Examination of the relationship of the rate of protein evolution and breadth (in terms of the number of tissues) of gene expression has revealed that the evolutionary rate is low for broadly expressed genes in humans ( D uret and M ouchiroud 2000). This points to selection based on polypeptide length, in addition to the classic explanation of selection on individual amino acid sites to ensure protein function ( L i 1997 N ei and K umar 2000). However, a negative relationship between peptide length and expression level has been observed in humans ( E isenberg and L evanon 2003 U rrutia and H urst 2003). This relationship is less clear in invertebrates (see contrasting findings in D uret and M ouchiroud 1999 M arais and D uret 2001 C astillo-D avis et al. The effect of selection exerted by the gene expression level is revealed by the negative relationship between transcript abundance and protein length in yeast ( C oghlan and W olfe 2000 A kashi 2003). 1988 S harp and L i 1989 P owell and M oriyama 1997). Selection on mutations that do not alter amino acids (synonymous substitutions) is evident in the codon usage bias, which enhances the translational efficiency in invertebrates ( S hields et al. NATURAL selection acts on the molecular evolution of protein and DNA sequences in many different ways. These results provide insights into the differential relationship and effect of the increasing complexity of animal body form on evolutionary rates of proteins. Precambrian genes exhibit a more pronounced difference in protein evolutionary rates (up to three times) between the genes with high and low expression levels as compared to the vertebrate-specific genes, which appears to be due to the narrower breadth of expression of the vertebrate-specific genes. The most highly expressed genes actually show the lowest total number of substitutions per polypeptide, consistent with cumulative effects of purifying selection on individual amino acid replacements.
We find that the intensity of gene expression relates inversely to the rate of protein sequence evolution on a genomic scale. To understand how natural selection operates on proteins that appear to have arisen in earlier and later phases of animal evolution, we have contrasted patterns of mouse proteins that have homologs in invertebrate and protist genomes (Precambrian genes) with those that do not have such detectable homologs (vertebrate-specific genes). Here we have examined how the rates of evolution of proteins encoded by the vertebrate genomes are modulated by the amount (intensity) of gene expression. In mammals, the highly expressed genes have a shorter gene length in the genome and the breadth of expression is known to constrain the rate of protein evolution. In highly expressed genes in invertebrates, these footprints are seen in the higher codon usage bias and lower synonymous divergence. Natural selection leaves its footprints on protein-coding sequences by modulating their silent and replacement evolutionary rates.
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