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PNNL Team Cracks Most of a Schmutz-Cleaning Bacterium s Proteome

SAN FRANCISCO, Aug. 16 - Scientists at the US Department of Energy's Pacific Northwest National Laboratory have identified 61 percent of the proteome of the microbe Deinococcus radiodurans.

 

More than 1,900 of the bug's proteins were identified using a two-step mass spectrometry process, according to the researchers, who claim their work represents the most complete proteome reporting of any organism.

 

In the first step, tandem mass spectrometers--a Thermo Finnigan LCQ ion trap and a 7 Tesla Fourier-transform ion cyclotron resonance machine--were used to identify biomarkers for proteins. The team then used an 11.5 Tesla FTICR mass spectrometer to validate the results by measuring the mass of the peptides.

 

"Once we've identified the protein biomarkers, we never have to repeat the identification step, thereby speeding up our experiments," said Richard Smith, a PNNL principal investigator. "As a result we not only have a much more complete view of the proteome than existed previously, but we also can follow changes to it much faster."

 

Which is what researchers plan to do next.

 

"It's not enough to know whether something's there. We need to know how much is there," said Mary Lipton, a senior research scientist at PNNL.

 

To do this, Lipton said, the researchers will subject D. radiodurans to changing conditions in order to find out how the proteins change.

 

D. radiodurans is a radiation-resistant microbe known to survive in extreme environments. It was selected for study because the DOE is interested in its potential role to clean environmentally contaminated sites, said Lipton. The DOE's Genomes to Life program gave PNNL roughly $1 million to identify the microbe's proteome.

 

D. radiodurans is also of interest because of its ability to repair its DNA. This could provide insight to methods to block DNA repair in cancer cells, said Lipton.

 

Other authors of the paper, which appears in the Aug. 20 Proceedings of the National Academy of Sciences, include researchers from Louisiana State University and the Uniformed Services University of the Health Sciences in Bethesda, Md.

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