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Navarro-Muñoz JC, Selem-Mojica N, Mullowney MW, Kautsar SA, Tryon JH, Parkinson EI, De Los Santos ELC, Yeong M, Cruz-Morales P, Abubucker S, Roeters A, Lokhorst W, Fernandez-Guerra A, Cappelini LTD, Goering AW, Thomson RJ, Metcalf WW, Kelleher NL, Barona-Gomez F, Medema MH. A computational framework to explore large-scale biosynthetic diversity. Nat Chem Biol 2020; 16:60-68. [PMID: 31768033 PMCID: PMC6917865 DOI: 10.1038/s41589-019-0400-9] [Citation(s) in RCA: 388] [Impact Index Per Article: 97.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 10/04/2019] [Indexed: 01/06/2023]
Abstract
Genome mining has become a key technology to exploit natural product diversity. Although initially performed on a single-genome basis, the process is now being scaled up to mine entire genera, strain collections and microbiomes. However, no bioinformatic framework is currently available for effectively analyzing datasets of this size and complexity. In the present study, a streamlined computational workflow is provided, consisting of two new software tools: the 'biosynthetic gene similarity clustering and prospecting engine' (BiG-SCAPE), which facilitates fast and interactive sequence similarity network analysis of biosynthetic gene clusters and gene cluster families; and the 'core analysis of syntenic orthologues to prioritize natural product gene clusters' (CORASON), which elucidates phylogenetic relationships within and across these families. BiG-SCAPE is validated by correlating its output to metabolomic data across 363 actinobacterial strains and the discovery potential of CORASON is demonstrated by comprehensively mapping biosynthetic diversity across a range of detoxin/rimosamide-related gene cluster families, culminating in the characterization of seven detoxin analogues.
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Affiliation(s)
- Jorge C Navarro-Muñoz
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
- Fungal Natural Products Group, Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Nelly Selem-Mojica
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Mexico
| | | | - Satria A Kautsar
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | - James H Tryon
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Elizabeth I Parkinson
- Carl R. Woese Institute for Genomic Biology and Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | | | - Marley Yeong
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | - Pablo Cruz-Morales
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Mexico
| | - Sahar Abubucker
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
- Sanofi, Cambridge, MA, USA
| | - Arne Roeters
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | - Wouter Lokhorst
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | - Antonio Fernandez-Guerra
- Microbial Genomics and Bioinformatics, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | | | | | - Regan J Thomson
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - William W Metcalf
- Carl R. Woese Institute for Genomic Biology and Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
| | - Francisco Barona-Gomez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Mexico.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands.
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Exploitation of Potentially New Antibiotics from Mangrove Actinobacteria in Maowei Sea by Combination of Multiple Discovery Strategies. Antibiotics (Basel) 2019; 8:antibiotics8040236. [PMID: 31783564 PMCID: PMC6963217 DOI: 10.3390/antibiotics8040236] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/05/2022] Open
Abstract
Rediscovery of known antibiotics from actinobacteria, especially Streptomyces, has become a bottleneck issue. Nowadays, more specific identification and dereplication could be acquired by a combination of modern analytic techniques with various databases. In this study, 261 actinobacterial strains were isolated from 8 mangrove soil samples by culture-dependent method. A total of 83 strains were selected to evaluate antibacterial activities and mechanisms by disc diffusion method and a unique double fluorescent protein reporter system (pDualrep2), respectively. Thirty-two strains exhibited antagonistic activity against at least one of the “ESKAPE” pathogens. Four Streptomyces strains (B475, B486, B353, and B98) showed strong inhibitory activity against Gram-positive bacteria and induced DNA damage SOS response. One Micromonospora strain (B704) exhibited inhibitory activity against several pathogens and induced attenuation-based translational inhibitors reporter. Seven members of quinoxaline-type antibiotics including quinomycin A, quinomycin monosulfoxide, and other five putative new analogues were found from the culture broth of strain B475 by a combination of anti-MRSA guide, HPTLC, HPLC-UV, and UPLC-UV-HRESIMS/MS analysis, Chemspider searching, and MS/MS-based molecular networking analysis. In conclusion, this study not only demonstrated that mangrove is a rich source of actinobacteria with the potentially new antibiotics but showed rapid dereplication of known antibiotics in the early stage can improve efficiency for the discovery of new antibiotics.
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53
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Cao L, Gurevich A, Alexander KL, Naman CB, Leão T, Glukhov E, Luzzatto-Knaan T, Vargas F, Quinn R, Bouslimani A, Nothias LF, Singh NK, Sanders JG, Benitez RAS, Thompson LR, Hamid MN, Morton JT, Mikheenko A, Shlemov A, Korobeynikov A, Friedberg I, Knight R, Venkateswaran K, Gerwick WH, Gerwick L, Dorrestein PC, Pevzner PA, Mohimani H. MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. Cell Syst 2019; 9:600-608.e4. [PMID: 31629686 DOI: 10.1016/j.cels.2019.09.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/23/2019] [Accepted: 09/12/2019] [Indexed: 12/22/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that contain antibiotics and a variety of other bioactive compounds. The existing methods for discovery of RiPPs by combining genome mining and computational mass spectrometry are limited to discovering specific classes of RiPPs from small datasets, and these methods fail to handle unknown post-translational modifications. Here, we present MetaMiner, a software tool for addressing these challenges that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just eight genomic and metagenomic datasets, MetaMiner discovered 31 known and seven unknown RiPPs from diverse microbial communities, including human microbiome and lichen microbiome, and microorganisms isolated from the International Space Station.
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Affiliation(s)
- Liu Cao
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alexey Gurevich
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Kelsey L Alexander
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, USA
| | - C Benjamin Naman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Tiago Leão
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Robby Quinn
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Louis Felix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Nitin K Singh
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA
| | - Rodolfo A S Benitez
- Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA
| | - Luke R Thompson
- Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, USA; Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, CA, USA
| | - Md-Nafiz Hamid
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA; Interdepartmental program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - James T Morton
- Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Alexander Shlemov
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Anton Korobeynikov
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Department of Mathematics and Mechanics, St. Petersburg State University, St. Petersburg, Russia
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA; Interdepartmental program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, San Diego, CA, USA; Department of Bioengineering, University of California, San Diego, San Diego, CA, USA
| | | | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, San Diego, CA, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, San Diego, CA, USA
| | - Hosein Mohimani
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA.
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54
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Zhang C, Straight PD. Antibiotic discovery through microbial interactions. Curr Opin Microbiol 2019; 51:64-71. [DOI: 10.1016/j.mib.2019.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/05/2019] [Accepted: 06/20/2019] [Indexed: 01/09/2023]
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Kim Tiam S, Gugger M, Demay J, Le Manach S, Duval C, Bernard C, Marie B. Insights into the Diversity of Secondary Metabolites of Planktothrix Using a Biphasic Approach Combining Global Genomics and Metabolomics. Toxins (Basel) 2019; 11:E498. [PMID: 31461939 PMCID: PMC6784222 DOI: 10.3390/toxins11090498] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/14/2019] [Accepted: 08/22/2019] [Indexed: 12/19/2022] Open
Abstract
Cyanobacteria are an ancient lineage of slow-growing photosynthetic bacteria and a prolific source of natural products with diverse chemical structures and potent biological activities and toxicities. The chemical identification of these compounds remains a major bottleneck. Strategies that can prioritize the most prolific strains and novel compounds are of great interest. Here, we combine chemical analysis and genomics to investigate the chemodiversity of secondary metabolites based on their pattern of distribution within some cyanobacteria. Planktothrix being a cyanobacterial genus known to form blooms worldwide and to produce a broad spectrum of toxins and other bioactive compounds, we applied this combined approach on four closely related strains of Planktothrix. The chemical diversity of the metabolites produced by the four strains was evaluated using an untargeted metabolomics strategy with high-resolution LC-MS. Metabolite profiles were correlated with the potential of metabolite production identified by genomics for the different strains. Although, the Planktothrix strains present a global similarity in terms of a biosynthetic cluster gene for microcystin, aeruginosin, and prenylagaramide for example, we found remarkable strain-specific chemodiversity. Only few of the chemical features were common to the four studied strains. Additionally, the MS/MS data were analyzed using Global Natural Products Social Molecular Networking (GNPS) to identify molecular families of the same biosynthetic origin. In conclusion, we depict an efficient, integrative strategy for elucidating the chemical diversity of a given genus and link the data obtained from analytical chemistry to biosynthetic genes of cyanobacteria.
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Affiliation(s)
- Sandra Kim Tiam
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Muriel Gugger
- Institut Pasteur, Collection des Cyanobactéries, 28 rue du Dr Roux, 75724 Paris Cedex 05, France
| | - Justine Demay
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Séverine Le Manach
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Charlotte Duval
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Cécile Bernard
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Benjamin Marie
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France.
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Paulo BS, Sigrist R, Angolini CFF, De Oliveira LG. New Cyclodepsipeptide Derivatives Revealed by Genome Mining and Molecular Networking. ChemistrySelect 2019. [DOI: 10.1002/slct.201900922] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Bruno S. Paulo
- Department of Organic ChemistryUniversity of CampinasUNICAMPCidade Universitária Zeferino Vaz s/n, P.O. Box 6154 13083-970, Campinas SP (Brazil
| | - Renata Sigrist
- Department of Organic ChemistryUniversity of CampinasUNICAMPCidade Universitária Zeferino Vaz s/n, P.O. Box 6154 13083-970, Campinas SP (Brazil
| | - Célio F. F. Angolini
- Center for Natural and Human SciencesFederal University of ABC (UFABC), 09210–580 Santo André SP (Brazil
| | - Luciana G. De Oliveira
- Department of Organic ChemistryUniversity of CampinasUNICAMPCidade Universitária Zeferino Vaz s/n, P.O. Box 6154 13083-970, Campinas SP (Brazil
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Niu G, Li W. Next-Generation Drug Discovery to Combat Antimicrobial Resistance. Trends Biochem Sci 2019; 44:961-972. [PMID: 31256981 DOI: 10.1016/j.tibs.2019.05.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 12/16/2022]
Abstract
The widespread emergence of antibiotic-resistant pathogens poses a severe threat to public health. This problem becomes even worse with a coincident decline in the supply of new antibiotics. Conventional bioactivity-guided natural product discovery has failed to meet the urgent need for new antibiotics, largely due to limited resources and high rediscovery rates. Recent advances in cultivation techniques, analytical technologies, and genomics-based approaches have greatly expanded our access to previously underexploited microbial sources. These strategies will enable us to access new reservoirs of microorganisms and unleash their chemical potentials, thus opening new opportunities for the discovery of next-generation drugs to address the growing concerns of antimicrobial resistance.
