The Experts below are selected from a list of 255 Experts worldwide ranked by ideXlab platform
Evgeny Nudler - One of the best experts on this subject based on the ideXlab platform.
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srna mediated control of Transcription Termination in e coli
Cell, 2016Co-Authors: Vitaly Epshtein, Nadezda Sedlyarova, Ilya Shamovsky, Binod K Bharati, Jiandong Chen, Susan Gottesman, Renee Schroeder, Evgeny NudlerAbstract:Summary Bacterial small RNAs (sRNAs) have been implicated in various aspects of post-Transcriptional gene regulation. Here, we demonstrate that sRNAs also act at the level of Transcription Termination. We use the rpoS gene, which encodes a general stress sigma factor σ S , as a model system, and show that sRNAs DsrA, ArcZ, and RprA bind the rpoS 5′UTR to suppress premature Rho-dependent Transcription Termination, both in vitro and in vivo. sRNA-mediated antiTermination markedly stimulates Transcription of rpoS during the transition to the stationary phase of growth, thereby facilitating a rapid adjustment of bacteria to global metabolic changes. Next generation RNA sequencing and bioinformatic analysis indicate that Rho functions as a global "attenuator" of Transcription, acting at the 5′UTR of hundreds of bacterial genes, and that its suppression by sRNAs is a widespread mode of bacterial gene regulation.
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riboswitch control of rho dependent Transcription Termination
Proceedings of the National Academy of Sciences of the United States of America, 2012Co-Authors: Kerry Hollands, Evgeny Nudler, Sergey Proshkin, Svetlana Sklyarova, Vitaly Epshtein, A S Mironov, Eduardo A GroismanAbstract:Riboswitches are RNA sensors that regulate gene expression upon binding specific metabolites or ions. Bacterial riboswitches control gene expression primarily by promoting intrinsic Transcription Termination or by inhibiting translation initiation. We now report a third general mechanism of riboswitch action: governing the ability of the RNA-dependent helicase Rho to terminate Transcription. We establish that Rho promotes Transcription Termination in the Mg 2+ -sensingmgtAriboswitch from Salmonella entericaserovar Typhimurium and the flavin mononucleotide-sensing ribB riboswitch from Escherichia coli when the corresponding riboswitch ligands are present. The Rho-specific inhibitor bicyclomycin enabled Transcription of the coding regions at these two loci in bacteria experiencing repressing concentrations of the riboswitch ligands in vivo. A mutation in the mgtA leader that favors the “high Mg 2+ ” conformation of the riboswitch promoted Rho-dependent Transcription Termination in vivo and in vitro and enhanced the ability of the RNA to stimulate Rho’s ATPase activity in vitro. These effects were overcome by mutations in a C-rich region of the mRNA that is alternately folded at high and low Mg 2+ , suggesting a role for this region in regulating the activity of Rho. Our results reveal a potentially widespread mode of gene regulation whereby riboswitches dictate whether a protein effector can interact with the Transcription machinery to prematurely terminate Transcription.
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an allosteric path to Transcription Termination
Molecular Cell, 2007Co-Authors: Vitaly Epshtein, Christopher J Cardinale, Andrei E Ruckenstein, Sergei Borukhov, Evgeny NudlerAbstract:Transcription Termination signals in bacteria occur in RNA as a strong hairpin followed by a stretch of U residues at the 3' terminus. To release the transcript, RNA polymerase (RNAP) is thought to translocate forward without RNA synthesis. Here we provide genetic and biochemical evidence supporting an alternative model in which extensive conformational changes across the enzyme lead to Termination without forward translocation. In this model, flexible parts of the RNA exit channel (zipper, flap, and zinc finger) assist the initial step of hairpin folding (nucleation). The hairpin then invades the RNAP main channel, causing RNA:DNA hybrid melting, structural changes of the catalytic site, and DNA-clamp opening induced by interaction with the G(trigger)-loop. Our results envision the elongation complex as a flexible structure, not a rigid body, and establish basic principles of the Termination pathway that are likely to be universal in prokaryotic and eukaryotic systems.
