1
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Paulsel TQ, Williams GJ. Current State-of-the-Art Toward Chemoenzymatic Synthesis of Polyketide Natural Products. Chembiochem 2023; 24:e202300386. [PMID: 37615926 PMCID: PMC10964317 DOI: 10.1002/cbic.202300386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 08/25/2023]
Abstract
Polyketide natural products have significant promise as pharmaceutical targets for human health and as molecular tools to probe disease and complex biological systems. While the biosynthetic logic of polyketide synthases (PKS) is well-understood, biosynthesis of designer polyketides remains challenging due to several bottlenecks, including substrate specificity constraints, disrupted protein-protein interactions, and protein solubility and folding issues. Focusing on substrate specificity, PKSs are typically interrogated using synthetic thioesters. PKS assembly lines and their products offer a wealth of information when studied in a chemoenzymatic fashion. This review provides an overview of the past two decades of polyketide chemoenzymatic synthesis and their contributions to the field of chemical biology. These synthetic strategies have successfully yielded natural product derivatives while providing critical insights into enzymatic promiscuity and mechanistic activity.
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Affiliation(s)
- Thaddeus Q Paulsel
- Department of Chemistry, NC State University Dabney Hall, Room 208, Campus Box 8204, 2620 Yarbrough Dr., NC State University, Raleigh, NC 27695, USA
- Comparative Medicine Institute, NC State University, 1060 William Moore Dr., NC State University, Raleigh, NC 27607, USA
| | - Gavin J Williams
- Department of Chemistry, NC State University Dabney Hall, Room 208, Campus Box 8204, 2620 Yarbrough Dr., NC State University, Raleigh, NC 27695, USA
- Comparative Medicine Institute, NC State University, 1060 William Moore Dr., NC State University, Raleigh, NC 27607, USA
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2
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Sigrist R, Luhavaya H, McKinnie SMK, Ferreira da Silva A, Jurberg ID, Moore BS, Gonzaga de Oliveira L. Nonlinear Biosynthetic Assembly of Alpiniamide by a Hybrid cis/ trans-AT PKS-NRPS. ACS Chem Biol 2020; 15:1067-1077. [PMID: 32195572 DOI: 10.1021/acschembio.0c00081] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Alpiniamide A is a linear polyketide produced by Streptomyces endophytic bacteria. Despite its relatively simple chemical structure suggestive of a linear assembly line biosynthetic construction involving a hybrid polyketide synthase-nonribosomal peptide synthetase enzymatic protein machine, we report an unexpected nonlinear synthesis of this bacterial natural product. Using a combination of genomics, heterologous expression, mutagenesis, isotope-labeling, and chain terminator experiments, we propose that alpiniamide A is assembled in two halves and then ligated into the mature molecule. We show that each polyketide half is constructed using orthogonal biosynthetic strategies, employing either cis- or trans-acyl transferase mechanisms, thus prompting an alternative proposal for the operation of this PKS-NRPS.
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Affiliation(s)
- Renata Sigrist
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
| | - Hanna Luhavaya
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Shaun M. K. McKinnie
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Amanda Ferreira da Silva
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
| | - Igor D. Jurberg
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Luciana Gonzaga de Oliveira
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
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3
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Kilgour SL, Jenkins R, Tosin M. A Photoactivatable Small-Molecule Probe for the In Vivo Capture of Polyketide Intermediates. Chemistry 2019; 25:16511-16514. [PMID: 31617624 PMCID: PMC6972646 DOI: 10.1002/chem.201903661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/26/2019] [Indexed: 01/24/2023]
Abstract
A photolabile carba(dethia) malonyl N-acetylcysteamine derivative was devised and prepared for the trapping of biosynthetic polyketide intermediates following light activation. From the lasalocid A polyketide assembly in a mutant strain of the soil bacterium Streptomyces lasaliensis, a previously undetected cyclised intermediate was identified and characterised, providing a new outlook on the timing of substrate processing.
