Methods and compositions for PPO herbicide resistance

Abstract

The present invention relates to biotechnology and provides novel recombinant DNA molecules and engineered proteins for conferring tolerance to protoporphyrinogen oxidase-inhibiting herbicides. The present invention also provides herbicide-tolerant transgenic plants, seeds, cells, and plant parts containing the recombinant DNA molecules, as well as methods for their use. [Selection diagram] None

Description

Technical Field

[0001] Cross - Reference to Related Applications This application claims the benefit of priority of U.S. Provisional Application No. 62 / 599,386, filed Dec. 15, 2017, the disclosure of which is hereby incorporated by reference in its entirety.

[0002] The present invention relates to the fields of agriculture, plant biotechnology, and molecular biology. More specifically, the present invention relates to recombinant DNA molecules encoding engineered proteins that provide resistance to herbicides that inhibit protoporphyrinogen oxidase and methods of using them.

[0003] Incorporation of Sequence Listing A sequence listing in computer - readable form is submitted with this application by electronic submission and is hereby incorporated by reference in its entirety. This sequence listing is contained in a file named MONS429WO_ST25.txt, which is 296 kilobytes in size (measured in the operating system MS Windows) and was created on Dec. 13, 2018.

Background Art

[0004] Agricultural crop production often utilizes transgenic traits created using biotechnology. Transgenic traits can be generated by introducing heterologous genes, also known as introduced genes, into plants. The expression of introduced genes in plants confers traits such as herbicide resistance. Examples of herbicide-resistant transgenic traits include glyphosate resistance, glufosinate resistance, and dicamba resistance. With the increasing number of weed species resistant to commonly used herbicides, new herbicide resistance traits are needed in this field. Particularly targeted herbicides include those that inhibit protoporphyrinogen oxidase (PPO, EC 1.3.3.4), known as PPO herbicides. PPO herbicides provide control over a wide variety of herbicide-resistant weeds, and therefore, traits conferring resistance to these herbicides are particularly useful in cropping systems when combined with one or more other herbicide resistance traits. The present invention provides a novel, manipulated herbicide-resistant protoporphyrinogen oxidase that is useful for providing PPO herbicide resistance in plants. [Overview of the project]

[0005] In one embodiment, the present invention provides a recombinant DNA molecule comprising a heterologous promoter operably linked to a nucleic acid molecule encoding a protein having herbicide-resistant protoporphyrinogen oxidase activity, wherein the protein has at least about 50% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 1 to 23, and comprises at least a first amino acid substitution at a position corresponding to residues 125 to 146 of SEQ ID NO: 1, The substitutions are L125I, L125V, R126A, Y127W, P128A, P128D, P128E, P128K, P128L, P128Q, P128R, P128S, P128T, R129A, R129E, R129G, R129H, R129I, R129K, R129L, R129N, R129Q, R129S, Y130L, R131A, W132A, W132F, W132I, W132K, W132L, W132P, W1 32R, W132S, W132T, W132V, W132Y, I133A, D134A, D134N, D134Q, D134T, K135A, K135Q, K135R, K135S, K135T, K135V, V1 36A, M137A, M137C, M137I, M137L, M137S, M137V, I138L, I138M, I138V, Q139A, Q139C, Q139E, Q139G, Q139H, Q139K, Q1 Selected from the group consisting of 39L, Q139M, Q139R, Q139S, L140A, L140C, L140F, L140G, L140H, L140I, L140M, L140N, L140Q, L140S, L140T, L140V, L140W, L140Y, I141V, M142L, M142S, M142V, R143A, M144A, T145A, G146A, G146D, G146H, G146K, and G146N.In a particular embodiment, the protein has at least about 50% sequence identity with respect to an amino acid sequence selected from the group consisting of SEQ ID NOs: 1 to 23, at least about 60% sequence identity, at least about 70% sequence identity, at least about 80% sequence identity, at least about 85% sequence identity, at least about 90% sequence identity, at least about 91% sequence identity, at least about 92% sequence identity, at least about 93% sequence identity, at least about 94% sequence identity, at least about 95% sequence identity, and less than It has at least approximately 96% sequence identity, at least approximately 97% sequence identity, at least approximately 98% sequence identity, and at least approximately 99% sequence identity, and includes at least a first amino acid substitution at a position corresponding to residues 125-146 of SEQ ID NO: 1, wherein the substitution is L125I, L125V, R126A, Y127W, P128A, P128D, P128E, P128K, P128L, P128Q, P128R, P128S, P128T, R129A, R129E, R129G, R129H, R129I, R129K, R129L, R129N, R129Q, R129S, Y130L, R131A, W132A, W132F, W132I, W132K, W132L, W132P, W132R, W132S, W132T, W132V, W132Y, I133A, D134A, D134N, D134Q, D134T, K135A, K135Q, K135R, K135S, K135T, K135V, V136A, M137A, M137C, M137I, M137L, M137S, M137V, I138L, I138M, I138V, Q Selected from the group consisting of 139A, Q139C, Q139E, Q139G, Q139H, Q139K, Q139L, Q139M, Q139R, Q139S, L140A, L140C, L140F, L140G, L140H, L140I, L140M, L140N, L140Q, L140S, L140T, L140V, L140W, L140Y, I141V, M142L, M142S, M142V, R143A, M144A, T145A, G146A, G146D, G146H, G146K, and G146N.In some embodiments, the protein contains at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten of the amino acid substitutions. In another embodiment, the protein has at least about 90% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs. 24-124 and 249-263. In yet another embodiment, the protein contains a HemG class protoporphyrinogen oxidase enzyme. In a further embodiment, at least the first amino acid substitution is located in the long insert loop of such a HemG class protoporphyrinogen oxidase enzyme. In yet another embodiment, the recombinant DNA molecule of the present invention is contained in the genome of a plant cell.

[0006] In a particular embodiment, a heterologous promoter, for example, a promoter functional in plant cells, is operably linked to a nucleic acid molecule encoding a protein having herbicide-resistant protoporphyrinogen oxidase activity, wherein the protein has at least 50% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 1 to 23, and has at least a first amino acid at positions corresponding to residues 125 to 146 of SEQ ID NO: 1. This includes no acid substitution, and the substitution is L125I, L125V, R126A, Y127W, P128A, P128D, P128E, P128K, P128L, P128Q, P128R, P128S, P128T, R129A, R129E, R129G, R129H, R129I, R129K, R129L, R129N, R129Q, R129S, Y130L, R131A, W132A, W132F, W132I, W132K, W132L, W1 32P, W132R, W132S, W132T, W132V, W132Y, I133A, D134A, D134N, D134Q, D134T, K135A, K135Q, K135R, K135S, K135T, K13 5V, V136A, M137A, M137C, M137I, M137L, M137S, M137V, I138L, I138M, I138V, Q139A, Q139C, Q139E, Q139G, Q139H, Q139K The DNA molecules are selected from the group consisting of Q139L, Q139M, Q139R, Q139S, L140A, L140C, L140F, L140G, L140H, L140I, L140M, L140N, L140Q, L140S, L140T, L140V, L140W, L140Y, I141V, M142L, M142S, M142V, R143A, M144A, T145A, G146A, G146D, G146H, G146K, and G146N. The resulting DNA molecule may further contain a transport sequence that functions to localize the protein within the cell.

[0007] In another aspect, the present invention provides a DNA construct comprising a recombinant DNA molecule provided herein, such as a recombinant DNA molecule comprising a heterologous promoter operably linked to a nucleic acid molecule encoding a protein having herbicide-resistant protoporphyrinogen oxidase activity, wherein the protein has at least 50% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 1 to 23, and corresponds to residues 125 to 146 of SEQ ID NO: 1. The following amino acids are included in the following positions: L125I, L125V, R126A, Y127W, P128A, P128D, P128E, P128K, P128L, P128Q, P128R, P128S, P128T, R129A, R129E, R129G, R129H, R129I, R129K, R129L, R129N, R129Q, R129S, Y130L, R131A, W132A, W132F, W132I, W132K , W132L, W132P, W132R, W132S, W132T, W132V, W132Y, I133A, D134A, D134N, D134Q, D134T, K135A, K135Q, K135R, K135S, K1 35T, K135V, V136A, M137A, M137C, M137I, M137L, M137S, M137V, I138L, I138M, I138V, Q139A, Q139C, Q139E, Q139G, Q139H, The group is selected from Q139K, Q139L, Q139M, Q139R, Q139S, L140A, L140C, L140F, L140G, L140H, L140I, L140M, L140N, L140Q, L140S, L140T, L140V, L140W, L140Y, I141V, M142L, M142S, M142V, R143A, M144A, T145A, G146A, G146D, G146H, G146K, and G146N. In another embodiment, the manipulated protein is encoded by a recombinant DNA molecule provided herein.

[0008] In a further embodiment, the present invention provides transgenic plants, seeds, cells, or plant parts comprising recombinant DNA molecules provided herein, such as recombinant DNA molecules comprising heterologous promoters operably linked to nucleic acid molecules encoding a protein having herbicide-resistant protoporphyrinogen oxidase activity, wherein the protein has at least 50% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 1 to 23, and sequence number The first amino acid substitution includes at least one amino acid substitution at the position corresponding to residues 125-146 of compound 1, wherein the substitution is L125I, L125V, R126A, Y127W, P128A, P128D, P128E, P128K, P128L, P128Q, P128R, P128S, P128T, R129A, R129E, R129G, R129H, R129I, R129K, R129L, R129N, R129Q, R129S, Y130L, R131A, W132A, W132F, W132I, W132K, W132L, W132P, W132R, W132S, W132T, W132V, W132Y, I133A, D134A, D134N, D134Q, D134T, K135A, K135Q, K135R, K135S, K135T, K135V, V136A, M137A, M137C, M137I, M137L, M137S, M137V, I138L, I138M, I138V, Q139A, Q139C, Q139E, Q139G, Q The herbicides are selected from the group consisting of 139H, Q139K, Q139L, Q139M, Q139R, Q139S, L140A, L140C, L140F, L140G, L140H, L140I, L140M, L140N, L140Q, L140S, L140T, L140V, L140W, L140Y, I141V, M142L, M142S, M142V, R143A, M144A, T145A, G146A, G146D, G146H, G146K, and G146N. In one embodiment, the transgenic plant, seed, cell, or plant part is resistant to at least one PPO herbicide.In another embodiment, the PPO herbicide is selected from the group consisting of asifluorphen, homesaphen, lactofen, fluoroglycofen ethyl, oxyfluorphen, flumioxazine, azaphenidine, carfentrazone ethyl, sulfentrazone, fluthiaset methyl, oxadiargyl, oxadiazone, pyraflufen ethyl, saflufenacil, and S-3100. In a further embodiment, the transgenic plant, seed, cell, or plant part is resistant to at least the second herbicide.

[0009] In another embodiment, the present invention provides a method for conferring PPO herbicide resistance to a plant, seed, cell, or plant part, comprising heterologously expressing an engineered protein of the present invention in the plant, seed, cell, or plant part. In some embodiments, the herbicide resistance is to at least one PPO herbicide selected from the group consisting of asifluorphene, homesaphene, lactofen, fluoroglycofen ethyl, oxyfluorphene, flumioxazine, azaphenidine, carfentrazone ethyl, sulfentrazone, fluthiaset methyl, oxaziargyl, oxadiazone, pyraflufen ethyl, saflufenacil, and S-3100.

[0010] In another embodiment, the present invention provides a step of transforming plant cells with a recombinant DNA molecule provided herein, such as a recombinant DNA molecule containing a heterologous promoter operably linked to a nucleic acid molecule encoding a protein having herbicide-resistant protoporphyrinogen oxidase activity, wherein the protein has at least 50% sequence identity with an amino acid sequence selected from the group consisting of SEQ ID NOs: 1 to 23, and at least at the positions corresponding to residues 125 to 146 of SEQ ID NO: 1. Both include a first amino acid substitution, where the substitution is L125I, L125V, R126A, Y127W, P128A, P128D, P128E, P128K, P128L, P128Q, P128R, P128S, P128T, R129A, R129E, R129G, R129H, R129I, R129K, R129L, R129N, R129Q, R129S, Y130L, R131A, W132A, W132F, W132I, W132K, W132L, W132P, W132R, W132S, W 132T, W132V, W132Y, I133A, D134A, D134N, D134Q, D134T, K135A, K135Q, K135R, K135S, K135T, K135V, V136A, M137A, M137C, M137I, M1 37L, M137S, M137V, I138L, I138M, I138V, Q139A, Q139C, Q139E, Q139G, Q139H, Q139K, Q139L, Q139M, Q139R, Q139S, L140A, L140C, L14 A method for producing herbicide-resistant plants is provided, comprising the steps of: a) selecting from the group consisting of 0F, L140G, L140H, L140I, L140M, L140N, L140Q, L140S, L140T, L140V, L140W, L140Y, I141V, M142L, M142S, M142V, R143A, M144A, T145A, G146A, G146D, G146H, G146K, and G146N; and b) regenerating a plant from the plant cells containing the recombinant DNA molecule. In one embodiment, the method further comprises the step of selecting the plant or its progeny for PPO herbicide resistance. In another embodiment, the method further comprises the step of crossing the regenerated plant with itself or with a second plant to produce progeny.

