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Academic literature on the topic 'Carboxyl-terminal domain CTD'
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Journal articles on the topic "Carboxyl-terminal domain CTD"
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Baskaran, R., M. E. Dahmus, and J. Y. Wang. "Tyrosine phosphorylation of mammalian RNA polymerase II carboxyl-terminal domain." Proceedings of the National Academy of Sciences 90, no. 23 (1993): 11167–71. http://dx.doi.org/10.1073/pnas.90.23.11167.
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The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II is composed of tandem repeats of the consensus sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser. Phosphorylation of the CTD occurs during formation of the initiation complex and is correlated with the transition from complex assembly to elongation. Previously, serine and threonine residues within the CTD have been shown to be modified by the addition of phosphate and by the addition of O-linked GlcNAc. Our results establish that the CTD is also modified in vivo by phosphorylation on tyrosine. Furthermore, a nuclear tyrosine kinase encoded by the c-abl protooncogene phosphorylates the CTD to a high stoichiometry in vitro. Under conditions of maximum phosphorylation, approximately 30 mol of phosphate are incorporated per mol of CTD. The observation that the CTD is not phosphorylated by c-Src tyrosine kinase under identical conditions indicates that the CTD is not a substrate of all tyrosine kinases. Phosphorylation of tyrosine residues within the CTD may modulate the interaction of RNA polymerase II with the preinitiation complex and, hence, may be important in regulating gene expression.
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Palancade, Beno��t, and Olivier Bensaude. "Investigating RNA polymerase II carboxyl-terminal domain (CTD) phosphorylation." European Journal of Biochemistry 270, no. 19 (2003): 3859–70. http://dx.doi.org/10.1046/j.1432-1033.2003.03794.x.
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Kataoka, Masakazu, Takeshi Tanaka, Toshiyuki Kohno, and Yusuke Kajiyama. "The Carboxyl-Terminal Domain of TraR, a Streptomyces HutC Family Repressor, Functions in Oligomerization." Journal of Bacteriology 190, no. 21 (2008): 7164–69. http://dx.doi.org/10.1128/jb.00843-08.
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ABSTRACT Efficient conjugative transfer of the Streptomyces plasmid pSN22 is accomplished by regulated expression of the tra operon genes, traA, traB, and spdB. The TraR protein is the central transcriptional repressor regulating the expression of the tra operon and itself and is classified as a member of the HutC subfamily in the helix-turn-helix (HTH) GntR protein family. Sequence information predicts that the N-terminal domain (NTD) of TraR, containing an HTH motif, functions in binding of DNA to the cis element; however, the function of the C-terminal region remains obscure, like that for many other GntR family proteins. Here we demonstrate the domain structure of the TraR protein and explain the role of the C-terminal domain (CTD). The TraR protein can be divided into two structural domains, the NTD of M1 to R95 and the CTD of Y96 to E246, revealed by limited proteolysis. Domain expression experiments revealed that both domains retained their function. An in vitro pull-down assay using recombinant TraR proteins revealed that TraR oligomerization depended on the CTD. A bacterial two-hybrid system interaction assay revealed that the minimum region necessary for this binding is R95 to P151. A mutant TraR protein in which Leu121 was replaced by His exhibited a loss of both oligomerization ability and repressor function. An in vitro cross-linking assay revealed preferential tetramer formation by TraR and the minimum CTD. These results indicate that the C-terminal R95-to-P151 region of TraR functions to form an oligomer, preferentially a tetramer, that is essential for the repressor function of TraR.
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Lin, Alice V., and Valley Stewart. "Functional roles for the GerE-family carboxyl-terminal domains of nitrate response regulators NarL and NarP of Escherichia coli K-12." Microbiology 156, no. 10 (2010): 2933–43. http://dx.doi.org/10.1099/mic.0.040469-0.
