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J. Biol. Chem., Vol. 276, Issue 45, 41850-41855, November 9, 2001
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From the 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 termination. 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.
Alternate Paradigm for Intrinsic Transcription Termination in
Eubacteria*,
,§, and¶
Department of Microbiology and Cell Biology,
Indian Institute of Science, Bangalore 560012, India and
¶ Jawaharlal Nehru Centre for Advanced Scientific Research,
Bangalore 560064, India
*
The research was supported by grants from the Indian Council
of Medical Research, Government of India.The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
The on-line version of this article (available at
http://www.jbc.org) contains a list of terminator
sequences used to optimize the algorithm.
§
Recipient of an Indian Academy of Sciences fellowship.
To whom correspondence should be addressed. Tel.:
91-80-360-0668; Fax: 91-80-360-2697; E-mail:
vraj@mcbl.iisc.ernet.in.
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