Methods and compositions for cellular and metabolic engineering

• US 6,309,883 B1
• Filed: 01/24/2000
• Issued: 10/30/2001
• Est. Priority Date: 02/17/1994
• Status: Expired due to Term

• Current Assignee: Codexis, Inc.
• Original Assignee: Maxygen Inc.
• Inventors: Minshull, Jeremy, Stemmer, Willem P. C.
• Primary Examiner(s): WHISENANT, ETHAN C
• Application Number:
  US09/490,642
• Time in Patent Office: 645 Days
• Field of Search: 435/440, 435/6, 536/23.1, 536/24.3, 935/76, 935/77, 935/78
• US Class Current: 435/440
• CPC Class Codes: C07K 14/43595 from coelenteratae, e.g. medusae
• CPC Class Codes: C07K 14/545 IL-1
• CPC Class Codes: C07K 16/00 Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies antibodies with enzymatic activity, e.g. abzymes C12N9/0002
• CPC Class Codes: C07K 2317/565 Complementarity determining region [CDR]
• CPC Class Codes: C07K 2317/622 Single chain antibody (scFv)
• CPC Class Codes: C12N 15/10 Processes for the isolation, preparation or purification of DNA or RNA chemical preparation of DNA or RNA C07H21/00; preparation of non-structural polynucleotides from microorganisms or with enzymes C12P19/34
• CPC Class Codes: C12N 15/1027 by DNA shuffling, e.g. RSR, STEP, RPR
• CPC Class Codes: C12N 15/1034 Isolating an individual clone by screening libraries
• CPC Class Codes: C12N 15/1037 Screening libraries presented on the surface of microorganisms, e.g. phage display, E. coli display
• CPC Class Codes: C12N 15/52 Genes encoding for enzymes or proenzymes
• CPC Class Codes: C12N 15/64 General methods for preparing the vector, for introducing it into the cell or for selecting the vector-containing host
• CPC Class Codes: C12N 9/2471 Beta-galactosidase (3.2.1.23), i.e. exo-(1-->4)-beta-D-galactanase
• CPC Class Codes: C12N 9/86 acting on amide bonds in cyclic amides, e.g. penicillinase (3.5.2)
• CPC Class Codes: C12Q 1/6811 Selection methods for production or design of target specific oligonucleotides or binding molecules
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2525/161 incorporating target specific and non-target specific sites
• CPC Class Codes: C12Y 302/01023 Beta-galactosidase (3.2.1.23), i.e. exo-(1-->4)-beta-D-galactanase
• CPC Class Codes: C40B 40/02 Libraries contained in or displayed by microorganisms, e.g. bacteria or animal cells; Libraries contained in or displayed by vectors, e.g. plasmids; Libraries containing only microorganisms or vectors

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.

Claims

1. A method of recombining one or more nucleic acids, the method comprising:

introducing one or more sets of nucleic acids into a plurality of cells, thereby providing a plurality of modified cells, each of the plurality of modified cells comprising at least one member of the one or more sets of nucleic acids;

transferring at least a first member of the one or more sets of nucleic acids from a first of the plurality of modified cells into at least a second of the plurality of modified cells;

permitting recombination to occur between the at least one member of the one or more sets of nucleic acids and a nucleic acid present in the second of the plurality of modified cells to produce a recombinant nucleic acid;

introducing the recombinant nucleic acid into a third cell and permitting recombination between the recombinant nucleic acid and a third member present in a third cell of the plurality of modified cells, or between the recombinant nucleic acid and the first member or the second member, thereby producing a further recombined nucleic acid; and

,

screening the further recombined nucleic acid for one or more properties or one or more encoded activities, thereby providing a selected recombinant nucleic acid.

2. The method of claim 1, comprising further recombining the selected recombinant nucleic acid with one or more additional nucleic acids and selecting the resulting further recombined nucleic acid to produce a further recombined selected nucleic acid.

4. The method of claim 2 or 3, comprising screening the further recombined selected nucleic acid for one or more encoded activities, thereby providing a multiply recombined multiply selected nucleic acid.

