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Meena SN, Wajs-Bonikowska A, Girawale S, Imran M, Poduwal P, Kodam KM. High-Throughput Mining of Novel Compounds from Known Microbes: A Boost to Natural Product Screening. Molecules 2024; 29:3237. [PMID: 38999189 PMCID: PMC11243205 DOI: 10.3390/molecules29133237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024] Open
Abstract
Advanced techniques can accelerate the pace of natural product discovery from microbes, which has been lagging behind the drug discovery era. Therefore, the present review article discusses the various interdisciplinary and cutting-edge techniques to present a concrete strategy that enables the high-throughput screening of novel natural compounds (NCs) from known microbes. Recent bioinformatics methods revealed that the microbial genome contains a huge untapped reservoir of silent biosynthetic gene clusters (BGC). This article describes several methods to identify the microbial strains with hidden mines of silent BGCs. Moreover, antiSMASH 5.0 is a free, accurate, and highly reliable bioinformatics tool discussed in detail to identify silent BGCs in the microbial genome. Further, the latest microbial culture technique, HiTES (high-throughput elicitor screening), has been detailed for the expression of silent BGCs using 500-1000 different growth conditions at a time. Following the expression of silent BGCs, the latest mass spectrometry methods are highlighted to identify the NCs. The recently emerged LAESI-IMS (laser ablation electrospray ionization-imaging mass spectrometry) technique, which enables the rapid identification of novel NCs directly from microtiter plates, is presented in detail. Finally, various trending 'dereplication' strategies are emphasized to increase the effectiveness of NC screening.
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Affiliation(s)
- Surya Nandan Meena
- Department of Chemistry, Savitribai Phule Pune University, Pune 411007, India; (S.N.M.); (K.M.K.)
| | - Anna Wajs-Bonikowska
- Institute of Natural Products and Cosmetics, Faculty of Biotechnology and Food Sciences, Łódz University of Technology, Stefanowskiego Street 2/22, 90-537 Łódz, Poland
| | - Savita Girawale
- Department of Chemistry, Savitribai Phule Pune University, Pune 411007, India; (S.N.M.); (K.M.K.)
| | - Md Imran
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Preethi Poduwal
- Department of Biotechnology, Dhempe College of Arts and Science, Miramar, Goa 403001, India;
| | - Kisan M. Kodam
- Department of Chemistry, Savitribai Phule Pune University, Pune 411007, India; (S.N.M.); (K.M.K.)
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de Carvalho LC, de Almeida Junior A, Ribeiro FS, Angolini CFF. Unveiling Microbial Chemical Interactions Based on Metabolomics Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:51-70. [PMID: 37843805 DOI: 10.1007/978-3-031-41741-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Microorganisms are ubiquitous in diverse habitats and studying their chemical interactions with the environment and comprehend its complex relations with both hosts and environment, are crucial for the development of strategies to control microbial diseases. This chapter discusses the importance of studying microorganisms with agricultural benefits, using specialized metabolites as examples. Herein we highlight the challenges and opportunities in utilizing microorganisms as alternatives to synthetic pesticides and fertilizers in agriculture. Genome-guided investigations and improved analytical methodologies are necessary to characterize diverse and complex biomolecules produced by microorganisms. Predicting and isolating bioproducts based on genetic information have become a focus for researchers, aided by tools like antiSMASH, BiG-SCAPE, PRISM, and others. However, translating genomic data into practical applications can be complex. Therefore, integrating genomics, transcriptomics, and metabolomics enhances chemical characterization, aiding in discovering new metabolic pathways and specialized metabolites. Additionally, elicitation is one promising strategy to enhance beneficial metabolite production. Finally, identify and characterize microbial secondary metabolites remain challenging due to their low production, complex chemical structure characterization and different environmental factors necessary for metabolite in vitro production.
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Affiliation(s)
- Laís Castro de Carvalho
- Mass Spectrometry and Chemical Ecology Laboratory (MC-CELL), Center for Natural and Human Sciences, University of ABC (UFABC), São Paulo, Brazil
| | - Arnaldo de Almeida Junior
- Mass Spectrometry and Chemical Ecology Laboratory (MC-CELL), Center for Natural and Human Sciences, University of ABC (UFABC), São Paulo, Brazil
| | - Fernanda Silva Ribeiro
- Mass Spectrometry and Chemical Ecology Laboratory (MC-CELL), Center for Natural and Human Sciences, University of ABC (UFABC), São Paulo, Brazil
| | - Célio Fernando Figueiredo Angolini
- Mass Spectrometry and Chemical Ecology Laboratory (MC-CELL), Center for Natural and Human Sciences, University of ABC (UFABC), São Paulo, Brazil.
