In a paper published in PNAS August 12, Richard Smith of the Pacific Northwest National Laboratory and colleagues at Louisiana State University and the Uniformed Services University of Health Sciences describe an analysis of the Deinococcus radiodurans proteome. Using global enzymatic digestion, liquid chromatography separations, and Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry, the authors identified 61 percent of the predicted proteome of D. radiodurans using the peptides as accurate mass tags. Smith et. al. also identified 715 proteins previously considered either hypothetical or conserved hypothetical. The proteome analysis, the authors claim, is the most thorough of any organism to date.
Delving into a proteomic analysis of the components of the human spliceosome, Matthias Mann of the Protein Interaction Laboratory at the University of Southern Denmark and his colleagues have published a report in Genome Biology describing their results. Rather than resort to protein separation by 2D gel electrophoresis, Mann and his team first purified splicing complexes that formed on two separate pre-mRNAs, and then identified the components by tandem mass spectrometry analysis of the enzymatically-digested crude mixture. The team used differential mass range pulsing on a quadrupole time-of-flight mass spectrometer to identify a total of 311 proteins, including 96 that had not been previously characterized. Fifty-five of these proteins contained domains that suggested a role in splicing or RNA processing. In addition, Mann and his colleagues also identified 20 proteins linked to transcription, indicating a relationship between this mechanism and splicing.
Reporting in the August 12 issue of PNAS, researchers at the Joint Center for Structural Genomics at the Scripps Research Institute, the Genomics Institute of the Novartis Research Foundation, Stanford University, and the San Diego Supercomputing Center describe a high-throughput approach to expressing, crystallizing and determining the structure of the proteome of Thermotoga maritima. Led by Scott Lesley, Peter Schultz, and Raymond Stevens, the team successfully cloned and attempted to crystallize 1,376 of the 1,877 predicted genes in the T. maritima genome, and identified crystallization conditions for 432, or 23 percent, of the predicted proteome. Although the authors included actual structures from only two of the proteins, TM0423 glycerol dehy-drogenase and TM0449 thymidylate synthase-complementing protein, in the paper, they write that their platform had enabled them to express, purify, and process the majority of the the T. maritima proteome “in a matter of months.”