Universal Biases in Protein Composition of Model

ABSTRACT The levels of cellular organization in living organisms are the results of a variety of selection pressures. We have investigated here the final outcome of this integrated selective process in proteins of the best known microbial models Esche-richia coli, Bacillus subtilis, and Methanococcus jannaschii, supposed to have undergone separate evolution for more than 1 billion years. Using multi-variate analysis methods, including correspon-dence analysis, we studied the overall amino acid composition of all proteins making a proteome. Starting from and further developing previous re-sults that had pointed out some general forces driv-ing the amino acid composition of the proteomes of these model bacteria, we explored the correlations existing between the structure and functions of the proteins forming a proteome and their amino acid composition. The electric charge of amino acids measured against hydrophobicity creates a highly homogeneous cluster, made exclusively of proteins that are core components of the cytoplasmic mem-brane of the cell (integral inner membrane pro-teins). A second bias is imposed by the GC content of the genome, indicating that protein functions are so robust with respect to amino acid changes that they can accommodate a large shift in the nucleo-tide content of the genome. A remarkable role of aromatic amino acids was uncovered. Expressed orphan proteins are enriched in these residues, suggesting that they might participate in a process of gain of function during evolution. Proteins 2005