Relative predicted protein levels of functionally associated proteins are conserved across organisms - PubMed (original) (raw)
Relative predicted protein levels of functionally associated proteins are conserved across organisms
Gila Lithwick et al. Nucleic Acids Res. 2005.
Abstract
We show that the predicted protein levels of functionally related proteins change in a coordinated fashion over many unicellular organisms. For each protein, we created a profile containing a protein abundance measure in each of a set of organisms. We show that for functionally related proteins these profiles tend to be correlated. Using the Codon Adaptation Index as a predictor of protein abundance in 48 unicellular organisms, we demonstrated this phenomenon for two types of functional relations: for proteins that physically interact and for proteins involved in consecutive steps within a metabolic pathway. Our results suggest that the protein abundance levels of functionally related proteins co-evolve.
Figures
Figure 1
Illustration of protein abundance profiles. The predicted abundance levels of two proteins, each with orthologs in four organisms, are shown. The first is represented by filled triangles, and the second by open circles. The correlation coefficient between these two abundance profiles can be computed. The connecting lines in the plot are for illustration only.
Figure 2
Main steps of the analysis for a four-organism group. Each step is detailed in Materials and Methods. After performing the analysis on each four-organism group, the number of groups that resulted in significant _P_-values was compared with that expected at random in order to obtain the significance of the overall analysis.
Figure 3
CAI profiles within proteobacteria for the α and β subunits of the F0F1–ATP synthase (COG0056 and COG0055, respectively). Normalized CAI values for proteobacterial genomes are shown. For each organism, the normalization was based on the mean and standard deviation of all its proteins that appear in the COG database. The genomes represented here are Campylobacter jejuni (Cje), Neisseria meningitidis Z2491 (Nme), Agrobacterium tumefaciens (Atu), Brucella melitensis (Bme), Caulobacter vibrioides (Cvi), Mesorhizobium loti (Mlo), Rickettsia conorii (Rco), Rickettsia prowazekii (Rpr), Sinorhizobium meliloti (Sme), Escherichia coli K12 (Eco), Haemophilus influenzae (Hin), Pasteurella multocida (Pmu), Salmonella typhimurium (Sty), Vibrio cholerae (Vch), Xylella fastidiosa (Xfa) and Yersinia pestis (Ype). The connecting lines in the plot are for illustration only.
Figure 4
CAI profiles for the β and β′ subunits of the DNA-directed RNA polymerase (COG0085 and COG0086, respectively). The normalized CAI values for 46 genomes are shown here. For each organism, the normalization was based on the mean and standard deviation of all its proteins that appear in the COG database. The two organisms not represented were left out due to a large difference in the CAI values of their paralogs (see Materials and Methods). The connecting lines in the plot are for illustration only.
Figure 5
Correlation coefficients between neighboring proteins in the histidine biosynthesis pathway of γ-proteobacteria. Consecutive proteins within the pathway are shown, with the corresponding COG name in parentheses. Next to the arrows, Spearman correlation coefficients between the consecutive proteins are shown, and the number of organisms over which the correlation was calculated is shown in parentheses. HisB and HisI are each composed of two domains, and are thus each represented by two COGs. The correlation between COG0140 and COG0139 is marked ‘nr’, since the γ-proteobacteria proteins within these two COGs are identical. COG0118 and COG0107 form a heterodimer, and the Spearman correlation coefficient for these proteins, over seven organisms, is one. The correlation coefficient of the preceding protein (COG0106) with both of these proteins is identical, as are the correlation coefficients of the successive protein (COG0131) with both of these proteins.
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