Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:2.7.7.6 (RNA polymerase)
34,946 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Cyclin-dependent kinases (CDKs) are the central components of eukaryotic cell cycle regulation. Phosphorylation of CDKs at a conserved threonine residue is required for their full activity and is mediated by a CDK-activating kinase (CAK). The CAK R2 from rice belongs to those CAKs that phosphorylate not only CDKs but also the C-terminal domain (CTD) of RNA polymerase II. We showed that R2 is a nuclear protein with increased expression and increased CTD kinase activity in S-phase. Increasing R2 abundance through a transgenic approach accelerated S-phase progression and overall growth rate in suspension cells. In planta, the CTD kinase activity of R2 was induced by a growth-promoting signal. R2 regulation, therefore, may constitute a plant-specific adaptive mechanism that is used to adjust the rate of cell proliferation in response to a changing environment.
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PMID:The rice cyclin-dependent kinase-activating kinase R2 regulates S-phase progression. 1182 8

The initial waves of gene induction caused by GnRH in the LbetaT2 gonadotrope cell line have recently been identified using microarrays. We now investigate the relationship of the concentration of GnRH to the level of biosynthesis induced. Using an optimized custom cDNA microarray, we show that a large number of genes are induced in a concentration-dependent fashion. Detailed time course studies of the induction of six induced transcripts using quantitative real-time PCR suggest that the amplitude, but not the temporal pattern, depends on the concentration of GnRH. The early genes appear to show a delay in gene induction, followed by a linear phase of increase. The relationship of rate of synthesis and GnRH concentration was studied by mathematical modeling of the induction of two genes, gly96 and tis11. In both cases, only the rates of increase, but not the lag times, are influenced by the concentration of GnRH exposure. Western blot analyses for c-Jun and Egr1 show that the levels of nuclear protein for these transcription factors also depend on the concentration of GnRH. These studies indicate that, despite the complex signaling network connecting the receptor to the activated genes, the biosynthetic rate of RNA polymerase at induced genes is correlated with the concentration of GnRH at the GnRH receptor.
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PMID:Coupling of GnRH concentration and the GnRH receptor-activated gene program. 1204 3

Ku is an abundant nuclear protein with an essential function in the repair of DNA double-strand breaks. Various observations suggest that Ku also interacts with the cellular transcription machinery, although the mechanism and significance of this interaction are not well understood. In the present study, we investigated the subnuclear distribution of Ku in normally growing human cells by using confocal microscopy, chromatin immunoprecipitation, and protein immunoprecipitation. All three approaches indicated association of Ku with RNA polymerase II (RNAP II) elongation sites. This association occurred independently of the DNA-dependent protein kinase catalytic subunit and was highly selective. There was no detectable association with the initiating isoform of RNAP II or with the general transcription initiation factors. In vitro protein-protein interaction assays demonstrated that the association of Ku with elongation proteins is mediated, in part, by a discrete C-terminal domain in the Ku80 subunit. Functional disruption of this interaction with a dominant-negative mutant inhibited transcription in vitro and in vivo and suppressed cell growth. These results suggest that association of Ku with transcription sites is important for maintenance of global transcription levels. Tethering of double-strand break repair proteins to defined subnuclear structures may also be advantageous in maintenance of genome stability.
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PMID:Subnuclear localization of Ku protein: functional association with RNA polymerase II elongation sites. 1239 Nov 74

