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Nucleic Acids Research Advance Access originally published online on August 18, 2006
Nucleic Acids Research 2006 34(15):4245-4257; doi:10.1093/nar/gkl521
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Nucleic Acids Research, 2006, Vol. 34, No. 15 4245-4257
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

Mycobacterial transcriptional signals: requirements for recognition by RNA polymerase and optimal transcriptional activity

Nisheeth Agarwal and Anil K. Tyagi*

Department of Biochemistry, University of Delhi South Campus Benito Juarez Road, New Delhi 110 021, India

*To whom correspondence should be addressed. Tel: +91 11 24110970; Fax: +91 11 24115270; Email: akt1003{at}rediffmail.com

Received April 17, 2006. Revised July 6, 2006. Accepted July 6, 2006.

Majority of the promoter elements of mycobacteria do not function well in other eubacterial systems and analysis of their sequences has established the presence of only single conserved sequence located at the –10 position. Additional sequences for the appropriate functioning of these promoters have been proposed but not characterized, probably due to the absence of sufficient number of strong mycobacterial promoters. In the current study, we have isolated functional promoter-like sequences of mycobacteria from the pool of random DNA sequences. Based on the promoter activity in Mycobacterium smegmatis and score assigned by neural network promoter prediction program, we selected one of these promoter sequences, namely A37 for characterization in order to understand the structure of housekeeping promoters of mycobacteria. A37–RNAP complexes were subjected to DNase I footprinting and subsequent mutagenesis. Our results demonstrate that in addition to –10 sequences, DNA sequence at –35 site can also influence the activity of mycobacterial promoters by modulating the promoter recognition by RNA polymerase and subsequent formation of open complex. We also provide evidence that despite exhibiting similarities in –10 and –35 sequences, promoter regions of mycobacteria and Escherichia coli differ from each other due to differences in their requirement of spacer sequences between the two positions.

Present address: Nisheeth Agarwal, Johns Hopkins University, 1550 Orleans Street, Cancer Research Building II, Room No. 1.76, Baltimore, Maryland 21231 (USA)


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