Home LiteratureArticle Details
PMID: 18250311 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

Evolution of polyketide synthases in bacteria.

Ridley CP, Lee HY, Khosla C

Abstract

The emergence of resistant strains of human pathogens to current antibiotics, along with the demonstrated ability of polyketides as antimicrobial agents, provides strong motivation for understanding how polyketide antibiotics have evolved and diversified in nature. Insights into how bacterial polyketide synthases (PKSs) acquire new metabolic capabilities can guide future laboratory efforts in generating the next generation of polyketide antibiotics. Here, we examine phylogenetic and structural evidence to glean answers to two general questions regarding PKS evolution. How did the exceptionally diverse chemistry of present-day PKSs evolve? And what are the take-home messages for the biosynthetic engineer?

MeSH Terms
Bacteria/enzymology Base Sequence Evolution, Molecular Gene Transfer, Horizontal Macrolides/chemistry Molecular Sequence Data Multigene Family Phylogeny Polyketide Synthases/chemistry,genetics Protein Structure, Secondary Protein Structure, Tertiary Recombination, Genetic
Chemicals
Macrolides Polyketide Synthases
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Ridley Christian P
Departments of Chemistry, Chemical Engineering, and Biochemistry, Stanford University, Stanford, CA 94305, USA.
Lee Ho Young
Khosla Chaitan
References (49)
49 references, click to expand
  1. Genetic Contributions to Understanding Polyketide Synthases.
    Chem Rev. 1997 Nov 10;97(7):2465-2498 PMID: 11851466
  2. GenBank.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D21-5 PMID: 17202161
  3. The chalcone synthase superfamily of type III polyketide synthases.
    Nat Prod Rep. 2003 Feb;20(1):79-110 PMID: 12636085
  4. Pathogenic fungus harbours endosymbiotic bacteria for toxin production.
    Nature. 2005 Oct 6;437(7060):884-8 PMID: 16208371
  5. A gene cluster encoding resistomycin biosynthesis in Streptomyces resistomycificus; exploring polyketide cyclization beyond linear and angucyclic patterns.
    J Am Chem Soc. 2004 Mar 3;126(8):2298-9 PMID: 14982421
  6. The 2.7-Angstrom crystal structure of a 194-kDa homodimeric fragment of the 6-deoxyerythronolide B synthase.
    Proc Natl Acad Sci U S A. 2006 Jul 25;103(30):11124-9 PMID: 16844787
  7. Crystal structure of the priming beta-ketosynthase from the R1128 polyketide biosynthetic pathway.
    Structure. 2002 Nov;10(11):1559-68 PMID: 12429097
  8. MrBayes 3: Bayesian phylogenetic inference under mixed models.
    Bioinformatics. 2003 Aug 12;19(12):1572-4 PMID: 12912839
  9. The complete gene cluster of the antitumor agent gilvocarcin V and its implication for the biosynthesis of the gilvocarcins.
    J Am Chem Soc. 2003 Jul 2;125(26):7818-9 PMID: 12822997
  10. Type I polyketide synthase requiring a discrete acyltransferase for polyketide biosynthesis.
    Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3149-54 PMID: 12598647
  11. Molecular analysis of the benastatin biosynthetic pathway and genetic engineering of altered fatty acid-polyketide hybrids.
    J Am Chem Soc. 2007 May 9;129(18):6022-30 PMID: 17439117
  12. Ablation of the otcC gene encoding a post-polyketide hydroxylase from the oxytetracyline biosynthetic pathway in Streptomyces rimosus results in novel polyketides with altered chain length.
    J Biol Chem. 2005 Nov 11;280(45):37455-60 PMID: 16148009
  13. The enzymology of combinatorial biosynthesis.
    Crit Rev Biotechnol. 2003;23(2):95-147 PMID: 12889743
  14. Characterization of the biosynthetic gene cluster for the antifungal polyketide soraphen A from Sorangium cellulosum So ce26.
    Gene. 2002 Feb 20;285(1-2):257-67 PMID: 12039053
  15. The acyltransferase homologue from the initiation module of the R1128 polyketide synthase is an acyl-ACP thioesterase that edits acetyl primer units.
    Biochemistry. 2004 Jul 27;43(29):9546-55 PMID: 15260498
  16. An unusually large multifunctional polypeptide in the erythromycin-producing polyketide synthase of Saccharopolyspora erythraea.
    Nature. 1990 Nov 8;348(6297):176-8 PMID: 2234082
  17. Type II polyketide synthases: gaining a deeper insight into enzymatic teamwork.
    Nat Prod Rep. 2007 Feb;24(1):162-90 PMID: 17268612
  18. A Type II polyketide synthase from the gram-negative Bacterium Stigmatella aurantiaca is involved in Aurachin alkaloid biosynthesis.
    Angew Chem Int Ed Engl. 2007;46(15):2712-6 PMID: 17335090
  19. Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes.
    Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15670-5 PMID: 14676319
  20. Biosynthesis of the antitumor agent chartreusin involves the oxidative rearrangement of an anthracyclic polyketide.
    Chem Biol. 2005 May;12(5):579-88 PMID: 15911378
  21. Assembly-line enzymology for polyketide and nonribosomal Peptide antibiotics: logic, machinery, and mechanisms.
    Chem Rev. 2006 Aug;106(8):3468-96 PMID: 16895337
  22. An antibiotic factory caught in action.
    Nat Struct Mol Biol. 2004 Sep;11(9):888-93 PMID: 15286722
