1
|
Jian X, Pang F, Hobson C, Jenner M, Alkhalaf LM, Challis GL. Antibiotic Skeletal Diversification via Differential Enoylreductase Recruitment and Module Iteration in trans-Acyltransferase Polyketide Synthases. J Am Chem Soc 2024; 146:6114-6124. [PMID: 38389455 PMCID: PMC10921412 DOI: 10.1021/jacs.3c13667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024]
Abstract
Microorganisms are remarkable chemists capable of assembling complex molecular architectures that penetrate cells and bind biomolecular targets with exquisite selectivity. Consequently, microbial natural products have wide-ranging applications in medicine and agriculture. How the "blind watchmaker" of evolution creates skeletal diversity is a key question in natural products research. Comparative analysis of biosynthetic pathways to structurally related metabolites is an insightful approach to addressing this. Here, we report comparative biosynthetic investigations of gladiolin, a polyketide antibiotic from Burkholderia gladioli with promising activity against multidrug-resistant Mycobacterium tuberculosis, and etnangien, a structurally related antibiotic produced by Sorangium cellulosum. Although these metabolites have very similar macrolide cores, their C21 side chains differ significantly in both length and degree of saturation. Surprisingly, the trans-acyltransferase polyketide synthases (PKSs) that assemble these antibiotics are almost identical, raising intriguing questions about mechanisms underlying structural diversification in this important class of biosynthetic assembly line. In vitro reconstitution of key biosynthetic transformations using simplified substrate analogues, combined with gene deletion and complementation experiments, enabled us to elucidate the origin of all the structural differences in the C21 side chains of gladiolin and etnangien. The more saturated gladiolin side chain arises from a cis-acting enoylreductase (ER) domain in module 1 and in trans recruitment of a standalone ER to module 5 of the PKS. Remarkably, module 5 of the gladiolin PKS is intrinsically iterative in the absence of the standalone ER, accounting for the longer side chain in etnangien. These findings have important implications for biosynthetic engineering approaches to the creation of novel polyketide skeletons.
Collapse
Affiliation(s)
- Xinyun Jian
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
- Warwick
Integrative Synthetic Biology Centre, University
of Warwick, Coventry CV4 7AL, U.K.
- Department
of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- ARC
Centre of Excellence for Innovations in Protein and Peptide Science, Monash University, Clayton, VIC 3800, Australia
| | - Fang Pang
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Christian Hobson
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Matthew Jenner
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
- Warwick
Integrative Synthetic Biology Centre, University
of Warwick, Coventry CV4 7AL, U.K.
| | - Lona M. Alkhalaf
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Gregory L. Challis
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
- Warwick
Integrative Synthetic Biology Centre, University
of Warwick, Coventry CV4 7AL, U.K.
- Department
of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- ARC
Centre of Excellence for Innovations in Protein and Peptide Science, Monash University, Clayton, VIC 3800, Australia
| |
Collapse
|
2
|
Saggu SK, Nath A, Kumar S. Myxobacteria: biology and bioactive secondary metabolites. Res Microbiol 2023; 174:104079. [PMID: 37169232 DOI: 10.1016/j.resmic.2023.104079] [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: 01/19/2023] [Revised: 04/22/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
Myxobacteria are Gram-negative eubacteria and they thrive in a variety of habitats including soil rich in organic matter, rotting wood, animal dung and marine environment. Myxobacteria are a promising source of new compounds associated with diverse bioactive spectrum and unique mode of action. The genome information of myxobacteria has revealed many orphan biosynthetic pathways indicating that these bacteria can be the source of several novel natural products. In this review, we highlight the biology of myxobacteria with emphasis on their habitat, life cycle, isolation methods and enlist all the bioactive secondary metabolites purified till date and their mode of action.
Collapse
Affiliation(s)
- Sandeep Kaur Saggu
- Department of Biotechnology, Kanya Maha Vidyalaya, Jalandhar, Punjab, India - 144004.
| | - Amar Nath
- University Centre of Excellence in Research, Baba Farid University of Health Sciences, Faridkot, Punjab India 151203.
| | - Shiv Kumar
- Guru Gobind Singh Medical College, Baba Farid University of Health Sciences, Faridkot, Punjab India 151203.
| |
Collapse
|
3
|
Liu L, Wang W, Chen M, Zhang Y, Mao H, Wang D, Chen Y, Li P. Characterization of three succinyl-CoA acyltransferases involved in polyketide chain assembly. Appl Microbiol Biotechnol 2023; 107:2403-2412. [PMID: 36929192 DOI: 10.1007/s00253-023-12481-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/18/2023]
Abstract
Polyketides are a class of natural products with astonishing structural diversities, fascinating biological activities, and a versatile of applications. In polyketides biosynthesis, acyltransferases (ATs) are the 'gatekeeping' enzymes selecting the specific CoA-activated acyl groups as building blocks and transferring them onto the phosphopantetheine arm of acyl carrier proteins (ACPs) to enable the following condensation reactions to assemble the polyketide chain. Herein, the Art2 protein from aurantinins, a group of the antibacterial polyketides, is characterized in vitro as an AT that can load a CoA-activated succinyl unit onto the first ACP domain of Art17 (ACPArt17-1). In addition, another two proteins, GbnB and EtnB, involved in the biosynthesis of gladiolin and etnangien respectively, were traced by literature mining, homologous searching, and product structure analysis and then identified as functional succinyl-CoA ATs by the ACPArt17-1 assays. Taken together, by the assay method employing ACPArt17-1 as an acyl acceptor, we identified three ATs that can introduce a succinyl unit into the polyketide assembly line, which enriches the toolbox of polyketide biosynthetic enzymes and sets a stage for incorporating a succinyl unit into polyketide backbones in synthetic biological manners. KEY POINTS: • Three acyltransferases that are able to load ACP with a succinyl unit were characterized in vitro. • ACPArt17-1 can be used as an acceptor to assay succinyl-CoA AT from different polyketides. • The succinyl unit can be incorporated into polyketides assembly process.
Collapse
Affiliation(s)
- Lilu Liu
- 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
| | - Wenzhao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Meng 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
| | - Yuwei Zhang
- 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
| | - 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
| | - Dacheng Wang
- 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.
| |
Collapse
|
4
|
Lacey HJ, Chen R, Vuong D, Lacey E, Rutledge PJ, Chooi YH, Piggott AM, Booth TJ. Resorculins: hybrid polyketide macrolides from Streptomyces sp. MST-91080. Org Biomol Chem 2023; 21:2531-2538. [PMID: 36876905 DOI: 10.1039/d2ob02332f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Fourteen-membered macrolides are a class of compounds with significant clinical value as antibacterial agents. As part of our ongoing investigation into the metabolites of Streptomyces sp. MST-91080, we report the discovery of resorculins A and B, unprecedented 3,5-dihydroxybenzoic acid (α-resorcylic acid)-containing 14-membered macrolides. We sequenced the genome of MST-91080 and identified the putative resorculin biosynthetic gene cluster (rsn BGC). The rsn BGC is hybrid of type I and type III polyketide synthases. Bioinformatic analysis revealed that the resorculins are relatives of known hybrid polyketides: kendomycin and venemycin. Resorculin A exhibited antibacterial activity against Bacillus subtilis (MIC 19.8 μg mL-1), while resorculin B showed cytotoxic activity against the NS-1 mouse myeloma cell line (IC50 3.6 μg mL-1).
Collapse
Affiliation(s)
- Heather J Lacey
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
- School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Rachel Chen
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
- School of Natural Sciences, Macquarie University, NSW 2109, Australia
| | - Peter J Rutledge
- School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Andrew M Piggott
- School of Natural Sciences, Macquarie University, NSW 2109, Australia
| | - Thomas J Booth
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| |
Collapse
|
5
|
Winter AJ, Rowe MT, Weir ANM, Akter N, Mbatha SZ, Walker PD, Williams C, Song Z, Race PR, Willis CL, Crump MP. Programmed Iteration Controls the Assembly of the Nonanoic Acid Side Chain of the Antibiotic Mupirocin. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202212393. [PMID: 38505625 PMCID: PMC10947060 DOI: 10.1002/ange.202212393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/11/2022]
Abstract
Mupirocin is a clinically important antibiotic produced by Pseudomonas fluorescens NCIMB 10586 that is assembled by a complex trans-AT polyketide synthase. The polyketide fragment, monic acid, is esterified by a 9-hydroxynonanoic acid (9HN) side chain which is essential for biological activity. The ester side chain assembly is initialised from a 3-hydroxypropionate (3HP) starter unit attached to the acyl carrier protein (ACP) MacpD, but the fate of this species is unknown. Herein we report the application of NMR spectroscopy, mass spectrometry, chemical probes and in vitro assays to establish the remaining steps of 9HN biosynthesis. These investigations reveal a complex interplay between a novel iterative or "stuttering" KS-AT didomain (MmpF), the multidomain module MmpB and multiple ACPs. This work has important implications for understanding the late-stage biosynthetic steps of mupirocin and will be important for future engineering of related trans-AT biosynthetic pathways (e.g. thiomarinol).