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Affiliation(s)
| | - Robert Jenkins
- Department of ChemistryUniversity of WarwickLibrary RoadCoventryCV4 7ALUK
| | - Manuela Tosin
- Department of ChemistryUniversity of WarwickLibrary RoadCoventryCV4 7ALUK
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4
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Kilgour SL, Kilgour DPA, Prasongpholchai P, O'Connor PB, Tosin M. A Light-Activated Acyl Carrier Protein "Trap" for Intermediate Capture in Type II Iterative Polyketide Biocatalysis. Chemistry 2019; 25:16515-16518. [PMID: 31596972 PMCID: PMC6972679 DOI: 10.1002/chem.201903662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 10/03/2019] [Indexed: 01/24/2023]
Abstract
A discrete acyl carrier protein (ACP) bearing a photolabile nonhydrolysable carba(dethia) malonyl pantetheine cofactor was chemoenzymatically prepared and utilised for the trapping of biosynthetic polyketide intermediates following light activation. From the in vitro assembly of the polyketides SEK4 and SEK4b, by the type II actinorhodin "minimal" polyketide synthase (PKS), a range of putative ACP-bound diketides, tetraketides, pentaketides and hexaketides were identified and characterised by FT-ICR-MS, providing direct insights on active site accessibility and substrate processing for this enzyme class.
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Affiliation(s)
| | - David P. A. Kilgour
- Department of Chemistry and ForensicsNottingham Trent UniversityNottinghamNG11 8NSUK
| | | | - Peter B. O'Connor
- Department of ChemistryUniversity of WarwickLibrary RoadCoventryCV4 7ALUK
| | - Manuela Tosin
- Department of ChemistryUniversity of WarwickLibrary RoadCoventryCV4 7ALUK
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5
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Tao W, Chen L, Zhao C, Wu J, Yan D, Deng Z, Sun Y. In Vitro Packaging Mediated One-Step Targeted Cloning of Natural Product Pathway. ACS Synth Biol 2019; 8:1991-1997. [PMID: 31487454 DOI: 10.1021/acssynbio.9b00248] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Direct cloning of natural product pathways for efficient refactoring and heterologous expression has become an important strategy for microbial natural product research and discovery, especially for those kept silent or poorly expressed in the original strains. Accordingly, the development of convenient and efficient cloning approaches is becoming increasingly necessary. Here we presented an in vitro packaging mediated cloning approach that combines CRISPR/Cas9 system with in vitro λ packaging system, for targeted cloning of natural product pathways. In such a scheme, pathways of Tü3010 (27.4 kb) and sisomicin (40.7 kb) were respectively cloned, and stuR was further depicted to positively regulate Tü3010 production. In vitro packaging mediated approach not only enables to activate cryptic pathways, but also facilitates refactoring or interrogating the pathways in conjunction with various gene editing systems. This approach features an expedited, convenient, and generic manner, and it is conceivable that it may be widely adopted for targeted cloning of the natural product pathways.
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Affiliation(s)
- Weixin Tao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
| | - Li Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
| | - Chunhua Zhao
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People’s Republic of China
| | - Jing Wu
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, People’s Republic of China
| | - Dazhong Yan
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, People’s Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
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6
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Zhang JJ, Tang X, Moore BS. Genetic platforms for heterologous expression of microbial natural products. Nat Prod Rep 2019; 36:1313-1332. [PMID: 31197291 PMCID: PMC6750982 DOI: 10.1039/c9np00025a] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Covering: 2005 up to 2019Natural products are of paramount importance in human medicine. Not only are most antibacterial and anticancer drugs derived directly from or inspired by natural products, many other branches of medicine, such as immunology, neurology, and cardiology, have similarly benefited from natural product-based drugs. Typically, the genetic material required to synthesize a microbial specialized product is arranged in a multigene biosynthetic gene cluster (BGC), which codes for proteins associated with molecule construction, regulation, and transport. The ability to connect natural product compounds to BGCs and vice versa, along with ever-increasing knowledge of biosynthetic machineries, has spawned the field of genomics-guided natural product genome mining for the rational discovery of new chemical entities. One significant challenge in the field of natural product genome mining is how to rapidly link orphan biosynthetic genes to their associated chemical products. This review highlights state-of-the-art genetic platforms to identify, interrogate, and engineer BGCs from diverse microbial sources, which can be broken into three stages: (1) cloning and isolation of genomic loci, (2) heterologous expression in a host organism, and (3) genetic manipulation of cloned pathways. In the future, we envision natural product genome mining will be rapidly accelerated by de novo DNA synthesis and refactoring of whole biosynthetic pathways in combination with systematic heterologous expression methodologies.
