresses a potent kasOp * The expression cassette contains a gusA reporter gene under the control of the promoter (Myronovskyi et al. 2011, Appl Environ Microbiol 77, 5370-5383) and an optimized synthetic strong SR40 RBS (Bai et al. 2015, Proc Natl Acad Sci USA 112, 12181-12186). The activity of this combination is 1897 U / g GUS and ermEp * This was 47-fold higher than that of the same expression cassette under the promoter.

[0057] Example 3 A polynucleotide encoding a fusion polypeptide of the vsi signal peptide sequence and the red fluorescent protein (mRFP) reporter gene was prepared, with an NheI site inserted between the signal peptide sequence and mRFP. The entire vsi-mRFP cassette, as an 800 bp NdeI-NotI DNA fragment, was replaced with gusA in pMU1s-kasOpSR40gusA of Example 2 to obtain the pMU1s-kasOpSR40vsi3mRFPA vector (Figure 3). This also expressed the strong kasOp * The construct contained a promoter, an optimized synthetic strong SR40 RBS and a Vsi signal peptide. This construct potently secreted mRFP (27 886 FU). SDS-PAGE revealed the correct band for secreted mRFP in rich TSB medium (Figure 4).

[0058] Example 4 kasOp *The 900 bp KpnI-NotI expression cassette containing the promoter, the optimized SR40 RBS, and the vsi-mRFP reporter fusion gene with a single NdeI site inserted at the ATG codon was cloned into the standard E. coli cloning vector pBluescript II SK (Stratagene) digested with the same enzymes to obtain pBS-kasOpSR40vsi3mRFP. This fragment was subsequently cloned from this plasmid as a 900 bp KpnI-SacI fragment in the standard E. coli cloning vector LITMUS 28 (New England BioLabs) digested with the same enzymes to obtain pLit-kasOpSR40vsi3mRFP (Figure 5). This plasmid was verified by nucleotide sequencing and was used as a vector for cloning all e40 genes into the vector according to the invention. The entire e40 gene from the ATG start codon and its signal peptide sequence (e40 prepro) (with and without the 6xHis tag located at the C-terminus) were PCR amplified from the pIJ86 / e40His plasmid with an NdeI site at the ATG start codon and SpeI and HindIII sites after the e40 stop codon. The PCR amplified and purified 1200 bp DNA fragment was digested with NdeI and SpeI and cloned into AvrII and NdeI digested pLit-kasOpSR40vsi3mRFP to obtain pLit-e40 or pLit-e40His, respectively (Figure 6). Several positive clones were analyzed by restriction enzyme mapping and subsequently verified by nucleotide sequencing.

[0059] To prepare vsi-e40pre gene fusions, containing a fusion of Vsi and the proenzyme E40pre, the e40pre gene (with and without the 6xHis tag located at the C-terminus) was PCR amplified using pIJ86 / e40His plasmid as a template and proofreading Pfu DNA polymerase with primers that inserted an NheI site at the Ala34 codon and primers that inserted SpeI and HindIII sites after the e40 stop codon. The PCR amplified and purified 1100 bp DNA fragment was digested with NheI and HindIII and cloned into NheI and HindIII digested pLitkasOpSR40vsi3mRFP to obtain pLit-vsie40pre or pLit-vsi40Hispre, respectively (Figure 8). Several positive clones were analyzed by restriction enzyme mapping and subsequently verified by nucleotide sequencing. Sequencing of the clones revealed one clone in which the synthetic primers generated a mutation replacing the His38 CAC codon with a Gln38 CAA codon, and this plasmid was picked for further analysis and labeled pLitvsi40HQHispre.

[0060] To prepare vsi-e40mat gene fusions containing the fusion of Vsi and the mature enzyme E40mat, the e40mat gene (with and without the 6xHis tag located at the C-terminus) was PCR amplified using pIJ86 / e40His plasmid as a template and proofreading Pfu DNA polymerase with primers that inserted an NheI site at the Ala73 codon and further changed the Ala74 codon to Ser, and primers that inserted SpeI and HindIII sites after the e40 stop codon. The PCR amplified and purified 1000 bp DNA fragment was digested with NheI and HindIII and cloned into NheI and HindIII digested pLit-kasOpSR40vsi3mRFP to obtain pLit-vsie40mat or pLit-vsi40Hismat, respectively (Figure 8). Several positive clones were analyzed by restriction enzyme mapping and subsequently verified by nucleotide sequencing.