5. The method of claim 2 or 3, wherein the further recombining comprises in vitro recombination.

6. The method of claim 5, wherein the further recombining comprises recursive in vitro recombination.

7. The method of claim 2 or 3, wherein the further recombining comprises in vivo recombination.

8. The method of claim 7, wherein the further recombining step comprises recursive in vivo recombination.

9. The method of claim 1 or 3, wherein the one or more sets of nucleic acids comprise one or more nucleic acid produced by in vitro sequence recombination.

10. The method of claim 1 or 3, wherein the one or more sets of nucleic acids comprise one or more nucleic acid produced by recursive in vitro recombination.

11. The method of claim 1 or 3, wherein the one or more sets of nucleic acids comprise one or more nucleic acid produced by in vivo recombination.

12. The method of claim 1 or 3, wherein the one or more sets of nucleic acids comprise one or more nucleic acid produced by recursive in vivo sequence recombination.

13. The method of claim 1 or 3, wherein the one or more sets of nucleic acids comprise one or more nucleic acid produced by mutation.

14. The method of claim 13, wherein the one or more sets of nucleic acids are produced by error prone PCR.

15. The method of claim 1 or 3, wherein the step of introducing the one or more sets of nucleic acids into the plurality of cells comprises packaging members of one or more of the one or more sets into phage vectors and transducing the resulting phage library into a plurality of cells, thereby producing the plurality of modified cells.

16. The method of claim 1 or 3, wherein the step of introducing the one or more sets of nucleic acids into the plurality of cells comprises packaging members of one or more of the one or more sets into viral vectors and transducing the resulting viral library into a plurality of cells, thereby producing the plurality of modified cells.

17. The method of claim 1 or 3, wherein the step of introducing the one or more sets of nucleic acids into the plurality of cells comprises electroporating members of one or more of the one or more sets into a plurality of cells, thereby producing the plurality of modified cells.

18. The method of claim 1 or 3, wherein the step of introducing the one or more sets of nucleic acids into the plurality of cells comprises electronic pulse introduction of members of one or more of the one or more sets into a plurality of cells, thereby producing the plurality of modified cells.

19. The method of claim 1 or 3, wherein the step of introducing the one or more sets of nucleic acids into the plurality of cells comprises biolistically introducing members of one or more of the one or more sets into a plurality of cells, thereby producing the plurality of modified cells.

20. The method of claim 1 or 3, wherein the step of introducing the one or more sets of nucleic acids into the plurality of cells comprises transferring members of one or more of the one or more sets into a plurality of cells via conjugative transfer, thereby producing the plurality of modified cells.

21. The method of claim 1 or 3, wherein the step of introducing the one or more sets of nucleic acids into the plurality of cells comprises transferring one or more of the one or more sets into the plurality of cells by fusing one or more cells comprising one or more members of the one or more sets with a plurality of cells, thereby producing the plurality of modified cells.

22. The method of claim 1 or 3, wherein the step of introducing the one or more sets of nucleic acids into the plurality of cells comprises transferring one or more members of the one or more sets of nucleic acids into a plurality of cells by fusing one or more library cells comprising members of the one or more sets with the one or more of the plurality of cells, wherein the fusing is induced by incubation of the library cells or the plurality of cells, or both, with a viral protein, or a chenmical agent.

23. The method of claim 22, wherein the viral protein comprises one or more of:

an influenza protein, an influenza viral hemagglutinin protein, HSV-1 g B, or HSV-1 g D.

24. The method of claim 22, wherein the chemical agent is PEG.

25. The method of claim 1 or 3, wherein the step of transferring at least a first member of the one or more sets of nucleic acids from a first of the plurality of modified cells into at least a second of the plurality of modified cells comprises packaging at least one member of one or more of the one or more sets into at least one phage vector and transducing the resulting at least one phage vector into the second modified cell.

26. The method of claim 1 or 3, wherein the step of transferring at least a first member of the one or more sets of nucleic acids from a first of the plurality of modified cells into at least a second of the plurality of modified cells comprises packaging at least one member of one or more of the one or more sets into at least one viral vector and transducing the resulting at least one viral vector into the second modified cell.

27. The method of claim 1 or 3, wherein the step of transferring at least a first member of the one or more sets of nucleic acids from a first of the plurality of modified cells into at least a second of the plurality of modified cells comprises electroporating at least one member of one or more of the one or more sets into the second modified cell.

