101
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Pfeifer BA, Admiraal SJ, Gramajo H, Cane DE, Khosla C. Biosynthesis of complex polyketides in a metabolically engineered strain of E. coli. Science 2001; 291:1790-2. [PMID: 11230695 DOI: 10.1126/science.1058092] [Citation(s) in RCA: 542] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The macrocyclic core of the antibiotic erythromycin, 6-deoxyerythronolide B (6dEB), is a complex natural product synthesized by the soil bacterium Saccharopolyspora erythraea through the action of a multifunctional polyketide synthase (PKS). The engineering potential of modular PKSs is hampered by the limited capabilities for molecular biological manipulation of organisms (principally actinomycetes) in which complex polyketides have thus far been produced. To address this problem, a derivative of Escherichia coli has been genetically engineered. The resulting cellular catalyst converts exogenous propionate into 6dEB with a specific productivity that compares well with a high-producing mutant of S. erythraea that has been incrementally enhanced over decades for the industrial production of erythromycin.
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Affiliation(s)
- B A Pfeifer
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305-5025, USA
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102
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Carreras CW, Ashley GW. Manipulation of polyketide biosynthesis for new drug discovery. EXS 2001; 89:89-108. [PMID: 10997284 DOI: 10.1007/978-3-0348-8393-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Modular polyketide synthases (PKS) are large multifunctional proteins which direct the condensation of activated short chain carboxylic acids into products of defined length and functionality using a dedicated set of active sites, or module, for each step in the polymerization. The structure of the product is directly related to the number, content and sequence of modules in a PKS. Technology is described which allows the rational manipulation of the biosynthesis of these compounds and enables the generation of specific novel polyketide structures. Examples of polyketide drugs whose structures may be manipulated using this technology are given.
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Affiliation(s)
- C W Carreras
- Department of New Technologies, Kosan Biosciences, Inc., Hayward, CA 94545, USA
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103
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Perham RN. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu Rev Biochem 2001; 69:961-1004. [PMID: 10966480 DOI: 10.1146/annurev.biochem.69.1.961] [Citation(s) in RCA: 489] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Multistep chemical reactions are increasingly seen as important in a growing number of complex biotransformations. Covalently attached prosthetic groups or swinging arms, and their associated protein domains, are essential to the mechanisms of active-site coupling and substrate channeling in a number of the multifunctional enzyme systems responsible. The protein domains, for which the posttranslational machinery in the cell is highly specific, are crucially important, contributing to the processes of molecular recognition that define and protect the substrates and the catalytic intermediates. The domains have novel folds and move by virtue of conformationally flexible linker regions that tether them to other components of their respective multienzyme complexes. Structural and mechanistic imperatives are becoming apparent as the assembly pathways and the coupling of multistep reactions catalyzed by these dauntingly complex molecular machines are unraveled.
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Affiliation(s)
- R N Perham
- Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
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104
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Chakraborty TK, Tapadar S. Diastereoselective opening of trisubstituted epoxy alcohols: application in the synthesis of (+)-prelactone C. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(00)02247-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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105
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Heathcote ML, Staunton J, Leadlay PF. Role of type II thioesterases: evidence for removal of short acyl chains produced by aberrant decarboxylation of chain extender units. CHEMISTRY & BIOLOGY 2001; 8:207-20. [PMID: 11251294 DOI: 10.1016/s1074-5521(01)00002-3] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Modular polyketide synthases (PKSs) function as molecular assembly lines in which polyketide chains are assembled by successive addition of chain extension units. At the end of the assembly line, there is usually a covalently linked type I thioesterase domain (TE I), which is responsible for release of the completed acyl chain from its covalent link to the synthase. Additionally, some PKS clusters contain a second thioesterase gene (TE II) for which there is no established role. Disruption of the TE II genes from several PKS clusters has shown that the TE II plays an important role in maintaining normal levels of antibiotic production. It has been suggested that the TE II fulfils this role by removing aberrant intermediates that might otherwise block the PKS complex. RESULTS We show that recombinant tylosin TE II behaves in vitro as a TE towards a variety of N-acetylcysteamine and p-nitrophenyl esters. The trends of hydrolytic activity determined by the kinetic parameter k(cat)/K(M) for the analogues tested indicates that simple fatty acyl chains are effective substrates. Analogues that modelled aberrant forms of putative tylosin biosynthetic intermediates were hydrolysed at low rates. CONCLUSIONS The behaviour of tylosin TE II in vitro is consistent with its proposed role as an editing enzyme. Aberrant decarboxylation of a malonate-derived moiety attached to an acyl carrier protein (ACP) domain may generate an acetate, propionate or butyrate residue on the ACP thiol. Our results suggest that removal of such groups is a significant role of TE II.
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Affiliation(s)
- M L Heathcote
- Cambridge Centre for Molecular Recognition and University Chemical Laboratory, University of Cambridge, UK
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106
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Metzler DE, Metzler CM, Sauke DJ. The Organization of Metabolism. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50020-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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107
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Abstract
Metabolic engineering of natural products is a science that has been built on the goals of traditional strain improvement with the availability of modern molecular biological technologies. In the past 15 years, the state of the art in metabolic engineering of natural products has advanced from the first proof-of-principle experiment based on minimal known genetics to a commonplace event using highly specific and sophisticated gene manipulation methods. With the availability of genes, host organisms, vector systems, and standard molecular biological tools, it is expected that metabolic engineering will be translated into industrial reality.
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Affiliation(s)
- W R Strohl
- Natural Products Drug Discovery-Microbiology, Merck Research Labs, Rahway, New Jersey 07065, USA.
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108
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Metzler DE, Metzler CM, Sauke DJ. Coenzymes. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50017-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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109
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Aparicio JF, Fouces R, Mendes MV, Olivera N, Martín JF. A complex multienzyme system encoded by five polyketide synthase genes is involved in the biosynthesis of the 26-membered polyene macrolide pimaricin in Streptomyces natalensis. CHEMISTRY & BIOLOGY 2000; 7:895-905. [PMID: 11094342 DOI: 10.1016/s1074-5521(00)00038-7] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND Polyene macrolides are a class of large macrocyclic polyketides that interact with membrane sterols, having antibiotic activity against fungi but not bacteria. Their rings include a chromophore of 3-7 conjugated double bonds which constitute the distinct polyene structure. Pimaricin is an archetype polyene, important in the food industry as a preservative to prevent mould contamination of foods, produced by Streptomyces natalensis. We set out to clone, sequence and analyse the gene cluster responsible for the biosynthesis of this tetraene. RESULTS A large cluster of 16 open reading frames spanning 84985 bp of the S. natalensis genome has been sequenced and found to encode 13 homologous sets of enzyme activities (modules) of a polyketide synthase (PKS) distributed within five giant multienzyme proteins (PIMS0-PIMS4). The total of 60 constituent active sites, 25 of them on a single enzyme (PIMS2), make this an exceptional multienzyme system. Eleven additional genes appear to govern modification of the polyketide-derived framework and export. Disruption of the genes encoding the PKS abolished pimaricin production. CONCLUSIONS The overall architecture of the PKS gene cluster responsible for the biosynthesis of the 26-membered polyene macrolide pimaricin has been determined. Eleven additional tailoring genes have been cloned and analysed. The availability of the PKS cluster will facilitate the generation of designer pimaricins by combinatorial biosynthesis approaches. This work represents the extensive description of a second polyene macrolide biosynthetic gene cluster after the one for the antifungal nystatin.
