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Relevant bibliographies by topics / Transcription by bacterial RNA polymerase

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Academic literature on the topic 'Transcription by bacterial RNA polymerase'

Author: Grafiati

Published: 4 June 2021

Last updated: 4 February 2022

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Journal articles on the topic "Transcription by bacterial RNA polymerase"

1

Djordjevic, Marko. "Modeling Transcription Initiation By Bacterial RNA Polymerase." Biophysical Journal 96, no. 3 (February 2009): 57a. http://dx.doi.org/10.1016/j.bpj.2008.12.193.

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Mosaei, Hamed, and John Harbottle. "Mechanisms of antibiotics inhibiting bacterial RNA polymerase." Biochemical Society Transactions 47, no. 1 (January 15, 2019): 339–50. http://dx.doi.org/10.1042/bst20180499.

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Abstract Transcription, the first phase of gene expression, is performed by the multi-subunit RNA polymerase (RNAP). Bacterial RNAP is a validated target for clinical antibiotics. Many natural and synthetic compounds are now known to target RNAP, inhibiting various stages of the transcription cycle. However, very few RNAP inhibitors are used clinically. A detailed knowledge of inhibitors and their mechanisms of action (MOA) is vital for the future development of efficacious antibiotics. Moreover, inhibitors of RNAP are often useful tools with which to dissect RNAP function. Here, we review the MOA of antimicrobial transcription inhibitors.

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Zhang, Nan, Vidya C. Darbari, Robert Glyde, Xiaodong Zhang, and Martin Buck. "The bacterial enhancer-dependent RNA polymerase." Biochemical Journal 473, no. 21 (October 27, 2016): 3741–53. http://dx.doi.org/10.1042/bcj20160741c.

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Transcription initiation is highly regulated in bacterial cells, allowing adaptive gene regulation in response to environment cues. One class of promoter specificity factor called sigma54 enables such adaptive gene expression through its ability to lock the RNA polymerase down into a state unable to melt out promoter DNA for transcription initiation. Promoter DNA opening then occurs through the action of specialized transcription control proteins called bacterial enhancer-binding proteins (bEBPs) that remodel the sigma54 factor within the closed promoter complexes. The remodelling of sigma54 occurs through an ATP-binding and hydrolysis reaction carried out by the bEBPs. The regulation of bEBP self-assembly into typically homomeric hexamers allows regulated gene expression since the self-assembly is required for bEBP ATPase activity and its direct engagement with the sigma54 factor during the remodelling reaction. Crystallographic studies have now established that in the closed promoter complex, the sigma54 factor occupies the bacterial RNA polymerase in ways that will physically impede promoter DNA opening and the loading of melted out promoter DNA into the DNA-binding clefts of the RNA polymerase. Large-scale structural re-organizations of sigma54 require contact of the bEBP with an amino-terminal glutamine and leucine-rich sequence of sigma54, and lead to domain movements within the core RNA polymerase necessary for making open promoter complexes and synthesizing the nascent RNA transcript.

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Szalewska-Pałasz, Agnieszka. "Properties of Escherichia coli RNA polymerase from a strain devoid of the stringent response alarmone ppGpp." Acta Biochimica Polonica 55, no. 2 (June 14, 2008): 317–23. http://dx.doi.org/10.18388/abp.2008_3078.

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The stringent response alarmone guanosine tetraphosphate (ppGpp) affects transcription from many promoters. ppGpp binds directly to the transcription enzyme of Escherichia coli, RNA polymerase. Analysis of the crystal structure of RNA polymerase with ppGpp suggested that binding of this nucleotide may result in some conformational or post-translational alterations to the enzyme. These changes might affect in vitro performance of the enzyme. Here, a comparison of the in vitro properties of RNA polymerases isolated from wild type and ppGpp-deficient bacteria shows that both enzymes do not differ in i) transcription activity of various promoters (e.g. sigma(70)-rrnB P1, lambdapL, T7A1), ii) response to ppGpp, iii) promoter-RNA polymerase open complex stability. Thus, it may be concluded that ppGpp present in the bacterial cell prior to purification of the RNA polymerase does not result in the alterations to the enzyme that could be permanent and affect its in vitro transcription capacity.

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Agapov, Aleksei, Artem Ignatov, Matti Turtola, Georgiy Belogurov, Daria Esyunina, and Andrey Kulbachinskiy. "Role of the trigger loop in translesion RNA synthesis by bacterial RNA polymerase." Journal of Biological Chemistry 295, no. 28 (May 21, 2020): 9583–95. http://dx.doi.org/10.1074/jbc.ra119.011844.

