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Nucleic Acids Research, 2002, Vol. 30, No. 3 675-684
© 2002 Oxford University Press

Conserved economics of transcription termination in eubacteria

Shyam Unniraman1, Ranjana Prakash1 and Valakunja Nagaraja1,2,*

1Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India and 2Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India

A secondary structure in the nascent RNA followed by a trail of U residues is believed to be necessary and sufficient to terminate transcription. Such structures represent an extremely economical mechanism of transcription termination since they function in the absence of any additional protein factors. We have developed a new algorithm, GeSTer, to identify putative terminators and analysed all available complete bacterial genomes. The algorithm classifies the structures into five classes. We find that potential secondary structure sequences are concentrated downstream of coding regions in most bacterial genomes. Interestingly, many of these structures are not followed by a discernible U-trail. However, irrespective of the nature of the trail sequence, the structures show a similar distribution, indicating that they serve the same purpose. In contrast, such a distribution is absent in archaeal genomes, indicating that they employ a distinct mechanism for transcription termination. The present algorithm represents the fastest and most accurate algorithm for identifying terminators in eubacterial genomes without being restricted by the classical Escherichia coli paradigm.

* To whom correspondence should be addressed. Tel: +91 80 360 0668; Fax: +91 80 360 2697; Email: vraj{at}mcbl.iisc.ernet.in


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