[0011] In another embodiment, the present invention provides a method for controlling or inhibiting weed growth in a plant growing area, comprising applying an effective amount of at least one PPO herbicide to a plant growing area containing a transgenic plant or seed, such as a transgenic plant or seed, as provided herein, which includes a recombinant DNA molecule comprising a heterologous promoter operably linked to a nucleic acid molecule encoding a protein having herbicide-resistant protoporphyrinogen oxidase activity, wherein the protein comprises Sequence IDs 1 to 23. It has at least 50% sequence identity with an amino acid sequence selected from the group and includes at least one first amino acid substitution at a position corresponding to residues 125-146 of SEQ ID NO: 1, wherein the substitution is L125I, L125V, R126A, Y127W, P128A, P128D, P128E, P128K, P128L, P128Q, P128R, P128S, P128T, R129A, R129E, R129G, R129H, R129I, R129K, R129L, R129N, R129Q, R129S, Y130L, R1 31A, W132A, W132F, W132I, W132K, W132L, W132P, W132R, W132S, W132T, W132V, W132Y, I133A, D134A, D134N, D134Q, D134T, K135A, K135Q, K13 5R, K135S, K135T, K135V, V136A, M137A, M137C, M137I, M137L, M137S, M137V, I138L, I138M, I138V, Q139A, Q139C, Q139E, Q139G, Q139H, Q139 Selected from the group consisting of K, Q139L, Q139M, Q139R, Q139S, L140A, L140C, L140F, L140G, L140H, L140I, L140M, L140N, L140Q, L140S, L140T, L140V, L140W, L140Y, I141V, M142L, M142S, M142V, R143A, M144A, T145A, G146A, G146D, G146H, G146K, and G146N, the transgenic plant or seed is resistant to PPO herbicides.In certain embodiments, the PPO herbicide is selected from the group consisting of asifluorphen, homesaphen, lactofen, fluoroglycofen ethyl, oxyfluorphen, flumioxazine, azaphenidine, carphenthrazone ethyl, sulfenthrazone, fluthiaset methyl, oxadiargyl, oxadiazone, pyraflufen ethyl, saflufenacil, and S-3100.

[0012] In another embodiment, the present invention provides a method for identifying nucleotide sequences encoding a protein having herbicide-resistant protoporphyrinogen oxidase activity, the method comprising: a) transforming an E. coli strain lacking herbicide-resistant PPO enzyme activity with a bacterial expression vector comprising a recombinant DNA molecule provided herein, such as a recombinant DNA molecule containing a heterologous promoter operably linked to a nucleic acid molecule encoding a protein having herbicide-resistant protoporphyrinogen oxidase activity, wherein the protein comprises Sequence IDs 1 to 23. It has at least 50% sequence identity with an amino acid sequence selected from the group, and includes at least a first amino acid substitution at a position corresponding to residues 125-146 of SEQ ID NO: 1, wherein the substitution is L125I, L125V, R126A, Y127W, P128A, P128D, P128E, P128K, P128L, P128Q, P128R, P128S, P128T, R129A, R129E, R129G, R129H, R129I, R129K, R129L, R129N, R129Q, R129S, Y130L, R131A, W132A, W132F, W132I, W132K, W132L, W132P, W132R, W132S, W132T, W132V, W132Y, I133A, D 134A, D134N, D134Q, D134T, K135A, K135Q, K135R, K135S, K135T, K135V, V1 36A, M137A, M137C, M137I, M137L, M137S, M137V, I138L, I138M, I138V, Q13 9A, Q139C, Q139E, Q139G, Q139H, Q139K, Q139L, Q139M, Q139R, Q139S, L140A a) transforming the organism using a protein selected from the group consisting of L140C, L140F, L140G, L140H, L140I, L140M, L140N, L140Q, L140S, L140T, L140V, L140W, L140Y, I141V, M142L, M142S, M142V, R143A, M144A, T145A, G146A, G146D, G146H, G146K, and G146N; b) growing the transformed E. coli to identify a protein having herbicide-resistant protoporphyrinogen oxidase activity.

[0013] In a further embodiment, the present invention relates to a) expressing a recombinant DNA molecule provided herein, such as a recombinant DNA molecule containing a heterologous promoter operably linked to a nucleic acid molecule encoding a protein having herbicide-resistant protoporphyrinogen oxidase activity, in plant cells, wherein the protein has at least 50% sequence identity with an amino acid sequence selected from the group consisting of SEQ ID NOs: 1 to 23, and at least at the positions corresponding to residues 125 to 146 of SEQ ID NO: 1. Both include a first amino acid substitution, where the substitution is L125I, L125V, R126A, Y127W, P128A, P128D, P128E, P128K, P128L, P128Q, P128R, P128S, P128T, R129A, R129E, R129G, R129H, R129I, R129K, R129L, R129N, R129Q, R129S, Y130L, R131A, W132A, W132F, W132I, W132K, W132L, W132P, W132R, W132S, W1 32T, W132V, W132Y, I133A, D134A, D134N, D134Q, D134T, K135A, K135Q, K135R, K135S, K135T, K135V, V136A, M137A, M137C, M137I, M137 L, M137S, M137V, I138L, I138M, I138V, Q139A, Q139C, Q139E, Q139G, Q139H, Q139K, Q139L, Q139M, Q139R, Q139S, L140A, L140C, L140F, The present invention provides a method for screening herbicide resistance genes, comprising: a) expressing a gene selected from the group consisting of L140G, L140H, L140I, L140M, L140N, L140Q, L140S, L140T, L140V, L140W, L140Y, I141V, M142L, M142S, M142V, R143A, M144A, T145A, G146A, G146D, G146H, G146K, and G146N; and b) identifying plant cells that exhibit resistance to PPO herbicides.

[0014] In another aspect, the present invention provides for obtaining a transgenic plant comprising a recombinant DNA molecule provided herein, such as a) a recombinant DNA molecule comprising a heterologous promoter operably linked to a nucleic acid molecule encoding a protein having herbicide-resistant protoporphyrinogen oxidase activity, wherein the protein has at least 50% sequence identity with an amino acid sequence selected from the group consisting of SEQ ID NOs: 1 to 23, and comprises at least a first amino acid substitution at a position corresponding to residues 125 to 146 of SEQ ID NO: 1, wherein the substitution is L1 25I, L125V, R126A, Y127W, P128A, P128D, P128E, P128K, P128L, P128Q, P1 28R, P128S, P128T, R129A, R129E, R129G, R129H, R129I, R129K, R129L, R1 29N, R129Q, R129S, Y130L, R131A, W132A, W132F, W132I, W132K, W132L, W1 32P, W132R, W132S, W132T, W132V, W132Y, I133A, D134A, D134N, D134Q, D13 4T, K135A, K135Q, K135R, K135S, K135T, K135V, V136A, M137A, M137C, M13 7I, M137L, M137S, M137V, I138L, I138M, I138V, Q139A, Q139C, Q139E, Q13 9G, Q139H, Q139K, Q139L, Q139M, Q139R, Q139S, L140A, L140C, L140F, L14 0G, L140H, L140I, L140M, L140N, L140Q, L140S, L140T, L140V, L140W, L140 The present invention provides a method for producing plants resistant to PPO herbicides and at least one other herbicides, comprising: a) obtaining a plant selected from the group consisting of Y, I141V, M142L, M142S, M142V, R143A, M144A, T145A, G146A, G146D, G146H, G146K, and G146N; b) crossing the plant with a second plant having resistance to at least one other herbicide; and c) selecting a progeny from the cross that has resistance to PPO herbicides and at least one other herbicide.

[0015] In another embodiment, the present invention relates to cultivating a transgenic plant in a crop growth environment comprising a recombinant DNA molecule provided herein, such as a recombinant DNA molecule containing a heterologous promoter operably linked to a nucleic acid molecule encoding a protein having herbicide-resistant protoporphyrinogen oxidase activity, wherein the protein has at least 50% sequence identity with an amino acid sequence selected from the group consisting of SEQ ID NOs: 1 to 23, and at least at the positions corresponding to residues 125 to 146 of SEQ ID NO: 1. The first amino acid substitution is included, wherein the substitution is L125I, L125V, R126A, Y127W, P128A, P128D, P128E, P128K, P128L, P128Q, P128R, P128S, P128T, R129A, R129E, R129G, R129H, R129I, R129K, R129L, R129N, R129Q, R129S, Y130L, R131A, W132A, W132F, W132I, W132K, W132L, W132P, W132R, W132S, W132T, W132V, W132Y, I133A, D134A, D134N, D134Q, D134T, K135A, K135Q, K135R, K135S, K135T, K135V, V136A, M137A, M137C, M137I, M137L, M137S, M137V, I138L, I1 38M, I138V, Q139A, Q139C, Q139E, Q139G, Q139H, Q139K, Q139L, Q139M, Q139R, Q139S, L140A, L140C, L140F, L140G, L140H, L140I, L140M, L140N The present invention provides a method for reducing the occurrence of herbicide-resistant weeds, comprising: a) cultivating a crop selected from the group consisting of L140Q, L140S, L140T, L140V, L140W, L140Y, I141V, M142L, M142S, M142V, R143A, M144A, T145A, G146A, G146D, G146H, G146K, and G146N; and b) applying a PPO herbicide and at least one other herbicide to the crop growing environment, wherein the crop plant is resistant to the PPO herbicide and at least one other herbicide.In one embodiment, the PPO herbicide is selected from the group consisting of asifluorphen, homesaphen, lactofen, fluoroglycofen ethyl, oxyfluorphen, flumioxazine, azaphenidine, carfentrazone ethyl, sulfentrazone, fluthiaset methyl, oxadiargyl, oxadiazone, pyraflufen ethyl, saflufenacil, and S-3100. In another embodiment, at least one other herbicide is selected from the group consisting of ACCase inhibitors, ALS inhibitors, EPSPS inhibitors, synthetic auxins, photosynthesis inhibitors, glutamine synthesis inhibitors, HPPD inhibitors, PPO inhibitors, and long-chain fatty acid inhibitors. In further embodiments, the ACCase inhibitor is aryloxyphenoxypropionate or cyclohexanedione; the ALS inhibitor is sulfonylurea, imidazolinone, triazoloyrimidine, or triazolinone; the EPSPS inhibitor is glyphosate; the synthetic auxin is phenoxyherbicide, benzoic acid, carboxylic acid, or semicarbazone; the photosynthesis inhibitor is triazine, triazinon, nitrile, benzothiadiazole, or urea; the glutamine synthesis inhibitor is glufosinate; the HPPD inhibitor is isoxazole, pyrazolone, or triketone; the PPO inhibitor is diphenyl ether, N-phenylphthalimide, aryltriazinon, or pyrimidinedione; or the long-chain fatty acid inhibitor is chloroacetamide, oxyacetamide, or pyrazole.