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DNA lesions can severely compromise transcription and block RNA synthesis by RNA polymerase (RNAP), leading to subsequent recruitment of DNA repair factors to the stalled transcription complex. Recent structural studies have uncovered molecular interactions of several DNA lesions within the transcription elongation complex. However, little is known about the role of key elements of the RNAP active site in translesion transcription. Here, using recombinantly expressed proteins, in vitro transcription, kinetic analyses, and in vivo cell viability assays, we report that point amino acid substitutions in the trigger loop, a flexible element of the active site involved in nucleotide addition, can stimulate translesion RNA synthesis by Escherichia coli RNAP without altering the fidelity of nucleotide incorporation. We show that these substitutions also decrease transcriptional pausing and strongly affect the nucleotide addition cycle of RNAP by increasing the rate of nucleotide addition but also decreasing the rate of translocation. The secondary channel factors DksA and GreA modulated translesion transcription by RNAP, depending on changes in the trigger loop structure. We observed that although the mutant RNAPs stimulate translesion synthesis, their expression is toxic in vivo, especially under stress conditions. We conclude that the efficiency of translesion transcription can be significantly modulated by mutations affecting the conformational dynamics of the active site of RNAP, with potential effects on cellular stress responses and survival.

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Harden, Timothy T., Christopher D. Wells, Larry J. Friedman, Robert Landick, Ann Hochschild, Jane Kondev, and Jeff Gelles. "Bacterial RNA polymerase can retain σ70 throughout transcription." Proceedings of the National Academy of Sciences 113, no. 3 (January 5, 2016): 602–7. http://dx.doi.org/10.1073/pnas.1513899113.

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Production of a messenger RNA proceeds through sequential stages of transcription initiation and transcript elongation and termination. During each of these stages, RNA polymerase (RNAP) function is regulated by RNAP-associated protein factors. In bacteria, RNAP-associated σ factors are strictly required for promoter recognition and have historically been regarded as dedicated initiation factors. However, the primary σ factor in Escherichia coli, σ70, can remain associated with RNAP during the transition from initiation to elongation, influencing events that occur after initiation. Quantitative studies on the extent of σ70 retention have been limited to complexes halted during early elongation. Here, we used multiwavelength single-molecule fluorescence-colocalization microscopy to observe the σ70–RNAP complex during initiation from the λ PR′ promoter and throughout the elongation of a long (>2,000-nt) transcript. Our results provide direct measurements of the fraction of actively transcribing complexes with bound σ70 and the kinetics of σ70 release from actively transcribing complexes. σ70 release from mature elongation complexes was slow (0.0038 s−1); a substantial subpopulation of elongation complexes retained σ70 throughout transcript elongation, and this fraction depended on the sequence of the initially transcribed region. We also show that elongation complexes containing σ70 manifest enhanced recognition of a promoter-like pause element positioned hundreds of nucleotides downstream of the promoter. Together, the results provide a quantitative framework for understanding the postinitiation roles of σ70 during transcription.

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Ouhammouch, Mohamed, Finn Werner, Robert O. J. Weinzierl, and E. Peter Geiduschek. "A Fully Recombinant System for Activator-dependent Archaeal Transcription." Journal of Biological Chemistry 279, no. 50 (October 14, 2004): 51719–21. http://dx.doi.org/10.1074/jbc.c400446200.

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The core components of the archaeal transcription apparatus closely resemble those of eukaryotic RNA polymerase II, while the DNA-binding transcriptional regulators are predominantly of bacterial type. Here we report the construction of an entirely recombinant system for positively regulated archaeal transcription. By omitting individual subunits, or sets of subunits, from thein vitroassembly of the 12-subunit RNA polymerase from the hyperthermophileMethanocaldococcus jannaschii, we describe a functional dissection of this RNA polymerase II-like enzyme, and its interactions with the general transcription factor TFE, as well as with the transcriptional activator Ptr2.

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Willkomm, Dagmar K., and Roland K. Hartmann. "6S RNA – an ancient regulator of bacterial RNA polymerase rediscovered." Biological Chemistry 386, no. 12 (December 1, 2005): 1273–77. http://dx.doi.org/10.1515/bc.2005.144.

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AbstractThe bacterial riboregulator 6S RNA was one of the first non-coding RNAs to be discovered in the late 1960s, but its cellular role remained enigmatic until the year 2000. 6S RNA, only recognized to be ubiquitous among bacteria in 2005, binds to RNA polymerase in a σ factor-dependent manner to repress transcription from a subgroup of promoters. The common feature of a double-stranded rod with a central bulge has led to the proposal that 6S RNA may mimic an open promoter complex.

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Pupov, Danil, Daria Esyunina, Andrey Feklistov, and Andrey Kulbachinskiy. "Single-strand promoter traps for bacterial RNA polymerase." Biochemical Journal 452, no. 2 (May 10, 2013): 241–48. http://dx.doi.org/10.1042/bj20130069.

