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J. Biol. Chem., Vol. 277, Issue 29, 26652-26661, July 19, 2002
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From the In Escherichia coli, the
two-component Cpx system comprising the CpxA sensor kinase and the CpxR
response regulator modulates gene expression in response to a variety
of stresses including membrane-protein damage, starvation, and high
osmolarity. To date, the few known CpxR-P target operons were mostly
identified by genetic screens. To facilitate the discovery of all
target operons, we derived a 15-bp weighted matrix for CpxR-P
recognition that takes into account the relative base frequency at each
nucleotide position. This matrix essentially consists of two tandem
5'-GTAAA-3' motifs separated by a 5-bp linker. All of the 15-bp
stretches on both strands of the E. coli MG1655 genome were
then scored for their degree of matching with the matrix and classified
in statistical deviation groups. The effectiveness of this screening is
indicated by the identification of eight new target operons (ung, ompC, psd, mviA,
aroK, rpoErseABC, secA, and aer)
among eleven candidates tested. Moreover, the matrix score correlates with the likelihood that a site is a true target and with the relative
site affinity for CpxR-P in vitro. Our data indicate that
some 100 operons are under direct CpxR-P control and that the signal
transduction pathway interacts with several other control circuits in
manners hitherto unanticipated.
Genome-wide Profiling of Promoter Recognition by the
Two-component Response Regulator CpxR-P in Escherichia
coli*
§¶
,,, and§§
Department of Microbiology and Molecular
Genetics and ** Department of Genetics, Harvard Medical
School, Boston, Massachusetts 02115
*
This work was supported by Public Health Service Grant
GM40993 from the National Institute of General Medical Sciences,
National Institutes of Health.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.
Former Postdoctoral D. Collen Fellow of the Belgian American
Educational Foundation.
Former predoctoral fellow of the Howard Hughes Medical Institute.
§§
To whom correspondence should be addressed: Dept. of Microbiology
and Molecular Genetics, Harvard Medical School, 200 Longwood Ave.,
Boston, MA 02115. Tel.: 617-432-1925; Fax: 617-738-7664; E-mail:
elin@hms.harvard.edu.
Copyright © 2002 by The American Society for Biochemistry and Molecular Biology, Inc.
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