Open AccessEscherichia coli DksA Binds to Free RNA Polymerase with Higher Affinity than to RNA Polymerase in an Open Complex
Author(s) -
Christopher Len,
Tamás Gaál,
Wilma Ross,
Richard L. Gourse
Publication year - 2009
Publication title -
journal of bacteriology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.652
H-Index - 246
eISSN - 1067-8832
pISSN - 0021-9193
DOI - 10.1128/jb.00621-09
Subject(s) - biology , rna polymerase , polymerase , escherichia coli , rna dependent rna polymerase , rna polymerase i , rna , microbiology and biotechnology , rna editing , genetics , dna , gene
The transcription factor DksA binds in the secondary channel of RNA polymerase (RNAP) and alters transcriptional output without interacting with DNA. Here we present a quantitative assay for measuring DksA binding affinity and illustrate its utility by determining the relative affinities of DksA for three different forms of RNAP. Whereas the apparent affinities of DksA for RNAP core and holoenzyme are the same, the apparent affinity of DksA for RNAP decreases almost 10-fold in an open complex. These results suggest that the conformation of RNAP present in an open complex is not optimal for DksA binding and that DNA directly or indirectly alters the interface between the two proteins.