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Besides canonical double-strand DNA promoters, multisubunit RNAPs (RNA polymerases) recognize a number of specific single-strand DNA and RNA templates, resulting in synthesis of various types of RNA transcripts. The general recognition principles and the mechanisms of transcription initiation on these templates are not fully understood. To investigate further the molecular mechanisms underlying the transcription of single-strand templates by bacterial RNAP, we selected high-affinity single-strand DNA aptamers that are specifically bound by RNAP holoenzyme, and characterized a novel class of aptamer-based transcription templates. The aptamer templates have a hairpin structure that mimics the upstream part of the open promoter bubble with accordingly placed specific promoter elements. The affinity of the RNAP holoenzyme to such DNA structures probably underlies its promoter-melting activity. Depending on the template structure, the aptamer templates can direct synthesis of productive RNA transcripts or effectively trap RNAP in the process of abortive synthesis, involving DNA scrunching, and competitively inhibit promoter recognition. The aptamer templates provide a novel tool for structure–function studies of transcription initiation by bacterial RNAP and its inhibition.

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Nielsen, Soren, Yulia Yuzenkova, and Nikolay Zenkin. "Mechanism of Eukaryotic RNA Polymerase III Transcription Termination." Science 340, no. 6140 (June 27, 2013): 1577–80. http://dx.doi.org/10.1126/science.1237934.

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Gene expression in organisms involves many factors and is tightly controlled. Although much is known about the initial phase of transcription by RNA polymerase III (Pol III), the enzyme that synthesizes the majority of RNA molecules in eukaryotic cells, termination is poorly understood. Here, we show that the extensive structure of Pol III–synthesized transcripts dictates the release of elongation complexes at the end of genes. The poly-T termination signal, which does not cause termination in itself, causes catalytic inactivation and backtracking of Pol III, thus committing the enzyme to termination and transporting it to the nearest RNA secondary structure, which facilitates Pol III release. Similarity between termination mechanisms of Pol III and bacterial RNA polymerase suggests that hairpin-dependent termination may date back to the common ancestor of multisubunit RNA polymerases.

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Dissertations / Theses on the topic "Transcription by bacterial RNA polymerase"

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Ferguson, Anna Louise. "Interactions of bacterial sigma subunits with core RNA polymerase." Thesis, University of York, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.341839.

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Southern, Emma. "The role of #sigma#'54 region II in transcription initiation." Thesis, University of East Anglia, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302057.

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Furman, Ran. "DksA Beyond the Stringent Response: Investigating the Functions of a Diverse Bacterial Transcription Factor." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1367584519.

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Tupin, Audrey. "Inhibiteurs de la transcription bactérienne : étude du mécanisme d'action de la lipiarmycine et dépendance au facteur de transcription σ." Thesis, Montpellier 1, 2010. http://www.theses.fr/2010MON13512/document.

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Le nombre croissant de bactéries résistantes aux antibiotiques et le problème des cellules persistantes rend urgent le développement de nouveaux antibiotiques et la compréhension de leur mécanisme d'action. L'ARN polymérase est l'enzyme centrale de la transcription et est une cible intéressante pour les antibiotiques. Dans cette étude, nous nous sommes particulièrement intéressés à un inhibiteur de l'ARN polymérase : la lipiarmycine. Il s'agit d'un inhibiteur de la transcription macrocyclique qui inhibe les bactéries à Gram + et qui est en essai clinique de phase III pour le traitement des infections liées à Clostridium difficile. L'objectif de ce travail a été de déterminer le mécanisme d'action de la lipiarmycine ainsi que le mécanisme de résistance à la molécule. Pour cela, nous avons dans un premier temps précisé et modélisé son site de liaison sur l'ARN polymérase. Puis, dans un deuxième temps, nous avons utilisé des approches génétiques et biochimiques afin de déterminer son mécanisme et l'effet de certaines mutations sur la transcription. Ces travaux ont mis à jour un nouveau mécanisme d'inhibition de la transcription
The growing number of antibiotic-resistant bacteria added to the problem caused by persistent cells stress the need for developing new antibiotics and for understanding their mechanism of action. RNA polymerase is the main enzyme of the transcription process and is an interesting target for antibiotics. In this study we focus on a particular inhibitor of RNA polymerase : lipiarmycin. It is a macrocyclic inhibitor of transcription inhibiting Gram + bacteria that is developed in phase III clinical trials for treatment of Clostridium difficile infections. The objective of this work was to determine the mechanism of action of lipiarmycin and the mechanism confering resistance against the molecule. We first define more precisely its binding site on RNA polymerase and then used genetic and biochemical approaches to determine its mechanism of action and the effect of some specific mutations on transcription. Our experiments reveal a new mechanism of t ranscription inhibitor action

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Chakraborty, Atanu. "Mechanism Of mom Gene Transactivation By Transcription Factor C Of Phage MU." Thesis, Indian Institute of Science, 2006. http://hdl.handle.net/2005/275.

