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Wang D, Mao H, Zhao Z, Liu L, Chen Y, Li P. Reprogramming of the Aurantinin Polyketide Assembly Line to Synthesize Auritriacids by Excising an Atypical Enoyl-CoA Hydratase Domain. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401708. [PMID: 38995095 DOI: 10.1002/advs.202401708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 06/14/2024] [Indexed: 07/13/2024]
Abstract
Modular polyketide synthases (PKSs) are capable of synthesizing diverse natural products with fascinating bioactivities. Canonical enoyl-CoA hydratases (ECHs) are components of the β-branching cassette that modifies the polyketide chain by adding a β-methyl branch. Herein, it is demonstrated that the deletion of an atypical ECHQ domain (featuring a Q280 residue) of Art21, a didomain protein contains an ECHQ domain and a thioesterase (TE) domain, reprograms the polyketide assembly line from synthesizing tetracyclic aurantinins (ARTs) to bicyclic auritriacids (ATAs) with much lower antibacterial activities. Genes encoding the ECHQ-TE didomain proteins distribute in many PKS gene clusters from different bacteria. Significantly, the ART PKS machinery can be directed to make ARTs, ATAs, or both of them by employing appropriate ECHQ-TE proteins, implying a great potential for using this reprogramming strategy in polyketide structure diversification.
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Affiliation(s)
- Dacheng Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huijin Mao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zelian Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- School of Life Sciences, Yunnan University, Kunming, 650500, China
| | - Lilu Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengwei Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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2
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Wu Y, Wang M, Liu L. Advances on structure, bioactivity, and biosynthesis of amino acid-containing trans-AT polyketides. Eur J Med Chem 2023; 262:115890. [PMID: 37907023 DOI: 10.1016/j.ejmech.2023.115890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/01/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023]
Abstract
Trans-AT polyketides represent a class of natural compounds utilizing independent acyltransferase during their biosynthesis. They are well known for their diverse chemical structures and potent bioactivities. Trans-AT polyketides are synthesized through biosynthetic gene clusters predominantly composed of polyketide synthases (PKS), but often found in hybrid with non-ribosomal peptide synthetases (NRPS). This genetic hybridization results in the incorporation of amino acid residues into polyketide structures, significantly enhancing their structural diversity. Numerous amino acid-containing trans-AT polyketides have been identified, drawing significant attention to the mechanisms underlying amino acid incorporation and their impact on the biological activity of polyketides. Here, we discussed their origins, structures, biological activities, and the specific roles of amino acids in modulating both the bioactivity and biosynthesis of 38 trans-AT polyketides containing amino acids for the first time. This comprehensive analysis will serve as a crucial reference for the exploration of novel compounds and the improvement of structures and activities.
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Affiliation(s)
- Yunqiang Wu
- Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China; Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China
| | - Min Wang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China.
| | - Liwei Liu
- Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China; Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China.
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3
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Abstract
Invertebrates, particularly sponges, have been a dominant source of new marine natural products. For example, lasonolide A (LSA) is a potential anticancer molecule isolated from the marine sponge Forcepia sp., with nanomolar growth inhibitory activity and a unique cytotoxicity profile against the National Cancer Institute 60-cell-line screen. Here, we identified the putative biosynthetic pathway for LSA. Genomic binning of the Forcepia sponge metagenome revealed a Gram-negative bacterium belonging to the phylum Verrucomicrobia as the candidate producer of LSA. Phylogenetic analysis showed that this bacterium, here named "Candidatus Thermopylae lasonolidus," only has 88.78% 16S rRNA identity with the closest relative, Pedosphaera parvula Ellin514, indicating that it represents a new genus. The lasonolide A (las) biosynthetic gene cluster (BGC) was identified as a trans-acyltransferase (AT) polyketide synthase (PKS) pathway. Compared with its host genome, the las BGC exhibits a significantly different GC content and pentanucleotide frequency, suggesting a potential horizontal acquisition of the gene cluster. Furthermore, three copies of the putative las pathway were identified in the candidate producer genome. Differences between the three las repeats were observed, including the presence of three insertions, two single-nucleotide polymorphisms, and the absence of a stand-alone acyl carrier protein in one of the repeats. Even though the verrucomicrobial producer shows signs of genome reduction, its genome size is still fairly large (about 5 Mbp), and, compared to its closest free-living relative, it contains most of the primary metabolic pathways, suggesting that it is in the early stages of reduction. IMPORTANCE While sponges are valuable sources of bioactive natural products, a majority of these compounds are produced in small quantities by uncultured symbionts, hampering the study and clinical development of these unique compounds. Lasonolide A (LSA), isolated from marine sponge Forcepia sp., is a cytotoxic molecule active at nanomolar concentrations, which causes premature chromosome condensation, blebbing, cell contraction, and loss of cell adhesion, indicating a novel mechanism of action and making it a potential anticancer drug lead. However, its limited supply hampers progression to clinical trials. We investigated the microbiome of Forcepia sp. using culture-independent DNA sequencing, identified genes likely responsible for LSA synthesis in an uncultured bacterium, and assembled the symbiont's genome. These insights provide future opportunities for heterologous expression and cultivation efforts that may minimize LSA's supply problem.
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Li X, Fu J, Li Y, Liu J, Gao R, Shi Y, Li Y, Sun H, Wang L, Li Y, Jiang B, Wu L, Hong B. Cytochrome P450 Monooxygenase for Catalyzing C-42 Hydroxylation of the Glycine-Derived Fragment in Hangtaimycin Biosynthesis. Org Lett 2022; 24:1388-1393. [PMID: 35138108 DOI: 10.1021/acs.orglett.2c00242] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A hybrid trans-AT PKS/NRPS gene cluster htm was identified with defined boundaries for hangtaimycin biosynthesis in Streptomyces spectabilis CPCC200148. Deoxyhangtaimycin, a new derivative of hangtaimycin, was identified from the htm11 gene knockout mutant. In vitro biochemical assays demonstrated that the cytochrome P450 monooxygenase Htm11 was responsible for the stereoselective hydroxylation of deoxyhangtaimycin to hangtaimycin. More importantly, deoxyhangtaimycin showed activity against influenza A virus at the micromolar level, highlighting its potential as an antiviral lead compound.
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Affiliation(s)
- Xingxing Li
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
| | - Jie Fu
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
| | - Yihua Li
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
| | - Jiachang Liu
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
| | - Rongmei Gao
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
| | - Yuanyuan Shi
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
| | - Yihong Li
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
| | - Hongmin Sun
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
| | - Lifei Wang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
| | - Yuhuan Li
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
| | - Bingya Jiang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
| | - Linzhuan Wu
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
| | - Bin Hong
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantan Xili, 100050 Beijing, China
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5
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Walker PD, Weir ANM, Willis CL, Crump MP. Polyketide β-branching: diversity, mechanism and selectivity. Nat Prod Rep 2021; 38:723-756. [PMID: 33057534 DOI: 10.1039/d0np00045k] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: 2008 to August 2020 Polyketides are a family of natural products constructed from simple building blocks to generate a diverse range of often complex chemical structures with biological activities of both pharmaceutical and agrochemical importance. Their biosynthesis is controlled by polyketide synthases (PKSs) which catalyse the condensation of thioesters to assemble a functionalised linear carbon chain. Alkyl-branches may be installed at the nucleophilic α- or electrophilic β-carbon of the growing chain. Polyketide β-branching is a fascinating biosynthetic modification that allows for the conversion of a β-ketone into a β-alkyl group or functionalised side-chain. The overall transformation is catalysed by a multi-protein 3-hydroxy-3-methylglutaryl synthase (HMGS) cassette and is reminiscent of the mevalonate pathway in terpene biosynthesis. The first step most commonly involves the aldol addition of acetate to the electrophilic carbon of the β-ketothioester catalysed by a 3-hydroxy-3-methylglutaryl synthase (HMGS). Subsequent dehydration and decarboxylation selectively generates either α,β- or β,γ-unsaturated β-alkyl branches which may be further modified. This review covers 2008 to August 2020 and summarises the diversity of β-branch incorporation and the mechanistic details of each catalytic step. This is extended to discussion of polyketides containing multiple β-branches and the selectivity exerted by the PKS to ensure β-branching fidelity. Finally, the application of HMGS in data mining, additional β-branching mechanisms and current knowledge of the role of β-branches in this important class of biologically active natural products is discussed.