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Affiliation(s)
- Guoqing Niu
- Biotechnology Research Center, Southwest University, Chongqing 400715, China; Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Southwest University, Chongqing 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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58
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Fox Ramos AE, Evanno L, Poupon E, Champy P, Beniddir MA. Natural products targeting strategies involving molecular networking: different manners, one goal. Nat Prod Rep 2019; 36:960-980. [PMID: 31140509 DOI: 10.1039/c9np00006b] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to 2019Landmark advances in bioinformatics tools have recently enhanced the field of natural products research, putting today's natural product chemists in the enviable position of being able to perform the efficient targeting/discovery of previously undescribed molecules by expediting the prioritization of the isolation workflow. Among these advances, MS/MS molecular networking has appeared as a promising approach to dereplicate complex natural product mixtures, leading to a real revolution in the "art of natural product isolation" by accelerating the pace of research of this field. This review illustrates through selected cornerstone studies the new thinking in natural product isolation by drawing a parallel between the different underlying philosophies behind the use of molecular networking in targeting natural products.
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Affiliation(s)
- Alexander E Fox Ramos
- Équipe "Pharmacognosie-Chimie des Substances Naturelles", BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.
| | - Laurent Evanno
- Équipe "Pharmacognosie-Chimie des Substances Naturelles", BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.
| | - Erwan Poupon
- Équipe "Pharmacognosie-Chimie des Substances Naturelles", BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.
| | - Pierre Champy
- Équipe "Pharmacognosie-Chimie des Substances Naturelles", BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.
| | - Mehdi A Beniddir
- Équipe "Pharmacognosie-Chimie des Substances Naturelles", BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.
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Genome mining for ribosomally synthesised and post-translationally modified peptides (RiPPs) reveals undiscovered bioactive potentials of actinobacteria. Antonie van Leeuwenhoek 2019; 112:1477-1499. [DOI: 10.1007/s10482-019-01276-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/14/2019] [Indexed: 01/22/2023]
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Nugroho AE, Morita H. Computationally-assisted discovery and structure elucidation of natural products. J Nat Med 2019; 73:687-695. [PMID: 31093833 PMCID: PMC6713678 DOI: 10.1007/s11418-019-01321-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/07/2019] [Indexed: 12/30/2022]
Abstract
Computer hardware development coupled with the development of quantum chemistry, new computational models and algorithms, and user-friendly interfaces have lowered the barriers to the use of computation in the discovery and structure elucidation of natural products. Consequently, the use of computational chemistry software as a tool to discover and determine the structure of natural products has become more common in recent years. In this review, we provide several examples of recent studies that used computer technology to facilitate the discovery and structure determination of various natural products.
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Affiliation(s)
- Alfarius Eko Nugroho
- Faculty of Pharmaceutical Sciences, Hoshi University, Ebara 2-4-41 Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Hiroshi Morita
- Faculty of Pharmaceutical Sciences, Hoshi University, Ebara 2-4-41 Shinagawa-ku, Tokyo, 142-8501, Japan.
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Subramani R, Sipkema D. Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products. Mar Drugs 2019; 17:E249. [PMID: 31035452 PMCID: PMC6562664 DOI: 10.3390/md17050249] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 12/18/2022] Open
Abstract
Rare actinomycetes are prolific in the marine environment; however, knowledge about their diversity, distribution and biochemistry is limited. Marine rare actinomycetes represent a rather untapped source of chemically diverse secondary metabolites and novel bioactive compounds. In this review, we aim to summarize the present knowledge on the isolation, diversity, distribution and natural product discovery of marine rare actinomycetes reported from mid-2013 to 2017. A total of 97 new species, representing 9 novel genera and belonging to 27 families of marine rare actinomycetes have been reported, with the highest numbers of novel isolates from the families Pseudonocardiaceae, Demequinaceae, Micromonosporaceae and Nocardioidaceae. Additionally, this study reviewed 167 new bioactive compounds produced by 58 different rare actinomycete species representing 24 genera. Most of the compounds produced by the marine rare actinomycetes present antibacterial, antifungal, antiparasitic, anticancer or antimalarial activities. The highest numbers of natural products were derived from the genera Nocardiopsis, Micromonospora, Salinispora and Pseudonocardia. Members of the genus Micromonospora were revealed to be the richest source of chemically diverse and unique bioactive natural products.
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Affiliation(s)
- Ramesh Subramani
- School of Biological and Chemical Sciences, Faculty of Science, Technology & Environment, The University of the South Pacific, Laucala Campus, Private Mail Bag, Suva, Republic of Fiji.
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
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Tuttle RN, Demko AM, Patin NV, Kapono CA, Donia MS, Dorrestein P, Jensen PR. Detection of Natural Products and Their Producers in Ocean Sediments. Appl Environ Microbiol 2019; 85:e02830-18. [PMID: 30737349 PMCID: PMC6450032 DOI: 10.1128/aem.02830-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 01/30/2019] [Indexed: 11/20/2022] Open
Abstract
Thousands of natural products have been identified from cultured microorganisms, yet evidence of their production in the environment has proven elusive. Technological advances in mass spectrometry, combined with public databases, now make it possible to address this disparity by detecting compounds directly from environmental samples. Here, we used adsorbent resins, tandem mass spectrometry, and next-generation sequencing to assess the metabolome of marine sediments and its relationship to bacterial community structure. We identified natural products previously reported from cultured bacteria, providing evidence they are produced in situ, and compounds of anthropogenic origin, suggesting this approach can be used as an indicator of environmental impact. The bacterial metabolite staurosporine was quantified and shown to reach physiologically relevant concentrations, indicating that it may influence sediment community structure. Staurosporine concentrations were correlated with the relative abundance of the staurosporine-producing bacterial genus Salinispora and production confirmed in strains cultured from the same location, providing a link between compound and candidate producer. Metagenomic analyses revealed numerous biosynthetic gene clusters related to indolocarbazole biosynthesis, providing evidence for noncanonical sources of staurosporine and a path forward to assess the relationships between natural products and the organisms that produce them. Untargeted environmental metabolomics circumvents the need for laboratory cultivation and represents a promising approach to understanding the functional roles of natural products in shaping microbial community structure in marine sediments.IMPORTANCE Natural products are readily isolated from cultured bacteria and exploited for useful purposes, including drug discovery. However, these compounds are rarely detected in the environments from which the bacteria are obtained, thus limiting our understanding of their ecological significance. Here, we used environmental metabolomics to directly assess chemical diversity in marine sediments. We identified numerous metabolites and, in one case, isolated strains of bacteria capable of producing one of the compounds detected. Coupling environmental metabolomics with community and metagenomic analyses provides opportunities to link compounds and producers and begin to assess the complex interactions mediated by specialized metabolites in marine sediments.
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Affiliation(s)
- Robert N Tuttle
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Alyssa M Demko
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Nastassia V Patin
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Clifford A Kapono
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Mohamed S Donia
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Pieter Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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63
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Bauermeister A, Pereira F, Grilo IR, Godinho CC, Paulino M, Almeida V, Gobbo‐Neto L, Prieto‐Davó A, Sobral RG, Lopes NP, Gaudêncio SP. Intra‐clade metabolomic profiling of MAR4
Streptomyces
from the Macaronesia Atlantic region reveals a source of anti‐biofilm metabolites. Environ Microbiol 2019; 21:1099-1112. [DOI: 10.1111/1462-2920.14529] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 01/09/2019] [Accepted: 01/09/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Anelize Bauermeister
- NPPNS‐Núcleo de Pesquisa em Produtos Naturais e Sintéticos, Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão PretoUniversidade de São Paulo, Avenida do Café, Monte Alegre 14040‐903 Ribeirão Preto São Paulo Brazil
| | - Florbela Pereira
- LAQV‐REQUIMTE, Departamento de Química, Faculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa 2829‐516 Caparica Portugal
| | - Inês R. Grilo
- UCIBIO‐REQUIMTE, Laboratório de Microbiologia Molecular de Bactérias Patogénicas, Departamento de Ciências da Vida, Faculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa 2829‐516 Caparica Portugal
| | - Camila C. Godinho
- NPPNS‐Núcleo de Pesquisa em Produtos Naturais e Sintéticos, Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão PretoUniversidade de São Paulo, Avenida do Café, Monte Alegre 14040‐903 Ribeirão Preto São Paulo Brazil
| | - Marisa Paulino
- UCIBIO‐REQUIMTE, Laboratório de Biotecnologia Azul e Biomedicina, Departamento de QuímicaFaculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa 2829‐516 Caparica Portugal
| | - Vanessa Almeida
- UCIBIO‐REQUIMTE, Laboratório de Biotecnologia Azul e Biomedicina, Departamento de QuímicaFaculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa 2829‐516 Caparica Portugal
| | - Leonardo Gobbo‐Neto
- NPPNS‐Núcleo de Pesquisa em Produtos Naturais e Sintéticos, Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão PretoUniversidade de São Paulo, Avenida do Café, Monte Alegre 14040‐903 Ribeirão Preto São Paulo Brazil
| | - Alejandra Prieto‐Davó
- Laboratorio de Ecología Microbiana y Productos Naturales MarinosUnidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México Sisal Yucatán Mexico
| | - Rita G. Sobral
- UCIBIO‐REQUIMTE, Laboratório de Microbiologia Molecular de Bactérias Patogénicas, Departamento de Ciências da Vida, Faculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa 2829‐516 Caparica Portugal
| | - Norberto P. Lopes
- NPPNS‐Núcleo de Pesquisa em Produtos Naturais e Sintéticos, Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão PretoUniversidade de São Paulo, Avenida do Café, Monte Alegre 14040‐903 Ribeirão Preto São Paulo Brazil
| | - Susana P. Gaudêncio
- LAQV‐REQUIMTE, Departamento de Química, Faculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa 2829‐516 Caparica Portugal
- UCIBIO‐REQUIMTE, Laboratório de Biotecnologia Azul e Biomedicina, Departamento de QuímicaFaculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa 2829‐516 Caparica Portugal
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64
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Özakin S, Ince E. Genome and metabolome mining of marine obligate Salinisporsatrains to discover new natural products. ACTA ACUST UNITED AC 2019; 43:28-36. [PMID: 30930633 PMCID: PMC6426641 DOI: 10.3906/biy-1807-136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Marine microorganisms are receiving more attention as a promising potential source of new natural products. In the present study, we performed genomic and metabolomic analyses to explore the metabolic potential of the obligate marine actinomycete genus Salinispora. The genomes of thirty Salinispora strains were prospected in search of biosynthetic gene clusters including polyketide synthase (PKS), nonribosomal peptide synthetase (NPRS), terpene, indole, lantibiotics, and siderophores. We determined considerable diversity of natural product biosynthetic gene clusters in their genome. There were a total of 1428 putative gene clusters involved in the biosynthesis of various bioactive natural products. Furthermore, 1509 ketosynthase (KS) and condensation (C) domains were detected by using NapDoS belonging to PKS and NRPS genes, respectively. Metabolic profiling was performed by a nontargeted LC-MS/MS approach combined with spectral networking using Global Natural Product Social Molecular Networking (GNPS). Dereplication and tentative identification of natural products were evaluated for common chemical properties and their associated pathways. Significant bioactive natural products such as lomaiviticin C, 7-OH-staurosporine, staurosporine, and cyanosporaside B were determined. More importantly, an unknown glycosylated compound associated with an NRPS/PKS-I hybrid gene cluster in Salinispora pacifica CNY703 was established through chemical and genomic analyses.
