Chapter 13 Genetic Engineering to Produce Polyketide Analogues

Methods in Enzymology

Volumn 459, Issue B, 2009, Pages 295-318

  Reeves, Christopher D ^a   Rodriguez, Eduardo ^b  

^a Amyris Biotechnologies Inc   (United States)

^b UNIVERSIDAD NACIONAL DE ROSARIO   (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; POLYKETIDE; POLYKETIDE SYNTHASE; MACROLIDE;

AMINO ACID SUBSTITUTION; BIOSYNTHESIS; CATALYSIS; CHROMOSOME; CROSSING OVER; ENZYME ASSAY; ENZYME STRUCTURE; ENZYME SYNTHESIS; GENE DELETION; GENE EXPRESSION; GENE MUTATION; GENETIC ENGINEERING; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; REVIEW; STRUCTURE ACTIVITY RELATION; ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; GENETICS; METABOLISM; METHODOLOGY;

GENETIC ENGINEERING; MACROLIDES; MODELS, BIOLOGICAL; POLYKETIDE SYNTHASES;

EID: 64049089208     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(09)04613-8     Document Type: Review

References (62)

1. Bedford D., Jacobsen J.R., Luo G., and Khosla C. A functional chimeric modular polyketide synthase generated via domain replacement. Chem. Biol. 3 (1996) 827-831
2. Boddy C.N., Hotta K., Tse M.L., Watts R.E., and Khosla C. Precursor-directed biosynthesis of epothilone in Escherichia coli. J. Am. Chem. Soc. 126 (2004) 7436-7437
3. Chandran S.S., Menzella H.G., Carney J.R., and Santi D. Activating hybrid modular interfaces in synthetic polyketide synthases by cassette replacement of ketosynthase domains. Chem. Biol. 13 (2006) 469-474
4. Cortes J., Wiesmann K.E., Roberts G.A., Brown M.J., Staunton J., and Leadlay P.F. Repositioning of a domain in a modular polyketide synthase to promote specific chain cleavage. Science 268 (1995) 1487-1489
5. Donadio S., and Katz L. Organization of the enzymatic domains in the multifunctional polyketide synthase involved in erythromycin formation in Saccharopolyspora erythraea. Gene 111 (1992) 51-60
6. Donadio S., McAlpine J.B., Sheldon P.J., Jackson M., and Katz L. An erythromycin analog produced by reprogramming of polyketide synthesis. Proc. Natl. Acad. Sci. USA 90 (1993) 7119-7123
7. Donadio S., Staver M.J., McAlpine J.B., Swanson S.J., and Katz L. Modular organization of genes required for complex polyketide biosynthesis. Science 252 (1991) 675-679
8. Donadio S., Staver M.J., McAlpine J.B., Swanson S.J., and Katz L. Biosynthesis of the erythromycin macrolactone and a rational approach for producing hybrid macrolides. Gene 115 (1992) 97-103
9. Fischbach M.A., and Walsh C.T. Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: Logic, machinery, and mechanisms. Chem. Rev. 106 (2006) 3468-3496
10. Goss R.J., Lanceron S.E., Wise N.J., and Moss S.J. Generating rapamycin analogues by directed biosynthesis: Starter acid substrate specificity of mono-substituted cyclohexane carboxylic acids. Org. Biomol. Chem. 4 (2006) 4071-4073
11. Haydock S.F., Aparicio J.F., Molnar I., Schwecke T., Khaw L.E., König A., Marsden A.F., Galloway I.S., Staunton J., and Leadlay P.F. Divergent sequence motifs correlated with the substrate specificity of (methyl)malonyl-CoA:acyl carrier protein transacylase domains in modular polyketide synthases. FEBS Lett. 374 (1995) 246-248
12. Heckman K.L., and Pease L.R. Gene splicing and mutagenesis by PCR-driven overlap extension. Nat. Protoc. 2 (2007) 924-932