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Affiliation(s)
- P D Walker
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - A N M Weir
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - C L Willis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - M P Crump
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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6
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Kačar D, Schleissner C, Cañedo LM, Rodríguez P, de la Calle F, Galán B, García JL. Genome of Labrenzia sp. PHM005 Reveals a Complete and Active Trans-AT PKS Gene Cluster for the Biosynthesis of Labrenzin. Front Microbiol 2019; 10:2561. [PMID: 31787953 PMCID: PMC6855096 DOI: 10.3389/fmicb.2019.02561] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 10/23/2019] [Indexed: 11/28/2022] Open
Abstract
The complete genome of the strain Labrenzia sp. PHM005, a free-living producer of a pederin analog 18-O-demethyl pederin, hereinafter labrenzin, has been sequenced. This strain contains two replicons comprising a circular chromosome of 6,167,349 bp and a circular plasmid (named p1BIR) of 19,450 bp. A putative gene cluster responsible for the synthesis of labrenzin (lab cluster) has been identified showing that it encodes a trans-AT mixed type PKS/NRPS biosynthetic pathway that is responsible for the synthesis of pederin and possibly an onnamide analog. The putative boundaries of the lab gene cluster were determined by genetic comparisons with other related strains, suggesting that the cluster consists of a 79-kb region comprising 3 genes encoding multidomain hybrid polyketide synthase/non-ribosomal peptide synthetase (PKS/NRPS) proteins (PKS4, PKS/NRPS13, and PKS/NRPS15), and 16 auxiliary enzymes. Transcriptomic analyses suggest that all the genes of the cluster are expressed in our culture conditions (i.e., in minimal medium in the absence of any specific inducer) at detectable levels. We have developed genetic tools to facilitate the manipulation of this strain and the functional characterization of the cluster genes. We have created a site-directed mutant unable to produce pederin, demonstrating experimentally for the first time the role of the cluster in the synthesis of pederin. This work paves the way to unravel the clues of the biosynthesis of pederin family compounds and opens the door to modify and overproduce these anticancer drugs for industrial and pharmaceutical purposes.
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Affiliation(s)
- Dina Kačar
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - Librada M Cañedo
- Research and Development Department, PharmaMar S.A., Madrid, Spain
| | - Pilar Rodríguez
- Research and Development Department, PharmaMar S.A., Madrid, Spain
| | | | - Beatriz Galán
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - José Luis García
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid, Spain
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7
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Walker PD, Williams C, Weir ANM, Wang L, Crosby J, Race PR, Simpson TJ, Willis CL, Crump MP. Control of β‐Branching in Kalimantacin Biosynthesis: Application of13C NMR to Polyketide Programming. Angew Chem Int Ed Engl 2019; 58:12446-12450. [DOI: 10.1002/anie.201905482] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/12/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Paul D. Walker
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | | | - Angus N. M. Weir
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Luoyi Wang
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - John Crosby
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Paul R. Race
- School of BiochemistryUniversity of Bristol University Walk Bristol BS8 1TD UK
| | - Thomas J. Simpson
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | | | - Matthew P. Crump
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
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8
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Walker PD, Williams C, Weir ANM, Wang L, Crosby J, Race PR, Simpson TJ, Willis CL, Crump MP. Control of β‐Branching in Kalimantacin Biosynthesis: Application of13C NMR to Polyketide Programming. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Paul D. Walker
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | | | - Angus N. M. Weir
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Luoyi Wang
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - John Crosby
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Paul R. Race
- School of BiochemistryUniversity of Bristol University Walk Bristol BS8 1TD UK
| | - Thomas J. Simpson
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | | | - Matthew P. Crump
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
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9
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Uria AR, Piel J, Wakimoto T. Biosynthetic Insights of Calyculin- and Misakinolide-Type Compounds in "Candidatus Entotheonella sp.". Methods Enzymol 2018; 604:287-330. [PMID: 29779656 DOI: 10.1016/bs.mie.2018.02.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Microbial symbionts are recognized as the important sources of numerous sponge-derived metabolites with potent biological activities. The limitation to cultivate the majority of potential symbionts has hampered attempts to explore and exploit their natural products for further development toward medical applications. Metagenomics-guided approaches have enabled cloning of natural product biosynthesis genes from uncultured microbial symbionts. Subsequent activation of biosynthesis genes in easily culturable bacteria could lead to the sustainable production of rare sponge-derived compounds. In this chapter, we highlight metagenomic strategies to reveal natural product biosynthetic pathways in sponge metagenomes based on the calyculin and misakinolide polyketides. Techniques to identify the compound producer are briefly discussed. We further describe examples of functional studies of the biosynthetic pathways of these two compound types with a special emphasis on the general experimental protocols for the activity assays of key proteins involved in their biosynthesis.
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Affiliation(s)
- Agustinus R Uria
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
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10
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Slocum ST, Lowell AN, Tripathi A, Shende VV, Smith JL, Sherman DH. Chemoenzymatic Dissection of Polyketide β-Branching in the Bryostatin Pathway. Methods Enzymol 2018; 604:207-236. [PMID: 29779653 PMCID: PMC6327954 DOI: 10.1016/bs.mie.2018.01.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
β-Branching is an expansion upon canonical polyketide synthase extension that allows for the installation of diverse chemical moieties in several natural products. Several of these moieties are unique among natural products, including the two vinyl methylesters found in the core structure of bryostatins. This family of molecules is derived from an obligate bacterial symbiont of a sessile marine bryozoan, Bugula neritina. Within this family, bryostatin 1 has been investigated as an anticancer, neuroprotective, and immunomodulatory compound. We have turned to the biosynthetic gene cluster within the bacterial symbiont to investigate the biosynthesis of bryostatins. Recent sequencing efforts resulted in the annotation of two missing genes: bryT and bryU. Using novel chemoenzymatic techniques, we have validated these as the missing enoyl-CoA hydratase and donor acyl carrier protein, essential components of the β-branching cassette of the bryostatin pathway. Together, this cassette installs the vinyl methylester moieties essential to the activity of bryostatins.
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Affiliation(s)
- Samuel T Slocum
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - Andrew N Lowell
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States
| | - Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States
| | - Vikram V Shende
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Chemistry, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, United States.
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11
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Maneesh A, Chakraborty K. Unprecedented antioxidative and anti-inflammatory aryl polyketides from the brown seaweed Sargassum wightii. Food Res Int 2017; 100:640-649. [PMID: 28873732 DOI: 10.1016/j.foodres.2017.07.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 06/28/2017] [Accepted: 07/02/2017] [Indexed: 11/15/2022]
Abstract
Previously undescribed aryl polyketide lactones, 4-(8-ethyl-tetrahydro-7-oxo-2H-pyran-5-yl)-propyl-4'-methylbenzoate (compound 1) and methyl-2-(12-oxo-7-phenyl-8-vinyl-1-oxa-4,9-cyclododecadien-3-yl)-acetate (compound 2) were purified from ethyl acetate-methanol fraction of the brown seaweed Sargassum wightii. The structures were proposed based on their NMR and mass spectrometric data. The antioxidative activities of the lactones were significantly greater (P<0.05) (IC50 1,1-diphenyl-2-picrylhydrazyl radical scavenging 0.24-0.32mg/mL) than α-tocopherol (IC50 0.63mg/mL). The title compounds displayed considerably greater 5-lipoxygenase inhibitory activity (IC50 0.56 and 0.29mg/mL, respectively) in conjunction with higher selectivity indices (anti-cycloxygense-1IC50/anti-cycloxygense-2IC50 >1) compared to non-steroidal anti-inflammatory drugs (SIaspirin 0.03, SIibuprofen 0.43). Putative biosynthetic pathway of title polyketide products through polyketide synthase enzyme cascade catalyzed reactions substantiated the structural attributions of the hitherto unreported aryl polyketides. This is the first report of the occurrence and characterization of two rare skeletal types, oxo-2H-pyranyl and oxa-cyclododecadienyl macrolactone featuring the aryl substituent from marine organisms with potential antioxidative and anti-inflammatory activities.
