Genome plasticity and systems evolution in Streptomyces.
Genome plasticity and systems evolution in Streptomyces.
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链霉菌的基因组可塑性和系统进化
DOI：
10.1186/1471-2105-13-s10-s8
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发表时间：
2012-06-25
影响因子：
3
通讯作者：
Wang Y
中科院分区：
文献类型：
--
作者：
Zhou Z;Gu J;Li YQ;Wang Y
链霉菌是一种丝状土壤细菌。他们最出名的是各种天然产品的生产商，如抗生素、抗真菌药物、抗寄生虫剂和抗癌剂，以及碳循环有机物质的分解者。它们也是研究基因调控网络、形态分化和胁迫反应的模式生物。从密切相关的链霉菌菌株获得的基因组组使评估基因组可塑性和系统适应的机制成为可能。我们给出了具有不同表型的五种链霉菌基因组的综合分析结果。这些链霉菌有一个由17,362个同源家族组成的泛基因组，其中包括核心基因组中的3,096个组分，非必需基因组中的5,066个组分，以及仅在一个物种中唯一存在的9,200个组分。核心基因组约占每个基因组谱系的33%-45%。它包含链霉菌生物学的重要基因，包括参与基因调节、分泌、次生代谢和形态分化的基因。大量的重复基因已被鉴定出来，其中4%-11%的基因组由谱系特异性扩展(LSE)组成，这表明频繁的基因重复或横向基因转移事件在塑造该属基因组多样性方面发挥了作用。观察到两种扩展模式，单基因扩展和染色体块扩展，代表不同规模的复制。我们的结果提供了基因组组成及其在基因调控网络和代谢网络中的潜在功能作用的目录。核心基因组组分揭示了链霉菌在土壤环境中维持成功生命周期的最低要求，反映了基因组进化和环境胁迫对所表达表型的影响。另一方面，更好地了解LSE基因家族将为菌株特异性表型的潜在机制带来丰富的新见解，如新抗生素的产生、发病机制和对环境挑战的适应性反应。
Streptomycetes 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. We 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. Our 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.