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TIGR, German Labs, and Qiagen Sequence Versatile Plant Microbe

NEW YORK, Dec. 3 - Researchers at The Institute for Genomic Research, a trio of German labs, and Qiagen have sequenced and analyzed the genome of a versatile soil bacterium.


The microbe, Pseudomonas putida, is considered in many scientific circles to be a "workhorse" model organism soil-bacteria research. According to TIGR, scientists can use P. putida's genome sequence to shed light on the microbe's "complex and versatile" metabolism, which they say may eventually spur new ways to remediate organic pollutants. In addition, comparative-genomic studies might also lead scientists to better understand related virulent organisms.


Found in most temperate and aerobic soil and water, P. putida, whose single circular chromosome contains nearly 6.2 million base pairs, can colonize the root area of crop plants, according to TIGR. As a result, researchers are trying to use the sequenced strain, KT2440, to develop pesticides and plant-growth promoters.


Additionally, an analysis found the fast-growing microbe to have certain metabolic pathways that lets it "transform" aromatic compounds like phenylalkanoates, ferulate, vanillate, and coniferyl- and coumaryl-alcohols, aldehydes, and acids, TIGR said.


Results of the research, supported by nearly $4 million in grants shared by the US Department of Energy and the German Ministry for Education and Research, are published in the December issue of Environmental Biology, which has devoted the entire issue to the microbe and other sepcies of the Pseudomonas genus.


For example, scientists compared the P. putida genome with related species to help rummage through its evolutionary baggage. One "revealing" comparison was with the genome of Pseudomonas aeruginosa, which happens to be an opportunistic pathogen that contributes to mortality in patients with cystic fibrosis, TIGR said.


In this case, the comparison identified "numerous" chemosensory systems, cell-attachment factors, and transport systems in P. putida that were believed to play a role in the virulence in P. aeruginosa, according to TIGR. For example researchers found a chromosomal region in the KT2440 genome that also exists in 85 percent of P. aeruginosa clinical isolates from sepsis and urinary-tract infections. "That suggests that those genes many not be specific for virulence," said Jonathan Eisen, an evolutionary biologist at TIGR.


What the researchers did find were "many genes" in P. aeruginosa but not P. putida that had not previously been linked with pathogenicity. "The identification of such genes may help biomedical researchers pinpoint potential targets for developing drugs or vaccines against this pathogen," TIGR said.


Collaborating with TIGR were the Medizinische Hochschule Hannover medical college, the Gesellschaft fuer Biotechnologische Forschung national research center for biotechnology; the Deutsches Krebsforschungszentrum cancer research center; and the sequencing and genomics center of Qiagen.

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