Automated Genome Mining of Ribosomal Peptide Natural Products
Ribosomally synthesized and posttranslationally modified peptides (RiPPs), especially from microbial sources, are a large group of bioactive natural products that are a promising source of new (bio)chemistry and bioactivity. In light of exponentially increasing microbial genome databases and improv...
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creator | Mohimani, Hosein Kersten, Roland D Liu, Wei-Ting Wang, Mingxun Purvine, Samuel O Wu, Si Brewer, Heather M Pasa-Tolic, Ljiljana Bandeira, Nuno Moore, Bradley S Pevzner, Pavel A Dorrestein, Pieter C |
description | Ribosomally synthesized and posttranslationally modified peptides (RiPPs), especially from microbial sources, are a large group of bioactive natural products that are a promising source of new (bio)chemistry and bioactivity. In light of exponentially increasing microbial genome databases and improved mass spectrometry (MS)-based metabolomic platforms, there is a need for computational tools that connect natural product genotypes predicted from microbial genome sequences with their corresponding chemotypes from metabolomic data sets. Here, we introduce RiPPquest, a tandem mass spectrometry database search tool for identification of microbial RiPPs, and apply it to lanthipeptide discovery. RiPPquest uses genomics to limit search space to the vicinity of RiPP biosynthetic genes and proteomics to analyze extensive peptide modifications and compute p-values of peptide-spectrum matches (PSMs). We highlight RiPPquest by connecting multiple RiPPs from extracts of Streptomyces to their gene clusters and by the discovery of a new class III lanthipeptide, informatipeptin, from Streptomyces viridochromogenes DSM 40736 to reflect that it is a natural product that was discovered by mass spectrometry based genome mining using algorithmic tools rather than manual inspection of mass spectrometry data and genetic information. The presented tool is available at cyclo.ucsd.edu. |
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In light of exponentially increasing microbial genome databases and improved mass spectrometry (MS)-based metabolomic platforms, there is a need for computational tools that connect natural product genotypes predicted from microbial genome sequences with their corresponding chemotypes from metabolomic data sets. Here, we introduce RiPPquest, a tandem mass spectrometry database search tool for identification of microbial RiPPs, and apply it to lanthipeptide discovery. RiPPquest uses genomics to limit search space to the vicinity of RiPP biosynthetic genes and proteomics to analyze extensive peptide modifications and compute p-values of peptide-spectrum matches (PSMs). We highlight RiPPquest by connecting multiple RiPPs from extracts of Streptomyces to their gene clusters and by the discovery of a new class III lanthipeptide, informatipeptin, from Streptomyces viridochromogenes DSM 40736 to reflect that it is a natural product that was discovered by mass spectrometry based genome mining using algorithmic tools rather than manual inspection of mass spectrometry data and genetic information. 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Biol</addtitle><description>Ribosomally synthesized and posttranslationally modified peptides (RiPPs), especially from microbial sources, are a large group of bioactive natural products that are a promising source of new (bio)chemistry and bioactivity. In light of exponentially increasing microbial genome databases and improved mass spectrometry (MS)-based metabolomic platforms, there is a need for computational tools that connect natural product genotypes predicted from microbial genome sequences with their corresponding chemotypes from metabolomic data sets. Here, we introduce RiPPquest, a tandem mass spectrometry database