Two modes of transcription initiation in vitro at the rrnB P1 promoter of Escherichia coli
- PMID: 8226874
Two modes of transcription initiation in vitro at the rrnB P1 promoter of Escherichia coli
Abstract
The rrnB P1 promoter of Escherichia coli (starting sequence C-4-A-3-C-2-C-1-A+1-C+2-U+3-G+4) forms a binary complex with RNA polymerase that is highly unstable and requires the presence of transcription substrates ATP and CTP for stabilizing the enzyme-DNA association (Gourse, R. L. (1988) Nucleic Acids Res. 16, 9789-9809). We show that in the absence of UTP and GTP the stabilization is accomplished by short RNA oligomers synthesized in an unusual "-3-->" mode whereby the primer initiated at the +1 site presumably slips back by three nucleotides into the -3 site and is then extended yielding stable ternary complexes. By contrast, short oligomers initiated in the conventional "+1-->" mode without slippage do not exert the stabilization effect and are readily aborted from the promoter complex. The stable -3-->ternary complexes carry sigma factor but otherwise resemble elongation complexes in their high salt stability and in the fact that they are formed with a mutant RNA polymerase deficient in promoter binding. A model is proposed explaining the stability of the -3-->ternary complexes by RNA slipping into a putative "tight RNA binding site" in RNA polymerase which is normally occupied by RNA during elongation.
Similar articles
-
Transcription of the Escherichia coli rrnB P1 promoter by the heat shock RNA polymerase (E sigma 32) in vitro.J Bacteriol. 1993 Feb;175(3):661-8. doi: 10.1128/jb.175.3.661-668.1993. J Bacteriol. 1993. PMID: 8423142 Free PMC article.
-
The bacterial DNA-binding protein H-NS represses ribosomal RNA transcription by trapping RNA polymerase in the initiation complex.J Mol Biol. 2000 May 19;298(5):737-48. doi: 10.1006/jmbi.2000.3708. J Mol Biol. 2000. PMID: 10801345
-
Factor-independent activation of Escherichia coli rRNA transcription. II. characterization of complexes of rrnB P1 promoters containing or lacking the upstream activator region with Escherichia coli RNA polymerase.J Mol Biol. 1991 Aug 5;220(3):569-83. doi: 10.1016/0022-2836(91)90101-b. J Mol Biol. 1991. PMID: 1651394
-
Antagonistic regulation of Escherichia coli ribosomal RNA rrnB P1 promoter activity by GreA and DksA.J Biol Chem. 2006 Jun 2;281(22):15238-48. doi: 10.1074/jbc.M601531200. Epub 2006 Apr 5. J Biol Chem. 2006. PMID: 16597620
-
Possible roles of σ-dependent RNA polymerase pausing in transcription regulation.RNA Biol. 2017 Dec 2;14(12):1678-1682. doi: 10.1080/15476286.2017.1356568. Epub 2017 Sep 13. RNA Biol. 2017. PMID: 28816625 Free PMC article. Review.
Cited by
-
Identification of an UP element consensus sequence for bacterial promoters.Proc Natl Acad Sci U S A. 1998 Aug 18;95(17):9761-6. doi: 10.1073/pnas.95.17.9761. Proc Natl Acad Sci U S A. 1998. PMID: 9707549 Free PMC article.
-
Topology of the RNA polymerase active center probed by chimeric rifampicin-nucleotide compounds.Proc Natl Acad Sci U S A. 1994 Dec 6;91(25):12036-40. doi: 10.1073/pnas.91.25.12036. Proc Natl Acad Sci U S A. 1994. PMID: 7991580 Free PMC article.
-
Bacterial RNA Polymerase-DNA Interaction-The Driving Force of Gene Expression and the Target for Drug Action.Front Mol Biosci. 2016 Nov 9;3:73. doi: 10.3389/fmolb.2016.00073. eCollection 2016. Front Mol Biosci. 2016. PMID: 27882317 Free PMC article. Review.
-
An intersubunit contact stimulating transcription initiation by E coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4.Genes Dev. 2003 May 15;17(10):1293-307. doi: 10.1101/gad.1079403. Genes Dev. 2003. PMID: 12756230 Free PMC article.
-
Activation of Escherichia coli rRNA transcription by FIS during a growth cycle.J Bacteriol. 1998 Mar;180(6):1525-32. doi: 10.1128/JB.180.6.1525-1532.1998. J Bacteriol. 1998. PMID: 9515922 Free PMC article.
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources
