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)

In Saccharomyces cerevisiae, Kin28 is a member of the cyclin-dependent kinase family. Kin28 is a subunit of the basal transcription factor holo-TFIIH and its trimeric sub-complex TFIIK. Kin28 is the primary kinase that phosphorylates the RNA polymerase II (RNA pol II) C-terminal domain (CTD) within a transcription initiation complex. Mediator, a global transcriptional co-activator, dramatically enhances the phosphorylation of the CTD of RNA pol II by holo-TFIIH in vitro. Using purified proteins we have determined that the subunits of TFIIK are sufficient for Mediator to enhance Kin28 CTD kinase activity and that Mediator enhances phosphorylation of a glutathione S-transferase-CTD fusion protein, despite the absence of multiple Mediator and/or TFIIH interactions with polymerase. Mediator does not stimulate the activity of several other CTD kinases, suggesting that the specific enhancement of TFIIH kinase activity results in Kin28 being the primary CTD kinase at initiation. In addition, we have found that Kin28 phosphorylates Mediator subunit Med4 in an assay, including purified holo-TFIIH, and either Mediator or recombinant Med4 alone. Furthermore, Kin28 appears to be, at least in part, responsible for the phosphorylation of Med4 in vivo. We have identified Thr-237 as the site of phosphorylation of Med4 by Kin28 in vitro. The mutation of Thr-237 to Ala has no effect on the growth of a yeast strain under normal conditions but confirms that Thr-237 is also the site of Med4 phosphorylation in vivo.
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PMID:Mutual targeting of mediator and the TFIIH kinase Kin28. 1512 97

A growing body of evidence supports the coordination of mRNA synthesis and its subsequent processing events. Nuclear proteins harboring both WW and FF protein interaction modules bind to splicing factors as well as RNA polymerase II and may serve to link transcription with splicing. To understand how WW domains coordinate the assembly of splicing complexes, we used glutathione S-transferase fusions containing WW domains from CA150 or FBP11 in pull-down experiments with HeLa cell nuclear extract. The WW domains associate preferentially with the U2 small nuclear ribonucleoprotein and with splicing factors SF1, U2AF, and components of the SF3 complex. Accordingly, WW domain-associating factors bind to the 3' part of a pre-mRNA to form a pre-spliceosome-like complex. We performed both in vitro and in vivo splicing assays to explore the role of WW/FF domain-containing proteins in this process. However, although CA150 is associated with the spliceosome, it appears to be dispensable for splicing in vitro. Nevertheless, in vivo depletion of CA150 substantially reduced splicing efficiency of a reporter pre-mRNA. Moreover, overexpression of CA150 fragments containing both WW and FF domains activated splicing and modulated alternative exon selection, probably by facilitating 3' splice site recognition. Our results suggest an essential role of WW/FF domain-containing factors in pre-mRNA splicing that likely occurs in concert with transcription in vivo.
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PMID:The WW domain-containing proteins interact with the early spliceosome and participate in pre-mRNA splicing in vivo. 1545 88

RNA polymerase II, and specifically the C-terminal domain (CTD) of its largest subunit, has been demonstrated to play important roles in capping, splicing, and 3' processing of mRNA precursors. But how the CTD functions in these reactions, especially splicing, is not well understood. To address some of the basic questions concerning CTD function in splicing, we constructed and purified two fusion proteins, a protein in which the CTD is positioned at the C terminus of the splicing factor ASF/SF2 (ASF-CTD) and an RS domain deletion mutant protein (ASFDeltaRS-CTD). Significantly, compared to ASF/SF2, ASF-CTD increased the reaction rate during the early stages of splicing, detected as a 20- to 60-min decrease in splicing lag time depending on the pre-mRNA substrate. The increased splicing rate correlated with enhanced production of prespliceosomal complex A and the early spliceosomal complex B but, interestingly, not the very early ATP-independent complex E. Additional assays indicate that the RS domain and CTD perform distinct functions, as exemplified by our identification of an activity that cooperates only with the CTD. Dephosphorylated ASFDeltaRS-CTD and a glutathione S-transferase-CTD fusion protein were both inactive, suggesting that an RNA-targeting domain and CTD phosphorylation were necessary. Our results provide new insights into the mechanism by which the CTD functions in splicing.
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PMID:The C-terminal domain of RNA polymerase II functions as a phosphorylation-dependent splicing activator in a heterologous protein. 1563 56

