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Parascandolo JS, Havemann J, Potter HK, Huang F, Riva E, Connolly J, Wilkening I, Song L, Leadlay PF, Tosin M. Insights into 6-Methylsalicylic Acid Bio-assembly by Using Chemical Probes. Angew Chem Int Ed Engl 2016; 55:3463-7. [PMID: 26833898 PMCID: PMC4797705 DOI: 10.1002/anie.201509038] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 11/19/2015] [Indexed: 01/21/2023]
Abstract
Chemical probes capable of reacting with KS (ketosynthase)-bound biosynthetic intermediates were utilized for the investigation of the model type I iterative polyketide synthase 6-methylsalicylic acid synthase (6-MSAS) in vivo and in vitro. From the fermentation of fungal and bacterial 6-MSAS hosts in the presence of chain termination probes, a full range of biosynthetic intermediates was isolated and characterized for the first time. Meanwhile, in vitro studies of recombinant 6-MSA synthases with both nonhydrolyzable and hydrolyzable substrate mimics have provided additional insights into substrate recognition, providing the basis for further exploration of the enzyme catalytic activities.
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Affiliation(s)
- James S Parascandolo
- Department of Chemistry, University of Warwick, Library Road, Coventry, CV4 7AL, UK
| | - Judith Havemann
- Department of Chemistry, University of Warwick, Library Road, Coventry, CV4 7AL, UK
| | - Helen K Potter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Fanglu Huang
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Elena Riva
- Department of Chemistry, University of Warwick, Library Road, Coventry, CV4 7AL, UK
| | - Jack Connolly
- Department of Chemistry, University of Warwick, Library Road, Coventry, CV4 7AL, UK
- School of Biosciences, The University of Birmingham, Birmingham, B15 2TT, UK
| | - Ina Wilkening
- Department of Chemistry, University of Warwick, Library Road, Coventry, CV4 7AL, UK
| | - Lijiang Song
- Department of Chemistry, University of Warwick, Library Road, Coventry, CV4 7AL, UK
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Manuela Tosin
- Department of Chemistry, University of Warwick, Library Road, Coventry, CV4 7AL, UK.
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102
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Xie X, Garg A, Keatinge-Clay AT, Khosla C, Cane DE. Epimerase and Reductase Activities of Polyketide Synthase Ketoreductase Domains Utilize the Same Conserved Tyrosine and Serine Residues. Biochemistry 2016; 55:1179-86. [PMID: 26863427 DOI: 10.1021/acs.biochem.6b00024] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The role of the conserved active site tyrosine and serine residues in epimerization catalyzed by polyketide synthase ketoreductase (PKS KR) domains has been investigated. Both mutant and wild-type forms of epimerase-active KR domains, including the intrinsically redox-inactive EryKR3° and PicKR3° as well as redox-inactive mutants of EryKR1, were incubated with [2-(2)H]-(2R,3S)-2-methyl-3-hydroxypentanoyl-SACP ([2-(2)H]-2) and 0.05 equiv of NADP(+) in the presence of the redox-active, epimerase-inactive EryKR6 domain. The residual epimerase activity of each mutant was determined by tandem equilibrium isotope exchange, in which the first-order, time-dependent washout of isotope from 2 was monitored by liquid chromatography-tandem mass spectrometry with quantitation of the deuterium content of the diagnostic pantetheinate ejection fragment (4). Replacement of the active site Tyr or Ser residues, alone or together, significantly reduced the observed epimerase activity of each KR domain with minimal effect on substrate binding. Our results demonstrate that the epimerase and reductase activities of PKS KR domains share a common active site, with both reactions utilizing the same pair of Tyr and Ser residues.
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Affiliation(s)
- Xinqiang Xie
- Department of Chemistry, Box H, Brown University , Providence, Rhode Island 02912-9108, United States
| | - Ashish Garg
- Department of Chemistry, Box H, Brown University , Providence, Rhode Island 02912-9108, United States
| | - Adrian T Keatinge-Clay
- Departments of Molecular Biosciences and Chemistry, The University of Texas at Austin , 1 University Station A5300, Austin, Texas 78712-0165, United States
| | - Chaitan Khosla
- Departments of Chemical Engineering, Chemistry, and Biochemistry, Stanford University , Stanford, California 94305, United States
| | - David E Cane
- Department of Chemistry, Box H, Brown University , Providence, Rhode Island 02912-9108, United States
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103
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Lowry B, Li X, Robbins T, Cane DE, Khosla C. A Turnstile Mechanism for the Controlled Growth of Biosynthetic Intermediates on Assembly Line Polyketide Synthases. ACS CENTRAL SCIENCE 2016; 2:14-20. [PMID: 26878060 PMCID: PMC4731828 DOI: 10.1021/acscentsci.5b00321] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Indexed: 05/09/2023]
Abstract
Vectorial polyketide biosynthesis on an assembly line polyketide synthase is the most distinctive property of this family of biological machines, while providing the key conceptual tool for the bioinformatic decoding of new antibiotic pathways. We now show that the action of the entire assembly line is synchronized by a previously unrecognized turnstile mechanism that prevents the ketosynthase domain of each module from being acylated by a new polyketide chain until the product of the prior catalytic cycle has been passed to the downstream module from the corresponding acyl carrier protein domain. The turnstile is closed by virtue of tight coupling to the signature decarboxylative condensation reaction catalyzed by the ketosynthase domain of each polyketide synthase module. Reopening of the turnstile is coupled to the eventual chain translocation step that vacates the module. At the maximal rate of substrate turnover, one would expect the chain release step to initiate a cascade of chain translocation events that sequentially migrate back upstream, thereby repriming each module and setting up the assembly line for the next round of polyketide chain elongation.
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Affiliation(s)
- Brian Lowry
- Departments
of Chemistry and Chemical Engineering, Stanford
University, Stanford, California 94305, United States
| | - Xiuyuan Li
- Departments
of Chemistry and Chemical Engineering, Stanford
University, Stanford, California 94305, United States
| | - Thomas Robbins
- Departments
of Chemistry and Chemical Engineering, Stanford
University, Stanford, California 94305, United States
| | - David E. Cane
- Department
of Chemistry, Brown University, Providence, Rhode Island 02912-9108, United States
| | - Chaitan Khosla
- Departments
of Chemistry and Chemical Engineering, Stanford
University, Stanford, California 94305, United States
- E-mail: . Tel: (650) 723-6538
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104
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Finzel K, Burkart MD. Traffic Control in Modular Polyketide Synthases. ACS CENTRAL SCIENCE 2016; 2:9-11. [PMID: 27163020 PMCID: PMC4827489 DOI: 10.1021/acscentsci.6b00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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105
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Hagen A, Poust S, Rond TD, Fortman JL, Katz L, Petzold CJ, Keasling JD. Engineering a Polyketide Synthase for In Vitro Production of Adipic Acid. ACS Synth Biol 2016; 5:21-7. [PMID: 26501439 DOI: 10.1021/acssynbio.5b00153] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polyketides have enormous structural diversity, yet polyketide synthases (PKSs) have thus far been engineered to produce only drug candidates or derivatives thereof. Thousands of other molecules, including commodity and specialty chemicals, could be synthesized using PKSs if composing hybrid PKSs from well-characterized parts derived from natural PKSs was more efficient. Here, using modern mass spectrometry techniques as an essential part of the design-build-test cycle, we engineered a chimeric PKS to enable production one of the most widely used commodity chemicals, adipic acid. To accomplish this, we introduced heterologous reductive domains from various PKS clusters into the borrelidin PKS' first extension module, which we previously showed produces a 3-hydroxy-adipoyl intermediate when coincubated with the loading module and a succinyl-CoA starter unit. Acyl-ACP intermediate analysis revealed an unexpected bottleneck at the dehydration step, which was overcome by introduction of a carboxyacyl-processing dehydratase domain. Appending a thioesterase to the hybrid PKS enabled the production of free adipic acid. Using acyl-intermediate based techniques to "debug" PKSs as described here, it should one day be possible to engineer chimeric PKSs to produce a variety of existing commodity and specialty chemicals, as well as thousands of chemicals that are difficult to produce from petroleum feedstocks using traditional synthetic chemistry.