Collapse
Affiliation(s)
| | | | | | - Nahida Akter
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
| | | | - Paul D. Walker
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
| | | | - Zhongshu Song
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
| | - Paul R. Race
- School of BiochemistryUniversity of BristolBristolBS8 1TDUK
| | | | | |
Collapse
|
6
|
Winter AJ, Rowe MT, Weir ANM, Akter N, Mbatha SZ, Walker PD, Williams C, Song Z, Race PR, Willis CL, Crump MP. Programmed Iteration Controls the Assembly of the Nonanoic Acid Side Chain of the Antibiotic Mupirocin. Angew Chem Int Ed Engl 2022; 61:e202212393. [PMID: 36227272 PMCID: PMC10098928 DOI: 10.1002/anie.202212393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/12/2022]
Abstract
Mupirocin is a clinically important antibiotic produced by Pseudomonas fluorescens NCIMB 10586 that is assembled by a complex trans-AT polyketide synthase. The polyketide fragment, monic acid, is esterified by a 9-hydroxynonanoic acid (9HN) side chain which is essential for biological activity. The ester side chain assembly is initialised from a 3-hydroxypropionate (3HP) starter unit attached to the acyl carrier protein (ACP) MacpD, but the fate of this species is unknown. Herein we report the application of NMR spectroscopy, mass spectrometry, chemical probes and in vitro assays to establish the remaining steps of 9HN biosynthesis. These investigations reveal a complex interplay between a novel iterative or "stuttering" KS-AT didomain (MmpF), the multidomain module MmpB and multiple ACPs. This work has important implications for understanding the late-stage biosynthetic steps of mupirocin and will be important for future engineering of related trans-AT biosynthetic pathways (e.g. thiomarinol).
Collapse
Affiliation(s)
| | - Matthew T. Rowe
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | | | - Nahida Akter
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | | | - Paul D. Walker
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | | | - Zhongshu Song
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | - Paul R. Race
- School of Biochemistry University of Bristol Bristol BS8 1TD UK
| | | | | |
Collapse
|
7
|
Approaches to Configuration Determinations of Flexible Marine Natural Products: Advances and Prospects. Mar Drugs 2022; 20:md20050333. [PMID: 35621984 PMCID: PMC9143581 DOI: 10.3390/md20050333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/07/2023] Open
Abstract
Flexible marine natural products (MNPs), such as eribulin and bryostatin, play an important role in the development of modern marine drugs. However, due to the multiple chiral centers and geometrical uncertainty of flexible systems, configuration determinations of flexible MNPs face great challenges, which, in turn, have led to obstacles in druggability research. To resolve this issue, the comprehensive use of multiple methods is necessary. Additionally, configuration assignment methods, such as X-ray single-crystal diffraction (crystalline derivatives, crystallization chaperones, and crystalline sponges), NMR-based methods (JBCA and Mosher’s method), circular dichroism-based methods (ECCD and ICD), quantum computational chemistry-based methods (NMR calculations, ECD calculations, and VCD calculations), and chemical transformation-based methods should be summarized. This paper reviews the basic principles, characteristics, and applicability of the methods mentioned above as well as application examples to broaden the research and applications of these methods and to provide a reference for the configuration determinations of flexible MNPs.
Collapse
|
8
|
Kirsch SH, Haeckl FPJ, Müller R. Beyond the approved: target sites and inhibitors of bacterial RNA polymerase from bacteria and fungi. Nat Prod Rep 2022; 39:1226-1263. [PMID: 35507039 DOI: 10.1039/d1np00067e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: 2016 to 2022RNA polymerase (RNAP) is the central enzyme in bacterial gene expression representing an attractive and validated target for antibiotics. Two well-known and clinically approved classes of natural product RNAP inhibitors are the rifamycins and the fidaxomycins. Rifampicin (Rif), a semi-synthetic derivative of rifamycin, plays a crucial role as a first line antibiotic in the treatment of tuberculosis and a broad range of bacterial infections. However, more and more pathogens such as Mycobacterium tuberculosis develop resistance, not only against Rif and other RNAP inhibitors. To overcome this problem, novel RNAP inhibitors exhibiting different target sites are urgently needed. This review includes recent developments published between 2016 and today. Particular focus is placed on novel findings concerning already known bacterial RNAP inhibitors, the characterization and development of new compounds isolated from bacteria and fungi, and providing brief insights into promising new synthetic compounds.
Collapse
Affiliation(s)
- Susanne H Kirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - F P Jake Haeckl
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.,Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
| |
Collapse
|
9
|
Covington BC, Seyedsayamdost MR. MetEx, a Metabolomics Explorer Application for Natural Product Discovery. ACS Chem Biol 2021; 16:2825-2833. [PMID: 34859662 DOI: 10.1021/acschembio.1c00737] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Advances in next-generation DNA sequencing technologies, bioinformatics, and mass spectrometry-based metabolite detection have ushered in a new era of natural product discovery. Microbial secondary metabolomes are complex, especially when otherwise silent biosynthetic genes are activated, and there is therefore a need for data analysis software to explore and map the resulting multidimensional datasets. To that end, we herein report the Metabolomics Explorer (MetEx), a publicly available web application for the analysis of parallel liquid chromatography-coupled mass spectrometry (LC-MS)-based metabolomics data. MetEx is a highly interactive application that facilitates visualization and analysis of complex metabolomics datasets, consisting of retention time, m/z, and MS intensity features, as a function of hundreds of conditions or elicitors. The software enables prioritization of leads from three-dimensional maps, extraction of two-dimensional slices from various higher order plots, organization of datasets by elicitor chemotypes, customizable library-based dereplication, and automatically scored lead selection. We describe the application of MetEx to the first UPLC-MS-guided high-throughput elicitor screen in which Burkholderia gladioli was challenged with 750 elicitors, and the resulting profiles were interrogated by UPLC-Qtof-MS and subsequently analyzed with the app. We demonstrate the utility of MetEx by reporting elicitors for several cryptic metabolite groups and by uncovering new natural products that remain to be characterized. MetEx is available at https://mo.princeton.edu/MetEx/.
Collapse
Affiliation(s)
- Brett C. Covington
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| |
Collapse
|
10
|
Bach E, Passaglia LMP, Jiao J, Gross H. Burkholderia in the genomic era: from taxonomy to the discovery of new antimicrobial secondary metabolites. Crit Rev Microbiol 2021; 48:121-160. [PMID: 34346791 DOI: 10.1080/1040841x.2021.1946009] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Species of Burkholderia are highly versatile being found not only abundantly in soil, but also as plants and animals' commensals or pathogens. Their complex multireplicon genomes harbour an impressive number of polyketide synthase (PKS) and nonribosomal peptide-synthetase (NRPS) genes coding for the production of antimicrobial secondary metabolites (SMs), which have been successfully deciphered by genome-guided tools. Moreover, genome metrics supported the split of this genus into Burkholderia sensu stricto (s.s.) and five new other genera. Here, we show that the successful antimicrobial SMs producers belong to Burkholderia s.s. Additionally, we reviewed the occurrence, bioactivities, modes of action, structural, and biosynthetic information of thirty-eight Burkholderia antimicrobial SMs shedding light on their diversity, complexity, and uniqueness as well as the importance of genome-guided strategies to facilitate their discovery. Several Burkholderia NRPS and PKS display unusual features, which are reflected in their structural diversity, important bioactivities, and varied modes of action. Up to now, it is possible to observe a general tendency of Burkholderia SMs being more active against fungi. Although the modes of action and biosynthetic gene clusters of many SMs remain unknown, we highlight the potential of Burkholderia SMs as alternatives to fight against new diseases and antibiotic resistance.
Collapse
Affiliation(s)
- Evelise Bach
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Junjing Jiao
- Department for Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Harald Gross
- Department for Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| |
Collapse
|
11
|
Li P, Chen M, Tang W, Guo Z, Zhang Y, Wang M, Horsman GP, Zhong J, Lu Z, Chen Y. Initiating polyketide biosynthesis by on-line methyl esterification. Nat Commun 2021; 12:4499. [PMID: 34301953 PMCID: PMC8302727 DOI: 10.1038/s41467-021-24846-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 07/09/2021] [Indexed: 12/04/2022] Open
Abstract
Aurantinins (ARTs) are antibacterial polyketides featuring a unique 6/7/8/5-fused tetracyclic ring system and a triene side chain with a carboxyl terminus. Here we identify the art gene cluster and dissect ART’s C-methyl incorporation patterns to study its biosynthesis. During this process, an apparently redundant methyltransferase Art28 was characterized as a malonyl-acyl carrier protein O-methyltransferase, which represents an unusual on-line methyl esterification initiation strategy for polyketide biosynthesis. The methyl ester bond introduced by Art28 is kept until the last step of ART biosynthesis, in which it is hydrolyzed by Art9 to convert inactive ART 9B to active ART B. The cryptic reactions catalyzed by Art28 and Art9 represent a protecting group biosynthetic logic to render the ART carboxyl terminus inert to unwanted side reactions and to protect producing organisms from toxic ART intermediates. Further analyses revealed a wide distribution of this initiation strategy for polyketide biosynthesis in various bacteria. Aurantinins are polyketides with unusual connectivities and broad antibacterial activity. Here the authors show the biosynthesis of aurantinins, which proceeds via an on-line methyl esterification at the terminus that enables the iterative chain elongations prior to condensation and cyclization.