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Affiliation(s)
- J F Aparicio
- Institute of Biotechnology INBIOTEC, Parque Científico de León, León, France.
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110
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Paterson I, Donghi M, Gerlach K. A Combinatorial Approach to Polyketide-Type Libraries by Iterative Asymmetric Aldol Reactions Performed on Solid Support We thank the European Commission (TMR Network ERB-FMR XCT 96-0011 and IHP Network HPRN-CT-2000-00014), EPSRC, Pfizer, and Merck for support. Angew Chem Int Ed Engl 2000; 39:3315-3319. [PMID: 11028089 DOI: 10.1002/1521-3773(20000915)39:18<3315::aid-anie3315>3.0.co;2-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- I Paterson
- University Chemical Laboratory Lensfield Road, Cambridge, CB2 1EW (UK)
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111
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Paterson I, Donghi M, Gerlach K. A Combinatorial Approach to Polyketide-Type Libraries by Iterative Asymmetric Aldol Reactions Performed on Solid Support. Angew Chem Int Ed Engl 2000. [DOI: 10.1002/1521-3757(20000915)112:18<3453::aid-ange3453>3.0.co;2-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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112
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Trauger JW, Kohli RM, Mootz HD, Marahiel MA, Walsh CT. Peptide cyclization catalysed by the thioesterase domain of tyrocidine synthetase. Nature 2000; 407:215-8. [PMID: 11001063 DOI: 10.1038/35025116] [Citation(s) in RCA: 239] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the biosynthesis of many macrocyclic natural products by multidomain megasynthases, a carboxy-terminal thioesterase (TE) domain is involved in cyclization and product release; however, it has not been determined whether TE domains can catalyse macrocyclization (and elongation in the case of symmetric cyclic peptides) independently of upstream domains. The inability to decouple the TE cyclization step from earlier chain assembly steps has precluded determination of TE substrate specificity, which is important for the engineered biosynthesis of new compounds. Here we report that the excised TE domain from tyrocidine synthetase efficiently catalyses cyclization of a decapeptide-thioester to form the antibiotic tyrocidine A, and can catalyse pentapeptide-thioester dimerization followed by cyclization to form the antibiotic gramicidin S. By systematically varying the decapeptide-thioester substrate and comparing cyclization rates, we also show that only two residues (one near each end of the decapeptide) are critical for cyclization. This specificity profile indicates that the tyrocidine synthetase TE, and by analogy many other TE domains, will be able to cyclize and release a broad range of new substrates and products produced by engineered enzymatic assembly lines.
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Affiliation(s)
- J W Trauger
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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113
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Abstract
Polyketide synthases catalyze the assembly of complex natural products from simple precursors such as propionyl-CoA and methylmalonyl-CoA in a biosynthetic process that closely parallels fatty acid biosynthesis. Like fatty acids, polyketides are assembled by successive decarboxylative condensations of simple precursors. But whereas the intermediates in fatty acid biosynthesis are fully reduced to generate unfunctionalized alkyl chains, the intermediates in polyketide biosynthesis may be only partially processed, giving rise to complex patterns of functional groups. Additional complexity arises from the use of different starter and chain extension substrates, the generation of chiral centers, and further functional group modifications, such as cyclizations. The structural and functional modularity of these multienzyme systems has raised the possibility that polyketide biosynthetic pathways might be rationally reprogrammed by combinatorial manipulation. An essential prerequisite for harnessing this biosynthetic potential is a better understanding of the molecular recognition features of polyketide synthases. Within this decade, a variety of genetic, biochemical, and chemical investigations have yielded insights into the tolerance and specificity of several architecturally different polyketide synthases. The results of these studies, together with their implications for biosynthetic engineering, are summarized in this review.
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Affiliation(s)
- C Khosla
- Department of Chemical Engineering, Stanford University, California 94305-5025, USA.
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114
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Lal R, Kumari R, Kaur H, Khanna R, Dhingra N, Tuteja D. Regulation and manipulation of the gene clusters encoding type-I PKSs. Trends Biotechnol 2000; 18:264-74. [PMID: 10802562 DOI: 10.1016/s0167-7799(00)01443-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Modular polyketide synthases are large, multifunctional enzyme complexes that are involved in the biosynthesis of important polyketides. Recent studies have revolutionized our understanding of the linear organization of polyketide-synthase-gene clusters. They have provided crucial information on the initiation, elongation and termination of polyketide chains, and thus a rational basis for the generation of novel compounds. Combinatorial libraries have helped this field to move from a random approach to a more empirical phase. The large number of diverse analogs of antibiotics that are presently produced demonstrate the enormous potential of combinatorial biosynthesis.
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Affiliation(s)
- R Lal
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India.
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115
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Kallow W, Kennedy J, Arezi B, Turner G, von Döhren H. Thioesterase domain of delta-(l-alpha-Aminoadipyl)-l-cysteinyl-d-valine synthetase: alteration of stereospecificity by site-directed mutagenesis. J Mol Biol 2000; 297:395-408. [PMID: 10715209 DOI: 10.1006/jmbi.2000.3566] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The carboxy-terminal thioesterase domain of delta-(l-alpha-aminoadipyl)-l-cysteinyl-d-valine synthetase catalyzes the hydrolytic release of the tripeptide product (LLD-ACV). By site-directed mutagenesis an S3599A change was introduced into the highly conserved GXSXG motif, resulting in a more than 95 % decrease of penicillin production. Purification of the modified multienzyme showed surprisingly only a 50 % reduction of the peptide formation rate, with the stereoisomer delta-(l-alpha-aminoadipyl)-l-cysteinyl-l-valine (LLL-ACV) as the dominating product. Thioesterases of ACV synthetases differ from other thioesterases integrated in non-ribosomal peptide synthetases in their direct association with an epimerase domain, and their respective GXSXG-seryl residue is apparently not essential in acyl transfer leading to peptide release. Instead, this motif may be involved in the control of tripeptide epimerization by selection of the isomer to be released, and the construct supports the presence of LLL-ACV as an intermediate in penicillin biosynthesis.
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Affiliation(s)
- W Kallow
- Institute of Biochemistry and Molecular Biology, Technical University Berlin, Germany
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116
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Xue Y, Sherman DH. Alternative modular polyketide synthase expression controls macrolactone structure. Nature 2000; 403:571-5. [PMID: 10676969 DOI: 10.1038/35000624] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Modular polyketide synthases are giant multifunctional enzymes that catalyse the condensation of small carboxylic acids such as acetate and propionate into structurally diverse polyketides that possess a spectrum of biological activities. In a modular polyketide synthase, an enzymatic domain catalyses a specific reaction, and three to six enzymatic domains involved in a condensation-processing cycle are organized into a module. A fundamental aspect of a modular polyketide synthase is that its module arrangement linearly specifies the structure of its polyketide product. Here we report a natural example in which alternative expression of the pikromycin polyketide synthase results in the generation of two macrolactone structures. Expression of the full-length modular polyketide synthase PikAIV in Streptomyces venezuelae generates the 14-membered ring macrolactone narbonolide, whereas expression of the amino-terminal truncated form of PikAIV leads to 'skipping' of the final condensation cycle in polyketide biosynthesis to generate the 12-membered ring macrolactone 10-deoxymethynolide. Our findings provide insight into the structure and function of modular polyketide synthases, as well as a new set of tools to generate structural diversity in polyketide natural products.