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Affiliation(s)
| | | | | | | | | | - Christopher J. Petzold
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
| | - Jay D. Keasling
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
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106
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Helfrich EJN, Piel J. Biosynthesis of polyketides by trans-AT polyketide synthases. Nat Prod Rep 2016; 33:231-316. [DOI: 10.1039/c5np00125k] [Citation(s) in RCA: 230] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review discusses the biosynthesis of natural products that are generated bytrans-AT polyketide synthases, a family of catalytically versatile enzymes that represents one of the major group of proteins involved in the production of bioactive polyketides.
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Affiliation(s)
- Eric J. N. Helfrich
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
| | - Jörn Piel
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
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107
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Weissman KJ. Genetic engineering of modular PKSs: from combinatorial biosynthesis to synthetic biology. Nat Prod Rep 2016; 33:203-30. [DOI: 10.1039/c5np00109a] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This reviews covers on-going efforts at engineering the gigantic modular polyketide synthases (PKSs), highlighting both notable successes and failures.
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Affiliation(s)
- Kira J. Weissman
- UMR 7365
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA)
- CNRS-Université de Lorraine
- Biopôle de l'Université de Lorraine
- 54505 Vandœuvre-lès-Nancy Cedex
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108
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Abstract
Polyketides are a structurally and functionally diverse family of bioactive natural products that have found widespread application as pharmaceuticals, agrochemicals, and veterinary medicines. In bacteria complex polyketides are biosynthesized by giant multifunctional megaenzymes, termed modular polyketide synthases (PKSs), which construct their products in a highly coordinated assembly line-like fashion from a pool of simple precursor substrates. Not only is the multifaceted enzymology of PKSs a fascinating target for study, but it also presents considerable opportunities for the reengineering of these systems affording access to functionally optimized unnatural natural products. Here we provide an introductory primer to modular polyketide synthase structure and function, and highlight recent advances in the characterization and exploitation of these systems.
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Affiliation(s)
- Marisa Till
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
- BrisSynBio Synthetic Biology Research Centre, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Paul R Race
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
- BrisSynBio Synthetic Biology Research Centre, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
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109
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Horsman ME, Hari TPA, Boddy CN. Polyketide synthase and non-ribosomal peptide synthetase thioesterase selectivity: logic gate or a victim of fate? Nat Prod Rep 2016; 33:183-202. [DOI: 10.1039/c4np00148f] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thioesterases (TEs) are product offloading enzymes from FAS, PKS, and NRPS complexes. We review the diversity, structure, and mechanism of PKS and NRPS TEs and analyze TE loading and release steps as possible logic gates with a view to predicting TE function in new pathways.
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Affiliation(s)
- Mark E. Horsman
- Department of chemistry
- Centre for Catalysis Research and Innovation
- University of Ottawa
- Canada
| | - Taylor P. A. Hari
- Department of chemistry
- Centre for Catalysis Research and Innovation
- University of Ottawa
- Canada
| | - Christopher N. Boddy
- Department of chemistry
- Centre for Catalysis Research and Innovation
- University of Ottawa
- Canada
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110
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References. Antibiotics (Basel) 2015. [DOI: 10.1128/9781555819316.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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111
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Abstract
Synthetic biology (SB) is an emerging discipline, which is slowly reorienting the field of drug discovery. For thousands of years, living organisms such as plants were the major source of human medicines. The difficulty in resynthesizing natural products, however, often turned pharmaceutical industries away from this rich source for human medicine. More recently, progress on transformation through genetic manipulation of biosynthetic units in microorganisms has opened the possibility of in-depth exploration of the large chemical space of natural products derivatives. Success of SB in drug synthesis culminated with the bioproduction of artemisinin by microorganisms, a tour de force in protein and metabolic engineering. Today, synthetic cells are not only used as biofactories but also used as cell-based screening platforms for both target-based and phenotypic-based approaches. Engineered genetic circuits in synthetic cells are also used to decipher disease mechanisms or drug mechanism of actions and to study cell-cell communication within bacteria consortia. This review presents latest developments of SB in the field of drug discovery, including some challenging issues such as drug resistance and drug toxicity.
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Affiliation(s)
| | - Pablo Carbonell
- Faculty of Life Sciences, SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- Department of Experimental and Health Sciences (DCEXS), Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Barcelona, Spain
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112
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Shelest E, Heimerl N, Fichtner M, Sasso S. Multimodular type I polyketide synthases in algae evolve by module duplications and displacement of AT domains in trans. BMC Genomics 2015; 16:1015. [PMID: 26611533 PMCID: PMC4661987 DOI: 10.1186/s12864-015-2222-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 11/16/2015] [Indexed: 11/16/2022] Open
Abstract
Background Polyketide synthase (PKS) catalyzes the biosynthesis of polyketides, which are structurally and functionally diverse natural products in microorganisms and plants. Here, we have analyzed available full genome sequences of microscopic and macroscopic algae for the presence of type I PKS genes. Results Type I PKS genes are present in 15 of 32 analyzed algal species. In chlorophytes, large proteins in the MDa range are predicted in most sequenced species, and PKSs with free-standing acyltransferase domains (trans-AT PKSs) predominate. In a phylogenetic tree, PKS sequences from different algal phyla form clades that are distinct from PKSs from other organisms such as non-photosynthetic protists or cyanobacteria. However, intermixing is observed in some cases, for example polyunsaturated fatty acid (PUFA) and glycolipid synthases of various origins. Close relationships between type I PKS modules from different species or between modules within the same multimodular enzyme were identified, suggesting module duplications during evolution of algal PKSs. In contrast to type I PKSs, nonribosomal peptide synthetases (NRPSs) are relatively rare in algae (occurrence in 7 of 32 species). Conclusions Our phylogenetic analysis of type I PKSs in algae supports an evolutionary scenario whereby integrated AT domains were displaced to yield trans-AT PKSs. Together with module duplications, the displacement of AT domains may constitute a major mechanism of PKS evolution in algae. This study advances our understanding of the diversity of eukaryotic PKSs and their evolutionary trajectories. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2222-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ekaterina Shelest
- Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany.
| | - Natalie Heimerl
- Institute of General Botany and Plant Physiology, Friedrich Schiller University, Dornburger Str. 159, 07743, Jena, Germany.
| | - Maximilian Fichtner
- Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany.
| | - Severin Sasso
- Institute of General Botany and Plant Physiology, Friedrich Schiller University, Dornburger Str. 159, 07743, Jena, Germany.
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113
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Wu H, Li W, Xin C, Zhang C, Wang Y, Ren S, Ren M, Zhao W, Yuan L, Xu Z, Yuan H, Geng M, Zhang L, Weaver DT, Zhang B. In vivo investigation to the macrolide-glycosylating enzyme pair DesVII/DesVIII in Saccharopolyspora erythraea. Appl Microbiol Biotechnol 2015; 100:2257-66. [PMID: 26552796 DOI: 10.1007/s00253-015-7036-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/07/2015] [Accepted: 09/17/2015] [Indexed: 11/25/2022]
Abstract
Glycosyltransferase DesVII and its auxiliary partner DesVIII from Streptomyces venezulae, homologs of EryCIII and EryCII in Saccharopolyspora erythraea, have previously been demonstrated to be flexible on their substrates in vitro. Herein, we investigated their in vivo function by interspecies complementation in the mutant strains of Sac. erythraea A226. As desVII and desVIII were concomitantly expressed in the ΔeryCIII mutant, the erythromycin A (Er-A) production was restored. Interestingly, co-expression of desVII and desVIII in the ΔeryBV mutant exhibited an increased Er-A yield by 15 % in comparison to A226. Hence, DesVII/DesVIII not only replaced EryCIII to upload D-desosamine to C5 position of 3-O-mycarosyl erythronolide B (MEB) but also in vivo attached L-mycarose, not D-desosamine to C3 position of erythronolide B (EB) with a higher activity than EryBV. Furthermore, expression of desVII in ΔeryCIII and ΔeryBV-CIII partially restored the Er-A production; however, no Er-A was detected while desVII was expressed in ΔeryBV. It was implicated that DesVII coupled with EryCII to form the DesVII/EryCII complex for attaching above two deoxysugars in the absence of EryCIII in Sac. erythraea. In addition, when desVII and desVIII were co-expressed in ΔeryBV-CII, Er-A was recovered with a lower yield than ΔeryBV-CIII. Our study presents an opportunity with Sac. erythraea as a cell factory for macrolide glycodiversification.
