Methods and compositions for cellular and metabolic engineering
DCFirst Claim
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1. A method of evolving a biocatalytic activity of a cell, comprising:
- (a) recombining at least a first and second DNA segment from at least one gene conferring ability to catalyze a reaction of interest, the segments differing from each other in at least two nucleotides, to produce a library of recombinant genes;
(b) screening the library to identify at least one recombinant gene from the library that confers enhanced ability to catalyze the reaction of interest by the cell relative to a wildtype form of the gene;
(c) recombining at least a segment from the at least one recombinant gene with a further DNA segment from the at least one gene, the same or different from said first and second DNA segments, to produce a second library of recombinant genes;
(d) screening the second library of recombinant genes to identify at least one further recombinant gene from the second library of recombinant genes that confers enhanced ability to catalyze the reaction of interest by the cell relative to a previous recombinant gene;
(e) repeating (c) and (d), as necessary, until the further recombinant gene confers a desired level of enhanced ability to catalyze the reaction of interest by the cell,wherein the reaction of interest is the ability to utilize a substrate as a nutrient source.
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Abstract
The present invention is generally directed to the evolution of new metabolic pathways and the enhancement of bioprocessing through a process herein termed recursive sequence recombination. Recursive sequence recombination entails performing iterative cycles of recombination and screening or selection to "evolve" individual genes, whole plasmids or viruses, multigene clusters, or even whole genomes. Such techniques do not require the extensive analysis and computation required by conventional methods for metabolic engineering.
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Citations
36 Claims
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1. A method of evolving a biocatalytic activity of a cell, comprising:
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(a) recombining at least a first and second DNA segment from at least one gene conferring ability to catalyze a reaction of interest, the segments differing from each other in at least two nucleotides, to produce a library of recombinant genes; (b) screening the library to identify at least one recombinant gene from the library that confers enhanced ability to catalyze the reaction of interest by the cell relative to a wildtype form of the gene; (c) recombining at least a segment from the at least one recombinant gene with a further DNA segment from the at least one gene, the same or different from said first and second DNA segments, to produce a second library of recombinant genes; (d) screening the second library of recombinant genes to identify at least one further recombinant gene from the second library of recombinant genes that confers enhanced ability to catalyze the reaction of interest by the cell relative to a previous recombinant gene; (e) repeating (c) and (d), as necessary, until the further recombinant gene confers a desired level of enhanced ability to catalyze the reaction of interest by the cell, wherein the reaction of interest is the ability to utilize a substrate as a nutrient source. - View Dependent Claims (4, 5, 6, 7, 8, 29, 32)
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2. A method of evolving a biocatalytic activity of a cell, comprising:
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(a) recombining at least a first and second DNA segment from at least one gene conferring ability to catalyze a reaction of interest, the segments differing from each other in at least two nucleotides, to produce a library of recombinant genes; (b) screening the library to identify at least one recombinant gene from the library that confers enhanced ability to catalyze the reaction of interest by cell relative to a wildtype form of the gene; (c) recombining at least a segment from the at least one recombinant gene with a further DNA segment from the at least one gene, the same or different from said first and second DNA segments, to produce a second library of recombinant genes; (d) screening the second library of recombinant genes to identify at least one further recombinant gene from the second library of recombinant genes that confers enhanced ability to catalyze the reaction of interest by the cell relative to a previous recombinant gene; (e) repeating (c) and (d), as necessary, until the further recombinant gene confers a desired level of enhanced ability to catalyze the reaction of interest by the cell, wherein the reaction of interest is the ability to detoxify a compound. - View Dependent Claims (18, 19)
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3. A method of evolving a biocatalytic activity of a cell, comprising:
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(a) recombining at least a first and second DNA segment from at least one gene conferring ability to catalyze a reaction of interest, the segments differing from each other in at least two nucleotides, to produce a library of recombinant genes; (b) screening the library to identify at least one recombinant gene from the library that confers enhanced ability to catalyze the reaction of interest by the cell relative to a wildtype form of the gene; (c) recombining at least a segment from the at least one recombinant gene with a further DNA segment from the at least one gene, the same or different from said first and second DNA segments, to produce a second library of recombinant genes; (d) screening the second library of recombinant genes to identify at least one further recombinant gene from the second library of recombinant genes that confers enhanced ability to catalyze the reaction of interest by the cell relative to a previous recombinant gene; (e) repeating (c) and (d), as necessary, until the further recombinant gene confers a desired level of enhanced ability to catalyze the reaction of interest by the cell wherein the reaction of interest is the ability to synthesize a compound of interest and wherein the compound of interest is selected from the group consisting of an amino acid, a polymer, vitamin C, and indigo. - View Dependent Claims (30, 31)
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9. A method of generating a new biocatalytic activity in a cell, comprising:
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(a) recombining at least first and second DNA segments from at least one gene conferring ability to catalyze a first enzymatic reaction related to a second enzymatic reaction of interest, the segments differing from each other in at least two nucleotides, to produce a library of recombinant genes; (b) screening at least one recombinant gene from the library that confers a new ability to catalyze the second reaction of interest; (c) recombining at least a segment from at least one recombinant gene with a further DNA segment from the at least one gene, the same or different from the first and second segments, to produce a further library of recombinant genes; (d) screening at least one further recombinant gene from the further library of recombinant genes that confers enhanced ability to catalyze the second reaction of interest in the cell relative to a previous recombinant gene; (e) repeating (c) and (d), as necessary, until the further recombinant gene confers a desired level of enhanced ability to catalyze the second reaction of interest in the cell.
