Pre-termination Transcription Complex: Structure and Function

Hao, Zhimin; Epshtein, Vitaly; Kim, Kelly H.; Proshkin, Sergey; Svetlov, Vladimir; Kamarthapu, Venu; Bharati, Binod K.; Миронов, А.; Walz, Thomas; Nudler, Evgeny

doi:10.1016/j.molcel.2020.11.013

Cited by 75 publications

(119 citation statements)

References 67 publications

(95 reference statements)

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“…The classical RDTT model posits that such directional ATPase-fueled movement from a Rut 'anchoring' site towards the transcript 3'-end allows Rho to catch up with RNAP and then disrupt the TEC (see: [19][20][21][22] and references within). However, a series of cryoEM structures from two recent studies 23,24 supports an alternative 'allosteric' model whereby EcRho first binds ribosome-free RNAP 25 . The Rho-RNAP interaction involves the N-terminal face of the EcRho hexamer (Figure 1A) and is stabilized by cofactors NusA and NusG that both bind EcRho and the RNAP 23,24 .…”

Section: Introductionmentioning

confidence: 99%

A Large Insertion Domain in the Rho Factor From a Low G + C, Gram-negative Bacterium is Critical for RNA Binding and Transcription Termination Activity

Simón

Delaleau

Schwartz

et al. 2021

Journal of Molecular Biology

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Rho-dependent termination of transcription (RDTT) is a critical regulatory mechanism specific to bacteria. In a subset of species including most Actinobacteria and Bacteroidetes, the Rho factor contains a large, poorly conserved N-terminal insertion domain (NID) of cryptic function. To date, only two NID-bearing Rho factors from high G+C Actinobacteria have been thoroughly characterized. Both can trigger RDTT at promoter-proximal sites or with structurally constrained transcripts that are unsuitable for the archetypal, NID-less Rho factor of Escherichia coli (EcRho). Here, we provide the first biochemical characterization of a NID-bearing Rho factor from a low G+C bacterium. We show that Bacteroides fragilis Rho (BfRho) is a bona fide RNA-dependent NTPase motor able to unwind long RNA:DNA duplexes and to disrupt transcription complexes. The large NID (~40% of total mass) strongly increases BfRho affinity for RNA, is strictly required for RDTT, but does not promote RDTT at promoter-proximal sites or with a structurally constrained transcript. Furthermore, the NID does not preclude modulation of RDTT by transcription factors NusA and NusG or by the Rho inhibitor bicyclomycin. Although the NID contains a prion-like Q/N-rich motif, it does not spontaneously trigger formation of -amyloids. Thus, despite its unusually large RNA binding domain, BfRho behaves more like the NID-less EcRho than NID-bearing counterparts from high G+C Actinobacteria. Our data highlight the evolutionary plasticity of Rho's N-terminal region and illustrate how RDTT is adapted to distinct genomic contents.

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Section: Introductionmentioning

confidence: 99%

A Large Insertion Domain in the Rho Factor From a Low G + C, Gram-negative Bacterium is Critical for RNA Binding and Transcription Termination Activity

Simón

Delaleau

Schwartz

et al. 2021

Journal of Molecular Biology

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“…r, however, has been shown to not only bind RNA polymerase at pause sites but throughout the transcription cycle (Epshtein et al, 2010;Mooney et al, 2009), lending support to the allosteric model. Specifically, the cryo-EM structures of E. coli RNA polymerase bound to r and the elongation factors NusA and NusG show that r forms intimate contacts with RNA polymerase independent of the RNA product (Hao et al, 2021;Said et al, 2021). It is proposed that only after r has bound the polymerase does r engage RNA.…”

Section: Transcription Terminationmentioning

confidence: 99%

“…Because r binds a subset of RNA polymerases and is sterically blocked from binding RNA polymerase on genes where ribosomes closely trail the polymerase, it is unlikely that direct association of r with RNA polymerase is used to terminate all r-dependent loci (Peters et al, 2011). Notably, conformational changes in RNA polymerase at pause sites and the poly C RNA sequence are important for r-induced termination in the allosteric and torpedo models (Ceruzzi et al, 1985;Hao et al, 2021;Jin et al, 1992;Said et al, 2021).…”

Section: Transcription Terminationmentioning

confidence: 99%

Understanding transcription across scales: From base pairs to chromosomes

Vos

2021

Molecular Cell

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“…In this case, the dC20 ligand might be too short to bridge several NTDs/NIDs and restrict their movements. It is also possible that the NIDs substitute for the lineage-specific motifs that stabilize the Ec(Rho:RNAP) complex 15,16 and become structurally organized only upon MtbRho interaction with RNAP 27 .…”

Section: The Mtbrho Hexamer Adopts An Open Ring Conformationmentioning

confidence: 99%

“…This composite PBS includes a YC-binding pocket (Y being a C or U residue) on each EcRho protomer that contributes to the specific recognition of transcript Rut sites 18,19 . The NTD also carries the residues contacting RNA polymerase (RNAP) identified in recent cryoEM structures of the EcRho:RNAP complex 15,16 .…”

Section: Introductionmentioning

confidence: 99%

Cryo-EM structure of the transcription termination factor Rho from Mycobacterium tuberculosis reveals mechanism of resistance to bicyclomycin

Saridakis

Vishwakarma

Lai-Kee-Him

et al. 2021

Preprint

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The bacterial Rho factor is a ring-shaped motor triggering genome-wide transcription termination and R-loop dissociation. Rho is essential in many species, including in Mycobacterium tuberculosis where rho gene inactivation leads to rapid death. Yet, the M. tuberculosis Rho [MtbRho] factor displays poor NTPase and helicase activities, and resistance to the natural Rho inhibitor bicyclomycin [BCM] that remain unexplained. Here, we address these unusual features by solving the cryo-EM structure of MtbRho at 3.3 Å resolution, providing a new framework for future antibiotic development. The MtbRho hexamer is poised into a pre-catalytic, open-ringed state wherein specific contacts stabilize ATP in intersubunit ATPase pockets, thereby explaining the cofactor preference of MtbRho. We reveal a leucine-to-methionine substitution that creates a steric bulk in BCM binding cavities near the positions of ATP γ-phosphates, and confers resistance to BCM at the expense of motor efficiency.

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Pre-termination Transcription Complex: Structure and Function

Cited by 75 publications

References 67 publications

A Large Insertion Domain in the Rho Factor From a Low G + C, Gram-negative Bacterium is Critical for RNA Binding and Transcription Termination Activity

A Large Insertion Domain in the Rho Factor From a Low G + C, Gram-negative Bacterium is Critical for RNA Binding and Transcription Termination Activity

Understanding transcription across scales: From base pairs to chromosomes

Cryo-EM structure of the transcription termination factor Rho from Mycobacterium tuberculosis reveals mechanism of resistance to bicyclomycin

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