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Affiliation(s)
- Hang Wu
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Weiwei Li
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Chen Xin
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Congming Zhang
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Yansheng Wang
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Shaohua Ren
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Min Ren
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Wei Zhao
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Li Yuan
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Zhongdong Xu
- School of Life Sciences, Hefei Normal University, Hefei, 230601, China
| | - Hualing Yuan
- School of Life Sciences, Hefei Normal University, Hefei, 230601, China
| | - Ming Geng
- School of Life Sciences, Hefei Normal University, Hefei, 230601, China
| | - Lixin Zhang
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China. .,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - David T Weaver
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Buchang Zhang
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
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114
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Iterative polyketide biosynthesis by modular polyketide synthases in bacteria. Appl Microbiol Biotechnol 2015; 100:541-57. [PMID: 26549236 DOI: 10.1007/s00253-015-7093-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 10/10/2015] [Accepted: 10/13/2015] [Indexed: 10/22/2022]
Abstract
Modular polyketide synthases (type I PKSs) in bacteria are responsible for synthesizing a significant percentage of bioactive natural products. This group of synthases has a characteristic modular organization, and each module within a PKS carries out one cycle of polyketide chain elongation; thus each module is non-iterative in function. It was possible to predict the basic structure of a polyketide product from the module organization of the PKSs, since there generally existed a co-linearity between the number of modules and the number of chain elongations. However, more and more bacterial modular PKSs fail to conform to the canonical rules, and a particularly noteworthy group of non-canonical PKSs is the bacterial iterative type I PKSs. This review covers recent examples of iteratively used modular PKSs in bacteria. These non-canonical PKSs give rise to a large array of natural products with impressive structural diversity. The molecular mechanism behind the iterations is often unclear, presenting a new challenge to the rational engineering of these PKSs with the goal of generating new natural products. Structural elucidation of these synthase complexes and better understanding of potential PKS-PKS interactions as well as PKS-substrate recognition may provide new prospects and inspirations for the discovery and engineering of new bioactive polyketides.
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115
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The structural biology of biosynthetic megaenzymes. Nat Chem Biol 2015; 11:660-70. [PMID: 26284673 DOI: 10.1038/nchembio.1883] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/02/2015] [Indexed: 01/27/2023]
Abstract
The modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) are among the largest and most complicated enzymes in nature. In these biosynthetic systems, independently folding protein domains, which are organized into units called 'modules', operate in assembly-line fashion to construct polymeric chains and tailor their functionalities. Products of PKSs and NRPSs include a number of blockbuster medicines, and this has motivated researchers to understand how they operate so that they can be modified by genetic engineering. Beginning in the 1990s, structural biology has provided a number of key insights. The emerging picture is one of remarkable dynamics and conformational programming in which the chemical states of individual catalytic domains are communicated to the others, configuring the modules for the next stage in the biosynthesis. This unexpected level of complexity most likely accounts for the low success rate of empirical genetic engineering experiments and suggests ways forward for productive megaenzyme synthetic biology.
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116
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Escudero L, Al-Refai M, Nieto C, Laatsch H, Malpartida F, Seco EM. New Rimocidin/CE-108 Derivatives Obtained by a Crotonyl-CoA Carboxylase/Reductase Gene Disruption in Streptomyces diastaticus var. 108: Substrates for the Polyene Carboxamide Synthase PcsA. PLoS One 2015; 10:e0135891. [PMID: 26284936 PMCID: PMC4540446 DOI: 10.1371/journal.pone.0135891] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/27/2015] [Indexed: 11/19/2022] Open
Abstract
The rimJ gene, which codes for a crotonyl-CoA carboxylase/reductase, lies within the biosynthetic gene cluster for two polyketides belonging to the polyene macrolide group (CE-108 and rimocidin) produced by Streptomyces diastaticus var. 108. Disruption of rimJ by insertional inactivation gave rise to a recombinant strain overproducing new polyene derivatives besides the parental CE-108 (2a) and rimocidin (4a). The structure elucidation of one of them, CE-108D (3a), confirmed the incorporation of an alternative extender unit for elongation step 13. Other compounds were also overproduced in the fermentation broth of rimJ disruptant. The new compounds are in vivo substrates for the previously described polyene carboxamide synthase PcsA. The rimJ disruptant strain, constitutively expressing the pcsA gene, allowed the overproduction of CE-108E (3b), the corresponding carboxamide derivative of CE-108D (3a), with improved pharmacological properties.
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Affiliation(s)
- Leticia Escudero
- Centro Nacional de Biotecnología (CNB-CSIC), Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Mahmoud Al-Refai
- Department of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstrasse 2, D-37077, Göttingen, Germany
| | - Cristina Nieto
- Centro Nacional de Biotecnología (CNB-CSIC), Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Hartmut Laatsch
- Department of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstrasse 2, D-37077, Göttingen, Germany
| | - Francisco Malpartida
- Centro Nacional de Biotecnología (CNB-CSIC), Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Elena M. Seco
- Centro Nacional de Biotecnología (CNB-CSIC), Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
- * E-mail:
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Lowry B, Walsh CT, Khosla C. In Vitro Reconstitution of Metabolic Pathways: Insights into Nature's Chemical Logic. Synlett 2015; 26:1008-1025. [PMID: 26207083 PMCID: PMC4507746 DOI: 10.1055/s-0034-1380264] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In vitro analysis of metabolic pathways is becoming a powerful method to gain a deeper understanding of Nature's core biochemical transformations. With astounding advancements in biotechnology, purification of a metabolic pathway's constitutive enzymatic components is becoming a tractable problem, and such in vitro studies allow scientists to capture the finer details of enzymatic reaction mechanisms, kinetics, and the identity of organic product molecules. In this review, we present eleven metabolic pathways that have been the subject of in vitro reconstitution studies in the literature in recent years. In addition, we have selected and analyzed subset of four case studies within these eleven examples that exemplify remarkable organic chemistry occurring within biology. These examples serves as tangible reminders that Nature's biochemical routes obey the fundamental principles of organic chemistry, and the chemical mechanisms are reminiscent of those featured in traditional synthetic organic routes. The illustrations of biosynthetic chemistry depicted in this review may inspire the development of biomimetic chemistries via abiotic chemical techniques.
