Steps towards the synthetic biology of polyketide biosynthesis

Aguirrezabalaga, 2000, Identification and expression of genes involved in biosynthesis of L-oleandrose and its intermediate L-olivose in the oleandomycin producer Streptomyces antibioticus, Antimicrob Agents Chemother, 44, 1266, 10.1128/AAC.44.5.1266-1275.2000

Alper, 2005, Tuning genetic control through promoter engineering, P Natl Acad Sci USA, 102, 12678, 10.1073/pnas.0504604102

Anand, 2012, Modeling holo-ACP:DH and holo-ACP:KR complexes of modular polyketide synthases: a docking and molecular dynamics study, BMC Struct Biol, 12, 21, 10.1186/1472-6807-12-10

Blin, 2013, antiSMASH 2.0-a versatile platform for genome mining of secondary metabolite producers, Nucleic Acids Res, 41, W204, 10.1093/nar/gkt449

Bonnett, 2011, Acyl-CoA subunit selectivity in the pikromycin polyketide synthase PikAIV: steady-state kinetics and active-site occupancy analysis by FTICR-MS, Chem Biol, 18, 1075, 10.1016/j.chembiol.2011.07.016

Breaker, 2008, Gene regulation by riboswitches, FASEB J, 22, 1, 10.1096/fasebj.22.1_supplement.97.3

Caffrey, 2003, Conserved amino acid residues correlating with ketoreductase stereospecificity in modular polyketide synthases, ChemBioChem, 4, 654, 10.1002/cbic.200300581

Campbell, 2010, Biosynthesis of lovastatin and related metabolites formed by fungal iterative PKS enzymes, Biopolymers, 93, 755, 10.1002/bip.21428

Chan, 2006, Hydroxymalonyl-acyl carrier protein (ACP) and aminomalonyl-ACP are two additional type I polyketide synthase extender units, P Natl Acad Sci USA, 103, 14349, 10.1073/pnas.0603748103

Chen, 2006, Structural and functional characterization of three polyketide synthase gene clusters in Bacillus amyloliquefaciens FZB 42, J Bacteriol, 188, 4024, 10.1128/JB.00052-06

Chen, 2007, Structure-based dissociation of a type I polyketide synthase module, Chem Biol, 14, 784, 10.1016/j.chembiol.2007.05.015

Donadio, 1991, Modular organization of genes required for complex polyketide biosynthesis, Science, 252, 675, 10.1126/science.2024119

Donadio, 1993, An erythromycin analog produced by reprogramming of polyketide synthesis, P Natl Acad Sci USA, 90, 7119, 10.1073/pnas.90.15.7119

Donadio, 2005, Comparative analysis and insights into the evolution of gene clusters for glycopeptide antibiotic biosynthesis, Mol Genet Genomics, 274, 40, 10.1007/s00438-005-1156-3

Doumith, 1999, Interspecies complementation in Saccharopolyspora erythraea: elucidation of the function of oleP1, oleG1 and oleG2 from the oleandomycin biosynthetic gene cluster of Streptomyces antibioticus and generation of new erythromycin derivatives, Mol Microbiol, 34, 1039, 10.1046/j.1365-2958.1999.01666.x

Eustaquio, 2009, Biosynthesis of the salinosporamide A polyketide synthase substrate chloroethylmalonyl-coenzyme A from S-adenosyl-L-methionine, P Natl Acad Sci USA, 106, 12295, 10.1073/pnas.0901237106

Gaisser, 2000, A defined system for hybrid macrolide biosynthesis in Saccharopolyspora erythraea, Mol Microbiol, 36, 391, 10.1046/j.1365-2958.2000.01856.x

Georg, 2011, cis-Antisense RNA, Another Level of Gene Regulation in Bacteria, Microbiol Mol Biol Rev, 75, 286, 10.1128/MMBR.00032-10

Goranovic, 2012, FK506 biosynthesis is regulated by two positive regulatory elements in Streptomyces tsukubaensis, BMC Microbiol, 12, 238, 10.1186/1471-2180-12-238

