Genome plasticity and systems evolution in Streptomyces

BMC Bioinformatics

Proceedings

Yong-Quan Li¹  Zhan Zhou²  Jianying Gu³  Yufeng Wang⁴ 

[1] College of Life Sciences, Zhejiang University, 310058, Hangzhou, P. R. China;College of Life Sciences, Zhejiang University, 310058, Hangzhou, P. R. China;Department of Biology, University of Texas at San Antonio, 78249, San Antonio, TX, USA;Department of Biology, College of Staten Island, City University of New York, 10314, Staten Island, NY, USA;Department of Biology, University of Texas at San Antonio, 78249, San Antonio, TX, USA;South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, 78249, San Antonio, TX, USA;

关键词: Streptomyces;    Secondary Metabolism;    Sigma Factor;    Lateral Gene Transfer;    Core Genome;   

DOI  :  10.1186/1471-2105-13-S10-S8

来源: Springer

【 摘 要 】

BackgroundStreptomycetes are filamentous soil-dwelling bacteria. They are best known as the producers of a great variety of natural products such as antibiotics, antifungals, antiparasitics, and anticancer agents and the decomposers of organic substances for carbon recycling. They are also model organisms for the studies of gene regulatory networks, morphological differentiation, and stress response. The availability of sets of genomes from closely related Streptomyces strains makes it possible to assess the mechanisms underlying genome plasticity and systems adaptation.ResultsWe present the results of a comprehensive analysis of the genomes of five Streptomyces species with distinct phenotypes. These streptomycetes have a pan-genome comprised of 17,362 orthologous families which includes 3,096 components in the core genome, 5,066 components in the dispensable genome, and 9,200 components that are uniquely present in only one species. The core genome makes up about 33%-45% of each genome repertoire. It contains important genes for Streptomyces biology including those involved in gene regulation, secretion, secondary metabolism and morphological differentiation. Abundant duplicate genes have been identified, with 4%-11% of the whole genomes composed of lineage-specific expansions (LSEs), suggesting that frequent gene duplication or lateral gene transfer events play a role in shaping the genome diversification within this genus. Two patterns of expansion, single gene expansion and chromosome block expansion are observed, representing different scales of duplication.ConclusionsOur results provide a catalog of genome components and their potential functional roles in gene regulatory networks and metabolic networks. The core genome components reveal the minimum requirement for streptomycetes to sustain a successful lifecycle in the soil environment, reflecting the effects of both genome evolution and environmental stress acting upon the expressed phenotypes. A better understanding of the LSE gene families will, on the other hand, bring a wealth of new insights into the mechanisms underlying strain-specific phenotypes, such as the production of novel antibiotics, pathogenesis, and adaptive response to environmental challenges.

【 授权许可】

Unknown   
© Zhou et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.