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Affiliation(s)
- Jia Jia Zhang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA.
| | - Xiaoyu Tang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA.
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA. and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA
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7
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Greule A, Stok JE, De Voss JJ, Cryle MJ. Unrivalled diversity: the many roles and reactions of bacterial cytochromes P450 in secondary metabolism. Nat Prod Rep 2019; 35:757-791. [PMID: 29667657 DOI: 10.1039/c7np00063d] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: 2000 up to 2018 The cytochromes P450 (P450s) are a superfamily of heme-containing monooxygenases that perform diverse catalytic roles in many species, including bacteria. The P450 superfamily is widely known for the hydroxylation of unactivated C-H bonds, but the diversity of reactions that P450s can perform vastly exceeds this undoubtedly impressive chemical transformation. Within bacteria, P450s play important roles in many biosynthetic and biodegradative processes that span a wide range of secondary metabolite pathways and present diverse chemical transformations. In this review, we aim to provide an overview of the range of chemical transformations that P450 enzymes can catalyse within bacterial secondary metabolism, with the intention to provide an important resource to aid in understanding of the potential roles of P450 enzymes within newly identified bacterial biosynthetic pathways.
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Affiliation(s)
- Anja Greule
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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8
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Gulick AM, Aldrich CC. Trapping interactions between catalytic domains and carrier proteins of modular biosynthetic enzymes with chemical probes. Nat Prod Rep 2019; 35:1156-1184. [PMID: 30046790 DOI: 10.1039/c8np00044a] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to early 2018 The Nonribosomal Peptide Synthetases (NRPSs) and Polyketide Synthases (PKSs) are families of modular enzymes that produce a tremendous diversity of natural products, with antibacterial, antifungal, immunosuppressive, and anticancer activities. Both enzymes utilize a fascinating modular architecture in which the synthetic intermediates are covalently attached to a peptidyl- or acyl-carrier protein that is delivered to catalytic domains for natural product elongation, modification, and termination. An investigation of the structural mechanism therefore requires trapping the often transient interactions between the carrier and catalytic domains. Many novel chemical probes have been produced to enable the structural and functional investigation of multidomain NRPS and PKS structures. This review will describe the design and implementation of the chemical tools that have proven to be useful in biochemical and biophysical studies of these natural product biosynthetic enzymes.
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Affiliation(s)
- Andrew M Gulick
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 955 Main St, Buffalo, NY 14203, USA.
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9
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Naowarojna N, Cheng R, Chen L, Quill M, Xu M, Zhao C, Liu P. Mini-Review: Ergothioneine and Ovothiol Biosyntheses, an Unprecedented Trans-Sulfur Strategy in Natural Product Biosynthesis. Biochemistry 2018; 57:3309-3325. [PMID: 29589901 DOI: 10.1021/acs.biochem.8b00239] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
As one of the most abundant elements on earth, sulfur is part of many small molecular metabolites and is key to their biological activities. Over the past few decades, some general strategies have been discovered for the incorporation of sulfur into natural products. In this review, we summarize recent efforts in elucidating the biosynthetic details for two sulfur-containing metabolites, ergothioneine and ovothiol. Their biosyntheses involve an unprecedented trans-sulfur strategy, a combination of a mononuclear non-heme iron enzyme-catalyzed oxidative C-S bond formation reaction and a PLP enzyme-mediated C-S lyase reaction.
