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J. Biol. Chem., Vol. 277, Issue 49, 47420-47427, December 6, 2002
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From the Department of Chemistry and Biochemistry and the Molecular
Biology Institute, University of California, Los Angeles,
California 90095-1569
Promoter Use by
38 (rpoS)
RNA Polymerase
AMINO ACID CLUSTERS FOR DNA BINDING AND ISOMERIZATION*
38 is a non-essential but
highly homologous member of the 70 family of
transcription factors. In vitro mutagenesis and in
vivo screening were used to identify 22 critical amino acids in
the promoter interaction domain of Escherichia coli
38. Electrophoretic mobility shift assay studies
showed that residues involved in duplex DNA binding largely segregated
into distinct regions that coincided with those of 70.
However, the majority of these amino acids were in non-conserved positions. Analysis indicates that this region of the two s probably has a common overall organization but differs in how its amino acids
are used to form functional open complexes. Placement of the mutations
on the known 70 holoenzyme structure shows two clusters;
one appears to be used for duplex DNA recognition and the other for the
subsequent isomerization events. Permanganate assays for DNA melting
support this view.
*
This work was supported by National Institutes of Health
Grant GM35754.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.
To whom correspondence should be addressed: Dept. of Chemistry and
Biochemistry and the Molecular Biology Inst., University of California,
P. O. Box 951569, Los Angeles, CA 90095-1569. Tel.: 310-825-1620; Fax:
310-267-2302; E-mail: gralla@chem.ucla.edu.
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