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Indirect Read-out of the Promoter DNA by RNA Polymerase in the Closed Complex

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Title Indirect Read-out of the Promoter DNA by RNA Polymerase in the Closed Complex
 
Creator Debnath, Subrata
Roy, Neeladri Sekhar
Bera, Indrani
Ghoshal, Nanda
Roy, Siddhartha
 
Subject Structural Biology & Bioinformatics
 
Description Transcription is initiated when RNA polymerase
recognizes the duplex promoter DNA in the closed
complex. Due to its transient nature, the closed
complex has not been well characterized. How the
initial promoter recognition occurs may offer
important clues to regulation of transcription initiation.
In this article, we have carried out single-base
pair substitution experiments on two Escherichia coli
promoters belonging to two different classes, the
�35 and the extended �10, under conditions which
stabilize the closed complex. Single-base pair substitution
experiments indicate modest base-specific
effects on the stability of the closed complex of both
promoters. Mutations of base pairs in the �10 region
affect the closed complexes of two promoters differently,
suggesting different modes of interaction of
the RNA polymerase and the promoter in the two
closed complexes. Two residues on p70 which have
been suggested to play important role in promoter
recognition, Q437 and R436, were mutated and
found to have different effects on the closedcomplex
stability. DNA circular dichroism (CD) and
FRET suggest that the promoter DNA in the closed
complex is distorted. Modeling suggests two
different orientations of the recognition helix of the
RNA polymerase in the closed complex. We propose
that the RNA polymerase recognizes the sequence
dependent conformation of the promoter DNA in
the closed complex
 
Publisher Oxford University Press
 
Date 2013
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://www.eprints.iicb.res.in/1818/1/NUCLEIC_ACIDS_RESEARCH___41__(_1)366%2D377;2013[20].pdf
Debnath, Subrata and Roy, Neeladri Sekhar and Bera, Indrani and Ghoshal, Nanda and Roy, Siddhartha (2013) Indirect Read-out of the Promoter DNA by RNA Polymerase in the Closed Complex. Nucleic Acids Research, 41 (1). pp. 366-377.
 
Relation http://dx.doi.org/10.1093/nar/gks1018
http://www.eprints.iicb.res.in/1818/