The RNA–DNA Hybrid Maintains the Register of Transcription by Preventing Backtracking of RNA Polymerase

Nudler, Evgeny; Mustaev, Arkady; Goldfarb, Alex; Lukhtanov, Evgeny A.

doi:10.1016/s0092-8674(00)80180-4

Cited by 420 publications

(459 citation statements)

References 44 publications

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“…32, whereas the RNA-RNA (folding) contribution is obtained from the VIENNARNA package (33). The number of hypertranslocated configurations is bounded by the length of the hybrid, whereas the backtracked ones are fixed at 9, to account for paused complexes known to backtrack by Ͼ6 nt (36). Increasing backtracking beyond 9 nt does not affect our results in the presence of RNA folding (see below).…”

Section: Statistical Mechanics Approachmentioning

confidence: 99%

“…[Note that, as in the gel experiments used to identify transcriptional pauses (36)(37)(38), a pause site refers to the transcript length for which pausing occurs, without reference to the precise backtracked position along the template.] The cutoff parameter, (0 Ͻ Ͻ 1), is determined by optimizing the statistical significance of our predictions over all experimental templates.…”

Section: Statistical Mechanics Approachmentioning

confidence: 99%

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Thermodynamic and kinetic modeling of transcriptional pausing

Tadigotla

Maoiléidigh

Sengupta

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

106

185

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We present a statistical mechanics approach for the prediction of backtracked pauses in bacterial transcription elongation derived from structural models of the transcription elongation complex (EC). Our algorithm is based on the thermodynamic stability of the EC along the DNA template calculated from the sequence-dependent free energy of DNA–DNA, DNA–RNA, and RNA–RNA base pairing associated with ( i ) the translocational and size fluctuations of the transcription bubble; ( ii ) changes in the associated DNA–RNA hybrid; and ( iii ) changes in the cotranscriptional RNA secondary structure upstream of the RNA exit channel. The calculations involve no adjustable parameters except for a cutoff used to discriminate paused from nonpaused complexes. When applied to 100 experimental pauses in transcription elongation by Escherichia coli RNA polymerase on 10 DNA templates, the approach produces statistically significant results. We also present a kinetic model for the rate of recovery of backtracked paused complexes. A crucial ingredient of our model is the incorporation of kinetic barriers to backtracking resulting from steric clashes of EC with the cotranscriptionally generated RNA secondary structure, an aspect not included explicitly in previous attempts at modeling the transcription elongation process.

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Section: Statistical Mechanics Approachmentioning

confidence: 99%

Section: Statistical Mechanics Approachmentioning

confidence: 99%

Thermodynamic and kinetic modeling of transcriptional pausing

Tadigotla

Maoiléidigh

Sengupta

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

106

185

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show abstract

“…After misincorporation, the mismatched nucleotide at position +1 of the RNA is frayed away from the template, thereby pausing RNAP. Pausing is the first step in backtracking [63,[76][77][78][79][80][81][82][83]. The frayed nucleotide then inhibits RNA extension, because it prevents NTP binding, but favors backtracking, because the bp in position +1 is disrupted.…”

Section: Model For Transcriptional Proofreadingmentioning

confidence: 99%

RNA polymerase fidelity and transcriptional proofreading

Sydow

Cramer

2009

Current Opinion in Structural Biology

144

133

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Whereas mechanisms underlying the fidelity of DNA polymerases (DNAPs) have been investigated in detail, RNA polymerase (RNAP) fidelity mechanisms remained poorly understood. New functional and structural studies now suggest how RNAPs select the correct nucleoside triphosphate (NTP) substrate to prevent transcription errors, and how the enzymes detect and remove a misincorporated nucleotide during proofreading. Proofreading begins with fraying of the misincorporated nucleotide away from the DNA template, which pauses transcription. Subsequent backtracking of RNAP by one position enables nucleolytic cleavage of an RNA dinucleotide that contains the misincorporated nucleotide. Since cleavage occurs at the same active site that is used for polymerization, the RNAP proofreading mechanism differs from that used by DNAPs, which contain a distinct nuclease specific active site.

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“…Although efficient cleavage occurs in vitro only in the presence of a stimulatory factor, hydrolytic transcript cleavage is an intrinsic activity of the RNAP (Orlova et al 1994;Rudd et al 1994) and is believed to be promoted by the RNAP active center (Rudd et al 1994). The active center can approach the scissile phosphodiester bond by upstream sliding of RNAP along the transcript (Komissarova and Kashlev 1997;Nudler et al 1997), as shown in Figure 7, structure III (the endonucleolysis-ready form). Structure III is incapable of transcript elongation.…”

Section: Structure and Properties Of A Transcription Elongation Complexmentioning

confidence: 99%

The Nun protein of bacteriophage HK022 inhibits translocation of Escherichia coliRNA polymerase without abolishing its catalytic activities

Hung¹,

Gottesman²

1997

Genes Dev.

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Bacteriophage HK022 Nun protein blocks transcription elongation by Escherichia coli RNA polymerase in vitro without dissociating the transcription complex. Nun is active on complexes located at any template site tested. Ultimately, only the 3 -OH terminal nucleotide of the nascent transcript in an arrested complex can turn over; it is removed by pyrophosphate and restored with NTPs. This suggests that Nun inhibits the translocation of RNA polymerase without abolishing its catalytic activities. Unlike spontaneously arrested complexes, Nun-arrested complexes cannot be reactivated by transcription factor GreB. The various complexes show distinct patterns of nucleotide incorporation and pyrophosphorolysis before or after treatment with Nun, suggesting that the configuration of RNAP, transcript, and template DNA is different in each complex.

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The RNA–DNA Hybrid Maintains the Register of Transcription by Preventing Backtracking of RNA Polymerase

Cited by 420 publications

References 44 publications

Thermodynamic and kinetic modeling of transcriptional pausing

Thermodynamic and kinetic modeling of transcriptional pausing

RNA polymerase fidelity and transcriptional proofreading

The Nun protein of bacteriophage HK022 inhibits translocation of Escherichia coliRNA polymerase without abolishing its catalytic activities

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