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MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities.
Cao, Liu; Gurevich, Alexey; Alexander, Kelsey L; Naman, C Benjamin; Leão, Tiago; Glukhov, Evgenia; Luzzatto-Knaan, Tal; Vargas, Fernando; Quinn, Robby; Bouslimani, Amina; Nothias, Louis Felix; Singh, Nitin K; Sanders, Jon G; Benitez, Rodolfo A S; Thompson, Luke R; Hamid, Md-Nafiz; Morton, James T; Mikheenko, Alla; Shlemov, Alexander; Korobeynikov, Anton; Friedberg, Iddo; Knight, Rob; Venkateswaran, Kasthuri; Gerwick, William H; Gerwick, Lena; Dorrestein, Pieter C; Pevzner, Pavel A; Mohimani, Hosein.
Afiliación
  • Cao L; Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.
  • Gurevich A; Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
  • Alexander KL; 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.
  • Naman CB; 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 P
  • Leão T; 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.
  • Glukhov E; 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.
  • Luzzatto-Knaan T; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA.
  • Vargas F; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA.
  • Quinn R; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA.
  • Bouslimani A; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA.
  • Nothias LF; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA.
  • Singh NK; Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
  • Sanders JG; Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA.
  • Benitez RAS; Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA.
  • Thompson LR; 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 Sc
  • Hamid MN; 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.
  • Morton JT; 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.
  • Mikheenko A; Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
  • Shlemov A; Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
  • Korobeynikov A; 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.
  • Friedberg I; 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.
  • Knight R; 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
  • Venkateswaran K; Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
  • Gerwick WH; 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.
  • Gerwick L; 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.
  • Dorrestein PC; 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.
  • Pevzner PA; 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.
  • Mohimani H; Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA. Electronic address: hoseinm@andrew.cmu.edu.
Cell Syst ; 9(6): 600-608.e4, 2019 12 18.
Article en En | MEDLINE | ID: mdl-31629686
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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Texto completo: 1 Base de datos: MEDLINE Asunto principal: Procesamiento Proteico-Postraduccional / Biología Computacional / Microbiota Límite: Humans Idioma: En Revista: Cell Syst Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos
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Texto completo: 1 Base de datos: MEDLINE Asunto principal: Procesamiento Proteico-Postraduccional / Biología Computacional / Microbiota Límite: Humans Idioma: En Revista: Cell Syst Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos