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Literature DB >> 24174214

Bioinformatics tools for genome mining of polyketide and non-ribosomal peptides.

Abstract

Microbial natural products have played a key role in the development of clinical agents in nearly all therapeutic areas. Recent advances in genome sequencing have revealed that there is an incredible wealth of new polyketide and non-ribosomal peptide natural product diversity to be mined from genetic data. The diversity and complexity of polyketide and non-ribosomal peptide biosynthesis has required the development of unique bioinformatics tools to identify, annotate, and predict the structures of these natural products from their biosynthetic gene clusters. This review highlights and evaluates web-based bioinformatics tools currently available to the natural product community for genome mining to discover new polyketides and non-ribosomal peptides.

Entities: Chemical

Mesh：

Substances：

Year: 2013 PMID： 24174214 DOI： 10.1007/s10295-013-1368-1

Source DB: PubMed Journal: J Ind Microbiol Biotechnol ISSN： 1367-5435 Impact factor: 3.346

67 in total

1. Functional analysis of environmental DNA-derived type II polyketide synthases reveals structurally diverse secondary metabolites.

Authors: Zhiyang Feng; Dimitris Kallifidas; Sean F Brady
Journal: Proc Natl Acad Sci U S A Date: 2011-07-18 Impact factor: 11.205

2. A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles.

Authors: Jörn Piel
Journal: Proc Natl Acad Sci U S A Date: 2002-10-14 Impact factor: 11.205

3. Biosynthesis of the anti-parasitic agent megalomicin: transformation of erythromycin to megalomicin in Saccharopolyspora erythraea.

Authors: Y Volchegursky; Z Hu; L Katz; R McDaniel
Journal: Mol Microbiol Date: 2000-08 Impact factor: 3.501

4. Biochemical analysis of the biosynthetic pathway of an anticancer tetracycline SF2575.

Authors: Lauren B Pickens; Woncheol Kim; Peng Wang; Hui Zhou; Kenji Watanabe; Shuichi Gomi; Yi Tang
Journal: J Am Chem Soc Date: 2009-12-09 Impact factor: 15.419

5. Chirality of peptide bond-forming condensation domains in nonribosomal peptide synthetases: the C5 domain of tyrocidine synthetase is a (D)C(L) catalyst.

Authors: Susan L Clugston; Stephan A Sieber; Mohamed A Marahiel; Christopher T Walsh
Journal: Biochemistry Date: 2003-10-21 Impact factor: 3.162

6. Emergent gene order in a model of modular polyketide synthases.

Authors: Benjamin Callahan; Mukund Thattai; Boris I Shraiman
Journal: Proc Natl Acad Sci U S A Date: 2009-10-28 Impact factor: 11.205

7. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

Authors: Marnix H Medema; Kai Blin; Peter Cimermancic; Victor de Jager; Piotr Zakrzewski; Michael A Fischbach; Tilmann Weber; Eriko Takano; Rainer Breitling
Journal: Nucleic Acids Res Date: 2011-06-14 Impact factor: 16.971

8. Towards prediction of metabolic products of polyketide synthases: an in silico analysis.

Authors: Gitanjali Yadav; Rajesh S Gokhale; Debasisa Mohanty
Journal: PLoS Comput Biol Date: 2009-04-10 Impact factor: 4.475

9. SMART 6: recent updates and new developments.

Authors: Ivica Letunic; Tobias Doerks; Peer Bork
Journal: Nucleic Acids Res Date: 2008-10-31 Impact factor: 16.971

10. In silico analysis of methyltransferase domains involved in biosynthesis of secondary metabolites.

Authors: Mohd Zeeshan Ansari; Jyoti Sharma; Rajesh S Gokhale; Debasisa Mohanty
Journal: BMC Bioinformatics Date: 2008-10-25 Impact factor: 3.169

36 in total

Review 1. Genetic manipulation of secondary metabolite biosynthesis for improved production in Streptomyces and other actinomycetes.

Authors: Richard H Baltz
Journal: J Ind Microbiol Biotechnol Date: 2015-09-12 Impact factor: 3.346

2. Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors.

Authors: Jeremy G Owen; Zachary Charlop-Powers; Alexandra G Smith; Melinda A Ternei; Paula Y Calle; Boojala Vijay B Reddy; Daniel Montiel; Sean F Brady
Journal: Proc Natl Acad Sci U S A Date: 2015-03-23 Impact factor: 11.205

3. MbtH homology codes to identify gifted microbes for genome mining.

Authors: Richard H Baltz
Journal: J Ind Microbiol Biotechnol Date: 2013-11-07 Impact factor: 3.346

4. Discovery of the Tiancilactone Antibiotics by Genome Mining of Atypical Bacterial Type II Diterpene Synthases.

Authors: Liao-Bin Dong; Jeffrey D Rudolf; Ming-Rong Deng; Xiaohui Yan; Ben Shen
Journal: Chembiochem Date: 2018-05-27 Impact factor: 3.164

5. Computational structural enzymology methodologies for the study and engineering of fatty acid synthases, polyketide synthases and nonribosomal peptide synthetases.

Authors: Andrew J Schaub; Gabriel O Moreno; Shiji Zhao; Hau V Truong; Ray Luo; Shiou-Chuan Tsai
Journal: Methods Enzymol Date: 2019-04-22 Impact factor: 1.600