Environmental signatures in proteome properties

摘要

In a broad study of >100 eukaryotic and prokaryotic species in this issue of PNAS, Knight et al. (1) characterize eukaryotic and prokaryotic proteomes by "theoretical 2D-gels," two-dimensional plots where each protein is represented by its molecular weight and isoelectric point. The difference in patterns between proteome 2D-gels turns out to have little or no relation to phylogeny. Instead, a variety of comparisons seem to indicate that theoretical 2D-gels are shaped by the cellular environment and the ecological niche of the corresponding species. Knight et al. conclude that environmental variability causes a greater variability in the general properties of membrane proteins (at the cell-environment interface) and that metabolic specialization (evidenced by differential usage of carbon substrates) correlates better with the general properties of nonmembrane proteins. The notion that environmental factors influence the properties of a proteome is not new. It was developed in relation to protein characters related to the dimensions represented in the theoretical 2D-gels of Knight et al., i.e., amino acid usages (more specifically the usage of the "charged" residues Asp, Glu, Lys, Arg, and His and of the other ionizable residues Cys and Tyr) and protein length.