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Affiliation(s)
- Nathchar Naowarojna
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Ronghai Cheng
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Li Chen
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States.,Key Laboratory of Combinatory Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences , Wuhan University , Wuhan , Hubei 430072 , People's Republic of China
| | - Melissa Quill
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Meiling Xu
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Changming Zhao
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States.,Key Laboratory of Combinatory Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences , Wuhan University , Wuhan , Hubei 430072 , People's Republic of China
| | - Pinghua Liu
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
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10
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Ho YTC, Leng DJ, Ghiringhelli F, Wilkening I, Bushell DP, Kostner O, Riva E, Havemann J, Passarella D, Tosin M. Novel chemical probes for the investigation of nonribosomal peptide assembly. Chem Commun (Camb) 2018. [PMID: 28627528 DOI: 10.1039/c7cc02427d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Chemical probes were devised and evaluated for the capture of biosynthetic intermediates involved in the bio-assembly of the nonribosomal peptide echinomycin. Putative intermediate peptide species were isolated and characterised, providing fresh insights into pathway substrate flexibility and paving the way for novel chemoenzymatic approaches towards unnatural peptides.
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Affiliation(s)
- Y T Candace Ho
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Daniel J Leng
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Francesca Ghiringhelli
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK. and Department of Chemistry, Universita' degli Studi di Milano, Via Golgi, 19 20133 Milano, Italy
| | - Ina Wilkening
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Dexter P Bushell
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Otto Kostner
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK. and Institut für Organische Chemie, Universität Wien, Währinger Str., 38 1090 Wien, Austria
| | - Elena Riva
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Judith Havemann
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Daniele Passarella
- Department of Chemistry, Universita' degli Studi di Milano, Via Golgi, 19 20133 Milano, Italy
| | - Manuela Tosin
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
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11
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Sánchez-Hidalgo M, González I, Díaz-Muñoz C, Martínez G, Genilloud O. Comparative Genomics and Biosynthetic Potential Analysis of Two Lichen-Isolated Amycolatopsis Strains. Front Microbiol 2018; 9:369. [PMID: 29593664 PMCID: PMC5859366 DOI: 10.3389/fmicb.2018.00369] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/16/2018] [Indexed: 11/15/2022] Open
Abstract
Actinomycetes have been extensively exploited as one of the most prolific secondary metabolite-producer sources and continue to be in the focus of interest in the constant search of novel bioactive compounds. The availability of less expensive next generation genome sequencing techniques has not only confirmed the extraordinary richness and broad distribution of silent natural product biosynthetic gene clusters among these bacterial genomes, but also has allowed the incorporation of genomics in bacterial taxonomy and systematics. As part of our efforts to isolate novel strains from unique environments, we explored lichen-associated microbial communities as unique assemblages to be studied as potential sources of novel bioactive natural products with application in biotechnology and drug discovery. In this work, we have studied the whole genome sequences of two new Amycolatopsis strains (CA-126428 and CA-128772) isolated from tropical lichens, and performed a comparative genomic analysis with 41 publicly available Amycolatopsis genomes. This work has not only permitted to infer and discuss their taxonomic position on the basis of the different phylogenetic approaches used, but has also allowed to assess the richness and uniqueness of the biosynthetic pathways associated to primary and secondary metabolism, and to provide a first insight on the potential role of these bacteria in the lichen-associated microbial community.
