Relevant bibliographies by topics / Rho-dependent termination

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  1. Journal articles
  2. Dissertations / Theses
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Academic literature on the topic 'Rho-dependent termination'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Rho-dependent termination"

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Ciampi, M. Sofia. "Rho-dependent terminators and transcription termination." Microbiology 152, no. 9 (September 1, 2006): 2515–28. http://dx.doi.org/10.1099/mic.0.28982-0.

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Rho-dependent transcription terminators participate in sophisticated genetic regulatory mechanisms, in both bacteria and phages; they occur in regulatory regions preceding the coding sequences of genes and within coding sequences, as well as at the end of transcriptional units, to prevent readthrough transcription. Most Rho-dependent terminators have been found in enteric bacteria, but they also occur in Gram-positive bacteria and may be widespread among bacteria. Rho-dependent termination requires both cis-acting elements, on the mRNA, and trans-acting factors. The only cis-acting element common to Rho-dependent terminators is richness in rC residues. Additional sequence elements have been observed at different Rho termination sites. These ‘auxiliary elements' may assist in the termination process; they differ among terminators, their occurrence possibly depending on the function and sequence context of the terminator. Specific nucleotides required for termination have also been identified at Rho sites. Rho is the main factor required for termination; it is a ring-shaped hexameric protein with ATPase and helicase activities. NusG, NusA and NusB are additional factors participating in the termination process. Rho-dependent termination occurs by binding of Rho to ribosome-free mRNA, C-rich sites being good candidates for binding. Rho's ATPase is activated by Rho–mRNA binding, and provides the energy for Rho translocation along the mRNA; translocation requires sliding of the message into the central hole of the hexamer. When a polymerase pause site is encountered, the actual termination occurs, and the transcript is released by Rho's helicase activity. Many aspects of this process are still being studied. The isolation of mutants suppressing termination, site-directed mutagenesis of cis-acting elements in Rho-dependent termination, and biochemistry, are and will be contributing to unravelling the still undefined aspects of the Rho termination machinery. Analysis of the more sophisticated regulatory mechanisms relying on Rho-dependent termination may be crucial in identifying new essential elements for termination.
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Richardson, John P. "Rho-dependent transcription termination." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1048, no. 2-3 (April 1990): 127–38. http://dx.doi.org/10.1016/0167-4781(90)90048-7.

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Richardson, John P., and E. Cristy Ruteshouser. "rho Factor-dependent transcription termination." Journal of Molecular Biology 189, no. 3 (June 1986): 413–19. http://dx.doi.org/10.1016/0022-2836(86)90313-x.

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Richardson, John P. "Rho-dependent termination and ATPases in transcript termination." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1577, no. 2 (September 2002): 251–60. http://dx.doi.org/10.1016/s0167-4781(02)00456-6.

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Hinde, Paul, Padraig Deighan, and Charles J. Dorman. "Characterization of the Detachable Rho-Dependent Transcription Terminator of the fimE Gene in Escherichia coli K-12." Journal of Bacteriology 187, no. 24 (December 15, 2005): 8256–66. http://dx.doi.org/10.1128/jb.187.24.8256-8266.2005.

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ABSTRACT The fim genetic switch in the chromosome of Escherichia coli K-12 is an invertible DNA element that harbors the promoter for transcription of the downstream fim structural genes and a transcription terminator that acts on the upstream fimE regulatory gene. Switches oriented appropriately for structural gene transcription also allow fimE mRNA to read through, whereas those in the opposite orientation terminate the fimE message. We show here that termination is Rho dependent and is suppressed in a rho mutant or by bicyclomycin treatment when fimE mRNA is expressed by the fimE gene, either from a multicopy recombinant plasmid or in its native chromosomal location. Two cis-acting elements within the central portion of the 314-bp invertible DNA switch were identified as contributors to Rho-dependent termination and dissected. These fim sequence elements show similarities to well-characterized Rho utilization (rut) sites and consist of a boxA motif and a C-rich and G-poor region of approximately 40 bp. Deletion of the boxA motif alone had only a subtle negative effect on Rho function. However, when this element was deleted in combination with the C-rich, G-poor region, Rho function was considerably decreased. Altering the C-to-G ratio in favor of G in this portion of the switch also strongly attenuated transcription termination. The implications of the existence of a fimE-specific Rho-dependent terminator within the invertible switch are discussed in the context of the fim regulatory circuit.
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Hao, Zhitai, Vladimir Svetlov, and Evgeny Nudler. "Rho-dependent transcription termination: a revisionist view." Transcription 12, no. 4 (August 8, 2021): 171–81. http://dx.doi.org/10.1080/21541264.2021.1991773.