[0016] This patent or application document includes at least one drawing drawn in color. A copy of this patent or patent application publication, including the color drawing(s), will be provided by the Patent Office upon request and payment of the necessary fees. [Brief explanation of the drawing]

[0017] [Figure 1A]This diagram shows the sequence alignment of long-chain insert loops of a subset of 23 microbial HemG PPO enzymes, with conserved long-chain insert loops highlighted in black. The sequences are arranged in descending order of overall sequence identity to H_N90 (SEQ ID NO: 1). HemG001 and HemG003 represent HemG PPO proteins with overall sequence identity to H_N90 exceeding 70%. The next 15 sequences, not enclosed in boxes, represent HemG PPO proteins with overall sequence identity to H_N90 between 50% and 70%. The last 5 sequences enclosed in boxes represent HemG PPO proteins with overall sequence identity to H_N90 between 40% and 50%. [Figure 1B] This diagram shows the sequence alignment of long-chain insert loops of a subset of 23 microbial HemG PPO enzymes, with conserved long-chain insert loops highlighted in black. The sequences are arranged in descending order of overall sequence identity to H_N90 (SEQ ID NO: 1). HemG001 and HemG003 represent HemG PPO proteins with overall sequence identity to H_N90 exceeding 70%. The next 15 sequences, not enclosed in boxes, represent HemG PPO proteins with overall sequence identity to H_N90 between 50% and 70%. The last 5 sequences enclosed in boxes represent HemG PPO proteins with overall sequence identity to H_N90 between 40% and 50%. [Figure 2] A universal genetic code table is presented showing all possible mRNA triplet codons (where T in DNA molecules is replaced by U in RNA molecules) and the amino acids encoded by each codon. [Figure 3]This diagram shows all the mutations found at each residue within the long insert loop of H_N90 (SEQ ID NO: 1) through microbial genome screening. The black box spanning the top represents the native H_N90 sequence. The boxes below the H_N90 sequence list each of the 20 amino acids. The numbers listed above the H_N90 sequence indicate the relative amino acid position. The gray shaded areas represent amino acid mutations identified in groups with 50% or more sequence identity. The gray vertical striped areas represent amino acid mutations identified in groups with 40% to 50% sequence identity. The remaining white, unfilled boxes represent amino acid mutations not observed in the initial microbial dataset with 40% or more overall sequence identity. [Figure 4] The diagram shows the results obtained from the enzyme function assay. The black box spanning the top represents the natural H_N90 sequence (SEQ ID NO: 1). The boxes below the H_N90 sequence list each of the 20 amino acids. The numbers listed above the H_N90 sequence indicate the relative amino acid position. Gray vertical stripes indicate that the amino acid modification caused enzyme dysfunction. Light gray shading with black text indicates that the amino acid modification caused impaired enzyme function. Dark gray shading with white text indicates that the amino acid change maintained the enzyme fully functionally. The black shading represents the natural amino acids in the H_N90 sequence. The remaining white, unfilled boxes represent amino acid mutations not tested in this assay. [Figure 5]This shows a graph version of the results obtained from the herbicide resistance assay. Resistance was measured in comparison to H_N90 resistance. The black box spanning the top represents the natural H_N90 sequence (SEQ ID NO: 1). The boxes below the H_N90 sequence list each of the 20 amino acids. The numbers listed above the H_N90 sequence are the relative amino acid positions. Gray vertical stripes represent relative resistance scores of 0-24, indicating that the amino acid modification conferred little to no herbicide resistance. Gray horizontal stripes represent relative resistance scores of 25-49, indicating that the amino acid modification conferred weak herbicide resistance. Light gray filled-in shading with black text represents relative resistance scores of 50-74, indicating that the amino acid modification conferred moderate herbicide resistance. Dark gray shaded areas with white text represent relative resistance scores between 75 and 100, indicating that the amino acid modification conferred good herbicide resistance. Dark gray shaded areas with thick black borders represent amino acid modifications showing relative resistance scores greater than 100, indicating that the amino acid modification conferred better herbicide resistance than H_N90. Black shaded areas represent native amino acids in the H_N90 sequence. The remaining unfilled white boxes represent amino acid mutations not tested in this assay.

[0018] A brief explanation of arrays Sequence ID 1 is the amino acid sequence of H_N90.

[0019] Sequence IDs 2 through 10 are amino acid sequences of microbial HemG PPO enzymes that have a conserved long-chain insert loop.

[0020] Sequence IDs 11 to 23 are amino acid sequences of diverse HemG PPO enzymes that have mutations within the long insert loop.

[0021] SEQ ID NO: 24 to SEQ ID NO: 124 and SEQ ID NO: 249 to SEQ ID NO: 263 are the amino acid sequences of 116 recombinant HemG PPO variants, each incorporating a mutation with respect to the long-chain insert loop.

[0022] SEQ ID NO: 125 is the DNA sequence encoding SEQ ID NO: 1.

[0023] SEQ ID NO: 126 to SEQ ID NO: 147 are the DNA sequences encoding SEQ ID NO: 2 to SEQ ID NO: 23, respectively.

[0024] SEQ ID NO: 148 to SEQ ID NO: 248 and SEQ ID NO: 264 to SEQ ID NO: 278 are the DNA sequences encoding SEQ ID NO: 24 to SEQ ID NO: 124 and SEQ ID NO: 249 to SEQ ID NO: 263, respectively.

MODE FOR CARRYING OUT THE INVENTION

[0025] The following explanations and definitions are provided to better define the present invention and guide those skilled in the art in implementing the present invention. Unless otherwise noted, terms should be understood according to conventional usage by those with ordinary knowledge in the relevant technical field.

[0026] Protoporphyrinogen oxidase functions in both chlorophyll and heme biosynthetic pathways, in which it converts protoporphyrinogen IX to protoporphyrin IX. Herbicide-resistant protoporphyrinogen oxidase is useful for producing cells, plants, and seeds that are not susceptible to the application of one or more PPO herbicides, and is also useful in agricultural and weed control methods. The present invention provides novel engineered proteins that are herbicide-resistant protoporphyrinogen oxidase, as well as recombinant DNA molecules encoding them, compositions containing them, and methods of using them. For example, in one embodiment, the present invention provides a DNA construct comprising a recombinant DNA molecule encoding an engineered herbicide-resistant protoporphyrinogen oxidase for expression in cells, plants, and seeds. In another embodiment, the present invention provides an engineered protein having herbicide-resistant protoporphyrinogen oxidase activity. In another embodiment, the present invention provides methods and compositions for obtaining and improving herbicide-resistant protoporphyrinogen oxidase using protein manipulation and bioinformatics tools. The present invention further provides methods and compositions for producing cells, plants, and seeds that are resistant to PPO herbicides, as well as methods for weed control using such cells, plants, and seeds.

[0027] The present invention provides novel engineered proteins and recombinant DNA molecules that encode them. As used herein, the term "engineered" refers to non-natural DNA, proteins, cells, or organisms created by human intervention that are not normally found in nature. "Engineered protein," "engineered enzyme," or "engineered PPO" refers to a protein, enzyme, or PPO whose amino acid sequence is devised and produced in a laboratory using one or more techniques of biotechnology, protein design, or protein manipulation, such as molecular biology, protein biochemistry, bacterial transformation, plant transformation, site-directed mutagenesis, directed evolution using random mutagenesis, genome editing, gene editing, gene cloning, DNA ligation, DNA synthesis, protein synthesis, and DNA shuffling. For example, an engineered protein may have one or more deletions, insertions, or substitutions compared to the coding sequence of a wild-type protein, each deletion, insertion, or substitution may consist of one or more amino acids. Using genetic engineering, DNA molecules encoding engineered proteins, such as engineered PPO, which is herbicide-resistant and contains at least one amino acid substitution compared to the wild-type PPO protein, can be created.

[0028] Examples of manipulated proteins provided herein include L125I, L125V, R126A, Y127W, P128A, P128D, P128E, P128K, P128L, P128Q, P128R, P128S, P128T, R129A, R129E, R129G, R129H, R129I, R129K, R129L, R129N, R129Q, R129S, Y130L, and R131A. , W132A, W132F, W132I, W132K, W132L, W132P, W132R, W132S, W132T, W132V, W132Y, I133A, D134A, D134N, D 134Q, D134T, K135A, K135Q, K135R, K135S, K135T, K135V, V136A, M137A, M137C, M137I, M137L, M137S, M137 V, I138L, I138M, I138V, Q139A, Q139C, Q139E, Q139G, Q139H, Q139K, Q139L, Q139M, Q139R, Q139S, L140A, L140C, L140F, L140G, L140H, L140I, L140M, L140N, L140Q, L140S, L140T, L140V, L140W, L140Y, I141V, M14 Herbicide-resistant PPO comprising one or more amino acid substitutions selected from 2L, M142S, M142V, R143A, M144A, T145A, G146A, G146D, G146H, G146K, and G146N (including all possible combinations thereof), wherein the positions of the amino acid substitutions are relative to the amino acid positions described in Sequence ID No. 1. In specific embodiments, the manipulated proteins provided herein may contain one, two, three, four, five, six, seven, eight, nine, ten, or more of any combination of such substitutions.

[0029] In one embodiment, the manipulated protein provided by the present invention has herbicide-resistant protoporphyrinogen oxidase activity. As used herein, “herbicide-resistant protoporphyrinogen oxidase” means the ability of protoporphyrinogen oxidase to maintain at least a portion of its protoporphyrinogen oxidase activity in the presence of one or more PPO herbicides. The term “protoporphyrinogen oxidase activity” means the ability to catalyze the 6-electron oxidation (removal of electrons) of protoporphyrinogen IX to form protoporphyrin IX, that is, to catalyze the dehydrogenation of protoporphyrinogen to form protoporphyrin. The enzymatic activity of protoporphyrinogen oxidase can be measured by any means known in the art, for example, by an enzyme assay in which the production of protoporphyrinogen oxidase products or the consumption of protoporphyrinogen oxidase substrates in the presence of one or more PPO herbicides is measured via fluorescence, high-performance liquid chromatography (HPLC), or mass spectrometry (MS). Another example of an assay for measuring the enzymatic activity of protoporphyrinogen oxidase is a bacterial assay, such as the assay described herein, in which recombinant protoporphyrinogen oxidase is expressed in bacterial cells otherwise lacking PPO activity, and the ability of recombinant protoporphyrinogen oxidase to complement this knockout phenotype is measured. As used herein, "hemG knockout strain" means an organism or cell of an organism such as E. coli that is unable to grow on heme-free growth medium or lacks hemG activity to such an extent that its growth in the absence of heme is detectably impaired compared to a strain that is otherwise isogeneic and contains functional hemG.For example, a hemG knockout strain of E. coli may be prepared in accordance with the knowledge of the art, for example, in accordance with the E. coli HemG PPO sequence (Ecogene accession number EG11485, Sasarman et al., “Nucleotide sequence of the hemG gene involved in the protoporphyrinogen oxidase activity of E. coli K12”, Can J Microbiol 39:1155-1161, 1993).

[0030] The manipulated protein, in particular, is a modified V max , K m , K i ,I C 50The novel proteins may be produced by altering or modifying the wild-type protein sequence to produce novel proteins having modified properties or novel combinations of useful protein properties, such as substrate specificity, inhibitor / herbicide specificity, substrate selectivity, ability to interact with other intracellular components such as partner proteins or membranes, and protein stability. The modifications may be carried out at specific amino acid positions in the protein, or by substituting a typical amino acid found at the same position in nature (i.e., in the wild-type protein) with an alternative amino acid. The amino acid modifications may be carried out as single amino acid substitutions in the protein sequence, or in combination with one or more other modifications, such as one or more other amino acid substitutions, deletions, or additions. In one embodiment of the present invention, the engineered protein has modified protein properties, such as the property of conferring reduced sensitivity to one or more herbicides compared to the wild-type protein, or the property of conferring resistance to one or more herbicides to transgenic plants expressing the engineered protein.In one embodiment, the present invention therefore relates to L125I, L125V, R126A, Y127W, P128A, P128D, P128E, P128K, P128L, P128Q, P128R, P128S, P128T, R129A, R129E, R129G, R129H, R129I, R129K, R129L, R129N, R129Q, R129S, Y130L, R131A, W132A, W132F, W132I, W132K, W132L, W132P, W132R, W132S, W132T, W132V, W132Y, I133A, D134A, D134N, D134Q, D134T, K135A, K135Q, K13 5R, K135S, K135T, K135V, V136A, M137A, M137C, M137I, M137L, M137S, M137V, I138L, I138M, I138V, Q139A, Q139C, Q 139E, Q139G, Q139H, Q139K, Q139L, Q139M, Q139R, Q139S, L140A, L140C, L140F, L140G, L140H, L140I, L140M, L140 N, L140Q, L140S, L140T, L140V, L140W, L140Y, I141V, M142L, M142S, M142V, R143A, M144A, T145A, G146A, G146D, G1 This invention provides engineered proteins, such as PPO enzymes having herbicide-resistant protoporphyrinogen oxidase activity, having one or more amino acid substitutions selected from the group consisting of 46H, G146K, and G146N, and all combinations thereof, and recombinant DNA molecules encoding them, where the positions of the amino acid substitutions are relative to the amino acid positions described in Sequence ID No. 1. In specific embodiments, the engineered proteins provided herein contain one, two, three, four, five, six, seven, eight, nine, ten, or more of any combination of such substitutions, where the modifications are made at positions corresponding to equivalent positions in position and function in the amino acid sequence provided as Sequence ID No. 1. The amino acid sequences of recombinant or engineered HemG variant PPOs are provided in Table 1. [Table 1-1] [Table 1-2]

[0031] By aligning the amino acid sequence of the PPO enzyme to be mutated with the amino acid sequence of a PPO enzyme possessing herbicide-resistant protoporphyrinogen oxidase activity, similar modifications can be performed at similar positions on any PPO enzyme. An example of a sequence encoding a PPO enzyme possessing herbicide-resistant protoporphyrinogen oxidase activity that can be used for alignment is Sequence ID No. 1. Figures 1A and 1B show alignments of H_N90, the PPO enzyme of Sequence ID No. 1, example known PPO enzymes (Sequence IDs No. 2-10), and various PPO enzymes (Sequence IDs No. 11-23). ​​Using sequence identity information as shown in Figures 1A and 1B, it is well within the skill of those skilled in the art to generate PPO enzymes possessing herbicide-resistant protoporphyrinogen oxidase activity by performing the amino acid modifications described herein on, for example, the proteins of Sequence IDs No. 2-23. The amino acid sequences of the microorganism HemG PPO are provided in Table 2. [Table 2]

[0032] As used herein, the term “recombinant” refers to non-natural DNA, proteins, cells, seeds, or organisms that are the result of genetic engineering and are produced by human intervention. “Recombinant DNA molecule” is a DNA molecule containing a DNA sequence that does not exist naturally and is therefore the result of human intervention, such as a DNA molecule containing at least two heterogeneous DNA molecules. An example of a recombinant DNA molecule is the DNA molecule provided herein that encodes herbicide-resistant protoporphyrinogen oxidase operably linked to a heterogeneous promoter. “Recombinant protein” is a protein containing an amino acid sequence that does not exist naturally and is therefore the result of human intervention, such as an engineered protein. Recombinant cells, seeds, or organisms are cells, seeds, or organisms containing transgenic or heterogeneous DNA or proteins, such as transgenic plant cells, seeds, or plants containing the DNA constructs or engineered proteins of the present invention.