Guell, 2011, Bacterial transcriptomics: what is beyond the RNA horiz-ome?, Nat Rev Microbiol, 9, 658, 10.1038/nrmicro2620

Han, 2011, Development of a Streptomyces venezuelae-based combinatorial biosynthetic system for the production of glycosylated derivatives of doxorubicin and its biosynthetic intermediates, Appl Environ Microbiol, 77, 4912, 10.1128/AEM.02527-10

Hertweck, 2009, The biosynthetic logic of polyketide diversity, Angew Chem Int Ed Engl, 48, 4688, 10.1002/anie.200806121

Hurteloup, 1986, Clinical studies with new anthracyclines epirubicin, idarubicin, esorubicin, Drugs Exp Clin Res, 12, 233

Ishihama, 2010, Prokaryotic genome regulation: multifactor promoters, multitarget regulators and hierarchic networks, FEMS Microbiol Rev, 34, 628, 10.1111/j.1574-6976.2010.00227.x

Jacobsen, 1997, Precursor-directed biosynthesis of erythromycin analogs by an engineered polyketide synthase, Science, 277, 367, 10.1126/science.277.5324.367

Kantola, 2003, Expanding the scope of aromatic polyketides by combinatorial biosynthesis, Comb Chem High Throughput Screening, 6, 501, 10.2174/138620703106298680

Kao, 1994, Engineered biosynthesis of a triketide lactone from an incomplete modular polyketide synthase, J Am Chem Soc, 116, 11612, 10.1021/ja00104a069

Kao, 1995, Manipulation of macrolide ring size by directed mutagenesis of a modular polyketide synthase, J Am Chem Soc, 117, 9105, 10.1021/ja00140a043

Kapur, 2012, Reprogramming a module of the 6-deoxyerythronolide B synthase for iterative chain elongation, P Natl Acad Sci USA, 109, 4110, 10.1073/pnas.1118734109

Kennedy, 2008, Mutasynthesis, chemobiosynthesis, and back to semi-synthesis: combining synthetic chemistry and biosynthetic engineering for diversifying natural products, Nat Prod Rep, 25, 25, 10.1039/B707678A

Knight TF 2003 Idempotent vector design for standard assembly of BioBricks MIT Synthetic Biology Working Group Technical Reports

Koskinen, 2005, Polyketide stereotetrads in natural products, Chem Soc Rev, 34, 677, 10.1039/b417466f

Lai, 2006, Carrier protein structure and recognition in polyketide and nonribosomal peptide biosynthesis, Biochemistry, 45, 14869, 10.1021/bi061979p

Lesnik, 2009, Regulatory elements in tetracycline-encoding gene clusters: the otcG gene positively regulates the production of oxytetracycline in Streptomyces rimosus, Food Technol Biotechnol, 47, 323

Liu, 2009, Biosynthesis of salinosporamides from alpha, beta-unsaturated fatty acids: implications for extending polyketide synthase diversity, J Am Chem Soc, 131, 10376, 10.1021/ja9042824

Lockless, 2009, Traceless protein splicing utilizing evolved split inteins, P Natl Acad Sci USA, 106, 10999, 10.1073/pnas.0902964106

Long, 2002, Engineering specificity of starter unit selection by the erythromycin-producing polyketide synthase, Mol Microbiol, 43, 1215, 10.1046/j.1365-2958.2002.02815.x

Ma, 2007, Biochemical characterization of the minimal polyketide synthase domains in the lovastatin nonaketide synthase LovB, FEBS J, 274, 2854, 10.1111/j.1742-4658.2007.05818.x

Masschelein, 2013, A PKS/NRPS/FAS hybrid gene cluster from Serratia plymuthica RVH1 encoding the biosynthesis of three broad spectrum, zeamine-related antibiotics, PLoS One, 8, 1, 10.1371/journal.pone.0054143

McDaniel, 1997, Gain-of-function mutagenesis of a modular polyketide synthase, J Am Chem Soc, 119, 4309, 10.1021/ja9702531

