Comparative systems biology across an evolutionary gradient within the Shewanella genus
Comparative systems biology across an evolutionary gradient within the Shewanella genus
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DOI：
10.1073/pnas.0902000106
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发表时间：
2009-09-15
影响因子：
11.1
通讯作者：
Tiedje, James M.
中科院分区：
文献类型：
--
作者：
Konstantinidis, Konstantinos T.;Serres, Margrethe H.;Tiedje, James M.
基因型差异在多大程度上转化为表型变异仍然是一个鲜为人知的问题，对微生物学的几个基础概念至关重要，包括物种定义。在这里，我们利用10个密切相关的希瓦氏菌菌株和物种的完整的基因组序列，表达的蛋白质组学图谱和生理学研究来提供定量的见解。我们的分析表明，尽管在这些基因组中存在广泛的水平基因转移，但生物之间的基因型和表型相似性通常可以从它们的进化亲缘关系中预测出来。预测的效力取决于被评估生物的生态专门化程度。利用这些基因组形成的进化亲缘关系梯度，我们能够将生态的影响从进化分化中部分分离出来，并根据它们的进化速度对不同的细胞功能进行排序。我们的排名还显示，当这些生物在相同条件下生长时，这些生物之间的全细胞蛋白表达差异相对大于基因组水平的差异，这表明基因调控和表达的相似性应该是（新）物种描述的另一个重要参数。总的来说，我们的结果为开始对细菌种类和属的系统级理解提供了重要的新信息。
To what extent genotypic differences translate to phenotypic variation remains a poorly understood issue of paramount importance for several cornerstone concepts of microbiology including the species definition. Here, we take advantage of the completed genomic sequences, expressed proteomic profiles, and physiological studies of 10 closely related Shewanella strains and species to provide quantitative insights into this issue. Our analyses revealed that, despite extensive horizontal gene transfer within these genomes, the genotypic and phenotypic similarities among the organisms were generally predictable from their evolutionary relatedness. The power of the predictions depended on the degree of ecological specialization of the organisms evaluated. Using the gradient of evolutionary relatedness formed by these genomes, we were able to partly isolate the effect of ecology from that of evolutionary divergence and to rank the different cellular functions in terms of their rates of evolution. Our ranking also revealed that whole-cell protein expression differences among these organisms, when the organisms were grown under identical conditions, were relatively larger than differences at the genome level, suggesting that similarity in gene regulation and expression should constitute another important parameter for ( new) species description. Collectively, our results provide important new information toward beginning a systems-level understanding of bacterial species and genera.