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Affiliation(s)
- Y Xue
- Department of Microbiology and Biological Process Technology Institute, University of Minnesota, Minneapolis 55455, USA
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117
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Tang L, Fu H, McDaniel R. Formation of functional heterologous complexes using subunits from the picromycin, erythromycin and oleandomycin polyketide synthases. CHEMISTRY & BIOLOGY 2000; 7:77-84. [PMID: 10662693 DOI: 10.1016/s1074-5521(00)00073-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND Recently developed tools for the genetic manipulation of modular polyketide synthases (PKSs) have advanced the development of combinatorial biosynthesis technologies for drug discovery. Although many of the current techniques involve engineering individual domains or modules of the PKS, few experiments have addressed the ability to combine entire protein subunits from different modular PKSs to create hybrid polyketide pathways. We investigated this possibility by in vivo assembly of heterologous PKS complexes using natural and altered subunits from related macrolide PKSs. RESULTS The pikAI and pikAII genes encoding subunits 1 and 2 (modules 1-4) of the picromycin PKS (PikPKS) and the eryAIII gene encoding subunit 3 (modules 5-6) of the 6-deoxyerythronolide B synthase (DEBS) were cloned in two compatible Streptomyces expression vectors. A strain of Streptomyces lividans co-transformed with the two vectors produced the hybrid macrolactone 3-hydroxynarbonolide. Co-expression of the same pik genes with the gene for subunit 3 of the oleandomycin PKS (OlePKS) was also successful. A series of hybrid polyketide pathways was then constructed by combining PikPKS subunits 1 and 2 with modified DEBS3 subunits containing engineered domains in modules 5 or 6. We also report the effect of junction location in a set of DEBS-PikPKS fusions. CONCLUSIONS We show that natural as well as engineered protein subunits from heterologous modular PKSs can be functionally assembled to create hybrid polyketide pathways. This work represents a new strategy that complements earlier domain engineering approaches for combinatorial biosynthesis in which complete modules or PKS protein subunits, in addition to individual enzymatic domains, are used as building blocks for PKS engineering.
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Affiliation(s)
- L Tang
- Incorporated, KOSAN Biosciences, Hayward, CA 94545, USA. tang@kosan. com
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118
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Wilkinson B, Foster G, Rudd BA, Taylor NL, Blackaby AP, Sidebottom PJ, Cooper DJ, Dawson MJ, Buss AD, Gaisser S, Böhm IU, Rowe CJ, Cortés J, Leadlay PF, Staunton J. Novel octaketide macrolides related to 6-deoxyerythronolide B provide evidence for iterative operation of the erythromycin polyketide synthase. CHEMISTRY & BIOLOGY 2000; 7:111-7. [PMID: 10662692 DOI: 10.1016/s1074-5521(00)00076-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
BACKGROUND The macrolide antibiotic erythromycin A, like other complex aliphatic polyketides, is synthesised by a bacterial modular polyketide synthase (PKS). Such PKSs, in contrast to other fatty acid and polyketide synthases which work iteratively, contain a separate set or module of enzyme activities for each successive cycle of polyketide chain extension, and the number and type of modules together determine the structure of the polyketide product. Thus, the six extension modules of the erythromycin PKS (DEBS) together catalyse the production of the specific heptaketide 6-deoxyerythronolide B. RESULTS A mutant strain of the erythromycin producer Saccharopolyspora erythraea, which accumulates the aglycone intermediate erythronolide B, was found unexpectedly to produce two novel octaketides, both 16-membered macrolides. These compounds were detectable in fermentation broths of wild-type S. erythraea, but not in a strain from which the DEBS genes had been specifically deleted. From their structures, both of these octaketides appear to be aberrant products of DEBS in which module 4 has 'stuttered', that is, has catalysed two successive cycles of chain extension. CONCLUSIONS The isolation of novel DEBS-derived octaketides provides the first evidence that an extension module in a modular PKS has the potential to catalyse iterative rounds of chain elongation like other type I FAS and PKS systems. The factors governing the extent of such 'stuttering' remain to be determined.
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Affiliation(s)
- B Wilkinson
- Bioprocessing Unit, Glaxo Wellcome Research and Development, Medicines Research Centre, Stevenage, SG1 2NY, UK.
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119
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Bioactive Fungal Natural Products Through Classic and Biocombinatorial Approaches. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1572-5995(00)80027-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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120
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Bycroft M, Weissman KJ, Staunton J, Leadlay PF. Efficient purification and kinetic characterization of a bimodular derivative of the erythromycin polyketide synthase. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:520-6. [PMID: 10632721 DOI: 10.1046/j.1432-1327.2000.01025.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Modular polyketide synthases (PKSs), such as the 6-deoxyerythronolide B synthase (DEBS), are giant multienzymes that biosynthesize a number of clinically important natural products. The modular nature of PKSs suggests the possibility of a combinatorial approach to the synthesis of novel bioactive polyketides, but the efficacy of such a strategy depends critically on gaining fundamental insight into PKS structure and function, most directly through experiments with purified PKS proteins. Several recent investigations into important aspects of the activity of these enzymes have used only partially purified proteins (often 3-4% of total protein), reflecting how difficult it is to purify these multienzymes in amounts adequate for kinetic and structural analysis. We report here the steady-state kinetic analysis of a typical bimodular PKS, 6-deoxyerythronolide B synthase 1-thioesterase (DEBS 1-TE), purified from recombinant Saccharopolyspora erythraea JCB101 by a new, high-yielding procedure consisting of three steps: ammonium sulfate precipitation, hydrophobic interaction chromatography and size-exclusion chromatography. The method provides 13-fold purification with a recovery of 11% of the applied PKS activity. The essentially homogeneous synthase exhibits an intrinsic methylmalonyl-CoA hydrolase activity, which competes with polyketide chain extension. The most reliable value for the kcat for synthesis of (3S,5R)-dihydroxy-(2R,4R)-dimethyl-n-heptanoic acid-delta-lactone is 0.84 min-1, and the apparent Km for (2RS)-methylmalonyl-CoA is 17 microM. This kcat is approximately 10-fold lower than the value reported previously for a differently engineered version of the truncated PKS, DEBS 1+TE. The difference likely reflects the fact that the DEBS 1-TE contains a hybrid acyl carrier protein (ACP) domain in its second module, which lowers its catalytic efficiency.
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Affiliation(s)
- M Bycroft
- Cambridge Centre for Molecular Recognition, Department of Organic Chemistry, University of Cambridge, UK
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121
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122
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Abstract
In a new golden age, polyketides are investigated and manipulated with the tools of molecular biology and genetics; hybrid polyketides can be produced. Pharmaceutical companies hope to find new and useful polyketide products, including antibiotics, anthelminthics, and immunosuppressants. This review describes the past developments (largely chemical) on which the present investigations are based, attempts to make sense of the expanding scope of polyketides, looks at the shifting research focus around polyketides, presents a working definition in biosynthetic terms, and takes note of recent work in combinatorial biosynthesis. Also discussed is the failure of the classical enzymological approach to polyketide biosynthesis.