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10. A method of optimizing expression of a gene product, the method comprising:
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(a) recombining at least a first and second DNA segments from at least one gene conferring ability to produce the gene product, the segments differing from each other in at least two nucleotides, to produce a library of recombinant genes; (b) screening the library to identify at least one recombinant gene from the library that confers optimized expression of the gene product relative to a wildtype form of the gene; (c) recombining at least a segment from the at least one recombinant gene with a further DNA segment from the at least one gene, the same or different from said first and second DNA segments, to produce a second library of recombinant genes; (d) screening the second library of recombinant genes to identify at least one further recombinant gene from the second library of recombinant genes that confers optimized ability to produce the gene product relative to a previous recombinant gene; (e) repeating (c) and (d), as necessary, until the further recombinant gene confers a desired level of optimized ability to express the gene product wherein at least one recombining step is performed in vivo. - View Dependent Claims (11, 12, 13)
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14. A method of evolving a biosensor for a compound A of interest, the method comprising:
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(a) recombining at least first and second DNA segments from at least one gene conferring ability to detect a structurally related compound B, the segments differing from each other in at least two nucleotides, to produce a library of recombinant genes; (b) screening at least one recombinant gene from the library that confers optimized ability to detect compound A relative to a wildtype form of the gene; (c) recombining at least a segment from the at least one recombinant gene with a further DNA segment from the at least one gene, the same or different from the first and second segments, to produce a further library of recombinant genes; (d) screening at least one further recombinant gene from the further library of recombinant genes that confers optimized ability to detect compound A relative to a previous recombinant gene; (e) repeating (c) and (d), as necessary, until the further recombinant gene confers a desired level of optimized ability to detect compound A. - View Dependent Claims (15, 16, 17)
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20. A method of evolving a biocatalytic activity of a cell, comprising:
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(a) recombining at least a first and second DNA segment from at least one gene conferring ability of a dioxygenase to catalyze a reaction of interest, the segments differing from each other in at least two nucleotides, to produce a library of recombinant genes; (b) screening the library to identify at least one recombinant gene from the library that confers enhanced ability to catalyze the reaction of interest by the cell relative to a wildtype form of the gene; (c) recombining at least a segment from the at least one recombinant gene with a further DNA segment from the at least one gene, the same or different from said first and second DNA segments, to produce a second library of recombinant genes; (d) screening the second library of recombinant genes to identify at least one further recombinant gene from the second library of recombinant genes that confers enhanced ability to catalyze the reaction of interest by the cell relative to a previous recombinant gene; (e) repeating (c) and (d), as necessary, until the further recombinant gene confers a desired level of enhanced ability to catalyze the reaction of interest by the cell. - View Dependent Claims (21)
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22. A method of evolving a biocatalytic activity of a cell, comprising:
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(a) recombining at least a first and second DNA segment from at least one gene conferring to the cell the ability to be resistant to a heavy metal, the segments differing from each other in at least two nucleotides, to produce a library of recombinant genes; (b) screening the library to identify at least one recombinant gene from the library that confers enhanced ability to catalyze the reaction of interest by the cell relative to a wildtype form of the gene; (c) recombining at least a segment from the at least one recombinant gene with a further DNA segment from the at least one gene, the same or different from said first and second DNA segments, to produce a second library of recombinant genes; (d) screening the second library of recombinant genes to identify at least one further recombinant gene from the second library of recombinant genes that confers enhanced ability to catalyze the reaction of interest by the cell relative to a previous recombinant gene; (e) repeating (c) and (d), as necessary, until further recombinant gene confers a desired level of enhanced ability of resistance to the heavy metal. - View Dependent Claims (23)
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24. A method of evolving a biocatalytic activity of a cell, comprising:
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(a) recombining at least a first and second DNA segment from at least one gene conferring ability to catalyze a reaction of interest, the segments differing from each other in at least two nucleotides, to produce a library of recombinant genes; (b) screening the library to identify at least one recombinant gene from the library that confers enhanced ability to catalyze the reaction of interest by the cell relative to a wildtype form of the gene; (c) recombining at least a segment from the at least one recombinant gene with a further DNA segment from the at least one gene, the same or different from said first and second DNA segments, to produce a second library of recombinant genes; (d) screening the second library of recombinant genes to identify at least one further recombinant gene from the second library of recombinant genes that confers enhanced ability to catalyze the reaction of interest by the cell relative to a previous recombinant gene; (e) repeating (c) and (d), as necessary, until the further recombinant gene confers a desired level of enhanced ability to catalyze the reaction of interest by the cell, wherein the reaction of interest is the ability to biocatalyze desulfurization of oil. - View Dependent Claims (25)
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26. A method of optimizing production of a metabolite by a metabolic pathway, the method comprising:
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(a) recombining at least a first and second DNA segments from at least one gene conferring ability to produce the metabolite, the segments differing from each other in at least two nucleotides, to produce a library of recombinant genes; (b) screening the library to identify at least one recombinant gene from the library that confers optimized production of the metabolite relative to a wildtype form of the gene; (c) recombining at least a segment from the at least one recombinant gene with a further DNA segment from the at least one gene, the same or different from said first and second DNA segments, to produce a second library of recombinant genes; (d) screening the second library of recombinant genes to identify at least one further recombinant gene from the second library of recombinant genes that confers optimized ability to produce the metabolite relative to a previous recombinant gene; (e) repeating (c) and (d), as necessary, until the further recombinant gene confers a desired level of optimized production of the metabolite. - View Dependent Claims (27, 28)
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33. A method of evolving a biocatalytic activity of a cell, comprising:
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(a) recombining at least a first and second DNA segment from at least one gene conferring ability to catalyze a reaction of interest, the segments differing from each other in at least two nucleotides, to produce a library of recombinant genes; (b) screening the library to identify at least one recombinant gene from the library that confers enhanced ability to catalyze the reaction of interest by the cell relative to a wildtype form of the gene; (c) recombining at least a segment from the at least one recombinant gene with a further DNA segment from the at least one gene, the same or different from said first and second DNA segments, to produce a second library of recombinant genes; (d) screening the second library of recombinant genes to identify at least one further recombinant gene from the second library of recombinant genes that confers enhanced ability to catalyze the reaction of interest by the cell relative to a previous recombinant gene; (e) repeating (c) and (d), as necessary, until the further recombinant gene confers a desired level of enhanced ability to catalyze the reaction of interest by the cell wherein the reaction of interest is the ability to synthesize a compound of interest and wherein the compound of interest is an isoprenoid.
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34. A method of evolving a biocatalytic activity of a cell, comprising:
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(a) recombining at least a first and second DNA segment from at least one gene conferring ability to catalyze a reaction of interest, the segments differing from each other in at least two nucleotides, to produce a library of recombinant genes; (b) screening the library to identify at least one recombinant gene from the library that confers enhanced ability to catalyze the reaction of interest by the cell relative to a wildtype form of the gene; (c) recombining at least a segment from the at least one recombinant gene with a further DNA segment from the at least one gene, the same or different from said first and second DNA segments, to produce a second library of recombinant genes; (d) screening the second library of recombinant genes to identify at least one further recombinant gene from the second library of recombinant genes that confers enhanced ability to catalyze the reaction of interest by the cell relative to a previous recombinant gene; (e) repeating (c) and (d), as necessary, until the further recombinant gene confers a desired level of enhanced ability to catalyze the reaction of interest by the cell wherein the reaction of interest is the ability to synthesize a compound of interest and wherein the compound of interest is a polyketide.
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35. A method of evolving a biocatalytic activity of a cell, comprising:
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(a) recombining at least a first and second DNA segment from at least one gene conferring ability to catalyze a reaction of interest, the segments differing from each other in at least two nucleotides, to produce a library of recombinant genes; (b) screening the library to identify at least one recombinant gene from the library that confers enhanced ability to catalyze the reaction of interest by the cell relative to a wildtype form of the gene; (c) recombining at least a segment from the at least one recombinant gene with a further DNA segment from the at least one gene, the same or different from said first and second DNA segments, to produce a second library of recombinant genes; (d) screening the second library of recombinant genes to identify at least one further recombinant gene from the second library of recombinant genes that confers enhanced ability to catalyze the reaction of interest by the cell relative to a previous recombinant gene; (e) repeating (c) and (d), as necessary, until the further recombinant gene confers a desired level of enhanced ability to catalyze the reaction of interest by the cell wherein the reaction of interest is the ability to synthesize a compound of interest and wherein the compound of interest is a carotenoid.
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36. A method of evolving a biocatalytic activity of a cell, comprising:
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(a) recombining at least a first and second DNA segment from at least one gene conferring ability to catalyze a reaction of interest, the segments differing from each other in at least two nucleotides, to produce a library of recombinant genes; (b) screening the library to identify at least one recombinant gene from the library that confers enhanced ability to catalyze the reaction of interest by the cell relative to a wildtype form of the gene; (c) recombining at least a segment from the at least one recombinant gene with a further DNA segment from the at least one gene, the same or different from said first and second DNA segments, to produce a second library of recombinant genes; (d) screening the second library of recombinant genes to identify at least one further recombinant gene from the second library of recombinant genes that confers enhanced ability to catalyze the reaction of interest by the cell relative to a previous recombinant gene; (e) repeating (c) and (d), as necessary, until the further recombinant gene confers a desired level of enhanced ability to catalyze the reaction of interest by the cell wherein the reaction of interest is the ability to synthesize a compound of interest and wherein the compound of interest is an antibiotic.
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Specification