28. The method of claim 1 or 3, wherein the step of transferring at least a first member of the one or more sets of nucleic acids from a first of the plurality of modified cells into at least a second of the plurality of modified cells comprises electronic pulse transfer of at least one member of one or more of the one or more sets into the second modified cell.

29. The method of claim 1 or 3, wherein the step of transferring at least a first member of the one or more sets of nucleic acids from a first of the plurality of modified cells into at least a second of the plurality of modified cells comprises biolistically transferring at least one member of one or more of the one or more sets into the second modified cell.

30. The method of claim 1 or 3, wherein the step of transferring at least a first member of the one or more sets of nucleic acids from a first of the plurality of modified cells into at least a second of the plurality of modified cells is performed via conjugative transfer of the first member from the first modified cell into the second modified cell.

31. The method of claim 1 or 3, wherein the step of transferring at least a first member of the one or more sets of nucleic acids from a first of the plurality of modified cells into at least a second of the plurality of modified cells is performed by fusing the first and second cell.

32. The method of claim 1 or 3, wherein the step of transferring at least a first member of the one or more sets of nucleic acids from a first of the plurality of modified cells into at least a second of the plurality of modified cells is performed by fusing the first and second cell, wherein the fusing is induced by incubation of the first and second cells with a viral protein, or a chemical agent.

33. The method of claim 32, wherein the viral protein comprises one or more of:

an influenza protein, an influenza viral hemagglutinin protein, HSV-1 g B, or HSV-1 g D.

34. The method of claim 32, wherein the chemical agent is PEG.

35. The method of claim 1 or 3, wherein the step of introducing the recombinant nucleic acid into the third cell comprises packaging the recombinant nucleic acid into at least one phage vector and transducing the resulting at least one phage vector into the third cell.

36. The method of claim 1 or 3, wherein the step of introducing the recombinant nucleic acid into the third cell comprises packaging the recombinant nucleic acid into at least one viral vector and transducing the resulting at least one viral vector into the third cell.

37. The method of claim 1 or 3, wherein the step of introducing the recombinant nucleic acids into the third cell comprises electroporating the recombinant nucleic acid into the third cell.

38. The method of claim 1 or 3, wherein the step of introducing the recombinant nucleic acid into the third cell comprises pulse introducing the recombinant nucleic acid into the third cell.

39. The method of claim 1 or 3, wherein the step of introducing the recombinant nucleic acid into the third cell comprises biolistically introducing the recombinant nucleic acid into the third cell.

40. The method of claim 1 or 3, wherein the step of introducing the recombinant nucleic acid into the third cell is performed via conjugative transfer of the recombinant nucleic acid into the third cell.

41. The method of claim 1 or 3, wherein the step of introducing the recombinant nucleic acid into the third cell comprises fusing the second and third cells.

42. The method of claim 1 or 3, wherein the step of introducing the recombinant nucleic acid into the third cell comprises fusing the second and third cells, wherein the fusing is induced bit incubation of the second and third cells with a viral protein, or a chemical agent.

43. The method of claim 42, wherein the viral protein comprises one or more of:

an influenza protein, an influenza viral hemagglutinin protein, HSV-1 g B, or HSV-1 g D.

44. The method of claim 42, wherein the chemical agent is PEG.

45. The method of claim 1 or 3, wherein the plurality of modified cells comprise one or more mutator cells.

46. The method of claim 45, wherein the mutator cells are selected from the group consisting of:

Mut L cells, Mut S cells, Mut D cells, Mut T cells, Mut H cells, and Human Ataxia Telengiecta cells.

47. The method of claim 1 or 3, wherein a plurality of members of the one or more sets of nucleic acids are at least about 50% identical.

48. The method of claim 1 or 3, wherein the members of the one or more sets of nucleic acids are at least about 70% identical.

49. The method of claim 1 or 3, wherein the members of the one or more sets of nucleic acids are at least about 80% identical.

50. The method of claim 1 or 3, wherein the members of the one or more sets of nucleic acids are at least about 90% identical.

51. The method of claim 1 or 3, wherein the members of the one or more sets of nucleic acids differ from each other in about 5 to about 20 positions.

52. The method of claim 1 or 3, wherein at least one of the one or more sets of nucleic acids have less than 10 members.

53. The method of claim 1 or 3, wherein at least one of the one or more sets of nucleic acids have more than 10⁵ members.