13. Horton R.M., Ho S.N., Pullen J.K., Hunt H.D., Cai Z., and Pease L.R. Gene splicing by overlap extension. Methods Enzymol. 217 (1993) 270-279
14. Hu Z., Reid R., and Gramajo H. The leptomycin gene cluster and its heterologous expression in Streptomyces lividans. J. Antibiot. (Tokyo) 58 (2005) 625-633
15. Jacobsen J.R., Hutchinson C.R., Cane D.E., and Khosla C. Precursor-directed biosynthesis of erythromycin analogs by an engineered polyketide synthase. Science 277 (1997) 367-369
16. Jaoua S., Neff S., and Schupp T. Transfer of mobilizable plasmids to Sorangium cellulosum and evidence for their integration into the chromosome. Plasmid 28 (1992) 157-165
17. Julien B., Tian Z.Q., Reid R., and Reeves C.D. Analysis of the ambruticin and jerangolid gene clusters of Sorangium cellulosum reveals unusual mechanisms of polyketide biosynthesis. Chem. Biol. 13 (2006) 1277-1286
18. Kato Y., Bai L., Xue Q., Revill W.P., Yu T.W., and Floss H.G. Functional expression of genes involved in the biosynthesis of the novel polyketide chain extension unit, methoxymalonyl-acyl carrier protein, and engineered biosynthesis of 2-desmethyl-2-methoxy-6-deoxyerythronolide B. J. Am. Chem. Soc. 124 (2002) 5268-5269
19. Katz L., and Donadio S. Polyketide synthesis: Prospects for hybrid antibiotics. Annu. Rev. Microbiol. 47 (1993) 875-912
20. Keatinge-Clay A. Crystal structure of the erythromycin polyketide synthase dehydratase. J. Mol. Biol. 384 (2008) 941-953
21. Keatinge-Clay A.T. A tylosin ketoreductase reveals how chirality is determined in polyketides. Chem. Biol. 14 (2007) 898-908
22. Keatinge-Clay A.T., and Stroud R.M. The structure of a ketoreductase determines the organization of the beta-carbon processing enzymes of modular polyketide synthases. Structure 14 (2006) 737-748
23. Khosla C., Tang Y., Chen A.Y., Schnarr N.A., and Cane D.E. Structure and mechanism of the 6-deoxyerythronolide B synthase. Annu. Rev. Biochem. 76 (2007) 195-221
24. Kieser T., Bibb M.J., Buttner M.J., Chater K.F., and Hopwood D.A. Practical Streptomyces Genetics (2000), John Innes Foundation, Norwich, UK
25. Kim W., Lee J.S., Lee D., Cai X.F., Shin J.C., Lee K., Lee C.H., Ryu S., Paik S.G., Lee J.J., and Hong Y.S. Mutasynthesis of geldanamycin by the disruption of a gene producing starter unit: Generation of structural diversity at the benzoquinone ring. Chembiochem 8 (2007) 1491-1494
26. Kinoshita K., Williard P.G., Khosla C., and Cane D.E. Precursor-directed biosynthesis of 16-membered macrolides by the erythromycin polyketide synthase. J. Am. Chem. Soc. 123 (2001) 2495-2502
27. Kopp M., Irschik H., Gross F., Perlova O., Sandmann A., Gerth K., and Müller R. Critical variations of conjugational DNA transfer into secondary metabolite multiproducing Sorangium cellulosum strains So ce12 and So ce56: Development of a mariner-based transposon mutagenesis system. J. Biotechnol. 107 (2004) 29-40
28. Kumar P., Khosla C., and Tang Y. Manipulation and analysis of polyketide synthases. Methods Enzymol. 388 (2004) 269-293
29. Maier T., Leibundgut M., and Ban N. The crystal structure of a mammalian fatty acid synthase. Science 321 (2008) 1315-1322
30. McDaniel R., Kao C.M., Hwang S.J., and Khosla C. Engineered intermodular and intramodular polyketide synthase fusions. Chem. Biol. 4 (1997) 667-674