[0033] As used herein, “wild-type” means naturally occurring. “Wild-type DNA molecule” and “wild-type protein” refer to the naturally occurring version of a DNA molecule or protein, i.e., a version of a DNA molecule or protein that exists in nature. The wild-type version of a DNA molecule or protein may be useful for comparison with recombinant or engineered DNA molecules or proteins. An example of a wild-type protein useful for comparison with engineered proteins provided by this invention is the PPO enzyme derived from E. cloacae (H_N90), provided as SEQ ID NO: 1.

[0034] A "wild-type plant" is a naturally occurring plant. Such wild-type plants can also be useful for comparison with plants containing recombinant or engineered DNA molecules or proteins. Examples of wild-type plants useful for comparison with plants containing recombinant or engineered DNA molecules or proteins may be the same species of plant as plants containing engineered DNA molecules or proteins, such as proteins that confer herbicide resistance traits, and are therefore genetically distinct from plants containing herbicide resistance traits.

[0035] In certain embodiments, wild-type plants may also be used or referred to as “control plants.” As used herein, “control” means an experimental control designed for comparative purposes. For example, a control plant in transgenic plant analysis is the same species of plant as the experimental plant (i.e., the plant under test), but does not contain the transgenic insert, recombinant DNA molecule, or DNA construct of the experimental plant. Examples of control plants useful for comparison with transgenic plants include, for comparison with maize, non-transgenic LH244 maize (ATCC deposit number PTA-1173); for comparison with soybean plants, non-transgenic A3555 soybean (ATCC deposit number PTA-10207); for comparison with cotton plants, non-transgenic Coker 130 (Plant Variety Protection (PVP) number 8900252); for comparison with rapeseed or Brassica napus, non-transgenic Brassica napus variety 65037 fertility recovery line (Canada Plant Breeders' Rights Application 06-5517); and for comparison with wheat plants, non-transgenic wheat variety Samson germplasm (PVP 1994).

[0036] As used herein, the terms “DNA” or “DNA molecule” refer to a double-stranded DNA molecule of genomic or synthetic origin (i.e., a polymer of deoxyribonucleotide bases or polynucleotide molecules) read from the 5' (upstream) end to the 3' (downstream) end. As used herein, the term “DNA sequence” refers to the nucleotide sequence of a DNA molecule. The nomenclature used herein corresponds to that of the Federal Rules of the United States Code § 1.822, Title 37, and is set forth in the tables in WIPO Standard ST.25 (1998), Appendix 2, Tables 1 and 3.

[0037] This disclosure applies to L125I, L125V, R126A, Y127W, P128A, P128D, P128E, P128K, P128L, P128Q, P128R, P128S, P128T, R129A, R129E, R129G, R129H, R129I, R129K, R129L, R129N, R129Q, R129S, Y130L, R131A, W132A, W132F, W132I, W132K , W132L, W132P, W132R, W132S, W132T, W132V, W132Y, I133A, D134A, D134N, D134Q, D134T, K135A, K135Q, K135 R, K135S, K135T, K135V, V136A, M137A, M137C, M137I, M137L, M137S, M137V, I138L, I138M, I138V, Q139A, Q13 9C, Q139E, Q139G, Q139H, Q139K, Q139L, Q139M, Q139R, Q139S, L140A, L140C, L140F, L140G, L140H, L140I, L1 40M, L140N, L140Q, L140S, L140T, L140V, L140W, L140Y, I141V, M142L, M142S, M142V, R143A, M144A, T145A, G We provide a nucleic acid molecule encoding a protein having herbicide-resistant protoporphyrinogen oxidase activity, having one or more amino acid substitutions selected from the group consisting of 146A, G146D, G146H, G146K, and G146N, and all combinations thereof, wherein the positions of the amino acid substitutions are relative to the amino acid positions described in Sequence ID No. 1.

[0038] As used herein, the term “protein-coding DNA molecule” refers to a DNA molecule containing a DNA sequence that codes for a protein. As used herein, the term “protein” refers to a chain of amino acids linked by peptide (amide) bonds, and includes both polypeptide chains that are folded or arranged in a biologically functional manner, and polypeptide chains that are not. As used herein, “protein-coding sequence” means a DNA sequence that codes for a protein. As used herein, “sequence” means a sequential arrangement of nucleotides or amino acids. “DNA sequence” may refer to a series of nucleotides or a DNA molecule containing a series of nucleotides, and “protein sequence” may refer to a series of amino acids or a protein containing a series of amino acids. The boundaries of a protein-coding sequence are typically determined by a translation start codon at the 5' end and a translation stop codon at the 3' end.

[0039] As used herein, the term “isolated” means separating a molecule at least partially from other molecules that are typically associated with it in its natural state. In one embodiment, the term “isolated” refers to a DNA molecule that is separated in its natural state from nucleic acids that would normally be adjacent to it. For example, a DNA molecule that codes for a protein naturally present in bacteria would be an isolated DNA molecule if the DNA molecule that codes for that protein were not present in the naturally found bacterial DNA. Thus, a DNA molecule that is fused or operably ligated to one or more other DNA molecules that would not be associated in nature, for example, as a result of recombinant DNA or plant transformation techniques, is considered isolated herein. Such a molecule is considered isolated even if it is incorporated into the chromosome of a host cell or present in nucleic acid solution together with other DNA molecules.

[0040] DNA molecules, or fragments thereof, can be isolated and manipulated as disclosed herein using several methods well known in the art. For example, polymerase chain reaction (PCR) techniques can be used to amplify a specific start DNA molecule or to produce a variant of the original molecule. DNA molecules, or fragments thereof, can also be obtained by other techniques, such as by directly synthesizing the fragments by chemical means, as is commonly done using automated oligonucleotide synthesizers.

[0041] Due to the degeneracy of the genetic code, various different DNA sequences can encode proteins, such as the modified or engineered proteins disclosed herein. For example, Figure 2 provides a universal genetic code table showing all possible mRNA triplet codons (where T in the DNA molecule is replaced by U in the RNA molecule) and the amino acids encoded by each codon. DNA sequences encoding PPO enzymes having the amino acid substitutions described herein can be produced by introducing mutations into the DNA sequence encoding the wild-type PPO enzyme using methods known in the art and the information provided in Figure 2. It is well within the skill of those skilled in the art to produce alternative DNA sequences encoding the same or essentially the same modified or engineered proteins as those described herein. These variants or alternative DNA sequences are within the scope of the embodiments described herein. As used herein, a reference to “essentially the same” sequences refers to sequences encoding amino acid substitutions, deletions, additions, or insertions that do not significantly alter the functional activity of the protein encoded by the DNA molecules of the embodiments described herein. Allele variants of nucleotide sequences encoding wild-type or engineered proteins are also included within the scope of the embodiments described herein. Substitutions of amino acids other than those specifically exemplified or naturally occurring in wild-type or engineered PPO enzymes are also intended to fall within the scope of the embodiments described herein, insofar as the PPO enzyme having such substitutions still retains substantially the same functional activity as described herein.

[0042] If it is desirable to provide sequences useful for DNA manipulation (such as restriction enzyme recognition sites or recombination-based cloning sites), sequences preferred in plants (such as plant codon usage frequencies or Kozak consensus sequences), or sequences useful for designing DNA constructs (such as spacer or linker sequences), the recombinant DNA molecules of the present invention may be synthesized and modified, either completely or partially, by methods known in the art. The present invention includes recombinant DNA molecules and engineered proteins having at least 50%, at least 60%, at least 70%, 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%, and at least 99% sequence identity to any of the recombinant DNA molecules or amino acid sequences provided herein, and having herbicide-resistant protoporphyrinogen oxidase activity. As used herein, the terms “sequence identity percentage” or “sequence identity %” refer to the percentage of identical nucleotides or amino acids in the linear polynucleotide or amino acid sequences of the reference ("inquiry") sequence (or its complementary strand) compared to the test ("subject") sequence (or its complementary strand), when the two sequences are optimally aligned (using appropriate nucleotide or amino acid insertions, deletions, or gaps that total less than 20 percent of the reference sequence across the comparison window).Optimal sequence alignment for aligning comparison windows is well known to those skilled in the art and may be performed, for example, using default parameters, by tools such as the local identity algorithm of Smith and Waterman, the identity alignment algorithm of Needleman and Wunsch, and the similarity search method of Pearson and Lipman, as well as by computer implementations of these algorithms, such as GAP, BESTFIT, FASTA, and TFASTA, available as part of the sequence analysis software package of GCG® Wisconsin Package® (Accelrys Inc., San Diego, CA), MEGAlign (DNAStar Inc., 1228 S. Park St., Madison, WI 53715), and MUSCLE (version 3.6) (RC Edgar, “MUSCLE: multiple sequence alignment with high accuracy and high throughput” Nucleic Acids Research 32(5):1792-7(2004)). The "identity fraction" for aligned segments of a test sequence and a reference sequence is calculated by dividing the number of identical components shared by the two aligned sequences in the segment of the aligned reference sequence—that is, in the entire reference sequence or a smaller specified portion of the reference sequence—by the total number of components. The sequence identity percentage is expressed as the identity fraction multiplied by 100. The comparison of one or more sequences may be of the full sequence, a portion thereof, or a longer sequence.

[0043] As used herein, “DNA construct” means a recombinant DNA molecule containing two or more heterologous DNA sequences. DNA constructs are useful for the expression of transgenes and may be contained in vectors and plasmids. DNA constructs may be used in vectors for transformation (i.e., introduction of heterologous DNA into host cells) to produce recombinant bacteria or transgenic plants and cells (and may also be contained in plasmid DNA or genomic DNA of transgenic plants, seeds, cells, or plant parts as such). As used herein, “vector” means any recombinant DNA molecule that can be used for bacterial or plant transformation. The DNA molecules provided by the present invention can be inserted into a vector as part of a DNA construct having, for example, a DNA molecule operably linked to a heterologous gene expression element that functions to affect the expression of an engineered protein encoded by the DNA molecule in a plant. Methods for preparing and using DNA constructs and vectors are well known in the art and are detailed in manuals and laboratory reports, for example, Michael R. Green and Joseph Sambrook, “Molecular Cloning: A Laboratory Manual” (Fourth Edition), ISBN: 978-1-936113-42-2, Cold Spring Harbor Laboratory Press, NY (2012). Components for DNA constructs, or vectors containing DNA constructs, include one or more gene expression elements operably ligated to a transcriptionable nucleic acid sequence, such as: a promoter for expressing operably ligated DNA, an operably ligated protein-coding DNA molecule, and an operably ligated 3' untranslated region (UTR). Gene expression elements useful in carrying out the present invention include, but are not limited to, one or more of the following types of elements: promoters, 5'UTRs, enhancers, readers, cis-acting elements, introns, transport sequences, 3'UTRs, and one or more selectable marker transgenes.

[0044] The term "transgene" refers to a DNA molecule artificially incorporated into the genome of an organism as a result of human intervention, such as by plant transformation. As used herein, the term "transgenic" means including a transgene; for example, "transgenic plant" refers to a plant that contains a transgene in its genome, and "transgenic trait" refers to a characteristic or phenotype that is transmitted or conferred by the presence of a transgene incorporated into the plant genome. As a result of such genome modification, a transgenic plant is distinctly different from the associated wild-type plant, and a transgenic trait is a trait not naturally found in the wild-type plant. The transgenic plants of the present invention include recombinant DNA molecules and engineered proteins provided by the present invention.