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Affiliation(s)
- Süleyman Özakin
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego , La Jolla, California , USA.,Department of Biology, Faculty of Science, Dicle University , Diyarbakır , Turkey
| | - Ebru Ince
- Department of Biology, Faculty of Science, Dicle University , Diyarbakır , Turkey
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65
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A selective genome-guided method for environmental Burkholderia isolation. J Ind Microbiol Biotechnol 2019; 46:345-362. [PMID: 30680473 DOI: 10.1007/s10295-018-02121-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/19/2018] [Indexed: 12/31/2022]
Abstract
The genus Burkholderia is an emerging source of novel natural products chemistry, yet to date few methods exist for the selective isolation of strains of this genus from the environment. More broadly, tools to efficiently design selection media for any given genus would be of significant value to the natural products and microbiology communities. Using a modification of the recently published SMART protocol, we have developed a two-stage isolation protocol for strains from the genus Burkholderia. This method uses a combination of selective agar isolation media and multiplexed PCR profiling to derive Burkholderia strains from environmental samples with 95% efficiency. Creation of this new method paves the way for the systematic exploration of natural products chemistry from this important genus and offers new insight into potential methods for selective isolation method development for other priority genera.
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66
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Integrated Genomic and Metabolomic Approach to the Discovery of Potential Anti-Quorum Sensing Natural Products from Microbes Associated with Marine Samples from Singapore. Mar Drugs 2019; 17:md17010072. [PMID: 30669697 PMCID: PMC6356914 DOI: 10.3390/md17010072] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 01/18/2019] [Accepted: 01/20/2019] [Indexed: 12/17/2022] Open
Abstract
With 70% of the Earth's surface covered in water, the marine ecosystem offers immense opportunities for drug discovery and development. Due to the decreasing rate of novel natural product discovery from terrestrial sources in recent years, many researchers are beginning to look seaward for breakthroughs in new therapeutic agents. As part of an ongoing marine drug discovery programme in Singapore, an integrated approach of combining metabolomic and genomic techniques were initiated for uncovering novel anti-quorum sensing molecules from bacteria associated with subtidal samples collected in the Singapore Strait. Based on the culture-dependent method, a total of 102 marine bacteria strains were isolated and the identities of selected strains were established based on their 16S rRNA gene sequences. About 5% of the marine bacterial organic extracts showed quorum sensing inhibitory (QSI) activity in a dose-dependent manner based on the Pseudomonas aeruginosa QS reporter system. In addition, the extracts were subjected to mass spectrometry-based molecular networking and the genome of selected strains were analysed for known as well as new biosynthetic gene clusters. This study revealed that using integrated techniques, coupled with biological assays, can provide an effective and rapid prioritization of marine bacterial strains for downstream large-scale culturing for the purpose of isolation and structural elucidation of novel bioactive compounds.
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67
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Contador CA, Rodríguez V, Andrews BA, Asenjo JA. Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora. BMC SYSTEMS BIOLOGY 2019; 13:11. [PMID: 30665399 PMCID: PMC6341766 DOI: 10.1186/s12918-019-0683-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 01/11/2019] [Indexed: 11/10/2022]
Abstract
BACKGROUND There is little published regarding metabolism of Salinispora species. In continuation with efforts performed towards this goal, this study is focused on new insights into the metabolism of the three-identified species of Salinispora using constraints-based modeling. At present, only one manually curated genome-scale metabolic model (GSM) for Salinispora tropica strain CNB-440T has been built despite the role of Salinispora strains in drug discovery. RESULTS Here, we updated, and expanded the scope of the model of Salinispora tropica CNB-440T, and GSMs were constructed for two sequenced type strains covering the three-identified species. We also constructed a Salinispora core model that contains the genes shared by 93 sequenced strains and a few non-conserved genes associated with essential reactions. The models predicted no auxotrophies for essential amino acids, which was corroborated experimentally using a defined minimal medium (DMM). Experimental observations suggest possible sulfur accumulation. The Core metabolic content shows that the biosynthesis of specialised metabolites is the less conserved subsystem. Sets of reactions were analyzed to explore the differences between the reconstructions. Unique reactions associated to each GSM were mainly due to genome sequence data except for the ST-CNB440 reconstruction. In this case, additional reactions were added from experimental evidence. This reveals that by reaction content the ST-CNB440 model is different from the other species models. The differences identified in reaction content between models gave rise to different functional predictions of essential nutrient usage by each species in DMM. Furthermore, models were used to evaluate in silico single gene knockouts under DMM and complex medium. Cluster analysis of these results shows that ST-CNB440, and SP-CNR114 models are more similar when considering predicted essential genes. CONCLUSIONS Models were built for each of the three currently identified Salinispora species, and a core model representing the conserved metabolic capabilities of Salinispora was constructed. Models will allow in silico metabolism studies of Salinispora strains, and help researchers to guide and increase the production of specialised metabolites. Also, models can be used as templates to build GSMs models of closely related organisms with high biotechnology potential.
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Affiliation(s)
- Carolina A. Contador
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Vida Rodríguez
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Barbara A. Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Juan A. Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
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68
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Pancrace C, Ishida K, Briand E, Pichi DG, Weiz AR, Guljamow A, Scalvenzi T, Sassoon N, Hertweck C, Dittmann E, Gugger M. Unique Biosynthetic Pathway in Bloom-Forming Cyanobacterial Genus Microcystis Jointly Assembles Cytotoxic Aeruginoguanidines and Microguanidines. ACS Chem Biol 2019; 14:67-75. [PMID: 30556994 DOI: 10.1021/acschembio.8b00918] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The cyanobacterial genus Microcystis is known to produce an elaborate array of structurally unique and biologically active natural products, including hazardous cyanotoxins. Cytotoxic aeruginoguanidines represent a yet unexplored family of peptides featuring a trisubstituted benzene unit and farnesylated arginine derivatives. In this study, we aimed at assigning these compounds to a biosynthetic gene cluster by utilizing biosynthetic attributes deduced from public genomes of Microcystis and the sporadic distribution of the metabolite in axenic strains of the Pasteur Culture Collection of Cyanobacteria. By integrating genome mining with untargeted metabolomics using liquid chromatography with mass spectrometry, we linked aeruginoguanidine (AGD) to a nonribosomal peptide synthetase gene cluster and coassigned a significantly smaller product to this pathway, microguanidine (MGD), previously only reported from two Microcystis blooms. Further, a new intermediate class of compounds named microguanidine amides was uncovered, thereby further enlarging this compound family. The comparison of structurally divergent AGDs and MGDs reveals an outstanding versatility of this biosynthetic pathway and provides insights into the assembly of the two compound subfamilies. Strikingly, aeruginoguanidines and microguanidines were found to be as widespread as the hepatotoxic microcystins, but the occurrence of both toxin families appeared to be mutually exclusive.