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Affiliation(s)
- Brian Lowry
- Department of Chemical Engineering, Stanford University, 443 Via Ortega, Stanford, CA 94305, USA;
| | - Christopher T Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA 94305
| | - Chaitan Khosla
- Department of Chemical Engineering, Stanford University, 443 Via Ortega, Stanford, CA 94305, USA; ; Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA 94305 ; Department of Chemistry, 333 Campus Drive Mudd Building, Stanford University, Stanford, CA 94305, USA;
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Zhang G, Li Y, Fang L, Pfeifer BA. Tailoring pathway modularity in the biosynthesis of erythromycin analogs heterologously engineered in E. coli. SCIENCE ADVANCES 2015; 1:e1500077. [PMID: 26601183 PMCID: PMC4640655 DOI: 10.1126/sciadv.1500077] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/11/2015] [Indexed: 05/26/2023]
Abstract
Type I modular polyketide synthases are responsible for potent therapeutic compounds that include avermectin (antihelinthic), rapamycin (immunosuppressant), pikromycin (antibiotic), and erythromycin (antibiotic). However, compound access and biosynthetic manipulation are often complicated by properties of native production organisms, prompting an approach (termed heterologous biosynthesis) illustrated in this study through the reconstitution of the erythromycin pathway through Escherichia coli. Using this heterologous system, 16 tailoring pathways were introduced, systematically producing eight chiral pairs of deoxysugar substrates. Successful analog formation for each new pathway emphasizes the remarkable flexibility of downstream enzymes to accommodate molecular variation. Furthermore, analogs resulting from three of the pathways demonstrated bioactivity against an erythromycin-resistant Bacillus subtilis strain. The approach and results support a platform for continued molecular diversification of the tailoring components of this and other complex natural product pathways in a manner that mirrors the modular nature of the upstream megasynthases responsible for aglycone polyketide formation.
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Gao BW, Wang XH, Liu X, Shi SP, Tu PF. Rapid preparation of (methyl)malonyl coenzyme A and enzymatic formation of unusual polyketides by type III polyketide synthase from Aquilaria sinensis. Bioorg Med Chem Lett 2015; 25:1279-83. [PMID: 25677661 DOI: 10.1016/j.bmcl.2015.01.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 01/07/2015] [Accepted: 01/21/2015] [Indexed: 10/24/2022]
Abstract
(Methyl)malonyl coenzyme A was rapidly and effectively synthesized by a two-step procedure involving preparation of N-hydroxysuccinimidyl (methyl)malonate from (methyl)Meldrum's acid, and followed by transesterification with coenzyme A. The synthesized (methyl)malonyl coenzyme A could be well accepted and assembled to 4-hydroxy phenylpropionyl coenzyme A by type III polyketide synthase from Aquilaria sinensis to produce dihydrochalcone and 4-hydroxy-3,5-dimethyl-6-(4-hydroxyphenethyl)-2H-pyrone as well as 4-hydroxy-3,5-dimethyl-6-(5-(4-hydroxyphenyl)-3-oxopentan-2-yl)-2H-pyrone.
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Affiliation(s)
- Bo-Wen Gao
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China; School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China; Baotou Medical College, Baotou 014060, China
| | - Xiao-Hui Wang
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xiao Liu
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - She-Po Shi
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China.
| | - Peng-Fei Tu
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China.
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Cacho RA, Tang Y, Chooi YH. Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi. Front Microbiol 2015; 5:774. [PMID: 25642215 PMCID: PMC4294208 DOI: 10.3389/fmicb.2014.00774] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 12/17/2014] [Indexed: 12/20/2022] Open
Abstract
Genomics has revolutionized the research on fungal secondary metabolite (SM) biosynthesis. To elucidate the molecular and enzymatic mechanisms underlying the biosynthesis of a specific SM compound, the important first step is often to find the genes that responsible for its synthesis. The accessibility to fungal genome sequences allows the bypass of the cumbersome traditional library construction and screening approach. The advance in next-generation sequencing (NGS) technologies have further improved the speed and reduced the cost of microbial genome sequencing in the past few years, which has accelerated the research in this field. Here, we will present an example work flow for identifying the gene cluster encoding the biosynthesis of SMs of interest using an NGS approach. We will also review the different strategies that can be employed to pinpoint the targeted gene clusters rapidly by giving several examples stemming from our work.
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Affiliation(s)
- Ralph A Cacho
- Chemical and Biomolecular Engineering Department, University of California Los Angeles, Los Angeles, CA, USA
| | - Yi Tang
- Chemical and Biomolecular Engineering Department, University of California Los Angeles, Los Angeles, CA, USA ; Chemistry and Biochemistry Department, University of California Los Angeles, Los Angeles, CA, USA
| | - Yit-Heng Chooi
- Plant Sciences Division, Research School of Biology, The Australian National University Canberra, ACT, Australia
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Gajzlerska W, Kurkowiak J, Turło J. Use of three-carbon chain compounds as biosynthesis precursors to enhance tacrolimus production in Streptomyces tsukubaensis. N Biotechnol 2015; 32:32-9. [DOI: 10.1016/j.nbt.2014.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Revised: 07/06/2014] [Accepted: 07/17/2014] [Indexed: 01/11/2023]
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Wu H, Chen M, Mao Y, Li W, Liu J, Huang X, Zhou Y, Ye BC, Zhang L, Weaver DT, Zhang B. Dissecting and engineering of the TetR family regulator SACE_7301 for enhanced erythromycin production in Saccharopolyspora erythraea. Microb Cell Fact 2014; 13:158. [PMID: 25391994 PMCID: PMC4258057 DOI: 10.1186/s12934-014-0158-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 10/23/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Saccharopolyspora erythraea was extensively utilized for the industrial-scale production of erythromycin A (Er-A), a macrolide antibiotic commonly used in human medicine. Yet, S. erythraea lacks regulatory genes in the erythromycin biosynthetic gene (ery) cluster, hampering efforts to enhance Er-A production via the engineering of regulatory genes. RESULTS By the chromosome gene inactivation technique based on homologous recombination with linearized DNA fragments, we have inactivated a number of candidate TetR family transcriptional regulators (TFRs) and identified one TFR (SACE_7301) positively controlling erythromycin biosynthesis in S. erythraea A226. qRT-PCR and EMSA analyses demonstrated that SACE_7301 activated the transcription of erythromycin biosynthetic gene eryAI and the resistance gene ermE by interacting with their promoter regions with low affinities, similar to BldD (SACE_2077) previously identified to regulate erythromycin biosynthesis and morphological differentiation. Therefore, we designed a strategy for overexpressing SACE_7301 with 1 to 3 extra copies under the control of PermE* in A226. Following up-regulated transcriptional expression of SACE_7301, eryAI and ermE, the SACE_7301-overexpressed strains all increased Er-A production over A226 proportional to the number of copies. Likewise, when SACE_7301 was overexpressed in an industrial S. erythraea WB strain, Er-A yields of the mutants WB/7301, WB/2×7301 and WB/3×7301 were respectively increased by 17%, 29% and 42% relative to that of WB. In a 5 L fermentor, Er-A accumulation increased to 4,230 mg/L with the highest-yield strain WB/3×7301, an approximately 27% production improvement over WB (3,322 mg/L). CONCLUSIONS We have identified and characterized a TFR, SACE_7301, in S. erythraea that positively regulated erythromycin biosynthesis, and overexpression of SACE_7301 in wild-type and industrial S. erythraea strains enhanced Er-A yields. This study markedly improves our understanding of the unusual regulatory mechanism of erythromycin biosynthesis, and provides a novel strategy towards Er-A overproduction by engineering transcriptional regulators of S. erythraea.
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Affiliation(s)
- Hang Wu
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Meng Chen
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Yongrong Mao
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Weiwei Li
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Jingtao Liu
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China. .,Beijing Institute of Cell Biotechnology, Beijing, 100043, China.
| | - Xunduan Huang
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Ying Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China.
| | - Bang-Ce Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China.
| | - Lixin Zhang
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China. .,CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - David T Weaver
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Buchang Zhang
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
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Hari TPA, Labana P, Boileau M, Boddy CN. An evolutionary model encompassing substrate specificity and reactivity of type I polyketide synthase thioesterases. Chembiochem 2014; 15:2656-61. [PMID: 25354333 DOI: 10.1002/cbic.201402475] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Indexed: 11/10/2022]
Abstract
Bacterial polyketides are a rich source of chemical diversity and pharmaceutical agents. Understanding the biochemical basis for their biosynthesis and the evolutionary driving force leading to this diversity is essential to take advantage of the enzymes as biocatalysts and to access new chemical diversity for drug discovery. Biochemical characterization of the thioesterase (TE) responsible for 6-deoxyerythronolide macrocyclization shows that a small, evolutionarily accessible change to the substrate can increase the chemical diversity of products, including macrodiolide formation. We propose an evolutionary model in which TEs are by nature non-selective for the type of chemistry they catalyze, producing a range of metabolites. As one metabolite becomes essential for improving fitness in a particular environment, the TE evolves to enrich for that corresponding reactivity. This hypothesis is supported by our phylogenetic analysis, showing convergent evolution of macrodiolide-forming TEs.