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Affiliation(s)
- Marina Sánchez-Hidalgo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores de Andalucía, Granada, Spain
| | - Ignacio González
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores de Andalucía, Granada, Spain
| | - Cristian Díaz-Muñoz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores de Andalucía, Granada, Spain
| | - Germán Martínez
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores de Andalucía, Granada, Spain
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores de Andalucía, Granada, Spain
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12
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Hong H, Samborskyy M, Usachova K, Schnatz K, Leadlay PF. Sulfation and amidinohydrolysis in the biosynthesis of giant linear polyenes. Beilstein J Org Chem 2017; 13:2408-2415. [PMID: 29234468 PMCID: PMC5704753 DOI: 10.3762/bjoc.13.238] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 10/13/2017] [Indexed: 12/24/2022] Open
Abstract
Clethramycin from Streptomyces malaysiensis DSM4137, and mediomycins (produced together with clethramycin from Streptomyces mediocidicus), are near-identical giant linear polyenes apparently constructed from, respectively, a 4-guanidinobutanoate or 4-aminobutanoate starter unit and 27 polyketide extender units, and bearing a specific O-sulfonate modification at the C-29 hydroxy group. We show here that mediomycins are actually biosynthesised not by use of a different starter unit but by direct late-stage deamidination of (desulfo)clethramycin. A gene (slf) encoding a candidate sulfotransferase has been located in both gene clusters. Deletion of this gene in DSM4137 led to accumulation of desulfoclethramycin only, instead of a mixture of desulfoclethramycin and clethramycin. The mediomycin gene cluster does not encode an amidinohydrolase, but when three candidate amidinohydrolase genes from elsewhere in the S. mediocidicus genome were individually expressed in Escherichia coli and assayed, only one of them (medi4948), located 670 kbp away from the mediomycin gene cluster on the chromosome, catalysed the removal of the amidino group from desulfoclethramycin. Subsequent cloning of medi4948 into DSM4137 caused mediomycins A and B to accumulate at the expense of clethramycin and desulfoclethramycin, respectively, a rare case where an essential biosynthetic gene is not co-located with other pathway genes. Clearly, both desulfoclethramycin and clethramycin are substrates for this amidinohydrolase. Also, purified recombinant sulfotransferase from DSM4137, in the presence of 3'-phosphoadenosine-5'-phosphosulfate as donor, efficiently converted mediomycin B to mediomycin A in vitro. Thus, in the final steps of mediomycin A biosynthesis deamidination and sulfotransfer can take place in either order.
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Affiliation(s)
- Hui Hong
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | | | - Katharina Schnatz
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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13
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Li J, Tang X, Awakawa T, Moore BS. Enzymatic C−H Oxidation-Amidation Cascade in the Production of Natural and Unnatural Thiotetronate Antibiotics with Potentiated Bioactivity. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705239] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jie Li
- Center of Marine Biotechnology and Biomedicine; Scripps Institution of Oceanography; University of California at San Diego; 9500 Gilman Drive La Jolla CA 92093-0204 USA
| | - Xiaoyu Tang
- Center of Marine Biotechnology and Biomedicine; Scripps Institution of Oceanography; University of California at San Diego; 9500 Gilman Drive La Jolla CA 92093-0204 USA
| | - Takayoshi Awakawa
- Center of Marine Biotechnology and Biomedicine; Scripps Institution of Oceanography; University of California at San Diego; 9500 Gilman Drive La Jolla CA 92093-0204 USA
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Bradley S. Moore
- Center of Marine Biotechnology and Biomedicine; Scripps Institution of Oceanography; University of California at San Diego; 9500 Gilman Drive La Jolla CA 92093-0204 USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California at San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
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14
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Li J, Tang X, Awakawa T, Moore BS. Enzymatic C-H Oxidation-Amidation Cascade in the Production of Natural and Unnatural Thiotetronate Antibiotics with Potentiated Bioactivity. Angew Chem Int Ed Engl 2017; 56:12234-12239. [PMID: 28833969 DOI: 10.1002/anie.201705239] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/28/2017] [Indexed: 11/10/2022]
Abstract
The selective activation of unreactive hydrocarbons by biosynthetic enzymes has inspired new synthetic methods in C-H bond activation. Herein, we report the unprecedented two-step biosynthetic conversion of thiotetromycin to thiotetroamide C involving the tandem oxidation and amidation of an unreactive ethyl group. We detail the genetic and biochemical basis for the terminal amidation in thiotetroamide C biosynthesis, which involves a uniquely adapted cytochrome P450-amidotransferase enzyme pair and highlights the first oxidation-amidation enzymatic cascade reaction leading to the selective formation of a primary amide group from a chemically inert alkyl group. Motivated by the ten-fold increase in antibiotic potency of thiotetroamide C ascribed to the acetamide group and the unusual enzymology involved, we enzymatically interrogated diverse thiolactomycin analogues and prepared an unnatural thiotetroamide C analogue with potentiated bioactivity compared to the parent molecule.