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Affiliation(s)
- Claire Pancrace
- Collection des Cyanobactéries, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
- UMR UPMC 113, CNRS 7618, IRD 242, INRA 1392, PARIS 7 113, UPEC, IEES Paris, 4 Place Jussieu, 75005 Paris, France
| | - Keishi Ishida
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Enora Briand
- Laboratoire Phycotoxines, Ifremer, rue de l’Ile d’Yeu, 44311 Nantes, France
| | - Douglas Gatte Pichi
- Department of Microbiology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Golm, Germany
| | - Annika R. Weiz
- Department of Microbiology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Golm, Germany
| | - Arthur Guljamow
- Department of Microbiology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Golm, Germany
| | - Thibault Scalvenzi
- Collection des Cyanobactéries, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Nathalie Sassoon
- Collection des Cyanobactéries, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Elke Dittmann
- Department of Microbiology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Golm, Germany
| | - Muriel Gugger
- Collection des Cyanobactéries, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
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69
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Chen LY, Cui HT, Su C, Bai FW, Zhao XQ. Analysis of the complete genome sequence of a marine-derived strain Streptomyces sp. S063 CGMCC 14582 reveals its biosynthetic potential to produce novel anti-complement agents and peptides. PeerJ 2019; 7:e6122. [PMID: 30627488 PMCID: PMC6321760 DOI: 10.7717/peerj.6122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/12/2018] [Indexed: 12/12/2022] Open
Abstract
Genome sequences of marine streptomycetes are valuable for the discovery of useful enzymes and bioactive compounds by genome mining. However, publicly available complete genome sequences of marine streptomycetes are still limited. Here, we present the complete genome sequence of a marine streptomycete Streptomyces sp. S063 CGMCC 14582. Species delineation based on the pairwise digital DNA-DNA hybridization and genome comparison ANI (average nucleotide identity) value showed that Streptomyces sp. S063 CGMCC 14582 possesses a unique genome that is clearly different from all of the other available genomes. Bioactivity tests showed that Streptomyces sp. S063 CGMCC 14582 produces metabolites with anti-complement activities, which are useful for treatment of numerous diseases that arise from inappropriate activation of the human complement system. Analysis of the genome reveals no biosynthetic gene cluster (BGC) which shows even low similarity to that of the known anti-complement agents was detected in the genome, indicating that Streptomyces sp. S063 CGMCC 14582 may produce novel anti-complement agents of microbial origin. Four BGCs which are potentially involved in biosynthesis of non-ribosomal peptides were disrupted, but no decrease of anti-complement activities was observed, suggesting that these four BGCs are not involved in biosynthesis of the anti-complement agents. In addition, LC-MS/MS analysis and subsequent alignment through the Global Natural Products Social Molecular Networking (GNPS) platform led to the detection of novel peptides produced by the strain. Streptomyces sp. S063 CGMCC 14582 grows rapidly and is salt tolerant, which benefits efficient secondary metabolite production via seawater-based fermentation. Our results indicate that Streptomyces sp. S063 has great potential to produce novel bioactive compounds, and also is a good host for heterologous production of useful secondary metabolites for drug discovery.
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Affiliation(s)
- Liang-Yu Chen
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,School Life Science and Biotechnology, Dalian University of Technology, Dalian, Liaoning, China
| | - Hao-Tian Cui
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chun Su
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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70
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Li Z, Zhu D, Shen Y. Discovery of novel bioactive natural products driven by genome mining. Drug Discov Ther 2018; 12:318-328. [DOI: 10.5582/ddt.2018.01066] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Zhongyue Li
- Key Laboratory of Chemical Biology, School of Pharmaceutical Sciences, Shandong University
| | - Deyu Zhu
- School of Basic Medical Sciences, Shandong University
| | - Yuemao Shen
- Key Laboratory of Chemical Biology, School of Pharmaceutical Sciences, Shandong University
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71
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Bauermeister A, Velasco-Alzate K, Dias T, Macedo H, Ferreira EG, Jimenez PC, Lotufo TMC, Lopes NP, Gaudêncio SP, Costa-Lotufo LV. Metabolomic Fingerprinting of Salinispora From Atlantic Oceanic Islands. Front Microbiol 2018; 9:3021. [PMID: 30619120 PMCID: PMC6297358 DOI: 10.3389/fmicb.2018.03021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 11/22/2018] [Indexed: 11/13/2022] Open
Abstract
Salinispora (Micromonosporaceae) is an obligate marine bacterium genus consisting of three species that share over 99% 16S rRNA identity. The genome and biosynthetic pathways of the members of this genus have been widely investigated due to their production of species-specific metabolites. However, despite the species’ high genetic similarity, site-specific secondary metabolic gene clusters have been found in Salinispora strains collected at different locations. Therefore, exploring the metabolic expression of Salinispora recovered from different sites may furnish insights into their environmental adaptation or their chemical communication and, further, may lead to the discovery of new natural products. We describe the first occurrence of Salinispora strains in sediments from the Saint Peter and Saint Paul Archipelago (a collection of islets in Brazil) in the Atlantic Ocean, and we investigate the metabolic profiles of these strains by employing mass-spectrometry-based metabolomic approaches, including molecular networking from the Global Natural Products Social Molecular Networking platform. Furthermore, we analyze data from Salinispora strains recovered from sediments from the Madeira Archipelago (Portugal, Macaronesia) in order to provide a wider metabolomic investigation of Salinispora strains from the Atlantic Oceanic islands. Overall, our study evidences a broader geographic influence on the secondary metabolism of Salinispora than was previously proposed. Still, some biosynthetic gene clusters, such as those corresponding to typical chemical signatures of S. arenicola, like saliniketals and rifamycins, are highly conserved among the assessed strains.
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Affiliation(s)
- Anelize Bauermeister
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.,Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Karen Velasco-Alzate
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Tiago Dias
- UCIBIO-REQUIMTE, Departamento de Química, Laboratório de Biotecnologia Azul e Biomedicina, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal.,UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Laboratório de Biotecnologia Azul e Biomedicina, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Helena Macedo
- UCIBIO-REQUIMTE, Departamento de Química, Laboratório de Biotecnologia Azul e Biomedicina, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal.,UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Laboratório de Biotecnologia Azul e Biomedicina, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Elthon G Ferreira
- Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Paula C Jimenez
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.,Departamento de Ciências do Mar, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Tito M C Lotufo
- Instituto Oceanográfico, Universidade de São Paulo, São Paulo, Brazil
| | - Norberto P Lopes
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Susana P Gaudêncio
- UCIBIO-REQUIMTE, Departamento de Química, Laboratório de Biotecnologia Azul e Biomedicina, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal.,UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Laboratório de Biotecnologia Azul e Biomedicina, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Letícia V Costa-Lotufo
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
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72
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Castro-Falcón G, Millán-Aguiñaga N, Roullier C, Jensen PR, Hughes CC. Nitrosopyridine Probe To Detect Polyketide Natural Products with Conjugated Alkenes: Discovery of Novodaryamide and Nocarditriene. ACS Chem Biol 2018; 13:3097-3106. [PMID: 30272441 DOI: 10.1021/acschembio.8b00598] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An optimized nitroso-based probe that facilitates the discovery of conjugated alkene-containing natural products in unprocessed extracts was developed. It chemoselectively reacts with conjugated olefins via a nitroso-Diels-Alder cyclization to yield derivatives with a distinct chromophore and an isotopically unique bromine atom that can be rapidly identified using liquid chromatography/mass spectrometry and a bioinformatics tool called MeHaloCoA (Marine Halogenated Compound Analysis). The probe is ideally employed when genome-mining techniques identify strains containing polyketide gene clusters with two or more repeating KS-AT-DH-KR-ACP domain sequences, which are required for the biosynthesis of conjugated alkenes. Comparing the reactivity and spectral properties of five brominated arylnitroso reagents with model compounds spiramycin, bufalin, rapamycin, and rifampicin led to the identification of 5-bromo-2-nitrosopyridine as the most suitable probe structure. The utility of the dienophile probe was then demonstrated in bacterial extracts. Tylactone, novodaryamide and daryamide A, piperazimycin A, and the saccharamonopyrones A and B were cleanly labeled in extracts from their respective bacterial producers, in high regioselectivity but with varying degrees of diastereoselectivity. Further application of the method led to the discovery of a new natural product called nocarditriene, containing an unprecedented epoxy-2,3,4,5-tetrahydropyridine structure, from marine-derived Nocardiopsis strain CNY-503.
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Affiliation(s)
- Gabriel Castro-Falcón
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Natalie Millán-Aguiñaga
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Catherine Roullier
- Mer Molécules Santé - EA2160, Université de Nantes, 44035 Nantes-cedex 1, France
| | - Paul R. Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Chambers C. Hughes
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
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73
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Mohimani H, Gurevich A, Shlemov A, Mikheenko A, Korobeynikov A, Cao L, Shcherbin E, Nothias LF, Dorrestein PC, Pevzner PA. Dereplication of microbial metabolites through database search of mass spectra. Nat Commun 2018; 9:4035. [PMID: 30279420 PMCID: PMC6168521 DOI: 10.1038/s41467-018-06082-8] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 08/14/2018] [Indexed: 12/24/2022] Open
Abstract
Natural products have traditionally been rich sources for drug discovery. In order to clear the road toward the discovery of unknown natural products, biologists need dereplication strategies that identify known ones. Here we report DEREPLICATOR+, an algorithm that improves on the previous approaches for identifying peptidic natural products, and extends them for identification of polyketides, terpenes, benzenoids, alkaloids, flavonoids, and other classes of natural products. We show that DEREPLICATOR+ can search all spectra in the recently launched Global Natural Products Social molecular network and identify an order of magnitude more natural products than previous dereplication efforts. We further demonstrate that DEREPLICATOR+ enables cross-validation of genome-mining and peptidogenomics/glycogenomics results.
