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MBE Advance Access published online on June 30, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp132
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© The Author 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Letter

The consequences of base pair composition biases for regulatory network organization in prokaryotes

Otto X. Cordero* and Paulien Hogeweg

Theoretical Biology and Bioinformatics, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands

* Author to whom correspondence should be addressed. E-mail: ottoxcordero{at}gmail.com; Tel: +31 30 253 1497; Fax: +31 30 253 9043

Received for publication June 4, 2009. Accepted for publication June 23, 2009.

Given the dramatic variation GC content observed in prokaryotes, from ~ 20% to ~ 75% GC, one wonders if these extreme biases in base pair composition affect the evolution of transcription factor binding sites. This letter shows that, along the wide range of GC content variation in bacteria, bacterial binding sites keep a high frequency of AT bases, roughly independently of the background base pair composition of intergenic regions. As a result, the equilibrium base pair frequencies of binding sites depart the most from those of background DNA in GC rich genomes. This not only implies a higher specificity, but also a higher coding barrier for binding sites in GC rich genomes. In accordance, we observe that the average percentage of divergently transcribed regions increases with the GC content of the genome, suggesting the use of a more efficient coding strategy.

Key Words: Evolution • Gene regulation • GC content • Binding sites


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