Escherichia coli DksA binds to Free RNA polymerase with higher affinity than to RNA polymerase in an open complex.
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.
Lennon
Christopher W
CW
Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA.
Gaal
Tamas
T
Ross
Wilma
W
Gourse
Richard L
RL
D001665:Binding Sites; D020134:Catalytic Domain; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D005296:Ferrous Compounds / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D020035:Holoenzymes; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation
D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D005296:Ferrous Compounds; D020035:Holoenzymes; C090751:dksA protein, E coli; D012321:DNA-Directed RNA Polymerases