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Proteomics brings researchers closer to understanding microbes that produce acid mine drainage

e the biofilm matrix upon which all community members depend," Banfield said. "It's like it's a slave."

The team also was able to identify important acid-stable proteins, including the iron oxidizing protein in Leptospirillum group II bacterium, that may have technological applications in the longer term, Banfield said.

The "proteogenomic" technique Banfield and her team used to extract the proteome from the biofilm involved dicing up all the proteins in a melange of the organisms, then determining at ORNL the masses of these short proteins, called peptides, with "shotgun" mass spectrometry. To identify the peptides from their masses, they turned back to the genomes. The genomes they obtained last year allowed them to predict the proteins in each member of the biofilm community, and from that predict the protein fragments that would result if they were all chopped up. Correlating the two allowed them to reconstruct the complete proteins and then associate each protein with a particular organism.

"This work illustrates the power of the genome sequencing done at the Department of Energy's Joint Genome Institute to contribute to understanding the microbiological communities living at contaminated sites," said Dr. Raymond L. Orbach, director of DOE's Office of Science. "Now scientists can investigate not only the community genome, but also the resulting community proteome for enzymes and pathways that can help clean up some of the worst environmental sites in the nation. This underscores the value of basic research carried out by the DOE Genomics:GTL Program that can develop novel approaches and solutions to national challenges."

Banfield is continuing her studies of the Richmond Mine biofilm and acid producing biofilms elsewhere, which includes work with the Joint Genome Institute to obtain more genomes of community members.

"We really want to know how the environment drives the community, how the environment selects for the memb
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Source:UC Berkeley


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