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© 2010 van Dijk et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: van Dijk ADJ, Morabito G, Fiers M, van Ham RCHJ, Angenent GC, et al. (2010) Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction. PLoS Comput Biol 6(11): e1001017. doi:10.1371/journal.pcbi.1001017

Abstract

Protein sequences encompass tertiary structures and contain information about specific molecular interactions, which in turn determine biological functions of proteins. Knowledge about how protein sequences define interaction specificity is largely missing, in particular for paralogous protein families with high sequence similarity, such as the plant MADS domain transcription factor family. In comparison to the situation in mammalian species, this important family of transcription regulators has expanded enormously in plant species and contains over 100 members in the model plant species Arabidopsis thaliana. Here, we provide insight into the mechanisms that determine protein-protein interaction specificity for the Arabidopsis MADS domain transcription factor family, using an integrated computational and experimental approach. Plant MADS proteins have highly similar amino acid sequences, but their dimerization patterns vary substantially. Our computational analysis uncovered small sequence regions that explain observed differences in dimerization patterns with reasonable accuracy. Furthermore, we show the usefulness of the method for prediction of MADS domain transcription factor interaction networks in other plant species. Introduction of mutations in the predicted interaction motifs demonstrated that single amino acid mutations can have a large effect and lead to loss or gain of specific interactions. In addition, various performed bioinformatics analyses shed light on the way evolution has shaped MADS domain transcription factor interaction specificity. Identified protein-protein interaction motifs appeared to be strongly conserved among orthologs, indicating their evolutionary importance. We also provide evidence that mutations in these motifs can be a source for sub- or neo-functionalization. The analyses presented here take us a step forward in understanding protein-protein interactions and the interplay between protein sequences and network evolution.

Details

Title
Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction
Author
Dijk, D Jvan; Morabito, Giuseppa; Fiers, Martijn; Ham, H Jvan; Angenent, Gerco C; Immink, Richard GH
Pages
e1001017
Section
Research Article
Publication year
2010
Publication date
Nov 2010
Publisher
Public Library of Science
ISSN
1553734X
e-ISSN
15537358
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
1313167136
Copyright
© 2010 van Dijk et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: van Dijk ADJ, Morabito G, Fiers M, van Ham RCHJ, Angenent GC, et al. (2010) Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction. PLoS Comput Biol 6(11): e1001017. doi:10.1371/journal.pcbi.1001017