Collapse
Affiliation(s)
- Pengwei Li
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Meng Chen
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wei Tang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhengyan Guo
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuwei Zhang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Min Wang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong, China
| | - Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Jin Zhong
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agriculture University, Nanjing, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
12
|
Menche D. Design and Synthesis of Simplified Polyketide Analogs: New Modalities beyond the Rule of 5. ChemMedChem 2021; 16:2068-2074. [PMID: 33755304 PMCID: PMC8360190 DOI: 10.1002/cmdc.202100150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Indexed: 12/29/2022]
Abstract
Natural products provide important lead structures for development of pharmaceutical agents or present attractive tools for medicinal chemistry. However, structurally complex and thus less accessible metabolites defying conventional drug-like properties, as expressed by Pfizer's rule of five, have received less attention as medicinal leads. Traditionally, research focus has been on realizing total syntheses rather than developing more readily available analogs to resolve the critical supply issue. However, very recent studies with complex myxobacterial polyketides have demonstrated that considerable structural simplification may be realized with retention of biological potencies. The context, underlying rationale and importance of tailored synthetic strategies of three such case studies are presented, which may inspire further related activities and may eventually help exploiting the largely untapped biological potential of complex metabolites in general.
Collapse
Affiliation(s)
- Dirk Menche
- Kekulé-Institut für Organische Chemie und BiochemieUniversität BonnGerhard-Domagk-Strasse 153121BonnGermany
| |
Collapse
|
13
|
Spindler S, Wingen LM, Schönenbroicher M, Seul M, Adamek M, Essig S, Kurz M, Ziemert N, Menche D. Modular Fragment Synthesis and Bioinformatic Analysis Propose a Revised Vancoresmycin Stereoconfiguration. Org Lett 2021; 23:1175-1180. [PMID: 33356317 DOI: 10.1021/acs.orglett.0c03957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Elaborate fragments of the proposed stereostructure of the complex polyketide antibiotic vancoresmycin have been synthesized in a stereoselective fashion based on a modular and convergent approach. Significant nuclear magnetic resonance differences in one of these subunits compared with the natural product question the proposed stereoconfiguration. Consequently, an extensive bioinformatics analysis of the biosynthetic gene cluster was carried out, leading to a revised stereoconfigurational proposal for this highly potent antibiotic.
Collapse
Affiliation(s)
- Stefanie Spindler
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Str. 1, D-53121 Bonn, Germany
| | - Lukas M Wingen
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Str. 1, D-53121 Bonn, Germany
| | - Max Schönenbroicher
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Str. 1, D-53121 Bonn, Germany
| | - Maximilian Seul
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Str. 1, D-53121 Bonn, Germany
| | - Martina Adamek
- Interfaculty Institute of Microbiology and Infection Medicine, German Centre for Infection Research (DZIF), Partnersite Tuebingen, Auf der Morgenstelle 28, D-72076 Tübingen, Germany
| | | | - Michael Kurz
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, D-65926 Frankfurt am Main, Germany
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine, German Centre for Infection Research (DZIF), Partnersite Tuebingen, Auf der Morgenstelle 28, D-72076 Tübingen, Germany
| | - Dirk Menche
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Str. 1, D-53121 Bonn, Germany
| |
Collapse
|
14
|
Yin Z, Dickschat JS. Cis double bond formation in polyketide biosynthesis. Nat Prod Rep 2021; 38:1445-1468. [PMID: 33475122 DOI: 10.1039/d0np00091d] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Covering: up to 2020Polyketides form a large group of bioactive secondary metabolites that usually contain one or more double bonds. Although most of the double bonds found in polyketides are trans or E-configured, several cases are known in which cis or Z-configurations are observed. Double bond formation by polyketide synthases (PKSs) is widely recognised to be catalysed by ketoreduction and subsequent dehydration of the acyl carrier protein (ACP)-tethered 3-ketoacyl intermediate in the PKS biosynthetic assembly line with a specific stereochemical course in which the ketoreduction step determines the usual trans or more rare cis double bond configuration. Occasionally, other mechanisms for the installation of cis double bonds such as double bond formation during chain release or post-PKS modifications including, amongst others, isomerisations or double bond installations by oxidation are observed. This review discusses the peculiar mechanisms of cis double bond formation in polyketide biosynthesis.
Collapse
Affiliation(s)
- Zhiyong Yin
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
| | | |
Collapse
|
15
|
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.
Collapse
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.
| |
Collapse
|
16
|
Zhang W. Heck macrocyclization in natural product total synthesis. Nat Prod Rep 2021; 38:1109-1135. [PMID: 33662070 DOI: 10.1039/d0np00087f] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: 1981-2020 Heck macrocyclization is a logical extension of the award-winning Mizoroki-Heck reaction. Through covalent linking of two otherwise discrete coupling partners, the resultant chimeric substrate is transformed into a large ring with enhanced rigidity and unique functional group disposition. Pioneered in the early 1980s, this methodology has evolved into a competent option for creating diverse macrocycles. Despite its growing influence, hitherto no systematic survey has ever appeared in the literature. The present review delineates the state-of-the-art of Heck macrocyclization in the context of natural product synthesis. Sixteen selected cases, each examined from a different perspective, coalesce into the view that the title reaction is a viable tool for synthesis-enabled macrocycle research.
Collapse
Affiliation(s)
- Weicheng Zhang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, People's Republic of China.
| |
Collapse
|
17
|
Rivas A, Areal A, Mora P, Álvarez R, de Lera AR. Synthesis of Symmetrical and Nonsymmetrical Polyenes by Iterative and Bidirectional Palladium-Catalyzed Cross-Coupling Reactions. Chemistry 2020; 26:13543-13567. [PMID: 32267574 DOI: 10.1002/chem.202000624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/08/2020] [Indexed: 11/06/2022]
Abstract
Bifunctional unsaturated reagents designed to undergo palladium-catalyzed cross-coupling reactions with complementary polyenyl connective fragments are highly useful for the undoubtedly challenging synthesis of polyenes. The current toolkit of building blocks for the bidirectional formation of Csp2 -Csp2 single bonds of polyenes includes homo-bisfunctionalized reagents with equal or unequal reactivity (due to steric and/or electronic factors), and hetero-bisfunctionalized counterparts containing either two different nucleophiles, two electrophiles or one of these functionalities and a latent nucleophile that can be unmasked when desired. The combination of these bifunctional linchpin reagents using tactics that modulate the reactivity of each terminus in order to achieve the required connection have streamlined the synthesis of polyenes of great complexity using (iterative) cross-coupling methods for Csp2 -Csp2 bond formation. Reaction conditions for the Pd-catalyzed cross-coupling reactions are mild and functional-group-tolerant, and therefore these protocols allow to construct the polyene structures using shorter unsaturated reactants with the desired geometries, since in general the products preserve the stereochemical information of the connected cross-coupling partners.
Collapse
Affiliation(s)
- Aurea Rivas
- Departamento de Química Orgánica, Facultade de Química, CINBIO and IIS Galicia Sur, Universidade de Vigo, 36310, Vigo, Spain
| | - Andrea Areal
- Departamento de Química Orgánica, Facultade de Química, CINBIO and IIS Galicia Sur, Universidade de Vigo, 36310, Vigo, Spain
| | - Paula Mora
- Departamento de Química Orgánica, Facultade de Química, CINBIO and IIS Galicia Sur, Universidade de Vigo, 36310, Vigo, Spain
| | - Rosana Álvarez
- Departamento de Química Orgánica, Facultade de Química, CINBIO and IIS Galicia Sur, Universidade de Vigo, 36310, Vigo, Spain
| | - Angel R de Lera
- Departamento de Química Orgánica, Facultade de Química, CINBIO and IIS Galicia Sur, Universidade de Vigo, 36310, Vigo, Spain
| |
Collapse
|
18
|
Low ZJ, Xiong J, Xie Y, Ma GL, Saw H, Thi Tran H, Wong SL, Pang LM, Fong J, Lu P, Hu JF, Yang L, Miao Y, Liang ZX. Discovery, biosynthesis and antifungal mechanism of the polyene-polyol meijiemycin. Chem Commun (Camb) 2019; 56:822-825. [PMID: 31848534 DOI: 10.1039/c9cc08908j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Produced by a newly isolated Streptomycetes strain, meijiemycin is a gigantic linear polyene-polyol that exhibits structural features not seen in other members of the polyene-polyol family. We propose a biosynthetic mechanism and demonstrate that meijiemycin inhibits hyphal growth by inducing the aggregation of ergosterol and restructuring of the fungal plasma membrane.
