NRPquest: Coupling mass spectrometry and genome mining for nonribosomal peptide discovery

TitleNRPquest: Coupling mass spectrometry and genome mining for nonribosomal peptide discovery
Publication TypeJournal Article
Year of Publication2014
AuthorsMohimani H., Liu W.T, Kersten RD, Moore BS, Dorrestein PC, Pevzner P.A
JournalJournal of Natural Products
Volume77
Pagination1902-1909
Date Published2014/08
Type of ArticleArticle
ISBN Number0163-3864
Accession NumberWOS:000340861800019
Keywordsadenylation domains; antibiotics; bacillus-subtilis; biosynthesis; cyanobacterium; gene clusters; natural-products; protein identification; search; structure elucidation; tyrocidine
Abstract

Nonribosomal peptides (NRPs) such as vancomycin and daptomycin are among the most effective antibiotics. While NRPs are biomedically important, the computational techniques for sequencing these peptides are still in their infancy. The recent emergence of mass spectrometry techniques for NRP analysis (capable of sequencing an NRP from small amounts of nonpurified material) revealed an enormous diversity of NRPs. However, as many NRPs have nonlinear structure (e.g., cyclic or branched-cyclic peptides), the standard de novo sequencing tools (developed for linear peptides) are not applicable to NRP analysis. Here, we introduce the first NRP identification algorithm, NRPquest, that performs mutation-tolerant and modification-tolerant searches of spectral data sets against a database of putative NRPs. In contrast to previous studies aimed at NRP discovery (that usually report very few NRPs), NRPquest revealed nearly a hundred NRPs (including unknown variants of previously known peptides) in a single study. This result indicates that NRPquest can potentially make MS-based NRP identification as robust as the identification of linear peptides in traditional proteomics.

DOI10.1021/np500370c
Short TitleJ. Nat. Prod.
Integrated Research Themes: 
Student Publication: 
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