In vitro studies of transcript initiation by Escherichia coli RNA polymerase. 3. Influences of individual DNA elements within the promoter recognition region on abortive initiation and promoter escape
- PMID: 12667071
- DOI: 10.1021/bi026962v
In vitro studies of transcript initiation by Escherichia coli RNA polymerase. 3. Influences of individual DNA elements within the promoter recognition region on abortive initiation and promoter escape
Abstract
Abortive initiation and promoter escape are two principal biochemical reactions occurring in the latter stage of transcript initiation. We have analyzed the influences of individual DNA elements within the promoter recognition region (PRR) on these reactions by measuring the quantitative initiation parameters that describe abortive initiation and promoter escape; these parameters are the abortive rate, the productive rate, the abortive:productive ratio, the abortive probability, and the maximum size of abortive transcripts. Changes in the individual DNA elements within the PRR can have a substantial effect on each of these parameters. The discriminator region and the -10 element primarily influence the abortive probability at positions 2-5 and 6-10, respectively, while the -10 and -35 conserved hexamers and the spacer region affect the abortive probability at positions 11-15. Surprisingly, transcription of a consensus promoter invariably gives a higher abortive yield, a higher abortive probability, a longer abortive ladder, and a lower productive rate than promoter variants carrying even a single deviation in the consensus hexamers. These results suggest that strong RNA polymerase-PRR interactions stall the polymerase at the promoter, thereby reducing the rate of promoter escape and consequently enhancing the extent of abortive initiation.
Similar articles
-
In vitro studies of transcript initiation by Escherichia coli RNA polymerase. 2. Formation and characterization of two distinct classes of initial transcribing complexes.Biochemistry. 2003 Apr 8;42(13):3787-97. doi: 10.1021/bi0269613. Biochemistry. 2003. PMID: 12667070
-
In vitro studies of transcript initiation by Escherichia coli RNA polymerase. 1. RNA chain initiation, abortive initiation, and promoter escape at three bacteriophage promoters.Biochemistry. 2003 Apr 8;42(13):3777-86. doi: 10.1021/bi026954e. Biochemistry. 2003. PMID: 12667069
-
An alternate mechanism of abortive release marked by the formation of very long abortive transcripts.Biochemistry. 2007 Nov 6;46(44):12687-99. doi: 10.1021/bi701236f. Epub 2007 Oct 11. Biochemistry. 2007. PMID: 17929835
-
Promoter clearance and escape in prokaryotes.Biochim Biophys Acta. 2002 Sep 13;1577(2):191-207. doi: 10.1016/s0167-4781(02)00452-9. Biochim Biophys Acta. 2002. PMID: 12213652 Review.
-
[Interactions of DNA-dependent bacterial RNA polymerase with promoters].Mol Biol (Mosk). 2007 May-Jun;41(3):423-32. Mol Biol (Mosk). 2007. PMID: 17685221 Review. Russian.
Cited by
-
Alteration of the -35 and -10 sequences and deletion the upstream sequence of the -35 region of the promoter A1 of the phage T7 in dsDNA confirm the contribution of non-specific interactions with E. coli RNA polymerase to the transcription initiation process.Front Mol Biosci. 2024 Jan 8;10:1335409. doi: 10.3389/fmolb.2023.1335409. eCollection 2023. Front Mol Biosci. 2024. PMID: 38259683 Free PMC article.
-
Functional dissection of the catalytic mechanism of mammalian RNA polymerase II.Biochem Cell Biol. 2005 Aug;83(4):497-504. doi: 10.1139/o05-061. Biochem Cell Biol. 2005. PMID: 16094453 Free PMC article. Review.
-
The interaction between sigma70 and the beta-flap of Escherichia coli RNA polymerase inhibits extension of nascent RNA during early elongation.Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4488-93. doi: 10.1073/pnas.0409850102. Epub 2005 Mar 10. Proc Natl Acad Sci U S A. 2005. PMID: 15761057 Free PMC article.
-
Recent Advances in Understanding σ70-Dependent Transcription Initiation Mechanisms.J Mol Biol. 2019 Sep 20;431(20):3947-3959. doi: 10.1016/j.jmb.2019.04.046. Epub 2019 May 11. J Mol Biol. 2019. PMID: 31082441 Free PMC article. Review.
-
Open complex scrunching before nucleotide addition accounts for the unusual transcription start site of E. coli ribosomal RNA promoters.Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):E1787-95. doi: 10.1073/pnas.1522159113. Epub 2016 Mar 14. Proc Natl Acad Sci U S A. 2016. PMID: 26976590 Free PMC article.
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources
