Polyketide biosynthesis: understanding and exploiting modularity

Polyketide–based pharmaceuticals are some of our most important medicines. They are constructed in micro–organisms (typically bacteria and fungi) by gigantic enzyme catalysts called polyketide synthases (PKSs). The organization of PKSs into molecular assembly lines makes them particularly appealing targets for genetic engineering because, in principle, an alteration in the enzyme organization might translate into a predictable change in polyketide structure. Excitingly, this has been shown repeatedly to work in practice, but the efficiency of the engineered PKSs is frequently too low to be useful for large–scale drug synthesis. To reach this goal, researchers need a deeper understanding of the structure and function of these proteins, which are among the most complex in nature. This review highlights some recent experiments which are providing key information about the molecular organization, mechanism and orchestration of these magnificent catalysts, and opening up fresh prospects of truly combinatorial biosynthesis of novel polyketides as leads in drug discovery.

[1]  P. Leadlay,et al.  Identification of DEBS 1, DEBS 2 and DEBS 3, the multienzyme polypeptides of the erythromycin‐producing polyketide synthase from Saccharopolyspora erythraea , 1992, FEBS letters.

[2]  Bernard R Brooks,et al.  Molecular architecture and mechanism of an icosahedral pyruvate dehydrogenase complex: a multifunctional catalytic machine , 2002, The EMBO journal.

[3]  C. Starks,et al.  Isolation and characterization of new epothilone analogues from recombinant Myxococcus xanthus fermentations. , 2003 .

[4]  J R Jacobsen,et al.  Precursor-directed biosynthesis of erythromycin analogs by an engineered polyketide synthase. , 1997, Science.

[5]  Christine J. Martin,et al.  Heterologous expression in Saccharopolyspora erythraea of a pentaketide synthase derived from the spinosyn polyketide synthase. , 2003, Organic & biomolecular chemistry.

[6]  M. Staver,et al.  Cloning of genes involved in erythromycin biosynthesis from Saccharopolyspora erythraea using a novel actinomycete-Escherichia coli cosmid. , 1990, Gene.

[7]  R McDaniel,et al.  Construction of desosamine containing polyketide libraries using a glycosyltransferase with broad substrate specificity. , 2001, Chemistry & biology.

[8]  J R Jacobsen,et al.  Tolerance and specificity of polyketide synthases. , 1999, Annual review of biochemistry.

[9]  Sarojini Adusumilli,et al.  Giant plasmid-encoded polyketide synthases produce the macrolide toxin of Mycobacterium ulcerans. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[10]  S. Gaisser,et al.  Sugaring the pill by design , 1998, Nature Biotechnology.

[11]  R. Lill,et al.  New erythromycin derivatives from Saccharopolyspora erythraea using sugar O‐methyltransferases from the spinosyn biosynthetic gene cluster , 2001, Molecular microbiology.

[12]  J. Thornton,et al.  Structural characterisation and functional significance of transient protein-protein interactions. , 2003, Journal of molecular biology.

[13]  J. Staunton,et al.  Active-site residue, domain and module swaps in modular polyketide synthases , 2003, Journal of Industrial Microbiology and Biotechnology.

[14]  D. Cane,et al.  Quantitative analysis of loading and extender acyltransferases of modular polyketide synthases. , 2003, Biochemistry.

[15]  J B McAlpine,et al.  Modular organization of genes required for complex polyketide biosynthesis. , 1991, Science.

[16]  J. Bu’lock,et al.  Novel avermectins produced by mutational biosynthesis. , 1991, The Journal of antibiotics.

[17]  Sabine Gaisser,et al.  Direct production of ivermectin-like drugs after domain exchange in the avermectin polyketide synthase of Streptomyces avermitilis ATCC31272. , 2003, Organic & biomolecular chemistry.

[18]  P. Leadlay,et al.  Repositioning of a domain in a modular polyketide synthase to promote specific chain cleavage. , 1995, Science.

[19]  W. Gerwick,et al.  The barbamide biosynthetic gene cluster: a novel marine cyanobacterial system of mixed polyketide synthase (PKS)-non-ribosomal peptide synthetase (NRPS) origin involving an unusual trichloroleucyl starter unit. , 2002, Gene.

[20]  Kenji Watanabe,et al.  Understanding Substrate Specificity of Polyketide Synthase Modules by Generating Hybrid Multimodular Synthases* , 2003, Journal of Biological Chemistry.

[21]  P. Leadlay,et al.  Evaluating precursor-directed biosynthesis towards novel erythromycins through in vitro studies on a bimodular polyketide synthase. , 1998, Chemistry & biology.

[22]  Gitanjali Yadav,et al.  NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases , 2004, Nucleic Acids Res..

