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Alternate Paradigm for Intrinsic Transcription Termination in Eubacteria

Unniraman, Shyam and Prakash, Ranjana and Nagaraja, Valakunja (2001) Alternate Paradigm for Intrinsic Transcription Termination in Eubacteria. In: The Journal of Biological Chemistry, 276 (45). pp. 41850-41855.


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Intrinsic transcription terminators are functionally defined as sites that bring about termination in vitro with purified RNA polymerase alone. Based on studies in escherichia coli, intrinsic termination requires a palindromic stretch followed by a trail of T( or U) residues in the coding strand. We have developed a highly efficient algorithm to identify hairpin potential sequences in bacterial genomes in order to build a general model for intrinsic transcription ermination. The algorithm was applied to analyze the Mycobacterium tuberculosis genome. We find that hairpin potential sequences are concentrated in the immediate downstream of stop codons. However, most of these structures either lack the U trail entirely or have a mixed A/U trail reflecting an evolutionarily relaxed requirement for the U trail in the mycobacterial genome. Predicted atypical structures were shown to work efficiently as terminators both inside the mycobacterial cell and in vitro with purified RNA polymerase. The results are discussed in light of the kinetic competition models for transcription termination. The algorithm identifies 90% of experimentally tested terminators in bacteria and is an invaluable tool in identifying transcription units in whole genomes

Item Type: Journal Article
Publication: The Journal of Biological Chemistry
Publisher: The American Society for Biochemistry and Molecular Biology
Keywords: Intrinsic transcription;RNA polymerase
Department/Centre: Division of Biological Sciences > Microbiology & Cell Biology
Date Deposited: 30 Sep 2004
Last Modified: 19 Sep 2010 04:14
URI: http://eprints.iisc.ac.in/id/eprint/1107

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