search tool for identification of microbial RiPPs, and apply it to lanthipeptide discovery. RiPPquest uses genomics to limit search space to the vicinity of RiPP biosynthetic genes and proteomics to analyze extensive peptide modifications and compute p-values of peptide-spectrum matches (PSMs). We highlight RiPPquest by connecting multiple RiPPs from extracts of Streptomyces to their gene clusters and by the discovery of a new class III lanthipeptide, informatipeptin, from Streptomyces viridochromogenes DSM 40736 to reflect that it is a natural product that was discovered by mass spectrometry based genome mining using algorithmic tools rather than manual inspection of mass spectrometry data and genetic information. The presented tool is available at cyclo.ucsd.edu.</description><subject>Amino Acid Sequence</subject><subject>Biological Products - metabolism</subject><subject>Databases, Genetic</subject><subject>Drug Discovery - methods</subject><subject>Environmental Molecular Sciences Laboratory</subject><subject>Genome, Bacterial</subject><subject>Genomics - methods</subject><subject>Molecular Sequence Data</subject><subject>Multigene Family</subject><subject>Peptides - chemistry</subject><subject>Peptides - genetics</subject><subject>Protein Processing, Post-Translational</subject><subject>Proteomics - methods</subject><subject>Ribosomes - chemistry</subject><subject>Ribosomes - genetics</subject><subject>Streptomyces - chemistry</subject><subject>Streptomyces - genetics</subject><subject>Tandem Mass Spectrometry - methods</subject><issn>1554-8929</issn><issn>1554-8937</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>N~.</sourceid><sourceid>EIF</sourceid><recordid>eNptkV1LHTEQhkOpVD32wj8gS0GwF0fztdnNhYKItYL9QOx1mE0mnsjZ5LjJFvz3rhw9WOjVzDAP77zMS8g-o8eMcnZiu5pSpvXiA9lhdS3nrRbNx03P9TbZzfmBUilUqz-RbS5bypXQO-T0fCyph4KuusKYeqx-hBjifZV8dRu6lKflsvqNqxIcVj-hjMPLPCQ32pL3yJaHZcbPr3VG_ny7vLv4Pr_5dXV9cX4zB6nbMm9FJxshobZCgUVoJEjVqNpjqx145y1ziB0F4b3jYJl2QvHGCVAdMg9iRs7Wuqux69FZjGWyYVZD6GF4MgmC-XcTw8Lcp79Gcla3Sk8CX9YCKZdgsg0F7cKmGNEWw1jDuJYTdPR6ZUiPI-Zi-pAtLpcQMY3ZsFoqzqmaPjcjX9eoHVLOA_qNF0bNSyZmk8nEHrw3vyHfQpiAwzUANpuHNA5x-uV_hJ4BWI2UNg</recordid><startdate>20140718</startdate><enddate>20140718</enddate><creator>Mohimani, Hosein</creator><creator>Kersten, Roland D</creator><creator>Liu, Wei-Ting</creator><creator>Wang, Mingxun</creator><creator>Purvine, Samuel O</creator><creator>Wu, Si</creator><creator>Brewer, Heather M</creator><creator>Pasa-Tolic, Ljiljana</creator><creator>Bandeira, Nuno</creator><creator>Moore, Bradley S</creator><creator>Pevzner, Pavel A</creator><creator>Dorrestein, Pieter C</creator><general>American Chemical Society</general><scope>N~.</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>OTOTI</scope><scope>5PM</scope></search><sort><creationdate>20140718</creationdate><title>Automated Genome Mining of Ribosomal Peptide Natural Products</title><author>Mohimani, Hosein ; Kersten, Roland D ; Liu, Wei-Ting ; Wang, Mingxun ; Purvine, Samuel O ; Wu, Si ; Brewer, Heather M ; Pasa-Tolic, Ljiljana ; Bandeira, Nuno ; Moore, Bradley S ; Pevzner, Pavel A ; Dorrestein, Pieter C</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a498t-83b4734a5c36acea74a46765fe89dafdfc1deeb0a3ffd2ac19d3627d3a6be1fa3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Amino Acid Sequence</topic><topic>Biological Products - metabolism</topic><topic>Databases, Genetic</topic><topic>Drug Discovery - methods</topic><topic>Environmental Molecular Sciences Laboratory</topic><topic>Genome, Bacterial</topic><topic>Genomics - methods</topic><topic>Molecular Sequence Data</topic><topic>Multigene Family</topic><topic>Peptides - chemistry</topic><topic>Peptides - genetics</topic><topic>Protein Processing, Post-Translational</topic><topic>Proteomics - methods</topic><topic>Ribosomes - chemistry</topic><topic>Ribosomes - genetics</topic><topic>Streptomyces - chemistry</topic><topic>Streptomyces - genetics</topic><topic>Tandem Mass Spectrometry - methods</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mohimani, Hosein</creatorcontrib><creatorcontrib>Kersten, Roland D</creatorcontrib><creatorcontrib>Liu, Wei-Ting</creatorcontrib><creatorcontrib>Wang, Mingxun</creatorcontrib><creatorcontrib>Purvine, Samuel O</creatorcontrib><creatorcontrib>Wu, Si</creatorcontrib><creatorcontrib>Brewer, Heather M</creatorcontrib><creatorcontrib>Pasa-Tolic, Ljiljana</creatorcontrib><creatorcontrib>Bandeira, Nuno</creatorcontrib><creatorcontrib>Moore, Bradley S</creatorcontrib><creatorcontrib>Pevzner, Pavel A</creatorcontrib><creatorcontrib>Dorrestein, Pieter C</creatorcontrib><creatorcontrib>Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)</creatorcontrib><collection>American Chemical Society (ACS) Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>ACS Chemical Biology, 9(7):1545-1551</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mohimani, Hosein</au><au>Kersten, Roland D</au><au>Liu, Wei-Ting</au><au>Wang, Mingxun</au><au>Purvine, Samuel O</au><au>Wu, Si</au><au>Brewer, Heather M</au><au>Pasa-Tolic, Ljiljana</au><au>Bandeira, Nuno</au><au>Moore, Bradley S</au><au>Pevzner, Pavel A</au><au>Dorrestein, Pieter C</au><aucorp>Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Automated Genome Mining of Ribosomal Peptide Natural Products</atitle><jtitle>ACS Chemical Biology, 9(7):1545-1551</jtitle><addtitle>ACS Chem. Biol</addtitle><date>2014-07-18</date><risdate>2014</risdate><volume>9</volume><issue>7</issue><spage>1545</spage><epage>1551</epage><pages>1545-1551</pages><issn>1554-8929</issn><eissn>1554-8937</eissn><abstract>Ribosomally synthesized and posttranslationally modified peptides (RiPPs), especially from microbial sources, are a large group of bioactive natural products that are a promising source of new (bio)chemistry and bioactivity. In light of exponentially increasing microbial genome databases and improved mass spectrometry (MS)-based metabolomic platforms, there is a need for computational tools that connect natural product genotypes predicted from microbial genome sequences with their corresponding chemotypes from metabolomic data sets. Here, we introduce RiPPquest, a tandem mass spectrometry database search tool for identification of microbial RiPPs, and apply it to lanthipeptide discovery. RiPPquest uses genomics to limit search space to the vicinity of RiPP biosynthetic genes and proteomics to analyze extensive peptide modifications and compute p-values of peptide-spectrum matches (PSMs). We highlight RiPPquest by connecting multiple RiPPs from extracts of Streptomyces to their gene clusters and by the discovery of a new class III lanthipeptide, informatipeptin, from Streptomyces viridochromogenes DSM 40736 to reflect that it is a natural product that was discovered by mass spectrometry based genome mining using algorithmic tools rather than manual inspection of mass spectrometry data and genetic information. The presented tool is available at cyclo.ucsd.edu.</abstract><cop>United States</cop><pub>American Chemical Society</pub><pmid>24802639</pmid><doi>10.1021/cb500199h</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Amino Acid Sequence Biological Products - metabolism Databases, Genetic Drug Discovery - methods Environmental Molecular Sciences Laboratory Genome, Bacterial Genomics - methods Molecular Sequence Data Multigene Family Peptides - chemistry Peptides - genetics Protein Processing, Post-Translational Proteomics - methods Ribosomes - chemistry Ribosomes - genetics Streptomyces - chemistry Streptomyces - genetics Tandem Mass Spectrometry - methods |
title | Automated Genome Mining of Ribosomal Peptide Natural Products |
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