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Affiliation(s)
- Hosein Mohimani
- Computational Biology Department, School of Computer Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
| | - Alexey Gurevich
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Alexander Shlemov
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Anton Korobeynikov
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- Department of Statistical Modelling, St. Petersburg State University, St. Petersburg, Russia
| | - Liu Cao
- Computational Biology Department, School of Computer Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Egor Shcherbin
- National Research University Higher School of Economics, St. Petersburg, Russia
| | - Louis-Felix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Department of Pharmacology and Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
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74
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Genome mining of Streptomyces xinghaiensis NRRL B-24674 T for the discovery of the gene cluster involved in anticomplement activities and detection of novel xiamycin analogs. Appl Microbiol Biotechnol 2018; 102:9549-9562. [PMID: 30232534 DOI: 10.1007/s00253-018-9337-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/10/2018] [Accepted: 08/15/2018] [Indexed: 12/13/2022]
Abstract
Marine actinobacterium Streptomyces xinghaiensis NRRL B-24674T has been characterized as a novel species, but thus far, its biosynthetic potential remains unexplored. In this study, the high-quality genome sequence of S. xinghaiensis NRRL B-24674T was obtained, and the production of anticomplement agents, xiamycin analogs, and siderophores was investigated by genome mining. Anticomplement compounds are valuable for combating numerous diseases caused by the abnormal activation of the human complement system. The biosynthetic gene cluster (BGC) nrps1 resembles that of complestatins, which are potent microbial-derived anticomplement agents. The identification of the nrps1 BGC revealed a core peptide that differed from that in complestatin; thus, we studied the anticomplement activity of this strain. The culture broth of S. xinghaiensis NRRL B-24674T displayed good anticomplement activity. Subsequently, the disruption of the genes in the nrps1 BGC resulted in the loss of anticomplement activity, confirming the involvement of this BGC in the biosynthesis of anticomplement agents. In addition, the mining of the BGC tep5, which resembles that of the antiviral pentacyclic indolosesquiterpene xiamycin, resulted in the discovery of nine xiamycin analogs, including three novel compounds. In addition to the BGCs responsible for desferrioxamine B, neomycin, ectoine, and carotenoid, 18 BGCs present in the genome are predicted to be novel. The results of this study unveil the potential of S. xinghaiensis as a producer of novel anticomplement agents and provide a basis for further exploration of the biosynthetic potential of S. xinghaiensis NRRL B-24674T for the discovery of novel bioactive compounds by genome mining.
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75
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Du C, van Wezel GP. Mining for Microbial Gems: Integrating Proteomics in the Postgenomic Natural Product Discovery Pipeline. Proteomics 2018; 18:e1700332. [PMID: 29708658 PMCID: PMC6175363 DOI: 10.1002/pmic.201700332] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/09/2018] [Indexed: 12/23/2022]
Abstract
Natural products (NPs) are a major source of compounds for medical, agricultural, and biotechnological industries. Many of these compounds are of microbial origin, and, in particular, from Actinobacteria or filamentous fungi. To successfully identify novel compounds that correlate to a bioactivity of interest, or discover new enzymes with desired functions, systematic multiomics approaches have been developed over the years. Bioinformatics tools harness the rapidly expanding wealth of genome sequence information, revealing previously unsuspected biosynthetic diversity. Varying growth conditions or application of elicitors are applied to activate cryptic biosynthetic gene clusters, and metabolomics provide detailed insights into the NPs they specify. Combining these technologies with proteomics-based approaches to profile the biosynthetic enzymes provides scientists with insights into the full biosynthetic potential of microorganisms. The proteomics approaches include enrichment strategies such as employing activity-based probes designed by chemical biology, as well as unbiased (quantitative) proteomics methods. In this review, the opportunities and challenges in microbial NP research are discussed, and, in particular, the application of proteomics to link biosynthetic enzymes to the molecules they produce, and vice versa.
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Affiliation(s)
- Chao Du
- Microbial Biotechnology & Health Programme Institute of BiologyLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
| | - Gilles P. van Wezel
- Microbial Biotechnology & Health Programme Institute of BiologyLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
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76
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Giordano D, Costantini M, Coppola D, Lauritano C, Núñez Pons L, Ruocco N, di Prisco G, Ianora A, Verde C. Biotechnological Applications of Bioactive Peptides From Marine Sources. Adv Microb Physiol 2018; 73:171-220. [PMID: 30262109 DOI: 10.1016/bs.ampbs.2018.05.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This review is an overview on marine bioactive peptides with promising activities for the development of alternative drugs to fight human pathologies. In particular, we focus on potentially prolific producers of peptides in microorganisms, including sponge-associated bacteria and marine photoautotrophs such as microalgae and cyanobacteria. Microorganisms are still poorly explored for drug discovery, even if they are highly metabolically plastic and potentially amenable to culturing. This offers the possibility of obtaining a continuous source of bioactive compounds to satisfy the challenging demands of pharmaceutical industries. This review targets peptides because of the variety of potent biological activities demonstrated by these molecules, including antiviral, antimicrobial, antifungal, antioxidant, anticoagulant, antihypertensive, anticancer, antidiabetic, antiobesity, and calcium-binding bioactivities. Several of these peptides have already gained recognition as effective drug agents in recent years. We also focus on cutting-edge omic approaches for the discovery of novel compounds for pharmacological applications. With rapid depletion of natural resources, omic technologies may be the solution to efficiently produce a vast variety of novel peptides with unique pharmacological potential.
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Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy; Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Maria Costantini
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy; Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Daniela Coppola
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy
| | - Chiara Lauritano
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Laura Núñez Pons
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Nadia Ruocco
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy; Department of Biology, University of Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cinthia, Napoli, Italy; Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Napoli, Italy
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy
| | - Adrianna Ianora
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy; Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy; Dipartimento di Biologia, Università Roma 3, Roma, Italy.
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77
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Parkinson EI, Tryon JH, Goering AW, Ju KS, McClure RA, Kemball JD, Zhukovsky S, Labeda DP, Thomson RJ, Kelleher NL, Metcalf WW. Discovery of the Tyrobetaine Natural Products and Their Biosynthetic Gene Cluster via Metabologenomics. ACS Chem Biol 2018; 13:1029-1037. [PMID: 29510029 DOI: 10.1021/acschembio.7b01089] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Natural products (NPs) are a rich source of medicines, but traditional discovery methods are often unsuccessful due to high rates of rediscovery. Genetic approaches for NP discovery are promising, but progress has been slow due to the difficulty of identifying unique biosynthetic gene clusters (BGCs) and poor gene expression. We previously developed the metabologenomics method, which combines genomic and metabolomic data to discover new NPs and their BGCs. Here, we utilize metabologenomics in combination with molecular networking to discover a novel class of NPs, the tyrobetaines: nonribosomal peptides with an unusual trimethylammonium tyrosine residue. The BGC for this unusual class of compounds was identified using metabologenomics and computational structure prediction data. Heterologous expression confirmed the BGC and suggests an unusual mechanism for trimethylammonium formation. Overall, the discovery of the tyrobetaines shows the great potential of metabologenomics combined with molecular networking and computational structure prediction for identifying interesting biosynthetic reactions and novel NPs.
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Affiliation(s)
- Elizabeth I. Parkinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - James H. Tryon
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Anthony W. Goering
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Kou-San Ju
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Ryan A. McClure
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jeremy D. Kemball
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Sara Zhukovsky
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - David P. Labeda
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS National Center for Agricultural Utilization Research, Peoria, Illinois 61604, United States
| | - Regan J. Thomson
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - William W. Metcalf
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Microbiology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801 United States
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78
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Wolff H, Bode HB. The benzodiazepine-like natural product tilivalline is produced by the entomopathogenic bacterium Xenorhabdus eapokensis. PLoS One 2018; 13:e0194297. [PMID: 29596433 PMCID: PMC5875774 DOI: 10.1371/journal.pone.0194297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/28/2018] [Indexed: 01/05/2023] Open
Abstract
The pyrrolobenzodiazepine tilivalline (1) was originally identified in the human gut pathobiont Klebsiella oxytoca, the causative agent of antibiotic-associated hemorrhagic colitis. Here we show the identification of tilivalline and analogs thereof in the entomopathogenic bacterium Xenorhabdus eapokensis as well as the identification of its biosynthesis gene cluster encoding a bimodular non-ribosomal peptide synthetase. Heterologous expression of both genes in E. coli resulted in the production of 1 and from mutasynthesis and precursor directed biosynthesis 11 new tilivalline analogs were identified in X. eapokensis. These results allowed the prediction of the tilivalline biosynthesis being similar to that in K. oxytoca.
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Affiliation(s)
- Hendrik Wolff
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B. Bode
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, Frankfurt am Main, Germany
- * E-mail:
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79
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Coley PD, Endara MJ, Kursar TA. Consequences of interspecific variation in defenses and herbivore host choice for the ecology and evolution of Inga, a speciose rainforest tree. Oecologia 2018; 187:361-376. [PMID: 29428967 DOI: 10.1007/s00442-018-4080-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/26/2017] [Indexed: 01/08/2023]
Abstract
We summarize work on a speciose Neotropical tree genus, Inga (Fabaceae), examining how interspecific variation in anti-herbivore defenses may have evolved, how defenses shape host choice by herbivores and how they might regulate community composition and influence species radiations. Defenses of expanding leaves include secondary metabolites, extrafloral nectaries, rapid leaf expansion, trichomes, and synchrony and timing of leaf production. These six classes of defenses are orthogonal, supporting independent evolutionary trajectories. Moreover, only trichomes show a phylogenetic signature, suggesting evolutionary lability in nearly all defenses. The interspecific diversity in secondary metabolite profiles does not arise from the evolution of novel compounds, but from novel combinations of common compounds, presumably due to changes in gene regulation. Herbivore host choice is determined by plant defensive traits, not host phylogeny. Neighboring plants escape each other's pests if their defenses differ enough, thereby enforcing the high local diversity typical of tropical forests. Related herbivores feed on hosts with similar defenses, implying that there are phylogenetic constraints placed on the herbivore traits that are associated with host use. Divergence in defensive traits among Inga appears to be driven by herbivore pressure. However, the lack of congruence between herbivore and host phylogeny suggests that herbivores are tracking defenses, choosing hosts based on traits for which they already have adaptations. There is, therefore, an asymmetry in the host-herbivore evolutionary arms race.
