Published online 6 June 2005
Article |
Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes
Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012, India
*To whom correspondence should be addressed. Tel: +91 80 2293 2534; Fax: +91 80 2360 0535; Email: mb{at}mbu.iisc.ernet.in
Received February 23, 2005. Revised April 21, 2005. Accepted May 13, 2005.
During the process of transcription, RNA polymerase can exactly locate a promoter sequence in the complex maze of a genome. Several experimental studies and computational analyses have shown that the promoter sequences apparently possess some special properties, such as unusual DNA structures and low stability, which make them distinct from the rest of the genome. But most of these studies have been carried out on a particular set of promoter sequences or on promoter sequences from similar organisms. To examine whether the promoters from a wide variety of organisms share these special properties, we have carried out an analysis of sets of promoters from bacteria, vertebrates and plants. These promoters were analyzed with respect to the prediction of three different properties, such as DNA curvature, bendability and stability, which are relevant to transcription. All the promoter sequences are predicted to share certain features, such as stability and bendability profiles, but there are significant differences in DNA curvature profiles and nucleotide composition between the different organisms. These similarities and differences are correlated with some of the known facts about transcription process in the promoters from the three groups of organisms.
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