[0045] As used herein, the term “heterogeneous” refers to a relationship between two or more things that are not typically related in nature, for example, originating from different sources or not typically found together in nature in any other way. For example, a DNA molecule or a protein may be heterogeneous if it is not typically found together in nature or in the same association with another DNA molecule, protein, cell, plant, seed, or organism. In certain embodiments, a first DNA molecule is heterogeneous with a second DNA molecule if the two DNA molecules are not typically found together in nature in the same association. For example, a protein-coding recombinant DNA molecule is heterogeneous with a operably linked promoter if such a combination is not typically found in nature. Similarly, a protein is heterogeneous with a second operably linked protein, such as a transport peptide, if such a combination is not typically found in nature. In another embodiment, a recombinant DNA molecule encoding a PPO enzyme is heterogeneous with a operably linked promoter that is functional in a plant cell if such a combination is not typically found in nature. Recombinant DNA molecules can also be heterogeneous to the cell, seed, or organism into which they are inserted, in which case they would not naturally exist.

[0046] A “heterogeneous protein” is a protein that is present in plants, seeds, cells, tissues, or organisms that do not exist in nature, or that is operably linked to a protein that does not exist in nature. An example of a heterogeneous protein is an engineered PPO enzyme containing at least the first amino acid substitution described herein, which is expressed in any plant, seed, cell, tissue, or organism. Another example is a protein that is operably linked to a second protein, such as a transport peptide or herbicide-resistant protein, that does not exist in nature, using genetic engineering techniques, or a protein that is introduced into plant cells that do not exist in nature.

[0047] As used herein, “operatably linked” means two or more DNA molecules or two or more proteins linked in such a manner that one can influence the function of the other. The operatably linked DNA molecules or proteins may be part of a single contiguous molecule, and may be adjacent or not. For example, a promoter is operatably linked to a protein-coding DNA molecule in a DNA construct if the two DNA molecules are positioned such that the promoter can influence the expression of a transgene.

[0048] The DNA constructs of the present invention may include a promoter operably ligated to a protein-coding DNA molecule provided by the present invention, thereby driving the expression of the manipulated protein. Promoters useful in carrying out the present invention include promoters that function in cells to express the operably ligated DNA molecule, such as bacterial or plant promoters. Plant promoters are diverse and well known in the art, and include, for example, inductive, viral, synthetic, constitutive, temporally regulated, spatially regulated, or spatio-temporally regulated promoters.

[0049] In one embodiment of the present invention, the DNA construct provided herein comprises a DNA sequence encoding a transport sequence operably ligated to a heterologous DNA sequence encoding a PPO enzyme, thereby facilitating the intracellular localization of the protein molecule. Transport sequences are known in the art as signal sequences, target peptides, target sequences, localization sequences, and transport peptides. Examples of transport sequences include chloroplast transport peptides (CTPs), mitochondrial transport sequences (MTSs), or chloroplast-mitochondrial dual transport peptides. By facilitating the intracellular localization of proteins, transport sequences can increase the accumulation of recombinant proteins, protect proteins from proteolysis, or improve the level of herbicide resistance, thereby reducing the level of damage to cells, seeds, or organisms after herbicide application. CTPs and other target molecules that may be used in connection with the present invention are well known in the art. The DNA sequence encoding the transport sequence may be operably ligated to a DNA sequence encoding a PPO enzyme, such as those provided herein. Such a operable ligation may involve the removal of the start methionine codon (ATG) at the 5' end of the PPO sequence, but this is not necessary, and the transport sequence aims to facilitate the intracellular localization of the protein molecule regardless of whether the start methionine codon is removed or not.

[0050] As used herein, “transgene expression,” “expressing a transgene,” “protein expression,” and “expressing a protein” mean the production of a protein through the process of transcribing a DNA molecule into messenger RNA (mRNA), translating the mRNA into a polypeptide chain, and ultimately folding this polypeptide chain into a protein. A protein-coding DNA molecule may be operably linked in a DNA construct to a heterologous promoter for use in expressing the protein in cells transformed with recombinant DNA molecules.

[0051] In one embodiment, the present invention provides cells, tissues, plants, and seeds comprising the recombinant DNA molecule or engineered protein of the present invention. These cells, tissues, plants, and seeds comprising the recombinant DNA molecule or engineered protein exhibit resistance to one or more PPO herbicides.

[0052] One method of producing such cells, tissues, plants, and seeds is by plant transformation. Methods for transforming host plant cells that are suitable for use in conjunction with the present invention include any method by which DNA can be introduced into cells (e.g., recombinant DNA constructs are stably incorporated into plant chromosomes), and these are well known in the art. Two effective and widely used methods for cell transformation are agrobacterium-mediated transformation and particulate gun-mediated transformation. Particulate gun methods are illustrated, for example, in U.S. Patents 5,550,318, 5,538,880, 6,160,208, and 6,399,861. Agrobacterium-mediated transformation is described, for example, in U.S. Patent 5,591,616, which is incorporated herein by reference in its entirety. Cells having the recombinant DNA molecule or engineered protein of the present invention can be selected, for example, by their encoded enzyme activity, before or after regenerating such cells into plants, based on the presence of the recombinant DNA molecule or engineered protein.

[0053] Another method for producing cells, plants, and seeds according to the present invention involves genome modification using site-directed integration or genome editing. Targeted modification of the plant genome through the use of genome editing techniques can be used to create improved plant lines through modification of plant genomic DNA. As used herein, “site-directed integration” refers to a genome editing technique that enables targeted insertion of one or more nucleic acids of interest into the plant genome. Suitable methods for modifying wild-type DNA sequences or existing transgenic sequences, or for inserting DNA into the plant genome at predetermined chromosomal sites, include any methods known in the art. Examples of methods include the use of sequence-specific nucleases such as zinc finger nucleases, manipulated or natural meganucleases, TALE-endonucleases, or RNA-inducible endonucleases (e.g., clustered regularly interspersed short palindromic repeat (CRISPR) / Cas9, CRISPR / Cpf1, CRISPR / CasX, CRISPR / CasY, CRISPR / Cascade). Some embodiments relate to genome editing methods that introduce precise base pair modifications in plant genomes using single-stranded oligonucleotides, as described by Sauer et al., Plant Physiology 170(4):1917-1928 (2016). Genome editing methods for modifying, deleting, or inserting nucleic acid sequences into genomic DNA are known in the art.

[0054] In certain embodiments, the present invention provides a plant genome having a sequence encoding an engineered protein, such as the engineered PPO coding sequence of the present invention, or modification or replacement of an existing coding sequence, such as a PPO coding sequence or another existing transgenic insert, within an expression cassette containing such an engineered protein. Some embodiments relate to the use of known genome editing methods, such as zinc finger nucleases, engineered or natural meganucleases, TALE-endonucleases, or RNA-inducible endonucleases (e.g., Clustered Regularly Interspersed Short Palindromic Repeat (CRISPR) / Cas9, CRISPR / Cpf1, CRISPR / CasX, CRISPR / CasY, CRISPR / Cascade).

[0055] Accordingly, some embodiments may also relate to recombinant DNA constructs comprising expression cassettes(or more) encoding site-specific nucleases and, optionally, any associated proteins(or more) for performing genome modifications. These nuclease expression cassettes(or more) may reside in the same molecule or vector as an expression cassette (cis) containing a donor template for templated editing or a nucleic acid sequence encoding a PPO protein, as described herein, or on a separate molecule or vector (trans). Several methods for site-specific integration are known in the art, involving different sequence-specific nucleases (or protein complexes or guide RNA or both) that cleave genomic DNA at a desired genomic site or locus to produce double-strand breaks (DSBs) or breaks. As understood in the art, during the process of repairing DSBs or breaks introduced by nuclease enzymes, donor template DNA, transgenes, or expression cassettes may become integrated into the genome at the DSB or break site. The presence of homologous arms(s) in the DNA to be inserted may facilitate the adoption and targeting of insertion sequences into the plant genome via homologous recombination during the repair process, although the insertion event may also occur through non-homologous end joining (NHEJ).

[0056] As used herein, the term “double-strand break inducer” refers to any agent capable of inducing double-strand breaks (DSBs) in DNA molecules. In some embodiments, the double-strand break inducer is a site-directed genome modification enzyme.

[0057] As used herein, the term “site-directed genome modifying enzyme” refers to any enzyme capable of modifying a nucleotide sequence in a sequence-specific manner. In some embodiments, the site-directed genome modifying enzyme modifies the genome by inducing single-strand breaks. In some embodiments, the site-directed genome modifying enzyme modifies the genome by inducing double-strand breaks. In some embodiments, the site-directed genome modifying enzyme includes cytidine deaminase. In some embodiments, the site-directed genome modifying enzyme includes adenine deaminase. In this disclosure, site-directed genome modifying enzymes include endonucleases, recombinases, transposases, deaminases, helicases, and any combination thereof. In some embodiments, the site-directed genome modifying enzyme is a sequence-specific nuclease.

[0058] In one embodiment, endonucleases include meganucleases, zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), algonauts (non-limiting examples of algonaut proteins include Thermus thermophilus algonaut (TtAgo), Pyrococcus furiosus algonaut (PfAgo), and Natronobacterium gregoryi algonaut (NgAgo)), RNA-induced nucleases, such as CRISPR-related nucleases (non-limiting examples of CRISPR-related nucleases include Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csn1 and Csx12), Cas10, Csy1, Csy2, Csy3, Cse1, Cse2, Csc1, Cs Selected from c2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx15, Csf1, Csf2, Csf3, Csf4, Cpf1, CasX, CasY, their homologs, or modified versions thereof.

[0059] In some embodiments, the site-directed genome modification enzyme is a recombinase. Non-limiting examples of recombinases include tyrosine recombinases conjugated to DNA recognition motifs provided herein, selected from the group consisting of Cre recombinase, Gin recombinase, Flp recombinase, and Tnp1 recombinase. In some embodiments, the Cre recombinase or Gin recombinase provided herein is ligated to a zinc finger DNA-binding domain, or a TALE DNA-binding domain, or a Cas9 nuclease. In other embodiments, the serine recombinase conjugated to DNA recognition motifs provided herein is selected from the group consisting of PhiC31 integrase, R4 integrase, and TP-901 integrase. In yet another embodiment, the DNA transposase conjugated to a DNA-binding domain provided herein is selected from the group consisting of TALE-piggyBac and TALE-Mutator.

[0060] Any of the target DNAs provided herein can be incorporated into a target site in a chromosomal sequence by introducing the target DNA and the provided site-specific genome modification enzyme. Any of the methods provided herein can utilize any of the site-specific genome modification enzymes provided herein.

[0061] In one embodiment, the present invention provides cells, plants, and seeds that are resistant to PPO inhibitor herbicides. Such cells, plants, and seeds are useful in agricultural methods such as weed control and crop production.

[0062] As used herein, “herbicide” means any molecule used to control, inhibit, or interfere with the growth of one or more plants. Examples of herbicides include, among others, acetyl-CoA carboxylase (ACCase) inhibitors (e.g., aryloxyphenoxypropionate and cyclohexanedione); acetolactic acid synthase (ALS) inhibitors (e.g., sulfonylurea, imidazolinone, triazolopyrimidine, and triazolinone); 5-enolpyruvirshikimate-3-phosphate synthase (EPSPS) inhibitors (e.g., glyphosate); synthetic auxins (e.g., phenoxybenzoic acid, carboxylic acid, semicarbazone); photosynthesis (photosystem II) inhibitors (e.g., triazine, triazinon, nitrile, benzothiadiazole, and urea); glutamine synthase (GS) inhibitors (e.g., g These include rufosinate and bialafos, 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitors (e.g., isoxazole, pyrazolone, and triketone), protoporphyrinogen oxidase (PPO) inhibitors (e.g., diphenyl ether, N-phenylphthalimide, aryltriazinon, and pyrimidinedione), very long-chain fatty acid inhibitors (e.g., chloroacetamide, oxyacetamide, and pyrazole), cellulose biosynthesis inhibitors (e.g., indadiphram), photosystem I inhibitors (e.g., paraquat), microtubule aggregation inhibitors (e.g., pendimethalin), and phytoendesaturase (PDS) inhibitors (e.g., norflurazone).

