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 Luzzatto-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 Korobeynikov; Iddo Friedberg; Rob Knight; Kasthuri Venkateswaran; William H. Gerwick; Lena Gerwick; Pieter C. Dorrestein; Pavel A. Pevzner; Hosein Mohimani

doi: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

Liu Cao, Alexey Gurevich, Kelsey L. Alexander, C. Benjamin Naman, Tiago Leão, Evgenia Glukhov, Tal Luzzatto-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

Research output: Contribution to journal › Article › peer-review

Abstract

We have developed an efficient method for discovering ribosomally synthesized and post-translationally modified peptides with unknown post-translational modifications from microbial communities through the database search of mass spectra against peptides predicted by genome or metagenome mining. Searching eight datasets collected from various environments—including human microbiome, marine cyanobacteria, and International Space Station—resulted in the discovery of seven unknown RiPPs.

Original language	English
Pages (from-to)	600-608.e4
Journal	Cell Systems
Volume	9
Issue number	6
DOIs	https://doi.org/10.1016/j.cels.2019.09.004
State	Published - 18 Dec 2019
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2019 Elsevier Inc.

Keywords

computational mass spectrometry
metagenomics
microbial metabolites
natural products discovery
ribosomally synthesized and post-translationally modified peptides

ASJC Scopus subject areas

Pathology and Forensic Medicine
Histology
Cell Biology

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10.1016/j.cels.2019.09.004

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Cao, L., Gurevich, A., Alexander, K. L., Naman, C. B., Leão, T., Glukhov, E., Luzzatto-Knaan, T., Vargas, F., Quinn, R., Bouslimani, A., Nothias, L. F., Singh, N. K., Sanders, J. G., Benitez, R. A. S., Thompson, L. R., Hamid, M. N., Morton, J. T., Mikheenko, A., Shlemov, A., ... Mohimani, H. (2019). MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. Cell Systems, 9(6), 600-608.e4. https://doi.org/10.1016/j.cels.2019.09.004

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

abstract = "We have developed an efficient method for discovering ribosomally synthesized and post-translationally modified peptides with unknown post-translational modifications from microbial communities through the database search of mass spectra against peptides predicted by genome or metagenome mining. Searching eight datasets collected from various environments—including human microbiome, marine cyanobacteria, and International Space Station—resulted in the discovery of seven unknown RiPPs.",

keywords = "computational mass spectrometry, metagenomics, microbial metabolites, natural products discovery, ribosomally synthesized and post-translationally modified peptides",

author = "Liu Cao and Alexey Gurevich and Alexander, {Kelsey L.} and Naman, {C. Benjamin} and Tiago Le{\~a}o and Evgenia Glukhov and Tal Luzzatto-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 Hamid, {Md Nafiz} 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",

note = "Publisher Copyright: {\textcopyright} 2019 Elsevier Inc.",

year = "2019",

month = dec,

day = "18",

doi = "10.1016/j.cels.2019.09.004",

language = "English",

volume = "9",

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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 2019, 'MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities', Cell Systems, vol. 9, no. 6, pp. 600-608.e4. https://doi.org/10.1016/j.cels.2019.09.004

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T1 - MetaMiner

T2 - 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 - Luzzatto-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 - 2019/12/18

Y1 - 2019/12/18

N2 - We have developed an efficient method for discovering ribosomally synthesized and post-translationally modified peptides with unknown post-translational modifications from microbial communities through the database search of mass spectra against peptides predicted by genome or metagenome mining. Searching eight datasets collected from various environments—including human microbiome, marine cyanobacteria, and International Space Station—resulted in the discovery of seven unknown RiPPs.

AB - We have developed an efficient method for discovering ribosomally synthesized and post-translationally modified peptides with unknown post-translational modifications from microbial communities through the database search of mass spectra against peptides predicted by genome or metagenome mining. Searching eight datasets collected from various environments—including human microbiome, marine cyanobacteria, and International Space Station—resulted in the discovery of seven unknown RiPPs.

KW - computational mass spectrometry

KW - metagenomics

KW - microbial metabolites

KW - natural products discovery

KW - ribosomally synthesized and post-translationally modified peptides

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DO - 10.1016/j.cels.2019.09.004

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AN - SCOPUS:85076261727

SN - 2405-4712

VL - 9

SP - 600-608.e4

JO - Cell Systems

JF - Cell Systems

IS - 6

ER -

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

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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