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NarL and NarP are paralogous response regulators that control anaerobic gene expression in response to the favoured electron acceptors nitrate and nitrite. Their DNA-binding carboxyl termini are in the widespread GerE–LuxR–FixJ subfamily of tetrahelical helix–turn–helix domains. Previous biochemical and crystallographic studies with NarL suggest that dimerization and DNA binding by the carboxyl-terminal domain (CTD) is inhibited by the unphosphorylated amino-terminal receiver domain. We report here that NarL-CTD and NarP-CTD, liberated from their receiver domains, activated transcription in vivo from the class II napF and yeaR operon control regions, but failed to activate from the class I narG and fdnG operon control regions. Alanine substitutions were made to examine requirements for residues in the NarL DNA recognition helix. Substitutions for Val-189 and Arg-192 blocked DNA binding as assayed both in vivo and in vitro, whereas substitution for Arg-188 had a strong effect only in vivo. Similar results were obtained with the corresponding residues in NarP. Finally, Ala substitutions identified residues within the NarL CTD as important for transcription activation. Overall, results are congruent with those obtained for other GerE-family members, including GerE, TraR, LuxR and FixJ.
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Tellier, Michael, Justyna Zaborowska, Livia Caizzi, et al. "CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation." Nucleic Acids Research 48, no. 14 (2020): 7712–27. http://dx.doi.org/10.1093/nar/gkaa514.
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Abstract Cyclin-dependent kinase 12 (CDK12) phosphorylates the carboxyl-terminal domain (CTD) of RNA polymerase II (pol II) but its roles in transcription beyond the expression of DNA damage response genes remain unclear. Here, we have used TT-seq and mNET-seq to monitor the direct effects of rapid CDK12 inhibition on transcription activity and CTD phosphorylation in human cells. CDK12 inhibition causes a genome-wide defect in transcription elongation and a global reduction of CTD Ser2 and Ser5 phosphorylation. The elongation defect is explained by the loss of the elongation factors LEO1 and CDC73, part of PAF1 complex, and SPT6 from the newly-elongating pol II. Our results indicate that CDK12 is a general activator of pol II transcription elongation and indicate that it targets both Ser2 and Ser5 residues of the pol II CTD.
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Bensaude, Olivier, François Bonnet, Céline Cassé, Marie-Françoise Dubois, Van Trung Nguyen, and Benoit Palancade. "Regulated phosphorylation of the RNA polymerase II C-terminal domain (CTD)." Biochemistry and Cell Biology 77, no. 4 (1999): 249–55. http://dx.doi.org/10.1139/o99-047.
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The largest subunit of RNA polymerase II has an intriguing feature in its carboxyl-terminal domain (CTD) that consists of multiple repeats of an evolutionary conserved motif of seven amino acids. CTD phosphorylation plays a pivotal role in controlling mRNA synthesis and maturation. In exponentially growing cells, the phosphate turnover on the CTD is fast; it is blocked by common inhibitors of transcription, such as 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole and actinomycin D. Transcription-independent changes in CTD phosphorylation are observed at critical developmental stages, such as meiosis and early development.Key words: RNA polymerase II, phosphorylation, transcription inhibitors, cyclin-dependent kinases, development.
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Hausmann, Stéphane, Hisashi Koiwa, Shankarling Krishnamurthy, Michael Hampsey, and Stewart Shuman. "Different Strategies for Carboxyl-terminal Domain (CTD) Recognition by Serine 5-specific CTD Phosphatases." Journal of Biological Chemistry 280, no. 45 (2005): 37681–88. http://dx.doi.org/10.1074/jbc.m505292200.
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Lu, Richard, Hina Z. Ghory, and Alan Engelman. "Genetic Analyses of Conserved Residues in the Carboxyl-Terminal Domain of Human Immunodeficiency Virus Type 1 Integrase." Journal of Virology 79, no. 16 (2005): 10356–68. http://dx.doi.org/10.1128/jvi.79.16.10356-10368.2005.
