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Automated genome mining of ribosomal peptide natural products.

Mohimani H, Kersten RD, Liu WT, Wang M, Purvine SO, Wu S, Brewer HM, Pasa-Tolic L, Bandeira N, Moore BS, Pevzner PA, Dorrestein PC - ACS Chem. Biol. (2014)

Bottom Line: Ribosomally synthesized and posttranslationally modified peptides (RiPPs), especially from microbial sources, are a large group of bioactive natural products that are a promising source of new (bio)chemistry and bioactivity.1 In light of exponentially increasing microbial genome databases and improved mass spectrometry (MS)-based metabolomic platforms, there is a need for computational tools that connect natural product genotypes predicted from microbial genome sequences with their corresponding chemotypes from metabolomic data sets.RiPPquest uses genomics to limit search space to the vicinity of RiPP biosynthetic genes and proteomics to analyze extensive peptide modifications and compute p-values of peptide-spectrum matches (PSMs).The presented tool is available at cyclo.ucsd.edu.

View Article: PubMed Central - PubMed

Affiliation: Department of Electrical and Computer Engineering, University of California San Diego , La Jolla, California 92093, United States.

ABSTRACT
Ribosomally synthesized and posttranslationally modified peptides (RiPPs), especially from microbial sources, are a large group of bioactive natural products that are a promising source of new (bio)chemistry and bioactivity.1 In light of exponentially increasing microbial genome databases and improved mass spectrometry (MS)-based metabolomic platforms, there is a need for computational tools that connect natural product genotypes predicted from microbial genome sequences with their corresponding chemotypes from metabolomic data sets. Here, we introduce RiPPquest, a tandem mass spectrometry database search tool for identification of microbial RiPPs, and apply it to lanthipeptide discovery. RiPPquest uses genomics to limit search space to the vicinity of RiPP biosynthetic genes and proteomics to analyze extensive peptide modifications and compute p-values of peptide-spectrum matches (PSMs). We highlight RiPPquest by connecting multiple RiPPs from extracts of Streptomyces to their gene clusters and by the discovery of a new class III lanthipeptide, informatipeptin, from Streptomyces viridochromogenes DSM 40736 to reflect that it is a natural product that was discovered by mass spectrometry based genome mining using algorithmic tools rather than manual inspection of mass spectrometry data and genetic information. The presented tool is available at cyclo.ucsd.edu.

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Characterizationof class III lanthipeptide informatipeptin from Streptomycesviridochromogenes DSM 40736 by RiPPquest. (a)PSM of informatipeptin. (b) Gene cluster analysis of informatipeptin.(c) Predicted structures of informatipeptin. Abbreviation: N/A = notannotated.
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fig2: Characterizationof class III lanthipeptide informatipeptin from Streptomycesviridochromogenes DSM 40736 by RiPPquest. (a)PSM of informatipeptin. (b) Gene cluster analysis of informatipeptin.(c) Predicted structures of informatipeptin. Abbreviation: N/A = notannotated.

Mentions: In addition to known lanthipeptides, RiPPquestyielded a PSM of an unknown lanthipeptide from LC-MS/MS data of an n-butanol extract of S. viridochromogenes DSM 40736, which was previously inspected manually11(Figure 2A). Analysis of the correspondinggene cluster of the identified peptide revealed a lanthionine synthetaseSSQG_07268, which lacks zinc ligand residues and thus indicates aclass III lanthipeptide (Figure 2B, SI Table S2). We termed the new peptide informatipeptin,as it is the first natural product chemotype to be connected to itsgenotype in a microbial genome sequence by a genome mining algorithm.From FT-MS/MS analysis and sequence similarity to other class IIIlanthipeptides from S. chartreusis, S. erythraea, C. acidiphila, S. coelicolor,and S. griseus (SI Figures S5and S6), we deduced that the Ser21/Ser24/Cys28-motif and theSer30/Ser33/Cys37-motif are converted to either labionin or lanthionine.This leaves us with four structural candidates of two lanthionines,two labionins, or one lanthionine and one labionin in the peptide(Figure 2C). Based on the closest sequencesimilarity to avermipeptins from S. avermitilis andtheir characterized one lanthionine-one labionin modification,26 we predict the same Lan/Lab ratio in informatipeptin.The fact that RiPPquest found all these peptides, including a newlanthipeptide in a single study illustrates the power of automatedpeptidogenomics for RiPP studies and that natural products can bediscovered informatically.