31. McDaniel R., Thamchaipenet A., Gustafsson C., Fu H., Betlach M., and Ashley G. Multiple genetic modifications of the erythromycin polyketide synthase to produce a library of novel "unnatural" natural products. Proc. Natl. Acad. Sci. USA 96 (1999) 1846-1851
32. Menzella H.G., Reid R., Carney J.R., Chandran S.S., Reisinger S.J., Patel K.G., Hopwood D.A., and Santi D.V. Combinatorial polyketide biosynthesis by de novo design and rearrangement of modular polyketide synthase genes. Nat. Biotechnol. 23 (2005) 1171-1176
33. Moss S.J., Martin C.J., and Wilkinson B. Loss of co-linearity by modular polyketide synthases: A mechanism for the evolution of chemical diversity. Nat. Prod. Rep. 21 (2004) 575-593
34. Mutka S.C., Carney J.R., Liu Y., and Kennedy J. Heterologous production of epothilone C and D in Escherichia coli. Biochemistry 45 (2006) 1321-1330
35. Oliynyk M., Brown M.J., Cortes J., Staunton J., and Leadlay P.F. A hybrid modular polyketide synthase obtained by domain swapping. Chem. Biol. 3 (1996) 833-839
36. Patel K., Piagentini M., Rascher A., Tian Z.Q., Buchanan G.O., Regentin R., Hu Z., Hutchinson C.R., and McDaniel R. Engineered biosynthesis of geldanamycin analogs for Hsp90 inhibition. Chem. Biol. 11 (2004) 1625-1633
37. Peiru S., Menzella H.G., Rodriguez E., Carney J., and Gramajo H. Production of the potent antibacterial polyketide erythromycin C in Escherichia coli. Appl. Environ. Microbiol. 71 (2005) 2539-2547
38. Petkovic H., Lill R.E., Sheridan R.M., Wilkinson B., McCormick E.L., McArthur H.A., Staunton J., Leadlay P.F., and Kendrew S.G. A novel erythromycin, 6-desmethyl erythromycin D, made by substituting an acyltransferase domain of the erythromycin polyketide synthase. J. Antibiot. (Tokyo) 56 (2003) 543-551
39. Reeves C.D., Chung L.M., Liu Y., Xue Q., Carney J.R., Revill W.P., and Katz L. A new substrate specificity for acyl transferase domains of the ascomycin polyketide synthase in Streptomyces hygroscopicus. J. Biol. Chem. 277 (2002) 9155-9159
40. Reeves C.D., Murli S., Ashley G.W., Piagentini M., Hutchinson C.R., and McDaniel R. Alteration of the substrate specificity of a modular polyketide synthase acyltransferase domain through site-specific mutations. Biochemistry 40 (2001) 15464-15470
41. Reeves C.D., Ward S.L., Revill W.P., Suzuki H., Marcus M., Petrakovsky O.V., Marquez S., Fu H., Dong S.D., and Katz L. Production of hybrid 16-membered macrolides by expressing combinations of polyketide synthase genes in engineered Streptomyces fradiae hosts. Chem. Biol. 11 (2004) 1465-1472
42. Reid R., Piagentini M., Rodriguez E., Ashley G., Viswanathan N., Carney J., Santi D.V., Hutchinson C.R., and McDaniel R. A model of structure and catalysis for ketoreductase domains in modular polyketide synthases. Biochemistry 42 (2003) 72-79
43. Revill W.P., Voda J., Reeves C.R., Chung L., Schirmer A., Ashley G., Carney J.R., Fardis M., Carreras C.W., Zhou Y., Feng L., Tucker E., et al. Genetically engineered analogs of ascomycin for nerve regeneration. J. Pharmacol. Exp. Ther. 302 (2002) 1278-1285
44. Rodriguez E., Hu Z., Ou S., Volchegursky Y., Hutchinson C.R., and McDaniel R. Rapid engineering of polyketide overproduction by gene transfer to industrially optimized strains. J. Ind. Microbiol. Biotechnol. 30 (2003) 480-488