[0063] As used herein, "PPO herbicide" refers to a chemical substance that targets and inhibits the enzymatic activity of protoporphyrinogen oxidase (PPO), which catalyzes the dehydrogenation of protoporphyrinogen IX to form protoporphyrin IX, a precursor of heme and chlorophyll. Inhibition of protoporphyrinogen oxidase leads to the formation of reactive oxygen species, resulting in cell membrane disruption and ultimately the death of vulnerable cells. PPO herbicides are well known and commercially available in the art.Examples of PPO herbicides include diphenyl ethers (acifluorphen, its salts and esters, acronifen, bifenox, its salts and esters, ethoxyfen, its salts and esters, fluoronitrofen, furyloxyfen, halosaphene, clomethoxyfen, fluoroglycofen, its salts and esters, lactofen, its salts and esters, oxyfluorphene, and homesaphene, its salts and esters, etc.), thiadiazoles (fluthiasetmethyl and thidiadimine, etc.), pyrimidinedione or phenyluracil (benzfenzione, butaphenacil, ethyl[3-2-chloro-4-fluoro-5-(1-methyl-6-trifluoromethyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidine-3-yl)phenoxy]-2-pyridyloxy]acetate (CAS registry number 353292-31-6 and referred to as S-3100 herein), flupropasil (e.g., saflufenacil and thiafenacil), phenylpyrazole (e.g., fluazolate, pyraflufen, and pyraflufen ethyl), oxadiazole (e.g., oxaziargyl and oxadiazone), triazolinone (e.g., azaphenidine, bencarbazone, carfentrazone, their salts and esters, and sulfenthrazone), oxazolidinedione (e.g., pentoxazone), N-phenylphthalimide (e.g., synidone-ethyl, flumicrolac) Examples include, but are not limited to, flumicrolac-pentyl and flumioxazin, benzoxazinon derivatives (such as 1,5-dimethyl-6-thioxo-3-(2,2,7-trifluoro-3,4-dihydro-3-oxo-4-propa-2-inyl-2H-1,4-benzoxazin-6-yl)-1,3,5-triazinan-2,4-dione), flufenpyru and flufenpyru-ethyl, pyraclonil, and profluazole. Protoporphyrinogen oxidase and the cells, seeds, plants, and plant parts provided by the present invention exhibit herbicide resistance to one or more PPO herbicides.

[0064] As used herein, “herbicide-tolerant” or “herbicide-tolerance” means the ability to be unaffected, in whole or in part, by the presence or application of one or more herbicides, for example, to resist the toxic effects of a herbicide when applied. A cell or organism is “herbicide-tolerant” if it is able to maintain at least some normal growth or phenotype in the presence of one or more herbicides. A trait is a herbicide-tolerant trait if its presence can confer improved tolerance to a cell, plant, or seed to a wild-type or control cell, plant, or seed. A crop containing a herbicide-tolerant trait can continue to grow and is minimally affected by the presence of a herbicide. A target enzyme is “herbicide-tolerant” if it exhibits improved enzymatic activity in the presence of a herbicide compared to a wild-type or control enzyme. Herbicide resistance can be complete or partial insensitivity to a particular herbicide and can be expressed as a percentage (%) of resistance or insensitivity to that particular herbicide.

[0065] The plants intended to be produced using the herbicide-resistant traits of the present invention may include any plants, including, for example, crop plants such as soybeans (Glycine max), maize (Zea mays), cotton (Gossypium genus), and Brassica plants.

[0066] Herbicides may be applied to plant growing areas containing plants and seeds provided by the present invention as a method for controlling weeds. The plants and seeds provided by the present invention contain herbicide-resistant traits and are therefore resistant to the application of one or more PPO herbicides. The application of herbicides may be at the recommended commercial rate (1X) or any fraction or multiple thereof, for example, twice the recommended commercial rate (2X). The rate of herbicides may be expressed as pound-ae equivalents per acre (lb ae / acre) or gram-ae equivalents per hectare (g ae / ha), or as pound-ai active ingredient per acre (lb ai / acre) or gram-ai active ingredient per hectare (g ai / ha), depending on the herbicide and formulation. The application of herbicides includes at least one PPO herbicide. The plant growing area may or may not contain weed plants at the time of herbicide application. The herbicidal effective dose of a PPO herbicide(s) for use in a given area to control weeds may range from approximately 0.1X to approximately 30X of the label rate(s) over the growing season. Table 3 provides 1X label rates for some example PPO herbicides. One acre is equivalent to 2.47105 hectares, and one pound is equivalent to 453.592 grams. Herbicide rates can be converted between British and metric systems as follows: (lb ai / ac) multiplied by 1.12 = (kg ai / ha) and (kg ai / ha) multiplied by 0.89 = (lb ai / ac). [Table 3]

[0067] Herbicide application may be sequential with one PPO herbicide, two PPO herbicides, a combination of several PPO herbicides, or any other suitable herbicide, or mixed with them in a tank. Multiple applications of one or more herbicides (in combination or individually), such as two applications (pre-planting and post-germination application or pre-germination and post-germination application, etc.) or three applications (pre-planting, pre-germination, and post-germination application or pre-germination and two post-germination applications, etc.), may be used throughout the growing season in areas containing the transgenic plants of the present invention for the control of a wide variety of dicotyledonous weeds, monocotyledonous weeds, or both.

[0068] As used herein, “weed” means any unwanted plant. A plant may be considered undesirable in general for agricultural or horticultural purposes (e.g., Amaranthus species) or may be considered undesirable under specific circumstances (e.g., one species of crop plant in a field of different species, also known as a wild plant).

[0069] The transgenic plants, progeny, seeds, plant cells, and plant parts of the present invention may also contain one or more additional traits. Additional traits may be introduced by crossing a plant containing a transgene comprising a recombinant DNA molecule provided by the present invention with another plant containing one or more additional traits. As used herein, “crossing” means breeding two individual plants to produce progeny plants. Thus, two plants may be crossed to produce progeny containing the desired traits derived from each parent. As used herein, “progeny” means offspring of any generation of the parent plants, and the transgenic progeny contains DNA constructs inherited from at least one parent plant, as provided by the present invention.

[0070] Additional traits may also be introduced by co-transformation with DNA constructs for the additional transgenic trait(s) along with DNA constructs containing recombinant DNA molecules provided by the present invention (for example, with all DNA constructs present as part of the same vector used for plant transformation), or by inserting the additional trait(s) into a transgenic plant containing DNA constructs provided by the present invention or vice versa (for example, by using either plant transformation or genome editing on the transgenic plant or plant cells). Such additional traits include, but are not limited to, increased insect resistance, increased water use efficiency, increased yield performance, increased drought resistance, increased seed quality, improved nutritional quality, hybrid seed production, and herbicide tolerance, and the traits herein are measured in comparison to wild-type plants. Examples of additional herbicide resistance traits may include transgenic or non-transgenic resistance to one or more herbicides, particularly ACCase inhibitors (e.g., aryloxyphenoxypropionates and cyclohexanediones), ALS inhibitors (e.g., sulfonylureas, imidazolinones, triazolopyrimidines, and triazolinones), EPSPS inhibitors (e.g., glyphosate), synthetic auxins (e.g., phenoxybenzoic acid, carboxylic acids, semicarbazones), photosynthesis inhibitors (e.g., triazines, triazinones, nitriles, benzothiadiazoles, and ureas), glutamine synthesis inhibitors (e.g., glufosinate), HPPD inhibitors (e.g., isoxazoles, pyrazolones, and triketones), PPO inhibitors (e.g., diphenyl ethers, N-phenylphthalimides, aryltriazinones, and pyrimidinediones), and long-chain fatty acid inhibitors (e.g., chloroacetamindes, oxyacetamides, and pyrazoles).Examples of herbicide-resistant proteins useful for generating additional herbicide-resistant traits are well known in the art, such as glyphosate-resistant 5-enolpyruvirshikimic acid 3-phosphate synthase (e.g., CP4 Examples include, but are not limited to, EPSPS (2mEPSPS), glyphosate oxidoreductase (GOX), glyphosate N-acetyltransferase (GAT), herbicide-resistant acetolactic acid synthase (ALS) / acetohydroxy acid synthase (AHAS), herbicide-resistant 4-hydroxyphenylpyruvate dioxygenase (HPPD), dicamba monooxygenase (DMO), phosphinothricin acetyltransferase (PAT), herbicide-resistant glutamine synthetase (GS), 2,4-dichlorophenoxypropionate dioxygenase (TfdA), R-2,4-dichlorophenoxypropionate dioxygenase (RdpA), S-2,4-dichlorophenoxypropionate dioxygenase (SdpA), herbicide-resistant protoporphyrinogen oxidase (PPO), and cytochrome P450 monooxygenase. Examples of insect resistance traits may include, among others, resistance to one or more insect members within one or more of the orders Lepidoptera, Coleoptera, Hemiptera, Thysanoptera, Diptera, Hymenoptera, and Orthoptera. Such additional traits are well known to those skilled in the art, and a list of such transgenic traits is provided, for example, by the Animal and Plant Health Inspection Service (APHIS) of the United States Department of Agriculture (USDA).

[0071] Transgenic plants and progeny resistant to PPO herbicides may be used by any propagation method known in the art. In plant lines containing two or more traits, these traits may be independently isolated, linked, or, in plant lines containing three or more transgenic traits, a combination of both. Backcrossing to parent plants and outcrossing with non-transgenic plants are also attempted, as is vegetative propagation. Descriptions of propagation methods commonly used for different traits and crops are well known to those skilled in the art. Various assays may be performed to confirm the presence of a transgene(s) in a particular plant or seed. Such assays include, for example, molecular biological assays such as Southern blotting and Northern blotting, PCR, and DNA sequencing; biochemical assays such as detection of the presence of protein products by immunological means (ELISA and Western blotting) or by enzymatic function; plant part assays such as leaf or root assays; and analytical assays of the phenotype of the whole plant.

[0072] The gene transfer of a transgenic trait into a plant genotype is achieved as a result of a backcross conversion process. A plant genotype into which a transgenic trait has been transferred may be referred to as a backcross conversion genotype, strain, inbred strain, or hybrid strain. Similarly, a plant genotype lacking the desired transgenic trait may be referred to as an unconverted genotype, strain, inbred strain, or hybrid strain.

[0073] As used herein, the term “including” means “including, but not limited to.”

[0074] Having described the present invention in detail, it will become clear that modifications, variations, and equivalent embodiments are possible without departing from the scope of the invention as defined in the appended claims. Furthermore, it should be understood that the examples in this disclosure are provided as non-limiting examples. [Examples]

[0075] Example 1: Sequence diversity within long-chain loops of microbial HemG proteins We investigated the diversity of HemG PPO enzymes within the long insert loop of this protein. The long insert loop characterizes microbial HemG PPO enzymes and is approximately 25 residues long, including the major conserved residues (Boynton et al., Biochemistry (2009) 48:6705-6711).

[0076] Genome analysis was performed using a starter set of 1,013 HemG PPO sequences from various microorganisms. An algorithm was designed to capture both the overall sequence diversity and the diversity within the long-chain insert loop of this protein. These sequences were then grouped based on their overall sequence similarity within the starter set.

[0077] To create the first group, all sequences with 70% or greater sequence identity to HemG PPO H_N90 (SEQ ID NO: 1), which possesses herbicide-resistant protoporphyrinogen oxidase activity, were identified from the starting set. The analysis was then repeated to identify sequences with 70% or greater sequence identity to any sequence identified in the first analysis. Finally, the search was repeated a third time to identify sequences with 70% or greater sequence identity to any sequence identified in the second analysis. The results of the three analyses were pooled together to create the first group, representing a total of 273 HemG PPO sequences from three iterations of the 70% or greater sequence identity analysis.

[0078] A second group was created by focusing on the remaining ungrouped sequences from the starting set. All sequences with 50% to 70% sequence identity to HemG PPO H_N90 were identified. The analysis was then repeated to identify sequences with 70% or more sequence identity to any sequence identified in the first analysis. Finally, the search was repeated a third time to identify sequences with 70% or more sequence identity to any sequence identified in the second analysis. The results of the three analyses were pooled together to create a second group representing sequences from all three iterative analyses, totaling 278 HemG PPO sequences.

[0079] A third group was created by focusing on the remaining ungrouped sequences from the starting set. All sequences with 40% to 50% sequence identity to HemG PPO H_N90 were identified. The analysis was then repeated to identify sequences with 70% or more sequence identity to any sequence identified in the first analysis. A third search was performed to identify sequences with 70% or more sequence identity to any sequence identified in the second analysis, but this final iteration did not capture any additional sequences from the starting set. The results of the two analyses were pooled together to create a third group representing sequences from both iterations, totaling 66 HemG PPO sequences.

[0080] Next, these three groups of sequences were used to analyze the mutations found at each of the 25 amino acids within the long insert loops. The long insert loop sequences from each PPO were identified and combined. Surprisingly, the sequence mutations within this domain were found to be similar for the first and second groups, even though, when combined, the sequences from these two groups had up to 50% of the overall sequence mutations and represented 551 diverse sequences. Figure 3 provides an overview of the mutations found within the long insert loops among the 617 sequences from the three groups. Among the 25 amino acid positions of the long insert loops, 211 different amino acids were identified from the 617 HemG PPO sequences. Figures 1A and 1B show the sequence alignment of the long insert loops (highlighted in black) for a subset of 23 microbial HemG PPO sequences.

[0081] A group of 17 HemG PPO sequences was selected to represent the mutations found within the long-chain insert loops. When compared using pairwise sequence alignment, the protein sequences of these 17 diverse HemG PPO enzymes exhibited identity percentages ranging from approximately 15% to 98% across the entire length of the sequence. These 17 diverse HemG PPO enzymes were tested for protoporphyrinogen oxidase activity and herbicide resistance.