[23]  C R Hutchinson,et al.  Alteration of the substrate specificity of a modular polyketide synthase acyltransferase domain through site-specific mutations. , 2001, Biochemistry.

[24]  P. Leadlay,et al.  A hybrid modular polyketide synthase obtained by domain swapping. , 1996, Chemistry & biology.

[25]  L. Miercke,et al.  Crystal structure of the macrocycle-forming thioesterase domain of the erythromycin polyketide synthase: Versatility from a unique substrate channel , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[26]  P. Leadlay,et al.  An unusually large multifunctional polypeptide in the erythromycin-producing polyketide synthase of Saccharopolyspora erythraea , 1990, Nature.

[27]  William H Gerwick,et al.  Structure and biosynthesis of the jamaicamides, new mixed polyketide-peptide neurotoxins from the marine cyanobacterium Lyngbya majuscula. , 2004, Chemistry & biology.

[28]  James Staunton,et al.  Evidence for a double-helical structure for modular polyketide synthases , 1996, Nature Structural Biology.

[29]  Kira J Weissman,et al.  The structure of docking domains in modular polyketide synthases. , 2003, Chemistry & biology.

[30]  Christine J. Martin,et al.  Skipping in a hybrid polyketide synthase. Evidence for ACP-to-ACP chain transfer. , 2002, Chemistry & biology.

[31]  C M Kao,et al.  Engineered intermodular and intramodular polyketide synthase fusions. , 1997, Chemistry & biology.

[32]  D. Sherman,et al.  Biosynthesis of desosamine: construction of a new macrolide carrying a genetically designed sugar moiety. , 1999, Organic letters.

[33]  D. Cane,et al.  Substrate specificity of the loading didomain of the erythromycin polyketide synthase. , 2000, Biochemistry.

[34]  Jörn Piel,et al.  A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[35]  K. Hiratsu,et al.  The large linear plasmid pSLA2‐L of Streptomyces rochei has an unusually condensed gene organization for secondary metabolism , 2003, Molecular microbiology.

[36]  R. Müller,et al.  Multiple hybrid polyketide synthase/non-ribosomal peptide synthetase gene clusters in the myxobacterium Stigmatella aurantiaca. , 2001, Gene.

[37]  D. Cane,et al.  Assessing the balance between protein-protein interactions and enzyme-substrate interactions in the channeling of intermediates between polyketide synthase modules. , 2001, Journal of the American Chemical Society.

[38]  D. Cane,et al.  Selective protein-protein interactions direct channeling of intermediates between polyketide synthase modules. , 2001, Biochemistry.

[39]  R. Müller,et al.  Myxobacteria: proficient producers of novel natural products with various biological activities--past and future biotechnological aspects with the focus on the genus Sorangium. , 2003, Journal of biotechnology.

[40]  Gitanjali Yadav,et al.  SEARCHPKS: a program for detection and analysis of polyketide synthase domains , 2003, Nucleic Acids Res..

[41]  James Staunton,et al.  Analysis of the biosynthetic gene cluster for the polyether antibiotic monensin in Streptomyces cinnamonensis and evidence for the role of monB and monC genes in oxidative cyclization , 2003, Molecular microbiology.

[42]  Christopher M Thomas,et al.  Characterization of the mupirocin biosynthesis gene cluster from Pseudomonas fluorescens NCIMB 10586. , 2003, Chemistry & biology.

[43]  J. Staunton,et al.  Polyketide biosynthesis: a millennium review. , 2001, Natural product reports.

[44]  C. Méndez,et al.  Generation of hybrid elloramycin analogs by combinatorial biosynthesis using genes from anthracycline-type and macrolide biosynthetic pathways. , 2000, Journal of molecular microbiology and biotechnology.

[45]  J. Holton,et al.  High-resolution structure of the HNF-1alpha dimerization domain. , 2000, Biochemistry.

[46]  R. Stroud,et al.  Insights into channel architecture and substrate specificity from crystal structures of two macrocycle-forming thioesterases of modular polyketide synthases. , 2002, Biochemistry.

[47]  J. N. Mark Glover,et al.  Crystal structure of the heterodimeric bZIP transcription factor c-Fos–c-Jun bound to DNA , 1995, Nature.

[48]  C. Khosla,et al.  Role of linkers in communication between protein modules. , 2000, Current opinion in chemical biology.

[49]  Gitanjali Yadav,et al.  Computational approach for prediction of domain organization and substrate specificity of modular polyketide synthases. , 2003, Journal of molecular biology.

[50]  D. Cane,et al.  Precursor-directed biosynthesis: biochemical basis of the remarkable selectivity of the erythromycin polyketide synthase toward unsaturated triketides. , 2002, Chemistry & biology.

[51]  R. Perham,et al.  Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. , 2000, Annual review of biochemistry.

[52]  D. Cane,et al.  Dissecting and exploiting intermodular communication in polyketide synthases. , 1999, Science.

[53]  Brian O. Bachmann,et al.  A genomics-guided approach for discovering and expressing cryptic metabolic pathways , 2003, Nature Biotechnology.

[54]  P. Leadlay,et al.  Intermediates released from a polyether-producing polyketide synthase provide insight into the mechanism of oxidative cyclization. , 2003, Angewandte Chemie.

[55]  Hui Hong,et al.  Identification of a Phosphopantetheinyl Transferase for Erythromycin Biosynthesis in Saccharopolyspora erythraea. , 2004 .

[56]  D. Macneil,et al.  Insights about the biosynthesis of the avermectin deoxysugar L-oleandrose through heterologous expression of Streptomyces avermitilis deoxysugar genes in Streptomyces lividans. , 2001, Chemistry & biology.

[57]  Chaitan Khosla,et al.  Quantitative analysis of the relative contributions of donor acyl carrier proteins, acceptor ketosynthases, and linker regions to intermodular transfer of intermediates in hybrid polyketide synthases. , 2002, Biochemistry.

[58]  P. Leadlay,et al.  Divergent sequence motifs correlated with the substrate specificity of (methyl)malonyl‐CoA:acyl carrier protein transacylase domains in modular polyketide synthases , 1995, FEBS letters.

[59]  P. Leadlay,et al.  Knowledge-based design of bimodular and trimodular polyketide synthases based on domain and module swaps: a route to simple statin analogues. , 1999, Chemistry & biology.

[60]  Daniel W. Udwary,et al.  A method for prediction of the locations of linker regions within large multifunctional proteins, and application to a type I polyketide synthase. , 2002, Journal of molecular biology.

[61]  D. Hopwood,et al.  Nucleotide sequence and deduced functions of a set of cotranscribed genes of Streptomyces coelicolor A3(2) including the polyketide synthase for the antibiotic actinorhodin. , 1992, The Journal of biological chemistry.

[62]  P. Leadlay,et al.  Limited proteolysis and active-site studies of the first multienzyme component of the erythromycin-producing polyketide synthase. , 1994, Journal of Biological Chemistry.

[63]  R J Heath,et al.  Identification and Analysis of the Acyl Carrier Protein (ACP) Docking Site on β-Ketoacyl-ACP Synthase III* , 2001, The Journal of Biological Chemistry.

[64]  H. Liesegang,et al.  Structural and Functional Characterization of Gene Clusters Directing Nonribosomal Synthesis of Bioactive Cyclic Lipopeptides in Bacillus amyloliquefaciens Strain FZB42 , 2004, Journal of bacteriology.

[65]  B. Shen,et al.  Type I polyketide synthase requiring a discrete acyltransferase for polyketide biosynthesis , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[66]  J R Jacobsen,et al.  A functional chimeric modular polyketide synthase generated via domain replacement. , 1996, Chemistry & biology.

[67]  P. Leadlay,et al.  Evidence from engineered gene fusions for the repeated use of a module in a modular polyketide synthase. , 2003, Chemical communications.

[68]  D. Cane,et al.  Mechanism and specificity of the terminal thioesterase domain from the erythromycin polyketide synthase. , 1999, Chemistry & biology.

[69]  Camilla M. Kao,et al.  Manipulation of macrolide ring size by directed mutagenesis of a modular polyketide synthase , 1995 .

[70]  P. Leadlay,et al.  6-Deoxyerythronolide-B synthase 2 from Saccharopolyspora erythraea. Cloning of the structural gene, sequence analysis and inferred domain structure of the multifunctional enzyme. , 1992, European journal of biochemistry.

[71]  P. Leadlay,et al.  Stereospecific acyl transfers on the erythromycin-producing polyketide synthase. , 1994, Science.

[72]  D. Hopwood,et al.  Molecular cloning of the whole biosynthetic pathway of a Streptomyces antibiotic and its expression in a heterologous host , 1984, Nature.

[73]  A. Maureen Rouhi,et al.  Rediscovering natural products , 2003 .

[74]  David H Sherman,et al.  An unexpected interaction between the modular polyketide synthases, erythromycin DEBS1 and pikromycin PikAIV, leads to efficient triketide lactone synthesis. , 2002, Biochemistry.

[75]  J. Rohr,et al.  Identification of a sugar flexible glycosyltransferase from Streptomyces olivaceus, the producer of the antitumor polyketide elloramycin. , 2001, Chemistry & biology.