Universal Features in the Genome-level Evolution of Protein Domains
Correspondence: (Login to view email address)
- Universita' di Milano, Dip. Fisica
- University of Utrecht,
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- Document Type:
- Manuscript
- Date:
- Received 11 July 2008 17:49 UTC; Posted 16 July 2008
- Subjects:
- Genetics & Genomics, Bioinformatics, Evolutionary Biology
- Abstract:
Protein domains are found on genomes with notable statistical distributions, which bear a high degree of similarity. Previous work has shown how these distributions can be accounted for by simple models, where the main ingredients are probabilities of duplication, innovation, and loss of domains. However, no one so far has addressed the issue that these distributions follow definite trends depending on protein-coding genome size only. We present a stochastic duplication/innovation model, falling in the class of so-called Chinese Restaurant Processes, able to explain this feature of the data. Using only two universal parameters, related to a minimal number of domains and to the relative weight of innovation to duplication, the model reproduces two important aspects: (a) the populations of domain classes (the sets, related to homology classes, containing realizations of the same domain in different proteins) follow common power-laws whose cutoff is dictated by genome size, and (b) the number of domain families is universal and markedly sublinear in genome size. An important ingredient of the model is that the innovation probability decreases with genome size. We propose the possibility to interpret this as a global constraint given by the cost of expanding an increasingly complex interactome. Finally, we introduce a variant of the model where the choice of a new domain relates to its occurrence in genomic data, and thus accounts for fold specificity. Both models have general quantitative agreement with data from hundreds of genomes, which indicates the coexistence of the well-known specificity of proteomes with robust self-organizing phenomena related to the basic evolutionary ``moves’’ of duplication and innovation.
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- This document is licensed to the public under the Creative Commons Attribution 3.0 License
- How to cite this document:
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Cosentino Lagomarsino, Marco, Sellerio, Alessandro, Heijning, Philip, and Bassetti, Bruno. Universal Features in the Genome-level Evolution of Protein Domains. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2008.1376.2> (2008)
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Other versions of this document in Nature Precedings
Version number Document title Date v1 Posted 30 November 2007 Other versions of this document elsewhere on the web
