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

Kang, Jin Young; Olinares, Paul Dominic B.; Chen, James; Campbell, Elizabeth A.; Mustaev, Arkady; Chait, Brian T.; Gottesman, Max E.; Darst, Seth A.

doi:10.7554/elife.25478

Cited by 126 publications

(237 citation statements)

References 53 publications

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“…1A), a part of the b lobe domain (Belogurov et al, 2010). The b 0 clamp and b lobe form two pincers of the crab-claw-shaped RNAP (Zhang et al, 1999) that lie on two sides of the main channel, which contains the active site and the nucleic acids in the EC Kang et al, 2017). The clamp domain makes up much of the b 0 pincer and undergoes swinging motions that open the channel to permit entry of nucleic acids during initiation or close the channel around the nucleic acids to enable processive elongation (Gnatt et al, 2001;Chakraborty et al, 2012;Feklistov et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Locking the nontemplate DNA to control transcription

Nedialkov

Svetlov

Belogurov

et al. 2018

Molecular Microbiology

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Universally conserved NusG/Spt5 factors reduce RNA polymerase pausing and arrest. In a widely accepted model, these proteins bridge the RNA polymerase clamp and lobe domains across the DNA channel, inhibiting the clamp opening to promote pause-free RNA synthesis. However, recent structures of paused transcription elongation complexes show that the clamp does not open and suggest alternative mechanisms of antipausing. Among these mechanisms, direct contacts of NusG/Spt5 proteins with the nontemplate DNA in the transcription bubble have been proposed to prevent unproductive DNA conformations and thus inhibit arrest. We used Escherichia coli RfaH, whose interactions with DNA are best characterized, to test this idea. We report that RfaH stabilizes the upstream edge of the transcription bubble, favoring forward translocation, and protects the upstream duplex DNA from exonuclease cleavage. Modeling suggests that RfaH loops the nontemplate DNA around its surface and restricts the upstream DNA duplex mobility. Strikingly, we show that RfaH-induced DNA protection and antipausing activity can be mimicked by shortening the nontemplate strand in elongation complexes assembled on synthetic scaffolds. We propose that remodeling of the nontemplate DNA controls recruitment of regulatory factors and R-loop formation during transcription elongation across all life.

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Section: Introductionmentioning

confidence: 99%

Locking the nontemplate DNA to control transcription

Nedialkov

Svetlov

Belogurov

et al. 2018

Molecular Microbiology

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“…The near-atomic resolution X-ray crystal structure of E. coli RNAP was determined first as holoenzyme containing σ 70 (Murakami, 2013). X-ray crystal and cryo-electron microscopy (cryo-EM) structures of E. coli RNAP are now available in several forms such as holoenzymes containing alternative σ factors (Liu et al, 2016; Yang et al, 2015), promoter DNA complexes (Glyde et al, 2017; Zuo and Steitz, 2015), elongation complex (Kang et al, 2017), in complex with transcription factors (Bae et al, 2013; Liu et al, 2017; Molodtsov et al, 2018), and with inhibitors/antibiotics (Bae et al, 2015; Chen et al, 2017; Degen et al, 2014; Molodtsov et al, 2015; Molodtsov et al, 2013), providing details of the structure and function of E. coli RNAP transcription and regulation.…”

Section: Introductionmentioning

confidence: 99%

An Introduction to the Structure and Function of the Catalytic Core Enzyme of Escherichia coli RNA Polymerase

Sutherland

Murakami

2018

EcoSal Plus

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RNA polymerase (RNAP) is the essential enzyme responsible for transcribing the genetic information stored in DNA to RNA. Understanding the structure and function of RNAP is important for those who study basic principles in gene expression, such as the mechanisms of transcription and its regulation, as well as translational sciences such as antibiotic development. With over a half-century of investigations, there is a wealth of information available on the structure and function of Escherichia coli RNAP. This review introduces the structural features of E. coli RNAP, organized by subunit, giving information on the function, location, and conservation of these features to early stage investigators who have just started their research of E. coli RNAP.

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“…Spt4–Spt5 binds directly to RNAP and stabilizes a closed‐clamp configuration that facilitates elongation and TEC stability (Wada et al ., ; Grohmann et al ., ; Martinez‐Rucobo et al ., ; Guo et al ., ; Bernecky et al ., ; Ehara et al ., ; Kang et al ., ; Vos et al ., ). As pausing and subsequent backtracking can be influenced by inter‐domain movements of RNAP (Martinez‐Rucobo et al ., ; Chakraborty et al ., ; Weixlbaumer et al ., ; Hein et al ., ; Jun et al ., ; Blombach et al ., ; Feklistov et al ., ; Kang et al ., ; Duchi et al ., ), we sought to determine whether Spt4–Spt5 binding to RNAP would reduce pausing or accelerate transcription on protein‐free and histone‐bound templates. Addition of either Spt4 or Spt5 alone (Fig.…”

Section: Resultsmentioning

confidence: 99%

TFS and Spt4/5 accelerate transcription through archaeal histone‐based chromatin

Sanders

Lammers

Marshall

et al. 2019

Molecular Microbiology

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Summary RNA polymerase must surmount translocation barriers for continued transcription. In Eukarya and most Archaea, DNA‐bound histone proteins represent the most common and troublesome barrier to transcription elongation. Eukaryotes encode a plethora of chromatin‐remodeling complexes, histone‐modification enzymes and transcription elongation factors to aid transcription through nucleosomes, while archaea seemingly lack machinery to remodel/modify histone‐based chromatin and thus must rely on elongation factors to accelerate transcription through chromatin‐barriers. TFS (TFIIS in Eukarya) and the Spt4–Spt5 complex are universally encoded in archaeal genomes, and here we demonstrate that both elongation factors, via different mechanisms, can accelerate transcription through archaeal histone‐based chromatin. Histone proteins in Thermococcus kodakarensis are sufficiently abundant to completely wrap all genomic DNA, resulting in a consistent protein barrier to transcription elongation. TFS‐enhanced cleavage of RNAs in backtracked transcription complexes reactivates stalled RNAPs and dramatically accelerates transcription through histone‐barriers, while Spt4–Spt5 changes to clamp‐domain dynamics play a lesser‐role in stabilizing transcription. Repeated attempts to delete TFS, Spt4 and Spt5 from the T. kodakarensis genome were not successful, and the essentiality of both conserved transcription elongation factors suggests that both conserved elongation factors play important roles in transcription regulation in vivo, including mechanisms to accelerate transcription through downstream protein barriers.

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

Cited by 126 publications

References 53 publications

Locking the nontemplate DNA to control transcription

Locking the nontemplate DNA to control transcription

An Introduction to the Structure and Function of the Catalytic Core Enzyme of Escherichia coli RNA Polymerase

TFS and Spt4/5 accelerate transcription through archaeal histone‐based chromatin

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