TY - JOUR
T1 - Region 3.2 of the factor controls the stability of rRNA promoter complexes and potentiates their repression by DksA
AU - Pupov, Danil
AU - Petushkov, Ivan
AU - Esyunina, Daria
AU - Murakami, Katsuhiko S.
AU - Kulbachinskiy, Andrey
N1 - Funding Information:
Russian Science Foundation [16-14-10377 to D.E.] (analysis of rRNA transcription); Russian Foundation for Basic Research [RFBR 16-34-60237 to D.E., 17-04-02133 to D.P.]; National Institutes of Health (NIH) [GM087350 to K.S.M.]. Funding for open access charge: Russian Science Foundation [16-14-10377]. Conflict of interest statement. None declared.
Publisher Copyright:
© The Author(s) 2018.
PY - 2018/11/30
Y1 - 2018/11/30
N2 - The factor drives promoter recognition by bacterial RNA polymerase (RNAP) and is also essential for later steps of transcription initiation, including RNA priming and promoter escape. Conserved region 3.2 of the primary factor (‘ finger’) directly contacts the template DNA strand in the open promoter complex and facilitates initiating NTP binding in the active center of RNAP. Ribosomal RNA promoters are responsible for most RNA synthesis during exponential growth but should be silenced during the stationary phase to save cell resources. In Escherichia coli, the silencing mainly results from the action of the secondary channel factor DksA, which together with ppGpp binds RNAP and dramatically decreases the stability of intrinsically unstable rRNA promoter complexes. We demonstrate that this switch depends on the finger that destabilizes RNAP–promoter interactions. Mutations in the finger moderately decrease initiating NTP binding but significantly increase promoter complex stability and reduce DksA affinity to the RNAP–rRNA promoter complex, thus making rRNA transcription less sensitive to DksA/ppGpp both in vitro and in vivo. Thus, destabilization of rRNA promoter complexes by the finger makes them a target for robust regulation by the stringent response factors under stress conditions.
AB - The factor drives promoter recognition by bacterial RNA polymerase (RNAP) and is also essential for later steps of transcription initiation, including RNA priming and promoter escape. Conserved region 3.2 of the primary factor (‘ finger’) directly contacts the template DNA strand in the open promoter complex and facilitates initiating NTP binding in the active center of RNAP. Ribosomal RNA promoters are responsible for most RNA synthesis during exponential growth but should be silenced during the stationary phase to save cell resources. In Escherichia coli, the silencing mainly results from the action of the secondary channel factor DksA, which together with ppGpp binds RNAP and dramatically decreases the stability of intrinsically unstable rRNA promoter complexes. We demonstrate that this switch depends on the finger that destabilizes RNAP–promoter interactions. Mutations in the finger moderately decrease initiating NTP binding but significantly increase promoter complex stability and reduce DksA affinity to the RNAP–rRNA promoter complex, thus making rRNA transcription less sensitive to DksA/ppGpp both in vitro and in vivo. Thus, destabilization of rRNA promoter complexes by the finger makes them a target for robust regulation by the stringent response factors under stress conditions.
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U2 - 10.1093/nar/gky919
DO - 10.1093/nar/gky919
M3 - Article
C2 - 30321408
AN - SCOPUS:85061162813
SN - 0305-1048
VL - 46
SP - 11477
EP - 11487
JO - Nucleic acids research
JF - Nucleic acids research
IS - 21
ER -