Collapse
Affiliation(s)
- Zhen Jie Low
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Juan Xiong
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore. and School of Pharmacy, Fudan University, Shanghai, China
| | - Ying Xie
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Howard Saw
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Hoa Thi Tran
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Soo Lin Wong
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - July Fong
- The Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 637551, Singapore
| | - Peng Lu
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Jin-Feng Hu
- School of Pharmacy, Fudan University, Shanghai, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore. and The Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 637551, Singapore
| |
Collapse
|
19
|
Gregory K, Salvador LA, Akbar S, Adaikpoh BI, Stevens DC. Survey of Biosynthetic Gene Clusters from Sequenced Myxobacteria Reveals Unexplored Biosynthetic Potential. Microorganisms 2019; 7:E181. [PMID: 31238501 PMCID: PMC6616573 DOI: 10.3390/microorganisms7060181] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 01/31/2023] Open
Abstract
Coinciding with the increase in sequenced bacteria, mining of bacterial genomes for biosynthetic gene clusters (BGCs) has become a critical component of natural product discovery. The order Myxococcales, a reputable source of biologically active secondary metabolites, spans three suborders which all include natural product producing representatives. Utilizing the BiG-SCAPE-CORASON platform to generate a sequence similarity network that contains 994 BGCs from 36 sequenced myxobacteria deposited in the antiSMASH database, a total of 843 BGCs with lower than 75% similarity scores to characterized clusters within the MIBiG database are presented. This survey provides the biosynthetic diversity of these BGCs and an assessment of the predicted chemical space yet to be discovered. Considering the mere snapshot of myxobacteria included in this analysis, these untapped BGCs exemplify the potential for natural product discovery from myxobacteria.
Collapse
Affiliation(s)
- Katherine Gregory
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Laura A Salvador
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Shukria Akbar
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Barbara I Adaikpoh
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - D Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| |
Collapse
|
20
|
Chen H, Bian Z, Ravichandran V, Li R, Sun Y, Huo L, Fu J, Bian X, Xia L, Tu Q, Zhang Y. Biosynthesis of polyketides by trans-AT polyketide synthases in Burkholderiales. Crit Rev Microbiol 2019; 45:162-181. [PMID: 31218924 DOI: 10.1080/1040841x.2018.1514365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Widely used as drugs and agrochemicals, polyketides are a family of bioactive natural products, with diverse structures and functions. Polyketides are produced by megaenzymes termed as polyketide synthases (PKSs). PKS biosynthetic pathways are divided into the cis-AT PKSs and trans-AT PKSs; a division based mainly on the absence of an acyltransferase (AT) domain in the trans-AT PKS modules. In trans-AT biosynthesis, the AT activity is contributed via one or several independent proteins, and there are few other characteristics that distinguish trans-AT PKSs from cis-AT PKSs, especially in the formation of the β-branch. The trans-AT PKSs constitute a major PKS pathway, and many are found in Burkholderia species, which are prevalent in the environment and prolific sources of polyketides. This review summarizes studies from 1973 to 2017 on the biosynthesis of natural products by trans-AT PKSs from Burkholderia species.
Collapse
Affiliation(s)
- Hanna Chen
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China.,b State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science , Hunan Normal University , Changsha , People's Republic of China
| | - Zhilong Bian
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Vinothkannan Ravichandran
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Ruijuan Li
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Yi Sun
- c Institute of Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , People's Republic of China
| | - Liujie Huo
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Jun Fu
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Xiaoying Bian
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Liqiu Xia
- b State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science , Hunan Normal University , Changsha , People's Republic of China
| | - Qiang Tu
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Youming Zhang
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China.,b State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science , Hunan Normal University , Changsha , People's Republic of China
| |
Collapse
|
21
|
Pérez-Victoria I, Oves-Costales D, Lacret R, Martín J, Sánchez-Hidalgo M, Díaz C, Cautain B, Vicente F, Genilloud O, Reyes F. Structure elucidation and biosynthetic gene cluster analysis of caniferolides A–D, new bioactive 36-membered macrolides from the marine-derived Streptomyces caniferus CA-271066. Org Biomol Chem 2019; 17:2954-2971. [DOI: 10.1039/c8ob03115k] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The structures of caniferolides A–D have been determined combining NMR and bioinformatics prediction of the absolute configuration.
Collapse
|
22
|
Kim MC, Machado H, Jang KH, Trzoss L, Jensen PR, Fenical W. Integration of Genomic Data with NMR Analysis Enables Assignment of the Full Stereostructure of Neaumycin B, a Potent Inhibitor of Glioblastoma from a Marine-Derived Micromonospora. J Am Chem Soc 2018; 140:10775-10784. [PMID: 30085661 DOI: 10.1021/jacs.8b04848] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The microbial metabolites known as the macrolides are some of the most successful natural products used to treat infectious and immune diseases. Describing the structures of these complex metabolites, however, is often extremely difficult due to the presence of multiple stereogenic centers inherent in this class of polyketide-derived metabolites. With the availability of genome sequence data and a better understanding of the molecular genetics of natural product biosynthesis, it is now possible to use bioinformatic approaches in tandem with spectroscopic tools to assign the full stereostructures of these complex metabolites. In our quest to discover and develop new agents for the treatment of cancer, we observed the production of a highly cytotoxic macrolide, neaumycin B, by a marine-derived actinomycete bacterium of the genus Micromonospora. Neaumycin B is a complex polycyclic macrolide possessing 19 asymmetric centers, usually requiring selective degradation, crystallization, derivatization, X-ray diffraction analysis, synthesis, or other time-consuming approaches to assign the complete stereostructure. As an alternative approach, we sequenced the genome of the producing strain and identified the neaumycin gene cluster ( neu). By integrating the known stereospecificities of biosynthetic enzymes with comprehensive NMR analysis, the full stereostructure of neaumycin B was confidently assigned. This approach exemplifies how mining gene cluster information while integrating NMR-based structure data can achieve rapid, efficient, and accurate stereostructural assignments for complex macrolides.
Collapse
Affiliation(s)
- Min Cheol Kim
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - Henrique Machado
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - Kyoung Hwa Jang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - Lynnie Trzoss
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States.,Center for Microbiome Innovation , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093-0204 , United States.,Moores Comprehensive Cancer Center , University of California, San Diego , La Jolla , California 92093-0204 , United States
| |
Collapse
|
23
|
Curran SC, Hagen A, Poust S, Chan LJG, Garabedian BM, de Rond T, Baluyot MJ, Vu JT, Lau AK, Yuzawa S, Petzold CJ, Katz L, Keasling JD. Probing the Flexibility of an Iterative Modular Polyketide Synthase with Non-Native Substrates in Vitro. ACS Chem Biol 2018; 13:2261-2268. [PMID: 29912551 DOI: 10.1021/acschembio.8b00422] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the search for molecular machinery for custom biosynthesis of valuable compounds, the modular type I polyketide synthases (PKSs) offer great potential. In this study, we investigate the flexibility of BorM5, the iterative fifth module of the borrelidin synthase, with a panel of non-native priming substrates in vitro. BorM5 differentially extends various aliphatic and substituted substrates. Depending on substrate size and substitution BorM5 can exceed the three iterations it natively performs. To probe the effect of methyl branching on chain length regulation, we engineered a BorM5 variant capable of incorporating methylmalonyl- and malonyl-CoA into its intermediates. Intermediate methylation did not affect overall chain length, indicating that the enzyme does not to count methyl branches to specify the number of iterations. In addition to providing regulatory insight about BorM5, we produced dozens of novel methylated intermediates that might be used for production of various hydrocarbons or pharmaceuticals. These findings enable rational engineering and recombination of BorM5 and inform the study of other iterative modules.
Collapse
Affiliation(s)
- Samuel C. Curran
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Andrew Hagen
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
| | - Sean Poust
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
| | - Leanne Jade G. Chan
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Brett M. Garabedian
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Tristan de Rond
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Marian-Joy Baluyot
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jonathan T. Vu
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Andrew K. Lau
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
| | - Satoshi Yuzawa
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Christopher J. Petzold
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Leonard Katz
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| |
Collapse
|
24
|
de Frias UA, Pereira GKB, Guazzaroni ME, Silva-Rocha R. Boosting Secondary Metabolite Production and Discovery through the Engineering of Novel Microbial Biosensors. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7021826. [PMID: 30079350 PMCID: PMC6069586 DOI: 10.1155/2018/7021826] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/11/2018] [Indexed: 01/05/2023]
Abstract
Bacteria are a source of a large number of secondary metabolites with several biomedical and biotechnological applications. In recent years, there has been tremendous progress in the development of novel synthetic biology approaches both to increase the production rate of secondary metabolites of interest in native producers and to mine and reconstruct novel biosynthetic gene clusters in heterologous hosts. Here, we present the recent advances toward the engineering of novel microbial biosensors to detect the synthesis of secondary metabolites in bacteria and in the development of synthetic promoters and expression systems aiming at the construction of microbial cell factories for the production of these compounds. We place special focus on the potential of Gram-negative bacteria as a source of biosynthetic gene clusters and hosts for pathway assembly, on the construction and characterization of novel promoters for native hosts, and on the use of computer-aided design of novel pathways and expression systems for secondary metabolite production. Finally, we discuss some of the potentials and limitations of the approaches that are currently being developed and we highlight new directions that could be addressed in the field.
