Hopping and Flipping of RNA Polymerase on DNA during Recycling for Reinitiation after Intrinsic Termination in Bacterial Transcription

Kang, Wooyoung; Hwang, Seungha; Kang, Jin Young; Kang, Changwon; Hohng, Sungchul

doi:10.3390/ijms22052398

Cited by 10 publications

(17 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Among the several single-molecule assays that we established to explore the intrinsic and ρ-dependent termination mechanisms by E. coli RNAP ( 29 , 37 , 38 ), three assays were performed in this study on assorted ρ-dependent terminators, and their experimental schemes and representative results are briefed here. DNA templates each contain the T7A1 promoter and a ρ-dependent terminator, and are each labeled with biotin at the upstream end for surface immobilization and fluorescently with reddish Cy5 at the downstream end for individual real-time monitoring (Figure 1A ).…”

Section: Resultsmentioning

confidence: 99%

Transcriptional pause extension benefits the stand-by rather than catch-up Rho-dependent termination

Song

Hwang

Munasingha

et al. 2023

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

Transcriptional pause is essential for all types of termination. In this single-molecule study on bacterial Rho factor-dependent terminators, we confirm that the three Rho-dependent termination routes operate compatibly together in a single terminator, and discover that their termination efficiencies depend on the terminational pauses in unexpected ways. Evidently, the most abundant route is that Rho binds nascent RNA first and catches up with paused RNA polymerase (RNAP) and this catch-up Rho mediates simultaneous releases of transcript RNA and template DNA from RNAP. The fastest route is that the catch-up Rho effects RNA-only release and leads to 1D recycling of RNAP on DNA. The slowest route is that the RNAP-prebound stand-by Rho facilitates only the simultaneous rather than sequential releases. Among the three routes, only the stand-by Rho's termination efficiency positively correlates with pause duration, contrary to a long-standing speculation, invariably in the absence or presence of NusA/NusG factors, competitor RNAs or a crowding agent. Accordingly, the essential terminational pause does not need to be long for the catch-up Rho's terminations, and long pauses benefit only the stand-by Rho's terminations. Furthermore, the Rho-dependent termination of mgtA and ribB riboswitches is controlled mainly by modulation of the stand-by rather than catch-up termination.

show abstract

Section: Resultsmentioning

confidence: 99%

Transcriptional pause extension benefits the stand-by rather than catch-up Rho-dependent termination

Song

Hwang

Munasingha

et al. 2023

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

show abstract

“…Alternatively, the mismatch effects may not be related to hyper-translocation but with something else. For example, a DNA region around the −12 position interacts with RNAP in the recent X-ray crystal structures 7 , 16 , and such interaction may be hypothetically important for termination.…”

Section: Resultsmentioning

confidence: 99%

Rho-dependent transcription termination proceeds via three routes

et al. 2022

Self Cite

View full text Add to dashboard Cite

Rho is a general transcription termination factor in bacteria, but many aspects of its mechanism of action are unclear. Diverse models have been proposed for the initial interaction between the RNA polymerase (RNAP) and Rho (catch-up and stand-by pre-terminational models); for the terminational release of the RNA transcript (RNA shearing, RNAP hyper-translocation or displacing, and allosteric models); and for the post-terminational outcome (whether the RNAP dissociates or remains bound to the DNA). Here, we use single-molecule fluorescence assays to study those three steps in transcription termination mediated by E. coli Rho. We find that different mechanisms previously proposed for each step co-exist, but apparently occur on various timescales and tend to lead to specific outcomes. Our results indicate that three kinetically distinct routes take place: (1) the catch-up mode leads first to RNA shearing for RNAP recycling on DNA, and (2) later to RNAP displacement for decomposition of the transcriptional complex; (3) the last termination usually follows the stand-by mode with displacing for decomposing. This three-route model would help reconcile current controversies on the mechanisms.

show abstract

“…Recently, a new mechanism of proximity-based transcription coupling was observed. Using single-molecule microscopy, Harden et al 16 and Kang et al 17,18 observed that RNAP can remain bound to DNA after termination for at least hundreds of seconds in vitro. This post-termination RNAP-DNA complex may retain a partially open bubble in the DNA 19 .…”

Section: Introductionmentioning

confidence: 99%

RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons

Tenenbaum

Inlow

Friedman

et al. 2023

Preprint

View full text Add to dashboard Cite

DNA transcription initiates after an RNA polymerase (RNAP) molecule binds to the promoter of a gene. In bacteria, the canonical picture is that RNAP comes from the cytoplasmic pool of freely diffusing RNAP molecules. Recent experiments suggest the possible existence of a separate pool of polymerases, competent for initiation, which freely slide on the DNA after having terminated one round of transcription. Promoter-dependent transcription reinitiation from this pool of post-termination RNAP may lead to coupled initiation at nearby operons, but it is unclear whether this can occur over the distance- and time-scales needed for it to function widely on a bacterial genome in vivo. Here, we mathematically model the hypothesized reinitiation mechanism as a diffusion-to-capture process and compute the distances over which significant inter-operon coupling can occur and the time required. These quantities depend on previously uncharacterized molecular association and dissociation rate constants between DNA, RNAP and the transcription initiation factor σ70; we measure these rate constants using single-molecule experiments in vitro. Our combined theory/experimental results demonstrate that efficient coupling can occur at physiologically relevant σ70 concentrations and on timescales appropriate for transcript synthesis. Coupling is efficient over terminator-promoter distances up to ~1,000 bp, which includes the majority of terminator-promoter nearest neighbor pairs in the E. coli genome. The results suggest a generalized mechanism that couples the transcription of nearby operons and breaks the paradigm that each binding of RNAP to DNA can produce at most one messenger RNA.

show abstract

Hopping and Flipping of RNA Polymerase on DNA during Recycling for Reinitiation after Intrinsic Termination in Bacterial Transcription

Cited by 10 publications

References 27 publications

Transcriptional pause extension benefits the stand-by rather than catch-up Rho-dependent termination

Transcriptional pause extension benefits the stand-by rather than catch-up Rho-dependent termination

Rho-dependent transcription termination proceeds via three routes

RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons

Contact Info

Product

Resources

About