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Regulation of transcription initiation is the major determining event employed by the cell to control gene expression and subsequent cellular processes. The weak promoters, with low basal transcription activities, are activated by activators. Bacteriophage Mu mom gene, which encodes a unique DNA modification function, is detrimental to cell when expressed early or in large quantities. Mu has designed a complex, well-controlled and orchestrated regulatory network for mom expression to ensure its synthesis only in late lytic cycle. The phage encoded transcription activator protein C activates the gene by promoter unwinding of the DNA and thereby recruiting of RNAP to the promoter. C protein functions as a dimer for DNA binding and transcription activation. Mutagenesis and chemical crosslinking studies revealed that the leucine zipper motif, and not the coiled coil motif in the N terminal region, is responsible for C dimerization. The DNA binding domain of C is a HTH domain which is preceded by the leucine zipper motif. The C protein is one of the few examples in the bacterial proteins containing both leucine zipper and HTH domain. Most of the transcription activators either influence initial binding of RNAP or conversion of closed to open complex formation. Very few activators act at subsequent steps of promoter-polymerase interaction. Earlier studies showed high level of transcription from a mutant mom promoter, tin7. Addition of C further increased transcription from Ptin7 indicating that C may have a role beyond polymerase recruitment. Each steps of transcription initiation have been dissected using the Ptin7 and a positive control (pc) mutant of C, R105D. The results revealed multi-step transcription activation mechanism for C protein at Pmom. C recruits RNAP at Pmom and subsequently increases the productive RNAP-promoter complex and enhances promoter clearance. To further understand the C mediated transactivation mechanism, interaction between C and RNAP was assessed. C interacts with holo and core RNAP only in presence of DNA. Positive control mutants of C, F95A and R015D, were found to be compromised in RNAP interactions. These mutants were efficient in RNAP recruitment to Pmom but do not enhance promoter clearance. Trypsin cleavage protection experiment indicated that probably C protein interacts with b¢ subunit of RNAP. Interaction between C and RNAP appears to enhance the formation of productive RNAP-promoter complex leading to promoter clearance. The connection between activator-polymerase interaction and transcription activation is well documented where the recruitment of RNAP is influenced. In case of activators acting at post recruitment steps of initiation, the role of polymerase contact is poorly understood. Our study shows that activator-polymerase interaction can lead to increased promoter clearance at Pmom by overcoming abortive initiation.

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Duval-Valentin, Guy. "Reconnaissance proteines-acides nucleiques : etudes structurales et dynamiques de l'interaction de l'arn-polymerase d'e. coli sur deux promoteurs aux comportements heterologues." Paris 6, 1987. http://www.theses.fr/1987PA066354.

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Fernández, Coll Llorenç. "Secondary channel of the RNA polymerase, a target for transcriptional regulation in bacteria." Doctoral thesis, Universitat de Barcelona, 2015. http://hdl.handle.net/10803/298719.