[0082] A protoporphyrinogen oxidase bacterial screening system was used to test proteins for protoporphyrinogen oxidase activity, thereby confirming their functional PPO enzyme status. This screening system utilized a functional rescue assay in E. coli strains containing gene knockouts against the E. coli HemG PPO enzyme (referred to herein as H_N10, corresponding to SEQ ID NO: 2). HemG knockout E. coli strains were transformed with bacterial expression vectors containing expression cassettes for one of the PPO enzymes and cultured on LB medium. HemG knockout E. coli strains showed minimal growth on conventional bacterial media (e.g., LB medium), but normal growth could be restored by supplementing the bacterial medium with free heme or by expressing functional protoporphyrinogen oxidase in the cells. Two controls were used for comparison: green fluorescent protein (GFP) and untransformed cells. Two of the HemG PPO enzymes (HemG014 and HemG015) were unable to rescue the hemG knockout E. coli strain (lacking protoporphyrinogen oxidase activity). These two enzymes showed partial rescue with slower growth (intermediate), while the remaining 13 showed a complete rescue phenotype (functional). The results are shown in Table 4.

[0083] A protoplast herbicide resistance assay was designed to test 17 diverse HemG PPO enzymes for herbicide resistance in plant cells. Recombinant DNA molecules encoding 17 diverse HemG PPO enzymes (codon-optimized for expression in dicotyledonous plants) were synthesized and cloned into a plant transformation vector. The expression construct contained a plant promoter, a chloroplast transport peptide, and a recombinant DNA molecule encoding one of the 17 diverse HemG PPO enzymes operably ligated to the 3' untranslated region. Soybean protoplasts were transformed with the plant transformation vector using standard methods. Transformed protoplasts were grown in the presence of the PPO herbicide S-3100 or a dummy treatment (negative control) at a concentration of 1.0 μM. The protoplasts were then assayed for PPO herbicide resistance and standardized against a score of HemG PPO enzyme H_N90 set to 100. The assay was performed in two batches over four replicate experiments. The relative resistance scores were averaged for each, and the standard error was calculated (SE). The GFP control assay had a resistance score of 0, confirming that soybean protoplasts are not resistant to PPO herbicides in the absence of herbicide resistance proteins. Two of the diverse HemG PPO enzymes (HemG014 and HemG015) provided no resistance at all, while the other 14 provided resistance scores ranging from 24 to 89 compared to H_N90. The results are shown in Table 4.

[0084] Next, 15 of the diverse HemG PPO enzymes were expressed in transgenic plants, and the transgenic plants were analyzed for PPO herbicide resistance. Recombinant DNA molecules encoding the 15 diverse HemG PPO enzymes (codon-optimized for expression in dicotyledonous or monocotyledonous plants) were synthesized and cloned into plant transformation vectors. The expression constructs contained a plant promoter, a chloroplast transport peptide, and a recombinant DNA molecule encoding one of the 15 diverse HemG PPO enzymes operably ligated to the 3' untranslated region.

[0085] Maize cells were transformed with Agrobacterium tumefaciens and their vectors using standard methods known in the art. The regenerated R0 transgenic plantlets were grown in a greenhouse. To evaluate resistance, the plants were sprayed with the PPO herbicide S3100 at a rate of 80 g / ha at approximately the V2–V4 growth stage. The plants were evaluated for damage 1–14 days after treatment, and the damage score was recorded. The percentage of plants with a visible damage score of 20% or less was calculated for each of the various HemG PPO enzymes for all plants. Any construct in which 25% or more of individual plants showed good resistance (visible damage score of 20% or less) was considered effective in conferring herbicide resistance. Eight of the diverse HemG PPO enzymes (HemG001, HemG002, HemG003, HemG004, HemG005, HemG006, HemG011, and HemG012) provided a significant number of maize plants demonstrating resistance to PPO herbicides (less than 20% damage after treatment). The results are shown in Table 4.

[0086] Soybean cells were transformed with Agrobacterium tumefaciens and their vectors using standard methods known in the art. The regenerated R0 transgenic plantlets were grown in a greenhouse. To evaluate resistance, the plants were sprayed with the PPO herbicide S3100 at a rate of 20 g / ha at approximately the V2–V4 growth stage. The plants were evaluated for damage 1–14 days after treatment, and the damage score was recorded. The percentage of plants with a visible damage score of 20% or less was calculated for each of the various HemG PPO enzymes for all plants. Any construct in which 25% or more of individual plants showed good resistance (visible damage score of 20% or less) was considered effective in conferring herbicide resistance. Ten of the diverse HemG PPO enzymes (HemG001, HemG002, HemG003, HemG004, HemG005, HemG006, HemG007, HemG009, HemG011, and HemG013) provided a substantial number of soybean plants demonstrating resistance to PPO herbicides (less than 20% damage after treatment). The results are shown in Table 4. [Table 4]

[0087] Of 15 diverse HemG PPO enzymes tested in stably transformed corn and / or soybeans, 10 were found to be effective in conferring herbicide resistance (producing more than 25% of plants with a visible damage score of 20% or less). The sequences of these HemG PPO enzymes effective in conferring herbicide resistance to plants are provided as HemG001 (SEQ ID NO: 11), HemG002 (SEQ ID NO: 12), HemG003 (SEQ ID NO: 13), HemG004 (SEQ ID NO: 14), HemG005 (SEQ ID NO: 15), HemG006 (SEQ ID NO: 16), HemG007 (SEQ ID NO: 17), HemG009 (SEQ ID NO: 19), HemG011 (SEQ ID NO: 21), and HemG013 (SEQ ID NO: 23).

[0088] Example 2: Functional Characterization of Long-Chain Insert Loop Variants The long insert loop of the HemG protein is described as essential for PPO enzyme function, and many of its residues are reported to be highly conserved (Boynton et al., Biochemistry (2009) 48:6705-6711). Recombinant HemG PPO enzymes were created by introducing amino acid mutations into the long insert loop, and the changes in enzyme function were then analyzed in bacterial assays.

[0089] The protoporphyrinogen oxidase bacterial screening system described in Example 2 was used to test variant proteins for protoporphyrinogen oxidase activity. This assay provides a rapid and easy means of assaying variant proteins for protoporphyrinogen oxidase activity.

[0090] A recombinant HemG PPO enzyme incorporating mutations into a long insert loop was designed as follows. Each amino acid in the long insert loop was considered independently and ranked in order of priority based on the amount of mutation identified at that position and how much of that mutation was found in which of the sequence sets. Based on this evaluation, 21 of the 25 amino acids in the long insert loop were selected for mutagenesis. Mutations were induced in the H_N90 sequence to represent the mutations observed at each of these 21 positions, resulting in 109 single-amino acid variants. Furthermore, alanine scanning mutagenesis was performed using the H_N90 sequence to generate mutants with alanine at each position in the long insert loop that was not already alanine in H_N90, resulting in 10 additional variants. A total of 119 single-amino acid variants were then used for screening.

[0091] Next, recombinant DNA molecules encoding these 119 variants were synthesized and cloned into expression constructs in bacterial transformation vectors. For each variant, the entire nucleotide sequence was maintained identical to that of the H_N90 nucleotide sequence, except for codons corresponding to mutant amino acids. Each expression construct contained a plant promoter, an APG6 chloroplast transport peptide, and a recombinant DNA molecule encoding one of the 119 variants operably ligated to the 3' untranslated region. The positive control consisted of an expression construct containing a plant promoter, an APG6 chloroplast transport peptide, and an H_N90 coding sequence operably ligated to the 3' untranslated region. Each vector was individually introduced into hemG knockout E. coli strains for transformation. As negative controls, pseudo-transformation (without the presence of a vector) and vectors for expressing green fluorescent protein (GFP) were individually introduced into hemG knockout E. coli strains for transformation.

[0092] Each of the 119 variants was screened for its ability to restore normal growth in hemG knockout E. coli strains on LB plates. All plates were scored blindly and independently by three individuals for no growth (variant does not complement), slow growth (variant has reduced enzyme function), or normal growth (variant has full enzyme function and provides full complementation). Growth was measured based on colony size, not the number of colonies on the plate, and the three individuals agreed on all assessments. Table 5 shows the assay results. In this assay, 105 of the 119 variants restored normal growth, suggesting that these variants have full PPO function. Six of the 119 variants showed colony growth at a significantly slower growth rate, suggesting that these variants have reduced PPO function. Eight of the 119 variants showed no colony growth, suggesting that these variants lack PPO function. All positive controls showed complementarity as expected, but the H_N10 construct exhibited slower growth than the H_N90 construct. Figure 4 shows a chart of the results of this assay. [Table 5-1] [Table 5-2] [Table 5-3] [Table 5-4]

[0093] The results of this assay suggest that while the long insert loop is highly conserved in the HemG PPO protein, there is flexibility in many of the residues within this loop regarding the maintenance of enzyme function. This was unexpected, given that published reports (Zwerschke, D., Karrie, S., Jahn, D. and Jahn, M. (2014) Biosci. Rep. 34(4), art:e00124. doi:10.1042 / BSR20140081) state that changes in residues within the long insert loop lead to loss of enzyme function. In this assay, altered enzyme function was found in mutations, particularly at the positions of G123, L125, Y127, I138, L140, I141, M142, and G147, indicating that changes at these locations are important for altering enzyme function.

[0094] Example 3: Analysis of herbicide resistance characteristics of long-chain insert loop variants We created recombinant HemG PPO enzymes by introducing amino acid mutations within long-chain insert loops and analyzed their effects on herbicide sensitivity in plants. To determine whether the variants could confer resistance to PPO herbicides in plant cells, we designed a protoplast herbicide resistance assay.

[0095] Soybean protoplasts were transformed using a standard method with the same expression construct described in Example 2, but with a plant transformation vector. Transformed protoplasts were grown in the presence of 1.0 μM PPO herbicide S-3100 or a dummy treatment (negative control). The protoplasts were then assayed for PPO herbicide resistance and expressed relative to GFP control and H_N90 (to allow for the derivation of relative resistance scores to enable inter-experimental comparisons). The assay was performed in two batches over four replicate experiments. Relative resistance scores were averaged for each, and the standard error (SE) was calculated. The GFP control assay yielded a resistance score of 0, confirming that soybean protoplasts were not resistant to PPO herbicide in the absence of herbicide resistance proteins. The N-N90 assay yielded a resistance score of 100. Table 6 shows the assay results. Thirteen variants conferred little to no resistance (equivalent to untransformed or GFP controls), six variants conferred weak resistance (equivalent to H_N90 control without CTP), nine variants conferred slight resistance (equivalent to H_N10 control), and 79 variants conferred good resistance (equivalent to H_N90 control with CTP). Twelve variants had relative resistance scores greater than 100 (better than H_N90 control with CTP). The amino acid changes in these 12 variants were located at seven residue positions, four of which resulted in more than one variant with a tendency to score above 100. This suggests that these seven amino acid sites are particularly targeted for improved herbicide resistance. Figure 5 shows a chart of the results of this assay. [Table 6-1] [Table 6-2] [Table 6-3] [Table 6-4] [Table 6-5]

[0096] A subset of 39 variants (plus a control) was selected for further analysis. These variants were tested for resistance to three additional PPO herbicides—flumioxazine, sulfenthrazone, and lactofen—in an assay similar to the S-3100 resistance assay described above. Transformed protoplasts were treated with flumioxazine (5 nM), sulfenthrazone (1 μM), and lactofen (1 μM). Table 7 shows the assay results. Of the 39 variants tested, 30 showed good resistance to flumioxazine, sulfenthrazone, or lactofen, and 9 showed poor resistance (indicated as "PT," with a resistance score below 50). Of the 30 variants showing good resistance, 8 showed changes exceeding experimental variability compared to S-3100 in resistance to one or more herbicides. Of these eight variants, four conferred higher resistance to one or more herbicides (indicated as "higher" in Table 7 below), while four variants conferred lower resistance to one or more herbicides (indicated as "lower" in Table 7 below). Variants marked "NSD" had resistance scores where the difference in resistance scores was less than the standard error for a given data point. [Table 7-1] [Table 7-2]

[0097] Of the eight variants that demonstrated significant differences in resistance scores to flumioxazine, sulfenthrazone, or lactofen compared to their resistance scores to S-3100, six variants were located at hydrophobic residues M137, L140, and M142. The region spanning residues M137–M142 contains numerous hydrophobic residues (particularly I, L, V, M, and A). Analysis of this hydrophobic region suggests that these residues are uniquely important in modulating the functionality of the enzyme variants. Furthermore, these residues are uniquely important in modulating resistance to different PPO inhibitor herbicides.