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Affiliation(s)
- R Bentley
- Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260, USA.
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123
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Abstract
Erythromycin, a complex polyketide antibiotic belonging to the macrolide class, is produced as a natural product by the bacterium Saccharopolyspora erythraea. The genes encoding the enzymes responsible for the synthesis of the antibiotic have been cloned and sequenced, revealing that the polyketide backbone of the molecule in produced by a polyketide synthase (PKS) composed of multifunctional proteins that contain discrete functional domains for each step of synthesis. Genetic manipulation of the PKS-encoding genes can result in predictable changes in the structure of the polyketide component of erythromycin, many of which are not easily achievable through standard chemical derivatization or synthesis. Many of the changes can be combined to lead to the further generation of navel structures. Whereas genetic engineering of the erythromycin structure has been practiced for a number of years, the re cent and continuing discoveries of modular PKSs for the synthesis of many other important complex polyketides has raised the possibility of generating novel structures in these molecules by genetic manipulation, as well.
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Affiliation(s)
- L Katz
- Kosan Biosciences, Inc., Hayward, California 94545, USA.
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124
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Large K, Mirjalili N, Peacock ML, Zormpaidis V, Walsh M, Cavanagh M, Leadlay P, Ison A. Lipase activity in Streptomycetes. Enzyme Microb Technol 1999. [DOI: 10.1016/s0141-0229(99)00080-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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125
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Keating TA, Walsh CT. Initiation, elongation, and termination strategies in polyketide and polypeptide antibiotic biosynthesis. Curr Opin Chem Biol 1999; 3:598-606. [PMID: 10508662 DOI: 10.1016/s1367-5931(99)00015-0] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Progress in sequence analysis of biosynthetic gene clusters encoding polyketides and nonribosomal peptides and in the reconstitution of in vitro activities continues to reveal new insights into the growth of these natural products' acyl chains, which have been revealed as a series of elongating, covalent, acyl enzyme intermediates on their multimodular scaffolds. Studies that focus on the three stages of natural product biosynthesis - initiation, elongation, and termination - have yielded crucial information on monomer substrate specificity, domain and module portability, and product release mechanisms, all of which are important not only for an understanding of this exquisite enzymatic machinery, but also for the rational construction of new, functional synthetases and synthases that are a goal of combinatorial biosynthesis.
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Affiliation(s)
- T A Keating
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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126
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Shaw-Reid CA, Kelleher NL, Losey HC, Gehring AM, Berg C, Walsh CT. Assembly line enzymology by multimodular nonribosomal peptide synthetases: the thioesterase domain of E. coli EntF catalyzes both elongation and cyclolactonization. CHEMISTRY & BIOLOGY 1999; 6:385-400. [PMID: 10375542 DOI: 10.1016/s1074-5521(99)80050-7] [Citation(s) in RCA: 137] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
BACKGROUND EntF is a 142 kDa four domain (condensation-adenylation-peptidyl carrier protein-thioesterase) nonribosomal peptide synthetase (NRPS) enzyme that assembles the Escherichia coli N-acyl-serine trilactone siderophore enterobactin from serine, dihydroxybenzoate (DHB) and ATP with three other enzymes (EntB, EntD and EntE). To assess how EntF forms three ester linkages and cyclotrimerizes the covalent acyl enzyme DHB-Ser-S-PCP (peptidyl carrier protein) intermediate, we mutated residues of the proposed catalytic Ser-His-Asp triad of the thioesterase (TE) domain. RESULTS The Ser1138-->Cys mutant (kcat decreased 1000-fold compared with wild-type EntF) releases both enterobactin (75%) and linear (DHB-Ser)2 dimer (25%) as products. The His 1271-->Ala mutant (kcat decreased 10,000-fold compared with wild-type EntF) releases only enterobactin, but accumulates both DHB-Ser-O-TE and (DHB-Ser)2-O-TE acyl enzyme intermediates. Electrospray ionization and Fourier transform mass spectrometry of proteolytic digests were used to analyze the intermediates. CONCLUSIONS These results establish that the TE domain of EntF is both a cyclotrimerizing lactone synthetase and an elongation catalyst for ester-bond formation between covalently tethered DHB-Ser moieties, a new function for chain-termination TE domains found at the carboxyl termini of multimodular NRPSs and polyketide synthases.
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Affiliation(s)
- C A Shaw-Reid
- Department of Biological Chemistry and Molecular Pharmacology, 240 Longwood Avenue, Harvard Medical School, Boston, MA 02115, USA
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127
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Bender CL, Alarcón-Chaidez F, Gross DC. Pseudomonas syringae phytotoxins: mode of action, regulation, and biosynthesis by peptide and polyketide synthetases. Microbiol Mol Biol Rev 1999; 63:266-92. [PMID: 10357851 PMCID: PMC98966 DOI: 10.1128/mmbr.63.2.266-292.1999] [Citation(s) in RCA: 516] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Coronatine, syringomycin, syringopeptin, tabtoxin, and phaseolotoxin are the most intensively studied phytotoxins of Pseudomonas syringae, and each contributes significantly to bacterial virulence in plants. Coronatine functions partly as a mimic of methyl jasmonate, a hormone synthesized by plants undergoing biological stress. Syringomycin and syringopeptin form pores in plasma membranes, a process that leads to electrolyte leakage. Tabtoxin and phaseolotoxin are strongly antimicrobial and function by inhibiting glutamine synthetase and ornithine carbamoyltransferase, respectively. Genetic analysis has revealed the mechanisms responsible for toxin biosynthesis. Coronatine biosynthesis requires the cooperation of polyketide and peptide synthetases for the assembly of the coronafacic and coronamic acid moieties, respectively. Tabtoxin is derived from the lysine biosynthetic pathway, whereas syringomycin, syringopeptin, and phaseolotoxin biosynthesis requires peptide synthetases. Activation of phytotoxin synthesis is controlled by diverse environmental factors including plant signal molecules and temperature. Genes involved in the regulation of phytotoxin synthesis have been located within the coronatine and syringomycin gene clusters; however, additional regulatory genes are required for the synthesis of these and other phytotoxins. Global regulatory genes such as gacS modulate phytotoxin production in certain pathovars, indicating the complexity of the regulatory circuits controlling phytotoxin synthesis. The coronatine and syringomycin gene clusters have been intensively characterized and show potential for constructing modified polyketides and peptides. Genetic reprogramming of peptide and polyketide synthetases has been successful, and portions of the coronatine and syringomycin gene clusters could be valuable resources in developing new antimicrobial agents.
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Affiliation(s)
- C L Bender
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, Oklahoma 74078-3032, USA.