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Gene expression begins by an enzymatic complex known as RNA polymerase (RNApol). The basic unit (core) of RNApol in bacteria is formed by 5 protein subunits (α2ββ’ω). The three-dimensional structure of the RNApol defines two spaces that play a relevant role during transcription, defined as primary and secondary channel. The holoenzyme needs the binding of a σ subunit to recognise promoter sequences and initiate the transcription process. Transcription is a dynamic process controlled at different steps. Genetic regulation during transcription initiation has been highly studied, and several mechanisms of regulation exist. However, the aim of this project is to study some aspects of the regulation during transcription elongation. It has been described that the alamone ppGpp, as well as several proteins, such as GreA, GreB or DksA, enter within the secondary channel and interact directly with the catalytic centre of the RNApol. The swap between the different factors that bind to the secondary channel of the RNApol may cause changes in the expression pattern. It has been postulated that DksA and ppGpp act as cofactors, however, a previous study performed in our research group, indicated that the phenotype of ppGpp and DksA deficiencies were not always identical, letting us suggest that the occupancy degree of the secondary channel of the RNApol may have significant impact in the expression pattern in E. coli. The data obtained clearly indicate that upregulation of some genes, such as fliC, that occurs in absence of DksA, was the result of the vacancy of the secondary channel generated in a dksA strain rather than being the result of DksA having a direct repressor effect. We suggested that in the absence of DksA, the interactions of other proteins, such as GreA, are promoted and responsible of the upregulation observed. In this project, functional, structural and phylogenetical studies of the protein GreA were performed to determine which amino acids are important for i) the functionality of GreA, ii) the ability to bind to the secondary channel of the RNApol or iii) the capacity to compete with other factors, such as DksA. We have determined that greA overexpression produces a negative effect of the bacterial growth. Moreover, this negative effect is enhanced in absence of DksA, highlighting the hypothesis of a competition between factors that bind into the secondary channel. The effect of this competition between GreA and DksA was also determined studying the expression of the fliC gene. Our data showed that both, GreA and DksAare required for fliC expression but act at different levels in the regulatory cascade of flagella expression regulation. GreA may control fliC expression during transcription elongation whereas DksA may act during transcription initiation. Changes in the amount of GreA, could affect the competition between factors that bind to the secondary channel of the RNApol. Therefore, we have determined the expression pattern of greA. Transcriptional studies showed a crosstalk between the different factors that bind into the secondary channel of the RNApol exists. Finally, transcriptomic studies were performed to determine the effect of ppGpp and DksA on the expression pattern of Salmonella enterica serovar Typhimurium. The results obtained indicate : i) the effect of the possible competence between the factors that interact into the secondary channel of the RNApol and ii) the effect of ppGpp and DksA on the expression of several virulence factors as well as different mobile elements present in Salmonella.
El control de l’expressió gènica en bacteris recau principalment sobre un complex enzimàtic anomenat ARN polimerasa (ARNpol). A procariotes, la seva unitat bàsica (core) està formada per 5 subunitats proteiques (a2bb’w). S’han determinat dos canals entre les diferents subunitats de l’ARNpol: el canal primari, on es desenvolupa la transcripció, i el canal secundari, que comunica el medi exterior amb el centre catalític de l’ARNpol. Tot i així, aquest holoenzim necessita la unió d’una subunitat σ per ser capaç de reconèixer una seqüència promotora i iniciar la transcripció. S’han descrit diferents factors, tant proteics com no proteics, que poden interaccionar amb el canal secundari de l’ARNpol i causar alteracions a l’expressió gènica. En aquesta tesi ens hem centrat en la possible competència entre els diferents factors que poden interaccionar amb el canal secundari de l’ARNpol. Estudis anterior duts a terme en el nostre grup d’investigació, ens van permetre postular una possible competència entre els diferents factors que interaccionen amb el canal secundari de l’ARNpol, més concretament entre les proteïnes GreA i DksA. Aquesta competència provocaria alteracions en el patró d’expressió gènica d’Escherichia coli. En aquest treball s’han dut a terme estudis funcionals, estructurals i filogenètics de la proteïna GreA que ens han permès determinar quins aminoàcids, i com a conseqüència quins dominis, podrien ser importants per la funcionalitat de la proteïna, la seva capacitat d’unir-se a l’ARNpol i la seva capacitat de competir amb altres factors. A més, hem estudiat quin efecte té la competència entre els diferents factors que interaccionen amb el canal secundari sobre l’expressió d’un gen diana. Canvis en els nivells de la proteïna GreA, poden afectar la competència pel canal secundari de l’ARNpol Per això hem determinat el patró d’expressió del gen greA, així com l’existència d’una regulació creuada entre les diferents proteïnes que interaccionen amb el canal secundari. Finalment, hem dut a terme un estudi transcriptòmic en Salmonella enterica serovar Typhimurium, amb l’objectiu de determinar quin és l’efecte d’aquesta competència en l’expressió de factors de virulència.

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Neugebauer, Karla M., Inna Grishina, Anita S. Bledau, and Imke Listerman. "Extragenic Accumulation of RNA Polymerase II Enhances Transcription by RNA Polymerase III." PLOS, 2007. https://tud.qucosa.de/id/qucosa%3A27951.

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Recent genomic data indicate that RNA polymerase II (Pol II) function extends beyond conventional transcription of primarily protein-coding genes. Among the five snRNAs required for pre-mRNA splicing, only the U6 snRNA is synthesized by RNA polymerase III (Pol III). Here we address the question of how Pol II coordinates the expression of spliceosome components, including U6. We used chromatin immunoprecipitation (ChIP) and high-resolution mapping by PCR to localize both Pol II and Pol III to snRNA gene regions. We report the surprising finding that Pol II is highly concentrated ∼300 bp upstream of all five active human U6 genes in vivo. The U6 snRNA, an essential component of the spliceosome, is synthesized by Pol III, whereas all other spliceosomal snRNAs are Pol II transcripts. Accordingly, U6 transcripts were terminated in a Pol III-specific manner, and Pol III localized to the transcribed gene regions. However, synthesis of both U6 and U2 snRNAs was α-amanitin-sensitive, indicating a requirement for Pol II activity in the expression of both snRNAs. Moreover, both Pol II and histone tail acetylation marks were lost from U6 promoters upon α-amanitin treatment. The results indicate that Pol II is concentrated at specific genomic regions from which it can regulate Pol III activity by a general mechanism. Consequently, Pol II coordinates expression of all RNA and protein components of the spliceosome.

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Neugebauer, Karla M., Inna Grishina, Anita S. Bledau, and Imke Listerman. "Extragenic Accumulation of RNA Polymerase II Enhances Transcription by RNA Polymerase III." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-184076.

