Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins

Center for Models of Life, Niels Bohr Institute, Blegdamsvej 17, DK-2100 Copenhagen Ø, Denmark.
Biology Direct (Impact Factor: 4.04). 02/2007; 2:32. DOI: 10.1186/1745-6150-2-32
Source: PubMed

ABSTRACT Background: The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic parameters of these three basic processes is contained in the proteome-wide distribution of sequence identities of pairs of paralogous proteins. Results: We introduce a simple mathematical framework based on a stochastic birth-and-death model that allows one to extract some of this information and apply it to the set of all pairs of paralogous proteins in H. pylori, E. coli, S. cerevisiae, C. elegans, D. melanogaster, and H. sapiens. It was found that the histogram of sequence identities p generated by an all-to-all alignment of all protein sequences encoded in a genome is well fitted with a power-law form ∼ p−γ with the value of the exponent γ around 4 for the majority of organisms used in this study. This implies that the intra-protein variability of substitution rates is best described by the Gamma-distribution with the exponent α ≈ 0.33. Different features of the shape of such histograms allow us to quantify the ratio between the genome-wide average deletion/duplication rates and the amino-acid substitution rate. 1 Conclusions: We separately measure the short-term (“raw”) duplication and deletion rates r ∗ dup, r ∗ del which

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    • "However, inclusion of paralogous sequences can potentially introduce noises in generating protein sequence conservation profiles since, compared with orthologs, protein paralogs are more likely to diverge in sequence and in cellular functions. On average the amino acid sequence identity between paralogous protein pairs is only 30% (Axelsen et al., 2007). "
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