[0061] Example 5 kasOp * All cassettes, including the promoter, RBS, and e40 (under its original signal peptide or Vsi signal peptide, with or without a 6xHis tag at the end) were cloned into a 1400 bp KpnI-EcoRV DNA fragments pLit-e40, pLit-e40His, pLit-vsie40pre, pLit-e40Hispre, pLitvsie40HQHispre, pLit-vsie40mat, and pLit-vsie40Hismat (Figures 6 and 8) were cloned into pMU1skasOpSR40gusA digested with KpnI and EcoRV (Figure 7), resulting in pMU1s-e40, pMU1s-e40His, pMU1s-vsie40pre, pMU1s-vsie40Hispre, pMU1s-vsie40HQHispre, pMU1s-vsie40mat, and pMU1s-vsie40Hismat vectors (Figure 9). Several positive clones were analyzed by restriction enzyme mapping and subsequently verified by nucleotide sequencing. All constructs can be integrated into a single location in the chromosome of S. lividans TK24 using a phage PhiBT1-based integration system after conjugation of the plasmids into S. lividans TK24 with apramycin resistance (AprR) selection. The final constructs are stable and do not require AprR selection.

[0062] Example 6 kasOp *All cassettes, including the promoter, RBS, and e40 (under its original signal peptide or Vsi signal peptide, with or without a 6xHis tag at the end) were cloned into a 1400 bp KpnI-EcoRV DNA fragments from pLit-e40, pLit-e40His, pLit-vsie40pre, pLit-e40Hispre, pLitvsie40HQHispre, pLit-vsie40mat, and pLit-vsie40Hismat (Figures 6 and 8) were cloned into pIJ86 digested with KpnI and HindIII to obtain pIJ86-kasOpe40, pIJ86-kasOpe40His, pIJ86-vsie40pre, pIJ86-vsie40Hispre, pIJ86-vsie40HQHispre, pIJ86-vsie40mat, and pIJ86-vsie40Hismat vectors (Figure 10). Several positive clones were analyzed by restriction enzyme mapping and subsequently verified by nucleotide sequencing. All constructs can replicate in S. lividans TK24 at high copy number (approximately 100-300 copies) after conjugation of the plasmids into S. lividans TK24 with AprR selection, but permanent AprR selection is required and some instability has been reported.

[0063] Finally, the 1500 bp XbaI (Klenow filled)-HindIII fragment from the high copy number shuttle plasmid pIJ86 / e40His was cloned into the EcoRV and HindIII cut pMU1s-vsiRFPB vector to obtain pMU1s-ermEe40 (Figure 11). The plasmid was verified by sequencing.

[0064] Example 7 E40 activity was measured using the prior art strain S. lividans / pIJ86 / e40His. First, spore stocks were prepared after sporulation on solid Bennett and Apramycin (Apr) medium. Stability of the mixed spores and spores from five independent sporulated colonies was tested. Spore suspensions from 1 × 1 cm sporulation areas from confluent mixed spores (or five whole large single sporulated colonies) were inoculated into Erlenmeyer flasks (100 ml) containing 10 ml of medium V (glucose 20 g / L, yeast extract Difco 5 g / L, soy peptone Sigma Aldrich 10 g / L, NaCl 1.5 g / L), Apr was added to a final of 50 μg / ml, and the mixture was cultivated for 1 day at 30 °C at 200 rpm on a rotary shaker. Five beads (3.5 mm) were added and the cultivation continued for another day. 2 ml of this seed culture was inoculated into Erlenmeyer flasks (100 ml) containing 20 ml of medium P (sucrose 340 g / L, glucose 10 g / L, yeast extract 3 g / L, soybean peptone 5 g / L, malt extract 3 g / L) and Apr was added to a final concentration of 50 μg / ml and cultured under the same conditions. At the 2nd, 5th, 6th, 7th and 8th days, 1 ml of medium was taken into an Eppendorf tube, centrifuged (13000 rpm for 10 min), the supernatant was transferred to a new tube and stored at -20°C. E40 activity was measured by SSA protocol (Standard Activity Assay, SSA, performed in 96-well clear microtiter plates and measured with a Biotec microplate reader (A405)) by diluting the samples 40-fold. Equivalent E40 activity of approximately 20 AU / ml was measured in all five independent colonies and mixed cultures. Samples were also analyzed on SDS-PAGE and all showed an E40 38 kDa band (not shown).