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Affiliation(s)
- Jie Li
- Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0204, USA
| | - Xiaoyu Tang
- Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0204, USA
| | - Takayoshi Awakawa
- Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0204, USA.,Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Bradley S Moore
- Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0204, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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15
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Tang X, Li J, Moore BS. Minimization of the Thiolactomycin Biosynthetic Pathway Reveals that the Cytochrome P450 Enzyme TlmF Is Required for Five-Membered Thiolactone Ring Formation. Chembiochem 2017; 18:1072-1076. [PMID: 28393452 DOI: 10.1002/cbic.201700090] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Indexed: 11/10/2022]
Abstract
Thiolactomycin (TLM) belongs to a class of rare and unique thiotetronate antibiotics that inhibit bacterial fatty acid synthesis. Although this group of natural product antibiotics was first discovered over 30 years ago, the study of TLM biosynthesis remains in its infancy. We recently discovered the biosynthetic gene cluster (BGC) for TLM from the marine bacterium Salinispora pacifica CNS-863. Here, we report the investigation of TLM biosynthetic logic through mutagenesis and comparative metabolic analyses. Our results revealed that only four genes (tlmF, tlmG, tlmH, and tlmI) are required for the construction of the characteristic γ-thiolactone skeleton of this class of antibiotics. We further showed that the cytochrome P450 TlmF does not directly participate in sulfur insertion and C-S bond formation chemistry but rather in the construction of the five-membered thiolactone ring as, upon its deletion, we observed the alternative production of the six-membered δ-thiolactomycin. Our findings pave the way for future biochemical investigation of the biosynthesis of this structurally unique group of thiotetronic acid natural products.
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Affiliation(s)
- Xiaoyu Tang
- Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0204, USA
| | - Jie Li
- Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0204, USA
| | - Bradley S Moore
- Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0204, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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16
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Dunbar KL, Scharf DH, Litomska A, Hertweck C. Enzymatic Carbon-Sulfur Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5521-5577. [PMID: 28418240 DOI: 10.1021/acs.chemrev.6b00697] [Citation(s) in RCA: 345] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sulfur plays a critical role for the development and maintenance of life on earth, which is reflected by the wealth of primary metabolites, macromolecules, and cofactors bearing this element. Whereas a large body of knowledge has existed for sulfur trafficking in primary metabolism, the secondary metabolism involving sulfur has long been neglected. Yet, diverse sulfur functionalities have a major impact on the biological activities of natural products. Recent research at the genetic, biochemical, and chemical levels has unearthed a broad range of enzymes, sulfur shuttles, and chemical mechanisms for generating carbon-sulfur bonds. This Review will give the first systematic overview on enzymes catalyzing the formation of organosulfur natural products.
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Affiliation(s)
- Kyle L Dunbar
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Daniel H Scharf
- Life Sciences Institute, University of Michigan , 210 Washtenaw Avenue, Ann Arbor, Michigan 48109-2216, United States
| | - Agnieszka Litomska
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany.,Friedrich Schiller University , 07743 Jena, Germany
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17
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Havemann J, Yurkovich ME, Jenkins R, Harringer S, Tao W, Wen S, Sun Y, Leadlay PF, Tosin M. Chemical probing of thiotetronate bio-assembly. Chem Commun (Camb) 2017; 53:1912-1915. [DOI: 10.1039/c6cc09933e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemical ‘chain termination’ probes were utilised for the investigation of thiotetronate antibiotic biosynthesis in the filamentous bacteria Lentzea sp. and Streptomyces thiolactonus NRRL 15439.
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Affiliation(s)
| | | | | | | | - Weixin Tao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University)
- Ministry of Education
- Wuhan University School of Pharmaceutical Sciences
- Wuhan 430071
- People's Republic of China
| | - Shishi Wen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University)
- Ministry of Education
- Wuhan University School of Pharmaceutical Sciences
- Wuhan 430071
- People's Republic of China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University)
- Ministry of Education
- Wuhan University School of Pharmaceutical Sciences
- Wuhan 430071
- People's Republic of China
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