54. The method of claim 1 or 3, wherein at least one of the one or more sets of nucleic acids have more than 10⁷ members.

55. The method of claim 1 or 3, wherein at least one of the one or more sets of nucleic acids have more than 10⁹ members.

56. The method of claim 1 or 3, wherein at least one member of the one or more sets of nucleic acids is a full-length gene.

57. The method of claim 1 or 3, wherein at least one member of the one or more sets of nucleic acids is cloned into a vector which supplies one or more of:

a promoter, a polyadenylation sequence, or a regulatory sequence.

58. The method of claim 1 or 3, wherein the members of the one or more sets of nucleic acids are allelic or species variants.

59. The method of claim 1 or 3, wherein at least one member of the plurality of modified cells is selected or derived from one or more of:

a bacterial cell, gram-negative cell, gram-positive cell, a Streptomycetes cell, an Actinomycetes cell, a Corynebacteria cell, a Penicillium cell, a Bacillus cell, an Escherichia coli cell, a Pseudomonas cell, a Salmonella cell, an Erwinia cell, a eukaryotic cell, a mammalian cell, a mouse cell, a hamster cell, a primate cell, a human cell, an established cell line cell, a primary cell culture cell, a stem cell, an embryonic stem cell, a zygotes cell, a fibroblast cell, a lymphocyte cell, a Chinese hamster ovary (CHO) cell, a mouse fibroblast cell, an NIH3T3 cell, a kidney cell, a liver cell, a muscle cell, a skin cell, a plant cell, a maize cell, a rice cell, a wheat cell, a cotton cell, a soybean cell, a sugarcane cell, a tobacco cell, an arabidopsis cell;

a fish cell, an algal cell, a fungal cell, a Penicillium cell, a Fusarium cell, an Aspergillus cell, a Podospora cell, a Neurospora cell, an insect cell, a yeast cell, a Picchia cell, a Saccharomyces cell, or a nitrogen-fixation symbiotic cell.

60. The method of claim 1 or 3, wherein at least one member of the plurality of modified cells is selected or derived from a tissue or organism selected from the group consisting of:

a plant, a bacteria, a fungus, an algae, an intact animal tissue, a tissue culture, and an animal embryo.

61. The method of claim 1 or 3, wherein at least one member of the plurality of modified cells is selected or derived from one or more of:

E. coli, lactobacilli, Streptomycetes, Actinomycetes or filamentous fungi.

62. The method of claim 1 or 3, wherein at least one member of the plurality of modified cells is selected for one or more of:

pathogenicity, substrate range, environmental hardiness, presence of one or more key intermediates, ease of genetic manipulation, or likelihood of promiscuous transfer of genetic information to other organisms.

63. The method of claim 1 or 3, wherein at least one member of the plurality of modified cells is selected or derived from one or more cell which comprises a biphenyl catabolizing pathway.

64. The method of claim 1, 2, or 3, wherein one or more member of the one or more sets of nucleic acids, the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid comprises one or more of:

a plasmid, a cosmid, a chromosome, an episome, a YAC, a phage, a filamentous phage, a phage P1 clone, or a viral vector.

65. The method of claim 1, 2, or 3, wherein one or more member of the one or more sets of nucleic acids, the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid comprises cleaved genomic DNA.

66. The method of claim 1, 2, or 3, wherein one or more member of the one or more sets of nucleic acids, the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid comprises amplified genomic DNA.

67. The method of claim 1, 2, or 3, wherein one or more member of the one or more sets of nucleic acids, the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid comprises one or more metabolic pathway nucleic acids which encode at least one metabolic pathway.

68. The method of claim 1, 2, or 3, wherein one or more member of the one or more sets of nucleic acids, the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid are provided in or selected from a library of nucleic acids selected from the group consisting of:

a plasmid library, a cosmid library, a phage library, a chromosome library, a filamentous phage library, and a viral library.

69. The method of claim 1, 2, or 3, wherein one or more member of the one or more sets of nucleic acids, the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid are provided in or selected from a library of nucleic acids comprising variants of a single gene.

70. The method of claim 1, 2, or 3, wherein one or more member of the one or more sets of nucleic acids, the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid are provided in or selected from a library of nucleic acids comprising variants of more than one gene.

