HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search

Lee, Yi-Yuan; Guler, Mustafa; Chigumba, Desnor N.; Wang, Shen; Mittal, Neel; Miller, Cameron; Krummenacher, Benjamin; Liu, Haodong; Cao, Liu; Kannan, Aditya; Narayan, Keshav; Slocum, Samuel T.; Roth, Bryan L.; Gurevich, Alexey; Behsaz, Bahar; Kersten, Roland D.; Mohimani, Hosein

doi:10.1038/s41467-023-39905-4

Title: HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search

Journal Article · 14 July 2023 · Nature Communications

DOI: https://doi.org/10.1038/s41467-023-39905-4 · OSTI ID:1989754

;

; Chigumba, Desnor N.; Wang, Shen; Mittal, Neel; Miller, Cameron; Krummenacher, Benjamin; Liu, Haodong;

;

; Narayan, Keshav; Slocum, Samuel T.;

;

; Behsaz, Bahar; Kersten, Roland D.;

Abstract Recent analyses of public microbial genomes have found over a million biosynthetic gene clusters, the natural products of the majority of which remain unknown. Additionally, GNPS harbors billions of mass spectra of natural products without known structures and biosynthetic genes. We bridge the gap between large-scale genome mining and mass spectral datasets for natural product discovery by developing HypoRiPPAtlas, an Atlas of hypothetical natural product structures, which is ready-to-use for in silico database search of tandem mass spectra. HypoRiPPAtlas is constructed by mining genomes using seq2ripp, a machine-learning tool for the prediction of ribosomally synthesized and post-translationally modified peptides (RiPPs). In HypoRiPPAtlas, we identify RiPPs in microbes and plants. HypoRiPPAtlas could be extended to other natural product classes in the future by implementing corresponding biosynthetic logic. This study paves the way for large-scale explorations of biosynthetic pathways and chemical structures of microbial and plant RiPP classes.

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Sponsoring Organization:: USDOE

Grant/Contract Number:: NONE; SC0021340

OSTI ID:: 1989754

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 14; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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