Protein census of Leptospira interrogans

A census of proteins in a bacterial cell was conducted for the first time ever. By "census," I don't mean merely identifying all cellular proteins (which can be accomplished by shotgun tandem mass spectrometry). What I mean is counting the number of copies of every protein. The bacterium targeted for the census was the spirochete Leptospira interrogans. Like the census conducted here in the U.S. every ten years, some proteins were missed. The strategy developed by Malmström and colleagues, as described in the August 6 issue of Nature, allowed them to determine the abundance of 1,864 (or 83%) of the 2,221 proteins that were detectable by tandem mass spectrometry (MS) in Leptospira interrogans that had been grown in standard Leptospira culture medium.

The results of the protein census are compiled in the bar graph below. Proteins with related biological functions were grouped together and are color coded. The "Proteome" bar tabulates the number of different proteins in each group.
The next bar, "Copies per cell (control)," gives you an idea of how much of the protein expression machinery in L. interrogans is directed towards the synthesis of proteins in each functional category. The percentage reflects the amounts and size of the proteins in each category. For example, proteins of unknown function (hypothetical proteins) represent only 12.7% (blue) of the total protein synthesis capacity even though they constitute 30% of the identified proteins and over 40% of all genes in L. interrogans. I would surmise that these hypothetical proteins would account for a more sizable fraction of total protein synthesis under some other condition that L. interrogans would encounter during its life cycle (e.g., during infection).

The other observation noted by the authors is that L. interrogans gears 15% of its protein synthesis effort to make a small number of proteins deemed to be components of the "external encapsulating structure" (green), which is a fancy Gene Ontology term encompassing abundant Leptospira proteins that have been demonstrated to be in the inner or outer membrane. Most of the 15% is accounted for by five outer membrane proteins: LipL32, Loa22, LipL41, LipL21, and LipL36, the functions of which are not entirely clear. The five proteins are among the 10 most abundant proteins in L. interrogans.

The last bar shows the effect of the antibiotic ciprofloxacin ("cipro") on global protein levels in L. interrogans. The most striking change is the massive increase in 15 proteins of unknown function (light blue) leading them to constitute ~20% of the total protein content. As ciprofloxacin is an inhibitor of DNA gyrase, transcription of the genes encoding the 15 proteins may be extremely sensitive to DNA topology.

Did the enormous increase in the copy number of the 15 proteins following ciprofloxacin treatment increase the total number of protein molecules in L. interrogans? The authors found little change in the total cellular protein content:

Interestingly, this large redistribution of the proteome did not significantly change the total cellular protein concentration. Therefore, the large increase in the abundance of [the 15 proteins of unknown function] after ciprofloxacin exposure was compensated by a slight reduction of other high abundant protein classes.... This indicates that in L. interrogans, the cells strive to maintain a certain total number of protein components, that is, a constant cellular proteome concentration.

Featured paper

Malmström, J., Beck M., Schmidt, A., Lange, V., Deutsch, E.W., and Aebersold, R. (2009). Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature 460(7256):762-765. DOI: 10.1038/nature08184