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128
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129
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Butler AR, Bate N, Cundliffe E. Impact of thioesterase activity on tylosin biosynthesis in Streptomyces fradiae. CHEMISTRY & BIOLOGY 1999; 6:287-92. [PMID: 10322123 DOI: 10.1016/s1074-5521(99)80074-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND The polyketide lactone, tylactone, is produced in Streptomyces fradiae by the TylG complex of five multifunctional proteins. As with other type I polyketide synthases, the enzyme catalysing the final elongation step (TylGV) possesses an integral thioesterase domain that is believed to be responsible for chain termination and ring closure to form tylactone, which is then glycosylated to yield tylosin. In common with other macrolide producers, S. fradiae also possesses an additional thioesterase gene (orf5) located within the cluster of antibiotic biosynthetic genes. The function of the Orf5 protein is addressed here. RESULTS Disruption of orf5 reduced antibiotic accumulation in S. fradiae by at least 85%. Under such circumstances, the strain accumulated desmycosin (demycarosyl-tylosin) due to a downstream polar effect on the expression of orf6, which encodes a mycarose biosynthetic enzyme. High levels of desmycosin production were restored in the disrupted strain by complementation with intact orf5, or with the corresponding thioesterase gene, nbmB, from S. narbonensis, but not with DNA encoding the integral thioesterase domain of TylGV. CONCLUSIONS Polyketide metabolism in S. fradiae is strongly dependent on the thioesterase activity encoded by orf5 (tylO). It is proposed that the TylG complex might operate with a significant error frequency and be prone to blockage with aberrant polyketides. A putative editing activity associated with TylO might be essential to unblock the polyketide synthase complex and thereby promote antibiotic accumulation.
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Affiliation(s)
- A R Butler
- Department of Biochemistry University of Leicester Leicester, LE1 7RH, UK
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130
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Gokhale RS, Tsuji SY, Cane DE, Khosla C. Dissecting and exploiting intermodular communication in polyketide synthases. Science 1999; 284:482-5. [PMID: 10205055 DOI: 10.1126/science.284.5413.482] [Citation(s) in RCA: 236] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Modular polyketide synthases catalyze the biosynthesis of medicinally important natural products through an assembly-line mechanism. Although these megasynthases display very precise overall selectivity, we show that their constituent modules are remarkably tolerant toward diverse incoming acyl chains. By appropriate engineering of linkers, which exist within and between polypeptides, it is possible to exploit this tolerance to facilitate the transfer of biosynthetic intermediates between unnaturally linked modules. This protein engineering strategy also provides insights into the evolution of modular polyketide synthases.
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Affiliation(s)
- R S Gokhale
- Department of Chemical Engineering, Stanford University, Stanford CA 94305-5025, USA
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131
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Holzbaur IE, Harris RC, Bycroft M, Cortes J, Bisang C, Staunton J, Rudd BA, Leadlay PF. Molecular basis of Celmer's rules: the role of two ketoreductase domains in the control of chirality by the erythromycin modular polyketide synthase. CHEMISTRY & BIOLOGY 1999; 6:189-95. [PMID: 10099131 DOI: 10.1016/s1074-5521(99)80035-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
BACKGROUND Polyketides are compounds that possess medically significant activities. The modular nature of the polyketide synthase (PKS) multienzymes has generated interest in bioengineering new PKSs. Rational design of novel PKSs, however, requires a greater understanding of the stereocontrol mechanisms that operate in natural PKS modules. RESULTS The N-acetyl cysteamine (NAC) thioester derivative of the natural beta-keto diketide intermediate was incubated with DEBS1-TE, a derivative of the erythromycin PKS that contains only modules 1 and 2. The reduction products of the two ketoreductase (KR) domains of DEBS1-TE were a mixture of the (2S, 3R) and (2R,3S) isomers of the corresponding beta-hydroxy diketide NAC thioesters. Repeating the incubation using a DEBS1-TE mutant that only contains KR1 produced only the (2S,3R) isomer. CONCLUSIONS In contrast with earlier results, KR1 selects only the (2S) isomer and reduces it stereospecifically to the (2S, 3R)-3-hydroxy-2-methyl acyl product. The KR domain of module 1 controls the stereochemical outcome at both methyl-and hydroxyl-bearing chiral centres in the hydroxy diketide intermediate. Earlier work showed that the normal enzyme-bound ketoester generated in module 2 is not epimerised, however. The stereochemistry at C-2 is therefore established by a condensation reaction that exclusively gives the (2R)-ketoester, and the stereo-chemistry at C-3 by reduction of the keto group. Two different mechanisms of stereochemical control, therefore, operate in modules 1 and 2 of the erythromycin PKS. These results should provide a more rational basis for designing hybrid PKSs to generate altered stereochemistry in polyketide products.
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Affiliation(s)
- I E Holzbaur
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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132
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McDaniel R, Thamchaipenet A, Gustafsson C, Fu H, Betlach M, Ashley G. Multiple genetic modifications of the erythromycin polyketide synthase to produce a library of novel "unnatural" natural products. Proc Natl Acad Sci U S A 1999; 96:1846-51. [PMID: 10051557 PMCID: PMC26699 DOI: 10.1073/pnas.96.5.1846] [Citation(s) in RCA: 321] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structures of complex polyketide natural products, such as erythromycin, are programmed by multifunctional polyketide synthases (PKSs) that contain modular arrangements of functional domains. The colinearity between the activities of modular PKS domains and structure of the polyketide product portends the generation of novel organic compounds-"unnatural" natural products-by genetic manipulation. We have engineered the erythromycin polyketide synthase genes to effect combinatorial alterations of catalytic activities in the biosynthetic pathway, generating a library of >50 macrolides that would be impractical to produce by chemical methods. The library includes examples of analogs with one, two, and three altered carbon centers of the polyketide products. The manipulation of multiple biosynthetic steps in a PKS is an important milestone toward the goal of producing large libraries of unnatural natural products for biological and pharmaceutical applications.
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Affiliation(s)
- R McDaniel
- KOSAN Biosciences, Inc., 1450 Rollins Road, Burlingame, CA 94010, USA.
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133
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Gokhale RS, Hunziker D, Cane DE, Khosla C. Mechanism and specificity of the terminal thioesterase domain from the erythromycin polyketide synthase. CHEMISTRY & BIOLOGY 1999; 6:117-25. [PMID: 10021418 DOI: 10.1016/s1074-5521(99)80008-8] [Citation(s) in RCA: 127] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Polyketides are important compounds with antibiotic and anticancer activities. Several modular polyketide synthases (PKSs) contain a terminal thioesterase (TE) domain probably responsible for the release and concomitant cyclization of the fully processed polyketide chain. Because the TE domain influences qualitative aspects of product formation by engineered PKSs, its mechanism and specificity are of considerable interest. RESULTS The TE domain of the 6-deoxyerythronolide B synthase was overexpressed in Escherichia coli. When tested against a set of N-acetyl cysteamine thioesters the TE domain did not act as a cyclase, but showed significant hydrolytic specificity towards substrates that mimic important features of its natural substrate. Also the overall rate of polyketide chain release was strongly enhanced by a covalent connection between the TE domain and the terminal PKS module (by as much as 100-fold compared with separate TE and PKS 'domains'). CONCLUSIONS The inability of the TE domain alone to catalyze cyclization suggests that macrocycle formation results from the combined action of the TE domain and a PKS module. The chain-length and stereochemical preferences of the TE domain might be relevant in the design and engineered biosynthesis of certain novel polyketides. Our results also suggest that the TE domain might loop back to catalyze the release of polyketide chains from both terminal and pre-terminal modules, which may explain the ability of certain naturally occurring PKSs, such as the picromycin synthase, to generate both 12-membered and 14-membered macrolide antibiotics.
