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 Félix; Singh, Nitin Kumar; 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

doi:10.1016/j.cels.2019.09.004

Cited by 57 publications

(57 citation statements)

References 68 publications

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“…The high abundance of RiPPs in the human microbiome has been reported based on genome-mining, metabolomics, and computational MS approaches (30 -35). The development of novel and efficient software tools will allow expansion of the repertoire of RiPPs from diverse microbiomes, including those with unknown posttranslational modifications (36).…”

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confidence: 99%

The manifold roles of microbial ribosomal peptide–based natural products in physiology and ecology

Rebuffat

2020

Journal of Biological Chemistry

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confidence: 99%

The manifold roles of microbial ribosomal peptide–based natural products in physiology and ecology

Rebuffat

2020

Journal of Biological Chemistry

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“…RPL24 is associated with anticancer activity [50]. In addition, ribosomal synthesis and post-translationally modi ed peptides (RiPPs) are an important family of bioactive products [51]. These ndings all support the irreplaceable role of protein malonylation in the synthesis of bioactive substances.…”

Section: Discussionmentioning

confidence: 95%

Systematic Analysis of the Lysine Malonylome in Sanghuangporus Sanghuang

Wang

Zhang

et al. 2020

Preprint

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Background: Sanghuangporus sanghuang is a well-known traditional medicinal mushroom associated with mulberry, which has enormous economic and medical value. Despite being known for many years, proteomics studies of S. sanghuang have not been reported. In this paper, a series of technologies, such as high-performance liquid chromatography (HPLC) classification technology, malonyl peptide segment enrichment technology and proteomics technology, are combined to study the qualitative analysis of malonylation in S. sanghuang.Results: Strategies for qualitative proteomics included malonyl enrichment and high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS). In total, 714 malonyl modification sites were matched to 255 different proteins. The analysis indicated that malonyl modifications are involved in a wide range of acellular functions and displayed a distinct subcellular localization.Bioinformatics analysis indicates that malonylated proteins are engaged in different metabolic pathways, including glyoxylate and dicarboxylate metabolism, glycolysis/gluconeogenesis, and the tricarboxylic acid (TCA) cycle; consequently, a total of 26 enzymes related to triterpene and polysaccharide biosynthesis were found to be malonylated.Conclusions: These findings suggest that malonylation is associated with many metabolic pathways, particularly the metabolism of bioactive compounds. This paper provides the first comprehensive survey of malonylation in S. sanghuang.

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“…Some fully automated methods exist for linking mass spectra to molecular structures, by matching structural features predicted from genomics to those inferred from metabolomics. Specifically, for non-ribosomal peptides (NRPs) there is NRPquest, 26 and for ribosomally synthesized and post-translationally modified peptides (RiPPs) there are MetaMiner 48 and DeepRiPP. 50 the type of natural products they target, they share similar principles (Fig.…”

Section: Metabologenomic Integrationmentioning

confidence: 99%