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Affiliation(s)
- Anusree Maneesh
- Marine Bioprospecting Section of Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin 682018, Kerala, India
| | - Kajal Chakraborty
- Marine Bioprospecting Section of Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin 682018, Kerala, India.
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12
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Abstract
Oxidative cyclizations are important transformations that occur widely during natural product biosynthesis. The transformations from acyclic precursors to cyclized products can afford morphed scaffolds, structural rigidity, and biological activities. Some of the most dramatic structural alterations in natural product biosynthesis occur through oxidative cyclization. In this Review, we examine the different strategies used by nature to create new intra(inter)molecular bonds via redox chemistry. This Review will cover both oxidation- and reduction-enabled cyclization mechanisms, with an emphasis on the former. Radical cyclizations catalyzed by P450, nonheme iron, α-KG-dependent oxygenases, and radical SAM enzymes are discussed to illustrate the use of molecular oxygen and S-adenosylmethionine to forge new bonds at unactivated sites via one-electron manifolds. Nonradical cyclizations catalyzed by flavin-dependent monooxygenases and NAD(P)H-dependent reductases are covered to show the use of two-electron manifolds in initiating cyclization reactions. The oxidative installations of epoxides and halogens into acyclic scaffolds to drive subsequent cyclizations are separately discussed as examples of "disappearing" reactive handles. Last, oxidative rearrangement of rings systems, including contractions and expansions, will be covered.
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Affiliation(s)
- Man-Cheng Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Yi Zou
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA 94305
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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13
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Antibacterial polyketides from Bacillus amyloliquefaciens associated with edible red seaweed Laurenciae papillosa. Food Chem 2017; 218:427-434. [DOI: 10.1016/j.foodchem.2016.09.066] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/16/2016] [Accepted: 09/09/2016] [Indexed: 01/02/2023]
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14
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Ikon N, Ryan RO. On the origin of 3-methylglutaconic acid in disorders of mitochondrial energy metabolism. J Inherit Metab Dis 2016; 39:749-756. [PMID: 27091556 PMCID: PMC4988875 DOI: 10.1007/s10545-016-9933-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/17/2016] [Accepted: 03/31/2016] [Indexed: 01/06/2023]
Abstract
3-methylglutaconic acid (3MGA)-uria occurs in numerous inborn errors of metabolism (IEM) associated with compromised mitochondrial energy metabolism. This organic acid arises from thioester cleavage of 3-methylglutaconyl CoA (3MG CoA), an intermediate in leucine catabolism. In individuals harboring mutations in 3MG CoA hydratase (i.e., primary 3MGA-uria), dietary leucine is the source of 3MGA. In secondary 3MGA-uria, however, no leucine metabolism defects have been reported. While others have suggested 3MGA arises from aberrant isoprenoid shunting from cytosol to mitochondria, an alternative route posits that 3MG CoA arises in three steps from mitochondrial acetyl CoA. Support for this biosynthetic route in IEMs is seen by its regulated occurrence in microorganisms. The fungus, Ustilago maydis, the myxobacterium, Myxococcus xanthus and the marine cyanobacterium, Lyngbya majuscule, generate 3MG CoA (or acyl carrier protein derivative) in the biosynthesis of iron chelating siderophores, iso-odd chain fatty acids and polyketide/nonribosomal peptide products, respectively. The existence of this biosynthetic machinery in these organisms supports a model wherein, under conditions of mitochondrial dysfunction, accumulation of acetyl CoA in the inner mitochondrial space as a result of inefficient fuel utilization drives de novo synthesis of 3MG CoA. Since humans lack the downstream biosynthetic capability of the organisms mentioned above, as 3MG CoA levels rise, thioester hydrolysis yields 3MGA, which is excreted in urine as unspent fuel. Understanding the metabolic origins of 3MGA may increase its utility as a biomarker.
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Affiliation(s)
- Nikita Ikon
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA, 94609, USA
| | - Robert O Ryan
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA, 94609, USA.
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15
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Kleigrewe K, Gerwick L, Sherman DH, Gerwick WH. Unique marine derived cyanobacterial biosynthetic genes for chemical diversity. Nat Prod Rep 2016; 33:348-64. [PMID: 26758451 DOI: 10.1039/c5np00097a] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cyanobacteria are a prolific source of structurally unique and biologically active natural products that derive from intriguing biochemical pathways. Advancements in genome sequencing have accelerated the identification of unique modular biosynthetic gene clusters in cyanobacteria and reveal a wealth of unusual enzymatic reactions involved in their construction. This article examines several interesting mechanistic transformations involved in cyanobacterial secondary metabolite biosynthesis with a particular focus on marine derived modular polyketide synthases (PKS), nonribosomal peptide synthetases (NRPS) and combinations thereof to form hybrid natural products. Further, we focus on the cyanobacterial genus Moorea and the co-evolution of its enzyme cassettes that create metabolic diversity. Progress in the development of heterologous expression systems for cyanobacterial gene clusters along with chemoenzymatic synthesis makes it possible to create new analogs. Additionally, phylum-wide genome sequencing projects have enhanced the discovery rate of new natural products and their distinctive enzymatic reactions. Summarizing, cyanobacterial biosynthetic gene clusters encode for a large toolbox of novel enzymes that catalyze unique chemical reactions, some of which may be useful in synthetic biology.
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Affiliation(s)
- Karin Kleigrewe
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, USA.
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, USA.
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, USA. and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, USA
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16
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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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17
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Structural Basis for Cyclopropanation by a Unique Enoyl-Acyl Carrier Protein Reductase. Structure 2015; 23:2213-2223. [PMID: 26526850 DOI: 10.1016/j.str.2015.09.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/12/2015] [Accepted: 09/15/2015] [Indexed: 11/20/2022]
Abstract
The natural product curacin A, a potent anticancer agent, contains a rare cyclopropane group. The five enzymes for cyclopropane biosynthesis are highly similar to enzymes that generate a vinyl chloride moiety in the jamaicamide natural product. The structural biology of this remarkable catalytic adaptability is probed with high-resolution crystal structures of the curacin cyclopropanase (CurF ER), an in vitro enoyl reductase (JamJ ER), and a canonical curacin enoyl reductase (CurK ER). The JamJ and CurK ERs catalyze NADPH-dependent double bond reductions typical of enoyl reductases (ERs) of the medium-chain dehydrogenase reductase (MDR) superfamily. Cyclopropane formation by CurF ER is specified by a short loop which, when transplanted to JamJ ER, confers cyclopropanase activity on the chimeric enzyme. Detection of an adduct of NADPH with the model substrate crotonyl-CoA provides indirect support for a recent proposal of a C2-ene intermediate on the reaction pathway of MDR enoyl-thioester reductases.