71. The method of claim 1, 2, or 3, wherein one or more member of the one or more sets of nucleic acids, the recombinant nucleic acid, the further recombined nucleiic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid are provided in or selected from a library of nucleic acids comprising one or more genes in a biochemical pathway.

72. The method of claim 1, 2, or 3, wherein one or more member of the one or more sets of nucleic acids, the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid are provided in or selected from a library of genes isolated from one or more of:

a bacteria, an Alcaligenes, a Zoogloea, a Rhizobium, a Bacillus, a Azobacter, or a eukaryote.

73. The method of claim 1, 2, or 3, wherein one or more member of the one or more sets of nucleic acids, the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid comprises a nucleic acid which encodes a regulatory gene.

74. The method of claim 1, 2, or 3, wherein one or more member of the one or more sets of nucleic acids, the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid encodes one or more enzyme selected from the group consisting of:

an acylase, a dioxygenase, a monooxygenase, a carotenoid synthetic enzyme, a hydrolytic enzyme, a catabolic enzyme, a dibenzothiopene catabolizing enzyme, a nitroreductase, a benzene degrading enzyme, a nitrobenzene degrading enzyme, a nitrotoluene degrading enzyme, a toxin degrading enzyme, an industrial chemical degrading enzyme, an herbicide degrading enzyme, a cellulose degrading enzyme, a pesticide degrading enzyme a pollutant degrading enzyme, a xylene degrading enzyme a toluene degrading enzyme, a camphor degrading enzyme, a naphthalene degrading enzyme, a halogenated hydrocarbon degrading enzyme, a biphenyl degrading enzyme, a polychlorinated biphenyl (PCB) degrading enzyme, a polycyclic aromatic hydrocarbon (PHA) degrading enzyme, a polyhydroxybutyrate (PHB) degrading enzyme, a trichlorethylene degrading enzyme, a pentachlorophenyl (PCP) degrading enzyme, a trichloroethylene degrading enzyme, a paranitrobenzyl, esterase, a sesquiterpene synthase, an expandase, a penicillin amidase, a penicillin G amidase, an enzyme which modifies 7-aminodeacetooxycephalosporanic acid (7-ADCA), an enzyme which modifies a semi-synthetically produced cephalosporin, and an enzyme which modifies penicillin V.

75. The method of claim 74, wherein the enzyme is a polyhydroxybutyrate (PHB) degrading enzyme, wherein the one or more sets of nucleic acids are derived from one or more of:

an Alcaligenes bacteria, a Zoogloea bacteria, a Rhizobium bacteria, a Bacillus bacteria, or an Azobacter bacteria.

76. The method of claim 74, wherein the enzyme is a a biphenyl degrading enzyme and wherein the enzyme is expressed in at least one host cell which comprises a biphenyl catabolizing pathway.

77. The method of claim 74, wherein the enzyme is a cellulose degrading enzyme and wherein the one or more sets of nucleic acids are derived from one or more Agrobacterium tumefaciens.

78. The method of claim 74, wherein the enzyme is a carotenoid synthetic enzyme and wherein the one or more sets of nucleic acids are derived from one or more of:

Myxococcus xanthus, Rhodobacter sphaeroides, Thermus thermophilus, Erwina uredovora, Haematococcus pluvialis, E. coli, E. herbicola, or R. capsulatus.

79. The method of claim 1, 2, or 3, wherein one or more member of the one or more sets of nucleic acids, the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid encodes one or more enzyme which is resistant to inactivation by one or more epoxide.

80. The method of claim 1, 2, or 3, wherein the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid provides one or more organism, when expres,sed in the organism, with a new or improved ability to convert a pollutant into a nutrient source.

81. The method of claim 1, 2, or 3, wherein the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid provides one or more organism, when expressed in the organism, with a new or improved ability to degrade one or more toxin, industrial chemical, herbicide, pesticide or pollutant.

82. The method of claim 81, wherein the one or more toxin, industrial chemical, herbicide or pollutant comprises one or more of:

benzene, xylene, toluene, camphor, naphthalene, a halogenated hydrocarbon, a polychlorinated biphenyl (PCB), a polycyclic aromatic hydrocarbon (PHA), a trichlorethylene, a pentachlorophenyl (PCP) or trichloroethylene.

