Databases of the Thiotemplate Modular Systems (CSDB) and Their in Silico Recombinants (r-CSDB)

Overview

Journal J Ind Microbiol Biotechnol

Publisher Oxford University Press

Specialty Biotechnology

Date 2013 Mar 19

PMID 23504028

Citations 9

Authors

Janko Diminic

Jurica Zucko

Ida Trninic Ruzic

Ranko Gacesa

Daslav Hranueli

Paul F Long

John Cullum

Antonio Starcevic

Affiliations

Soon will be listed here.

Abstract

Modular biosynthetic clusters are responsible for the synthesis of many important pharmaceutical products. They include polyketide synthases (PKS clusters), non-ribosomal synthetases (NRPS clusters), and mixed clusters (containing both PKS and NRPS modules). The ClustScan database (CSDB) contains highly annotated descriptions of 170 clusters. The database has a hierarchical organization, which allows easy extraction of DNA and protein sequences of polypeptides, modules, and domains as well as an organization of the annotation so as to be able to predict the product chemistry to view it or export it in a standard SMILES format. The recombinant ClustScan database contains information about predicted recombinants between PKS clusters. The recombinants are generated by modeling homologous recombination and are associated with annotation and prediction of product chemistry automatically generated by the model. The database contains over 20,000 recombinants and is a resource for in silico approaches to detecting promising new compounds. Methods are available to construct the corresponding recombinants in the laboratory.

Citing Articles

Phylogenetic classification of natural product biosynthetic gene clusters based on regulatory mechanisms.

Rodriguez-Sanchez A, Gonzalez-Salazar L, Rodriguez-Orduna L, Cumsille A, Undabarrena A, Camara B Front Microbiol. 2023; 14:1290473.

PMID: 38029100 PMC: 10663231. DOI: 10.3389/fmicb.2023.1290473.

Genomic mining and diversity of assembly line polyketide synthases.

Kishore S, Khosla C Open Biol. 2023; 13(8):230096.

PMID: 37528731 PMC: 10394414. DOI: 10.1098/rsob.230096.

Acyltransferases as Tools for Polyketide Synthase Engineering.

Musiol-Kroll E, Wohlleben W Antibiotics (Basel). 2018; 7(3).

PMID: 30022008 PMC: 6164871. DOI: 10.3390/antibiotics7030062.

The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production.

Weber T, Kim H Synth Syst Biotechnol. 2017; 1(2):69-79.

PMID: 29062930 PMC: 5640684. DOI: 10.1016/j.synbio.2015.12.002.

Computational approaches to natural product discovery.

Medema M, Fischbach M Nat Chem Biol. 2015; 11(9):639-48.

PMID: 26284671 PMC: 5024737. DOI: 10.1038/nchembio.1884.

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