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ABSTRACT Results of in vitro assays identified residues in the C-terminal domain (CTD) of human immunodeficiency virus type 1 (HIV-1) integrase (IN) important for IN-IN and IN-DNA interactions, but the potential roles of these residues in virus replication were mostly unknown. Sixteen CTD residues were targeted here, generating 24 mutant viruses. Replication-defective mutants were typed as class I (blocked at integration) or class II (additional reverse transcription and/or assembly defects). Most defective viruses (15 of 17) displayed reverse transcription defects. In contrast, replication-defective HIV-1E246K synthesized near-normal cDNA levels but processing of Pr55 g ag was largely inhibited in virus-producing cells. Because single-round HIV-1E246K.Luc(R-) transduced cells at approximately 8% of the wild-type level, we concluded that the late-stage processing defect contributed significantly to the overall replication defect of HIV-1E246K. Results of complementation assays revealed that the CTD could function in trans to the catalytic core domain (CCD) in in vitro assays, and we since determined that certain class I and class II mutants defined a novel genetic complementation group that functioned in cells independently of IN domain boundaries. Seven of eight novel Vpr-IN mutant proteins efficiently trans-complemented class I active-site mutant virus, demonstrating catalytically active CTD mutant proteins during infection. Because most of these mutants inefficiently complemented a class II CCD mutant virus, the majority of CTD mutants were likely more defective for interactions with cellular and/or viral components that affected reverse transcription and/or preintegration trafficking than the catalytic activity of the IN enzyme.
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Oh, Yoon Seon, Eric J. Wang, Casey D. Gailey, David L. Brautigan, Benjamin L. Allen, and Zheng Fu. "Ciliopathy-Associated Protein Kinase ICK Requires Its Non-Catalytic Carboxyl-Terminal Domain for Regulation of Ciliogenesis." Cells 8, no. 7 (2019): 677. http://dx.doi.org/10.3390/cells8070677.
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Loss-of-function mutations in the human ICK (intestinal cell kinase) gene cause dysfunctional primary cilia and perinatal lethality which are associated with human ciliopathies. The enzyme that we herein call CAPK (ciliopathy-associated protein kinase) is a serine/threonine protein kinase that has a highly conserved MAPK-like N-terminal catalytic domain and an unstructured C-terminal domain (CTD) whose functions are completely unknown. In this study, we demonstrate that truncation of the CTD impairs the ability of CAPK to interact with and phosphorylate its substrate, kinesin family member 3A (KIF3A). We also find that deletion of the CTD of CAPK compromises both localization to the primary cilium and negative regulation of ciliogenesis. Thus, CAPK substrate recognition, ciliary targeting, and ciliary function depend on the non-catalytic CTD of the protein which is predicted to be intrinsically disordered.
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Shin, Hye Jin, Young-Eui Kim, Eui Tae Kim, and Jin-Hyun Ahn. "The chromatin-tethering domain of human cytomegalovirus immediate-early (IE) 1 mediates associations of IE1, PML and STAT2 with mitotic chromosomes, but is not essential for viral replication." Journal of General Virology 93, no. 4 (2012): 716–21. http://dx.doi.org/10.1099/vir.0.037986-0.
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Human cytomegalovirus (HCMV) immediate-early (IE) 1 protein associates with chromosomes in mitotic cells using its carboxyl-terminal 16 aa region. However, the role of this IE1 activity in viral growth has not been evaluated in the context of mutant virus infection. We produced a recombinant HCMV encoding mutant IE1 with the carboxyl-terminal chromosome-tethering domain (CTD) deleted. This IE1(ΔCTD) virus grew like the wild-type virus in fibroblasts, indicating that the CTD is not essential for viral replication in permissive cells. Unlike wild-type virus infections, PML and STAT2, which interact with IE1, did not accumulate at mitotic chromosomes in IE1(ΔCTD) virus-infected fibroblasts, demonstrating that their associations with chromosomes are IE1 CTD-dependent. IE1 SUMOylation did not affect IE1 association with chromosomes. Our results provide genetic evidence that the CTD is required for the associations of IE1, PML and STAT2 with mitotic chromosomes, but that these IE1-related activities are not essential for viral replication in fibroblasts.