83. The method of claim 1, 2, or 3, wherein the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid encode an enzyme with an improved catalytic activity, a new catalytic activity, altered substrate recognition, thermostability, stability in a non-aqueous solvent, or an altered expression level.

84. The method of claim 1, 2, or 3, wherein the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid provides one or more organism, when expressed in the organism, with a new or improved resistance to the presence of one or more heavy metal.

85. The method of claim 1, 2, or 3, wherein the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid provides one or more organism, when expressed in the organism one or more property selected from the group consisting of:

modified growth rate, ability to secrete a desired compound, an ability to tolerate an increased temperature, and an ability erate one or more environmental stress.

86. The method of claim 1, 2, or 3, wherein the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid provides one or more organism, when expressed in the organism, with a new or improved ability to reduce an organo-nitro compound or to permit the organism to survive in the presence of an organo-nitro compound.

87. The method of claim 1, 2, or 3, wherein the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid provides one or more organism, when expressed in the organism, with new or improved utilization of a nutrient source.

88. The method of claim 87, wherein the nutrient source is selected from the group consisting of:

lactose, whey, galactose, mannitol, xylan, cellobiose, cellulose and sucrose.

89. The method of claim 87, wherein the improved utilization of a nutrient source provides for production of compounds selected from the group consisting of:

ethanol, tryptophan, a rhamnolipid surfactant, xanthan gum, polysaccharide xanthan gum and polyhydroxylalkanoate.

90. The method of claim 1, 2, or 3, wherein the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid provides one or more organism, when expressed in the organism, new or improved production of one or more product selected from the group consisting of:

ethanol, tryptophan, a rhamnolipid surfactant, xanthan gum, polysaccharide xanthan gum, polyhydroxylalkanoate, phenylalanine, and 2-keto-L-gluconic acid.

91. The method of claim 1, 2, or 3, wherein the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid provides one or more organism, when expressed in the organism, with a new or improved ability to produce one or more metabolic intermediate.

92. The method of claim 91, wherein the metabolic intermediate is selected from the group consisting of:

an antibiotic, a vitamin, an amino acid, phenylalanine, an aromatic amino acid, ethanol, butanol, polysaccharide xanthan gum, xanthan gum, bacterial cellulose, a peptide, and a lipid.

93. The method of claim 1, 2, or 3, wherein the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid encodes an enzyme which produces one or more compound selected from the group consisting of:

a polyketide, a dye, a vitamin, an antibiotic, a carotenoid, a terpenoid, and an isoprenoid.

94. The method of claim 93, wherein the dye is indigo.

95. The method of claim 93, wherein the vitamin is vitamin C.

96. The method of claim 93, wherein the antibiotic is selected from the group consisting of:

a peptide, a peptidolactone, a thiopeptide, a beta-lactam, a glycopeptide, a lantibiotic, a microcin, a polyketide-derived antibiotic, an anthracyclin, a tetracyclin, a macrolide, an avermectin, a polyether, an ansamycins, chloramphenicol, an aminoglycoside, an aminocyclitol, a polyoxin, an agrocin, mederrhodin, dihydrogranatirhodin, 6-deoxyerythromycin A, isovalerylspiramycin, a hybrid macrolide and an isoprenoid.

97. The method of claim 93, wherein the polyketide is an antibiotic.

98. The method of claim 93, wherein the polyketide is selected from the group consisting of:

tetracycline, erythromycin, an anti-cancer agent, daunomycin, an immunosuppressant, FK506, rapamycin, monesin and avermectin.

99. The method of claim 93, wherein the isoprenoid is selected from the group consisting of:

an antibacterial isoprenoid and an antifungal isoprenoid.

100. The method of claim 93, wherein the carotinoid is selected from the group consisting of:

a ketocarotenoid, a myxobacton, a spheroidene, a spheroidenone, a lutein, an astaxanthin, a violaxanthin, a 4-ketorulene, a myxoxanthrophyll, an echinenone, a lycopene, a zeaxanthin, a monoglucoside, a diglucoside, an alpha carotene, a beta carotene, a gamma carotene, a delta carotene, a cryptoxanthin monoglucoside and a neoxanthin.