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Affiliation(s)
- R S Gokhale
- Department of Chemical Engineering, Stanford University, CA 94305-5025,USA
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134
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Gates PJ, Kearney GC, Jones R, Leadlay PF, Staunton J. Structural elucidation studies of erythromycins by electrospray tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 1999; 13:242-246. [PMID: 10097401 DOI: 10.1002/(sici)1097-0231(19990228)13:4<242::aid-rcm447>3.0.co;2-b] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Erythromycin A (EryA) was studied by electrospray ionisation tandem mass spectrometry (ESI-MS/MS) with the aim of developing a methodology for the structural elucidation of novel erythromycins developed by biological synthetic methods. Skimmer dissociation along with sequential mass spectrometry studies (up to MS5) have been employed in this study. In the low-resolution MS/MS analysis of the polyketides, there are several fragment ions that are easily assigned to various neutral losses. These have all been confirmed by accurate-mass measurements. There is also a series of peaks due to ring opening and fragmentation that can only be assigned by high-resolution MSn analysis. Further experiments were performed in deuterated media (D2O/CD3OD 50%) which, along with the high-resolution MSn of erythromycin analogues, has enabled us to identify some of the steps in the ring fragmentation, particularly the loss of the polyketide starter acid. This is an essential step for determining structural alterations in the novel polyketides, but further labelling experiments and studies on more erythromycin analogues are required before the complete fragmentation pathway can be confirmed.
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Affiliation(s)
- P J Gates
- Department of Chemistry, University of Cambridge, UK
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135
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Bender CL, Rangaswamy V, Loper J. POLYKETIDE PRODUCTION BY PLANT-ASSOCIATED PSEUDOMONADS. ANNUAL REVIEW OF PHYTOPATHOLOGY 1999; 37:175-196. [PMID: 11701821 DOI: 10.1146/annurev.phyto.37.1.175] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Polyketides constitute a huge family of structurally diverse natural products including antibiotics, chemotherapeutic compounds, and antiparasitics. Most of the research on polyketide synthesis in bacteria has focused on compounds synthesized by Streptomyces or other actinomycetes; however, plant-associated pseudomonads also produce a variety of compounds via the polyketide pathway including the phytotoxin coronatine, the antibiotic mupirocin, and the antifungal compounds pyoluteorin and 2,4-diacetylphloroglucinol. This review focuses on the mode of action, regulation, biosynthesis, and genetics of these four compounds and the potential use of Pseudomonas-derived polyketide synthases in the generation of novel compounds with unique activities.
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Affiliation(s)
- CL Bender
- Department of Entomology and Plant Pathology, 110 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma 74078-3032; e-mail: ;
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136
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Weissman KJ, Kearney GC, Leadlay PF, Staunton J. Structural elucidation studies of polyketide tetrasubstituted delta-lactones by gas chromatography/tandem mass spectrometry and electrospray mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 1999; 13:2103-2108. [PMID: 10523767 DOI: 10.1002/(sici)1097-0231(19991115)13:21<2103::aid-rcm760>3.0.co;2-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A series of tetrasubstituted polyketide delta-lactones were used to evaluate whether gas chromatography/tandem mass spectrometry (GC/MS/MS) and electrospray mass spectrometry (ESI-MS) are useful techniques for probing the structure and stereochemistry of such highly functionalised molecules. Analyses were performed with two commercially available mass spectrometers: a Finnigan/MAT GCQ instrument (CI source) and a Q-TOF Hybrid quadrupole time-of-flight instrument (ESI source). The analyses revealed that a range of variation in the structure and stereochemistry of the lactones did not affect the fragmentation pathway common to these molecules. By accurate mass determination (ESI-MS), the first two fragmentations were assigned to losses of water. Although it was anticipated that the initial dehydration would include the hydroxyl group at the 3-position of the lactones, evidence from deuterium- and (18)O-labelling studies suggests that the losses of water instead involve the oxygen atoms in the ester bond. Attempts to identify further the structures of daughter ions by GC/MS/MS were complicated by extensive rearrangements and non-specific hydrogen/deuterium migrations within the lactones. Together, these results illustrate the limitations of mass spectrometry in the structural elucidation of complex molecules. Copyright 1999 John Wiley & Sons, Ltd.
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Affiliation(s)
- KJ Weissman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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137
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Wilkinson (née Cutter) AL, Hanefeld U, Wilkinson B, Leadlay PF, Staunton J. Enantiospecific synthesis of tetrasubstituted δ-lactones. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(98)02243-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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138
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Weissman KJ, Bycroft M, Cutter AL, Hanefeld U, Frost EJ, Timoney MC, Harris R, Handa S, Roddis M, Staunton J, Leadlay PF. Evaluating precursor-directed biosynthesis towards novel erythromycins through in vitro studies on a bimodular polyketide synthase. CHEMISTRY & BIOLOGY 1998; 5:743-54. [PMID: 9862800 DOI: 10.1016/s1074-5521(98)90666-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
BACKGROUND Modular polyketide synthases (PKSs) catalyse the biosynthesis of complex polyketides using a different set of enzymes for each successive cycle of chain extension. Directed biosynthesis starting from synthetic diketides is a potentially valuable route to novel polyketides. We have used a purified bimodular derivative of the erythromycin-producing polyketide synthase (DEBS 1-TE) to study chain extension starting from a variety of diketide analogues and, in some cases, from the alternative acyl-CoA thioester substrates. RESULTS Chain initiation in vitro by DEBS 1-TE module 2 using a synthetic diketide analogue as a substrate was tolerant of significant structural variation in the starter unit of the synthetic diketide, but other changes completely abolished activity. Interestingly, a racemic beta-keto diketide was found to be reduced in situ on the PKS and utilised in place of its more complex hydroxy analogue as a substrate for chain extension. The presence of a diketide analogue strongly inhibited chain initiation via the loading module. Significantly higher concentrations of diketide N-acetylcysteamine analogues than their corresponding acyl-CoA thioesters are required to achieve comparable yields of triketide lactones. CONCLUSIONS Although a broad range of variation in the starter residue is acceptable, the substrate specificity of module 2 of a typical modular PKS in vitro is relatively intolerant of changes at C-2 and C-3. This will restrict the usefulness of approaches to synthesise novel erythromycins using synthetic diketides in vivo. The use of synthetic beta-keto diketides in vivo deserves to be explored.
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Affiliation(s)
- K J Weissman
- Cambridge Centre for Molecular Recognition Department of Organic Chemistry University of Cambridge Cambridge CB2 1EW UK
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139
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Affiliation(s)
- K A Reynolds
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, 800 East Leigh Street, Richmond, VA 23219, USA.
