Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora
Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora
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DOI：
10.1073/pnas.1324161111
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发表时间：
2014-03-25
影响因子：
11.1
通讯作者：
Jensen, Paul Robert
中科院分区：
文献类型：
--
作者：
Ziemert, Nadine;Lechner, Anna;Jensen, Paul Robert
基因组序列数据的获取挑战了传统的天然产物发现范式，揭示了大多数细菌生物合成途径的产物尚未被发现。尽管这项技术提供了深刻的见解，但人们对细菌中天然产物生物合成途径的多样性和分布以及它们如何进化以产生结构多样性知之甚少。在这里，我们分析来自75株海洋放线菌属Salinispora的基因组序列数据与聚酮化合物和非核糖体肽的生物合成，其产品占一些今天最重要的药物的途径。结果显示了高水平的多样性，共鉴定了124种途径，并通过持续测序预测了229种途径。最近的水平基因转移占大多数的途径，这只发生在一个或两个菌株。获得的途径被整合到基因组岛中，并且通常在物种内和物种之间交换。获取和转移事件在很大程度上涉及完整的途径，随后通过基因获得、丢失和复制以及分歧而进化。在不同菌株中，在精确的染色体位置上交换相似的途径类型表明整合机制包括途径水平的同源重组。尽管广泛的水平基因转移有明确的证据表明，物种水平的垂直遗传，支持的概念，次生代谢产物代表功能性状，帮助定义盐孢属物种。盐孢属次生代谢组的可塑性提供了一种有效的机制，以最大限度地提高人口水平的次生代谢物的多样性，同时限制任何个人的基因组内保持的途径的数量。
Access to genome sequence data has challenged traditional natural product discovery paradigms by revealing that the products of most bacterial biosynthetic pathways have yet to be discovered. Despite the insight afforded by this technology, little is known about the diversity and distributions of natural product biosynthetic pathways among bacteria and how they evolve to generate structural diversity. Here we analyze genome sequence data derived from 75 strains of the marine actinomycete genus Salinispora for pathways associated with polyketide and nonribosomal peptide biosynthesis, the products of which account for some of today's most important medicines. The results reveal high levels of diversity, with a total of 124 pathways identified and 229 predicted with continued sequencing. Recent horizontal gene transfer accounts for the majority of pathways, which occur in only one or two strains. Acquired pathways are incorporated into genomic islands and are commonly exchanged within and between species. Acquisition and transfer events largely involve complete pathways, which subsequently evolve by gene gain, loss, and duplication followed by divergence. The exchange of similar pathway types at the precise chromosomal locations in different strains suggests that the mechanisms of integration include pathway-level homologous recombination. Despite extensive horizontal gene transfer there is clear evidence of species-level vertical inheritance, supporting the concept that secondary metabolites represent functional traits that help define Salinispora species. The plasticity of the Salinispora secondary metabolome provides an effective mechanism to maximize population-level secondary metabolite diversity while limiting the number of pathways maintained within any individual genome.