Nucleic Acids Research, 2005, Vol. 33, No. 3 1051–1057 doi:10.1093/nar/gki261 Relative predicted protein levels of functionally associated proteins are conserved across organisms Gila Lithwick and Hanah Margalit* Department of Molecular Genetics and Biotechnology, The Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel Received January 3, 2005; Revised and Accepted February 1, 2005 ABSTRACT We show that the predicted protein levels of function- ally 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 con- secutive steps within a metabolic pathway. Our res- ults suggest that the protein abundance levels of functionally related proteins co-evolve. INTRODUCTION Over the past few years, the characterization and prediction of functional relations between proteins have been at the fore- front of genomic research. Several types of features, based on experimental results and computational analyses, were shown to be associated with functionally related and interacting pro- teins. It was shown that functionally associated proteins exhibit correlated mRNA expression proﬁles over a set of environmental conditions or different tissue types (1–4). In many cases, functionally linked proteins were shown to be encoded by genes that are conserved in evolution as neighbors (5–7); they were shown to undergo gene fusion events, such that individual genes in one genome were found to be fused into a single gene in another genome (8,9); and they were shown to co-occur in various organisms, either they were preserved together or eliminated together during evolution (10,11). This property of co-occurrence of functionally linked proteins across various organisms traditionally refers only to their presence or absence; however, it is appealing to conjec- ture that their relative protein abundance levels should be preserved in a coordinated fashion as well. Such a preservation of relative abundance levels across organisms is expected to be important for two types of functional associations: (i) for interacting proteins, where coordinated abundance levels may be needed in order to preserve the stoichiometry of the interaction; and (ii) for proteins within the same metabolic pathway, where a constant balance is needed between the relative abundance of the proteins within the pathway in order to ensure that the ﬂow of the pathway is maintained. To investigate whether the relative levels of functionally associated proteins are preserved during evolution, measured protein levels are needed. With such data at hand, one can generate a proﬁle for each protein, where each entry contains the abundance of the protein in a speciﬁc genome. These proﬁles can be analyzed in order to determine whether the proﬁles of functionally linked proteins are correlated. How- ever, since large-scale protein abundance data are scarce and are available only for a subset of proteins in a few organisms (12,13), this analysis is not feasible at present. An alternative approach would be to represent the protein levels by other measures that were shown to correlate with protein abundance, such as the mRNA level of the corresponding genes (13) or the degree of codon bias of the proteins (14–16). As to the former, the nature of available mRNA expression data prevents its use for the intended analysis. The mRNA expression is usually measured relative to background expression levels in a speciﬁc condition or set of conditions, and absolute expression levels are scarce. It is therefore impossible to compare the mRNA expression levels of pairs of proteins across different organ- isms. In addition, gene expression experiments in different genomes are often performed under different conditions, mak- ing the comparison of the expression of a gene in different organisms problematic. Another measure that was shown to correlate with the protein abundance level is the degree of codon bias of the protein (14,15,17,18). A common explana- tion for this phenomenon is based on the observation within several organisms that tRNA molecules corresponding to pre- ferred codons exist at higher levels (19–24). The mRNA sequences of highly abundant proteins have a greater bias toward these preferred codons, enabling their rapid translation *To whom correspondence should be addressed. Tel: +972 2 6758614; Fax: +972 2 6757308; Email: hanah@md.huji.ac.il ª The Author 2005. Published by Oxford University Press. All rights reserved. The online version of this article has been published under an open access model. 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