Collapse
Affiliation(s)
| | | | - María-Eugenia Guazzaroni
- Faculty of Philosophy, Science and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Rafael Silva-Rocha
- Medical School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| |
Collapse
|
25
|
The chejuenolide biosynthetic gene cluster harboring an iterative trans-AT PKS system in Hahella chejuensis strain MB-1084. J Antibiot (Tokyo) 2018; 71:495-505. [DOI: 10.1038/s41429-017-0023-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/21/2017] [Accepted: 12/25/2017] [Indexed: 11/08/2022]
|
26
|
Hu Y, Wang M, Wu C, Tan Y, Li J, Hao X, Duan Y, Guan Y, Shang X, Wang Y, Xiao C, Gan M. Identification and Proposed Relative and Absolute Configurations of Niphimycins C-E from the Marine-Derived Streptomyces sp. IMB7-145 by Genomic Analysis. JOURNAL OF NATURAL PRODUCTS 2018; 81:178-187. [PMID: 29308897 DOI: 10.1021/acs.jnatprod.7b00859] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Analysis of the whole genome sequence of Streptomyces sp. IMB7-145 revealed the presence of seven type I polyketide synthase biosynthetic gene clusters, one of which was highly homologous to the biosynthetic gene cluster of azalomycin F. Detailed bioinformatic analysis of the modular organization of the PKS gene suggested that this gene is responsible for niphimycin biosynthesis. Guided by genomic analysis, a large-scale cultivation ultimately led to the discovery and characterization of four new niphimycin congeners, namely, niphimycins C-E (1-3) and 17-O-methylniphimycin (4). The configurations of most stereocenters of niphimycins have not been determined to date. In the present study, the relative configurations were elucidated by spectroscopic analysis, including J-based analysis and the CNMR database method. Further, the full absolute configurations of niphimycins were completely proposed for the first time based on biosynthetic gene cluster analysis of the ketoreductase and enoylreductase domains for hydroxy- and methyl-bearing stereocenters. Compounds 1, 3, 4, and niphimycin Iα (5) showed antimicrobial activity against methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci (MIC: 8-64 μg/mL), as well as cytotoxicity against the human HeLa cancer cell line (IC50: 3.0-9.0 μM). In addition, compounds 1 and 5 displayed significant activity against several Mycobacterium tuberculosis clinical isolates (MIC: 4-32 μg/mL).
Collapse
Affiliation(s)
- Yuanyuan Hu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| | - Mian Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| | - Chunyan Wu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
- Beijing Key Laboratory of Bioactive Substances and Functional Foods, Beijing Union University , Beijing 100191, People's Republic of China
| | - Yi Tan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| | - Jiao Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| | - Xiaomeng Hao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| | - Yanbo Duan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| | - Yan Guan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| | - Xiaoya Shang
- Beijing Key Laboratory of Bioactive Substances and Functional Foods, Beijing Union University , Beijing 100191, People's Republic of China
| | - Yiguang Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| | - Chunling Xiao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| | - Maoluo Gan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| |
Collapse
|
27
|
Ho GM, Zulueta MML, Hung SC. Stereoselective one-pot synthesis of polypropionates. Nat Commun 2017; 8:679. [PMID: 28947767 PMCID: PMC5612996 DOI: 10.1038/s41467-017-00787-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 07/27/2017] [Indexed: 12/02/2022] Open
Abstract
Polypropionates—motifs with alternating methyl and hydroxy groups—are important segments of many natural products possessing high bioactivity and therapeutic value. Synthetic access to these structures remains an area of intensive interest, focusing on the establishment of the contiguous stereocentres and a desire for operational simplicity. Here we report an efficient strategy for the stereoselective assembly of polypropionates with three or four stereocentres through a three-step relay process that include Diels–Alder reaction, silylenol ether hydrolysis and Baeyer–Villiger oxidation. The stereochemistry and functionality of the resulting polypropionates depend on the substitution pattern of the diene and dienophile substrates of the Diels–Alder cycloaddition. More importantly, the relay sequence is effectively performed in one pot, and the product could potentially undergo the same sequence for further elaboration. Finally, the C1–C9 segment of the macrolide etnangien is constructed with four of the six stereogenic centres established using the relay sequence. Polypropionates are present in many natural products possessing high bioactivity and therapeutic value. Here the authors show a strategy for the stereoselective assembly of polypropionates with three or four stereocentres through a process that includes a Diels–Alder reaction, silylenol ether hydrolysis and Baeyer–Villiger oxidation.
Collapse
Affiliation(s)
- Guo-Ming Ho
- Genomics Research Center, Academia Sinica, 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Medel Manuel L Zulueta
- Genomics Research Center, Academia Sinica, 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Shang-Cheng Hung
- Genomics Research Center, Academia Sinica, 128, Section 2, Academia Road, Taipei, 115, Taiwan.
| |
Collapse
|
28
|
Masschelein J, Jenner M, Challis GL. Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights. Nat Prod Rep 2017. [PMID: 28650032 DOI: 10.1039/c7np00010c] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.
Collapse
Affiliation(s)
- J Masschelein
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - M Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - G L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| |
Collapse
|
29
|
Song L, Jenner M, Masschelein J, Jones C, Bull MJ, Harris SR, Hartkoorn RC, Vocat A, Romero-Canelon I, Coupland P, Webster G, Dunn M, Weiser R, Paisey C, Cole ST, Parkhill J, Mahenthiralingam E, Challis GL. Discovery and Biosynthesis of Gladiolin: A Burkholderia gladioli Antibiotic with Promising Activity against Mycobacterium tuberculosis. J Am Chem Soc 2017; 139:7974-7981. [DOI: 10.1021/jacs.7b03382] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lijiang Song
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Matthew Jenner
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Joleen Masschelein
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Cerith Jones
- Organisms
and Environment Research Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Matthew J. Bull
- Organisms
and Environment Research Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Simon R. Harris
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Ruben C. Hartkoorn
- Global
Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - Anthony Vocat
- Global
Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | | | - Paul Coupland
- Organisms
and Environment Research Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Gordon Webster
- Organisms
and Environment Research Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Matthew Dunn
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Rebecca Weiser
- Organisms
and Environment Research Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Christopher Paisey
- Organisms
and Environment Research Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Stewart T. Cole
- Global
Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Eshwar Mahenthiralingam
- Organisms
and Environment Research Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Gregory L. Challis
- Organisms
and Environment Research Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| |
Collapse
|
30
|
Flórez LV, Scherlach K, Gaube P, Ross C, Sitte E, Hermes C, Rodrigues A, Hertweck C, Kaltenpoth M. Antibiotic-producing symbionts dynamically transition between plant pathogenicity and insect-defensive mutualism. Nat Commun 2017; 8:15172. [PMID: 28452358 PMCID: PMC5414355 DOI: 10.1038/ncomms15172] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 03/06/2017] [Indexed: 11/17/2022] Open
Abstract
Pathogenic and mutualistic bacteria associated with eukaryotic hosts often lack distinctive genomic features, suggesting regular transitions between these lifestyles. Here we present evidence supporting a dynamic transition from plant pathogenicity to insect-defensive mutualism in symbiotic Burkholderia gladioli bacteria. In a group of herbivorous beetles, these symbionts protect the vulnerable egg stage against detrimental microbes. The production of a blend of antibiotics by B. gladioli, including toxoflavin, caryoynencin and two new antimicrobial compounds, the macrolide lagriene and the isothiocyanate sinapigladioside, likely mediate this defensive role. In addition to vertical transmission, these insect symbionts can be exchanged via the host plant and retain the ability to initiate systemic plant infection at the expense of the plant's fitness. Our findings provide a paradigm for the transition between pathogenic and mutualistic lifestyles and shed light on the evolution and chemical ecology of this defensive mutualism.