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The Natural Product Domain Seeker version 2 (NaPDoS2) webtool relates ketosynthase phylogeny to biosynthetic function. J Biol Chem 2022; 298:102480. [PMID: 36108739 PMCID: PMC9582728 DOI: 10.1016/j.jbc.2022.102480] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 12/01/2022] Open
Abstract
The Natural Product Domain Seeker (NaPDoS) webtool detects and classifies ketosynthase (KS) and condensation domains from genomic, metagenomic, and amplicon sequence data. Unlike other tools, a phylogeny-based classification scheme is used to make broader predictions about the polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes in which these domains are found. NaPDoS is particularly useful for the analysis of incomplete biosynthetic genes or gene clusters, as are often observed in poorly assembled genomes and metagenomes, or when loci are not clustered, as in eukaryotic genomes. To help support the growing interest in sequence-based analyses of natural product biosynthetic diversity, here we introduce version 2 of the webtool, NaPDoS2, available at http://napdos.ucsd.edu/napdos2. This update includes the addition of 1417 KS sequences, representing a major expansion of the taxonomic and functional diversity represented in the webtool database. The phylogeny-based KS classification scheme now recognizes 41 class and subclass assignments, including new type II PKS subclasses. Workflow modifications accelerate run times, allowing larger datasets to be analyzed. In addition, default parameters were established using statistical validation tests to maximize KS detection and classification accuracy while minimizing false positives. We further demonstrate the applications of NaPDoS2 to assess PKS biosynthetic potential using genomic, metagenomic, and PCR amplicon datasets. These examples illustrate how NaPDoS2 can be used to predict biosynthetic potential and detect genes involved in the biosynthesis of specific structure classes or new biosynthetic mechanisms.
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Cavas L, Kirkiz I. Characterization of siderophores from Escherichia coli strains through genome mining tools: an antiSMASH study. AMB Express 2022; 12:74. [PMID: 35704153 PMCID: PMC9200922 DOI: 10.1186/s13568-022-01421-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/08/2022] [Indexed: 11/23/2022] Open
Abstract
Although urinary tract infections (UTIs) affect many people, they are usually a disease observed in women. UTIs happen when exogenous and endogenous bacteria enter the urinary tract and colonize there. Cystitis and pyelonephritis occur when bacteria infect the bladder and the kidneys, respectively. UTIs become much serious if the bacteria causing the infection are antibiotic resistant. Since the pathogenic microorganisms have been adopted to current antibiotics via genetic variations, UTIs have become an even more severe health problem. Therefore, there is a great need for the discovery of novel antibiotics. Genome mining of nonpathogenic and pathogenic Escherichia coli strains for investigating secondary metabolites were conducted by the antiSMASH analysis. When the resulting secondary metabolites were examined, it was found that some of the siderophores are effective in UTIs. In conclusion, since the siderophore production in E. coli is directly related to UTIs, these molecules can be a good target for development of future pharmaceutical approaches and compounds. Siderophores can also be used in industrial studies due to their higher chelating affinity for iron. ![]()
Genome mining on nonpathogenic and pathogenic E. coli was studied. Comprehensive and comparative analysis of siderophores were investigated. The results may open a new gate on the development of new drugs on pathogenic E. coli-based diseases.
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Affiliation(s)
- Levent Cavas
- The Graduate School of Natural and Applied Sciences, Department of Biotechnology, Dokuz Eylül University, Kaynaklar Campus, 35390, İzmir, Türkiye. .,Dokuz Eylül University, Faculty of Science, Department of Chemistry, 35390, Kaynaklar Campus, İzmir, Türkiye.
| | - Ibrahim Kirkiz
- The Graduate School of Natural and Applied Sciences, Department of Biotechnology, Dokuz Eylül University, Kaynaklar Campus, 35390, İzmir, Türkiye
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Chen S, Zhang C, Zhang L. Investigation of the Molecular Landscape of Bacterial Aromatic Polyketides by Global Analysis of Type II Polyketide Synthases. Angew Chem Int Ed Engl 2022; 61:e202202286. [PMID: 35384223 DOI: 10.1002/anie.202202286] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Indexed: 12/17/2022]
Abstract
Aromatic polyketides biosynthesized by microorganisms are a prominent class of natural products widely used in clinical treatments. Although genome mining approaches have accelerated the discovery of these molecules, the molecular diversity, abundance, and distribution of bacterial aromatic polyketides at a global scale remain elusive. Here, we provide a global atlas of bacterial aromatic polyketides based on large-scale analysis of type II polyketide synthases. We first established the chain length factor protein as a marker that can predict both chemical class and molecular uniqueness of the biosynthetic product, and analyzed the abundance, taxonomic distribution, estimated structural diversity, and the total number of aromatic polyketides in bacteria. We further show the identification of oryzanaphthopyrans with an unprecedented angular naphthopyran scaffold from a rare actinobacterium by genome mining guided by the global atlas. These results serve as a compass for exploiting the entire type II polyketide synthase-derived aromatic polyketides in bacteria.
