MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities

Liu Cao, Alexey Gurevich, Kelsey L. Alexander, C. Benjamin Naman, Tiago Leão , Evgenia Glukhov, Tal TalLuzzatto-Knaan, Fernando Vargas, Robby Quinn, Amina Bouslimani, Louis Felix Nothias, Nitin K. Singh, Jon G. Sanders, Rodolfo A.S. Benitez, Luke R. Thompson, Md-Nafiz Hamid, James T. Morton, Alla Mikheenko, Alexander Shlemov, Anton KorobeynikovIddo Friedberg, Rob Knight, Kasthuri Venkateswaran, William H. Gerwick, Lena Gerwick, Pieter C Dorrestein, Pavel A. Pevzner, Hosein Mohimani

Результат исследований: Научные публикации в периодических изданияхстатья

Выдержка

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.
Язык оригиналаанглийский
ЖурналCell Systems
DOI
СостояниеЭлектронная публикация перед печатью - 16 окт 2019

Отпечаток

Biological Products
Microbiota
Peptides
Social Networking
Metagenomics
Lichens
Post Translational Protein Processing
Mass Spectrometry
Software
Genome
Anti-Bacterial Agents
Datasets

Цитировать

Cao, Liu ; Gurevich, Alexey ; Alexander, Kelsey L. ; Naman, C. Benjamin ; Leão , Tiago ; Glukhov, Evgenia ; TalLuzzatto-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. / MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. В: Cell Systems. 2019.
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title = "MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities",
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.",
keywords = "ribosomally synthesized and post-translationally modified peptides, computational mass spectrometry, Metagenomics, natural products discovery, microbial metabolites",
author = "Liu Cao and Alexey Gurevich and Alexander, {Kelsey L.} and Naman, {C. Benjamin} and Tiago Le{\~a}o and Evgenia Glukhov and Tal TalLuzzatto-Knaan and Fernando Vargas and Robby Quinn and Amina Bouslimani and Nothias, {Louis Felix} and Singh, {Nitin K.} and Sanders, {Jon G.} and Benitez, {Rodolfo A.S.} and Thompson, {Luke R.} and Md-Nafiz Hamid and Morton, {James T.} and Alla Mikheenko and Alexander Shlemov and Anton Korobeynikov and Iddo Friedberg and Rob Knight and Kasthuri Venkateswaran and Gerwick, {William H.} and Lena Gerwick and Dorrestein, {Pieter C} and Pevzner, {Pavel A.} and Hosein Mohimani",
year = "2019",
month = "10",
day = "16",
doi = "10.1016/j.cels.2019.09.004",
language = "English",
journal = "Cell Systems",
issn = "2405-4712",
publisher = "Cell Press",

}

Cao, L, Gurevich, A, Alexander, KL, Naman, CB, Leão , T, Glukhov, E, TalLuzzatto-Knaan, T, Vargas, F, Quinn, R, Bouslimani, A, Nothias, LF, Singh, NK, Sanders, JG, Benitez, RAS, Thompson, LR, Hamid, M-N, Morton, JT, Mikheenko, A, Shlemov, A, Korobeynikov, A, Friedberg, I, Knight, R, Venkateswaran, K, Gerwick, WH, Gerwick, L, Dorrestein, PC, Pevzner, PA & Mohimani, H 2019, 'MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities', Cell Systems. https://doi.org/10.1016/j.cels.2019.09.004

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 ; TalLuzzatto-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.

В: Cell Systems, 16.10.2019.

Результат исследований: Научные публикации в периодических изданияхстатья

TY - JOUR

T1 - MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities

AU - Cao, Liu

AU - Gurevich, Alexey

AU - Alexander, Kelsey L.

AU - Naman, C. Benjamin

AU - Leão , Tiago

AU - Glukhov, Evgenia

AU - TalLuzzatto-Knaan, Tal

AU - Vargas, Fernando

AU - Quinn, Robby

AU - Bouslimani, Amina

AU - Nothias, Louis Felix

AU - Singh, Nitin K.

AU - Sanders, Jon G.

AU - Benitez, Rodolfo A.S.

AU - Thompson, Luke R.

AU - Hamid, Md-Nafiz

AU - Morton, James T.

AU - Mikheenko, Alla

AU - Shlemov, Alexander

AU - Korobeynikov, Anton

AU - Friedberg, Iddo

AU - Knight, Rob

AU - Venkateswaran, Kasthuri

AU - Gerwick, William H.

AU - Gerwick, Lena

AU - Dorrestein, Pieter C

AU - Pevzner, Pavel A.

AU - Mohimani, Hosein

PY - 2019/10/16

Y1 - 2019/10/16

N2 - 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.

AB - 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.

KW - ribosomally synthesized and post-translationally modified peptides

KW - computational mass spectrometry

KW - Metagenomics

KW - natural products discovery

KW - microbial metabolites

UR - https://www.cell.com/cell-systems/fulltext/S2405-4712(19)30312-6

U2 - 10.1016/j.cels.2019.09.004

DO - 10.1016/j.cels.2019.09.004

M3 - Article

JO - Cell Systems

JF - Cell Systems

SN - 2405-4712

ER -