Collapse
Affiliation(s)
- Laura V. Flórez
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straβe 8, 07745 Jena, Germany
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 13, 55128 Mainz, Germany
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, HKI, Beutenbergstraβe 11a, 07745 Jena, Germany
| | - Paul Gaube
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straβe 8, 07745 Jena, Germany
| | - Claudia Ross
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, HKI, Beutenbergstraβe 11a, 07745 Jena, Germany
| | - Elisabeth Sitte
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, HKI, Beutenbergstraβe 11a, 07745 Jena, Germany
| | - Cornelia Hermes
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, HKI, Beutenbergstraβe 11a, 07745 Jena, Germany
| | - Andre Rodrigues
- Department of Biochemistry and Microbiology, UNESP-São Paulo State University, Av. 24A, n. 1515-Bela Vista, Rio Claro, São Paulo 13506-900, Brazil
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, HKI, Beutenbergstraβe 11a, 07745 Jena, Germany
- Chair for Natural Product Chemistry, Friedrich Schiller University, 07743 Jena, Germany
| | - Martin Kaltenpoth
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straβe 8, 07745 Jena, Germany
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 13, 55128 Mainz, Germany
| |
Collapse
|
31
|
Affiliation(s)
- Silke C. Wenzel
- Saarland University; Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology; Saarland University Campus, Building E8.1 66123 Saarbrücken Germany
| | - Rolf Müller
- Saarland University; Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology; Saarland University Campus, Building E8.1 66123 Saarbrücken Germany
| |
Collapse
|
32
|
Hong H, Sun Y, Zhou Y, Stephens E, Samborskyy M, Leadlay PF. Evidence for an iterative module in chain elongation on the azalomycin polyketide synthase. Beilstein J Org Chem 2016; 12:2164-2172. [PMID: 27829923 PMCID: PMC5082578 DOI: 10.3762/bjoc.12.206] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/23/2016] [Indexed: 11/28/2022] Open
Abstract
The assembly-line synthases that produce bacterial polyketide natural products follow a modular paradigm in which each round of chain extension is catalysed by a different set or module of enzymes. Examples of deviation from this paradigm, in which a module catalyses either multiple extensions or none are of interest from both a mechanistic and an evolutionary viewpoint. We present evidence that in the biosynthesis of the 36-membered macrocyclic aminopolyol lactones (marginolactones) azalomycin and kanchanamycin, isolated respectively from Streptomyces malaysiensis DSM4137 and Streptomyces olivaceus Tü4018, the first extension module catalyses both the first and second cycles of polyketide chain extension. To confirm the integrity of the azl gene cluster, it was cloned intact on a bacterial artificial chromosome and transplanted into the heterologous host strain Streptomyces lividans, which does not possess the genes for marginolactone production. When furnished with 4-guanidinobutyramide, a specific precursor of the azalomycin starter unit, the recombinant S. lividans produced azalomycin, showing that the polyketide synthase genes in the sequenced cluster are sufficient to accomplish formation of the full-length polyketide chain. This provides strong support for module iteration in the azalomycin and kanchanamycin biosynthetic pathways. In contrast, re-sequencing of the gene cluster for biosynthesis of the polyketide β-lactone ebelactone in Streptomyces aburaviensis has shown that, contrary to a recently-published proposal, the ebelactone polyketide synthase faithfully follows the colinear modular paradigm.
Collapse
Affiliation(s)
- Hui Hong
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Wuhan University, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
| | - Yongjun Zhou
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Emily Stephens
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Markiyan Samborskyy
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| |
Collapse
|
33
|
Kuzikov AV, Masamrekh RA, Khatri Y, Zavialova MG, Bernhardt R, Archakov AI, Shumyantseva VV. Scrutiny of electrochemically-driven electrocatalysis of C-19 steroid 1α-hydroxylase (CYP260A1) from Sorangium cellulosum So ce56. Anal Biochem 2016; 513:28-35. [PMID: 27567992 DOI: 10.1016/j.ab.2016.08.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/17/2016] [Accepted: 08/19/2016] [Indexed: 01/08/2023]
Abstract
Direct electrochemistry and bioelectrocatalysis of a newly discovered C-19 steroid 1α-hydroxylase (CYP260A1) from the myxobacterium Sorangium cellulosum So ce56 were investigated. CYP260A1 was immobilized on screen-printed graphite electrodes (SPE) modified with gold nanoparticles, stabilized by didodecyldimethylammonium bromide (SPE/DDAB/Au). Cyclic voltammograms in argon-saturated substrate free 0.1 M potassium phosphate buffer, pH 7.4, and in enzyme-substrate complex with androstenedione demonstrated a redox processes with a single redox couple of E(0') of -299 ± 16 mV and -297.5 ± 21 mV (vs. Ag/AgCl), respectively. CYP260A1 exhibited an electrocatalytic activity detected by an increase of the reduction current in the presence of dissolved oxygen and upon addition of the substrate (androstenedione) in the air-saturated buffer. The catalytic current of the enzyme correlated with substrate concentration in the electrochemical system and this dependence can be described by electrochemical Michaelis-Menten model. The products of CYP260A1-depended electrolysis at controlled working electrode potential of androstenedione were analyzed by mass-spectrometry. MS analysis revealed a mono-hydroxylated product of CYP260A1-dependent electrocatalytic reaction towards androstenedione.
Collapse
Affiliation(s)
- Alexey V Kuzikov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Moscow 119121, Russia; Pirogov Russian National Research Medical University, Ostrovitianov Street, 1, Moscow 117997, Russia
| | - Rami A Masamrekh
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Moscow 119121, Russia; Pirogov Russian National Research Medical University, Ostrovitianov Street, 1, Moscow 117997, Russia
| | - Yogan Khatri
- Institute of Biochemistry, Saarland University, Saarbruecken 66123, Germany
| | - Maria G Zavialova
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Rita Bernhardt
- Institute of Biochemistry, Saarland University, Saarbruecken 66123, Germany
| | - Alexander I Archakov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Moscow 119121, Russia; Pirogov Russian National Research Medical University, Ostrovitianov Street, 1, Moscow 117997, Russia
| | - Victoria V Shumyantseva
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Moscow 119121, Russia; Pirogov Russian National Research Medical University, Ostrovitianov Street, 1, Moscow 117997, Russia.
| |
Collapse
|
34
|
Steinmetz H, Li J, Fu C, Zaburannyi N, Kunze B, Harmrolfs K, Schmitt V, Herrmann J, Reichenbach H, Höfle G, Kalesse M, Müller R. Isolation, Structure Elucidation, and (Bio)Synthesis of Haprolid, a Cell-Type-Specific Myxobacterial Cytotoxin. Angew Chem Int Ed Engl 2016; 55:10113-7. [PMID: 27404448 DOI: 10.1002/anie.201603288] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 11/09/2022]
Abstract
Myxobacteria are well-established sources for novel natural products exhibiting intriguing bioactivities. We here report on haprolid (1) isolated from Byssovorax cruenta Har1. The compound exhibits an unprecedented macrolactone comprising four modified amino acids and a polyketide fragment. As configurational assignment proved difficult, a bioinformatic analysis of the biosynthetic gene cluster was chosen to predict the configuration of each stereocenter. In-depth analysis of the corresponding biosynthetic proteins established a hybrid polyketide synthase/nonribosomal peptide synthetase origin of haprolid and allowed for stereochemical assignments. A subsequent total synthesis yielded haprolid and corroborated all predictions made. Intriguingly, haprolid showed cytotoxicity against several cell lines in the nanomolar range whereas other cells were almost unaffected by treatment with the compound.
Collapse
Affiliation(s)
- Heinrich Steinmetz
- Helmholtz Center for Infection Research (HZI), Department Microbial Drugs, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Jun Li
- Institute for Organic Chemistry, Gottfried Leibniz Universität Hannover.,Centre of Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167, Hannover, Germany.,Helmholtz Center for Infection Research (HZI), Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Chengzhang Fu
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Pharmaceutical Biotechnology, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Nestor Zaburannyi
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Pharmaceutical Biotechnology, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Birgitte Kunze
- Helmholtz Center for Infection Research (HZI), Department Microbial Drugs, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Kirsten Harmrolfs
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Pharmaceutical Biotechnology, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Viktoria Schmitt
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Pharmaceutical Biotechnology, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Pharmaceutical Biotechnology, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Hans Reichenbach
- Helmholtz Center for Infection Research (HZI), Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Gerhard Höfle
- Helmholtz Center for Infection Research (HZI), Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Markus Kalesse
- Institute for Organic Chemistry, Gottfried Leibniz Universität Hannover. .,Centre of Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167, Hannover, Germany. .,Helmholtz Center for Infection Research (HZI), Inhoffenstrasse 7, 38124, Braunschweig, Germany.
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Pharmaceutical Biotechnology, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany.
| |
Collapse
|
35
|
Steinmetz H, Li J, Fu C, Zaburannyi N, Kunze B, Harmrolfs K, Schmitt V, Herrmann J, Reichenbach H, Höfle G, Kalesse M, Müller R. Isolierung, Strukturaufklärung und (Bio-)Synthese von Haprolid, einem zellspezifisch zytotoxischen myxobakteriellen Makrolidnaturstoff. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603288] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Heinrich Steinmetz
- Helmholtz-Zentrum für Infektionsforschung (HZI); Forschungsgruppe Mikrobielle Wirkstoffe; Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Jun Li
- Institut für Organische Chemie; Gottfried Wilhelm Leibniz Universität Hannover
- Biomolekulares Wirkstoffzentrum (BMWZ); Schneiderberg 1B 30167 Hannover Deutschland
- Helmholtz-Zentrum für Infektionsforschung (HZI); Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Chengzhang Fu
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Helmholtz-Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie; Universitätscampus E8.1; 66123 Saarbrücken Deutschland
| | - Nestor Zaburannyi
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Helmholtz-Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie; Universitätscampus E8.1; 66123 Saarbrücken Deutschland
| | - Birgitte Kunze
- Helmholtz-Zentrum für Infektionsforschung (HZI); Forschungsgruppe Mikrobielle Wirkstoffe; Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Kirsten Harmrolfs
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Helmholtz-Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie; Universitätscampus E8.1; 66123 Saarbrücken Deutschland
| | - Viktoria Schmitt
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Helmholtz-Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie; Universitätscampus E8.1; 66123 Saarbrücken Deutschland
| | - Jennifer Herrmann
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Helmholtz-Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie; Universitätscampus E8.1; 66123 Saarbrücken Deutschland
| | - Hans Reichenbach
- Helmholtz-Zentrum für Infektionsforschung (HZI); Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Gerhard Höfle
- Helmholtz-Zentrum für Infektionsforschung (HZI); Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Markus Kalesse
- Institut für Organische Chemie; Gottfried Wilhelm Leibniz Universität Hannover
- Biomolekulares Wirkstoffzentrum (BMWZ); Schneiderberg 1B 30167 Hannover Deutschland
- Helmholtz-Zentrum für Infektionsforschung (HZI); Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Rolf Müller
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Helmholtz-Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie; Universitätscampus E8.1; 66123 Saarbrücken Deutschland
| |
Collapse
|
36
|
Tautz T, Hoffmann J, Hoffmann T, Steinmetz H, Washausen P, Kunze B, Huch V, Kitsche A, Reichenbach H, Höfle G, Müller R, Kalesse M. Isolation, Structure Elucidation, Biosynthesis, and Synthesis of Antalid, a Secondary Metabolite from Polyangium species. Org Lett 2016; 18:2560-3. [DOI: 10.1021/acs.orglett.6b00810] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thomas Tautz
- Institute
for Organic Chemistry, Leibniz Universität Hannover, Schneiderberg
1B, D-30167 Hannover, Germany
| | - Judith Hoffmann
- Helmholtz
Institute for Pharmaceutical Research Saarland, Helmholtz Centre for
Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Building E8.1, D-66123 Saarbrücken, Germany
| | - Thomas Hoffmann
- Helmholtz
Institute for Pharmaceutical Research Saarland, Helmholtz Centre for
Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Building E8.1, D-66123 Saarbrücken, Germany
| | - Heinrich Steinmetz
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Peter Washausen
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Brigitte Kunze
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Volker Huch
- Institute
for Inorganic Chemistry, Saarland University, Building B2.2, D-66123 Saarbrücken, Germany
| | - Andreas Kitsche
- Institute
for Biostatistics, Leibniz Universität Hannover, Herrenhäuser
Straße 2, D-30419 Hannover, Germany
| | - Hans Reichenbach
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Gerhard Höfle
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Rolf Müller
- Helmholtz
Institute for Pharmaceutical Research Saarland, Helmholtz Centre for
Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Building E8.1, D-66123 Saarbrücken, Germany
| | - Markus Kalesse
- Institute
for Organic Chemistry, Leibniz Universität Hannover, Schneiderberg
1B, D-30167 Hannover, Germany
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| |
Collapse
|
37
|
Essig S, Schmalzbauer B, Bretzke S, Scherer O, Koeberle A, Werz O, Müller R, Menche D. Predictive Bioinformatic Assignment of Methyl-Bearing Stereocenters, Total Synthesis, and an Additional Molecular Target of Ajudazol B. J Org Chem 2016; 81:1333-57. [DOI: 10.1021/acs.joc.5b02844] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Sebastian Essig
- Institut
für Organische Chemie, Ruprecht-Karls Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Björn Schmalzbauer
- Kekulé-Institut
für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Sebastian Bretzke
- Institut
für Organische Chemie, Ruprecht-Karls Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Olga Scherer
- Institute
of Pharmacy, Friedrich Schiller Universität Jena, Philosophenweg
14, 07743 Jena, Germany
| | - Andreas Koeberle
- Institute
of Pharmacy, Friedrich Schiller Universität Jena, Philosophenweg
14, 07743 Jena, Germany
| | - Oliver Werz
- Institute
of Pharmacy, Friedrich Schiller Universität Jena, Philosophenweg
14, 07743 Jena, Germany
| | - Rolf Müller
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS) and Institut
for Pharmaceutical Biotechnology, Universität des Saarlandes, C 2.3, 66123 Saarbrücken, Germany
| | - Dirk Menche
- Kekulé-Institut
für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| |
Collapse
|
38
|
Shumyantseva V, Kuzikov A, Masamrekh R, Khatri Y, Zavialova M, Bernhardt R, Archakov A. Direct electrochemistry of CYP109C1, CYP109C2 and CYP109D1 from Sorangium cellulosum So ce56. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.01.162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
39
|
Hong H, Samborskyy M, Lindner F, Leadlay PF. An Amidinohydrolase Provides the Missing Link in the Biosynthesis of Amino Marginolactone Antibiotics. Angew Chem Int Ed Engl 2016; 55:1118-23. [PMID: 26630438 PMCID: PMC4737276 DOI: 10.1002/anie.201509300] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 01/23/2023]
Abstract
Desertomycin A is an aminopolyol polyketide containing a macrolactone ring. We have proposed that desertomycin A and similar compounds (marginolactones) are formed by polyketide synthases primed not with γ-aminobutanoyl-CoA but with 4-guanidinylbutanoyl-CoA, to avoid facile cyclization of the starter unit. This hypothesis requires that there be a final-stage de-amidination of the corresponding guanidino-substituted natural product, but no enzyme for such a process has been described. We have now identified candidate amidinohydrolase genes within the desertomycin and primycin clusters. Deletion of the putative desertomycin amidinohydrolase gene dstH in Streptomyces macronensis led to the accumulation of desertomycin B, the guanidino form of the antibiotic. Also, purified DstH efficiently catalyzed the in vitro conversion of desertomycin B into the A form. Hence this amidinohydrolase furnishes the missing link in this proposed naturally evolved example of protective-group chemistry.
Collapse
Affiliation(s)
- Hui Hong
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Markiyan Samborskyy
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Frederick Lindner
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- Institut für Organische Chemie, Leibniz Universität Hannover, Schneiderberg 1 B, 30167, Hannover, Germany
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
| |
Collapse
|
40
|
Helfrich EJN, Piel J. Biosynthesis of polyketides by trans-AT polyketide synthases. Nat Prod Rep 2016; 33:231-316. [DOI: 10.1039/c5np00125k] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review discusses the biosynthesis of natural products that are generated bytrans-AT polyketide synthases, a family of catalytically versatile enzymes that represents one of the major group of proteins involved in the production of bioactive polyketides.
Collapse
Affiliation(s)
- Eric J. N. Helfrich
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
| | - Jörn Piel
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
| |
Collapse
|
41
|
Weissman KJ. Genetic engineering of modular PKSs: from combinatorial biosynthesis to synthetic biology. Nat Prod Rep 2016; 33:203-30. [DOI: 10.1039/c5np00109a] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This reviews covers on-going efforts at engineering the gigantic modular polyketide synthases (PKSs), highlighting both notable successes and failures.
Collapse
Affiliation(s)
- Kira J. Weissman
- UMR 7365
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA)
- CNRS-Université de Lorraine
- Biopôle de l'Université de Lorraine
- 54505 Vandœuvre-lès-Nancy Cedex
| |
Collapse
|
42
|
Hong H, Samborskyy M, Lindner F, Leadlay PF. An Amidinohydrolase Provides the Missing Link in the Biosynthesis of Amino Marginolactone Antibiotics. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Hui Hong
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road Cambridge CB2 1GA UK
| | - Markiyan Samborskyy
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road Cambridge CB2 1GA UK
| | - Frederick Lindner
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road Cambridge CB2 1GA UK
- Institut für Organische Chemie; Leibniz Universität Hannover; Schneiderberg 1 B 30167 Hannover Germany
| | - Peter F. Leadlay
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road Cambridge CB2 1GA UK
| |
Collapse
|
43
|
Iterative polyketide biosynthesis by modular polyketide synthases in bacteria. Appl Microbiol Biotechnol 2015; 100:541-57. [PMID: 26549236 DOI: 10.1007/s00253-015-7093-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 10/10/2015] [Accepted: 10/13/2015] [Indexed: 10/22/2022]
Abstract
Modular polyketide synthases (type I PKSs) in bacteria are responsible for synthesizing a significant percentage of bioactive natural products. This group of synthases has a characteristic modular organization, and each module within a PKS carries out one cycle of polyketide chain elongation; thus each module is non-iterative in function. It was possible to predict the basic structure of a polyketide product from the module organization of the PKSs, since there generally existed a co-linearity between the number of modules and the number of chain elongations. However, more and more bacterial modular PKSs fail to conform to the canonical rules, and a particularly noteworthy group of non-canonical PKSs is the bacterial iterative type I PKSs. This review covers recent examples of iteratively used modular PKSs in bacteria. These non-canonical PKSs give rise to a large array of natural products with impressive structural diversity. The molecular mechanism behind the iterations is often unclear, presenting a new challenge to the rational engineering of these PKSs with the goal of generating new natural products. Structural elucidation of these synthase complexes and better understanding of potential PKS-PKS interactions as well as PKS-substrate recognition may provide new prospects and inspirations for the discovery and engineering of new bioactive polyketides.