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Hollands, K., S. Proshkin, S. Sklyarova, V. Epshtein, A. Mironov, E. Nudler, and E. A. Groisman. "Riboswitch control of Rho-dependent transcription termination." Proceedings of the National Academy of Sciences 109, no. 14 (March 19, 2012): 5376–81. http://dx.doi.org/10.1073/pnas.1112211109.

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Sevostyanova, Anastasia, and Eduardo A. Groisman. "An RNA motif advances transcription by preventing Rho-dependent termination." Proceedings of the National Academy of Sciences 112, no. 50 (November 16, 2015): E6835—E6843. http://dx.doi.org/10.1073/pnas.1515383112.

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The transcription termination factor Rho associates with most nascent bacterial RNAs as they emerge from RNA polymerase. However, pharmacological inhibition of Rho derepresses only a small fraction of these transcripts. What, then, determines the specificity of Rho-dependent transcription termination? We now report the identification of a Rho-antagonizing RNA element (RARE) that hinders Rho-dependent transcription termination. We establish that RARE traps Rho in an inactive complex but does not prevent Rho binding to its recruitment sites. Although translating ribosomes normally block Rho access to an mRNA, inefficient translation of an open reading frame in the leader region of the Salmonella mgtCBR operon actually enables transcription of its associated coding region by favoring an RNA conformation that sequesters RARE. The discovery of an RNA element that inactivates Rho signifies that the specificity of nucleic-acid binding proteins is defined not only by the sequences that recruit these proteins but also by sequences that antagonize their activity.
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Zhu, Anne Q., and Peter H. von Hippel. "Rho-dependent Termination within thetrp t‘ Terminator. I. Effects of Rho Loading and Template Sequence†." Biochemistry 37, no. 32 (August 1998): 11202–14. http://dx.doi.org/10.1021/bi9729110.

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Zhu, Anne Q., and Peter H. von Hippel. "Rho-dependent Termination within thetrp t ‘ Terminator. II. Effects of Kinetic Competition and Rho Processivity†." Biochemistry 37, no. 32 (August 1998): 11215–22. http://dx.doi.org/10.1021/bi972912s.

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Dissertations / Theses on the topic "Rho-dependent termination"

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Grylak-Mielnicka, Aleksandra. "Role of Rho-dependent transcription termination in the regulation of gene expression in Bacillus subtilis." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLS305.