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Affiliation(s)
- Phyllis D Coley
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA. .,Smithsonian Tropical Research Institute, Panama City, Republic of Panama.
| | - María-José Endara
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA.,Centro de Investigación de la Biodiversidad y Cambio Climático e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, EC170103, Quito, Ecuador
| | - Thomas A Kursar
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA.,Smithsonian Tropical Research Institute, Panama City, Republic of Panama
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80
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Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra. Nat Microbiol 2018; 3:319-327. [PMID: 29358742 DOI: 10.1038/s41564-017-0094-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 12/08/2017] [Indexed: 11/09/2022]
Abstract
Peptidic natural products (PNPs) include many antibiotics and other bioactive compounds. While the recent launch of the Global Natural Products Social (GNPS) molecular networking infrastructure is transforming PNP discovery into a high-throughput technology, PNP identification algorithms are needed to realize the potential of the GNPS project. GNPS relies on the assumption that each connected component of a molecular network (representing related metabolites) illuminates the 'dark matter of metabolomics' as long as it contains a known metabolite present in a database. We reveal a surprising diversity of PNPs produced by related bacteria and show that, contrary to the 'comparative metabolomics' assumption, two related bacteria are unlikely to produce identical PNPs (even though they are likely to produce similar PNPs). Since this observation undermines the utility of GNPS, we developed a PNP identification tool, VarQuest, that illuminates the connected components in a molecular network even if they do not contain known PNPs and only contain their variants. VarQuest reveals an order of magnitude more PNP variants than all previous PNP discovery efforts and demonstrates that GNPS already contains spectra from 41% of the currently known PNP families. The enormous diversity of PNPs suggests that biosynthetic gene clusters in various microorganisms constantly evolve to generate a unique spectrum of PNP variants that differ from PNPs in other species.
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81
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Adnani N, Chevrette MG, Adibhatla SN, Zhang F, Yu Q, Braun DR, Nelson J, Simpkins SW, McDonald BR, Myers CL, Piotrowski JS, Thompson CJ, Currie CR, Li L, Rajski SR, Bugni TS. Coculture of Marine Invertebrate-Associated Bacteria and Interdisciplinary Technologies Enable Biosynthesis and Discovery of a New Antibiotic, Keyicin. ACS Chem Biol 2017; 12:3093-3102. [PMID: 29121465 DOI: 10.1021/acschembio.7b00688] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Advances in genomics and metabolomics have made clear in recent years that microbial biosynthetic capacities on Earth far exceed previous expectations. This is attributable, in part, to the realization that most microbial natural product (NP) producers harbor biosynthetic machineries not readily amenable to classical laboratory fermentation conditions. Such "cryptic" or dormant biosynthetic gene clusters (BGCs) encode for a vast assortment of potentially new antibiotics and, as such, have become extremely attractive targets for activation under controlled laboratory conditions. We report here that coculturing of a Rhodococcus sp. and a Micromonospora sp. affords keyicin, a new and otherwise unattainable bis-nitroglycosylated anthracycline whose mechanism of action (MOA) appears to deviate from those of other anthracyclines. The structure of keyicin was elucidated using high resolution MS and NMR technologies, as well as detailed molecular modeling studies. Sequencing of the keyicin BGC (within the Micromonospora genome) enabled both structural and genomic comparisons to other anthracycline-producing systems informing efforts to characterize keyicin. The new NP was found to be selectively active against Gram-positive bacteria including both Rhodococcus sp. and Mycobacterium sp. E. coli-based chemical genomics studies revealed that keyicin's MOA, in contrast to many other anthracyclines, does not invoke nucleic acid damage.
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Affiliation(s)
- Navid Adnani
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Marc G. Chevrette
- Department
of Bacteriology, University of Wisconsin, Madison, Wisconsin 53705, United States
- Department
of Genetics, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Srikar N. Adibhatla
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Fan Zhang
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Qing Yu
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Doug R. Braun
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Justin Nelson
- Bioinformatics
and Computational Biology Program, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Scott W. Simpkins
- Bioinformatics
and Computational Biology Program, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Bradon R. McDonald
- Department
of Bacteriology, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Chad L. Myers
- Bioinformatics
and Computational Biology Program, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
- Department
of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
| | | | | | - Cameron R. Currie
- Department
of Bacteriology, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Scott R. Rajski
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Tim S. Bugni
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
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82
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Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality. Proc Natl Acad Sci U S A 2017; 114:E11121-E11130. [PMID: 29229817 DOI: 10.1073/pnas.1714381115] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bacterial natural products remain an important source of new medicines. DNA sequencing has revealed that a majority of natural product biosynthetic gene clusters (BGCs) maintained in bacterial genomes have yet to be linked to the small molecules whose biosynthesis they encode. Efforts to discover the products of these orphan BGCs are driving the development of genome mining techniques based on the premise that many are transcriptionally silent during normal laboratory cultivation. Here, we employ comparative transcriptomics to assess BGC expression among four closely related strains of marine bacteria belonging to the genus Salinispora The results reveal that slightly more than half of the BGCs are expressed at levels that should facilitate product detection. By comparing the expression profiles of similar gene clusters in different strains, we identified regulatory genes whose inactivation appears linked to cluster silencing. The significance of these subtle differences between expressed and silent BGCs could not have been predicted a priori and was only revealed by comparative transcriptomics. Evidence for the conservation of silent clusters among a larger number of strains for which genome sequences are available suggests they may be under different regulatory control from the expressed forms or that silencing may represent an underappreciated mechanism of gene cluster evolution. Coupling gene expression and metabolomics data established a bioinformatic link between the salinipostins and their associated BGC, while genetic manipulation established the genetic basis for this series of compounds, which were previously unknown from Salinispora pacifica.
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83
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Conde-Martínez N, Acosta-González A, Díaz LE, Tello E. Use of a mixed culture strategy to isolate halophilic bacteria with antibacterial and cytotoxic activity from the Manaure solar saltern in Colombia. BMC Microbiol 2017; 17:230. [PMID: 29216824 PMCID: PMC5721385 DOI: 10.1186/s12866-017-1136-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/27/2017] [Indexed: 12/04/2022] Open
Abstract
Background Water evaporation in solar salterns creates salinity gradients that promote the adaptation of microbial species to different salinities. This competitive habitat challenges the metabolic capabilities of microorganisms and promotes alterations in their production of secondary metabolites. Thus, solar salterns are a potentially important source of new natural products. In Colombia, the most important and representative solar saltern is located in Manaure (La Guajira) in the north of Colombia. The aim of this study was to develop an alternative screening strategy to select halophilic bacteria as producers of bioactive compounds from mixed microbial cultures rather than individual environmental isolates. Brine and sediment samples from different ponds (across a salinity gradient) were inoculated in seven different culture media to grow bacteria and archaea, allowing for a total of 40 different mixed cultures. An organic extract from each mixed culture was obtained and tested against multidrug resistant pathogens, including Klebsiella pneumoniae, vancomycin-resistant Enterococcus faecium, methicillin-resistant Staphylococcus aureus and Bacillus subtilis. In addition, the extracts were tested against two human cancer cell lines, cervical adenocarcinoma (SiHa) and lung carcinoma (A-549). Results Twenty-four of the forty extracts from mixed cultures obtained from brine and sediment samples from the Manaure solar saltern showed antibacterial activity against Bacillus subtilis. Two extracts, referred to as A1SM3–29 and A1SM3–36, were also active against a methicillin-resistant Staphylococcus aureus, with the latter extract also showing slight cytotoxic activity against the assayed human lung cancer cell line. From this mixed culture, nine isolates were cultivated, and their extracts were tested against the same pathogens, resulting in the identification of a Vibrio sp. strain (A1SM3–36-8) with antimicrobial activity that was similar to that observed for the mixed culture extract. The extract of this strain was subjected to a bioautography assay, and 3 different fractions exhibited antibacterial activity against methicillin-resistant Staphylococcus aureus. Based on the amount obtained for each fraction, F3 was selected to isolate and identify its metabolites. The major compound was identified by NMR and HRMS as 13-cis-docosenamide, an amide that has been previously reported to be an antimicrobial and cytotoxic compound. Conclusions Our results shows the utility of our strategy in detecting bioactive molecules in initial mixed cultures by biological assays, resulting in the isolation and characterization of Vibrio sp. A1SM3–36-8, a halophilic strain with great antibacterial and cytotoxic potential. Electronic supplementary material The online version of this article (10.1186/s12866-017-1136-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Natalia Conde-Martínez
- Bioscience Doctoral Program, Grupo de Investigación en Bioprospección, Faculty of Engineering, Universidad de La Sabana, Campus Puente del Común, Km 7, Autopista Norte de Bogotá, Chía, Colombia
| | - Alejandro Acosta-González
- Bioscience Doctoral Program, Grupo de Investigación en Bioprospección, Faculty of Engineering, Universidad de La Sabana, Campus Puente del Común, Km 7, Autopista Norte de Bogotá, Chía, Colombia
| | - Luis E Díaz
- Bioscience Doctoral Program, Grupo de Investigación en Bioprospección, Faculty of Engineering, Universidad de La Sabana, Campus Puente del Común, Km 7, Autopista Norte de Bogotá, Chía, Colombia
| | - Edisson Tello
- Bioscience Doctoral Program, Grupo de Investigación en Bioprospección, Faculty of Engineering, Universidad de La Sabana, Campus Puente del Común, Km 7, Autopista Norte de Bogotá, Chía, Colombia.
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84
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Vallet M, Vanbellingen QP, Fu T, Le Caer JP, Della-Negra S, Touboul D, Duncan KR, Nay B, Brunelle A, Prado S. An Integrative Approach to Decipher the Chemical Antagonism between the Competing Endophytes Paraconiothyrium variabile and Bacillus subtilis. JOURNAL OF NATURAL PRODUCTS 2017; 80:2863-2873. [PMID: 29139291 DOI: 10.1021/acs.jnatprod.6b01185] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
An integrative approach combining traditional natural products chemistry, molecular networking, and mass spectrometry imaging has been undertaken to decipher the molecular dialogue between the fungus Paraconiothyrium variabile and the bacterium Bacillus subtilis, which were isolated as endophytes from the conifer Cephalotaxus harringtonia and are characterized by a strong and mutual antibiosis. From this study, we highlight that bacterial surfactins and a fungal tetronic acid are involved in such competition and that the fungus is able to hydrolyze surfactins to fight against the bacterial partner.