101. The method of claim 1 or 3, further comprising propagating the first, second, or third cell, in culture.

102. The method of claim 1 or 3, wherein the screening comprises monitoring bioremediation or biodegradation of one or more toxin, industrial chemical, herbicide, pesticide or pollutant.

103. The method of claim 102, the one or more toxin, industrial chemical, herbicide or pollutant comprising one or more of:

benzene, xylene, toluene, camphor, naphthalene, a halogenated hydrocarbon, a polychlorinated biphenyl (PCB), a polycyclic aromatic hydrocarbon (PHA), a trichlorethylene, a pentachlorophenyl (PCP) or trichloroethylene.

104. The method of claim 1 or 3, wherein the screening step is performed in the same cell type as the recombinant cell is produced in.

105. The method of claim 1 or 3, wherein the screening step is performed in a different cell type than the recombinant cell is produced in.

106. The method of claim 1 or 3, wherein the screening comprises monitoring one or more reporter gene selected from the group consisting of:

luciferase, green fluorescence protein, and β

-galactosidase.

107. The method of claim 1 or 3, wherein the screening comprises monitoring one or more of:

fluorescence, bioluminescence, colony size, cell growth rate, a chromogenic substrate, or halo formation.

108. The method of claim 1 or 3, wherein the screening comprises performing an ELISA assay.

109. The method of claim 1 or 3, wherein the screening comprises performing a cell-cell activity assay.

110. The method of claim 2 or 3, wherein the screening comprises monitoring differential expression of a protein or nucleic acid expressed in a screened cell comprising the recombinant nucleic acid, the further recombined nucleic acid, or the further recombined selected nucleic acid.

111. The method of claim 1 or 3, wherein the screening comprises performing FACS.

112. The method of claim 1 or 3, wherein the screening comprises performing two-color FACS.

113. The method of claim 1 or 3, wherein the screening comprises monitoring gel microdroplets.

114. The method of claim 1 or 3, wherein the screening comprises detecting one or more molecule by mass spectometry.

115. The method of claim 1, 2, or 3, wherein a selected cell comprising the recombinant nucleic acid, the further recombined nucleic acid, the further recombined selected nucleic acid or the multiply recombined multiply selected nucleic acid is selected in a chemostat.

116. The method of claim 1 or 3, wherein the screening comprises selecting for one or more of:

an improved catalytic activity, a new catalytic activity, altered substrate recognition, thermostability, stability in a non-aqueous solvent, or an altered expression level.

117. The method of claim 1 or 3, wherein the screening comprises selecting one or more organism comprising the recombinant nucleic acid for one or more property selected from the group consisting of:

a modified growth rate, an ability to secrete a desired compound, an ability to tolerate an increased temperature, and an ability to tolerate one or more environmental stresses.

118. The method of claim 1 or 3, wherein the screening comprises monitoring the presence or absence of one or more secondary metabolite selected from the group consisting of:

a polyketide, a dye, a vitamin, an antibiotic, a carotenoid, a terpenoid, and an isoprenoid.

119. The method of claim 118, wherein the dye is indigo.

120. The method of claim 118, wherein the vitamin is vitamin C.

121. The method of claim 118, wherein the antibiotic is selected from the group consisting of:

a peptide, a peptidolactone, a thiopeptide, a beta-lactam, a glycopeptide, a lantibiotic, a microcin, a polyketide-derived antibiotic, an anthracyclin, a tetracyclin, a macrolide, an avermectin, a polyether, an ansamycins, chloramphenicol, an aminoglycoside, an aminocyclitol, a polyoxin, an agrocin, mederrhodin, dihydrogranatirhodin, 6-deoxyerythromycin A, isovalerylspiramycin, a hybrid macrolide and an isoprenoid.

122. The method of claim 118, wherein the polyketide is an antibiotic.

123. The method of claim 118, wherein the polyketide is selected from the group consisting of:

tetracycline, erythromycin, an anti-cancer agent, daunomycin, an immunosuppressant, FK506, rapamycin, monesin and avermectin.

124. The method of claim 118, wherein the isoprenoid is selected from the group consisting of:

an antibacterial isoprenoid and an antifungal isoprenoid.