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Recent genomic data indicate that RNA polymerase II (Pol II) function extends beyond conventional transcription of primarily protein-coding genes. Among the five snRNAs required for pre-mRNA splicing, only the U6 snRNA is synthesized by RNA polymerase III (Pol III). Here we address the question of how Pol II coordinates the expression of spliceosome components, including U6. We used chromatin immunoprecipitation (ChIP) and high-resolution mapping by PCR to localize both Pol II and Pol III to snRNA gene regions. We report the surprising finding that Pol II is highly concentrated ∼300 bp upstream of all five active human U6 genes in vivo. The U6 snRNA, an essential component of the spliceosome, is synthesized by Pol III, whereas all other spliceosomal snRNAs are Pol II transcripts. Accordingly, U6 transcripts were terminated in a Pol III-specific manner, and Pol III localized to the transcribed gene regions. However, synthesis of both U6 and U2 snRNAs was α-amanitin-sensitive, indicating a requirement for Pol II activity in the expression of both snRNAs. Moreover, both Pol II and histone tail acetylation marks were lost from U6 promoters upon α-amanitin treatment. The results indicate that Pol II is concentrated at specific genomic regions from which it can regulate Pol III activity by a general mechanism. Consequently, Pol II coordinates expression of all RNA and protein components of the spliceosome.

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10

White, Eleanor. "Transcription termination by RNA polymerase II." Thesis, University of Oxford, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.558432.

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RNA Polymerase II (Pol I1) is responsible for the transcription of all protein-encoding genes. Pol II termination is dependent on RNA processing signals (both terminal intron splice sites, and cleavage and polyadenylation signals) as well as specific terminator elements located downstream of the poly(A) site. Detailed analysis of the human ~- globin gene terminator has shown that it contains a sequence-specific region that promotes rapid Co-Transcriptional Cleavage (CoTC) of the nascent transcript - an essential but not well understood step in the human ~-globin gene termination process. In the first part of this thesis, the role of sequences within this CoTC-mediated terminator element in the termination process is investigated. Analysis of mutant terminator sequences indicate that homopolymer A tracts are important for Pol II termination. The second part of this study focuses on identifying the activity responsible for CoTC, by using the yeast S. pombe as a tool for genetic analysis. The results indicate that the human ~-globin gene terminator is inefficient in S. pombe, suggesting that a mammalian specific factor(s) are required. In the final part of this study, I describe an investigation into the possibility that the exosome subunit Dis3 or the RNase III enzyme Dicer are involved in CoTC mediated transcription termination. While Dis3 is not involved in the CoTC process my results on Dicer may imply a significant role. Lastly, I present a preliminary investigation into the effect of pre-mRNA processing and the carboxyl terminal domain (CTD) of Po 1 II on CoTC activity.

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Books on the topic "Transcription by bacterial RNA polymerase"

1

Artsimovitch, Irina, and Thomas J. Santangelo. Bacterial transcriptional control: Methods and protocols. New York: Humana Press, 2015.

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White, Robert J. RNA polymerase III transcription. Austin: R.G. Landes, 1994.

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J, White Robert. RNA polymerase III transcription. 2nd ed. Austin, TX: Landes Bioscience, 1998.

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RNA polymerase III transcription. 2nd ed. Berlin: Springer, 1998.

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White, Robert J. RNA Polymerase III Transcription. Berlin, Heidelberg: Springer Berlin Heidelberg, 1998. http://dx.doi.org/10.1007/978-3-662-03518-4.

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Emili, Andrew. Activation of RNA polymerase II mediated transcription. Ottawa: National Library of Canada = Bibliothèque nationale du Canada, 1997.

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Transcription of ribosomal RNA genes by eukaryotic RNA polymerase I. Berlin: Springer, 1998.

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Burns, Helen Dawn. Factors affecting open complex formation during transcription initiation by Escherichia coli RNA polymerase. Birmingham: University of Birmingham, 1995.

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Wisconsin--Madison), Steenbock Symposium (16th 1986 University of. RNA polymerase and the regulation of transcription: Proceedings of the Sixteenth Steenbock Symposium held July 13th through July 17th, 1986, at the University of Wisconsin--Madison, U.S.A. New York: Elsevier, 1987.

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Wu, Jiusheng. In vitro characterization of mutant yeast RNA polymerase II with reduced binding for transcription-elongation factor tfiis. Ottawa: National Library of Canada, 1996.

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Book chapters on the topic "Transcription by bacterial RNA polymerase"

1

Moran, Charles P. "RNA Polymerase and Transcription Factors." In Bacillus subtilis and Other Gram-Positive Bacteria, 651–67. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818388.ch45.

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Cohen, G. N. "Transcription: RNA Polymerase." In Microbial Biochemistry, 195–204. Dordrecht: Springer Netherlands, 2014. http://dx.doi.org/10.1007/978-94-017-8908-0_15.

