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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Comparative systems biology across an evolutionary gradient within the Shewanella genus
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Comparative systems biology across an evolutionary gradient within the Shewanella genus

机译：希瓦氏菌属内进化梯度上的比较系统生物学

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摘要

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.
机译：基因型差异在多大程度上转化为表型变异，仍然是人们对微生物学的几个基石概念（包括物种定义）至关重要的一个鲜为人知的问题。在这里，我们利用完整的基因组序列，表达的蛋白质组学概况以及对10个紧密相关的希瓦氏菌菌株和物种的生理学研究，提供了对该问题的定量见解。我们的分析表明，尽管在这些基因组中进行了广泛的水平基因转移，但通常可以从它们的进化相关性中预测生物之间的基因型和表型相似性。预测的力量取决于所评估生物的生态专业化程度。使用这些基因组形成的进化相关性梯度，我们能够部分地将生态学的影响与进化发散的影响区分开，并根据它们的进化速率对不同的细胞功能进行排名。我们的排名还显示，当这些生物在相同条件下生长时，它们之间的全细胞蛋白质表达差异要比基因组水平上的差异要大，这表明基因调控和表达的相似性应该构成另一个重要参数（ ）物种描述。总的来说，我们的结果为开始对细菌物种和属进行系统级了解提供了重要的新信息。

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  • 作者

    Konstantinos T. Konstantinidis; Margrethe H. Serres; Margaret F. Romine; Jorge L. M. Rodrigues; Jennifer Auchtung; Lee-Ann McCue; Mary S. Lipton; Anna Obraztsova; Carol S. Giometti; Kenneth H. Nealson; James K. Fredrickson; James M. Tiedje;

  • 作者单位

    School of Civil and Environmental Engineering and School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332;

    Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543;

    Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999 , Richland, WA 99352;

    Department of Biology, University of Texas, P.O. Box 19498, Arlington, TX 76019;

    Center for Microbial Ecology, Michigan State University, 540 Plant and Soil Sciences Building, East Lansing, Ml 48824;

    Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999 , Richland, WA 99352;

    Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999 , Richland, WA 99352;

    Department of Earth Sciences, University of Southern California, University Park Campus, Los Angeles, CA 90089;

    Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439;

    Department of Earth Sciences, University of Southern California, University Park Campus, Los Angeles, CA 90089;

    Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999 , Richland, WA 99352;

    Center for Microbial Ecology, Michigan State University, 540 Plant and Soil Sciences Building, East Lansing, Ml 48824;

  • 收录信息 美国《科学引文索引》(SCI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

    comparative genomics; evolution; proteomics; speciation; phenotype;

    机译：比较基因组学;演化;蛋白质组学物种表型;

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