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140
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Xue Y, Zhao L, Liu HW, Sherman DH. A gene cluster for macrolide antibiotic biosynthesis in Streptomyces venezuelae: architecture of metabolic diversity. Proc Natl Acad Sci U S A 1998; 95:12111-6. [PMID: 9770448 PMCID: PMC22793 DOI: 10.1073/pnas.95.21.12111] [Citation(s) in RCA: 271] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/1998] [Accepted: 07/31/1998] [Indexed: 11/18/2022] Open
Abstract
In a survey of microbial systems capable of generating unusual metabolite structural variability, Streptomyces venezuelae ATCC 15439 is notable in its ability to produce two distinct groups of macrolide antibiotics. Methymycin and neomethymycin are derived from the 12-membered ring macrolactone 10-deoxymethynolide, whereas narbomycin and pikromycin are derived from the 14-membered ring macrolactone, narbonolide. This report describes the cloning and characterization of the biosynthetic gene cluster for these antibiotics. Central to the cluster is a polyketide synthase locus (pikA) that encodes a six-module system comprised of four multifunctional proteins, in addition to a type II thioesterase (TEII). Immediately downstream is a set of genes for desosamine biosynthesis (des) and macrolide ring hydroxylation. The study suggests that Pik TEII plays a role in forming a metabolic branch through which polyketides of different chain length are generated, and the glycosyl transferase (encoded by desVII) has the ability to catalyze glycosylation of both the 12- and 14-membered ring macrolactones. Moreover, the pikC-encoded P450 hydroxylase provides yet another layer of structural variability by introducing regiochemical diversity into the macrolide ring systems. The data support the notion that the architecture of the pik gene cluster as well as the unusual substrate specificity of particular enzymes contributes to its ability to generate four macrolide antibiotics.
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Affiliation(s)
- Y Xue
- Department of Microbiology, University of Minnesota, Box 196, 1460 Mayo Memorial Building, Minneapolis, MN 55455, USA
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141
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Abstract
Polyketides and non-ribosomal peptides are two large families of complex natural products that are built from simple carboxylic acid or amino acid monomers, respectively, and that have important medicinal or agrochemical properties. Despite the substantial differences between these two classes of natural products, each is synthesized biologically under the control of exceptionally large, multifunctional proteins termed polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) that contain repeated, coordinated groups of active sites called modules, in which each module is responsible for catalysis of one complete cycle of polyketide or polypeptide chain elongation and associated functional group modifications. It has recently become possible to use molecular genetic methodology to alter the number, content, and order of such modules and, in so doing, to alter rationally the structure of the resultant products. This review considers the promise and challenges inherent in the combinatorial manipulation of PKS and NRPS structure in order to generate entirely "unnatural" products.
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Affiliation(s)
- D E Cane
- Department of Chemistry, Box H, Brown University, Providence, RI 02912-9108, USA
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142
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Rowe CJ, Cortés J, Gaisser S, Staunton J, Leadlay PF. Construction of new vectors for high-level expression in actinomycetes. Gene 1998; 216:215-23. [PMID: 9714812 DOI: 10.1016/s0378-1119(98)00327-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A new integrative vector (pCJR24) was constructed for use in the erythromycin producer Saccharopolyspora erythraea and in other actinomycetes. It includes the pathway-specific activator gene actII-ORF4 from the actinorhodin biosynthetic gene cluster of Streptomyces coelicolor. The actI promoter and the associated ribosome binding site are located upstream of an NdeI site (5'-CATATG-3') which encompasses the actI start codon allowing protein(s) to be produced at high levels in response to nutritional signals if these signals are faithfully mediated by the ActII-ORF4 activator. Several polyketide synthase genes were cloned in pCJR24 and overexpressed in S. erythraea after integration of the vector into the chromosome by homologous recombination, indicating the possibility that the S. coelicolor promoter/activator functions appropriately in S. erythraea. pCJR24-mediated recombination was also used to place the entire gene set for the erythromycin-producing polyketide synthase under the control of the actI promoter. The resulting strain produced copious quantities of erythromycins and precursor macrolides when compared with wild-type S. erythraea. The use of this system provides the means for rational strain improvement of antibiotic-producing actinomycetes.
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Affiliation(s)
- C J Rowe
- Cambridge Centre for Molecular Recognition and Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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143
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Carreras CW, Santi DV. Engineering of modular polyketide synthases to produce novel polyketides. Curr Opin Biotechnol 1998; 9:403-411. [PMID: 9751637 DOI: 10.1016/s0958-1669(98)80015-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Polyketides are important natural products produced by Actinomycetes and other organisms via the polymerization of coenzyme A-activated carboxylic acids. Modular polyketide synthases are large multifunctional enzymes that direct the biosynthetic process using a dedicated 'module' for each polymerization reaction, which specifies the unit to be polymerized, its oxidation state and stereochemistry. Over the past two years proof-of-principle has been demonstrated for technologies that modify or exchange modules to create hybrid enzymes that catalyze the biosynthesis of novel polyketides.
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Affiliation(s)
- CW Carreras
- Kosan Biosciences, Inc 1450 Rollins Road, Burlingame, CA 04010, USA
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144
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Böhm I, Holzbaur IE, Hanefeld U, Cortés J, Staunton J, Leadlay PF. Engineering of a minimal modular polyketide synthase, and targeted alteration of the stereospecificity of polyketide chain extension. CHEMISTRY & BIOLOGY 1998; 5:407-12. [PMID: 9710562 DOI: 10.1016/s1074-5521(98)90157-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND Polyketides are a large and structurally diverse group of natural products that include antibiotics, antifungal agents and immunosuppressant compounds. Polyketides are biosynthesised in filamentous bacteria on modular polyketide synthases (PKSs) in which each cycle of chain extension requires a different 'module' of enzymatic activities. The recently proposed dimeric model for modular PKSs predicts that even a single-module PKS should be catalytically active in the absence of other PKS components. Researchers are also interested in manipulating the stereochemical outcome of polyketide chain extension using genetic engineering of domains within each module. RESULTS We have constructed a minimal modular PKS from the erythromycin-producing PKS (DEBS) of Saccharopolyspora erythraea. The diketide synthase (DKS1-2) consists of a single chimaeric extension module, derived from the DEBS module 1 ketoacyl-ACP synthase (KS), sandwiched between a loading module and a chain-terminating thioesterase. When DKS1-2 was expressed in S. erythraea, the strain preferentially6 accumulated the diketide (2R, 3S)-2-methyl-3-hydroxy pentanoic acid. CONCLUSIONS These results demonstrate that, as predicted, even a single-module PKS is catalytically active in the absence of other DEBS proteins. In its normal context, the ketosynthase domain KS1 is thought to generate a (2S)-2methyl-3-hydroxy intermediate by epimerising the initial product of carbon-carbon chain formation, the (2R)-2-methyl-3-ketoester. The observed formation of the alternative (2R)-methyl-3-hydroxy product catalysed by DKS1-2 provides strong support for this proposal, and indicates how targeted alteration of stereospecificity can be achieved on a modular PKS.