Stringent starvation protein A (SspA) of Escherichia coli is an RNA polymerase-associated transcriptional activator for the lytic development of phage P1 and is essential for stationary phase-induced acid tolerance of E. coli. We report the crystal structure of Yersinia pestis SspA, which is 83% identical to E. coli SspA in amino acid sequence and is functionally complementary in supporting the lytic growth of phage P1 and acid resistance of an E. coli sspA mutant. The structure reveals that SspA assumes the characteristic fold of glutathione S-transferase (GST). However, SspA lacks GST activity and does not bind glutathione. Three regions of SspA are flexible, the N and C termini and the alpha2-helix. The structure also reveals a conserved surface-exposed pocket composed of residues from a loop between helices alpha3 and alpha4. The functional roles of these structural features were investigated by assessing the ability of deletion and site-directed mutants to confer acid resistance of E. coli and to activate transcription from a phage P1 late promoter, thereby supporting the lytic growth of phage P1. The results indicate that the flexible regions are not critical for SspA function, whereas the surface pocket is important for both transcriptional activation of the phage P1 late promoter and acid resistance of E. coli. The size, shape, and property of the pocket suggest that it mediates protein-protein interactions. SspA orthologs from Y. pestis, Vibrio cholerae, and Pseudomonas aeruginosa are all functional in acid resistance of E. coli, whereas only Y. pestis SspA supports phage P1 growth.
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PMID:Structural basis for the function of stringent starvation protein a as a transcription factor. 1573 7

The infected-cell protein 22 (ICP22), a regulatory protein encoded by the alpha22 gene of herpes simplex virus 1, is required for the optimal expression of a set of late viral proteins that includes the products of the U(S)11, U(L)38, and U(L)41 genes. ICP22 has two activities. Thus, ICP22 and the U(L)13 protein kinase mediate the activation of cdc2 and degradation of its partners, cyclins A and B. cdc2 and its new partner, the DNA polymerase accessory factor (U(L)42), bind topoisomerase IIalpha in an ICP22-dependent manner. In addition, ICP22 and U(L)13 mediate an intermediate phosphorylation of the carboxyl terminus of RNA polymerase II (RNA POL II). Here we report another function of ICP22. Thus, ICP22 physically interacts with cdk9, a constitutively active cyclin-dependent kinase involved in transcriptional regulation. A protein complex containing ICP22 and cdk9 phosphorylates in vitro the carboxyl-terminal domain of RNA POL II in a viral U(S)3 protein kinase-dependent fashion. Finally, the carboxyl-terminal domain of RNA POL II fused to glutathione S-transferase is phosphorylated in reaction mixtures containing complexes pulled down with ICP22 or cdk9 immune precipitated from lysates of wild-type parent virus or deltaU(L)13 but not deltaU(S)3 mutant-infected cells. The experiments described here place ICP22 and cdk9 in a complex with the carboxyl-terminal domain of RNA POL II. At the same time we confirm the requirement of ICP22 and the U(L)13 protein kinase in the posttranslational modification of RNA POL II that alters its electrophoretic mobility, although U(S)3 kinase appears to play a role in a cell-type-dependent fashion.
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PMID:The carboxyl-terminal domain of RNA polymerase II is phosphorylated by a complex containing cdk9 and infected-cell protein 22 of herpes simplex virus 1. 1589 Sep 14

Rabies virus P protein is a cofactor of RNA polymerase. We investigated other potential roles of P (CVS strain) by searching for cellular partners using two-hybrid screening. We isolated a cDNA encoding the signal transducer and activator of transcription 1 (STAT1) that is a critical component of interferon type I (IFN-alpha/beta) and type II (IFN-gamma) signaling. We confirmed this interaction by glutathione S-transferase-pull-down assay. Deletion mutant analysis indicated that the carboxy-terminal part of P interacted with a region containing the DNA-binding domain and the coiled-coil domain of STAT1. The expression of P protein inhibits IFN-alpha- and IFN-gamma-induced transcriptional responses, thus impairing the IFN-induced antiviral state. Mechanistic studies indicate that P protein does not induce STAT1 degradation and does not interfere with STAT1 phosphorylation but prevents IFN-induced STAT1 nuclear accumulation. These results indicate that rabies P protein overcomes the antiviral response of the infected cells.
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PMID:Rabies virus P protein interacts with STAT1 and inhibits interferon signal transduction pathways. 1625 75

Our aim was to isolate and characterize white spot syndrome virus (WSSV)-binding proteins from shrimp. After a blot of shrimp hemocyte membrane proteins was overlaid with a recombinant WSSV envelope protein (rVP28), the reactive bands on the blot were detected using anti-VP28 antibody. Among three membrane-associated molecules identified by liquid chromatography-tandem mass spectrometry, there was a 25-kDa protein that bound to both rVP28 and WSSV. Since it had a primary structure with high homology to the small GTP-binding protein Rab7, we named it Penaeus monodon Rab7 (PmRab7). The full-length PmRab7 cDNA was obtained, and results from a glutathione S-transferase pull-down assay confirmed specific binding to rVP28. Reverse transcriptase PCR analysis revealed PmRab7 expression in many tissues, and real-time PCR analysis revealed that expression was constitutive. Binding of PmRab7 to rVP28 or WSSV occurred in a dose-dependent manner and was inhibited by anti-Rab7 antibody. In an in vivo neutralization assay, the number of dead shrimp after challenge with WSSV plus PmRab7 (15%) or WSSV plus anti-Rab7 antibody (5%) was significantly lower than after challenge with WSSV alone (95%). In contrast to the WSSV-injected group, shrimp injected with WSSV plus PmRab7 or WSSV plus anti-Rab7 showed no WSSV-type histopathology. We conclude that PmRab7 is involved in WSSV infection in shrimp. This is the first study to identify a shrimp protein that binds directly to a major viral envelope protein of WSSV.
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PMID:PmRab7 is a VP28-binding protein involved in white spot syndrome virus infection in shrimp. 1704 Dec 24