125. The method of claim 118, wherein the carotinoid is selected from the group consisting of:

a ketocarotenoid, a myxobacton, a spheroidene, a spheroidenone, a lutein, an astaxanthin, a violaxanthin, a 4-ketorulene, a myxoxanthrophyll, an echinenone, a lycopene, a zeaxanthin, a monoglucoside, a diglucoside, an alpha carotene, a beta carotene, a gamma carotene, a delta carotene, a cryptoxanthin monoglucoside and a neoxanthin.

126. The method of claim 1 or 3, wherein the screening comprises monitoring one or more enzymatic activities of one or more enzymes selected from the group consisting of:

an acylase, a dioxygenase, a monooxygenase, a carotenoid synthetic enzyme, a hydrolytic enzyme, a catabolic enzyme, a nitroreductase, a benzene degrading enzyme, a nitrobenzene degrading enzyme, a nitrotoluene degrading enzyme, a toxin degrading enzyme, an industrial chemical degrading enzyme, an herbicide degrading enzyme, a cellulose degrading enzyme, a pesticide degrading enzyme a pollutant degrading enzyme, a xylene degrading enzyme, a toluene degrading enzyme, a camphor degrading enzyme, a naphthalene degrading enzyme, a halogenated hydrocarbon degrading enzyme, a polychlorinated biphenyl (PCB) degrading enzyme, a polycyclic aromatic hydrocarbon (PHA) degrading enzyme, a polyhydroxybutyrate (PHP) degrading enzyme, a trichlorethylene degrading enzyme, a pentachlorophenyl (PCP) degrading enzyme, a trichloroethylene degrading enzyme, a paranitrobenzyl, esterase, a sesquiterpene synthase, an expandase, a penicillin amidase, a penicillin G amidase, an enzyme which modifies 7-aminodeacetooxycephalosporanic acid (7-ADCA), an enzyme which modifies a semi-synthetically produced cephalosporin, and an enzyme which modifies penicillin V.

127. The method of claim 1 or 3, wherein the screening comprises monitoring degradation of one or more of:

a toxin, an industrial chemical, an herbicide, a pesticide a pollutant, PHB, or cellulose.

128. The method of claim 127 wherein the one or more toxin, industrial chemical, herbicide or pollutant comprises one or more of:

benzene, xylene, toluene, camphor, naphthalene, a halogenated hydrocarbon, a polychlorinated biphenyl (PCB), a polycyclic aromatic hydrocarbon (PHA), a trichlorethylene, a pentachlorophenyl (PCP) or trichloroethylene.

129. The method of claim 1 or 3, wherein the screening comprises monitoring synthesis of one or more carotenoid.

130. The method of claim 1 or 3, wherein the screening comprises monitoring resistance of an enzyme to an epoxide.

131. The method of claim 1 or 3, wherein the screening comprises monitoring resistance of a cell modified with the recombinant nucleic acid to a heavy metal.

132. The method of claim 1 or 3, wherein the screening comprises selecting an organism which expresses the recombinant nucleic acid for an ability to survive in the presence of an organo-nitro compound.

133. The method of claim 1 or 3, wherein the screening comprises selecting an organism for an ability to metabolize lactose, whey, galactose, mannitol, xylan, cellobiose, cellulose or sucrose.

134. The method of claim 1 or 3, wherein the screening comprises selecting, an organism for an ability to produce ethanol, tryptophan, a rhamnolipid surfactant, xanthan gum, polysaccharide xanthan gum, polyhydroxylalkanoate, phenylalanine, or 2-keto-L-gluconic acid.

3. A method of recombining one or more nucleic acids, the method comprising:

introducing one or more sets of nucleic acids into a plurality of cells, thereby providing a plurality of modified cells, each of the plurality of modified cells comprising at least one member of the one or more sets of nucleic acids;

transferring at least a first member of the one or more sets of nucleic acids from a first of the plurality of modified cells into at least a second of the plurality of modified cells;

permitting recombination to occur between the first member and a second member present in the second of the plurality of modified cells, thereby producing a recombinant nucleic acid;

screening the recombinant nucleic acid for one or more properties or one or more encoded activities; and

,

further recombining the selected recombinant nucleic acid with one or more additional nucleic acid, or with the first or second nucleic acid, thereby producing a further recombined selected nucleic acid.