McDaniel, 1999, Multiple genetic modifications of the erythromycin polyketide synthase to produce a library of novel “unnatural” natural products, P Natl Acad Sci USA, 96, 1846, 10.1073/pnas.96.5.1846

Medema, 2011a, The future of industrial antibiotic production: from random mutagenesis to synthetic biology, Bioeng Bugs, 2, 230, 10.4161/bbug.2.4.16114

Medema, 2011b, antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences, Nucleic Acids Res, 39, W339, 10.1093/nar/gkr466

Meier, 2009, The chemical biology of modular biosynthetic enzymes, Chem Soc Rev, 38, 2012, 10.1039/b805115c

Minotti, 2004, Anthracyclines: molecular advances and pharmacologic developments in antitumor activity and cardiotoxicity, Pharmacol Rev, 56, 185, 10.1124/pr.56.2.6

Mironov, 2004, Biogenesis and regulation of biosynthesis of erythromycins in Saccharopolyspora erythraea, Appl Biochem Microbiol, 40, 531, 10.1023/B:ABIM.0000046985.66328.7a

Mo, 2011, Biosynthesis of the allylmalonyl-CoA extender unit for the FK506 polyketide synthase proceeds through a dedicated polyketide synthase and facilitates the mutasynthesis of analogues, J Am Chem Soc, 133, 976, 10.1021/ja108399b

Moore, 2002, Biosynthesis and attachment of novel bacterial polyketide synthase starter units, Nat Prod Rep, 19, 70, 10.1039/b003939j

Olano, 2010, Post-PKS tailoring steps in natural product-producing actinomycetes from the perspective of combinatorial biosynthesis, Nat Prod Rep, 27, 571, 10.1039/b911956f

Oliynyk, 1996, A hybrid modular polyketide synthase obtained by domain swapping, Chem Biol, 3, 833, 10.1016/S1074-5521(96)90069-1

Park, 2010, Biosynthesis of rapamycin and its regulation: past achievements and recent progress, J Antibiot, 63, 434, 10.1038/ja.2010.71

Pfeifer, 2001, Biosynthesis of complex polyketides in a metabolically engineered strain of E-coli, Science, 291, 1790, 10.1126/science.1058092

Piel, 2010, Biosynthesis of polyketides by trans-AT polyketide synthases, Nat Prod Rep, 27, 996, 10.1039/b816430b

Pohl, 2001, Remarkably broad substrate tolerance of Malonyl-CoA synthetase, an enzyme capable of intracellular synthesis of polyketide precursors, J Am Chem Soc, 123, 5822, 10.1021/ja0028368

Ramos, 2008, Biosynthesis of elloramycin in Streptomyces olivaceus requires glycosylation by enzymes encoded outside the aglycon cluster, Microbiology, 154, 781, 10.1099/mic.0.2007/014035-0

Ranganathan, 1999, Knowledge-based design of bimodular and trimodular polyketide synthases based on domain and module swaps: a route to simple statin analogues, Chem Biol, 6, 731, 10.1016/S1074-5521(00)80020-4

Reid, 2003, A model of structure and catalysis for ketoreductase domains in modular polyketide synthases, Biochemistry, 42, 72, 10.1021/bi0268706

Rix, 2002, Modification of post-PKS tailoring steps through combinatorial biosynthesis, Nat Prod Rep, 19, 542, 10.1039/b103920m

Rodriguez, 2000, Generation of hybrid elloramycin analogs by combinatorial biosynthesis using genes from anthracycline-type and macrolide biosynthetic pathways, J Mol Microbiol Biotechnol, 2, 271

Rowe, 2001, Engineering a polyketide with a longer chain by insertion of an extra module into the erythromycin-producing polyketide synthase, Chem Biol, 8, 475, 10.1016/S1074-5521(01)00024-2

Shis, 2013, Library of synthetic transcriptional AND gates built with split T7 RNA polymerase mutants, P Natl Acad Sci USA, 110, 5028, 10.1073/pnas.1220157110

