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    Comparative systems biology across an evolutionary gradient within the Shewanella genus

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    Supplementary materials (1.921Mb)
    Date
    2009-07
    Author
    Konstantinidis, Konstantinos T.  Concept link
    Serres, Margrethe H.  Concept link
    Romine, Margaret F.  Concept link
    Rodrigues, Jorge L. M.  Concept link
    Auchtung, Jennifer  Concept link
    McCue, Lee-Ann  Concept link
    Lipton, Mary S.  Concept link
    Obraztsova, Anna Y.  Concept link
    Giometti, Carol S.  Concept link
    Nealson, Kenneth H.  Concept link
    Fredrickson, James K.  Concept link
    Tiedje, James M.  Concept link
    Metadata
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    Citable URI
    https://hdl.handle.net/1912/3191
    As published
    https://doi.org/10.1073/pnas.0902000106
    DOI
    10.1073/pnas.0902000106
    Abstract
    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 ten 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 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 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 towards beginning a systems-level understanding of bacterial species and genera.
    Description
    Author Posting. © The Authors, 2009. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 106 (2009): 15909-15914, doi:10.1073/pnas.0902000106.
    Collections
    • Josephine Bay Paul Center in Comparative Molecular Biology and Evolution
    Suggested Citation
    Preprint: Konstantinidis, Konstantinos T., Serres, Margrethe H., Romine, Margaret F., Rodrigues, Jorge L. M., Auchtung, Jennifer, McCue, Lee-Ann, Lipton, Mary S., Obraztsova, Anna Y., Giometti, Carol S., Nealson, Kenneth H., Fredrickson, James K., Tiedje, James M., "Comparative systems biology across an evolutionary gradient within the Shewanella genus", 2009-07, https://doi.org/10.1073/pnas.0902000106, https://hdl.handle.net/1912/3191
     
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