Automated genome mining of ribosomal peptide natural products.

Mohimani H, Kersten RD, Liu WT, Wang M, Purvine SO, Wu S, Brewer HM, Pasa-Tolic L, Bandeira N, Moore BS, Pevzner PA, Dorrestein PC - ACS Chem. Biol. (2014)

Characterizationof class III lanthipeptide informatipeptin from Streptomycesviridochromogenes DSM 40736 by RiPPquest. (a)PSM of informatipeptin. (b) Gene cluster analysis of informatipeptin.(c) Predicted structures of informatipeptin. Abbreviation: N/A = notannotated.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4215869&req=5

fig2: Characterizationof class III lanthipeptide informatipeptin from Streptomycesviridochromogenes DSM 40736 by RiPPquest. (a)PSM of informatipeptin. (b) Gene cluster analysis of informatipeptin.(c) Predicted structures of informatipeptin. Abbreviation: N/A = notannotated.
Mentions: In addition to known lanthipeptides, RiPPquestyielded a PSM of an unknown lanthipeptide from LC-MS/MS data of an n-butanol extract of S. viridochromogenes DSM 40736, which was previously inspected manually11(Figure 2A). Analysis of the correspondinggene cluster of the identified peptide revealed a lanthionine synthetaseSSQG_07268, which lacks zinc ligand residues and thus indicates aclass III lanthipeptide (Figure 2B, SI Table S2). We termed the new peptide informatipeptin,as it is the first natural product chemotype to be connected to itsgenotype in a microbial genome sequence by a genome mining algorithm.From FT-MS/MS analysis and sequence similarity to other class IIIlanthipeptides from S. chartreusis, S. erythraea, C. acidiphila, S. coelicolor,and S. griseus (SI Figures S5and S6), we deduced that the Ser21/Ser24/Cys28-motif and theSer30/Ser33/Cys37-motif are converted to either labionin or lanthionine.This leaves us with four structural candidates of two lanthionines,two labionins, or one lanthionine and one labionin in the peptide(Figure 2C). Based on the closest sequencesimilarity to avermipeptins from S. avermitilis andtheir characterized one lanthionine-one labionin modification,26 we predict the same Lan/Lab ratio in informatipeptin.The fact that RiPPquest found all these peptides, including a newlanthipeptide in a single study illustrates the power of automatedpeptidogenomics for RiPP studies and that natural products can bediscovered informatically.

Bottom Line: Ribosomally synthesized and posttranslationally modified peptides (RiPPs), especially from microbial sources, are a large group of bioactive natural products that are a promising source of new (bio)chemistry and bioactivity.1 In light of exponentially increasing microbial genome databases and improved mass spectrometry (MS)-based metabolomic platforms, there is a need for computational tools that connect natural product genotypes predicted from microbial genome sequences with their corresponding chemotypes from metabolomic data sets.RiPPquest uses genomics to limit search space to the vicinity of RiPP biosynthetic genes and proteomics to analyze extensive peptide modifications and compute p-values of peptide-spectrum matches (PSMs).The presented tool is available at cyclo.ucsd.edu.

View Article: PubMed Central - PubMed

Affiliation: Department of Electrical and Computer Engineering, University of California San Diego , La Jolla, California 92093, United States.

ABSTRACT
Ribosomally synthesized and posttranslationally modified peptides (RiPPs), especially from microbial sources, are a large group of bioactive natural products that are a promising source of new (bio)chemistry and bioactivity.1 In light of exponentially increasing microbial genome databases and improved mass spectrometry (MS)-based metabolomic platforms, there is a need for computational tools that connect natural product genotypes predicted from microbial genome sequences with their corresponding chemotypes from metabolomic data sets. Here, we introduce RiPPquest, a tandem mass spectrometry database search tool for identification of microbial RiPPs, and apply it to lanthipeptide discovery. RiPPquest uses genomics to limit search space to the vicinity of RiPP biosynthetic genes and proteomics to analyze extensive peptide modifications and compute p-values of peptide-spectrum matches (PSMs). We highlight RiPPquest by connecting multiple RiPPs from extracts of Streptomyces to their gene clusters and by the discovery of a new class III lanthipeptide, informatipeptin, from Streptomyces viridochromogenes DSM 40736 to reflect that it is a natural product that was discovered by mass spectrometry based genome mining using algorithmic tools rather than manual inspection of mass spectrometry data and genetic information. The presented tool is available at cyclo.ucsd.edu.

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