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18
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Chakraborty K, Thilakan B, Raola VK. Polyketide family of novel antibacterial 7-O-methyl-5'-hydroxy-3'-heptenoate-macrolactin from seaweed-associated Bacillus subtilis MTCC 10403. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:12194-208. [PMID: 25420039 DOI: 10.1021/jf504845m] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Seaweed-associated heterotrophic bacterial communities were screened to isolate potentially useful antimicrobial strains, which were characterized by phylogenetic analysis. The bacteria were screened for the presence of metabolite genes involved in natural product biosynthetic pathway, and the structural properties of secondary metabolites were correlated with the genes. Bioactivity-guided isolation of polyene antibiotic 7-O-methyl-5'-hydroxy-3'-heptenoate-macrolactin from Bacillus subtilis MTCC10403 associated with seaweed Anthophycus longifolius using mass spectrometry and extensive 2D-NMR studies was carried out. The newly isolated macrolactin compound is a bactericidal antibiotic with broad spectrum activity against human opportunistic clinical pathogens. The biosynthetic pathway of 7-O-methyl-5'-hydroxy-3'-heptenoate-macrolactin by means of a stepwise, decarboxylative condensation pathway established the PKS-assisted biosynthesis of the parent macrolactin and the side-chain 5-hydroxyhept-3-enoate moiety attached to the macrolactin ring system at C-7. Antimicrobial activity analysis combined with the results of amplifying genes encoding for polyketide synthetase and nonribosomal peptide synthetase showed that seaweed-associated bacteria had broad-spectrum antimicrobial activity. The present work may have an impact on the exploitation of macrolactins for pharmaceutical and biotechnological applications.
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Affiliation(s)
- Kajal Chakraborty
- Marine Biotechnology Division, Central Marine Fisheries Research Institute , Ernakulam North, P.B. No. 1603, Cochin, India
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19
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Essack M, Alzubaidy HS, Bajic VB, Archer JAC. Chemical compounds toxic to invertebrates isolated from marine cyanobacteria of potential relevance to the agricultural industry. Toxins (Basel) 2014; 6:3058-76. [PMID: 25356733 PMCID: PMC4247248 DOI: 10.3390/toxins6113058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 09/19/2014] [Accepted: 10/14/2014] [Indexed: 11/16/2022] Open
Abstract
In spite of advances in invertebrate pest management, the agricultural industry is suffering from impeded pest control exacerbated by global climate changes that have altered rain patterns to favour opportunistic breeding. Thus, novel naturally derived chemical compounds toxic to both terrestrial and aquatic invertebrates are of interest, as potential pesticides. In this regard, marine cyanobacterium-derived metabolites that are toxic to both terrestrial and aquatic invertebrates continue to be a promising, but neglected, source of potential pesticides. A PubMed query combined with hand-curation of the information from retrieved articles allowed for the identification of 36 cyanobacteria-derived chemical compounds experimentally confirmed as being toxic to invertebrates. These compounds are discussed in this review.
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Affiliation(s)
- Magbubah Essack
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Jeddah, Saudi Arabia.
| | - Hanin S Alzubaidy
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Jeddah, Saudi Arabia.
| | - Vladimir B Bajic
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Jeddah, Saudi Arabia.
| | - John A C Archer
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Jeddah, Saudi Arabia.
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20
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Haines AS, Dong X, Song Z, Farmer R, Williams C, Hothersall J, Płoskoń E, Wattana-Amorn P, Stephens ER, Yamada E, Gurney R, Takebayashi Y, Masschelein J, Cox RJ, Lavigne R, Willis CL, Simpson TJ, Crosby J, Winn PJ, Thomas CM, Crump MP. A conserved motif flags acyl carrier proteins for β-branching in polyketide synthesis. Nat Chem Biol 2013; 9:685-692. [PMID: 24056399 PMCID: PMC4658705 DOI: 10.1038/nchembio.1342] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 08/22/2013] [Indexed: 11/14/2022]
Abstract
Type I PKSs often utilise programmed β-branching, via enzymes of an “HMG-CoA synthase (HCS) cassette”, to incorporate various side chains at the second carbon from the terminal carboxylic acid of growing polyketide backbones. We identified a strong sequence motif in Acyl Carrier Proteins (ACPs) where β-branching is known. Substituting ACPs confirmed a correlation of ACP type with β-branching specificity. While these ACPs often occur in tandem, NMR analysis of tandem β-branching ACPs indicated no ACP-ACP synergistic effects and revealed that the conserved sequence motif forms an internal core rather than an exposed patch. Modelling and mutagenesis identified ACP Helix III as a probable anchor point of the ACP-HCS complex whose position is determined by the core. Mutating the core affects ACP functionality while ACP-HCS interface substitutions modulate system specificity. Our method for predicting β-carbon branching expands the potential for engineering novel polyketides and lays a basis for determining specificity rules.
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Affiliation(s)
- Anthony S Haines
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Xu Dong
- School of Chemistry, Cantock's Close, Clifton, Bristol, BS8 1TS, UK
| | - Zhongshu Song
- School of Chemistry, Cantock's Close, Clifton, Bristol, BS8 1TS, UK
| | - Rohit Farmer
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | | | - Joanne Hothersall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Eliza Płoskoń
- School of Chemistry, Cantock's Close, Clifton, Bristol, BS8 1TS, UK
| | | | - Elton R Stephens
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Erika Yamada
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Rachel Gurney
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Yuiko Takebayashi
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Joleen Masschelein
- Division of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 - box 2462, 3001 Heverlee, Belgium
| | - Russell J Cox
- School of Chemistry, Cantock's Close, Clifton, Bristol, BS8 1TS, UK
| | - Rob Lavigne
- Division of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 - box 2462, 3001 Heverlee, Belgium
| | | | - Thomas J Simpson
- School of Chemistry, Cantock's Close, Clifton, Bristol, BS8 1TS, UK
| | - John Crosby
- School of Chemistry, Cantock's Close, Clifton, Bristol, BS8 1TS, UK
| | - Peter J Winn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Matthew P Crump
- School of Chemistry, Cantock's Close, Clifton, Bristol, BS8 1TS, UK
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21
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Sucipto H, Wenzel SC, Müller R. Exploring Chemical Diversity of α-Pyrone Antibiotics: Molecular Basis of Myxopyronin Biosynthesis. Chembiochem 2013; 14:1581-9. [DOI: 10.1002/cbic.201300289] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Indexed: 01/30/2023]
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22
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Lohman JR, Bingman CA, Phillips GN, Shen B. Structure of the bifunctional acyltransferase/decarboxylase LnmK from the leinamycin biosynthetic pathway revealing novel activity for a double-hot-dog fold. Biochemistry 2013; 52:902-11. [PMID: 23320975 PMCID: PMC3567400 DOI: 10.1021/bi301652y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The β-branched C3 unit in leinamycin biosynthesis is installed by a set of four proteins, LnmFKLM. In vitro biochemical investigation confirmed that LnmK is a bifunctional acyltransferase/decarboxylase (AT/DC) that catalyzes first self-acylation using methylmalonyl-CoA as a substrate and subsequently transacylation of the methylmalonyl group to the phosphopantetheinyl group of the LnmL acyl carrier protein [Liu, T., Huang, Y., and Shen, B. (2009) J. Am. Chem. Soc. 131, 6900-6901]. LnmK shows no sequence homology to proteins of known function, representing a new family of AT/DC enzymes. Here we report the X-ray structure of LnmK. LnmK is homodimer with each of the monomers adopting a double-hot-dog fold. Cocrystallization of LnmK with methylmalonyl-CoA revealed an active site tunnel terminated by residues from the dimer interface. In contrast to canonical AT and ketosynthase enzymes that employ Ser or Cys as an active site residue, none of these residues are found in the vicinity of the LnmK active site. Instead, three tyrosines were identified, one of which, Tyr62, was established, by site-directed mutagenesis, to be the most likely active site residue for the AT activity of LnmK. LnmK represents the first AT enzyme that employs a Tyr as an active site residue and the first member of the family of double-hot-dog fold enzymes that displays an AT activity known to date. The LnmK structure sets the stage for probing of the DC activity of LnmK through site-directed mutagenesis. These findings highlight natural product biosynthetic machinery as a rich source of novel enzyme activities, mechanisms, and structures.