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Affiliation(s)
- Taylor P A Hari
- Departments of Chemistry and Biology, Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON K1N 6N5 (Canada)
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125
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Wang Y, Xu H, Harich KC, White RH. Identification and Characterization of a Tyramine–Glutamate Ligase (MfnD) Involved in Methanofuran Biosynthesis. Biochemistry 2014; 53:6220-30. [DOI: 10.1021/bi500879h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Yu Wang
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Huimin Xu
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Kim C. Harich
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Robert H. White
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
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Vederas JC. Explorations of fungal biosynthesis of reduced polyketides – a personal viewpoint. Nat Prod Rep 2014; 31:1253-9. [DOI: 10.1039/c4np00091a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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128
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Edwards AL, Matsui T, Weiss TM, Khosla C. Architectures of whole-module and bimodular proteins from the 6-deoxyerythronolide B synthase. J Mol Biol 2014; 426:2229-45. [PMID: 24704088 PMCID: PMC4284093 DOI: 10.1016/j.jmb.2014.03.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 03/24/2014] [Accepted: 03/27/2014] [Indexed: 10/25/2022]
Abstract
The 6-deoxyerythronolide B synthase (DEBS) is a prototypical assembly line polyketide synthase produced by the actinomycete Saccharopolyspora erythraea that synthesizes the macrocyclic core of the antibiotic erythromycin 6-deoxyerythronolide B. The megasynthase is a 2-MDa trimeric complex composed of three unique homodimers assembled from the gene products DEBS1, DEBS2, and DEBS3, which are housed within the erythromycin biosynthetic gene cluster. Each homodimer contains two clusters of catalytically independent enzymatic domains, each referred to as a module, which catalyzes one round of polyketide chain extension and modification. Modules are named sequentially to indicate the order in which they are utilized during synthesis of 6-deoxyerythronolide B. We report small-angle X-ray scattering (SAXS) analyses of a whole module and a bimodule from DEBS, as well as a set of domains for which high-resolution structures are available. In all cases, the solution state was probed under previously established conditions ensuring that each protein is catalytically active. SAXS data are consistent with atomic-resolution structures of DEBS fragments. Therefore, we used the available high-resolution structures of DEBS domains to model the architectures of the larger protein assemblies using rigid-body refinement. Our data support a model in which the third module of DEBS forms a disc-shaped structure capable of caging the acyl carrier protein domain proximal to each active site. The molecular envelope of DEBS3 is a thin elongated ellipsoid, and the results of rigid-body modeling suggest that modules 5 and 6 stack collinearly along the 2-fold axis of symmetry.
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Affiliation(s)
- Andrea L Edwards
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 14 2575 Sand Hill Road, MS69, Menlo Park, CA 94025, USA
| | - Thomas M Weiss
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 14 2575 Sand Hill Road, MS69, Menlo Park, CA 94025, USA
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
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Khosla C, Herschlag D, Cane DE, Walsh CT. Assembly line polyketide synthases: mechanistic insights and unsolved problems. Biochemistry 2014; 53:2875-83. [PMID: 24779441 PMCID: PMC4020578 DOI: 10.1021/bi500290t] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Two hallmarks of assembly line polyketide synthases have motivated an interest in these unusual multienzyme systems, their stereospecificity and their capacity for directional biosynthesis. In this review, we summarize the state of knowledge regarding the mechanistic origins of these two remarkable features, using the 6-deoxyerythronolide B synthase as a prototype. Of the 10 stereocenters in 6-deoxyerythronolide B, the stereochemistry of nine carbon atoms is directly set by ketoreductase domains, which catalyze epimerization and/or diastereospecific reduction reactions. The 10th stereocenter is established by the sequential action of three enzymatic domains. Thus, the problem has been reduced to a challenge in mainstream enzymology, where fundamental gaps remain in our understanding of the structural basis for this exquisite stereochemical control by relatively well-defined active sites. In contrast, testable mechanistic hypotheses for the phenomenon of vectorial biosynthesis are only just beginning to emerge. Starting from an elegant theoretical framework for understanding coupled vectorial processes in biology [Jencks, W. P. (1980) Adv. Enzymol. Relat. Areas Mol. Biol. 51, 75-106], we present a simple model that can explain assembly line polyketide biosynthesis as a coupled vectorial process. Our model, which highlights the important role of domain-domain interactions, not only is consistent with recent observations but also is amenable to further experimental verification and refinement. Ultimately, a definitive view of the coordinated motions within and between polyketide synthase modules will require a combination of structural, kinetic, spectroscopic, and computational tools and could be one of the most exciting frontiers in 21st Century enzymology.
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Affiliation(s)
- Chaitan Khosla
- Departments of Chemical Engineering, Chemistry, and Biochemistry, Stanford University , Stanford, California 94305, United States
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131
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Cummings M, Breitling R, Takano E. Steps towards the synthetic biology of polyketide biosynthesis. FEMS Microbiol Lett 2014; 351:116-25. [PMID: 24372666 PMCID: PMC4237116 DOI: 10.1111/1574-6968.12365] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 12/16/2013] [Accepted: 12/17/2013] [Indexed: 11/29/2022] Open
Abstract
Nature is providing a bountiful pool of valuable secondary metabolites, many of which possess therapeutic properties. However, the discovery of new bioactive secondary metabolites is slowing down, at a time when the rise of multidrug-resistant pathogens and the realization of acute and long-term side effects of widely used drugs lead to an urgent need for new therapeutic agents. Approaches such as synthetic biology are promising to deliver a much-needed boost to secondary metabolite drug development through plug-and-play optimized hosts and refactoring novel or cryptic bacterial gene clusters. Here, we discuss this prospect focusing on one comprehensively studied class of clinically relevant bioactive molecules, the polyketides. Extensive efforts towards optimization and derivatization of compounds via combinatorial biosynthesis and classical engineering have elucidated the modularity, flexibility and promiscuity of polyketide biosynthetic enzymes. Hence, a synthetic biology approach can build upon a solid basis of guidelines and principles, while providing a new perspective towards the discovery and generation of novel and new-to-nature compounds. We discuss the lessons learned from the classical engineering of polyketide synthases and indicate their importance when attempting to engineer biosynthetic pathways using synthetic biology approaches for the introduction of novelty and overexpression of products in a controllable manner.
