Genome mining strategies for ribosomally synthesised and post-translationally modified peptides

Russell, Alicia H; Truman, Andrew W.

doi:10.1016/j.csbj.2020.06.032

Cited by 77 publications

(64 citation statements)

References 110 publications

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“…RiPPs are grouped into families on the basis of their structural features and post-translational modifications (Funk and van der Donk, 2017). Several bioinformatic tools have been developed for the automatic recognition of RiPP BGCs in microbial genomes, which are usually based on recognizing elements, such as leader peptides or diagnostic RiPP-processing enzymes (Russell and Truman, 2020).…”

Section: Introductionmentioning

confidence: 99%

A biaryl-linked tripeptide from Planomonospora reveals a widespread class of minimal RiPP gene clusters

Zdouc

Alanjary

Zarazúa

et al. 2021

Cell Chemical Biology

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This article is made publicly available in the institutional repository of Wageningen University and Research, under the terms of article 25fa of the Dutch Copyright Act, also known as the Amendment Taverne. This has been done with explicit consent by the author.Article 25fa states that the author of a short scientific work funded either wholly or partially by Dutch public funds is entitled to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work.This publication is distributed under The Association of Universities in the Netherlands (VSNU) 'Article 25fa implementation' project. In this project research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication.You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and / or copyright owner(s) of this work. Any use of the publication or parts of it other than authorised under article 25fa of the Dutch Copyright act is prohibited. Wageningen University & Research and the author(s) of this publication shall not be held responsible or liable for any damages resulting from your (re)use of this publication.

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Section: Introductionmentioning

confidence: 99%

A biaryl-linked tripeptide from Planomonospora reveals a widespread class of minimal RiPP gene clusters

Zdouc

Alanjary

Zarazúa

et al. 2021

Cell Chemical Biology

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“…Benefited from rapid progress on DNA sequencing technology, in silico mining of genomes combined with molecular biology approaches has guided the discovery of a large number of new RiPPs natural products. In general, various algorithms, including antiSMASH, RiPPMiner, BAGEL4, RiPPER, and RiPP-PRISM can be used for mining the RiPP BGCs (Velasquez and Van der Donk, 2011 ; Poorinmohammad et al, 2019 ; Russell and Truman, 2020 ; Zhong et al, 2020 ). The most important characteristic of sactipeptide biosynthesis is the presence of radical SAM enzyme sactisynthase, which will direct the promising way for genome-mining discovery of sactipeptide.…”

Section: Distributions Of Sactipeptidesmentioning

confidence: 99%

Current Advancements in Sactipeptide Natural Products

Chen

Wang

et al. 2021

Front. Chem.

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Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing class of natural products that benefited from genome sequencing technology in the past two decades. RiPPs are widely distributed in nature and show diverse chemical structures and rich biological activities. Despite the various structural characteristic of RiPPs, they follow a common biosynthetic logic: a precursor peptide containing an N-terminal leader peptide and a C-terminal core peptide; in some cases,a follower peptide is after the core peptide. The precursor peptide undergoes a series of modification, transport, and cleavage steps to form a mature natural product with specific activities. Sactipeptides (Sulfur-to-alpha carbon thioether cross-linked peptides) belong to RiPPs that show various biological activities such as antibacterial, spermicidal and hemolytic properties. Their common hallmark is an intramolecular thioether bond that crosslinks the sulfur atom of a cysteine residue to the α-carbon of an acceptor amino acid, which is catalyzed by a rSAM enzyme. This review summarizes recent achievements concerning the discovery, distribution, structural elucidation, biosynthesis and application prospects of sactipeptides.

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“…Several widely used online platforms are still in active development, as listed in Table 1. Many of these selected tools have been extensively reviewed [21,[28][29][30][31][32][33][34]. Streptocollin [46], stackepeptins [47], bicereucin [48], curacozole [49], and lexapeptide [50] (Figure 1) are the recent examples of RiPPs in which their BGCs were discovered using the genome mining approach.…”

Section: Genome Mining Approachmentioning

confidence: 99%

“…Several widely used online platforms are still in active development, as listed in Table 1 . Many of these selected tools have been extensively reviewed [ 21 , 28 , 29 , 30 , 31 , 32 , 33 , 34 ].…”

Section: Bioinformatics- and Genomics-driven Discoverymentioning

confidence: 99%

Recent Advances in Discovery of Lead Structures from Microbial Natural Products: Genomics- and Metabolomics-Guided Acceleration

Sukmarini

2021

Molecules

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Natural products (NPs) are evolutionarily optimized as drug-like molecules and remain the most consistently successful source of drugs and drug leads. They offer major opportunities for finding novel lead structures that are active against a broad spectrum of assay targets, particularly those from secondary metabolites of microbial origin. Due to traditional discovery approaches’ limitations relying on untargeted screening methods, there is a growing trend to employ unconventional secondary metabolomics techniques. Aided by the more in-depth understanding of different biosynthetic pathways and the technological advancement in analytical instrumentation, the development of new methodologies provides an alternative that can accelerate discoveries of new lead-structures of natural origin. This present mini-review briefly discusses selected examples regarding advancements in bioinformatics and genomics (focusing on genome mining and metagenomics approaches), as well as bioanalytics (mass-spectrometry) towards the microbial NPs-based drug discovery and development. The selected recent discoveries from 2015 to 2020 are featured herein.

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Genome mining strategies for ribosomally synthesised and post-translationally modified peptides

Abstract: Graphical abstract

Cited by 77 publications

References 110 publications

A biaryl-linked tripeptide from Planomonospora reveals a widespread class of minimal RiPP gene clusters

A biaryl-linked tripeptide from Planomonospora reveals a widespread class of minimal RiPP gene clusters

Current Advancements in Sactipeptide Natural Products

Recent Advances in Discovery of Lead Structures from Microbial Natural Products: Genomics- and Metabolomics-Guided Acceleration

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