Preferential Interaction of the His Pause RNA Hairpin with RNA Polymerase Beta Subunit Residues 904-950 Correlates with Strong Transcriptional Pausing

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1997 Aug 5

PMID 9237994

Citations 15

Authors

D Wang

K Severinov

R Landick

Affiliations

Soon will be listed here.

Abstract

RNA secondary structures (hairpins) that form as the nascent RNA emerges from RNA polymerase are important components of many signals that regulate transcription, including some pause sites, all rho-independent terminators, and some antiterminators. At the his leader pause site, a 5-bp-stem, 8-nt-loop pause RNA hairpin forms 11 nt from the RNA 3' end and stabilizes a transcription complex conformation slow to react with NTP substrate. This stabilization appears to depend at least in part on an interaction with RNA polymerase. We tested for RNA hairpin interaction with the paused polymerase by crosslinking 5-iodoUMP positioned specifically in the hairpin loop. In the paused conformation, strong and unusual crosslinking of the pause hairpin to beta904-950 replaced crosslinking to beta' and to other parts of beta that occurred in nonpaused complexes prior to hairpin formation. These changes in nascent RNA interactions may inhibit reactive alignment of the RNA 3' end in the paused complex and be related to events at rho-independent terminators.

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References

Landick R, Colwell A, Stewart J . Insertional mutagenesis of a plasmid-borne Escherichia coli rpoB gene reveals alterations that inhibit beta-subunit assembly into RNA polymerase. J Bacteriol. 1990; 172(6):2844-54. PMC: 209080. DOI: 10.1128/jb.172.6.2844-2854.1990. View

Arndt K, CHAMBERLIN M . RNA chain elongation by Escherichia coli RNA polymerase. Factors affecting the stability of elongating ternary complexes. J Mol Biol. 1990; 213(1):79-108. DOI: 10.1016/S0022-2836(05)80123-8. View

dAubenton Carafa Y, BRODY E, Thermes C . Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures. J Mol Biol. 1990; 216(4):835-58. DOI: 10.1016/s0022-2836(99)80005-9. View

Yano R, Nomura M . Suppressor analysis of temperature-sensitive mutations of the largest subunit of RNA polymerase I in Saccharomyces cerevisiae: a suppressor gene encodes the second-largest subunit of RNA polymerase I. Mol Cell Biol. 1991; 11(2):754-64. PMC: 359727. DOI: 10.1128/mcb.11.2.754-764.1991. View

Cheng S, Lynch E, Leason K, Court D, Shapiro B, Friedman D . Functional importance of sequence in the stem-loop of a transcription terminator. Science. 1991; 254(5035):1205-7. DOI: 10.1126/science.1835546. View

Borukhov S, Severinov K, Kashlev M, Lebedev A, Bass I, Rowland G . Mapping of trypsin cleavage and antibody-binding sites and delineation of a dispensable domain in the beta subunit of Escherichia coli RNA polymerase. J Biol Chem. 1991; 266(35):23921-6. View

Reynolds R, Bermudez-Cruz R, CHAMBERLIN M . Parameters affecting transcription termination by Escherichia coli RNA polymerase. I. Analysis of 13 rho-independent terminators. J Mol Biol. 1992; 224(1):31-51. DOI: 10.1016/0022-2836(92)90574-4. View

Frankel A . Activation of HIV transcription by Tat. Curr Opin Genet Dev. 1992; 2(2):293-8. DOI: 10.1016/s0959-437x(05)80287-4. View

Lee D, Landick R . Structure of RNA and DNA chains in paused transcription complexes containing Escherichia coli RNA polymerase. J Mol Biol. 1992; 228(3):759-77. DOI: 10.1016/0022-2836(92)90862-e. View

10.

Richardson J . Transcription termination. Crit Rev Biochem Mol Biol. 1993; 28(1):1-30. DOI: 10.3109/10409239309082571. View

11.

Lewicki B, Margus T, Remme J, Nierhaus K . Coupling of rRNA transcription and ribosomal assembly in vivo. Formation of active ribosomal subunits in Escherichia coli requires transcription of rRNA genes by host RNA polymerase which cannot be replaced by bacteriophage T7 RNA polymerase. J Mol Biol. 1993; 231(3):581-93. DOI: 10.1006/jmbi.1993.1311. View

12.

Das A . Control of transcription termination by RNA-binding proteins. Annu Rev Biochem. 1993; 62:893-930. DOI: 10.1146/annurev.bi.62.070193.004333. View

13.

Chan C, Landick R . Dissection of the his leader pause site by base substitution reveals a multipartite signal that includes a pause RNA hairpin. J Mol Biol. 1993; 233(1):25-42. DOI: 10.1006/jmbi.1993.1482. View

14.

Willis M, Hicke B, Uhlenbeck O, Cech T, Koch T . Photocrosslinking of 5-iodouracil-substituted RNA and DNA to proteins. Science. 1993; 262(5137):1255-7. DOI: 10.1126/science.7694369. View

15.

Archambault J, Friesen J . Genetics of eukaryotic RNA polymerases I, II, and III. Microbiol Rev. 1993; 57(3):703-24. PMC: 372932. DOI: 10.1128/mr.57.3.703-724.1993. View

16.

Wilson K, von Hippel P . Stability of Escherichia coli transcription complexes near an intrinsic terminator. J Mol Biol. 1994; 244(1):36-51. DOI: 10.1006/jmbi.1994.1702. View

17.

McDowell J, Roberts J, Jin D, Gross C . Determination of intrinsic transcription termination efficiency by RNA polymerase elongation rate. Science. 1994; 266(5186):822-5. DOI: 10.1126/science.7526463. View

18.

WEILBAECHER R, Hebron C, Feng G, Landick R . Termination-altering amino acid substitutions in the beta' subunit of Escherichia coli RNA polymerase identify regions involved in RNA chain elongation. Genes Dev. 1994; 8(23):2913-27. DOI: 10.1101/gad.8.23.2913. View

19.

Wang D, Meier T, Chan C, Feng G, Lee D, Landick R . Discontinuous movements of DNA and RNA in RNA polymerase accompany formation of a paused transcription complex. Cell. 1995; 81(3):341-50. DOI: 10.1016/0092-8674(95)90387-9. View

20.

Nudler E, Kashlev M, Nikiforov V, Goldfarb A . Coupling between transcription termination and RNA polymerase inchworming. Cell. 1995; 81(3):351-7. DOI: 10.1016/0092-8674(95)90388-7. View