Collapse
|
44
|
Matilla MA, Leeper FJ, Salmond GPC. Biosynthesis of the antifungal haterumalide, oocydin A, in Serratia, and its regulation by quorum sensing, RpoS and Hfq. Environ Microbiol 2015; 17:2993-3008. [PMID: 25753587 PMCID: PMC4552970 DOI: 10.1111/1462-2920.12839] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/27/2015] [Accepted: 03/02/2015] [Indexed: 02/02/2023]
Abstract
Polyketides represent an important class of bioactive natural products with a broad range of biological activities. We identified recently a large trans-acyltransferase (AT) polyketide synthase gene cluster responsible for the biosynthesis of the antifungal, anti-oomycete and antitumor haterumalide, oocydin A (ooc). Using genome sequencing and comparative genomics, we show that the ooc gene cluster is widespread within biocontrol and phytopathogenic strains of the enterobacteria, Serratia and Dickeya. The analysis of in frame deletion mutants confirmed the role of a hydroxymethylglutaryl-coenzyme A synthase cassette, three flavin-dependent tailoring enzymes, a free-standing acyl carrier protein and two hypothetical proteins in oocydin A biosynthesis. The requirement of the three trans-acting AT domains for the biosynthesis of the macrolide was also demonstrated. Expression of the ooc gene cluster was shown to be positively regulated by an N-acyl-L-homoserine lactone-based quorum sensing system, but operating in a strain-dependent manner. At a post-transcriptional level, the RNA chaperone, Hfq, plays a key role in oocydin A biosynthesis. The Hfq-dependent regulation is partially mediated by the stationary phase sigma factor, RpoS, which was also shown to positively regulate the synthesis of the macrolide. Our results reveal differential regulation of the divergently transcribed ooc transcriptional units, highlighting the complexity of oocydin A production.
Collapse
Affiliation(s)
- Miguel A Matilla
- Department of Biochemistry, University of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK
| | - Finian J Leeper
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW, UK
| | - George P C Salmond
- Department of Biochemistry, University of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK,*For correspondence. E-mail ; Tel. +44 (0)1223 333650; Fax +44 (0)1223 766108
| |
Collapse
|
45
|
Synthesis of the all-syn C35–C39 stereopentad of etnangien by the γ-hydroxybutenolide approach. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.03.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
46
|
Sugimoto Y, Ishida K, Traitcheva N, Busch B, Dahse HM, Hertweck C. Freedom and Constraint in Engineered Noncolinear Polyketide Assembly Lines. ACTA ACUST UNITED AC 2015; 22:229-40. [DOI: 10.1016/j.chembiol.2014.12.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/26/2014] [Accepted: 12/06/2014] [Indexed: 10/24/2022]
|
47
|
Lu HH, Hinkelmann B, Tautz T, Li J, Sasse F, Franke R, Kalesse M. Paleo-soraphens: chemical total syntheses and biological studies. Org Biomol Chem 2015; 13:8029-36. [DOI: 10.1039/c5ob01249j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To provide a picture of the hypothetical evolutionary optimization of soraphen four additional paleo-soraphens and their biological profiles are described.
Collapse
Affiliation(s)
- Hai-Hua Lu
- Institute for Organic Chemistry and Centre for Biomolecular Drug Research (BMWZ)
- Leibniz Universität Hannover
- 30167 Hannover
- Germany
| | - Bettina Hinkelmann
- Department of Chemical Biology
- Helmholtz Centre for Infection Research (HZI)
- Braunschweig
- Germany
| | - Thomas Tautz
- Institute for Organic Chemistry and Centre for Biomolecular Drug Research (BMWZ)
- Leibniz Universität Hannover
- 30167 Hannover
- Germany
| | - Jun Li
- Institute for Organic Chemistry and Centre for Biomolecular Drug Research (BMWZ)
- Leibniz Universität Hannover
- 30167 Hannover
- Germany
| | - Florenz Sasse
- Department of Chemical Biology
- Helmholtz Centre for Infection Research (HZI)
- Braunschweig
- Germany
| | - Raimo Franke
- Department of Chemical Biology
- Helmholtz Centre for Infection Research (HZI)
- Braunschweig
- Germany
| | - Markus Kalesse
- Institute for Organic Chemistry and Centre for Biomolecular Drug Research (BMWZ)
- Leibniz Universität Hannover
- 30167 Hannover
- Germany
- Department of Chemical Biology
| |
Collapse
|
48
|
Bruns N, Collisi W, Bernecker S, Stadler M, Richter C, Schwalbe H, Kalesse M. Spirangien Derivatives from the MyxobacteriumSorangium cellulosum: Isolation, Structure Elucidation, and Biological Activity. European J Org Chem 2014. [DOI: 10.1002/ejoc.201403353] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
49
|
Schieferdecker S, König S, Weigel C, Dahse HM, Werz O, Nett M. Structure and biosynthetic assembly of gulmirecins, macrolide antibiotics from the predatory bacterium Pyxidicoccus fallax. Chemistry 2014; 20:15933-40. [PMID: 25287056 DOI: 10.1002/chem.201404291] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Indexed: 01/28/2023]
Abstract
The gulmirecins constitute a new class of glycosylated macrolides that were isolated from the predatory bacterium Pyxidicoccus fallax HKI 727. Their structures were solved by a combination of NMR spectroscopic experiments and chemical derivatization. Analysis of the annotated gulmirecin gene cluster complemented the configurational assignment and provided insights into the stereochemical course of the biosynthetic assembly. The gulmirecins exhibit strong activity against staphylococci, including methicillin-resistant Staphylococcus aureus, but no cytotoxic effects on human cells.
Collapse
Affiliation(s)
- Sebastian Schieferdecker
- Junior Research Group, "Secondary Metabolism of Predatory Bacteria", Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf-Reichwein-Str. 23, 07745 Jena (Germany), Fax: (+49) 3641-5320811
| | | | | | | | | | | |
Collapse
|
50
|
Piasecki SK, Zheng J, Axelrod AJ, Detelich M, Keatinge-Clay AT. Structural and functional studies of a trans-acyltransferase polyketide assembly line enzyme that catalyzes stereoselective α- and β-ketoreduction. Proteins 2014; 82:2067-77. [PMID: 24634061 PMCID: PMC4142079 DOI: 10.1002/prot.24561] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 02/19/2014] [Accepted: 03/06/2014] [Indexed: 11/06/2022]
Abstract
While the cis-acyltransferase modular polyketide synthase assembly lines have largely been structurally dissected, enzymes from within the recently discovered trans-acyltransferase polyketide synthase assembly lines are just starting to be observed crystallographically. Here we examine the ketoreductase (KR) from the first polyketide synthase module of the bacillaene nonribosomal peptide synthetase/polyketide synthase at 2.35-Å resolution. This KR naturally reduces both α- and β-keto groups and is the only KR known to do so during the biosynthesis of a polyketide. The isolated KR not only reduced an N-acetylcysteamine-bound β-keto substrate to a D-β-hydroxy product, but also an N-acetylcysteamine-bound α-keto substrate to an L-α-hydroxy product. That the substrates must enter the active site from opposite directions to generate these stereochemistries suggests that the acyl-phosphopantetheine moiety is capable of accessing very different conformations despite being anchored to a serine residue of a docked acyl carrier protein. The features enabling stereocontrolled α-ketoreduction may not be extensive since a KR that naturally reduces a β-keto group within a cis-acyltransferase polyketide synthase was identified that performs a completely stereoselective reduction of the same α-keto substrate to generate the D-α-hydroxy product. A sequence analysis of trans-acyltransferase KRs reveals that a single residue, rather than a three-residue motif found in cis-acyltransferase KRs, is predictive of the orientation of the resulting β-hydroxyl group.
Collapse
Affiliation(s)
- Shawn K. Piasecki
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Jianting Zheng
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Abram J. Axelrod
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Madeline Detelich
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Adrian T. Keatinge-Clay
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| |
Collapse
|