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Affiliation(s)
- Matthew Cummings
- Faculty of Life Sciences, Manchester Institute of Biotechnology, The University of ManchesterManchester, UK
| | - Rainer Breitling
- Faculty of Life Sciences, Manchester Institute of Biotechnology, The University of ManchesterManchester, UK
| | - Eriko Takano
- Faculty of Life Sciences, Manchester Institute of Biotechnology, The University of ManchesterManchester, UK
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Kirm B, Magdevska V, Tome M, Horvat M, Karničar K, Petek M, Vidmar R, Baebler S, Jamnik P, Fujs Š, Horvat J, Fonovič M, Turk B, Gruden K, Petković H, Kosec G. SACE_5599, a putative regulatory protein, is involved in morphological differentiation and erythromycin production in Saccharopolyspora erythraea. Microb Cell Fact 2013; 12:126. [PMID: 24341557 PMCID: PMC3878487 DOI: 10.1186/1475-2859-12-126] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 12/10/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Erythromycin is a medically important antibiotic, biosynthesized by the actinomycete Saccharopolyspora erythraea. Genes encoding erythromycin biosynthesis are organized in a gene cluster, spanning over 60 kbp of DNA. Most often, gene clusters encoding biosynthesis of secondary metabolites contain regulatory genes. In contrast, the erythromycin gene cluster does not contain regulatory genes and regulation of its biosynthesis has therefore remained poorly understood, which has for a long time limited genetic engineering approaches for erythromycin yield improvement. RESULTS We used a comparative proteomic approach to screen for potential regulatory proteins involved in erythromycin biosynthesis. We have identified a putative regulatory protein SACE_5599 which shows significantly higher levels of expression in an erythromycin high-producing strain, compared to the wild type S. erythraea strain. SACE_5599 is a member of an uncharacterized family of putative regulatory genes, located in several actinomycete biosynthetic gene clusters. Importantly, increased expression of SACE_5599 was observed in the complex fermentation medium and at controlled bioprocess conditions, simulating a high-yield industrial fermentation process in the bioreactor. Inactivation of SACE_5599 in the high-producing strain significantly reduced erythromycin yield, in addition to drastically decreasing sporulation intensity of the SACE_5599-inactivated strains when cultivated on ABSM4 agar medium. In contrast, constitutive overexpression of SACE_5599 in the wild type NRRL23338 strain resulted in an increase of erythromycin yield by 32%. Similar yield increase was also observed when we overexpressed the bldD gene, a previously identified regulator of erythromycin biosynthesis, thereby for the first time revealing its potential for improving erythromycin biosynthesis. CONCLUSIONS SACE_5599 is the second putative regulatory gene to be identified in S. erythraea which has positive influence on erythromycin yield. Like bldD, SACE_5599 is involved in morphological development of S. erythraea, suggesting a very close relationship between secondary metabolite biosynthesis and morphological differentiation in this organism. While the mode of action of SACE_5599 remains to be elucidated, the manipulation of this gene clearly shows potential for improvement of erythromycin production in S. erythraea in industrial setting. We have also demonstrated the applicability of the comparative proteomics approach for identifying new regulatory elements involved in biosynthesis of secondary metabolites in industrial conditions.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Hrvoje Petković
- Acies Bio, d,o,o, Tehnološki park 21, SI-1000, Ljubljana, Slovenia.
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133
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O'Brien RV, Davis RW, Khosla C, Hillenmeyer ME. Computational identification and analysis of orphan assembly-line polyketide synthases. J Antibiot (Tokyo) 2013; 67:89-97. [PMID: 24301183 DOI: 10.1038/ja.2013.125] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 10/30/2013] [Accepted: 10/31/2013] [Indexed: 01/13/2023]
Abstract
The increasing availability of DNA sequence data offers an opportunity for identifying new assembly-line polyketide synthases (PKSs) that produce biologically active natural products. We developed an automated method to extract and consolidate all multimodular PKS sequences (including hybrid PKS/non-ribosomal peptide synthetases) in the National Center for Biotechnology Information (NCBI) database, generating a non-redundant catalog of 885 distinct assembly-line PKSs, the majority of which were orphans associated with no known polyketide product. Two in silico experiments highlight the value of this search method and resulting catalog. First, we identified an orphan that could be engineered to produce an analog of albocycline, an interesting antibiotic whose gene cluster has not yet been sequenced. Second, we identified and analyzed a hitherto overlooked family of metazoan multimodular PKSs, including one from Caenorhabditis elegans. We also developed a comparative analysis method that identified sequence relationships among known and orphan PKSs. As expected, PKS sequences clustered according to structural similarities between their polyketide products. The utility of this method was illustrated by highlighting an interesting orphan from the genus Burkholderia that has no close relatives. Our search method and catalog provide a community resource for the discovery of new families of assembly-line PKSs and their antibiotic products.
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Affiliation(s)
| | - Ronald W Davis
- 1] Department of Biochemistry, Stanford University, Stanford, CA, USA [2] Stanford Genome Technology Center, 855 South California Avenue, Palo Alto, CA, USA
| | - Chaitan Khosla
- 1] Department of Chemistry, Stanford University, Stanford, CA, USA [2] Department of Biochemistry, Stanford University, Stanford, CA, USA [3] Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Maureen E Hillenmeyer
- 1] Department of Biochemistry, Stanford University, Stanford, CA, USA [2] Stanford Genome Technology Center, 855 South California Avenue, Palo Alto, CA, USA
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Lin TY, Borketey LS, Prasad G, Waters SA, Schnarr NA. Sequence, cloning, and analysis of the fluvirucin B1 polyketide synthase from Actinomadura vulgaris. ACS Synth Biol 2013; 2:635-42. [PMID: 23654262 DOI: 10.1021/sb4000355] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluvirucin B1 , produced by Actinomadura vulgaris, is a 14-membered macrolactam active against a variety of infectious fungi as well as influenza A. Despite considerable interest from the synthetic community, very little information is available regarding the biosynthetic origins of the fluvirucins. Herein, we report the identification and initial characterization of the fluvirucin B1 polyketide synthase and related enzymes. The cluster consists of five extender modules flanked by an N-terminal acyl carrier protein and C-terminal thioesterase domain. All but one of the synthase modules contain the full complement of tailoring domains (ketoreductase, dehydratase, and enoyl reductase) as determined by sequence homology with known polyketide synthases. Acitve site analyses of several key components of the cluster are performed to further verify that this gene cluster is associated with production of fluvirucin B1 . This work will both open doors toward a better understanding of macrolactam formation and provide an avenue to genetics-based diversification of fluvirucin structure.
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Affiliation(s)
- Tsung-Yi Lin
- Department of Chemistry, University of Massachusetts, 710 N. Pleasant Street,
Amherst, Massachusetts 01003, United States
| | - Lawrence S. Borketey
- Department of Chemistry, University of Massachusetts, 710 N. Pleasant Street,
Amherst, Massachusetts 01003, United States
| | - Gitanjeli Prasad
- Department of Chemistry, University of Massachusetts, 710 N. Pleasant Street,
Amherst, Massachusetts 01003, United States
| | - Stephanie A. Waters
- Department of Chemistry, University of Massachusetts, 710 N. Pleasant Street,
Amherst, Massachusetts 01003, United States
| | - Nathan A. Schnarr
- Department of Chemistry, University of Massachusetts, 710 N. Pleasant Street,
Amherst, Massachusetts 01003, United States
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Lowry B, Robbins T, Weng CH, O'Brien RV, Cane DE, Khosla C. In vitro reconstitution and analysis of the 6-deoxyerythronolide B synthase. J Am Chem Soc 2013; 135:16809-12. [PMID: 24161212 DOI: 10.1021/ja409048k] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Notwithstanding an extensive literature on assembly line polyketide synthases such as the 6-deoxyerythronolide B synthase (DEBS), a complete naturally occurring synthase has never been reconstituted in vitro from purified protein components. Here, we describe the fully reconstituted DEBS and quantitatively characterize some of the properties of the assembled system that have never been explored previously. The maximum turnover rate of the complete hexamodular system is 1.1 min(-1), comparable to the turnover rate of a truncated trimodular derivative (2.5 min(-1)) but slower than that of a bimodular derivative (21 min(-1)). In the presence of similar concentrations of methylmalonyl- and ethylmalonyl-CoA substrates, DEBS synthesizes multiple regiospecifically modified analogues, one of which we have analyzed in detail. Our studies lay the foundation for biochemically interrogating and rationally engineering polyketide assembly lines in an unprecedented manner.