[0065] Example 8 E40 activity was measured using two S. lividans strains, wild type TK24 and mutant S. lividans RedStrep1.3, fused with the prior art plasmids pIJ86, pIJ86 / e40, and pIJ86 / e40His. Sporulated cultures were inoculated into Erlenmeyer flasks (100 ml) containing 10 ml of Niedercorn medium (3% sucrose, 2% corn steep liquor, 0.2% ammonium sulfate, 0.7% CaCO3, pH 7, in distilled water), supplemented with Apr to a final of 50 μg / ml, and incubated at 30° C. for 2 days on a rotary shaker at 200 rpm.

[0066] 2 ml of this seed culture were inoculated into Erlenmeyer flasks (100 ml) containing 20 ml of medium P. E40 activity was measured by the SSA protocol described above using 40-fold dilutions of samples consisting of culture supernatants taken on days 3, 4, 5, 6 and 7. Vector pIJ86 alone showed only low background protease activity in both strains. E40 activity of both constructs pIJ86 / e40 and pIJ86 / e40His was approximately 15 AU / ml in strain TK24 and approximately 20 AU / ml in strain RedStrep1.3 (Figure 12).

[0067] Example 9 The E40 activity of wild-type S. lividans TK24 and the three mutants S. lividans RedStrep1.3;1.6;1.9 was measured using the control plasmid pMU1s-ermEe40 (FIG. 11). Cultures were prepared as in Example 8.

[0068] With the single-copy chromosomal integration construct pMU1s-ermEe40, E40 activity was much lower than that with the high-copy-number pIJ86 vector of Example 8: 1.13 AU / ml with pMU1s-ermEe40 in wild-type S. lividans TK24 and approximately three-fold higher in RedStrep1.6 and 1.9 strains (Figure 13).

[0069] Example 10 E40 activity was determined by kasOp *The wild-type S. lividans TK24 strain was ligated with four clones of the single-site integration plasmids pMU1s-e40 and pMU1s-e40His, which contain the promoter, the strong SR40 RBS, and e40 with its original signal peptide (without and with a C-terminal xHis tag). Cultures were prepared as in Example 8.

[0070] The three clones (No. 1, 2, 3) containing plasmid pMU1s-e40 had similar E40 activities of about 55 AU / ml, whereas clone No. 4 had much higher activity (260 AU / ml) (Figure 14A). Similarly, the three clones (No. 1, 2, 4) containing plasmid pMU1s-e40His had similar E40 activities of about 45 AU / ml, whereas clone No. 3 had much higher activity (180 AU / ml) (Figure 14B). Based on a comparison of the three similar clones with the single copy integration plasmid pMU1s-ermEe40 of Example 6, pMU1s-e40 and pMU1s-e40His show about 50-fold and 40-fold increases in E40 activity, respectively.

[0071] Example 11 kasOp * E40 activity was analyzed in four independent clones from wild-type S. lividans TK24 strain ligated with the high-copy vector pIJ86 containing e40 (without and with a C-terminal His tag) with a promoter, a strong SR40 RBS, and its native or vsi signal peptide (pIJ86-kasOpe40, pIJ86-kasOpe40His, pIJ86-vsie40pre, pIJ86-vsie40Hispre, pIJ86-vsie40HQHispre, pIJ86-vsie40mat, pIJ86-vsie40Hismat). As a result, the cloned cassette kasOpe40 *This high copy number vector containing the promoter, the strong SR40 RBS and e40 was shown to be highly unstable, either with the original signal peptide (Figure 15) or fused to the Vsi signal peptide (Figure 16) (without and with the C-terminal xHis tag). Indeed, in the case of the four clones of pIJ86-kasOpe40, one of the four clones had very high E40 activity (150AU / ml), one had an E40 activity of 40AU / ml, and the other two clones had zero activity (Figure 15A). Similarly, in the case of the four clones of pIJ86-kasOpe40His, one clone had a fairly high E40 activity (51AU / ml), one had an E40 activity of 38AU / ml, and the other two clones had zero activity (Figure 15B).