Ku antigen is an abundant nuclear protein with multiple functions that depend mainly on Ku's prolific and highly verstatile interactions with DNA. We have shown previously that the direct binding of Ku in vitro to negative regulatory element 1 (NRE1), a transcriptional regulatory element in the long terminal repeat of mouse mammary tumour virus, correlates with the regulation of viral transcription by Ku. In this study, we have sought to explore the interaction of Ku with NRE1 in vivo in yeast one-hybrid experiments. Unexpectedly, we observed that human Ku70 carrying a transcriptional activation domain from the yeast Gal4 protein induced transcription of yeast reporter genes pleiotrophically, independent of NRE1, promoter, reporter gene and chromosomal location. Ku80 with the same activation domain had no effect on transcription when expressed alone, but reconstituted activation when co-expressed with native human Ku70. The requirements for transcriptional activation by Ku-Gal4 activation domain proteins correlated with previous descriptions of the requirements for DNA sequence-independent DNA binding by Ku, but were distinct from determinants for DNA-end binding by a truncated Ku heterodimer determined recently by crystallography. These results suggest a preferential targeting of Ku to transcriptionally active chromatin that indicate a possible function for Ku within the RNA polymerase II holoenzyme.
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PMID:Evidence implicating Ku antigen as a structural factor in RNA polymerase II-mediated transcription. 1252 96

BRCA1 is a 220kDa nuclear protein with multiple functional domains. It interacts directly or indirectly with a variety of important proteins, including oncogene proteins (c-myc, E2F), tumor suppressor proteins (p53, RB, BRCA2), DNA damage repair proteins (RAD50, RAD51), cell-cycle regulators (cyclin, CDK), transcriptional regulators (RNA polymerase II) and others related to the important biological events. BRCA1 is likely to play an important role in the maintenance of genomic stability through its activities in cell-cycle progression, DNA damage repair, transcriptional regulation, and apoptosis. Here, the authors provided a review of the biochemistry structure of BRCA1 as well as its role in maintaining the genomic stability.
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PMID:[BRCA1 and genomic stability]. 1265 99

Transcription elongation factor S-II was originally purified as a specific stimulator of transcription by RNA polymerase II. Recent studies suggest that S-II participates in gene-specific transcriptional activation in vivo, despite the fact that it directly binds RNA polymerase II and does not recognize specific DNA sequences. In this study, under the hypothesis that S-II requires co-factors to regulate the expression of specific-genes in vivo, we searched for factors that directly interact with S-II using a yeast two-hybrid system, and isolated a novel nuclear protein, FESTA. FESTA is expressed specifically in kidney and spleen, supporting our notion that S-II participates in gene-specific regulation. Two mRNA isoforms of FESTA encoding proteins with different sizes were identified and named FESTA-S and FESTA-L. FESTA contains a serine-rich region and a C-terminal tail that are highly similar to those of the ELL-associated factor EAF1. Reporter gene assays indicated that both GAL4-FESTA-S and GAL4-FESTA-L fusion proteins have trans-activating ability. Furthermore, deletion of the C-terminal tail of FESTA dramatically reduced its trans-activating ability and abolished its interaction with S-II. This study is the first report of a transcriptional activator that directly interacts with S-II and contains a transcriptional activation domain that cooperates with S-II via direct interaction.
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PMID:Identification of a novel tissue-specific transcriptional activator FESTA as a protein that interacts with the transcription elongation factor S-II. 1276 Dec 97

Myb-binding protein 1a (Mybbp1a) is a novel nuclear protein localized predominantly, but not exclusively, in nucleoli. Although initially isolated as a c-Myb interacting protein, Mybbp1a is expressed ubiquitously, associates with a number of different transcription factors, and may play a role in both RNA polymerase I- and II-mediated transcriptional regulation. However, its precise function remains unclear. In this study we show that Mybbp1a is a nucleocytoplasmic shuttling protein and investigate the mechanisms responsible for both nuclear import and export. The carboxyl terminus of Mybbp1a, which contains seven short basic amino acid repeat sequences, is responsible for both nuclear and nucleolar localization, and this activity can be transferred to a heterologous protein. Deletion mapping demonstrated that these repeat sequences appear to act incrementally, with successive deletions resulting in a corresponding increase in the proportion of protein localized in the cytoplasm. Glutathione S-transferase pulldown experiments showed that the nuclear receptor importin-alpha/beta mediates Mybbp1a nuclear import. Interspecies heterokaryons were used to demonstrate that Mybbp1a was capable of shuttling between the nucleus and the cytoplasm. Deletion analysis and in vivo export studies using a heterologous assay system identified several nuclear export sequences which facilitate Mybbp1a nuclear export of Mybbp1a by CRM1-dependent and -independent pathways.
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PMID:Myb-binding protein 1a is a nucleocytoplasmic shuttling protein that utilizes CRM1-dependent and independent nuclear export pathways. 1294 9