Dissertations / Theses on the topic "Carboxyl-terminal domain CTD"
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Zhang, Da Jiang. "Involvement of the Polypyrimidine Tract-Binding Protein-Associated Splicing Factor (PSF) in the Hepatitis Delta Virus (HDV) RNA-Templated Transcription." Thèse, Université d'Ottawa / University of Ottawa, 2014. http://hdl.handle.net/10393/31095.
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Hepatitis delta virus (HDV) is the smallest known mammalian RNA virus, containing a genome of ~ 1700 nt. Replication of HDV is extremely dependent on the host transcription machinery. Previous studies indicated that RNA polymerase II (RNAPII) directly binds to and forms an active preinitiation complex on the right terminal stem-loop fragment (R199G) of HDV genomic RNA, and that the polypyrimidine tract-binding protein-associated splicing factor (PSF) directly binds to the same region. Further studies demonstrated that PSF also binds to the carboxyl-terminal domain (CTD) of RNAP II. In my thesis, co-immunoprecipitation assays were performed to show that PSF stimulates the interaction of RNAPII with R199G. Results of co-immunoprecipitation experiments also suggest that both the RNA recognition motif 2 (RRM2) and N-terminal proline-rich region (PRR) of PSF are required for the interaction between PSF and RNAPII, while the two RNA recognition motifs (RRM1 and RRM2) might be required for the interaction of PSF with R199G. Furthermore, in vitro run-off transcription assays suggest that PSF facilitates the HDV RNA transcription from the R199G template. Together, the above experiments suggest that PSF might act as a transcription factor for the RNAPII transcription of HDV RNA by linking the CTD of RNAPII and the HDV RNA promoter. My experiments provide a better understanding of the mechanism of HDV RNA-dependent transcription by RNAP II.
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Descostes, Nicolas. "Analyse bioinformatique des modifications post-traductionnelles du domaine carboxyl-terminal de l'Arn polymérase II." Thesis, Aix-Marseille, 2014. http://www.theses.fr/2014AIXM4089.
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Le processus transcriptionnel par l'ARN polymérase II (Pol II) chez les eucaryotes se déroule en trois étapes : L'initiation, l'élongation et la terminaison. De nombreux facteurs de transcription, des modifications de la chromatine (épigénétique) et des éléments régulateurs distants interviennent dans ce processus. La sous-unité RPB1 de l'ARN Pol II contient un domaine carboxyle terminale (CTD) composée d'une répétition de sept acides-aminés. Au travers de différentes modifications biochimiques, ce domaine coordonne le processus transcriptionnel par le recrutement de différents facteurs. Le CTD est également impliqué dans la coordination de la transcription au niveau de l'initiation, de l'élongation et de la terminaison par le biais de modifications épigénétiques et nucléosomales, mais aussi par l'action de régulateurs distants (enhancers) et probablement de changements de conformation tridimensionnelle du génome. Mon travail de thèse a consisté en l'étude de deux modifications biochimiques du CTD de l'ARN Pol II par traitement bioinformatique de données issues du séquençage haut-débit. J'ai pu montrer que la phosphorylation de la thréonine 4 influence l'élongation de la transcription chez l'humain. J'ai également montré que la phosphorylation de la tyrosine 1 est présente durant l'initiation, est préférentiellement localisée dans la direction anti-sens, est hyper-phosphorylée aux enhancers transcrits et tissus spécifiques et est une marque caractéristique de ces modules génomiques. Ce travail de doctorat a constitué une contribution à la compréhension du processus transcriptionnel chez l'humain par l'utilisation de méthodes bioinformatiques innovantes<br>The biggest subunit of eukaryotic RNA polymerase II contains a carboxy-terminal domain (CTD) that consists in a repetition of seven amino-acids ranging from 26 in yeast to 52 in mammals. Specific biochemical modifications of CTD residues have been linked to