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Cohen, Georges N. "Transcription. RNA polymerase." In Microbial Biochemistry, 97–101. Dordrecht: Springer Netherlands, 2004. http://dx.doi.org/10.1007/978-1-4020-2237-1_13.

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Cohen, Georges N. "Transcription: RNA Polymerase." In Microbial Biochemistry, 263–79. Dordrecht: Springer Netherlands, 2016. http://dx.doi.org/10.1007/978-94-017-7579-3_15.

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Cohen, G. N. "Transcription: RNA Polymerase." In Microbial Biochemistry, 179–87. Dordrecht: Springer Netherlands, 2010. http://dx.doi.org/10.1007/978-90-481-9437-7_15.

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White, Robert J. "Transcription." In RNA Polymerase III Transcription, 163–71. Berlin, Heidelberg: Springer Berlin Heidelberg, 1998. http://dx.doi.org/10.1007/978-3-662-03518-4_6.

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White, Robert J. "RNA Polymerase III." In RNA Polymerase III Transcription, 57–76. Berlin, Heidelberg: Springer Berlin Heidelberg, 1998. http://dx.doi.org/10.1007/978-3-662-03518-4_3.

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Drygin, Denis, and Ross Hannan. "RNA Polymerase I Transcription." In Encyclopedia of Cancer, 1–5. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-27841-9_7174-3.

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Drygin, Denis, and Ross Hannan. "RNA Polymerase I Transcription." In Encyclopedia of Cancer, 4095–99. Berlin, Heidelberg: Springer Berlin Heidelberg, 2016. http://dx.doi.org/10.1007/978-3-662-46875-3_7174.

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McAllister, W. T. "Transcription by T7 RNA Polymerase." In Mechanisms of Transcription, 15–25. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-60691-5_2.

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Conference papers on the topic "Transcription by bacterial RNA polymerase"

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Grierson, Patrick, Kate Lillard, Gregory Behbehani, Kelly Combs, Saumitri Bhattacharyya, Acharya Samir, and Joanna Groden. "Abstract PR3: The BLM helicase facilitates RNA polymerase l-mediated ribosomal RNA transcription." In Abstracts: Second AACR International Conference on Frontiers in Basic Cancer Research--Sep 14-18, 2011; San Francisco, CA. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.fbcr11-pr3.

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Belgacem, Ismail, Edith Grac, Delphine Ropers, and Jean-Luc Gouze. "Stability analysis of a reduced transcription-translation model of RNA polymerase." In 2014 IEEE 53rd Annual Conference on Decision and Control (CDC). IEEE, 2014. http://dx.doi.org/10.1109/cdc.2014.7039999.

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Leonidou, A., H. King, J. Gouge, and A. Vannini. "PO-250 Investigating BRF2-dependent RNA polymerase III transcription deregulation in cancer." In Abstracts of the 25th Biennial Congress of the European Association for Cancer Research, Amsterdam, The Netherlands, 30 June – 3 July 2018. BMJ Publishing Group Ltd, 2018. http://dx.doi.org/10.1136/esmoopen-2018-eacr25.283.

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Dass, Randall, Aishe Sarshad, Brittany Carson, Jennifer Feenstra, Amanpreet Kaur, Ales Obrdlik, Matthew Parks, et al. "Abstract A46: Wnt5a signals through DVL1 to repress ribosomal DNA transcription by RNA polymerase I." In Abstracts: AACR Special Conference on Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy; October 27-30, 2016; San Francisco, CA. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.transcontrol16-a46.

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Shah, Kalpit, Justin Foley, Michael L. Nickerson, Michael Dean, and Neil Bradbury. "Abstract 2379: Nuclear lemur tyrosine kinase-2 regulates RNA polymerase II dependent transcription in prostate cancer." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-2379.

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Andreeva, A. A., and N. V. Kudryakova. "Homonal regulation of gene expression of proteins associated with plastid RNA-bacterial polymerase during ontogenesis of Arabidopsis thaliana." In IX Congress of society physiologists of plants of Russia "Plant physiology is the basis for creating plants of the future". Kazan University Press, 2019. http://dx.doi.org/10.26907/978-5-00130-204-9-2019-41.

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Andreeva, A. A., M. N. Danilova, N. V. Kudryakova, and V. V. Kusnetsov. "GENES OF ARABIDOPSIS THALIANA PROTEINS ASSOCIATED WITH PLASTID RNA POLYMERASE OF BACTERIAL TYPE: EXPRESSION UNDER CONDITIONS OF ABIOTIC STRESS." In The All-Russian Scientific Conference with International Participation and Schools of Young Scientists "Mechanisms of resistance of plants and microorganisms to unfavorable environmental". SIPPB SB RAS, 2018. http://dx.doi.org/10.31255/978-5-94797-319-8-84-88.

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Sheng, Jinghao, Chi Luo, Yuxiang Jiang, Philip W. Hinds, Zhengping Xu, and Guo-fu Hu. "Abstract 1401: Transcription of angiogenin and ribonuclease 4 is regulated by RNA polymerase III elements and a CTCF-dependent intragenic chromatin loop." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-1401.

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Fleming, Paul, and Tara Dalton. "One-Step Reverse-Transcription PCR on a High-Throughput Micro-Fluidic Device." In ASME 2009 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2009. http://dx.doi.org/10.1115/sbc2009-206623.

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Abstract:

One step reverse-transcription polymerase chain reaction (RT-PCR) assays are an attractive option for further automating gene detection assays. One-step assays can reduce hands–on-time and the risk of sample crossover and contamination. The one-step chemistries are showing increasing use in virus detection and have been reported, in some cases, to be more appropriate than their two-step counterparts [1, 2]. Previous work presented by the Stokes Institute research group outlined a micro fluidic based continuous flow instrument which performed high throughput qPCR in nanolitre sized droplets [3]. This instrument had advantages over commercially available instruments in that it could process far more than the traditional 96 or 384 reaction setup in a single run and the reaction volume was reduced from 20–50 μl down to 30–100 nl sized droplets. Combining one-step chemistry with the technology offered by the devices being developed would lead to a high-throughput RNA-to-signal system capable of reverse transcribing and performing PCR on thousands of nanolitre sized reactions every day. It is envisaged that this technology will also lead to gene expression from single cells contained in nanolitre sized droplets. In this paper, a study was conducted in which an extra thermal region, manufactured from aluminium, was added to the existing continuous flow instruments. This region was maintained at a temperature suitable for reverse transcription, which was 48°C for the one-step kit tested. The thermal region was also a suitable length to maintain the sample at the required temperature for 15 minutes. Using a commercially available one step RT-PCR kit (TaqMan® RNA-to-CT™ 1-Step Kit, 4392653), the device was evaluated for its potential to perform one-step RT-PCR in continuously flowing nanolitre sized droplets. Electrophoresis gels were initially used in assessing specific amplification before an end-point detection method was utilized. RNA was extracted from the leukemic REH cell line with the housekeeping gene, glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) as the gene of interest. To investigate the possibility of further reducing sample preparation and facilitating further automation, amplification from cell lysates without nucleic acid extraction was carried out on the device. Cell lysates were prepared using the cell lysis buffer from the TaqMan® Gene Expression Cells-to-CT™ Kit (Cat #AM1728). It was found that the device was successful in one-step RT-PCR from extracted RNA samples and samples from cell lysates without nucleic acid extraction.

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Stoicescu, Ramona, Razvan-Alexandru Stoicescu, Codrin Gheorghe, Adina Honcea, and Iulian Bratu. "CONSIDERATIONS ON SARS-COV-2 DIAGNOSIS IN THE LABORATORY OF UNIVERSITY EMERGENCY CLINICAL HOSPITAL OF CONSTANTA." In GEOLINKS Conference Proceedings. Saima Consult Ltd, 2021. http://dx.doi.org/10.32008/geolinks2021/b1/v3/07.

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Coronaviruses are members of the Coronaviridae family. They are enveloped, non-segmented, positive-sense, single-stranded RNA viruses. Their genome size is about 30 kilobases (kb) which consist, at the 5’ end, of non-structural open reading frames (ORFs: ORF1a, ORF 1b) which code for 16 non structural proteins, and at the 3’ end the genes which code for four structural proteins including membrane (M), envelope (E), spike (S), and nucleocapsid (N) proteins. Due to the rapid spread of COVID-19, a reliable detection method is needed for patient diagnosis especially in the early stages of the disease. WHO has recommended nucleic acid amplification tests such as real-time reverse transcription-polymerase chain reaction (RT-PCR). The assay detects three SARS-CoV-2 RNA targets: the envelope (E) gene, the nucleocapsid (N) gene and a region of the open reading frame (ORF1) of the RNA-dependent RNA polymerase (RdRp) gene from SARS-CoV-2 virus isolate Wuhan-Hu-1. Our study was made in the first 3 months of the year 2021 using the real-time RT PCR results obtained in the Cellular Biology ward of the University Emergency Clinical Hospital. In our lab we are testing the inpatients from the hospital wards (Neurology, Pediatrics, Surgery, Internal medicine, ICU, Cardiology, etc.); we are also testing the outpatients from Dialysis and Oncology, 2 days prior to their therapy; we also test the health care personnel. The number of tests we performed was: in January 1456, with 399 positive results (27.4%), 33 deaths; in February 1273 tests, 221 positive (17.36%), 16 deaths; in March 1471 tests, 373 positive (25.36%), 37 deceased.

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