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The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication

Presser, Aviva and Elowitz, Michael B. and Kellis, Manolis and Kishony, Roy (2008) The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication. Proceedings of the National Academy of Sciences of the United States of America, 105 (3). pp. 950-954. ISSN 0027-8424. PMCID PMC2242688. doi:10.1073/pnas.0707293105. https://resolver.caltech.edu/CaltechAUTHORS:PREpnas08

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Abstract

Gene duplication is an important mechanism in the evolution of protein interaction networks. Duplications are followed by the gain and loss of interactions, rewiring the network at some unknown rate. Because rewiring is likely to change the distribution of network motifs within the duplicated interaction set, it should be possible to study network rewiring by tracking the evolution of these motifs. We have developed a mathematical framework that, together with duplication data from comparative genomic and proteomic studies, allows us to infer the connectivity of the preduplication network and the changes in connectivity over time. We focused on the whole-genome duplication (WGD) event in Saccharomyces cerevisiae. The model allowed us to predict the frequency of intergene interaction before WGD and the post duplication probabilities of interaction gain and loss. We find that the predicted frequency of self-interactions in the preduplication network is significantly higher than that observed in today's network. This could suggest a structural difference between the modern and ancestral networks, preferential addition or retention of interactions between ohnologs, or selective pressure to preserve duplicates of self-interacting proteins.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1073/pnas.0707293105DOIArticle
http://www.pnas.org/content/105/3/950.abstractPublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242688/PubMed CentralArticle
ORCID:
AuthorORCID
Elowitz, Michael B.0000-0002-1221-0967
Additional Information:© 2008 by the National Academy of Sciences. Edited by Leonid Kruglyak, Princeton University, Princeton, NJ, and accepted by the Editorial Board November 20, 2007 (received for review August 2, 2007). Published online before print January 16, 2008, doi: 10.1073/pnas.0707293105. This article is a PNAS Direct Submission. L.K. is a guest editor invited by the Editorial Board. We acknowledge N. Barkai, M. Brenner, A. DeLuna, E. Lieberman, I. Nachman, I. Wapinski, and K. Wolfe for their advice and helpful discussions and E. Lieberman and R. Milo for critical readings of the manuscript. This work was supported in part by National Institutes of Health Grants GM068763 (to M.B.E.) and R01GM081617 (to R.K.). A.P. was supported by a National Science Foundation Graduate Fellowship and a National Defense Science and Engineering Graduate Fellowship. Author contributions: A.P., M.B.E., and R.K. designed research; A.P. performed research; A.P., M.K., and R.K. analyzed data; and A.P., M.B.E., M.K., and R.K. wrote the paper. The authors declare no conflict of interest. This article contains supporting information online at www.pnas.org/cgi/content/full/0707293105/DC1.
Funders:
Funding AgencyGrant Number
NIHGM068763
NIHR01GM081617
National Defense Science and Engineering Graduate (NDSEG) FellowshipUNSPECIFIED
Subject Keywords:gene duplication; network motifs; self-interacting proteins; whole-genome duplication
Issue or Number:3
PubMed Central ID:PMC2242688
DOI:10.1073/pnas.0707293105
Record Number:CaltechAUTHORS:PREpnas08
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:PREpnas08
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:12177
Collection:CaltechAUTHORS
Deposited By: Archive Administrator
Deposited On:28 Oct 2008 06:05
Last Modified:08 Nov 2021 22:26

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