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Affiliation(s)
- Marine Vallet
- Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS , CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Quentin P Vanbellingen
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Tingting Fu
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Jean-Pierre Le Caer
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Serge Della-Negra
- Institut de Physique Nucléaire, UMR8608, IN2P3-CNRS, Université Paris-Sud, Université Paris-Saclay , 91406, Orsay, France
| | - David Touboul
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Katherine R Duncan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, HW608, University of Strathclyde , 161 Cathedral Street, Glasgow G4 ORE, U.K
| | - Bastien Nay
- Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS , CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Alain Brunelle
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Soizic Prado
- Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS , CP 54, 57 rue Cuvier, 75005 Paris, France
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85
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Chen R, Zhang Q, Tan B, Zheng L, Li H, Zhu Y, Zhang C. Genome Mining and Activation of a Silent PKS/NRPS Gene Cluster Direct the Production of Totopotensamides. Org Lett 2017; 19:5697-5700. [PMID: 29019409 DOI: 10.1021/acs.orglett.7b02878] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A 92 kb silent hybrid polyketide and nonribosomal peptide gene cluster in marine-derived Streptomyces pactum SCSIO 02999 was activated by genetically manipulating the regulatory genes, including the knockout of two negative regulators (totR5 and totR3) and overexpression of a positive regulator totR1, to direct the production of the known totopotensamides (TPMs) A (1) and B (3) and a novel sulfonate-containing analogue TPM C (2). Inactivation of totG led to accumulation of TPM B (3) lacking the glycosyl moiety, which indicated TotG as a dedicated glycosyltransferase in the biosynthesis of 1 and 2.
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Affiliation(s)
- Ruidong Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
| | - Bin Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
| | - Liujuan Zheng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
| | - Huixian Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
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86
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Machado H, Tuttle RN, Jensen PR. Omics-based natural product discovery and the lexicon of genome mining. Curr Opin Microbiol 2017; 39:136-142. [PMID: 29175703 PMCID: PMC5732065 DOI: 10.1016/j.mib.2017.10.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/28/2017] [Indexed: 11/29/2022]
Abstract
Genome sequencing and the application of omic techniques are driving many important advances in the field of microbial natural products research. Despite these gains, there remain aspects of the natural product discovery pipeline where our knowledge remains poor. These include the extent to which biosynthetic gene clusters are transcriptionally active in native microbes, the temporal dynamics of transcription, translation, and natural product assembly, as well as the relationships between small molecule production and detection. Here we touch on a number of these concepts in the context of continuing efforts to unlock the natural product potential revealed in genome sequence data and discuss nomenclatural issues that warrant consideration as the field moves forward.
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Affiliation(s)
- Henrique Machado
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA
| | - Robert N Tuttle
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA; Center for Microbiome Innovation, University of California, San Diego, USA.
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87
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Hufsky F, Böcker S. Mining molecular structure databases: Identification of small molecules based on fragmentation mass spectrometry data. MASS SPECTROMETRY REVIEWS 2017; 36:624-633. [PMID: 26763615 DOI: 10.1002/mas.21489] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 12/18/2015] [Indexed: 06/05/2023]
Abstract
Mass spectrometry (MS) is a key technology for the analysis of small molecules. For the identification and structural elucidation of novel molecules, new approaches beyond straightforward spectral comparison are required. In this review, we will cover computational methods that help with the identification of small molecules by analyzing fragmentation MS data. We focus on the four main approaches to mine a database of metabolite structures, that is rule-based fragmentation spectrum prediction, combinatorial fragmentation, competitive fragmentation modeling, and molecular fingerprint prediction. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:624-633, 2017.
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Affiliation(s)
- Franziska Hufsky
- Lehrstuhl für Bioinformatik, Friedrich-Schiller-Universität Jena, Ernst-Abbe-Platz 2, Jena, 07743, Germany
- Bioinformatik für Hochdurchsatzverfahren, Friedrich-Schiller-Universität Jena, Leutragraben 1, Jena, 07743, Germany
| | - Sebastian Böcker
- Lehrstuhl für Bioinformatik, Friedrich-Schiller-Universität Jena, Ernst-Abbe-Platz 2, Jena, 07743, Germany
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88
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Letzel AC, Li J, Amos GCA, Millán-Aguiñaga N, Ginigini J, Abdelmohsen UR, Gaudêncio SP, Ziemert N, Moore BS, Jensen PR. Genomic insights into specialized metabolism in the marine actinomycete Salinispora. Environ Microbiol 2017; 19:3660-3673. [PMID: 28752948 DOI: 10.1111/1462-2920.13867] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/18/2017] [Accepted: 07/21/2017] [Indexed: 11/28/2022]
Abstract
Comparative genomics is providing new opportunities to address the diversity and distributions of genes encoding the biosynthesis of specialized metabolites. An analysis of 119 genome sequences representing three closely related species of the marine actinomycete genus Salinispora reveals extraordinary biosynthetic diversity in the form of 176 distinct biosynthetic gene clusters (BGCs) of which only 24 have been linked to their products. Remarkably, more than half of the BGCs were observed in only one or two strains, suggesting they were acquired relatively recently in the evolutionary history of the genus. These acquired gene clusters are concentrated in specific genomic islands, which represent hot spots for BGC acquisition. While most BGCs are stable in terms of their chromosomal position, others migrated to different locations or were exchanged with unrelated gene clusters suggesting a plug and play type model of evolution that provides a mechanism to test the relative fitness effects of specialized metabolites. Transcriptome analyses were used to address the relationships between BGC abundance, chromosomal position and product discovery. The results indicate that recently acquired BGCs can be functional and that complex evolutionary processes shape the micro-diversity of specialized metabolism observed in closely related environmental bacteria.
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Affiliation(s)
- Anne-Catrin Letzel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Jing Li
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Gregory C A Amos
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Natalie Millán-Aguiñaga
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California 22800, Mexico
| | - Joape Ginigini
- Institute of Applied Sciences, Faculty of Science, Technology and Environment, University of the South Pacific, Laucala Campus, Private Mail Bag, Suva, Fiji
| | - Usama R Abdelmohsen
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Germany.,Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
| | - Susana P Gaudêncio
- Department of Chemistry, REQUIMTE, LAQV and UCIBIO, Faculty of Science and Technology, Universidade NOVA de Lisboa, Caparica 2529-516, Portugal
| | - Nadine Ziemert
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Interfaculty Institute of Microbiology and Infection Medicine Tuübingen, University of Tuübingen, Auf der Morgenstelle 28, Tuübingen 72076, Germany
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of 9500 Gilman Dr, La Jolla, CA 92093, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
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89
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Protasov ES, Axenov-Gribanov DV, Rebets YV, Voytsekhovskaya IV, Tokovenko BT, Shatilina ZM, Luzhetskyy AN, Timofeyev MA. The diversity and antibiotic properties of actinobacteria associated with endemic deepwater amphipods of Lake Baikal. Antonie van Leeuwenhoek 2017; 110:1593-1611. [PMID: 28721507 DOI: 10.1007/s10482-017-0910-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 07/08/2017] [Indexed: 02/03/2023]
Abstract
The emergence of pathogenic bacteria resistant to antibiotics increases the need for discovery of new effective antimicrobials. Unique habitats such as marine deposits, wetlands and caves or unexplored biological communities are promising sources for the isolation of actinobacteria, which are among the major antibiotic producers. The present study aimed at examining cultivated actinobacteria strains associated with endemic Lake Baikal deepwater amphipods and estimating their antibiotic activity. We isolated 42 actinobacterial strains from crustaceans belonging to Ommatogammarus albinus and Ommatogammarus flavus. To our knowledge, this is the first report describing the isolation and initial characterization of representatives of Micromonospora and Pseudonocardia genera from Baikal deepwater invertebrates. Also, as expected, representatives of the genus Streptomyces were the dominant group among the isolated species. Some correlations could be observed between the number of actinobacterial isolates, the depth of sampling and the source of the strains. Nevertheless, >70% of isolated strains demonstrated antifungal activity. The dereplication analysis of extract of one of the isolated strains resulted in annotation of several known compounds that can help to explain the observed biological activities. The characteristics of ecological niche and lifestyle of deepwater amphipods suggests that the observed associations between crustaceans and isolated actinobacteria are not random and might represent long-term symbiotic interactions.
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Affiliation(s)
| | - Denis V Axenov-Gribanov
- Institute of Biology, Irkutsk State University, Irkutsk, Russia. .,Baikal Research Centre, Irkutsk, Russia.
| | - Yuriy V Rebets
- Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrucken, Germany.,Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrucken, Germany
| | | | - Bogdan T Tokovenko
- Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrucken, Germany
| | - Zhanna M Shatilina
- Institute of Biology, Irkutsk State University, Irkutsk, Russia.,Baikal Research Centre, Irkutsk, Russia
| | - Andriy N Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrucken, Germany.,Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrucken, Germany
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90
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Aksenov AA, da Silva R, Knight R, Lopes NP, Dorrestein PC. Global chemical analysis of biology by mass spectrometry. Nat Rev Chem 2017. [DOI: 10.1038/s41570-017-0054] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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91
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Dhakal D, Pokhrel AR, Shrestha B, Sohng JK. Marine Rare Actinobacteria: Isolation, Characterization, and Strategies for Harnessing Bioactive Compounds. Front Microbiol 2017; 8:1106. [PMID: 28663748 PMCID: PMC5471306 DOI: 10.3389/fmicb.2017.01106] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 05/31/2017] [Indexed: 12/28/2022] Open
Abstract
Actinobacteria are prolific producers of thousands of biologically active natural compounds with diverse activities. More than half of these bioactive compounds have been isolated from members belonging to actinobacteria. Recently, rare actinobacteria existing at different environmental settings such as high altitudes, volcanic areas, and marine environment have attracted attention. It has been speculated that physiological or biochemical pressures under such harsh environmental conditions can lead to the production of diversified natural compounds. Hence, marine environment has been focused for the discovery of novel natural products with biological potency. Many novel and promising bioactive compounds with versatile medicinal, industrial, or agricultural uses have been isolated and characterized. The natural compounds cannot be directly used as drug or other purposes, so they are structurally modified and diversified to ameliorate their biological or chemical properties. Versatile synthetic biological tools, metabolic engineering techniques, and chemical synthesis platform can be used to assist such structural modification. This review summarizes the latest studies on marine rare actinobacteria and their natural products with focus on recent approaches for structural and functional diversification of such microbial chemicals for attaining better applications.
