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

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 languageEnglish
Pages (from-to)600-608.e4
Number of pages13
JournalCell Systems
Volume9
Issue number6
Early online date16 Oct 2019
DOIs
Publication statusPublished - 18 Dec 2019

Fingerprint

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

Scopus subject areas

  • Pathology and Forensic Medicine
  • Histology
  • Cell Biology

Cite this

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. / MetaMiner : A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. In: Cell Systems. 2019 ; Vol. 9, No. 6. pp. 600-608.e4.
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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.",
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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",
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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, 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; 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.

In: Cell Systems, Vol. 9, No. 6, 18.12.2019, p. 600-608.e4.

Research output

TY - JOUR

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

UR - http://www.scopus.com/inward/record.url?scp=85076261727&partnerID=8YFLogxK

UR - http://www.mendeley.com/research/metaminer-scalable-peptidogenomics-approach-discovery-ribosomal-peptide-natural-products-blind-modif

U2 - 10.1016/j.cels.2019.09.004

DO - 10.1016/j.cels.2019.09.004

M3 - Article

C2 - 31629686

VL - 9

SP - 600-608.e4

JO - Cell Systems

JF - Cell Systems

SN - 2405-4712

IS - 6

ER -