  23. Rational design of aromatic polyketide natural products by recombinant assembly of enzymatic subunits.
    Nature. 1995 Jun 15;375(6532):549-54 PMID: 7791871
  24. Evolutionary implications of bacterial polyketide synthases.
    Mol Biol Evol. 2005 Oct;22(10):2027-39 PMID: 15958783
  25. Mycobacterium ulcerans toxic macrolide, mycolactone modulates the host immune response and cellular location of M. ulcerans in vitro and in vivo.
    Cell Microbiol. 2005 Sep;7(9):1295-304 PMID: 16098217
  26. Priming type II polyketide synthases via a type II nonribosomal peptide synthetase mechanism.
    J Am Chem Soc. 2006 Feb 8;128(5):1428-9 PMID: 16448095
  27. Anticoccidial activity of frenolicin B and its derivatives.
    J Antibiot (Tokyo). 1985 Oct;38(10):1447-8 PMID: 4066499
  28. Modular organization of genes required for complex polyketide biosynthesis.
    Science. 1991 May 3;252(5006):675-9 PMID: 2024119
  29. Identification of the putative bryostatin polyketide synthase gene cluster from "Candidatus Endobugula sertula", the uncultivated microbial symbiont of the marine bryozoan Bugula neritina.
    J Nat Prod. 2007 Jan;70(1):67-74 PMID: 17253852
  30. Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences.
    Mol Biol Evol. 2005 Mar;22(3):792-802 PMID: 15590907
  31. Cloning and characterization of Streptomyces galilaeus aclacinomycins polyketide synthase (PKS) cluster.
    Gene. 2002 Jun 26;293(1-2):115-22 PMID: 12137949
  32. The FK520 gene cluster of Streptomyces hygroscopicus var. ascomyceticus (ATCC 14891) contains genes for biosynthesis of unusual polyketide extender units.
    Gene. 2000 Jun 13;251(1):81-90 PMID: 10863099
  33. The biosynthetic genes for disorazoles, potent cytotoxic compounds that disrupt microtubule formation.
    Gene. 2005 Oct 10;359:91-8 PMID: 16084035
  34. Cloning, nucleotide sequence, and heterologous expression of the biosynthetic gene cluster for R1128, a non-steroidal estrogen receptor antagonist. Insights into an unusual priming mechanism.
    J Biol Chem. 2000 Oct 27;275(43):33443-8 PMID: 10931852
  35. Polyketide chain length control by chain length factor.
    J Am Chem Soc. 2003 Oct 22;125(42):12708-9 PMID: 14558809
  36. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.
    Mol Biol Evol. 2007 Aug;24(8):1596-9 PMID: 17488738
  37. Cloning, sequencing and analysis of the enterocin biosynthesis gene cluster from the marine isolate 'Streptomyces maritimus': evidence for the derailment of an aromatic polyketide synthase.
    Chem Biol. 2000 Dec;7(12):943-55 PMID: 11137817
  38. A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles.
    Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14002-7 PMID: 12381784
  39. A role of the third complementarity-determining region in the affinity maturation of an antibody.
    J Biol Chem. 2001 Jul 20;276(29):27622-8 PMID: 11375987
  40. Cloning, sequencing and heterologous expression of the medermycin biosynthetic gene cluster of Streptomyces sp. AM-7161: towards comparative analysis of the benzoisochromanequinone gene clusters.
    Microbiology (Reading). 2003 Jul;149(Pt 7):1633-1645 PMID: 12855716
  41. Engineered biosynthesis of aklanonic acid analogues.
    J Am Chem Soc. 2005 Sep 7;127(35):12254-62 PMID: 16131203
  42. Molecular evolution of aromatic polyketides and comparative sequence analysis of polyketide ketosynthase and 16S ribosomal DNA genes from various streptomyces species.
    Appl Environ Microbiol. 2002 Sep;68(9):4472-9 PMID: 12200302
  43. The Streptomyces peucetius dpsC gene determines the choice of starter unit in biosynthesis of the daunorubicin polyketide.
    J Bacteriol. 1999 Aug;181(15):4690-5 PMID: 10419974
  44. Organization of the biosynthetic gene cluster for the polyketide anthelmintic macrolide avermectin in Streptomyces avermitilis.
    Proc Natl Acad Sci U S A. 1999 Aug 17;96(17):9509-14 PMID: 10449723
  45. The biosynthetic gene cluster for the polyketide immunosuppressant rapamycin.
    Proc Natl Acad Sci U S A. 1995 Aug 15;92(17):7839-43 PMID: 7644502
  46. Engineered biosynthesis of a novel amidated polyketide, using the malonamyl-specific initiation module from the oxytetracycline polyketide synthase.
    Appl Environ Microbiol. 2006 Apr;72(4):2573-80 PMID: 16597959
  47. TreeView: an application to display phylogenetic trees on personal computers.
    Comput Appl Biosci. 1996 Aug;12(4):357-8 PMID: 8902363
  48. Giant plasmid-encoded polyketide synthases produce the macrolide toxin of Mycobacterium ulcerans.
    Proc Natl Acad Sci U S A. 2004 Feb 3;101(5):1345-9 PMID: 14736915
  49. Dissecting the role of acyltransferase domains of modular polyketide synthases in the choice and stereochemical fate of extender units.
    Biochemistry. 1999 Feb 2;38(5):1643-51 PMID: 9931032
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
1091-6490
Published
2008-03-25
Epub
2008-00-04
Pages
4595-600
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC2290765
Subset
IM
Grants
NCI NIH HHS · R01 CA066736 · United States
NCI NIH HHS · R01 CA077248 · United States
NCI NIH HHS · CA 66736 · United States
NCI NIH HHS · CA 77248 · United States
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com