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Affiliation(s)
- Dipesh Dhakal
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea
| | - Anaya Raj Pokhrel
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea
| | - Biplav Shrestha
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea.,Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University Asan-siSouth Korea
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92
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Abstract
Covering: 2015. Previous review: Nat. Prod. Rep., 2016, 33, 382-431This review covers the literature published in 2015 for marine natural products (MNPs), with 1220 citations (792 for the period January to December 2015) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1340 in 429 papers for 2015), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.
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Affiliation(s)
- John W Blunt
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Robert A Keyzers
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Murray H G Munro
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
| | - Michèle R Prinsep
- Chemistry, School of Science, University of Waikato, Hamilton, New Zealand
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93
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Crüsemann M, O’Neill EC, Larson CB, Melnik AV, Floros DJ, da Silva RR, Jensen PR, Dorrestein PC, Moore BS. Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols. JOURNAL OF NATURAL PRODUCTS 2017; 80:588-597. [PMID: 28335604 PMCID: PMC5367486 DOI: 10.1021/acs.jnatprod.6b00722] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
In order to expedite the rapid and efficient discovery and isolation of novel specialized metabolites, while minimizing the waste of resources on rediscovery of known compounds, it is crucial to develop efficient approaches for strain prioritization, rapid dereplication, and the assessment of favored cultivation and extraction conditions. Herein we interrogated bacterial strains by systematically evaluating cultivation and extraction parameters with LC-MS/MS analysis and subsequent dereplication through the Global Natural Product Social Molecular Networking (GNPS) platform. The developed method is fast, requiring minimal time and sample material, and is compatible with high-throughput extract analysis, thereby streamlining strain prioritization and evaluation of culturing parameters. With this approach, we analyzed 146 marine Salinispora and Streptomyces strains that were grown and extracted using multiple different protocols. In total, 603 samples were analyzed, generating approximately 1.8 million mass spectra. We constructed a comprehensive molecular network and identified 15 molecular families of diverse natural products and their analogues. The size and breadth of this network shows statistically supported trends in molecular diversity when comparing growth and extraction conditions. The network provides an extensive survey of the biosynthetic capacity of the strain collection and a method to compare strains based on the variety and novelty of their metabolites. This approach allows us to quickly identify patterns in metabolite production that can be linked to taxonomy, culture conditions, and extraction methods, as well as informing the most valuable growth and extraction conditions.
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Affiliation(s)
- Max Crüsemann
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Ellis C. O’Neill
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Charles B. Larson
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Alexey V. Melnik
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dimitrios J Floros
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ricardo R. da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
- Research Support Center in Natural and Synthetic Products, Department of Physics and Chemistry, Faculty of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, 14040-903, Brazil
| | - Paul R. Jensen
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Pieter C. Dorrestein
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bradley S. Moore
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
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94
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Strong antibiotic production is correlated with highly active oxidative metabolism in Streptomyces coelicolor M145. Sci Rep 2017; 7:200. [PMID: 28298624 PMCID: PMC5427975 DOI: 10.1038/s41598-017-00259-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/10/2017] [Indexed: 11/08/2022] Open
Abstract
The Streptomyces genus is well known for its ability to produce bio-active secondary metabolites of great medical interest. However, the metabolic features accompanying these bio-productions remain to be defined. In this study, the comparison of related model strains producing differing levels of actinorhoddin (ACT), showed that S. lividans, a weak producer, had high TriAcylGlycerol (TAG) content indicative of a glycolytic metabolism. In contrast, the strong producer, S. coelicolor, was characterized by low TAG content, active consumption of its polyphosphate (PolyP) stores and extremely high ATP/ADP ratios. This indicated highly active oxidative metabolism that was correlated with induction of ACT biosynthesis. Interestingly, in conditions of phosphate limitation, the ppk mutant had TAG content and ACT production levels intermediary between those of S. lividans and S. coelicolor. This strain was characterized by high ADP levels indicating that Ppk was acting as an Adenosine Di Phosphate Kinase. Its absence resulted in energetic stress that is proposed to trigger an activation of oxidative metabolism to restore its energetic balance. This process, which is correlated with ACT biosynthesis, requires acetylCoA to fuel the Krebs cycle and phosphate for ATP generation by the ATP synthase coupled to the respiratory chain, resulting in low TAG and polyP content of the ACT producing strains.
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95
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Molecular Networking As a Drug Discovery, Drug Metabolism, and Precision Medicine Strategy. Trends Pharmacol Sci 2017; 38:143-154. [DOI: 10.1016/j.tips.2016.10.011] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/17/2016] [Accepted: 10/17/2016] [Indexed: 12/18/2022]
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96
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Covington BC, McLean JA, Bachmann BO. Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites. Nat Prod Rep 2017; 34:6-24. [PMID: 27604382 PMCID: PMC5214543 DOI: 10.1039/c6np00048g] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Covering: 2000 to 2016The labor-intensive process of microbial natural product discovery is contingent upon identifying discrete secondary metabolites of interest within complex biological extracts, which contain inventories of all extractable small molecules produced by an organism or consortium. Historically, compound isolation prioritization has been driven by observed biological activity and/or relative metabolite abundance and followed by dereplication via accurate mass analysis. Decades of discovery using variants of these methods has generated the natural pharmacopeia but also contributes to recent high rediscovery rates. However, genomic sequencing reveals substantial untapped potential in previously mined organisms, and can provide useful prescience of potentially new secondary metabolites that ultimately enables isolation. Recently, advances in comparative metabolomics analyses have been coupled to secondary metabolic predictions to accelerate bioactivity and abundance-independent discovery work flows. In this review we will discuss the various analytical and computational techniques that enable MS-based metabolomic applications to natural product discovery and discuss the future prospects for comparative metabolomics in natural product discovery.
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Affiliation(s)
- Brett C Covington
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA.
| | - John A McLean
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA. and Center for Innovative Technology, Vanderbilt University, 5401 Stevenson Center, Nashville, TN 37235, USA
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA.
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97
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McClure RA, Goering AW, Ju KS, Baccile JA, Schroeder FC, Metcalf WW, Thomson RJ, Kelleher NL. Elucidating the Rimosamide-Detoxin Natural Product Families and Their Biosynthesis Using Metabolite/Gene Cluster Correlations. ACS Chem Biol 2016; 11:3452-3460. [PMID: 27809474 DOI: 10.1021/acschembio.6b00779] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
As microbial genome sequencing becomes more widespread, the capacity of microorganisms to produce an immense number of metabolites has come into better view. Utilizing a metabolite/gene cluster correlation platform, the biosynthetic origins of a new family of natural products, the rimosamides, were discovered. The rimosamides were identified in Streptomyces rimosus and associated with their NRPS/PKS-type gene cluster based upon their high frequency of co-occurrence across 179 strains of actinobacteria. This also led to the discovery of the related detoxin gene cluster. The core of each of these families of natural products contains a depsipeptide bond at the point of bifurcation in their unusual branched structures, the origins of which are definitively assigned to nonlinear biosynthetic pathways via heterologous expression in Streptomyces lividans. The rimosamides were found to antagonize the antibiotic activity of blasticidin S against Bacillus cereus.
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Affiliation(s)
- Ryan A. McClure
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Anthony W. Goering
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Kou-San Ju
- Carl R.
Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Joshua A. Baccile
- Boyce Thompson
Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Frank C. Schroeder
- Boyce Thompson
Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - William W. Metcalf
- Carl R.
Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Microbiology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Regan J. Thomson
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil. L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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98
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New antibiotics from Nature’s chemical inventory. Bioorg Med Chem 2016; 24:6227-6252. [DOI: 10.1016/j.bmc.2016.09.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/07/2016] [Indexed: 01/07/2023]
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99
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Ortega MA, van der Donk WA. New Insights into the Biosynthetic Logic of Ribosomally Synthesized and Post-translationally Modified Peptide Natural Products. Cell Chem Biol 2016; 23:31-44. [PMID: 26933734 DOI: 10.1016/j.chembiol.2015.11.012] [Citation(s) in RCA: 200] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/10/2015] [Accepted: 11/10/2015] [Indexed: 10/24/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a large group of structurally diverse natural products. Their biological activities and unique biosynthetic pathways have sparked a growing interest in RiPPs. Furthermore, the relatively low genetic complexity associated with RiPP biosynthesis makes them excellent candidates for synthetic biology applications. This Review highlights recent developments in the understanding of the biosynthesis of several bacterial RiPP family members, the use of the RiPP biosynthetic machinery for generating novel macrocyclic peptides, and the implementation of tools designed to guide the discovery and characterization of novel RiPPs.
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Affiliation(s)
- Manuel A Ortega
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wilfred A van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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100
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Dereplication of peptidic natural products through database search of mass spectra. Nat Chem Biol 2016; 13:30-37. [PMID: 27820803 PMCID: PMC5409158 DOI: 10.1038/nchembio.2219] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 08/17/2016] [Indexed: 11/08/2022]
Abstract
Peptidic Natural Products (PNPs) are widely used compounds that include many antibiotics and a variety of other bioactive peptides. While recent breakthroughs in PNP discovery raised the challenge of developing new algorithms for their analysis, identification of PNPs via database search of tandem mass spectra remains an open problem. To address this problem, natural product researchers utilize dereplication strategies that identify known PNPs and lead to the discovery of new ones even in cases when the reference spectra are not present in existing spectral libraries. DEREPLICATOR is a new dereplication algorithm that enabled high-throughput PNP identification and that is compatible with large-scale mass spectrometry-based screening platforms for natural product discovery. After searching nearly one hundred million tandem mass spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure, DEREPLICATOR identified an order of magnitude more PNPs (and their new variants) than any previous dereplication efforts.
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