[0072] Similarly, for the four clones of plasmids pIJ86-vsie40pre, pIJ86-vsie40Hispre, pIJ86-vsie40HQHispre, pIJ86-vsie40mat, and pIJ86-vsie40Hismat of S. lividans TK24, E40 activity was very low (0.5-2.5 AU / ml) in all clones tested (Figure S16A-D). These results were surprising because their single-copy chromosomally integrated counterparts pMU1s-e40 and pMU1s-e40His had stable and high E40 activity (Figure S14).

[0073] Example 12 kasOp *High E40 activity was observed in all four clones using plasmids pMU1s-vsie40pre and pMU1s-vsie40Hispre, which contain the promoter, the strong SR40 RBS, and the proenzyme portion of e40 fused to the Vsi signal peptide (Figure 17). In the case of plasmid pMU1s-vsie40pre, there was an E40 activity of about 50 AU / ml, with one clone having an activity up to 85 AU / ml (Figure 17A). Similarly, plasmid pMU1s-vsie40Hispre had comparable E40 activity of about 30 AU / ml in three clones and 84 AU / ml in one clone (Figure 17B). Based on a comparison of these E40 activities with those from cells ligated with the control single copy integration plasmid pMU1s-ermEe40 of Example 9, the E40 activity of construct pMU1s-vsie40pre is increased by about 45-fold (75-fold in the most active clone) and the E40 activity of construct pMU1s-vsie40Hispre is increased by about 26-fold (even 75-fold in the most active clone). When these clones were compared to clones carrying the high copy number plasmid pIJ86 / e40His of TK24, the two best clones showed 5.6-fold higher E40 activity. Furthermore, these clones showed high stability.

[0074] kasOp * Plasmid pMU1s-vsie40HisHQpre, which contains the proenzyme portion of e40 with the promoter, strong RBS, and 38His / Gln mutations fused to the Vsi signal peptide, showed a partially reduced E40 activity compared to its wild-type variant (approximately 27 AU / ml).

[0075] Example 13 pMU1s-e40 and pMU1s-e40His were combined with S. lividans mutants RedStrep1.3, 1.6 and 1.9. E40 activity was analyzed in wild-type S. lividans TK24 strain along with the four clones previously analyzed in Example 10, as well as in four independent clones. For pMU1s-e40, E40 activity was clearly higher in RedStrep1.3 (75±13AU / ml) than in TK24 strain (56±7AU / ml). For pMU1s-e40, E40 activity was clearly higher in RedStrep1.3 (75±13AU / ml) than in TK24 (56±7AU / ml). E40 activity was also high in RedStrep1.6 (67±24AU / ml), whereas E40 activity in RedStrep1.9 was comparable to TK24 (52±7AU / ml) (FIG. 18A). For pMU1s-e40His, E40 activity was similar in all four strains: WT TK24 (33 ± 7 AU / ml), RedStrep1.3 (29 ± 6 AU / ml), RedStrep1.6 (31 ± 7 AU / ml), and RedStrep1.9 (31 ± 7 AU / ml) (Figure 18B).

[0076] Example 14 pMU1s-vsie40pre and pMU1s-vsie40Hispre (kasOp * The recombinant vector (containing the proenzyme portion of e40 fused to the promoter, strong SR40 RBS, and Vsi signal peptide) was ligated into RedStrep1.3, 1.6, and 1.9 mutants, and E40 activity was analyzed in four independent clones in wild-type S. lividans TK24 strain along with the four clones previously analyzed in Example 12. Recombinant cells were grown as in Example 8.

[0077] For the pMU1s-vsie40pre vector, E40 activity was higher in RedStrep1.3 (40 ± 13.3 AU / ml) than in TK24 (28.75 ± 6.2 AU / ml). E40 activity in RedStrep1.6 (29.75 ± 3.8 AU / ml) was similar to the WT TK24 strain (Figure 19A). For the pMU1s-vsie40Hispre vector, E40 activity was again higher in RedStrep1.3 (30 ± 3.5 AU / ml), similar in RedStrep1.6 (24.75 ± 0.9 AU / ml), RedStrep1.6 (31 ± 7 AU / ml), but lower in RedStrep1.9 (22 ± 2.9 AU / ml) (Figure 19B).