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Affiliation(s)
- I Böhm
- Cambridge Centre for Molecular Recognition, University of Cambridge, UK
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145
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Rangaswamy V, Mitchell R, Ullrich M, Bender C. Analysis of genes involved in biosynthesis of coronafacic acid, the polyketide component of the phytotoxin coronatine. J Bacteriol 1998; 180:3330-8. [PMID: 9642184 PMCID: PMC107286 DOI: 10.1128/jb.180.13.3330-3338.1998] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Coronafacic acid (CFA) is the polyketide component of coronatine (COR), a phytotoxin produced by the plant-pathogenic bacterium Pseudomonas syringae. The genes involved in CFA biosynthesis are encoded by a single transcript which encompasses 19 kb of the COR gene cluster. In the present study, the nucleotide sequence was determined for a 4-kb region located at the 3' end of the CFA biosynthetic gene cluster. Three open reading frames were identified and designated cfa8, cfa9, and tnp1; the predicted translation products of these genes showed relatedness to oxidoreductases, thioesterases, and transposases, respectively. The translational products of cfa8 and cfa9 were overproduced in Escherichia coli BL21; however, tnp1 was not translated in these experiments. Mutagenesis and complementation analysis indicated that cfa8 is required for the production of CFA and COR. Analysis of a cfa9 mutant indicated that this gene is dispensable for CFA and COR production but may increase the release of enzyme-bound products from the COR pathway; tnp1, however, had no obvious function in CFA or COR biosynthesis. A genetic strategy was used to produce CFA in a P. syringae strain which lacks the COR gene cluster; this approach will be useful in future studies designed to investigate biosynthetic products of the CFA gene cluster.
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Affiliation(s)
- V Rangaswamy
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater 74078-3032, USA
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146
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Guenzi E, Galli G, Grgurina I, Pace E, Ferranti P, Grandi G. Coordinate transcription and physical linkage of domains in surfactin synthetase are not essential for proper assembly and activity of the multienzyme complex. J Biol Chem 1998; 273:14403-10. [PMID: 9603952 DOI: 10.1074/jbc.273.23.14403] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial peptide synthetases have two common features that appear to be strictly conserved. 1) The enzyme subunits are co-regulated at both transcriptional and translational level. 2) The organization of the different enzymatic domains constituting the enzyme fulfills the "colinearity rule" according to which the order of the domains along the chromosome parallels their functional hierarchy. Considering the high degree of conservation of these features, one would expect that mutations such as transcription uncoupling and domain dissociations, deletions, duplications, and reshuffling would result in profound effects on the quality and quantity of synthesized peptides. To start testing this hypothesis, we designed two mutants. In one mutant, the operon structure of surfactin synthetase was destroyed, thus altering the concerted expression of the enzyme subunits. In the other mutant, the thioesterase domain naturally fused to the last amino acid binding domain of surfactin was physically dissociated and independently expressed. When the lipopeptides secreted by the mutant Bacillus subtilis strains were purified and characterized, they appeared to be expressed approximately at the same level of the wild type surfactin and to be identical to it, indicating that specific domain-domain interactions rather than coordinated transcription and translation play the major role in determining the correct assembly and activity of peptide synthetases.
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Affiliation(s)
- E Guenzi
- Department of Molecular Biology, Chiron S.p.A., Via Fiorentina, 1 53100, Siena, Italy
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147
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Abstract
Modular polyketide synthases that produce many clinically important natural products such as erythromycins and lovastatins have been engineered in many ways to produce novel natural products. The structural variations have included alterations to the substituents on the macrolide ring, including the starter acid residue, using either semi-synthetic methodology or genetic engineering. It is now also possible to produce shorter polyketide chains that are released either as lactone rings (6-, 8-, 12- and 14-membered rings) or linear products. The strategies for engineering polyketide synthases to produce specific natural products are now well established. Several of the macrolides produced recently have been elaborated to produce novel antibiotics.
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Affiliation(s)
- J Staunton
- Department of Chemistry, University of Cambridge, UK.
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148
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Weissman K, Smith C, Hanefeld U, Aggarwal R, Bycroft M, Staunton J, Leadlay P. Die Thioesterase der Polyketid-Synthase von Erythromycin: Einfluß der Acylkettenstruktur auf den Abkopplungsmechanismus der Substratanaloga von der Acyl-Enzym-Zwischenstufe. Angew Chem Int Ed Engl 1998. [DOI: 10.1002/(sici)1521-3757(19980518)110:10<1503::aid-ange1503>3.0.co;2-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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149
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McPherson M, Khosla C, Cane DE. Erythromycin Biosynthesis: The β-Ketoreductase Domains Catalyze the Stereospecific Transfer of the 4-pro-S Hydride of NADPH. J Am Chem Soc 1998. [DOI: 10.1021/ja980028z] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael McPherson
- Department of Chemistry, Box H, Brown University Providence, Rhode Island 02912-9108 Departments of Chemical Engineering, Chemistry and Biochemistry, Stanford University Stanford, California 94305-5025
| | - Chaitan Khosla
- Department of Chemistry, Box H, Brown University Providence, Rhode Island 02912-9108 Departments of Chemical Engineering, Chemistry and Biochemistry, Stanford University Stanford, California 94305-5025
| | - David E. Cane
- Department of Chemistry, Box H, Brown University Providence, Rhode Island 02912-9108 Departments of Chemical Engineering, Chemistry and Biochemistry, Stanford University Stanford, California 94305-5025
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150
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Kao CM, McPherson M, McDaniel RN, Fu H, Cane DE, Khosla C. Alcohol Stereochemistry in Polyketide Backbones Is Controlled by the β-Ketoreductase Domains of Modular Polyketide Synthases. J Am Chem Soc 1998. [DOI: 10.1021/ja973913a] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Camilla M. Kao
- Departments of Chemical Engineering Chemistry, and Biochemistry Stanford University Stanford, California 94305-5025 Department of Chemistry, Box H, Brown University Providence, Rhode Island 02912 KOSAN Biosciences, Inc., 1450 Rollins Road Burlingame, California 94010
| | - Michael McPherson
- Departments of Chemical Engineering Chemistry, and Biochemistry Stanford University Stanford, California 94305-5025 Department of Chemistry, Box H, Brown University Providence, Rhode Island 02912 KOSAN Biosciences, Inc., 1450 Rollins Road Burlingame, California 94010
| | - Robert N. McDaniel
- Departments of Chemical Engineering Chemistry, and Biochemistry Stanford University Stanford, California 94305-5025 Department of Chemistry, Box H, Brown University Providence, Rhode Island 02912 KOSAN Biosciences, Inc., 1450 Rollins Road Burlingame, California 94010
| | - Hong Fu
- Departments of Chemical Engineering Chemistry, and Biochemistry Stanford University Stanford, California 94305-5025 Department of Chemistry, Box H, Brown University Providence, Rhode Island 02912 KOSAN Biosciences, Inc., 1450 Rollins Road Burlingame, California 94010
| | - David E. Cane
- Departments of Chemical Engineering Chemistry, and Biochemistry Stanford University Stanford, California 94305-5025 Department of Chemistry, Box H, Brown University Providence, Rhode Island 02912 KOSAN Biosciences, Inc., 1450 Rollins Road Burlingame, California 94010
| | - Chaitan Khosla
- Departments of Chemical Engineering Chemistry, and Biochemistry Stanford University Stanford, California 94305-5025 Department of Chemistry, Box H, Brown University Providence, Rhode Island 02912 KOSAN Biosciences, Inc., 1450 Rollins Road Burlingame, California 94010
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