Transcription initiation factor DksA has diverse effects on RNA chain elongation.
Bacterial transcription factors DksA and GreB belong to a family of coiled-coil proteins that bind within the secondary channel of RNA polymerase (RNAP). These proteins display structural homology but play different regulatory roles. DksA disrupts RNAP interactions with promoter DNA and inhibits formation of initiation complexes, sensitizing rRNA synthesis to changes in concentrations of ppGpp and NTPs. Gre proteins remodel the RNAP active site and facilitate cleavage of the nascent RNA in elongation complexes. However, DksA and GreB were shown to have overlapping effects during initiation, and in vivo studies suggested that DksA may also function at post-initiation steps. Here we show that DksA has many features of an elongation factor: it inhibits both RNA chain extension and RNA shortening by exonucleolytic cleavage or pyrophosphorolysis and increases intrinsic termination in vitro and in vivo. However, DksA has no effect on Rho- or Mfd-mediated RNA release or nascent RNA cleavage in backtracked complexes, the regulatory target of Gre factors. Our results reveal that DksA effects on elongating RNAP are very different from those of GreB, suggesting that these regulators recognize distinct states of the transcription complex.
Department of Microbiology and The Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA.
Ran
R
Furman
Anastasiya
A
Sevostyanova
Irina
I
Artsimovitch
D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism*; D006159:Guanosine Tetraphosphate / Q000378:metabolism; D012313:RNA / Q000378:metabolism; D012234:Rho Factor / Q000378:metabolism; D014158:Transcription, Genetic; D035602:Transcriptional Elongation Factors / Q000737:chemistry / Q000378:metabolism*
D029968:Escherichia coli Proteins; C079667:GreB protein, E coli; D012234:Rho Factor; D035602:Transcriptional Elongation Factors; C090751:dksA protein, E coli; D006159:Guanosine Tetraphosphate; D012313:RNA; D012321:DNA-Directed RNA Polymerases