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Genome mining strategies for ribosomally synthesised and post-translationally modified peptides
- Source :
- Computational and Structural Biotechnology Journal, Computational and Structural Biotechnology Journal, Vol 18, Iss, Pp 1838-1851 (2020)
- Publication Year :
- 2020
- Publisher :
- Research Network of Computational and Structural Biotechnology, 2020.
-
Abstract
- Graphical abstract<br />Genome mining is a computational method for the automatic detection and annotation of biosynthetic gene clusters (BGCs) from genomic data. This approach has been increasingly utilised in natural product (NP) discovery due to the large amount of sequencing data that is now available. Ribosomally synthesised and post-translationally modified peptides (RiPPs) are a class of structurally complex NP with diverse bioactivities. RiPPs have recently been shown to occupy a much larger expanse of genomic and chemical space than previously appreciated, indicating that annotation of RiPP BGCs in genomes may have been overlooked in the past. This review provides an overview of the genome mining tools that have been specifically developed to aid in the discovery of RiPP BGCs, which have been built from an increasing knowledgebase of RiPP structures and biosynthesis. Given these recent advances, the application of targeted genome mining has great potential to accelerate the discovery of important molecules such as antimicrobial and anticancer agents whilst increasing our understanding about how these compounds are biosynthesised in nature.
- Subjects :
- PTM, post-translational modification
Bioinformatics
Genomic data
lcsh:Biotechnology
Sequencing data
Biophysics
Computational biology
Review Article
Biology
Biosynthesis
Biochemistry
Genome
Natural product
03 medical and health sciences
RiPP, Ribosomally synthesised and post-translationally modified peptide
0302 clinical medicine
ORF, open reading frame
Structural Biology
lcsh:TP248.13-248.65
Genome mining
Genetics
RiPP
Gene
030304 developmental biology
ComputingMethodologies_COMPUTERGRAPHICS
0303 health sciences
Antibiotic
BGC, biosynthetic gene cluster
Chemical space
Computer Science Applications
MS, mass spectrometry
HMM, hidden Markov model
030220 oncology & carcinogenesis
NP, natural product
DNN, deep neural network
Biotechnology
RTE, RiPP tailoring enzyme
Subjects
Details
- Language :
- English
- ISSN :
- 20010370
- Volume :
- 18
- Database :
- OpenAIRE
- Journal :
- Computational and Structural Biotechnology Journal
- Accession number :
- edsair.doi.dedup.....630c50f0b73e2f64ca715dc5ce82329e