A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network
10.1186/gb-2004-5-10-r76
Crossref journal-article
Springer Science and Business Media LLC
Genome Biology (297)
Abstract

Abstract Background Studying the evolution of the function of duplicated genes usually implies an estimation of the extent of functional conservation/divergence between duplicates from comparison of actual sequences. This only reveals the possible molecular function of genes without taking into account their cellular function(s). We took into consideration this latter dimension of gene function to approach the functional evolution of duplicated genes by analyzing the protein-protein interaction network in which their products are involved. For this, we derived a functional classification of the proteins using PRODISTIN, a bioinformatics method allowing comparison of protein function. Our work focused on the duplicated yeast genes, remnants of an ancient whole-genome duplication. Results Starting from 4,143 interactions, we analyzed 41 duplicated protein pairs with the PRODISTIN method. We showed that duplicated pairs behaved differently in the classification with respect to their interactors. The different observed behaviors allowed us to propose a functional scale of conservation/divergence for the duplicated genes, based on interaction data. By comparing our results to the functional information carried by GO annotations and sequence comparisons, we showed that the interaction network analysis reveals functional subtleties, which are not discernible by other means. Finally, we interpreted our results in terms of evolutionary scenarios. Conclusions Our analysis might provide a new way to analyse the functional evolution of duplicated genes and constitutes the first attempt of protein function evolutionary comparisons based on protein-protein interactions.

Bibliography

Baudot, A., Jacq, B., & Brun, C. (2004). A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network. Genome Biology, 5(10).

Authors 3
  1. Anaïs Baudot (first)
  2. Bernard Jacq (additional)
  3. Christine Brun (additional)
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Dates
Type When
Created 20 years, 11 months ago (Sept. 16, 2004, 2:23 a.m.)
Deposited 10 months, 4 weeks ago (Oct. 8, 2024, 6:37 a.m.)
Indexed 10 months, 4 weeks ago (Oct. 9, 2024, 12:23 a.m.)
Issued 20 years, 11 months ago (Sept. 15, 2004)
Published 20 years, 11 months ago (Sept. 15, 2004)
Published Online 20 years, 11 months ago (Sept. 15, 2004)
Funders 0

None

@article{Baudot_2004, title={A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network}, volume={5}, ISSN={1474-760X}, url={http://dx.doi.org/10.1186/gb-2004-5-10-r76}, DOI={10.1186/gb-2004-5-10-r76}, number={10}, journal={Genome Biology}, publisher={Springer Science and Business Media LLC}, author={Baudot, Anaïs and Jacq, Bernard and Brun, Christine}, year={2004}, month=sep }