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Affiliation(s)
- Shanchong Chen
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang Province, China.,Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Chi Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Lihan Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
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6
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Chen S, Zhang C, Zhang L. Investigation of the Molecular Landscape of Bacterial Aromatic Polyketides by Global Analysis of Type II Polyketide Synthases. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Shanchong Chen
- Zhejiang University Department of Chemistry Hangzhou CHINA
| | - Chi Zhang
- Westlake University School of Science Hangzhou CHINA
| | - Lihan Zhang
- Westlake University School of Science Shilongshan Rd.18Xihu District 310024 Hangzhou CHINA
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Hemmerling F, Piel J. Strategies to access biosynthetic novelty in bacterial genomes for drug discovery. Nat Rev Drug Discov 2022; 21:359-378. [PMID: 35296832 DOI: 10.1038/s41573-022-00414-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2022] [Indexed: 12/17/2022]
Abstract
Bacteria provide a rich source of natural products with potential therapeutic applications, such as novel antibiotic classes or anticancer drugs. Bioactivity-guided screening of bacterial extracts and characterization of biosynthetic pathways for drug discovery is now complemented by the availability of large (meta)genomic collections, placing researchers into the postgenomic, big-data era. The progress in next-generation sequencing and the rise of powerful computational tools provide unprecedented insights into unexplored taxa, ecological niches and 'biosynthetic dark matter', revealing diverse and chemically distinct natural products in previously unstudied bacteria. In this Review, we discuss such sources of new chemical entities and the implications for drug discovery with a particular focus on the strategies that have emerged in recent years to identify and access novelty.
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Affiliation(s)
- Franziska Hemmerling
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland.
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Zhang Q, Ren JW, Wang W, Zhai J, Yang J, Liu N, Huang Y, Chen Y, Pan G, Fan K. A Versatile Transcription-Translation in One Approach for Activation of Cryptic Biosynthetic Gene Clusters. ACS Chem Biol 2020; 15:2551-2557. [PMID: 32786260 DOI: 10.1021/acschembio.0c00581] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ever-growing drug resistance problem worldwide highlights the urgency to discover and develop new drugs. Microbial natural products are a prolific source of drugs. Genome sequencing has revealed a tremendous amount of uncharacterized natural product biosynthetic gene clusters (BGCs) encoded within microbial genomes, most of which are cryptic or express at very low levels under standard culture conditions. Therefore, developing effective strategies to awaken these cryptic BGCs is of great interest for natural product discovery. In this study, we designed and validated a Transcription-Translation in One (TTO) approach for activation of cryptic BGCs. This approach aims to alter the metabolite profiles of target strains by directly overexpressing exogenous rpsL (encoding ribosomal protein S12) and rpoB (encoding RNA polymerase β subunit) genes containing beneficial mutations for natural product production using a plug-and-play plasmid system. As a result, this approach bypasses the tedious screening work and overcomes the false positive problem in the traditional ribosome engineering approach. In this work, the TTO approach was successfully applied to activating cryptic BGCs in three Streptomyces strains, leading to the discovery of two aromatic polyketide antibiotics, piloquinone and homopiloquinone. We further identified a single BGC responsible for the biosynthesis of both piloquinone and homopiloquinone, which features an unusual starter unit incorporation step. This powerful strategy can be further exploited for BGC activation in strains even beyond streptomycetes, thus facilitating natural product discovery research in the future.
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Affiliation(s)
- Qian Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin-Wei Ren
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji’an Zhai
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Jing Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ning Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guohui Pan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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9
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Herisse M, Ishida K, Porter JL, Howden B, Hertweck C, Stinear TP, Pidot SJ. Identification and Mobilization of a Cryptic Antibiotic Biosynthesis Gene Locus from a Human-Pathogenic Nocardia Isolate. ACS Chem Biol 2020; 15:1161-1168. [PMID: 31697466 DOI: 10.1021/acschembio.9b00763] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The genus Nocardia contains >50 human pathogenic species that cause a range of illnesses from skin and soft tissue infections to lung and brain infections. However, despite their membership in the most prominent family of secondary metabolite producers (the Actinomycetes), the ability of Nocardia species, especially those that cause human infections, to produce secondary metabolites has not been as well studied. Using genome mining, we have investigated cryptic secondary metabolite biosynthesis gene clusters from Nocardia species and identified a conserved locus within human pathogenic strains of Nocardia brasiliensis and Nocardia vulneris. Direct capture and heterologous expression in a Streptomyces host activated the biosynthetic locus, revealing it to be the source of the brasiliquinones, benz[a]anthraquinone antibiotics whose biosynthetic pathway has remained hidden for over two decades, until now. Our findings highlight these hitherto neglected human pathogenic Nocardia as a source of diverse and important natural products.
