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Nucleic Acids Research, 2003, Vol. 31, No. 23 6770-6777
© 2003 Oxford University Press

Article

Conservation of DNA curvature signals in regulatory regions of prokaryotic genes

Ruy Jáuregui, Cei Abreu-Goodger, Gabriel Moreno-Hagelsieb1, Julio Collado-Vides1 and Enrique Merino*

Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Chamilpa, Cuernavaca Mor., 62210 México and 1 Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apdo Postal 565-A, Cuernavaca, Mor., 62100 México

*To whom correspondence should be addressed. Tel: +52 777 3291648; Fax: +52 777 3172388; Email: merino{at}ibt.unam.mx

DNA curvature plays a well-characterized role in many transcriptional regulation mechanisms. We present evidence for the conservation of curvature signals in putative regulatory regions of several archaeal and eubacterial genomes. Genes with highly curved upstream regions were identified in orthologous groups, based on the annotations of the Cluster of Orthologous Groups of proteins (COG) database. COGs possessing a significant number of genes with curvature signals were analyzed, and conserved properties were found in several cases. Curvature signals related to regulatory sites, previously described in single organisms, were located in a broad spectrum of bacterial genomes. Global regulatory proteins, such as HU, IHF and FIS, known to bind to curved DNA and to be autoregulated, were found to present conserved DNA curvature signals in their regulatory regions, emphasizing the fact that structural parameters of the DNA molecule are conserved elements in the process of transcriptional regulation of some systems. It is currently an open question whether these diverse systems are part of an integrated global regulatory response in different microorganisms.


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