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Transcription Termination and anti Termination in e coli
Genes to Cells, 2002Co-Authors: Evgeny Nudler, Max E. GottesmanAbstract:Transcription Termination in Escherichia coli is controlled by many factors. The sequence of the DNA template, the structure of the transcript, and the actions of auxiliary proteins all play a role in determining the efficiency of the process. Termination is regulated and can be enhanced or suppressed by host and phage proteins. This complex reaction is rapidly yielding to biochemical and structural analysis of the interacting factors. Below we review and attempt to unify into basic principles the remarkable recent progress in understanding Transcription Termination and anti-Termination.
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the mechanism of intrinsic Transcription Termination
Molecular Cell, 1999Co-Authors: Ivan Gusarov, Evgeny NudlerAbstract:Abstract In bacteria, an intrinsic Transcription Termination signal appears in RNA as a hairpin followed by approximately eight uridines (U stretch) at the 3′ terminus. This signal leads to rapid dissociation of the ternary elongation complex (TEC) into RNA, DNA, and an RNA polymerase. We demonstrate that the hairpin inactivates and then destabilizes TEC by weakening interactions in the RNA–DNA hybrid–binding site and the RNA-binding site that hold TEC together. Formation of the hairpin is restricted to the moment when TEC reaches the point of Termination and depends upon melting of four to five hybrid base pairs that follow the hairpin's stem. The U stretch–induced pausing at the point of Termination is crucial, providing additional time for hairpin formation. These results explain the mechanism of Termination and aid in understanding of how cellular factors modulate this process.
Gianni Dehò - One of the best experts on this subject based on the ideXlab platform.
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Autogenous regulation of Escherichia coli polynucleotide phosphorylase during cold acclimation by Transcription Termination and antiTermination.
Molecular Genetics and Genomics, 2007Co-Authors: Paolo Marchi, Federica Briani, Vera Longhi, Sandro Zangrossi, Elisa Gaetani, Gianni DehòAbstract:Adaptation of Escherichia coli at low temperature implicates a drastic reprogramming of gene expression patterns. Mechanisms operating downstream of Transcription initiation, such as control of Transcription Termination, mRNA stability and translatability, play a major role in controlling gene expression in the cold acclimation phase. It was previously shown that Rho-dependent Transcription Termination within pnp, the gene encoding polynucleotide phosphorylase (PNPase), was suppressed in pnp nonsense mutants, whereas it was restored by complementation with wild type allele. Using a tRNA gene as a reporter and the strong Rho-dependent Transcription terminator t imm of bacteriophage P4 as a tester, here we show that specific sites in the 5′-untranslated region of pnp mRNA are required for PNPase-sensitive cold-induced suppression of Rho-dependent Transcription Termination. We suggest that suppression of Rho-dependent Transcription Termination within pnp and its restoration by PNPase is an autogenous regulatory circuit that modulates pnp expression during cold acclimation.
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Antisense RNA-dependent Transcription Termination sites that modulate lysogenic development of satellite phage P4
Molecular Microbiology, 2000Co-Authors: Federica Briani, Daniela Ghisotti, Gianni DehòAbstract:In the lysogenic state, bacteriophage P4 prevents the expression of its own replication genes, which are encoded in the left operon, through premature Transcription Termination. The phage factor responsible for efficient Termination is a small, untranslated RNA (CI RNA), which acts as an antisense RNA and controls Transcription Termination by pairing with two complementary sequences (seqA and seqC) located within the leader region of the left operon. A Rho-dependent Termination site, timm, was previously shown to be involved in the control of P4 replication gene expression. In the present study, by making use of phage PhiR73 as a cloning vector and of suppressor tRNAGly as a reporter gene, we characterized two additional terminators, t1 and t4. Although Transcription Termination at neither site requires the Rho factor, only t1 has the typical structure of a Rho-independent terminator. t1 is located between the PLE promoter and the cI gene, whereas t4 is located between cI and timm. Efficient Termination at t1 requires the CI RNA and the seqA target sequence; in vitro, the CI RNA enhanced Termination at t1 in the absence of any bacterial factor. A P4 mutant, in which the t1 terminator has been deleted, can still lysogenize both Rho+ and Rho- strains and exhibits increased expression of CI RNA. These data indicate that t1 and the Rho-dependent timm terminators are not essential for lysogeny. t1 is involved in CI RNA autoregulation, whereas t4 appears to be the main terminator necessary to prevent expression of the lytic genes in the lysogenic state.