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Affiliation(s)
- Marion Herisse
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Jessica L. Porter
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Ben Howden
- Microbiological Diagnostic Unit, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
- Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
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10
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Jakočiūnas T, Klitgaard AK, Kontou EE, Nielsen JB, Thomsen E, Romero-Suarez D, Blin K, Petzold CJ, Gin JW, Tong Y, Gotfredsen CH, Charusanti P, Frandsen RJN, Weber T, Lee SY, Jensen MK, Keasling JD. Programmable polyketide biosynthesis platform for production of aromatic compounds in yeast. Synth Syst Biotechnol 2020; 5:11-18. [PMID: 32021916 PMCID: PMC6992897 DOI: 10.1016/j.synbio.2020.01.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 01/13/2020] [Indexed: 12/14/2022] Open
Abstract
To accelerate the shift to bio-based production and overcome complicated functional implementation of natural and artificial biosynthetic pathways to industry relevant organisms, development of new, versatile, bio-based production platforms is required. Here we present a novel yeast-based platform for biosynthesis of bacterial aromatic polyketides. The platform is based on a synthetic polyketide synthase system enabling a first demonstration of bacterial aromatic polyketide biosynthesis in a eukaryotic host.
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Affiliation(s)
- Tadas Jakočiūnas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Andreas K Klitgaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Eftychia Eva Kontou
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Julie Bang Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Emil Thomsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - David Romero-Suarez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | | | - Yaojun Tong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Pep Charusanti
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Rasmus J N Frandsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.,Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Michael K Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jay D Keasling
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.,Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Chemical and Biomolecular Engineering & Department of Bioengineering University of California, Berkeley, CA, USA.,Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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11
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Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH, Weber T. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81-W87. [PMID: 31032519 PMCID: PMC6602434 DOI: 10.1093/nar/gkz310] [Citation(s) in RCA: 1995] [Impact Index Per Article: 399.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/02/2019] [Accepted: 04/17/2019] [Indexed: 12/13/2022] Open
Abstract
Secondary metabolites produced by bacteria and fungi are an important source of antimicrobials and other bioactive compounds. In recent years, genome mining has seen broad applications in identifying and characterizing new compounds as well as in metabolic engineering. Since 2011, the 'antibiotics and secondary metabolite analysis shell-antiSMASH' (https://antismash.secondarymetabolites.org) has assisted researchers in this, both as a web server and a standalone tool. It has established itself as the most widely used tool for identifying and analysing biosynthetic gene clusters (BGCs) in bacterial and fungal genome sequences. Here, we present an entirely redesigned and extended version 5 of antiSMASH. antiSMASH 5 adds detection rules for clusters encoding the biosynthesis of acyl-amino acids, β-lactones, fungal RiPPs, RaS-RiPPs, polybrominated diphenyl ethers, C-nucleosides, PPY-like ketones and lipolanthines. For type II polyketide synthase-encoding gene clusters, antiSMASH 5 now offers more detailed predictions. The HTML output visualization has been redesigned to improve the navigation and visual representation of annotations. We have again improved the runtime of analysis steps, making it possible to deliver comprehensive annotations for bacterial genomes within a few minutes. A new output file in the standard JavaScript object notation (JSON) format is aimed at downstream tools that process antiSMASH results programmatically.
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Affiliation(s)
- Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Simon Shaw
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Katharina Steinke
- German Centre for Infection Research (DZIF), Interfaculty Institute of Microbiology and Infection Medicine, Auf der Morgenstelle 28, University of Tübingen, 72076 Tübingen, DE, Germany
| | - Rasmus Villebro
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Nadine Ziemert
- German Centre for Infection Research (DZIF), Interfaculty Institute of Microbiology and Infection Medicine, Auf der Morgenstelle 28, University of Tübingen, 72076 Tübingen, DE, Germany
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program) and BioInformatics Research Center, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, the Netherlands
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
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12
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Adamek M, Alanjary M, Ziemert N. Applied evolution: phylogeny-based approaches in natural products research. Nat Prod Rep 2019; 36:1295-1312. [DOI: 10.1039/c9np00027e] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here we highlight how phylogenetic analyses can be used to facilitate natural product discovery and structure elucidation.
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Affiliation(s)
- Martina Adamek
- Applied Natural Products Genome Mining
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen (IMIT)
- University of Tuebingen
- 72076 Tuebingen
- Germany
| | | | - Nadine Ziemert
- Applied Natural Products Genome Mining
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen (IMIT)
- University of Tuebingen
- 72076 Tuebingen
- Germany
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