scholarly journals Author response: Structural basis of transcription arrest by coliphage HK022 Nun in an Escherichia coli RNA polymerase elongation complex

2017 ◽  
Author(s):  
Jin Young Kang ◽  
Paul Dominic B Olinares ◽  
James Chen ◽  
Elizabeth A Campbell ◽  
Arkady Mustaev ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Author Response ◽  
Structural Basis ◽  
Elongation Complex

scholarly journals Structural basis of transcription arrest by coliphage HK022 Nun in an Escherichia coli RNA polymerase elongation complex

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Jin Young Kang ◽  
Paul Dominic B Olinares ◽  
James Chen ◽  
Elizabeth A Campbell ◽  
Arkady Mustaev ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Nucleic Acids ◽  
Rna Polymerase ◽  
Active Site ◽  
Terminal Segment ◽  
Structural Basis ◽  
Elongation Complex ◽  
Structural Framework ◽  
Cryo Electron Microscopy ◽  
Active Site Cleft

Coliphage HK022 Nun blocks superinfection by coliphage λ by stalling RNA polymerase (RNAP) translocation specifically on λ DNA. To provide a structural framework to understand how Nun blocks RNAP translocation, we determined structures of Escherichia coli RNAP ternary elongation complexes (TECs) with and without Nun by single-particle cryo-electron microscopy. Nun fits tightly into the TEC by taking advantage of gaps between the RNAP and the nucleic acids. The C-terminal segment of Nun interacts with the RNAP β and β’ subunits inside the RNAP active site cleft as well as with nearly every element of the nucleic acid scaffold, essentially crosslinking the RNAP and the nucleic acids to prevent translocation, a mechanism supported by the effects of Nun amino acid substitutions. The nature of Nun interactions inside the RNAP active site cleft suggests that RNAP clamp opening is required for Nun to establish its interactions, explaining why Nun acts on paused TECs.

Interaction of Escherichia coli RNA polymerase with DNA in an elongation complex arrested at a specific psoralen crosslink site

1988 ◽  
Vol 199 (2) ◽  
pp. 277-293 ◽  
Author(s):  
Yun-bo Shi ◽  
Howard Gamper ◽  
Bennett Van Houten ◽  
John E. Hearst
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Elongation Complex

scholarly journals Analysis of the PcrA-RNA polymerase complex reveals a helicase interaction motif and a role for PcrA/UvrD helicase in the suppression of R-loops.

2021 ◽  
Author(s):  
Inigo Urrutia ◽  
James Ault ◽  
Frank Sobott ◽  
Nigel Savery ◽  
Mark S Dillingham
Keyword(s):  
Rna Polymerase ◽  
Excision Repair ◽  
Structural Basis ◽  
Elongation Complex ◽  
Catalytic Core ◽  
Biochemical Assays ◽  
Nucleotide Excision ◽  
Hydrogen Deuterium ◽  
Partner Proteins

The PcrA/UvrD helicase binds directly to RNA polymerase (RNAP) but the structural basis for this interaction and its functional significance have remained unclear. In this work we used biochemical assays and hydrogen-deuterium exchange coupled to mass spectrometry to study the PcrA-RNAP complex. We find that PcrA binds tightly to a transcription elongation complex in a manner dependent on protein:protein interaction with the conserved PcrA C-terminal Tudor domain. The helicase binds predominantly to two positions on the surface of RNAP. The PcrA C-terminal domain engages a conserved region in a lineage-specific insert within the β subunit which we identify as a helicase interaction motif present in many other PcrA partner proteins, including the nucleotide excision repair factor UvrB. The catalytic core of the helicase binds near the RNA and DNA exit channels and blocking PcrA activity in vivo leads to the accumulation of R-loops. We propose a role for PcrA as an R-loop suppression factor that helps to minimise conflicts between transcription and other processes on DNA including replication.

scholarly journals Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli

2021 ◽  
pp. 101404
Author(s):  
M. Zuhaib Qayyum ◽  
Vadim Molodtsov ◽  
Andrew Renda ◽  
Katsuhiko S. Murakami
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Structural Basis

Mechanistic Model of the Elongation Complex of Escherichia coli RNA Polymerase

1998 ◽  
Vol 63 (0) ◽  
pp. 337-346 ◽  
Author(s):  
N. KORZHEVA ◽  
A. MUSTAEV ◽  
E. NUDLER ◽  
V. NIKIFOROV ◽  
A. GOLDFARB
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Mechanistic Model ◽  
Elongation Complex

scholarly journals Analysis of the PcrA-RNA polymerase complex reveals a helicase interaction motif and a role for PcrA/UvrD helicase in the suppression of R-loops

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Inigo Urrutia-Irazabal ◽  
James R Ault ◽  
Frank Sobott ◽  
Nigel J Savery ◽  
Mark Simon Dillingham
Keyword(s):  
Rna Polymerase ◽  
Excision Repair ◽  
Structural Basis ◽  
Elongation Complex ◽  
Catalytic Core ◽  
Biochemical Assays ◽  
Nucleotide Excision ◽  
Hydrogen Deuterium ◽  
Partner Proteins

The PcrA/UvrD helicase binds directly to RNA polymerase (RNAP) but the structural basis for this interaction and its functional significance have remained unclear. In this work we used biochemical assays and hydrogen-deuterium exchange coupled to mass spectrometry to study the PcrA-RNAP complex. We find that PcrA binds tightly to a transcription elongation complex in a manner dependent on protein:protein interaction with the conserved PcrA C-terminal Tudor domain. The helicase binds predominantly to two positions on the surface of RNAP. The PcrA C-terminal domain engages a conserved region in a lineage-specific insert within the β subunit which we identify as a helicase interaction motif present in many other PcrA partner proteins, including the nucleotide excision repair factor UvrB. The catalytic core of the helicase binds near the RNA and DNA exit channels and blocking PcrA activity in vivo leads to the accumulation of R-loops. We propose a role for PcrA as an R-loop suppression factor that helps to minimise conflicts between transcription and other processes on DNA including replication.

scholarly journals Structural basis of RNA polymerase I stalling at UV light-induced DNA damage

2018 ◽  
Vol 115 (36) ◽  
pp. 8972-8977 ◽  
Author(s):  
Marta Sanz-Murillo ◽  
Jun Xu ◽  
Georgiy A. Belogurov ◽  
Olga Calvo ◽  
David Gil-Carton ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Molecular Mechanisms ◽  
Mutational Analysis ◽  
Uv Light ◽  
Rna Polymerase I ◽  
Pyrimidine Dimer ◽  
Structural Basis ◽  
Elongation Complex ◽  
Pol I ◽  
Polymerase I

RNA polymerase I (Pol I) transcribes ribosomal DNA (rDNA) to produce the ribosomal RNA (rRNA) precursor, which accounts for up to 60% of the total transcriptional activity in growing cells. Pol I monitors rDNA integrity and influences cell survival, but little is known about how this enzyme processes UV-induced lesions. We report the electron cryomicroscopy structure of Pol I in an elongation complex containing a cyclobutane pyrimidine dimer (CPD) at a resolution of 3.6 Å. The structure shows that the lesion induces an early translocation intermediate exhibiting unique features. The bridge helix residue Arg1015 plays a major role in CPD-induced Pol I stalling, as confirmed by mutational analysis. These results, together with biochemical data presented here, reveal the molecular mechanism of Pol I stalling by CPD lesions, which is distinct from Pol II arrest by CPD lesions. Our findings open the avenue to unravel the molecular mechanisms underlying cell endurance to lesions on rDNA.

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