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Affiliation(s)
- Jeremy R. Lohman
- Department of Chemistry The Scripps Research institute, Jupiter, Florida 33485
| | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - George N. Phillips
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
,Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251
| | - Ben Shen
- Department of Chemistry The Scripps Research institute, Jupiter, Florida 33485
,Department of Molecular Therapeutics The Scripps Research institute, Jupiter, Florida 33485
,Department of Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research institute, Jupiter, Florida 33485
,To whom correspondence should be addressed: The Scripps Research Institute, 130 Scripps Way, #3A1, Jupiter, FL 33458; Tel: (561) 228-2456; Fax: (561) 228-2472;
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23
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Li Y, Luxenburger E, Müller R. An alternative isovaleryl CoA biosynthetic pathway involving a previously unknown 3-methylglutaconyl CoA decarboxylase. Angew Chem Int Ed Engl 2012; 52:1304-8. [PMID: 23225771 DOI: 10.1002/anie.201207984] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Yanyan Li
- Helmholtz Institut für Pharmazeutische Forschung Saarland, Helmholtz Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie, Universität des Saarlandes, 66041 Saarbrücken, Germany
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24
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Li Y, Luxenburger E, Müller R. Ein alternativer Isovaleryl-CoA-Biosyntheseweg: Beteiligung einer bisher unbekannten 3-Methylglutaconyl-CoA-Decarboxylase. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207984] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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25
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Matilla MA, Stöckmann H, Leeper FJ, Salmond GPC. Bacterial biosynthetic gene clusters encoding the anti-cancer haterumalide class of molecules: biogenesis of the broad spectrum antifungal and anti-oomycete compound, oocydin A. J Biol Chem 2012; 287:39125-38. [PMID: 23012376 PMCID: PMC3493953 DOI: 10.1074/jbc.m112.401026] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/05/2012] [Indexed: 01/16/2023] Open
Abstract
Haterumalides are halogenated macrolides with strong antitumor properties, making them attractive targets for chemical synthesis. Unfortunately, current synthetic routes to these molecules are inefficient. The potent haterumalide, oocydin A, was previously identified from two plant-associated bacteria through its high bioactivity against plant pathogenic fungi and oomycetes. In this study, we describe oocydin A (ooc) biosynthetic gene clusters identified by genome sequencing, comparative genomics, and chemical analysis in four plant-associated enterobacteria of the Serratia and Dickeya genera. Disruption of the ooc gene cluster abolished oocydin A production and bioactivity against fungi and oomycetes. The ooc gene clusters span between 77 and 80 kb and encode five multimodular polyketide synthase (PKS) proteins, a hydroxymethylglutaryl-CoA synthase cassette and three flavin-dependent tailoring enzymes. The presence of two free-standing acyltransferase proteins classifies the oocydin A gene cluster within the growing family of trans-AT PKSs. The amino acid sequences and organization of the PKS domains are consistent with the chemical predictions and functional peculiarities associated with trans-acyltransferase PKS. Based on extensive in silico analysis of the gene cluster, we propose a biosynthetic model for the production of oocydin A and, by extension, for other members of the haterumalide family of halogenated macrolides exhibiting anti-cancer, anti-fungal, and other interesting biological properties.
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Affiliation(s)
- Miguel A. Matilla
- From the Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW and
| | - Henning Stöckmann
- the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Finian J. Leeper
- the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - George P. C. Salmond
- From the Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW and
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26
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Akey DL, Gehret JJ, Khare D, Smith JL. Insights from the sea: structural biology of marine polyketide synthases. Nat Prod Rep 2012; 29:1038-49. [PMID: 22498975 DOI: 10.1039/c2np20016c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The world's oceans are a rich source of natural products with extremely interesting chemistry. Biosynthetic pathways have been worked out for a few, and the story is being enriched with crystal structures of interesting pathway enzymes. By far, the greatest number of structural insights from marine biosynthetic pathways has originated with studies of curacin A, a poster child for interesting marine chemistry with its cyclopropane and thiazoline rings, internal cis double bond, and terminal alkene. Using the curacin A pathway as a model, structural details are now available for a novel loading enzyme with remarkable dual decarboxylase and acetyltransferase activities, an Fe(2+)/α-ketoglutarate-dependent halogenase that dictates substrate binding order through conformational changes, a decarboxylase that establishes regiochemistry for cyclopropane formation, and a thioesterase with specificity for β-sulfated substrates that lead to terminal alkene offloading. The four curacin A pathway dehydratases reveal an intrinsic flexibility that may accommodate bulky or stiff polyketide intermediates. In the salinosporamide A pathway, active site volume determines the halide specificity of a halogenase that catalyzes for the synthesis of a halogenated building block. Structures of a number of putative polyketide cyclases may help in understanding reaction mechanisms and substrate specificities although their substrates are presently unknown.
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Affiliation(s)
- David L Akey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
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27
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Busche A, Gottstein D, Hein C, Ripin N, Pader I, Tufar P, Eisman EB, Gu L, Walsh CT, Sherman DH, Löhr F, Güntert P, Dötsch V. Characterization of molecular interactions between ACP and halogenase domains in the Curacin A polyketide synthase. ACS Chem Biol 2012; 7:378-86. [PMID: 22103656 DOI: 10.1021/cb200352q] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are large multidomain proteins present in microorganisms that produce bioactive compounds. Curacin A is such a bioactive compound with potent anti-proliferative activity. During its biosynthesis the growing substrate is bound covalently to an acyl carrier protein (ACP) that is able to access catalytic sites of neighboring domains for chain elongation and modification. While ACP domains usually occur as monomers, the curacin A cluster codes for a triplet ACP (ACP(I)-ACP(II)-ACP(III)) within the CurA PKS module. We have determined the structure of the isolated holo-ACP(I) and show that the ACPs are independent of each other within this tridomain system. In addition, we have determined the structure of the 3-hydroxyl-3-methylglutaryl-loaded holo-ACP(I), which is the substrate for the unique halogenase (Hal) domain embedded within the CurA module. We have identified the interaction surface of both proteins using mutagenesis and MALDI-based identification of product formation. Amino acids affecting product formation are located on helices II and III of ACP(I) and form a contiguous surface. Since the CurA Hal accepts substrate only when presented by one of the ACPs within the ACP(I)-ACP(II)-ACP(III) tridomain, our data provide insight into the specificity of the chlorination reaction.
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Affiliation(s)
- Alena Busche
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Center for Biomolecular
Magnetic Resonance, Max-von-Laue Str. 9, 60438 Frankfurt am Main,
Germany
| | - Daniel Gottstein
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Center for Biomolecular
Magnetic Resonance, Max-von-Laue Str. 9, 60438 Frankfurt am Main,
Germany
| | - Christopher Hein
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Center for Biomolecular
Magnetic Resonance, Max-von-Laue Str. 9, 60438 Frankfurt am Main,
Germany
| | - Nina Ripin
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Center for Biomolecular
Magnetic Resonance, Max-von-Laue Str. 9, 60438 Frankfurt am Main,
Germany
| | - Irina Pader
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Center for Biomolecular
Magnetic Resonance, Max-von-Laue Str. 9, 60438 Frankfurt am Main,
Germany
| | - Peter Tufar
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Center for Biomolecular
Magnetic Resonance, Max-von-Laue Str. 9, 60438 Frankfurt am Main,
Germany
| | - Eli B. Eisman
- Life Sciences Institute,
Departments
of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109,
United States
| | - Liangcai Gu
- Life Sciences Institute,
Departments
of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109,
United States
| | | | - David H. Sherman
- Life Sciences Institute,
Departments
of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109,
United States
| | - Frank Löhr
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Center for Biomolecular
Magnetic Resonance, Max-von-Laue Str. 9, 60438 Frankfurt am Main,
Germany
| | - Peter Güntert
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Center for Biomolecular
Magnetic Resonance, Max-von-Laue Str. 9, 60438 Frankfurt am Main,
Germany
- Frankfurt
Institute for Advanced
Studies, Goethe University Frankfurt, Ruth-Moufang-Str.