MKL1 (MRTF-A/MAL) is a member of the myocardin-related transcription factor family that plays a key role in the development and differentiation of smooth muscle cells (SMCs) via activation of serum response factor (SRF)-dependent SMC gene expression. MKL1 associates with SRF and stimulates its transcriptional activity. Here, by performing matrix-assisted laser desorption/ionization-time of flight mass spectrometric analysis combined with in vitro glutathione S-transferase pull-down assay, we identified 4 candidate proteins that associate with MKL1 through the N-terminus region of MKL1. SPT16, ATP citrate lyase, nucleolin and radixin were identified, and the physical and functional interactions between MKL1 and SPT16 were examined. SPT16 is a component of the FACT (facilitating chromatin transcription) complex that allows RNA polymerase II to traverse the nucleosomes. SPT16 associates with MKL1 in vitro and in vivo; moreover, SSRP1, another component of the FACT complex, associates with the N-terminus region of MKL1 in vitro. SPT16 synergistically activates the transcriptional activity of MKL1. These results show that the expression of nucleosomal SRF-dependent genes, including the SMC gene, is activated by MKL1 via activation of SRF and recruitment of the FACT complex.
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PMID:Modulation of SRF-dependent gene expression by association of SPT16 with MKL1. 1803 21

Using T-type maize cytoplasmic male sterile line (T-CMS) and maintainer line as experimental materials, we separated mitochondrial proteins from leaves at seedling, shooting, booting stages, mesocotyl, root and anther at meiosis of pollen mother cell, single-double nucleus stage of pollen grain by two-dimensional electrophoresis with immobilized pH3-10 gradients. About 150 mitochondrial protein spots in seedling leaves, 150 spots in mesocotyls, 150 spots in roots and 100 spots in meiosis anther were observed respectively in this investigation. 6 difference protein spots were identified by MALDI-TOF-MS analysis and NCBI database searching. r40c1 protein was present in mesocotyl of T-CMS and absent in maintainer line. Mature anther-specific protein, DNA-directed RNA polymerase 23kDa subunit, hexokinase II were present and glutathione S-transferase, putative polyprotein were absent in pollen aborted anther of T-CMS. Developmental changes in mitochondrial proteins were found in leaves but no differences were observed in T-CMS and its maintainer line. Obvious differences of mitochondrial proteins were found at single-double nucleus stage anther in T-CMS and maintainer line. These different proteins were considered to be associated to pollen aborted in T-CMS.
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PMID:[Different proteins in mitochondrial proteome of T-type maize cytoplasmic male-sterile line and its maintainer line]. 1819 83

Poplar plants (Populus deltoides x nigra, DN34) growing under hydroponic conditions were exposed to 50 mg L(-1) of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) for 24 h. The expression of genes potentially involved in the metabolism of toxic explosives was analyzed by reverse-transcriptase (RT) real-time PCR. Genes under study were selected by reference to corresponding genes that were previously shown to be upregulated in the model plant Arabidopsis thaliana by exposure to 2,4,6-trinitrotoluene (TNT) (Ekman et al., 2003. Plant Physiol., 133, 1397-1406). The target genes investigated include several genes encoding for enzymes known to be involved in the detoxification of xenobiotic pollutants, such as glutathione S-transferases (GSTs), cytochrome P-450s (CYPs), NADPH-dependent reductases, and peroxidases. Starting from A. thaliana TNT-inducible genes, corresponding Populus sequences were retrieved from the JGI Poplar Genome Project database and were used to design gene-specific primers. 18S ribosomal DNA (rDNA) was used as an internal standard and recorded gene expression levels were normalized by reference to nonexposed plants. In three separate experiments, five genes were found to be significantly amplified in leaf tissues by exposure to RDX, including GST (9.7 fold), CYP (1.6 fold), reductases (1.6-1.7 fold), and peroxidase (1.7 fold). In root tissues, only a single GST gene was found to be significantly amplified by exposure to RDX (2.0 fold). These results show, for the first time, that the exposure of poplar plants to RDX results in the induction of several genes that are potentially involved in explosive detoxification.
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PMID:Analysis of gene expression in poplar trees (Populus deltoides x nigra, DN34) exposed to the toxic explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). 1824 12


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