specific stages of the transcriptional process. The CTD acts as a recruitment platform for processing factors that are involved in initiation, promoter proximal pausing, early and productive elongation (alternative splicing), 3' processing, termination and epigenetics.During my PhD, I used bioinformatics and high-throughput sequencing data to study two novel biochemical modifications of the CTD in human. I showed, in collaboration with biologists and bioinformaticians, that threonine 4 phosphorylation is important for proper elongation and probably termination of transcription. I showed also that tyrosine 1 phosphorylation is present during early transcription, antisense transcription (at divergent promoters) and is hyperphosphorylated at transcribed and tissue specific enhancers.Overall my doctorate has contributed to the understanding of the transcriptional process in human through the use of innovative bioinformatic methods
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Feng, Yue. "Biochemical Characterization of Plant Small CTD Phosphatases and Application of CTD Phosphatase Mutant in Hyperaccumulation of Flavonoids in Arabidopsis." Thesis, 2010. http://hdl.handle.net/1969.1/ETD-TAMU-2010-08-8482.
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In addition to AtCPL1-4, the genome of Arabidopsis thaliana encodes a large number of putative acid phosphatases. The predicted Arabidopsis SCP1-like small phosphatases (SSP) are highly homologous to the catalytic domain of eukaryotic RNA polymerase II carboxyl terminal domain (pol II CTD) phosphatases. Among the family members, SSP4, SSP4b and SSP5 form a unique group characterized by long N-terminal extensions. These three SSPs showed similar and ubiquitous gene expression. SSP4 and SSP4b were localized exclusively in the nuclei, while SSP5 accumulated both in the nucleus and cytoplasm. In vitro observation revealed that SSP4 and SSP4b dephosphorylated the pol II CTD-PO4 at both Ser2 and Ser5 in the conserved heptad repeats; however, SSP5 dephosphorylated only Ser5 of CTD-PO4. These results indicate that Arabidopsis SSP family encodes active CTD phosphatases similarly to animal SCP1 family proteins and plant CPLs family proteins, but with distinct substrate specificities.
ssp mutants did not exhibit phenotypic abnormalities under normal growth conditions. However, ssp5 single mutants and ssp4 ssp4b ssp5 triple mutants showed enhanced sensitivity to ABA and glucose during seed germination. Yet, increased ABA-inducible gene expressions were not distinguishable in triple mutants compared to wild type plants upon ABA treatment. Unlike the ssp mutations, the cpl1 mutation strongly induced RD29A expression in response to cold, ABA and NaCl treatments. Thus, the cpl1 mutant is an ideal genetic background for an inducible gene expression system, in which the detrimental effect to host plants caused by a conventional constitutive expression could be avoided.
Production of flavonoid such as anthocyanins in Arabidopsis is relatively easy to monitor and is regulated by transcription factors such as PAP1. PAP1 activates the expression of multiple enzymes in the anthocyanin biosynthesis pathway; however, high level of flavonoid production could cause vegetative growth retardation. To optimize flavonoid accumulation, a three-component system was designed consisting of a cold inducible RD29A-PAP1 expression cassette, a feedforward effector RD29A-CBF3, and a mutation in host repressor CPL1. Transgenic cpl1 plants containing both homozygous PAP1 and CBF3 transgenes produced 30-fold higher level of total anthocyanins than control plants upon cold treatment. LC/MS/MS analysis showed the flavonoid profile in cold-induced transgenic plants resembled that of previously reported pap1-D plants but were enriched for kaempferol derivatives. Furthermore, PAP1 and environmental signals synergistically regulate flavonoid pathway to produce a flavonoid blend that has not been produced by PAP1 overexpression or cold treatment alone. These results delineate the usability of the three-component inducible system in plant metabolic engineering.