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A Rho-Dependent Transcription Termination Site Regulated by Bacteriophage P4 RNA Immunity Factor
Virology, 1996Co-Authors: Federica Briani, Daniela Ghisotti, Sandro Zangrossi, Gianni DehòAbstract:Abstract The genes required for replication of the temperate bacteriophage P4, which are coded by the phage left operon, are expressed from a constitutive promoter (P LE ). In the lysogenic state, repression of the P4 replication genes is achieved by premature Transcription Termination. The leader region of the left operon encodes all the genetic determinants required for prophage immunity, namely: (i) the P4 immunity factor, a short, stable RNA (CI RNA) that is generated by processing of the leader transcript; (ii) two specific target sequences that exhibit complementarity with the CI RNA. RNA–RNA interactions between the CI RNA and the target sites on the mRNA leader region are essential for Transcription Termination. To understand how Transcription Termination is elicited by the P4 immunity mechanism, it is relevant to identify the Transcription Termination site. This, however, could not be directly inferred from the 3′-end of the Transcription products because of the extensive and complex processing and degradation of the leader RNA. In this work, by making use of a tRNA gene as a reporter, we identify the Termination site of the immunity transcripts ( t imm ). This is a Rho-dependent terminator located within the first translated gene of the left operon and is regulated by P4 immunity. Analysis of the P4 Transcription pattern in Escherichia coli rho mutants suggests that Termination at t imm may also be important for the efficient processing of the CI RNA.
Eduardo A Groisman - One of the best experts on this subject based on the ideXlab platform.
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riboswitch control of rho dependent Transcription Termination
Proceedings of the National Academy of Sciences of the United States of America, 2012Co-Authors: Kerry Hollands, Evgeny Nudler, Sergey Proshkin, Svetlana Sklyarova, Vitaly Epshtein, A S Mironov, Eduardo A GroismanAbstract:Riboswitches are RNA sensors that regulate gene expression upon binding specific metabolites or ions. Bacterial riboswitches control gene expression primarily by promoting intrinsic Transcription Termination or by inhibiting translation initiation. We now report a third general mechanism of riboswitch action: governing the ability of the RNA-dependent helicase Rho to terminate Transcription. We establish that Rho promotes Transcription Termination in the Mg 2+ -sensingmgtAriboswitch from Salmonella entericaserovar Typhimurium and the flavin mononucleotide-sensing ribB riboswitch from Escherichia coli when the corresponding riboswitch ligands are present. The Rho-specific inhibitor bicyclomycin enabled Transcription of the coding regions at these two loci in bacteria experiencing repressing concentrations of the riboswitch ligands in vivo. A mutation in the mgtA leader that favors the “high Mg 2+ ” conformation of the riboswitch promoted Rho-dependent Transcription Termination in vivo and in vitro and enhanced the ability of the RNA to stimulate Rho’s ATPase activity in vitro. These effects were overcome by mutations in a C-rich region of the mRNA that is alternately folded at high and low Mg 2+ , suggesting a role for this region in regulating the activity of Rho. Our results reveal a potentially widespread mode of gene regulation whereby riboswitches dictate whether a protein effector can interact with the Transcription machinery to prematurely terminate Transcription.
Walter Keller - One of the best experts on this subject based on the ideXlab platform.
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independent functions of yeast pcf11p in pre mrna 3 end processing and in Transcription Termination
The EMBO Journal, 2003Co-Authors: Martin Sadowski, Bernhard Dichtl, Wolfgang Hubner, Walter KellerAbstract:Pcf11p, an essential subunit of the yeast cleavage factor IA, is required for pre-mRNA 3' end processing, binds to the C-terminal domain (CTD) of the largest subunit of RNA polymerase II (RNAP II) and is involved in Transcription Termination. We show that the conserved CTD interaction domain (CID) of Pcf11p is essential for cell viability. Interestingly, the CTD binding and 3' end processing activities of Pcf11p can be functionally uncoupled from each other and provided by distinct Pcf11p fragments in trans. Impaired CTD binding did not affect the 3' end processing activity of Pcf11p and a deficiency of Pcf11p in 3' end processing did not prevent CTD binding. Transcriptional run-on analysis with the CYC1 gene revealed that loss of cleavage activity did not correlate with a defect in Transcription Termination, whereas loss of CTD binding did. We conclude that Pcf11p is a bifunctional protein and that transcript cleavage is not an obligatory step prior to RNAP II Termination.