Cdk9 and its binding partner cyclin T1 comprise the positive elongation factor b (P-TEFb). P-TEFb phosphorylates the RNA polymerase II carboxyl-terminal-domain (CTD) allowing efficient transcription elongation. Recent studies showed that Cdk9 is a predominant nuclear protein, and here we investigated the functional requirement for nuclear localization of Cdk9. We found that the catalytic inactive kinase mutant (Cdk9dn) fails to accumulate in the nucleus showing a diffuse sub-cellular localization. In addition to the catalityc activity, nuclear localization of Cdk9 protein requires the presence of the phospho-acceptor sites at the C-terminus tail. Finally, enforced expression of wild-type cyclinT1, which enhances nuclear localization of Cdk9wt, fails to direct the Cdk9 mutants to the nucleus. Collectively, these findings implicate that nuclear localization of Cdk9 requires auto-phosphorylation of the kinase, and highlight the presence of a regulatory mechanism underlying the nuclear localization of the P-TEFb complex.
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PMID:Catalytic activity of Cdk9 is required for nuclear co-localization of the Cdk9/cyclin T1 (P-TEFb) complex. 1294 36

Phylogenetic studies of ticks have been increasing in recent years, particularly in the use of molecular data. However, all of the studies to date are either limited to the mitochondrial genome or to a few nuclear ribosomal genes. There is a need to explore the use of nuclear protein-encoding genes because these genes direct most aspects of the phenotypic traits in the development of an organism. We report here the test of a nuclear protein-encoding gene, RNA polymerase II, for the phylogenetic study of ticks. Thirty-eight ticks representing 26 species of hard and soft ticks were chosen for the study. The pairwise divergences among sampled species are ranged from 0.3 to 15.2% and most of the substitutions are transitions. In addition, the nucleotide composition is not obviously biased in POL II gene. The trees inferred from the POL II sequences using maximum parsimony (MP), neighbor joining (NJ), and maximum likelihood (ML) by PAUP* and MrBayes are largely concordant with the existing phylogenies. Our study demonstrated that POL II gene sequences contain strong phylogenetic signals in ticks at the generic and higher levels. POL II has proven to be a useful gene for resolving tick phylogeny.
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PMID:The use of the nuclear protein-encoding gene, RNA polymerase II, for tick molecular systematics. 1457 Jan 17

TATA-box-binding protein (TBP) is a highly conserved RNA polymerase II general transcription factor that binds to the core promoter and initiates assembly of the preinitiation complex. Two proteins with high homology to TBP have been found: TBP-related factor 1 (TRF1), described only in Drosophila melanogaster, and TRF2, which is broadly distributed in metazoans. Here, we report the identification and characterization of an additional TBP-related factor, TRF3. TRF3 is virtually identical to TBP in the C-terminal core domain, including all residues involved in DNA binding and interaction with other general transcription factors. Like other TBP family members, the N-terminal region of TRF3 is divergent. The TRF3 gene is present and expressed in vertebrates, from fish through humans, but absent from the genomes of the urochordate Ciona intestinalis and the lower eukaryotes D. melanogaster and Caenorhabditis elegans. TRF3 is a nuclear protein that is present in all human and mouse tissues and cell lines examined. Despite the highly homologous TBP-like C-terminal core domain, gel filtration analysis indicates that the native molecular weight of TRF3 is substantially less than that of TFIID. Interestingly, after mitosis, reimport of TRF3 into the nucleus occurs subsequent to TBP and other basal transcription factors. In summary, TRF3 is a highly conserved vertebrate-specific TRF whose phylogenetic conservation, expression pattern, and other properties are distinct from those of TBP and all other TRFs.
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PMID:TRF3, a TATA-box-binding protein-related factor, is vertebrate-specific and widely expressed. 1463 7


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