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Nerpa : A tool for discovering biosynthetic gene clusters of bacterial nonribosomal peptides. / Kunyavskaya, Olga; Tagirdzhanov, Azat M.; Caraballo-Rodríguez, Andrés Mauricio; Nothias, Louis Félix; Dorrestein, Pieter C.; Korobeynikov, Anton; Mohimani, Hosein; Gurevich, Alexey.

In: Metabolites, Vol. 11, No. 10, 693, 11.10.2021.

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

Harvard

Kunyavskaya, O, Tagirdzhanov, AM, Caraballo-Rodríguez, AM, Nothias, LF, Dorrestein, PC, Korobeynikov, A, Mohimani, H & Gurevich, A 2021, 'Nerpa: A tool for discovering biosynthetic gene clusters of bacterial nonribosomal peptides', Metabolites, vol. 11, no. 10, 693. https://doi.org/10.3390/metabo11100693

APA

Kunyavskaya, O., Tagirdzhanov, A. M., Caraballo-Rodríguez, A. M., Nothias, L. F., Dorrestein, P. C., Korobeynikov, A., Mohimani, H., & Gurevich, A. (2021). Nerpa: A tool for discovering biosynthetic gene clusters of bacterial nonribosomal peptides. Metabolites, 11(10), [693]. https://doi.org/10.3390/metabo11100693

Vancouver

Kunyavskaya O, Tagirdzhanov AM, Caraballo-Rodríguez AM, Nothias LF, Dorrestein PC, Korobeynikov A et al. Nerpa: A tool for discovering biosynthetic gene clusters of bacterial nonribosomal peptides. Metabolites. 2021 Oct 11;11(10). 693. https://doi.org/10.3390/metabo11100693

Author

Kunyavskaya, Olga ; Tagirdzhanov, Azat M. ; Caraballo-Rodríguez, Andrés Mauricio ; Nothias, Louis Félix ; Dorrestein, Pieter C. ; Korobeynikov, Anton ; Mohimani, Hosein ; Gurevich, Alexey. / Nerpa : A tool for discovering biosynthetic gene clusters of bacterial nonribosomal peptides. In: Metabolites. 2021 ; Vol. 11, No. 10.

BibTeX

@article{ebb3dc59833e4b1d805b99056708518c,
title = "Nerpa: A tool for discovering biosynthetic gene clusters of bacterial nonribosomal peptides",
abstract = "Microbial natural products are a major source of bioactive compounds for drug discovery. Among these molecules, nonribosomal peptides (NRPs) represent a diverse class of natural products that include antibiotics, immunosuppressants, and anticancer agents. Recent breakthroughs in natural product discovery have revealed the chemical structure of several thousand NRPs. However, biosynthetic gene clusters (BGCs) encoding them are known only for a few hundred compounds. Here, we developed Nerpa, a computational method for the high-throughput discovery of novel BGCs responsible for producing known NRPs. After searching 13,399 representative bacterial genomes from the RefSeq repository against 8368 known NRPs, Nerpa linked 117 BGCs to their prod-ucts. We further experimentally validated the predicted BGC of ngercheumicin from Photobacterium galatheae via mass spectrometry. Nerpa supports searching new genomes against thousands of known NRP structures, and novel molecular structures against tens of thousands of bacterial genomes. The availability of these tools can enhance our understanding of NRP synthesis and the function of their biosynthetic enzymes.",
keywords = "Bioinformatics, Biosynthetic gene clusters, Genome mining, Machine learning, Mass spectrometry, Natural products, Nonribosomal peptides, Software, software, MASS-SPECTROMETRY, natural products, mass spectrometry, DIVERSITY, ADENYLATION DOMAINS, RESOURCE, biosynthetic gene clusters, ANTIBIOTICS, NATURAL-PRODUCTS, machine learning, IDENTIFICATION, DATABASE SEARCH, PREDICTION, bioinformatics, POLYKETIDE, nonribosomal peptides, genome mining",
author = "Olga Kunyavskaya and Tagirdzhanov, {Azat M.} and Caraballo-Rodr{\'i}guez, {Andr{\'e}s Mauricio} and Nothias, {Louis F{\'e}lix} and Dorrestein, {Pieter C.} and Anton Korobeynikov and Hosein Mohimani and Alexey Gurevich",
note = "Publisher Copyright: {\textcopyright} 2021 by the authors. Licensee MDPI, Basel, Switzerland.",
year = "2021",
month = oct,
day = "11",
doi = "10.3390/metabo11100693",
language = "English",
volume = "11",
journal = "Metabolites",
issn = "2218-1989",
publisher = "MDPI AG",
number = "10",

