Transcript cleavage factors from E. coli

Borukhov, Sergei; Sagitov, V; Goldfarb, Alex

doi:10.1016/0092-8674(93)90121-6

Cited by 351 publications

(380 citation statements)

References 21 publications

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“…RNA cleavage leads to a new 3 0 -OH group at the RNA end at the polymerase active site, allowing RNA synthesis to resume [67][68][69]. RNAPs I and III possess a strong intrinsic RNA cleavage activity [70,71 ].…”

Section: Error Removal: Rnap Backtracking and Rna Cleavagementioning

confidence: 99%

RNA polymerase fidelity and transcriptional proofreading

Sydow

Cramer

2009

Current Opinion in Structural Biology

142

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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Section: Error Removal: Rnap Backtracking and Rna Cleavagementioning

confidence: 99%

RNA polymerase fidelity and transcriptional proofreading

Sydow

Cramer

2009

Current Opinion in Structural Biology

142

133

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“…The special configuration(s) of these paused complexes (Chan et al 1997) may render them resistant to full modification by Nun. Borukhov et al (1993) suggest that spontaneously arrested complexes arise when the RNAP active center and 3Ј terminus of the nascent transcript misalign. GreBstimulated cleavage removes the protruding 3Ј nucleotides and permits further elongation.…”

Section: How Nun Induces Transcription Arrestmentioning

confidence: 99%

“…Such complexes are particularly sensitive to endonucleolytic transcript cleavage stimulated by the E. coli GreB protein (Borukhov et al 1993). Transcript cleavage reactivates spontaneously arrested complexes, allowing elongation to continue from the new 3Ј-OH terminal nucleotide (Borukhov et al 1993;Nudler et al 1994). We asked if complexes arrested by Nun could also be reactivated by GreB.…”

Section: Nun-induced Transcription Arrest and Greb-stimulated Transcrmentioning

confidence: 99%

“…An RNAPassociated factor, such as GreA or GreB for E. coli RNAP (Borukhov et al 1992(Borukhov et al , 1993, or TFIIS for RNAPII (Izban and Luse 1992;Reines 1992;Guo and Price 1993) stimulates hydrolytic cleavage at a phosphodiester bond two or more nucleotides from the transcript 3Ј terminus. The small oligonucleotide product is released, whereas the upstream portion of the transcript remains engaged and can be elongated.…”

Section: Structure and Properties Of A Transcription Elongation Complexmentioning

confidence: 99%

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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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“…GreA is thought to block the secondary channel so that backtracked 3 0 RNA segments remain secluded in the cavity of the active center. 38 In the case of GreB, (which unlike GreA is a species-specific factor) the disengaged RNA segment freely exits into the secondary channel and does not interfere with GreB binding to TEC. Therefore, the role of GreB is thought to be to rescue arrested complexes.…”

Section: Overviewmentioning

confidence: 99%

Transcription elongation

2017

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This review is focused on recent progress in understanding how Escherichia coli RNAP polymerase translocates along the DNA template and the factors that affect this movement. We discuss the fundamental aspects of RNAP translocation, template signals that influence forward or backward movement, and host or phage factors that modulate translocation. Mechanism of transcription elongationTernary elongation complex (TEC) assembled by DNA template, RNA polymerase and emerging RNA product is the principal intermediate of transcription (Fig. 1). During the elongation step of RNA synthesis, the RNA product remains transiently base-paired to the template DNA strand, forming 9-10 bp RNA: DNA hybrid, 1 whereas the other DNA strand is separated from the template (Fig. 1). The resulting melted DNA region of 10-12 nt 2,3 is called the "transcription bubble." The crucial nucleic acid-protein interactions in TEC involve three principal functionally and structurally defined elements. 4 One of these, the downstream DNA binding site, encloses downstream DNA duplex and acts as a sliding clamp, whereas the two other sites resemble zip locks operationally. The rear zip lock clasps the upstream edge of the RNA:DNA hybrid and ensures displacement of RNA product from template during elongation, whereas the front zip lock, which coincides with RNAP active center, secludes the downstream boundary of the hybrid and also enables peeling of RNA from DNA upon backtracking RNAP. 1,5,6 Both front and rear zip locks accommodate the RNA:DNA hybrid in the hybrid binding site and maintain through topological contacts alone a constant configuration of nucleic acid scaffold upon RNAP lateral movement. Most interactions between the nucleic acid scaffold and RNAP in TEC are not sequence-specific. Some preference to dG residues has been demonstrated in the "core recognition element, CRE" of the b subunit (see below). However, these interactions do not seem to significantly affect TEC reactions, only in rare occasions contributing to RNAP escape from pausing. In X-ray structures of TEC, 7,8 the downstream DNA binding site is seen as a deep cleft formed by the b and b 0 subunits (Fig. 1). The RNA:DNA hybrid is accommodated in the main channel at the interface of the same subunits between the b 0 Bridge helix, b Fork loop II and the active center at its downstream end and the b 0 Rudder and b 0 Lid loops at its upstream end, which correspond to the front and rear zip locks respectively. After peeling from the DNA, the synthesized RNA transcript is channeled into an extended narrow cavity formed by the b 0 Lid and b 0 Zn-finger subdomains as well as the "Flap," which is a long flexible b subunit loop.Each individual step of RNA extension by RNA polymerase produces TEC in which the RNA 3 0 end occupies the iC1 site of the enzyme active center

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Transcript cleavage factors from E. coli

Cited by 351 publications

References 21 publications

RNA polymerase fidelity and transcriptional proofreading

RNA polymerase fidelity and transcriptional proofreading

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

Transcription elongation

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