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Affiliation(s)
- Brian Lowry
- Department of Chemical Engineering, ‡Department of Chemistry, §School of Medicine, and ⊥Medical Science Training Program, Stanford University , Stanford, California 94305, United States
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136
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Whicher JR, Smaga SS, Hansen DA, Brown WC, Gerwick WH, Sherman DH, Smith JL. Cyanobacterial polyketide synthase docking domains: a tool for engineering natural product biosynthesis. ACTA ACUST UNITED AC 2013; 20:1340-51. [PMID: 24183970 DOI: 10.1016/j.chembiol.2013.09.015] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 09/09/2013] [Accepted: 09/20/2013] [Indexed: 11/25/2022]
Abstract
Modular type I polyketide synthases (PKSs) are versatile biosynthetic systems that initiate, successively elongate, and modify acyl chains. Intermediate transfer between modules is mediated via docking domains, which are attractive targets for PKS pathway engineering to produce natural product analogs. We identified a class 2 docking domain in cyanobacterial PKSs and determined crystal structures for two docking domain pairs, revealing a distinct class 2 docking strategy for promoting intermediate transfer. The selectivity of class 2 docking interactions, demonstrated in binding and biochemical assays, could be altered by mutagenesis. We determined the ideal fusion location for exchanging class 1 and class 2 docking domains and demonstrated effective polyketide chain transfer in heterologous modules. Thus, class 2 docking domains are tools for rational bioengineering of a broad range of PKSs containing either class 1 or 2 docking domains.
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Affiliation(s)
- Jonathan R Whicher
- Chemical Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
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137
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Garg A, Khosla C, Cane DE. Coupled methyl group epimerization and reduction by polyketide synthase ketoreductase domains. Ketoreductase-catalyzed equilibrium isotope exchange. J Am Chem Soc 2013; 135:16324-7. [PMID: 24161343 DOI: 10.1021/ja408944s] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Incubation of [2-(2)H]-(2S,3R)-2-methyl-3-hydroxypentanoyl-SACP ([2-(2)H]-1a) with the epimerizing ketoreductase domain EryKR1 in the presence of a catalytic amount NADP(+) (0.05 equiv) resulted in time- and cofactor-dependent washout of deuterium from 1a, as a result of equilibrium isotope exchange of transiently generated [2-(2)H]-2-methyl-3-ketopentanoyl-ACP. Incubations of [2-(2)H]-(2S,3S)-2-methyl-3-hydroxy-pentanoyl-SACP with RifKR7 and with NysKR1 also resulted in time-dependent loss of deuterium. By contrast, incubations of [2-(2)H]-(2R,3S)-2-methyl-3-hydroxypentanoyl-SACP and [2-(2)H]-(2R,3R)-2-methyl-3-hydroxypentanoyl-SACP with the non-epimerizing ketoreductase domains EryKR6 and TylKR1, respectively, did not result in any significant washout of deuterium. The isotope exchange assay directly establishes that specific polyketide synthase ketoreductase domains also have an intrinsic epimerase activity, thus enabling mechanistic analysis of a key determinant of polyketide stereocomplexity.
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Affiliation(s)
- Ashish Garg
- Department of Chemistry, Brown University , Providence, Rhode Island 02912-9108, United States
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138
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Makitrynskyy R, Ostash B, Tsypik O, Rebets Y, Doud E, Meredith T, Luzhetskyy A, Bechthold A, Walker S, Fedorenko V. Pleiotropic regulatory genes bldA, adpA and absB are implicated in production of phosphoglycolipid antibiotic moenomycin. Open Biol 2013; 3:130121. [PMID: 24153004 PMCID: PMC3814723 DOI: 10.1098/rsob.130121] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Unlike the majority of actinomycete secondary metabolic pathways, the biosynthesis of peptidoglycan glycosyltransferase inhibitor moenomycin in Streptomyces ghanaensis does not involve any cluster-situated regulators (CSRs). This raises questions about the regulatory signals that initiate and sustain moenomycin production. We now show that three pleiotropic regulatory genes for Streptomyces morphogenesis and antibiotic production—bldA, adpA and absB—exert multi-layered control over moenomycin biosynthesis in native and heterologous producers. The bldA gene for tRNALeuUAA is required for the translation of rare UUA codons within two key moenomycin biosynthetic genes (moe), moeO5 and moeE5. It also indirectly influences moenomycin production by controlling the translation of the UUA-containing adpA and, probably, other as-yet-unknown repressor gene(s). AdpA binds key moe promoters and activates them. Furthermore, AdpA interacts with the bldA promoter, thus impacting translation of bldA-dependent mRNAs—that of adpA and several moe genes. Both adpA expression and moenomycin production are increased in an absB-deficient background, most probably because AbsB normally limits adpA mRNA abundance through ribonucleolytic cleavage. Our work highlights an underappreciated strategy for secondary metabolism regulation, in which the interaction between structural genes and pleiotropic regulators is not mediated by CSRs. This strategy might be relevant for a growing number of CSR-free gene clusters unearthed during actinomycete genome mining.
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Affiliation(s)
- Roman Makitrynskyy
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv 79005, Ukraine
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139
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Peirú S, Gramajo HC, Menzella HG. Recombinant approaches to large polyketide molecules as potential drugs. DRUG DISCOVERY TODAY. TECHNOLOGIES 2013; 7:e95-e146. [PMID: 24103720 DOI: 10.1016/j.ddtec.2010.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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140
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141
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Sinha R, Singh S, Srivastava P. Studies on process optimization methods for rapamycin production using Streptomyces hygroscopicus ATCC 29253. Bioprocess Biosyst Eng 2013; 37:829-40. [PMID: 24048754 DOI: 10.1007/s00449-013-1051-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 09/05/2013] [Indexed: 10/26/2022]
Abstract
Rapamycin is a high-value product finding immense use as a drug, in organ transplantation, and as a potential immunosuppressant. Optimization of fermentation parameters of rapamycin production by Streptomyces hygroscopicus NRRL 5491 has been carried out. The low titer value of rapamycin in the original producer strain limits its applicability at industrial level. This study aims at improving the production of rapamycin by optimizing the nutrient requirements. Addition of L-lysine increased the production of rapamycin up to a significant level which supports the fact that it acts as precursor for rapamycin production, as found in previous studies. Effect of optimized medium on the Streptomyces growth rate as well as rapamycin production has been studied. The optimization study incorporates one at a time parameter optimization studies followed by tool-based hybrid methodology. This methodology includes the Plackett-Burman design (PBD) method, artificial neural networks (ANN), and genetic algorithms (GA). PBD screened mannose, soyabean meal, and L-lysine concentrations as significant factors for rapamycin production. ANN was used to construct rapamycin production model. This strategy has led to a significant increase of rapamycin production up to 320.89 mg/L at GA optimized concentrations of 25.47, 15.39, and 17.48 g/L for mannose, soyabean meal, and L-lysine, respectively. The present study must find its application in scale-up study for industrial level production of rapamycin.
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Affiliation(s)
- Rupika Sinha
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
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142
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Li YY, Chang X, Yu WB, Li H, Ye ZQ, Yu H, Liu BH, Zhang Y, Zhang SL, Ye BC, Li YX. Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains. BMC Genomics 2013; 14:523. [PMID: 23902230 PMCID: PMC3733707 DOI: 10.1186/1471-2164-14-523] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 07/26/2013] [Indexed: 11/20/2022] Open
Abstract
Background S. erythraea is a Gram-positive filamentous bacterium used for the industrial-scale production of erythromycin A which is of high clinical importance. In this work, we sequenced the whole genome of a high-producing strain (E3) obtained by random mutagenesis and screening from the wild-type strain NRRL23338, and examined time-series expression profiles of both E3 and NRRL23338. Based on the genomic data and transcriptpmic data of these two strains, we carried out comparative analysis of high-producing strain and wild-type strain at both the genomic level and the transcriptomic level. Results We observed a large number of genetic variants including 60 insertions, 46 deletions and 584 single nucleotide variations (SNV) in E3 in comparison with NRRL23338, and the analysis of time series transcriptomic data indicated that the genes involved in erythromycin biosynthesis and feeder pathways were significantly up-regulated during the 60 hours time-course. According to our data, BldD, a previously identified ery cluster regulator, did not show any positive correlations with the expression of ery cluster, suggesting the existence of alternative regulation mechanisms of erythromycin synthesis in S. erythraea. Several potential regulators were then proposed by integration analysis of genomic and transcriptomic data. Conclusion This is a demonstration of the functional comparative genomics between an industrial S. erythraea strain and the wild-type strain. These findings help to understand the global regulation mechanisms of erythromycin biosynthesis in S. erythraea, providing useful clues for genetic and metabolic engineering in the future.