45. Rodriguez E., Ward S., Fu H., Revill W.P., McDaniel R., and Katz L. Engineered biosynthesis of 16-membered macrolides that require methoxymalonyl-ACP precursors in Streptomyces fradiae. Appl. Microbiol. Biotechnol. 66 (2004) 85-91
46. Ruan X., Pereda A., Stassi D.L., Zeidner D., Summers R.G., Jackson M., Shivakumar A., Kakavas S., Staver M.J., Donadio S., and Katz L. Acyltransferase domain substitutions in erythromycin polyketide synthase yield novel erythromycin derivatives. J. Bacteriol. 179 (1997) 6416-6425
47. Smith S., and Tsai S.C. The type I fatty acid and polyketide synthases: A tale of two megasynthases. Nat. Prod. Rep. 24 (2007) 1041-1072
48. Stassi D.L., Kakavas S.J., Reynolds K.A., Gunawardana G., Swanson S., Zeidner D., Jackson M., Liu H., Buko A., and Katz L. Ethyl-substituted erythromycin derivatives produced by directed metabolic engineering. Proc. Natl. Acad. Sci. USA 95 (1998) 7305-7309
49. Tang L., Chung L., Carney J.R., Starks C.M., Licari P., and Katz L. Generation of new epothilones by genetic engineering of a polyketide synthase in Myxococcus xanthus. J. Antibiot. (Tokyo) 58 (2005) 178-184
50. Tang L., Ward S., Chung L., Carney J.R., Li Y., Reid R., and Katz L. Elucidating the mechanism of cis double bond formation in epothilone biosynthesis. J. Am. Chem. Soc. 126 (2004) 46-47
51. Tang Y., Chen A.Y., Kim C.Y., Cane D.E., and Khosla C. Structural and mechanistic analysis of protein interactions in module 3 of the 6-deoxyerythronolide B synthase. Chem. Biol. 14 (2007) 931-943
52. Tang Y., Kim C.Y., Mathews II, Cane D.E., and Khosla C. The 2.7-Angstrom crystal structure of a 194-kDa homodimeric fragment of the 6-deoxyerythronolide B synthase. Proc. Natl. Acad. Sci. USA 103 (2006) 11124-11129
53. Van Lanen S.G., and Shen B. Advances in polyketide synthase structure and function. Curr. Opin. Drug Discov. Devel. 11 (2008) 186-195
54. Vetcher L., Tian Z.Q., McDaniel R., Rascher A., Revill W.P., Hutchinson C.R., and Hu Z. Rapid engineering of the geldanamycin biosynthesis pathway by Red/ET recombination and gene complementation. Appl. Environ. Microbiol. 71 (2005) 1829-1835
55. Walsh C.T. The chemical versatility of natural-product assembly lines. Acc. Chem. Res. 41 (2008) 4-10
56. Ward S.L., Desai R.P., Hu Z., Gramajo H., and Katz L. Precursor-directed biosynthesis of 6-deoxyerythronolide B analogues is improved by removal of the initial catalytic sites of the polyketide synthase. J. Ind. Microbiol. Biotechnol. 34 (2007) 9-15
57. Weissman K.J. Mutasynthesis - uniting chemistry and genetics for drug discovery. Trends Biotechnol. 25 (2007) 139-142
58. Weissman K.J., and Leadlay P.F. Combinatorial biosynthesis of reduced polyketides. Nat. Rev. Microbiol. 3 (2005) 925-936
59. Weissman K.J., and Muller R. Protein-protein interactions in multienzyme megasynthetases. Chembiochem 9 (2008) 826-848
60. Xia Z.J., Wang J., Hu W., Liu H., Gao X.Z., Wu Z.H., Zhang P.Y., and Li Y.Z. Improving conjugation efficacy of Sorangium cellulosum by the addition of dual selection antibiotics. J. Ind. Microbiol. Biotechnol. 35 (2008) 1157-1163
61. Xue Q., Ashley G., Hutchinson C.R., and Santi D.V. A multiplasmid approach to preparing large libraries of polyketides. Proc. Natl. Acad. Sci. USA 96 (1999) 11740-11745
62. Ziermann R., and Betlach M.C. Recombinant polyketide synthesis in Streptomyces: engineering of improved host strains. Biotechniques 26 (1999) 106-110