( n was even expressed. Now that we have ...)Fleshing out the genome

Before this study, nearly 40 percent of the genetic sequences in Shewanella oneidensis--of key interest to DOE for its potential in nuclear and heavy metal waste remediation--were considered as hypothetical. This work identified 538 of these genes that expressed functional proteins and messenger RNA, accounting for a third of the hypothetical genes. They enlisted analytic software to scour public databases and applied expression data to improve gene annotation, identifying similarities to known proteins for 97 percent of these hypothetical proteins. All told, computational and experimental evidence provided functional information for 256 more genes, or 48 percent, but they could confidently assign exact biochemical functions for only 16 proteins, or 3 percent. Finally, they introduced a seven-category system for annotating genomic proteins, ranked according to a functional assignment's precision and confidence.

Kolker said that "a big part of this was the proteomics"-- a systematic screening and identification of proteins, in this case those which were expressed in the microbe when subjected to stress. The proteomic analyses were done by four teams led by Kolker, Carol S. Giometti, Argonne National Laboratory (ANL); John R. Yates III; The Scripps Research Institute (TSRI); and Richard D. Smith, W.R. Wiley Environmental Molecular Sciences Laboratory, based at PNNL. BIATECH's analysis of this data included dealing with more than 2 million files.