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yhh1p cft1p directly links poly a site recognition and rna polymerase ii Transcription Termination
The EMBO Journal, 2002Co-Authors: Bernhard Dichtl, Diana Blank, Martin Sadowski, Wolfgang Hubner, Stefan Weiser, Walter KellerAbstract:RNA polymerase II (pol II) Transcription Termination requires co-Transcriptional recognition of a functional polyadenylation signal, but the molecular mechanisms that transduce this signal to pol II remain unclear. We show that Yhh1p/Cft1p, the yeast homologue of the mammalian AAUAAA interacting protein CPSF 160, is an RNA-binding protein and provide evidence that it participates in poly(A) site recognition. Interestingly, RNA binding is mediated by a central domain composed of predicted beta-propeller-forming repeats, which occurs in proteins of diverse cellular functions. We also found that Yhh1p/Cft1p bound specifically to the phosphorylated C-terminal domain (CTD) of pol II in vitro and in a two-hybrid test in vivo. Furthermore, Transcriptional run-on analysis demonstrated that yhh1 mutants were defective in Transcription Termination, suggesting that Yhh1p/Cft1p functions in the coupling of Transcription and 3'-end formation. We propose that direct interactions of Yhh1p/Cft1p with both the RNA transcript and the CTD are required to communicate poly(A) site recognition to elongating pol II to initiate Transcription Termination.
Marc Boudvillain - One of the best experts on this subject based on the ideXlab platform.
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Keeping up to speed with the Transcription Termination factor Rho motor
Transcription, 2020Co-Authors: Marc Boudvillain, Marcello Nollmann, Emmanuel MargeatAbstract:In bacteria, a subset of Transcription Termination events requires the participation of the Transcription Termination factor Rho. Rho is a homo-hexameric, ring-shaped, motor protein that uses the energy derived from its RNA-dependent ATPase activity to directionally unwind RNA and RNA-DNA helices and to dissociate Transcription elongation complexes. Despite a wealth of structural, biochemical and genetic data, the molecular mechanisms used by Rho to carry out its biological functions remain poorly understood. Here, we briefly discuss the most recent findings on Rho mechanisms and function and highlight important questions that remain to be addressed.
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regulatory interplay between small rnas and Transcription Termination factor rho
Biochimica et Biophysica Acta, 2020Co-Authors: Lionello Bossi, Nara Figueroabossi, Philippe Bouloc, Marc BoudvillainAbstract:Abstract The largest and best studied group of regulatory small RNAs (sRNAs) in bacteria act by modulating translation or turnover of messenger RNAs (mRNAs) through base-pairing interactions that typically take place near the 5′ end of the mRNA. This allows the sRNA to bind the complementary target sequence while the remainder of the mRNA is still being made, creating conditions whereby the action of the sRNA can extend to Transcriptional steps, most notably Transcription Termination. Increasing evidence corroborates the existence of a functional interplay between sRNAs and Termination factor Rho. Two general mechanisms have emerged. One mechanism operates in translated regions subjected to sRNA repression. By inhibiting ribosome binding co-Transcriptionally, the sRNA uncouples translation from Transcription, allowing Rho to bind the nascent RNA and promote Termination. In the second mechanism, which functions in 5′ untranslated regions, the sRNA antagonizes Termination directly by interfering with Rho binding to the RNA or the subsequent translocation along the RNA. Here, we review the above literature in the context of other mechanisms that underlie the participation of Rho-dependent Transcription Termination in gene regulation. This article is part of a Special Issue entitled: RNA and gene control in bacteria edited by Dr. M. Guillier and F. Repoila.
