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Characterization of structural features important for T7 RNAP elongation complex stability reveals competing complex conformations and a role for the non-template strand in RNA displacement

Identifieur interne : 001208 ( Istex/Checkpoint ); précédent : 001207; suivant : 001209

Characterization of structural features important for T7 RNAP elongation complex stability reveals competing complex conformations and a role for the non-template strand in RNA displacement

Auteurs : Vijaya Gopal [États-Unis] ; Luis G. Brieba [États-Unis] ; Richard Guajardo [États-Unis] ; William T. Mcallister [États-Unis] ; Rui Sousa [États-Unis]

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RBID : ISTEX:A9584748DE4781A7EB1992E66FB57FB90D837D14

English descriptors

Abstract

Abstract: We have characterized the roles of the phage T7 RNA polymerase (RNAP) thumb subdomain and the RNA binding activity of the N-terminal domain in elongation complex (EC) stability by evaluating how disrupting these structures affects the dissociation rates of halted ECs. Our results reveal distinct roles for these elements in EC stabilization. On supercoiled or partially single-stranded templates the enzyme with a deletion of the thumb subdomain is exceptionally unstable. However, on linear duplex templates the polymerase which has been proteolytically cleaved within the N-terminal domain is the most unstable. The differences in the effects of these RNAP modifications on the stability of ECs on the different templates appear to be due to differences in EC structure: on the linear duplex templates the RNA is properly displaced from the DNA, but on the supercoiled or partially single-stranded templates an extended RNA:DNA hybrid makes a larger contribution to the conformational state of the EC. The halted EC can therefore exist either in a conformation in which the RNA is displaced from the DNA and forms an interaction with the RNAP, or in a conformation in which a more extended RNA:DNA hybrid is present and the RNA:RNAP interaction is less extensive. The partitioning between these competing conformations appears to be a function of the energetics of template reannealing and the relative strengths of the RNA:RNAP interaction and the RNA:DNA hybrid.

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DOI: 10.1006/jmbi.1999.2836


Affiliations:


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ISTEX:A9584748DE4781A7EB1992E66FB57FB90D837D14

Le document en format XML

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<term>D.S.</term>
<term>EC</term>
<term>EtBr</term>
<term>NT</term>
<term>P.S.S.</term>
<term>RNA:DNA hybrid</term>
<term>RNAP</term>
<term>T7 RNA polymerase</term>
<term>ThΔ</term>
<term>elongation complex</term>
<term>processivity</term>
<term>transcription</term>
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<keywords scheme="Teeft" xml:lang="en">
<term>Acad</term>
<term>Active elongation</term>
<term>Apparent rnase</term>
<term>Bacteriophage</term>
<term>Base transcripts</term>
<term>Binary complexes</term>
<term>Binding activity</term>
<term>Binding site</term>
<term>Biochemistry</term>
<term>Biol</term>
<term>Chem</term>
<term>Coli</term>
<term>Coli rnap</term>
<term>Conformation</term>
<term>Cutoff membranes</term>
<term>Ddtmp incorporation</term>
<term>Ddttp</term>
<term>Degradation products</term>
<term>Denaturation</term>
<term>Dissociation rates</term>
<term>Dnase</term>
<term>Duplex</term>
<term>Duplex templates</term>
<term>Elongation</term>
<term>Enzyme</term>
<term>Enzyme forms</term>
<term>Enzyme reaction</term>
<term>Escherichia</term>
<term>Escherichia coli</term>
<term>Hairpin formation</term>
<term>Hybrid</term>
<term>Hybrid formation</term>
<term>Ikeda</term>
<term>Ikeda richardson</term>
<term>Intact enzyme</term>
<term>Intact enzymes</term>
<term>Lilley houghton</term>
<term>Linear duplex templates</term>
<term>Linear template</term>
<term>Linear templates</term>
<term>Linearized</term>
<term>Ltrate</term>
<term>Mcallister</term>
<term>Misincorporation</term>
<term>Molar amount</term>
<term>Multisubunit rnaps</term>
<term>Mutant</term>
<term>Natl</term>
<term>Natl acad</term>
<term>Ntps</term>
<term>Persistent hybrids</term>
<term>Plasmid</term>
<term>Polymerase</term>
<term>Poor activity</term>
<term>Proc</term>
<term>Processivity</term>
<term>Promoter</term>
<term>Proteolytic nicking</term>
<term>Reannealing</term>
<term>Reannealing template</term>
<term>Replication</term>
<term>Replication origins</term>
<term>Retenate</term>
<term>Rna</term>
<term>Rnap</term>
<term>Rnap elongation</term>
<term>Rnaps</term>
<term>Rnase</term>
<term>Room temperature</term>
<term>Runoff</term>
<term>Runoff product</term>
<term>Runoff transcript</term>
<term>Runoff transcription</term>
<term>Runoff transcripts</term>
<term>Short transcripts</term>
<term>Sousa</term>
<term>Stability figure</term>
<term>Strand</term>
<term>Strand invasion</term>
<term>Strand reannealing</term>
<term>Subdomain</term>
<term>Such conditions</term>
<term>Such hybrids</term>
<term>Such templates</term>
<term>Supercoiled</term>
<term>Supercoiled template</term>
<term>Supercoiled templates</term>
<term>Supercoiling</term>
<term>Synthetic promoters</term>
<term>Template</term>
<term>Template reannealing</term>
<term>Template strand</term>
<term>Template structure</term>
<term>Terminator</term>
<term>Thumb subdomain</term>
<term>Time point</term>
<term>Transcript</term>
<term>Transcript generation</term>
<term>Transcript synthesis</term>
<term>Transcription</term>
<term>Transcription bubble</term>
<term>Transcription reactions</term>
<term>Turnover</term>
<term>Turnover rate</term>
<term>Turnover rates</term>
<term>Unreacted</term>
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<div type="abstract" xml:lang="en">Abstract: We have characterized the roles of the phage T7 RNA polymerase (RNAP) thumb subdomain and the RNA binding activity of the N-terminal domain in elongation complex (EC) stability by evaluating how disrupting these structures affects the dissociation rates of halted ECs. Our results reveal distinct roles for these elements in EC stabilization. On supercoiled or partially single-stranded templates the enzyme with a deletion of the thumb subdomain is exceptionally unstable. However, on linear duplex templates the polymerase which has been proteolytically cleaved within the N-terminal domain is the most unstable. The differences in the effects of these RNAP modifications on the stability of ECs on the different templates appear to be due to differences in EC structure: on the linear duplex templates the RNA is properly displaced from the DNA, but on the supercoiled or partially single-stranded templates an extended RNA:DNA hybrid makes a larger contribution to the conformational state of the EC. The halted EC can therefore exist either in a conformation in which the RNA is displaced from the DNA and forms an interaction with the RNAP, or in a conformation in which a more extended RNA:DNA hybrid is present and the RNA:RNAP interaction is less extensive. The partitioning between these competing conformations appears to be a function of the energetics of template reannealing and the relative strengths of the RNA:RNAP interaction and the RNA:DNA hybrid.</div>
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