Sundermann, 2013, Enzyme-directed mutasynthesis: a combined experimental and theoretical approach to substrate recognition of a polyketide synthase, ACS Chem Biol, 8, 443, 10.1021/cb300505w

Tang, 2001, Construction of desosamine containing polyketide libraries using a glycosyltransferase with broad substrate specificity, Chem Biol, 8, 547, 10.1016/S1074-5521(01)00032-1

Temme, 2012, Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca, P Natl Acad Sci USA, 109, 7085, 10.1073/pnas.1120788109

Thattai, 2007, The origins of specificity in polyketide synthase protein interactions, PLoS Comput Biol, 3, 1827, 10.1371/journal.pcbi.0030186

Vagstad, 2013, Combinatorial domain swaps provide insights into the rules of fungal polyketide synthase programming and the rational synthesis of non-native aromatic products, Angew Chem Int Ed Engl, 52, 1718, 10.1002/anie.201208550

Vasanthakumar, 2013, Regulation of daunorubicin biosynthesis in Streptomyces peucetius - feed forward and feedback transcriptional control, J Basic Microbiol, 53, 636, 10.1002/jobm.201200302

Walsh, 2010, Natural products version 2.0: connecting genes to molecules, J Am Chem Soc, 132, 2469, 10.1021/ja909118a

Wang, 2011, Synthetic Biology, Pt B: Computer Aided Design and DNA Assembly, 409, 10.1016/B978-0-12-385120-8.00018-8

Wang, 2011, Production of doramectin by rational engineering of the avermectin biosynthetic pathway, Bioorg Med Chem Lett, 21, 3320, 10.1016/j.bmcl.2011.04.008

Weber, 2003, Exploiting the genetic potential of polyketide producing streptomycetes, J Biotechnol, 106, 221, 10.1016/j.jbiotec.2003.08.004

Weissman, 2005, Combinatorial biosynthesis of reduced polyketides, Nat Rev Microbiol, 3, 925, 10.1038/nrmicro1287

Weymouth-Wilson, 1997, The role of carbohydrates in biologically active natural products, Nat Prod Rep, 14, 99, 10.1039/np9971400099

Williams, 2013, Engineering polyketide synthases and nonribosomal peptide synthetases, Curr Opin Struct Biol, 23, 603, 10.1016/j.sbi.2013.06.012

Wilson, 2011, Structure and biosynthesis of the marine streptomycete ansamycin ansalactam A and its distinctive branched chain polyketide extender unit, J Am Chem Soc, 133, 1971, 10.1021/ja109226s

Wohlert, 1998, Novel hybrid tetracenomycins through combinatorial biosynthesis using a glycosyltransferase encoded by the elm genes in cosmid 16F4 and which shows a broad sugar substrate specificity, J Am Chem Soc, 120, 10596, 10.1021/ja981687e

Wu, 2000, The FK520 gene cluster of Streptomyces hygroscopicus var. ascomyceticus (ATCC 14891) contains genes for biosynthesis of unusual polyketide extender units, Gene, 251, 81, 10.1016/S0378-1119(00)00171-2

Xu, 2013, Thioesterase domains of fungal nonreducing polyketide synthases act as decision gates during combinatorial biosynthesis, J Am Chem Soc, 135, 10783, 10.1021/ja4041362

Yeh, 2013, Engineering fungal nonreducing polyketide synthase by heterologous expression and domain swapping, Org Lett, 15, 756, 10.1021/ol303328t

Yoon, 2002, Generation of multiple bioactive macrolides by hybrid modular polyketide synthases in Streptomyces venezuelae, Chem Biol, 9, 203, 10.1016/S1074-5521(02)00095-9

Yu, 2012, Type III polyketide synthases in natural product biosynthesis, LUBMB Life, 64, 285, 10.1002/iub.1005

Yuzawa, 2012, Role of a conserved arginine residue in linkers between the ketosynthase and acyltransferase domains of multimodular polyketide synthases, Biochemistry, 51, 3708, 10.1021/bi300399u