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Nucleic Acids Research, 2003, Vol. 31, No. 4 1234-1244
© 2003 Oxford University Press

Evolution of transcription factors and the gene regulatory network in Escherichia coli

M. Madan Babu* and Sarah A. Teichmann

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK

*To whom correspondence should be addressed. Tel: +44 1223 402041; Fax: +44 1223 213556; Email: madanm{at}mrc-lmb.cam.ac.uk

The most detailed information presently available for an organism’s transcriptional regulation network is that for the prokaryote Escherichia coli. In order to gain insight into the evolution of the E.coli regulatory network, we analysed information obtainable for the domains and protein families of the transcription factors and regulated genes. About three-quarters of the 271 transcription factors we identified are two-domain proteins, consisting of a DNA-binding domain along with a regulatory domain. The regulatory domains mainly bind small molecules. Many groups of transcription factors have identical domain architectures, and this implies that roughly three-quarters of the transcription factors have arisen as a consequence of gene duplication. In contrast, there is little evidence of duplication of regulatory regions together with regulated genes or of transcription factors together with regulated genes. Thirty-eight, out of the 121 transcription factors for which one or more regulated genes are known, regulate other transcription factors. This amplification effect, as well as large differences between the numbers of genes directly regulated by transcription factors, means that there are about 10 global regulators which each control many more genes than the other transcription factors.


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