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La transcription bactérienne est un processus dans lequel l'information codée dans l'ADN est transféré à l'ARN messager (ARNm). Au cours de la dernière étape de ce procédé, la terminaison de la transcription, l'ARNm est libéré et peut être utilisé pour la synthèse des protéines. Un type de terminaison de la transcription décrit chez les bactéries est la terminaison Rho-dépendante. Le rôle de Rho a été largement étudié dans le modèle à Gram négatif bactérie, Escherichia coli dans laquelle Rho est une protéine essentiel est abondant. En revanche, la connaissance de Rho chez les bactéries qui il ne sont pas essentiels et est présent en faibles quantités: par exemple Gram-positif Bacillus subtilis reste limité..Pour étudier le rôle de Rho dans le contrôle de l'expression des gènes chez B. subtilis plusieurs analyses à grande échelle ont été réalisées, y compris des tests d'interactions physiques et fonctionnelles et une analyse globale des changements observés dans l'expression des gènes en corrélation avec la production de protéines.En effet, un ensemble des Rho-spécifiques interactions physiques et fonctionnelles ont été établies. En outre, de nouveaux phénotypes de mutant dépourvu de rho ont été décrits ce qui élucider le rôle de Rho dans le contrôle des différents aspects de la physiologie cellulaire
Bacterial transcription is a process in which the information encoded in DNA is transferred to messenger RNA (mRNA). During the final step of this process, transcription termination, mRNA is released and can be used for protein synthesis. One type of transcription termination described in bacteria is Rho-dependent termination. The role of Rho has been widely investigated in model Gram-negative bacterium, Escherichia coli in which Rho is essential an abundant protein. In contrast, the knowledge about Rho inbacteria in which it is not essential and is present in low amounts, i. e. Gram-positive Bacillus subtilis remains limited.To investigate the role of Rho in control of gene expression in B. subtilis several large-scale analysis were performed. In effect, a set of Rho-specific physical and functional interactions were established. Additionally, new phenotypes of rho-null mutant were described unraveling the role of Rho in control of different aspects of cell physiology
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Mitra, Anirban. "Insights into Occurrence and Divergence of Intrinsic Terminators and Studies on Rho-Dependent Termination in Mycobacterium Tuberculosis." Thesis, 2013. http://etd.iisc.ernet.in/2005/3382.

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Two mechanisms, intrinsic and factor-dependent, have evolved for accomplishing the termination of transcription in eubacteria. In this thesis, the first chapter is an introduction to the topic that presents what is known about the mechanisms of termination. The properties of the primary and secondary ‘players’- intrinsic terminators, Rho protein, rho-dependent terminators, RNA polymerse and Nus factors - are presented and the known mechanisms by which termination functions are discussed. In Chapter 2, a detailed analysis of intrinsic terminators – their differential distribution, similarity and divergence - has been penned. The database, compiled using the program GeSTer (Genome Scanner for Terminators), comprises ~2000 sequences and is one of the largest of its kind. Furthermore, analyzing the data from over 700 bacteria reveals how different species have fine-tuned intrinsic terminators to suit their cellular needs. Non-canonical intrinsic terminators emerge to be a significant fraction of the observed structures. The conserved structural features of identified intrinsic terminators are discussed and the relationship between the two modes of termination is assessed. Chapter 3 deals with the importance of transcription termination in regulating horizontally acquired DNA. The results show that genomic islands are scarce in intrinsic terminators and thus constitute most likely sites for Rho-dependent termination. Plausible reasons for why such a scenario has evolved are discussed and a generally applicable model is presented. Chapters 4 and 5 focus on Rho protein from Mycobacterium tuberculosis. In silico identification of M. tuberculosisgenes that rely on MtbRho-dependent termination is followed by experimental validation. The data show that Rho-dependent termination is the predominant mechanism in this species.MtbRho is a majorly expressed protein that governs termination of protein-coding and non-protein coding genes. Further, MtbRho can productively interact with RNA that has considerable secondary structure. Such interactions cause conformational changes in the enzyme. Given that MtbRho has to function with a GC-rich transcriptome, the altered properties could have evolved for optimal function. Taken together, the thesis extends our current understanding of both modes of termination. The importance of non-canonical intrinsic terminators in mycobacteria and other organisms is discussed. The unusual function of Rho and its predominant role in mycobacteria is elucidated. Finally, the inter-relationship between the two modes of termination is also discussed.
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Book chapters on the topic "Rho-dependent termination"

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Nadiras, Cédric, Annie Schwartz, Mildred Delaleau, and Marc Boudvillain. "Evaluating the Effect of Small RNAs and Associated Chaperones on Rho-Dependent Termination of Transcription In Vitro." In Methods in Molecular Biology, 99–118. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7634-8_7.

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"rho-Dependent Transcription Termination." In Encyclopedia of Genetics, Genomics, Proteomics and Informatics, 1702. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6754-9_14614.

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Journal articles
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