[0078] Experimental data show that the PhiBT1 phage integrase-based integration vectors according to the present invention (pMU1s-e40, pMU1s-e40His, pMU1s-vsie40pre, pMU1s-vsie40Hispre, pMU1s-vsie40HHQHispre, pMU1s-vsie40mat, pMU1s-vsie40Hismat) provide stable and high production of E40. The pMU1s-e40 and pMU1s-e40His vectors were synthesized by kasOp * The best vectors contain a promoter, an optimal strong SR40 RBS, the original signal peptide sequence followed by the original e40 or e40His, producing an average of 50AU / ml or 35AU / ml of enzyme, respectively. Furthermore, the optimal host cell line for E40 production is S. lividans RedStrep1.3.

Claims

**Claim 1** A recombinant vector for the heterologous expression of a recombinant protein in a Streptomyces host cell, comprising: an expression cassette containing a promoter, a regulatory element, and a polynucleotide encoding a recombinant protein operably linked to the promoter and the regulatory element, - The promoter is an artificial kasO promoter (kasOp) having the sequence of SEQ ID NO: 10 ＊ ) and - the regulatory element is an optimized synthetic SR40 ribosome binding site (RBS) having the sequence of SEQ ID NO: 11; - the polynucleotide encoding the recombinant protein of interest encodes a recombinant protein containing an N-terminal signal peptide; and - the recombinant vector is a single-site integration vector. Recombinant vector. **Claim 2** The recombinant vector according to claim 1, wherein the recombinant protein is actinorhodin endopeptidase having the sequence containing SEQ ID NO: 1 or consisting of SEQ ID NO: 1; a biologically active fragment of E40; a naturally occurring allelic variant of E40; or an endopeptidase having a sequence having at least 60%, 70%, 80%, 90% or 95% identity to SEQ ID NO:

1. **Claim 3** The recombinant vector according to claim 2, wherein the recombinant protein is a histidine-tagged actinorhodin endopeptidase having the sequence of SEQ ID NO:

2. **Claim 4** The recombinant vector according to claim 1, wherein the signal peptide is the Vsi signal peptide of subtilisin inhibitor of Streptomyces venezuelae having the sequence of SEQ ID NO:

12. **Claim 5** The recombinant vector according to claim 2, wherein the signal peptide is the Vsi signal peptide of subtilisin inhibitor of Streptomyces venezuelae having the sequence of SEQ ID NO:

12. **Claim 6** The recombinant vector according to any one of claims 1 to 5, wherein the polynucleotide encoding the recombinant protein has a sequence containing the sequence of SEQ ID NO: 5, 6, 15, 16, 17 or 18. **Claim 7** The recombinant vector according to any one of claims 1 to 5, wherein the expression cassette has the sequence of SEQ ID NO: 20, 21, 22 or 23. **Claim 8** The recombinant vector according to any one of claims 1 to 5, which is a vector integrated into the attB site of Streptomyces. **Claim 9** The recombinant vector according to claim 8, which is a vector of the sequence of SEQ ID NO: 25, 26, 27 or 28.

10. A Streptomyces host cell for heterologous expression of a recombinant protein comprising the expression vector according to claims 1 to 5, preferably S. lividans host cell.

11. The host cell according to claim 10, which is an S. lividans host cell of the TK24 strain or the RedStrep 1.3, 1.6 or 1.9 strain.

12. The host cell according to claim 10, which is an S. lividans host cell of the DSM 33930 strain or the DSM 33931 strain.

13. Use of the recombinant vector according to any one of claims 1 to 5 for producing a recombinant protein, wherein the recombinant protein is secreted into the culture medium of the host cell.

14. Use of the host cell according to claim 10 for producing a recombinant protein, wherein the recombinant protein is secreted into the culture medium of the host cell.

15. A method for producing a recombinant protein, comprising the following steps: i) providing a recombinant host cell comprising the recombinant expression vector according to any one of claims 1 to 5; ii) culturing the recombinant host cell in a medium under conditions suitable for growth; iii) recovering the recombinant protein expressed by the recombinant host cell from the medium.

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