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143
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Abstract
Antibiotic discovery has a storied history. From the discovery of penicillin by Sir Alexander Fleming to the relentless quest for antibiotics by Selman Waksman, the stories have become like folklore used to inspire future generations of scientists. However, recent discovery pipelines have run dry at a time when multidrug-resistant pathogens are on the rise. Nature has proven to be a valuable reservoir of antimicrobial agents, which are primarily produced by modularized biochemical pathways. Such modularization is well suited to remodeling by an interdisciplinary approach that spans science and engineering. Herein, we discuss the biological engineering of small molecules, peptides, and non-traditional antimicrobials and provide an overview of the growing applicability of synthetic biology to antimicrobials discovery.
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Affiliation(s)
- Bijan Zakeri
- Synthetic Biology Group, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square, Cambridge MA 02139, USA
| | - Timothy K. Lu
- Synthetic Biology Group, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square, Cambridge MA 02139, USA
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144
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Williams GJ. Engineering polyketide synthases and nonribosomal peptide synthetases. Curr Opin Struct Biol 2013; 23:603-12. [PMID: 23838175 DOI: 10.1016/j.sbi.2013.06.012] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 06/14/2013] [Accepted: 06/17/2013] [Indexed: 01/05/2023]
Abstract
Naturally occurring polyketides and nonribosomal peptides with broad and potent biological activities continue to inspire the discovery of new and improved analogs. The biosynthetic apparatus responsible for the construction of these natural products has been the target of intensive protein engineering efforts. Traditionally, engineering has focused on substituting individual enzymatic domains or entire modules with those of different building block specificity, or by deleting various enzymatic functions, in an attempt to generate analogs. This review highlights strategies based on site-directed mutagenesis of substrate binding pockets, semi-rational mutagenesis, and whole-gene random mutagenesis to engineer the substrate specificity, activity, and protein interactions of polyketide and nonribosomal peptide biosynthetic machinery.
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Affiliation(s)
- Gavin J Williams
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States.
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145
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Musiol EM, Greule A, Härtner T, Kulik A, Wohlleben W, Weber T. The AT₂ domain of KirCI loads malonyl extender units to the ACPs of the kirromycin PKS. Chembiochem 2013; 14:1343-52. [PMID: 23828654 DOI: 10.1002/cbic.201300211] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Indexed: 11/06/2022]
Abstract
The antibiotic kirromycin is assembled by a hybrid modular polyketide synthases (PKSs)/nonribosomal peptide synthetases (NRPSs). Five of six PKSs of this complex assembly line do not have acyltransferase (AT) and have to recruit this activity from discrete AT enzymes. Here, we show that KirCI is a discrete AT which is involved in kirromycin production and displays a rarely found three-domain architecture (AT₁-AT₂-ER). We demonstrate that the second AT domain, KirCI-AT₂, but not KirCI-AT₁, is the malonyl-CoA-specific AT which utilizes this precursor for loading the acyl carrier proteins (ACPs) of the trans-AT PKS in vitro. In the kirromycin biosynthetic pathway, ACP5 is exclusively loaded with ethylmalonate by the enzyme KirCII and is not recognized as a substrate by KirCI. Interestingly, the excised KirCI-AT₂ can also transfer malonate to ACP5 and thus has a relaxed ACP-specificity compared to the entire KirCI protein. The ability of KirCI-AT₂ to load different ACPs provides opportunities for AT engineering as a potential strategy for polyketide diversification.
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Affiliation(s)
- Ewa Maria Musiol
- Mikrobiologie/Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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146
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Nakamura H, Balskus EP. Using Chemical Knowledge to Uncover New Biological Function: Discovery of the Cylindrocyclophane Biosynthetic Pathway. Synlett 2013; 24:1464-1470. [PMID: 31723311 PMCID: PMC6853628 DOI: 10.1055/s-0033-1338879] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
An understanding of organic chemistry can play a central role in uncovering enzymes with new biochemical functions. We have recently identified the enzymes involved in the biosynthesis of the cylindrocyclophanes, a structurally unique family of natural products, and found that this pathway employs a remarkable macrocyclization event that requires functionalization of an unactivated carbon atom. This work illustrates the potential of using chemically guided approaches for enzyme discovery.
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Affiliation(s)
- Hitomi Nakamura
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Emily P Balskus
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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147
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Jiang M, Pfeifer BA. Metabolic and pathway engineering to influence native and altered erythromycin production through E. coli. Metab Eng 2013; 19:42-9. [PMID: 23747605 DOI: 10.1016/j.ymben.2013.05.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 05/24/2013] [Accepted: 05/30/2013] [Indexed: 11/16/2022]
Abstract
The heterologous production of the complex antibiotic erythromycin through Escherichia coli provides a unique challenge in metabolic engineering. In addition to introducing the 19 foreign genes needed for heterologous biosynthesis, E. coli metabolism must be engineered to provide the propionyl-CoA and (2S)-methylmalonyl-CoA substrates required to allow erythromycin formation. In this work, three different pathways to propionyl-CoA were compared in the context of supporting E. coli erythromycin biosynthesis. The comparison revealed that alternative citramalate and threonine metabolic pathways (both starting from exogenous glycerol) were capable of supporting final compound formation equal to a proven pathway reliant upon exogenous propionate. Furthermore, two pathways to (2S)-methylmalonyl-CoA were compared in the production of a novel benzyl-erythromycin analog. A pathway dependent upon exogenous methylmalonate improved selectivity and facilitated antibiotic assessment of this new analog.
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Affiliation(s)
- Ming Jiang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Department of Chemical and Biological Engineering, The State University of New York at Buffalo, Buffalo, NY 14260, USA
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148
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149
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Dunn BJ, Khosla C. Engineering the acyltransferase substrate specificity of assembly line polyketide synthases. J R Soc Interface 2013; 10:20130297. [PMID: 23720536 DOI: 10.1098/rsif.2013.0297] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Polyketide natural products act as a broad range of therapeutics, including antibiotics, immunosuppressants and anti-cancer agents. This therapeutic diversity stems from the structural diversity of these small molecules, many of which are produced in an assembly line manner by modular polyketide synthases. The acyltransferase (AT) domains of these megasynthases are responsible for selection and incorporation of simple monomeric building blocks, and are thus responsible for a large amount of the resulting polyketide structural diversity. The substrate specificity of these domains is often targeted for engineering in the generation of novel, therapeutically active natural products. This review outlines recent developments that can be used in the successful engineering of these domains, including AT sequence and structural data, mechanistic insights and the production of a diverse pool of extender units. It also provides an overview of previous AT domain engineering attempts, and concludes with proposed engineering approaches that take advantage of current knowledge. These approaches may lead to successful production of biologically active 'unnatural' natural products.
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Affiliation(s)
- Briana J Dunn
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
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150
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Häckh M, Müller M, Lüdeke S. Substrate-Dependent Stereospecificity of Tyl-KR1: An Isolated Polyketide Synthase Ketoreductase Domain fromStreptomyces fradiae. Chemistry 2013; 19:8922-8. [DOI: 10.1002/chem.201300554] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Indexed: 11/11/2022]
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