[0098] The transformed protoplasts include diphenyl ethers (acifluorphene, its salts and esters, acroniphene, bifenox, its salts and esters, ethoxyphene, its salts and esters, fluoronitrophene, furyloxyphene, halosaphene, clomethoxyfene, fluoroglycofen, its salts and esters, lactofene salts and esters, oxyfluorphene, and homesaphene, its salts and esters, etc.), thiadiazoles (fluthiasetmethyl and thiadiamine, etc.), pyrimidinedione or phenyluracil (benzfenzione, butaphenacil, ethyl[3-2-chloro-4-fluoro-5-(1-methyl-6-trifluoromethyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidine-3-yl)phenoxy]-2-pyridyloxy]acetate (CAS registry number 353292-31-6 and referred to herein as S-3100) ), flupropasil, saflufenasil, and thiafenasil, etc., phenylpyrazole (fluazolate, pyraflufen, and pyraflufen ethyl, etc.), oxadiazole (oxaziargyl and oxadiazone, etc.), triazolinone (azaphenidine, bencarbazone, and carfentrazone, their salts and esters, etc.), oxazolidinedione (pentoxazone, etc.), N-phenylphthalimide (sinidone-ethyl, flumicronyl Other PPO herbicides may be used to attack the plants, such as lac and flumicorac-pentyl, benzoxazinon derivatives (1,5-dimethyl-6-thioxo-3-(2,2,7-trifluoro-3,4-dihydro-3-oxo-4-propa-2-inyl-2H-1,4-benzoxazine-6-yl)-1,3,5-triazinan-2,4-dione, flufenpyrus and flufenpyrus-ethyl, pyraclonil, and profluazole. A pseudo-treatment agent can be used as a negative control.

[0099] Example 4: Functional and herbicide resistance analysis of combinatorial albariant Variants are designed to include two or more amino acid modifications within the long insert loop of the HemG PPO sequence. These combinatorial valiant HemG PPO enzymes are then assayed to determine PPO activity. The DNA sequences of the combinatorial valiant HemG PPO are synthesized and cloned into expression cassettes. Bacterial transformation vectors containing the expression cassettes can be introduced into and transformed into hemG knockout E. coli strains for initial high-throughput bacterial rescue screening, as described in Example 2. The combinatorial valiantities are screened for their ability to restore normal growth in hemG knockout E. coli strains.

[0100] The combinatorial valiant HemG PPO enzyme is also assayed for its ability to confer resistance to PPO herbicides to plant cells. Soybean protoplasts are transformed using an expression cassette containing the DNA sequence of combinatorial valiant HemG PPO in combination with a plant transformation vector. Protoplast resistance assays are performed as described in Example 3 to screen combinatorial valiant enzymes for their ability to confer herbicide resistance to plant cells.

[0101] Example 5: Expression and testing of variant HemG PPO enzyme in plants The microbial HemG PPO variant described in the above examples may be expressed in stably transformed plants, and these plants can be analyzed for PPO herbicide resistance.

[0102] Twenty-five microbial HemG PPO variants were tested for herbicide resistance in stably transformed maize or soybean (or both). Plant transformation vectors were constructed containing a plant promoter, transport sequence, and recombinant DNA molecules encoding the variant HemG PPO enzyme operably ligated to the 3'UTR (with the protein coding sequence optimized for expression in monocots or dicots).

[0103] In maize, maize cells were transformed with a plant transformation vector using Agrobacterium tumefaciens and standard methods known in the art. The regenerated R0 transgenic plantlets were grown in a greenhouse. The R0 plants were sprayed with S3100 at a rate of 80 g / ha at approximately the V2-V4 growth stage. The plants were then evaluated for damage 1-14 days after treatment, and damage scores were recorded. Transgenic plants with a single copy of the transgenic DNA insert (i.e., single-event plants) were identified, and R0 plants containing only a single copy and passing the herbicide spray test were self-pollinated to produce R1 seeds.

[0104] In soybeans, excised embryos were transformed with plant transformation vectors using Agrobacterium tumefaciens and standard methods known in the art. The regenerated R0 transgenic plantlets were grown in a greenhouse. R0 plants were sprayed with S3100 at a rate of 20 g / ha at approximately the V2–V4 growth stage. The plants were then evaluated for damage 1–14 days after treatment, and damage scores were recorded. Transgenic plants with a single copy of the transgenic DNA insert (i.e., single-event plants) were identified, and R0 plants containing only a single copy and passing the herbicide spray test were self-pollinated to produce R1 seeds. For some variant HemG PPO enzymes, R1 plants were grown in a greenhouse and sprayed with S3100 at a rate of 60 g / ha at approximately the V2–V4 growth stage. The plants were then evaluated for damage 1–14 days after treatment, and damage scores were recorded.

[0105] Transgenic soybean and maize plants with a visible damage score of 20% or less were scored as having passed herbicide resistance screening and thus demonstrating resistance to PPO herbicides. The percentage of each variant HemG PPO enzyme that passed the herbicide resistance screening among the total number of plants was calculated. Any construct in which 25% or more of individual plants show good resistance (visible damage score of 20% or less) is considered effective in conferring herbicide resistance.

[0106] This study demonstrated that the results obtained from the protoplast assay (performed as described above) were consistent with the results obtained in the whole plant, confirming the effectiveness of using the protoplast assay as a screening tool. Of the 25 microbial HemG PPO variants tested in stably transformed maize or soybean (or both), 20 were found to be effective in conferring herbicide resistance (producing more than 25% of plants with a visible damage score of ≤20%). Of these 20, 14 showed higher efficacy results than the positive control H_N90. The results are provided in Table 8. [Table 8]

[0107] In cotton, excised embryos (Coker 130) can be transformed with Agrobacterium tumefaciens and their vectors using standard methods known in the art. The regenerated R0 transgenic plantlets are grown in a greenhouse and tested as described above.

[0108] These transgenic plants can be used to test resistance to other herbicides. This can be done, for example, by growing multiple transgenic plants for each HemG PPO and dividing the plants into groups. To evaluate resistance, these groups are sprayed with PPO herbicides (multiple are possible) (one PPO herbicide per group). For example, transgenic plants are sprayed with lactofen at a growth stage of approximately 2-4 true leaves at approximately 220 g ai / ha or 440 g ai / ha, or with flumioxazin at approximately 210 g / ha or 420 g / ha. The plants are then evaluated for damage 1-14 days after treatment, and the damage score is recorded. Transgenic plants that are not sprayed are used for phenotypic comparison with non-transgenic plants that are not sprayed.

Claims

1. A recombinant DNA molecule comprising a heterologous promoter operably linked to a nucleic acid molecule encoding a genetically engineered protein having herbicide-resistant protoporphyrinogen oxidase activity, wherein the protein comprises a HemG class protoporphyrinogen oxidase enzyme, and wherein the HemG class protoporphyrinogen oxidase enzyme is present at least at the positions corresponding to residues 125-146 of SEQ ID NO: 1 The first amino acid substitution is also manipulated to include L125I, L125V, R126A, Y127W, P128A, P128D, P128E, P128K, P128L, P128Q, P128R, P128S, P128T, R129A, R129E, R129G, R129H, R129I, R129K, R129L, R129N, R129Q, R129S, Y130L, R131A, W132A, W132F, W132I, W132 K, W132L, W132P, W132R, W132S, W132T, W132V, W132Y, I133A, D134A, D134N, D134Q, D134T, K135A, K135Q, K135R, K135S, K 135T, K135V, V136A, M137A, M137C, M137I, M137L, M137S, M137V, I138L, I138M, I138V, Q139A, Q139C, Q139E, Q139G, Q139H Selected from the group consisting of Q139K, Q139L, Q139M, Q139R, Q139S, L140A, L140C, L140F, L140G, L140H, L140I, L140M, L140N, L140Q, L140S, L140T, L140V, L140W, L140Y, I141V, M142L, M142S, M142V, R143A, M144A, T145A, G146A, G146D, G146H, G146K, and G146N, Here, the HemG class protoporphyrinogen oxidase enzyme is the recombinant DNA molecule having at least 90% sequence identity with an amino acid sequence selected from the group consisting of SEQ ID NOs: 24-124 and 249-263.

2. The recombinant DNA molecule according to claim 1, wherein the protein comprises at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten of the amino acid substitutions.

3. The recombinant DNA molecule according to claim 1, wherein the amino acid substitution is located in the long-chain insert loop in the enzyme.

4. The recombinant DNA molecule according to claim 1, wherein the heterologous promoter is functional in plant cells.

5. The recombinant DNA molecule according to claim 4, wherein the nucleic acid molecule is operably linked to a DNA molecule encoding a transport sequence that functions to localize the protein within a cell.

6. The recombinant DNA molecule according to claim 1, wherein the recombinant DNA molecule is contained in the genome of a plant cell.

7. A DNA construct comprising the recombinant DNA molecule described in claim 1.

8. A manipulated protein encoded by the recombinant DNA molecule described in claim 1.

9. A transgenic plant, seed, cell, or plant part comprising the recombinant DNA molecule described in claim 1.

10. The transgenic plant, seed, cell, or plant part according to claim 9, wherein the transgenic plant, seed, cell, or plant part is resistant to at least one PPO herbicide.

11. The transgenic plant, seed, cell, or plant part according to claim 10, wherein the PPO herbicide is selected from the group consisting of asyfluorphen, homesaphen, lactofen, fluoroglycofen ethyl, oxyfluorphen, flumioxazine, azaphenidine, carfentrazon ethyl, sulfentrazon, fluthiaset methyl, oxaziargyl, oxadiazon, pyraflufen ethyl, saflufenacil, thiafenacil, 1,5-dimethyl-6-thioxo-3-(2,2,7-trifluoro-3,4-dihydro-3-oxo-4-propa-2-inyl-2H-1,4-benzoxazin-6-yl)-1,3,5-triazinan-2,4-dione and S-3100.

12. The transgenic plant, seed, cell, or plant part according to claim 11, wherein the transgenic plant, seed, cell, or plant part is resistant to at least a second herbicide.

13. A method for conferring PPO herbicide resistance to a plant, seed, cell, or plant part, comprising heterologously expressing the manipulated protein described in claim 8 in the plant, seed, cell, or plant part.

14. The method according to claim 13, wherein the herbicide resistance is to at least one PPO herbicide selected from the group consisting of asifluorphen, homesaphen, lactofen, fluoroglycofen ethyl, oxyfluorphen, flumioxazine, azaphenidine, carfentrazon ethyl, sulfentrazon, fluthiaset methyl, oxaziargyl, oxadiazon, pyraflufen ethyl, saflufenacil, thiafenacil, 1,5-dimethyl-6-thioxo-3-(2,2,7-trifluoro-3,4-dihydro-3-oxo-4-propa-2-inyl-2H-1,4-benzoxazin-6-yl)-1,3,5-triazinan-2,4-dione and S-3100.

15. A method for producing herbicide-resistant plants, a) The step of transforming plant cells with the recombinant DNA molecule described in claim 1, b) A step of regenerating a plant from the plant cells containing the recombinant DNA molecule, The method, including the method described above.

16. The method according to claim 15, further comprising the step of selecting the plant or its progeny based on PPO herbicide resistance.

17. The method according to claim 15, further comprising the step of crossbreeding the regenerated plant with itself or with a second plant to produce offspring.

18. A method for controlling or inhibiting weed growth in a plant growing area, comprising applying an effective amount of at least one PPO herbicide to a plant growing area containing the transgenic plant or seeds described in claim 9, wherein the transgenic plant or seeds are resistant to the PPO herbicide.

19. The method according to claim 18, wherein the PPO herbicide is selected from the group consisting of asifluorphen, homesaphen, lactofen, fluoroglycofen ethyl, oxyfluorphen, flumioxazine, azaphenidine, carfentrazon ethyl, sulfentrazon, fluthiaset methyl, oxaziargyl, oxadiazon, pyraflufen ethyl, saflufenacil, thiafenacil, 1,5-dimethyl-6-thioxo-3-(2,2,7-trifluoro-3,4-dihydro-3-oxo-4-propa-2-inyl-2H-1,4-benzoxazin-6-yl)-1,3,5-triazinan-2,4-dione and S-3100.

20. A method for identifying a nucleotide sequence encoding a protein having herbicide-resistant protoporphyrinogen oxidase activity, wherein the method is a) Transforming an E. coli strain lacking herbicide-resistant PPO enzyme activity with a bacterial expression vector containing the recombinant DNA molecule described in claim 1, b) To propagate the transformed E. coli and identify proteins that have herbicide-resistant protoporphyrinogen oxidase activity, The method, including the method described above.

21. A method for screening herbicide resistance genes, a) Expressing the recombinant DNA molecule described in claim 1 in plant cells, b) Identifying plant cells that show resistance to PPO herbicides, The method, including the method described above.

22. A method for producing plants that are resistant to PPO herbicides and at least one other herbicide, a) To obtain the plant described in claim 9, b) Crossing the plant with a second plant which is resistant to at least one other herbicide, c) Selecting offspring plants that are resistant to the PPO herbicide and at least one other herbicide resulting from the cross, The method, including the method described above.

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