1, 60438 Frankfurt am Main, Germany
- Center for Priority Areas, Tokyo Metropolitan University, 1-1 minami-ohsawa, Hachioji,
Tokyo 192-0397, Japan
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Center for Biomolecular
Magnetic Resonance, Max-von-Laue Str. 9, 60438 Frankfurt am Main,
Germany
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28
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Grindberg RV, Ishoey T, Brinza D, Esquenazi E, Coates RC, Liu WT, Gerwick L, Dorrestein PC, Pevzner P, Lasken R, Gerwick WH. Single cell genome amplification accelerates identification of the apratoxin biosynthetic pathway from a complex microbial assemblage. PLoS One 2011; 6:e18565. [PMID: 21533272 PMCID: PMC3075265 DOI: 10.1371/journal.pone.0018565] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 03/08/2011] [Indexed: 01/11/2023] Open
Abstract
Filamentous marine cyanobacteria are extraordinarily rich sources of structurally novel, biomedically relevant natural products. To understand their biosynthetic origins as well as produce increased supplies and analog molecules, access to the clustered biosynthetic genes that encode for the assembly enzymes is necessary. Complicating these efforts is the universal presence of heterotrophic bacteria in the cell wall and sheath material of cyanobacteria obtained from the environment and those grown in uni-cyanobacterial culture. Moreover, the high similarity in genetic elements across disparate secondary metabolite biosynthetic pathways renders imprecise current gene cluster targeting strategies and contributes sequence complexity resulting in partial genome coverage. Thus, it was necessary to use a dual-method approach of single-cell genomic sequencing based on multiple displacement amplification (MDA) and metagenomic library screening. Here, we report the identification of the putative apratoxin. A biosynthetic gene cluster, a potent cancer cell cytotoxin with promise for medicinal applications. The roughly 58 kb biosynthetic gene cluster is composed of 12 open reading frames and has a type I modular mixed polyketide synthase/nonribosomal peptide synthetase (PKS/NRPS) organization and features loading and off-loading domain architecture never previously described. Moreover, this work represents the first successful isolation of a complete biosynthetic gene cluster from Lyngbya bouillonii, a tropical marine cyanobacterium renowned for its production of diverse bioactive secondary metabolites.
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Affiliation(s)
- Rashel V. Grindberg
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Thomas Ishoey
- J. Craig Venter Institute, San Diego, California, United States of America
| | - Dumitru Brinza
- Department of Computer Science and Engineering, Center for Algorithmic and Systems Biology, University of California San Diego, La Jolla, California, United States of America
| | - Eduardo Esquenazi
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - R. Cameron Coates
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Wei-ting Liu
- Departments of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
- Departments of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Pavel Pevzner
- Department of Computer Science and Engineering, Center for Algorithmic and Systems Biology, University of California San Diego, La Jolla, California, United States of America
| | - Roger Lasken
- J. Craig Venter Institute, San Diego, California, United States of America
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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29
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Mady ASA, Zolova OE, Millán MÁS, Villamizar G, de la Calle F, Lombó F, Garneau-Tsodikova S. Characterization of TioQ, a type II thioesterase from the thiocoraline biosynthetic cluster. MOLECULAR BIOSYSTEMS 2011; 7:1999-2011. [PMID: 21483938 DOI: 10.1039/c1mb05044c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
An antitumor agent thiocoraline is a thiodepsipeptide marine product derived from two Micromonospora sp. strains that inhibits protein synthesis by binding of its key 3-hydroxyquinaldic acid (3HQA) chromophores to duplex DNA. There are at least two potential pathways via which the 3HQA moiety could be biosynthesized from L-Trp. By biochemical characterization and by preparation of knockouts of an adenylation-thiolation enzyme, TioK, and of two type II thioesterases, TioP and TioQ, found in the thiocoraline biosynthetic gene cluster, we gained valuable insight into the pathway followed for the production of 3HQA.
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Affiliation(s)
- Ahmed S A Mady
- University of Michigan, Life Sciences Institute, 210 Washtenaw Ave, Ann Arbor, MI 48109, USA
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30
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Teta R, Gurgui M, Helfrich EJN, Künne S, Schneider A, Van Echten-Deckert G, Mangoni A, Piel J. Genome mining reveals trans-AT polyketide synthase directed antibiotic biosynthesis in the bacterial phylum bacteroidetes. Chembiochem 2011; 11:2506-12. [PMID: 21080397 DOI: 10.1002/cbic.201000542] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Roberta Teta
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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31
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Hochmuth T, Niederkrüger H, Gernert C, Siegl A, Taudien S, Platzer M, Crews P, Hentschel U, Piel J. Linking chemical and microbial diversity in marine sponges: possible role for poribacteria as producers of methyl-branched fatty acids. Chembiochem 2011; 11:2572-8. [PMID: 21077090 DOI: 10.1002/cbic.201000510] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Many marine sponges contain massive numbers of largely uncultivated, phylogenetically diverse bacteria that seem to be important contributors to the chemistry of these animals. Insights into the diversity, origin, distribution, and function of their metabolic gene communities are crucial to dissect the chemical ecology and biotechnological potential of sponge symbionts. This study reveals a sharp dichotomy between high and low microbial abundance sponges with respect to polyketide synthase (PKS) gene content, the presence of methyl-branched fatty acids, and the presence of members of the symbiotic candidate phylum "Poribacteria". For the symbiont-rich sponge Cacospongia mycofijiensis, a source of the tubulin-inhibiting fijianolides (=laulimalides), near-exhaustive large-scale sequencing of PKS gene-derived PCR amplicons was conducted. Although these amplicons exhibit high diversity at the sequence level, almost all of them belong to a single, architecturally unique group of PKSs present in "Poribacteria" and are proposed to synthesize methyl-branched fatty acids. Three components of this PKS were studied in vitro, providing initial insight into its biochemistry.
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Affiliation(s)
- Thomas Hochmuth
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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32
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Gu L, Eisman EB, Dutta S, Franzmann TM, Walter S, Gerwick WH, Skiniotis G, Sherman DH. Tandem Acyl Carrier Proteins in the Curacin Biosynthetic Pathway Promote Consecutive Multienzyme Reactions with a Synergistic Effect. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201005280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Liangcai Gu
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109 (USA)
- Department of Genetics, Harvard Medical School, Boston, MA 02115 (USA)
| | - Eli B. Eisman
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109 (USA)
| | - Somnath Dutta
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109 (USA)
| | - Titus M. Franzmann
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109 (USA)
| | - Stefan Walter
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109 (USA)
| | - William H. Gerwick
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093 (USA)
| | - Georgios Skiniotis
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109 (USA)
| | - David H. Sherman
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109 (USA)
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33
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Gulder TAM, Freeman MF, Piel J. The Catalytic Diversity of Multimodular Polyketide Synthases: Natural Product Biosynthesis Beyond Textbook Assembly Rules. Top Curr Chem (Cham) 2011. [PMID: 21360321 DOI: 10.1007/128_2010_113] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Bacterial multimodular polyketide synthases (PKSs) are responsible for the biosynthesis of a wide range of pharmacologically active natural products. These megaenzymes contain numerous catalytic and structural domains and act as biochemical templates to generate complex polyketides in an assembly line-like fashion. While the prototypical PKS is composed of only a few different domain types that are fused together in a combinatorial fashion, an increasing number of enzymes is being found that contain additional components. These domains can introduce remarkably diverse modifications into polyketides. This review discusses our current understanding of such noncanonical domains and their role in expanding the biosynthetic versatility of bacterial PKSs.
