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Hidden diversity in key environmental cleanup microbes found by systems biology assessment
Date:8/31/2009

l Engineering. Konstantinidis, who also holds a joint appointment in the School of Biology, led the research team in analyzing the data.

Using the traditional method for determining interrelatedness between microbial strains -- sequencing of the 16S ribosomal gene -- the researchers determined that the 10 strains belonged to the same genus. However, the technique was unable to distinguish between most of the strains or define general properties that would allow the researchers to differentiate one strain from another. To do that, they turned to genomic and whole-cell proteomic data.

By comparing the 10 Shewanella genomes, which were sequenced at the Department of Energy's Joint Genome Institute, the research team found that while some of the strains shared 98 percent of the same genes, other strains only shared 70 percent. Out of the almost 10,000 protein-coding genes in the 10 strains, nearly half -- 48 percent -- of the genes were strain-specific, and the differences in expressed proteins were consistently larger than their differences at the gene content level.

"These findings suggest that similarity in gene regulation and expression constitutes an important factor for determining phenotypic similarity or dissimilarity among the very closely related Shewanella genomes," noted Konstantinidis. "They also indicate that it might be time to start replacing the traditional microbiology approaches for identifying and classifying new species with genomics- or proteomics-based methods."

Upon further analysis, the researchers found that the genetic differences between strains frequently reflected environmental or ecological adaptation and specialization, which had also substantially altered the global metabolic and regulatory networks in some of the strains. The Shewanella organisms in the study appeared to gain most of their new functions by acquiring groups of genes as mobile genetic islands, selecting islands carrying ecologically
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Contact: Abby Vogel
avogel@gatech.edu
404-385-3364
Georgia Institute of Technology Research News
Source:Eurekalert  

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