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Transcription pausing by Escherichia coli RNA polymerase is modulated by downstream DNA sequences.
J Biol Chem. 1990 Sep 05; 265(25):15145-53.JB

Abstract

Escherichia coli RNA polymerase pauses immediately after transcription of certain sequences that can form stable secondary structures in the nascent RNA transcript; pausing appears to be essential for several types of bacterial transcription attenuation mechanisms. Because base changes that weaken the RNA secondary structures reduce the half-life of pausing by RNA polymerase, nascent transcript RNA hairpins are thought to cause pausing at these sites. We show here that, for the well characterized trpL pause site, the determinants of transcription pausing are not limited to the RNA hairpin, but include the not-yet-transcribed sequence of DNA immediately downstream from the pause site. We show that this effect extends to bases up to fourteen nucleotides downstream from the pause site, that placement of a oligo(dT) tract in the nontranscribed strand in this region does not convert the pause site to a termination site, and that shifting the position of pausing by one nucleotide downstream almost eliminates pausing. From an analysis of many variants of this downstream sequence, we argue that the effect of downstream sequence is not related simply to its GC content. We suggest that these effects are mediated by altered interactions between RNA polymerase and the DNA template downstream from the enzyme's active site.

Authors+Show Affiliations

Department of Biology, Washington University, St. Louis, Missouri 63130.No affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, U.S. Gov't, P.H.S.

Language

eng

PubMed ID

1697586

Citation

Lee, D N., et al. "Transcription Pausing By Escherichia Coli RNA Polymerase Is Modulated By Downstream DNA Sequences." The Journal of Biological Chemistry, vol. 265, no. 25, 1990, pp. 15145-53.
Lee DN, Phung L, Stewart J, et al. Transcription pausing by Escherichia coli RNA polymerase is modulated by downstream DNA sequences. J Biol Chem. 1990;265(25):15145-53.
Lee, D. N., Phung, L., Stewart, J., & Landick, R. (1990). Transcription pausing by Escherichia coli RNA polymerase is modulated by downstream DNA sequences. The Journal of Biological Chemistry, 265(25), 15145-53.
Lee DN, et al. Transcription Pausing By Escherichia Coli RNA Polymerase Is Modulated By Downstream DNA Sequences. J Biol Chem. 1990 Sep 5;265(25):15145-53. PubMed PMID: 1697586.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Transcription pausing by Escherichia coli RNA polymerase is modulated by downstream DNA sequences. AU - Lee,D N, AU - Phung,L, AU - Stewart,J, AU - Landick,R, PY - 1990/9/5/pubmed PY - 1990/9/5/medline PY - 1990/9/5/entrez SP - 15145 EP - 53 JF - The Journal of biological chemistry JO - J. Biol. Chem. VL - 265 IS - 25 N2 - Escherichia coli RNA polymerase pauses immediately after transcription of certain sequences that can form stable secondary structures in the nascent RNA transcript; pausing appears to be essential for several types of bacterial transcription attenuation mechanisms. Because base changes that weaken the RNA secondary structures reduce the half-life of pausing by RNA polymerase, nascent transcript RNA hairpins are thought to cause pausing at these sites. We show here that, for the well characterized trpL pause site, the determinants of transcription pausing are not limited to the RNA hairpin, but include the not-yet-transcribed sequence of DNA immediately downstream from the pause site. We show that this effect extends to bases up to fourteen nucleotides downstream from the pause site, that placement of a oligo(dT) tract in the nontranscribed strand in this region does not convert the pause site to a termination site, and that shifting the position of pausing by one nucleotide downstream almost eliminates pausing. From an analysis of many variants of this downstream sequence, we argue that the effect of downstream sequence is not related simply to its GC content. We suggest that these effects are mediated by altered interactions between RNA polymerase and the DNA template downstream from the enzyme's active site. SN - 0021-9258 UR - https://www.unboundmedicine.com/medline/citation/1697586/Transcription_pausing_by_Escherichia_coli_RNA_polymerase_is_modulated_by_downstream_DNA_sequences_ L2 - http://www.jbc.org/cgi/pmidlookup?view=long&pmid=1697586 DB - PRIME DP - Unbound Medicine ER -