}

RIS

TY - JOUR

T1 - Nerpa

T2 - A tool for discovering biosynthetic gene clusters of bacterial nonribosomal peptides

AU - Kunyavskaya, Olga

AU - Tagirdzhanov, Azat M.

AU - Caraballo-Rodríguez, Andrés Mauricio

AU - Nothias, Louis Félix

AU - Dorrestein, Pieter C.

AU - Korobeynikov, Anton

AU - Mohimani, Hosein

AU - Gurevich, Alexey

N1 - Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

PY - 2021/10/11

Y1 - 2021/10/11

N2 - Microbial natural products are a major source of bioactive compounds for drug discovery. Among these molecules, nonribosomal peptides (NRPs) represent a diverse class of natural products that include antibiotics, immunosuppressants, and anticancer agents. Recent breakthroughs in natural product discovery have revealed the chemical structure of several thousand NRPs. However, biosynthetic gene clusters (BGCs) encoding them are known only for a few hundred compounds. Here, we developed Nerpa, a computational method for the high-throughput discovery of novel BGCs responsible for producing known NRPs. After searching 13,399 representative bacterial genomes from the RefSeq repository against 8368 known NRPs, Nerpa linked 117 BGCs to their prod-ucts. We further experimentally validated the predicted BGC of ngercheumicin from Photobacterium galatheae via mass spectrometry. Nerpa supports searching new genomes against thousands of known NRP structures, and novel molecular structures against tens of thousands of bacterial genomes. The availability of these tools can enhance our understanding of NRP synthesis and the function of their biosynthetic enzymes.

AB - Microbial natural products are a major source of bioactive compounds for drug discovery. Among these molecules, nonribosomal peptides (NRPs) represent a diverse class of natural products that include antibiotics, immunosuppressants, and anticancer agents. Recent breakthroughs in natural product discovery have revealed the chemical structure of several thousand NRPs. However, biosynthetic gene clusters (BGCs) encoding them are known only for a few hundred compounds. Here, we developed Nerpa, a computational method for the high-throughput discovery of novel BGCs responsible for producing known NRPs. After searching 13,399 representative bacterial genomes from the RefSeq repository against 8368 known NRPs, Nerpa linked 117 BGCs to their prod-ucts. We further experimentally validated the predicted BGC of ngercheumicin from Photobacterium galatheae via mass spectrometry. Nerpa supports searching new genomes against thousands of known NRP structures, and novel molecular structures against tens of thousands of bacterial genomes. The availability of these tools can enhance our understanding of NRP synthesis and the function of their biosynthetic enzymes.

KW - Bioinformatics

KW - Biosynthetic gene clusters

KW - Genome mining

KW - Machine learning

KW - Mass spectrometry

KW - Natural products

KW - Nonribosomal peptides

KW - Software

KW - software

KW - MASS-SPECTROMETRY

KW - natural products

KW - mass spectrometry

KW - DIVERSITY

KW - ADENYLATION DOMAINS

KW - RESOURCE

KW - biosynthetic gene clusters

KW - ANTIBIOTICS

KW - NATURAL-PRODUCTS

KW - machine learning

KW - IDENTIFICATION

KW - DATABASE SEARCH

KW - PREDICTION

KW - bioinformatics

KW - POLYKETIDE

KW - nonribosomal peptides

KW - genome mining

UR - http://www.scopus.com/inward/record.url?scp=85117522451&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/f597c6da-a889-352b-952b-a5e1539666a8/

U2 - 10.3390/metabo11100693

DO - 10.3390/metabo11100693

M3 - Article

AN - SCOPUS:85117522451

VL - 11

JO - Metabolites

JF - Metabolites

SN - 2218-1989

IS - 10

M1 - 693

ER -

ID: 87636242