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34
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Gu L, Eisman EB, Dutta S, Franzmann TM, Walter S, Gerwick WH, Skiniotis G, Sherman DH. Tandem acyl carrier proteins in the curacin biosynthetic pathway promote consecutive multienzyme reactions with a synergistic effect. Angew Chem Int Ed Engl 2011; 50:2795-8. [PMID: 21387490 DOI: 10.1002/anie.201005280] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 01/12/2011] [Indexed: 11/10/2022]
Affiliation(s)
- Liangcai Gu
- Life Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, 48109, USA
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35
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Buchholz TJ, Rath CM, Lopanik NB, Gardner NP, Håkansson K, Sherman DH. Polyketide β-branching in bryostatin biosynthesis: identification of surrogate acetyl-ACP donors for BryR, an HMG-ACP synthase. ACTA ACUST UNITED AC 2011; 17:1092-100. [PMID: 21035732 DOI: 10.1016/j.chembiol.2010.08.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Revised: 08/10/2010] [Accepted: 08/17/2010] [Indexed: 10/18/2022]
Abstract
In vitro analysis of natural product biosynthetic gene products isolated from unculturable symbiotic bacteria is necessary to probe the functionalities of these enzymes. Herein, we report the biochemical characterization of BryR, the 3-hydroxy-3-methylglutaryl (HMG)-CoA synthase (HMGS) homolog implicated in β-branching at C13 and C21 of the core ring system from the bryostatin metabolic pathway (Bry). We confirmed the activity of BryR using two complementary methods, radio-SDS PAGE, and Fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS). The activity of BryR depended on pairing of the native acetoacetyl-BryM3 acceptor acyl carrier protein (ACP) with an appropriate donor acetyl-ACP from a heterologous HMGS cassette. Additionally, the ability of BryR to discriminate between various ACPs was assessed using a surface plasmon resonance (SPR)-based protein-protein binding assay. Our data suggest that specificity for a protein-bound acyl group is a distinguishing feature between HMGS homologs found in PKS or PKS/NRPS biosynthetic pathways and those of primary metabolism. These findings reveal an important example of molecular recognition between protein components that are essential for biosynthetic fidelity in natural product assembly and modification.
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Affiliation(s)
- Tonia J Buchholz
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
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36
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Zhang F, He HY, Tang MC, Tang YM, Zhou Q, Tang GL. Cloning and Elucidation of the FR901464 Gene Cluster Revealing a Complex Acyltransferase-less Polyketide Synthase Using Glycerate as Starter Units. J Am Chem Soc 2011; 133:2452-62. [DOI: 10.1021/ja105649g] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Feng Zhang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Hai-Yan He
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Man-Cheng Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yu-Min Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Qiang Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Gong-Li Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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37
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Huang Y, Huang SX, Ju J, Tang G, Liu T, Shen B. Characterization of the lnmKLM genes unveiling key intermediates for β-alkylation in leinamycin biosynthesis. Org Lett 2010; 13:498-501. [PMID: 21192727 DOI: 10.1021/ol102838y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Leinamycin (LNM, 1) biosynthesis is proposed to involve β-alkylation of the polyketide intermediate, catalyzed by LnmKLM. Inactivation of lnmK, lnmL, or lnmM afforded mutant strains that accumulated LNM K-1 (2), K-2 (3), K-3 (4), and isomers LNM K-1' (5), K-2' (6), and K-3' (7) whose polyketide origin was established by feeding experiments with sodium [1-(13)C]acetate. These findings confirm the indispensability of LnmKLM in 1 biosynthesis and suggest that β-alkylation proceeds on the growing polyketide intermediate while bound to the LNM polyketide synthase.
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Affiliation(s)
- Yong Huang
- Division of Pharmaceutical Sciences, University of Wisconsin, Madison, Wisconsin 53705-2222, USA
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38
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Conformational switch triggered by alpha-ketoglutarate in a halogenase of curacin A biosynthesis. Proc Natl Acad Sci U S A 2010; 107:14099-104. [PMID: 20660778 DOI: 10.1073/pnas.1006738107] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The CurA halogenase (Hal) catalyzes a cryptic chlorination leading to cyclopropane ring formation in the synthesis of the natural product curacin A. Hal belongs to a family of enzymes that use Fe(2+), O(2) and alpha-ketoglutarate (alphaKG) to perform a variety of halogenation reactions in natural product biosynthesis. Crystal structures of the enzyme in five ligand states reveal strikingly different open and closed conformations dependent on alphaKG binding. The open form represents ligand-free enzyme, preventing substrate from entering the active site until both alphaKG and chloride are bound, while the closed form represents the holoenzyme with alphaKG and chloride coordinated to iron. Candidate amino acid residues involved in substrate recognition were identified by site-directed mutagenesis. These new structures provide direct evidence of a conformational switch driven by alphaKG leading to chlorination of an early pathway intermediate.
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39
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Leggans EK, Akey DL, Smith JL, Fecik RA. A general scheme for synthesis of substrate-based polyketide labels for acyl carrier proteins. Bioorg Med Chem Lett 2010; 20:5939-42. [PMID: 20801036 DOI: 10.1016/j.bmcl.2010.05.089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 05/19/2010] [Accepted: 05/21/2010] [Indexed: 10/19/2022]
Abstract
A general strategy to enzymatically label acyl carrier proteins (ACPs) of polyketide synthases has been developed. Incorporation of a chloromethyl ketone or vinyl ketone moiety into polyketide chain elongation intermediate mimics allows for the synthesis of CoA adducts. These CoA adducts undergo enzymatic reaction with Sfp, a phosphopantetheinyl transferase, to afford labeled CurB carrier proteins.
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Affiliation(s)
- Erick K Leggans
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware Street SE, Room 456, Minneapolis, MN 55414-2959, USA
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40
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Abstract
This review discusses the biosynthesis of natural products that are generated by trans-AT polyketide synthases, a family of catalytically versatile enzymes that have recently been recognized as one of the major group of proteins involved in the production of bioactive polyketides. 436 references are cited.
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Affiliation(s)
- Jörn Piel
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Bonn, Germany.
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41
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Jones AC, Monroe EA, Eisman EB, Gerwick L, Sherman DH, Gerwick WH. The unique mechanistic transformations involved in the biosynthesis of modular natural products from marine cyanobacteria. Nat Prod Rep 2010; 27:1048-65. [PMID: 20442916 DOI: 10.1039/c000535e] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cyanobacteria are abundant producers of natural products well recognized for their bioactivity and utility in drug discovery and biotechnology applications. In the last decade, characterization of several modular gene clusters that code for the biosynthesis of these compounds has revealed a number of unusual enzymatic reactions. In this article, we review several mechanistic transformations identified in marine cyanobacterial biosynthetic pathways, with an emphasis on modular polyketide synthase(PKS)/non-ribosomal peptide synthetase (NRPS) gene clusters. In selected instances, we also make comparisons between cyanobacterial gene clusters derived from marine and freshwater strains. We then provide an overview of recent developments in cyanobacterial natural products biosynthesis made available through genome sequencing and new advances in bioinformatics and genetics.
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Affiliation(s)
- Adam C Jones
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA 92093, USA
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42
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Abstract
Mupirocin, a polyketide antibiotic produced by Pseudomonas fluorescens, is used to control the carriage of methicillin-resistant Staphylococcus aureus on skin and in nasal passages as well as for various skin infections. Low-level resistance to the antibiotic arises by mutation of the mupirocin target, isoleucyl-tRNA synthetase, whereas high-level resistance is due to the presence of an isoleucyl-tRNA synthetase with many similarities to eukaryotic enzymes. Mupirocin biosynthesis is carried out by a combination of type I multifunctional polyketide synthases and tailoring enzymes encoded in a 75 kb gene cluster. Chemical synthesis has also been achieved. This knowledge should allow the synthesis of new and modified antibiotics for the future.
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43
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Isolation and Purification of a New Kalimantacin/Batumin-Related Polyketide Antibiotic and Elucidation of Its Biosynthesis Gene Cluster. ACTA ACUST UNITED AC 2010; 17:149-59. [DOI: 10.1016/j.chembiol.2010.01.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 01/06/2010] [Accepted: 01/14/2010] [Indexed: 11/24/2022]
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44
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Fisch KM, Gurgui C, Heycke N, van der Sar SA, Anderson SA, Webb VL, Taudien S, Platzer M, Rubio BK, Robinson SJ, Crews P, Piel J. Polyketide assembly lines of uncultivated sponge symbionts from structure-based gene targeting. Nat Chem Biol 2009; 5:494-501. [PMID: 19448639 DOI: 10.1038/nchembio.176] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 03/25/2009] [Indexed: 11/09/2022]
Abstract
There is increasing evidence that uncultivated bacterial symbionts are the true producers of numerous bioactive compounds isolated from marine sponges. The localization and heterologous expression of biosynthetic genes could clarify this issue and provide sustainable supplies for a wide range of pharmaceuticals. However, identification of genes in the usually highly complex symbiont communities remains a challenging task. For polyketides, one of the most important groups of sponge-derived drug candidates, we have developed a general strategy that allows one to rapidly access biosynthetic gene clusters based on chemical moieties. Using this method, we targeted polyketide synthase genes from two different sponge metagenomes. We have obtained from a sponge-bacterial association a complete pathway for the rare and potent antitumor agent psymberin from Psammocinia aff. bulbosa. The data support the symbiont hypothesis and provide insights into natural product evolution in previously inaccessible bacteria.
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Affiliation(s)
- Katja M Fisch
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Bonn, Germany
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45
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Gu L, Wang B, Kulkarni A, Gehret JJ, Lloyd KR, Gerwick L, Gerwick WH, Wipf P, Håkansson K, Smith JL, Sherman DH. Polyketide decarboxylative chain termination preceded by o-sulfonation in curacin a biosynthesis. J Am Chem Soc 2009; 131:16033-5. [PMID: 19835378 PMCID: PMC2839324 DOI: 10.1021/ja9071578] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biosynthetic innovation in natural product systems is driven by the recruitment of new genes and enzymes into these complex pathways. Here, an unprecedented decarboxylative chain termination mechanism is described for the polyketide synthase of curacin A, an anticancer lead compound isolated from the marine cyanobacterium Lyngbya majuscula. The unusual chain termination module containing adjacent sulfotransferase (ST) and thioesterase (TE) catalytic domains embedded in CurM was biochemically characterized. The TE was proved to catalyze a hydrolytic chain release of the polyketide chain elongation intermediate. Moreover, a selective ST-mediated sulfonation of the (R)-beta-hydroxyl group was found to precede TE-mediated hydrolysis, triggering a successive decarboxylative elimination and resulting in the formation of a rare terminal olefin in the final metabolite.
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Affiliation(s)
- Liangcai Gu
- Life Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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46
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Busche AEL, Aranko AS, Talebzadeh-Farooji M, Bernhard F, Dötsch V, Iwaï H. Segmental isotopic labeling of a central domain in a multidomain protein by protein trans-splicing using only one robust DnaE intein. Angew Chem Int Ed Engl 2009; 48:6128-31. [PMID: 19591176 DOI: 10.1002/anie.200901488] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Alena E L Busche
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance and Cluster of Excellence Frankfurt Macromolecular Complexes (CEF), University of Frankfurt, 60438 Frankfurt, Germany
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47
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Hochmuth T, Piel J. Polyketide synthases of bacterial symbionts in sponges--evolution-based applications in natural products research. PHYTOCHEMISTRY 2009; 70:1841-1849. [PMID: 19443000 DOI: 10.1016/j.phytochem.2009.04.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 04/09/2009] [Accepted: 04/15/2009] [Indexed: 05/27/2023]
Abstract
Marine sponges are an unusually rich source of bioactive natural products with clinical potential. They also often harbor rich communities of symbiotic bacteria that have often been suspected as the true producers of sponge-derived compounds. To date, these bacteria can in most cases not be cultivated, but culture-independent methods, such as isolating and analyzing biosynthetic gene clusters using metagenomic strategies, have recently provided first insights into their chemical potential. This review summarizes recent work of our laboratory on the study of polyketide synthases (PKSs). These studies revealed two evolutionarily distinct, unusual PKS types that are commonly found in sponge metagenomes and were shown to be of bacterial origin. One, the sup PKS, dominates sponge metagenomic DNA libraries, occurs widespread in bacteriosponges and is to date exclusively known from such animals. Data suggest that it is a type of synthase that generates methyl-branched fatty acids, which are commonly present in sponges. The other PKS type, termed trans-acyltransferase (AT) PKS, is responsible for the biosynthesis of complex, bioactive polyketides, such as the onnamides, and also occurs in free-living bacteria. The diversity of PKS genes present in a single sponge metagenome can be enormous. However, the phylogenetic approaches outlined in this review can provide valuable insights into the PKS function and structures of polyketides and can assist in the targeted isolation of gene clusters.
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Affiliation(s)
- Thomas Hochmuth
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Bonn, Germany
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48
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Busche A, Aranko A, Talebzadeh-Farooji M, Bernhard F, Dötsch V, Iwaï H. Segmental Isotopic Labeling of a Central Domain in a Multidomain Protein by ProteinTrans-Splicing Using Only One Robust DnaE Intein. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200901488] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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49
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Evans BS, Kelleher NL. To cyclize or not to cyclize: catching enzyme evolution in the act. ACS Chem Biol 2009; 4:495-7. [PMID: 19606882 DOI: 10.1021/cb900154b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
If you look at the biggest genes in soil and marine bacteria, you tend to see the chemical blueprints for making natural products such as peptides and polyketides. Over the past decade, collective efforts of enzymologists working with synthetic and analytical chemists have been catching up with the data dump from microbial genome sequencing. Following this story line, we now understand how cyanobacteria construct scaffolds for the related natural products curacin and jamaicamide using subtle tweaks to non-standard biosynthetic machinery.
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Affiliation(s)
- Bradley S. Evans
- Department of Biochemistry
- The Institute of Genomic Biology, University of Illinois Urbana−Champaign, Urbana, Illinois 61802
| | - Neil L. Kelleher
- Department of Biochemistry
- Department of Chemistry
- The Institute of Genomic Biology, University of Illinois Urbana−Champaign, Urbana, Illinois 61802
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Liu T, Huang Y, Shen B. Bifunctional acyltransferase/decarboxylase LnmK as the missing link for beta-alkylation in polyketide biosynthesis. J Am Chem Soc 2009; 131:6900-1. [PMID: 19405532 DOI: 10.1021/ja9012134] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Beta-alkylations contribute to the vast structural diversity displayed by polyketide natural products. A unified pathway has been proposed for introduction of both beta-methyl and beta-ethyl branches catalyzed by hydroxymethylglutaryl-CoA synthase homologues that utilize acetyl- or propionyl-S-acyl carrier protein (ACP) as a substrate. While the origin of acetyl-S-ACP has been established, that of propionyl-S-ACP remains unknown. Here we report the characterization of LnmK from the leinamycin biosynthetic machinery as a bifunctional acyltransferase/decarboxylase (AT/DC) that derives propionyl-S-ACP from methylmalonyl-CoA, accounting for the missing link of the beta-ethyl or propionyl branch in polyketide biosynthesis. LnmK represents an emerging family of novel AT/DC enzymes and could be exploited by combinatorial biosynthesis methods to engineer novel polyketides, especially those with beta-alkyl branches.
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Affiliation(s)
- Tao Liu
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705-2222, USA
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