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)

The full-length E2 protein of human papillomavirus type 16 is believed to act as a trans-repressor of the viral p97 promoter. Previous reports have provided evidence that transcripts with the potential to encode the E2 protein contain the 880/2708 splice junction. We have further analyzed the structure of the E2-encoding transcripts. Employing the RNA polymerase chain reaction (PCR) technique and analyses of the RNA PCR products by Southern blot hybridization and DNA sequencing, we revealed the existence of a variety of alternatively spliced mRNAs, with the capacity to encode the full-length E2 protein. Two novel splice junctions were identified at nucleotides 880/2581 and 226/2708. E2 mRNAs characterized by the 880/2581 splice junction contain sequences from the E1 orf predicted to encode a truncated E1 polypeptide consisting mainly of the C terminal amino acids. Transcripts with the 226/2708 splice junction could encode a novel E6 protein, designated E6IV, containing C terminal amino acids derived from an out-of-frame region of the E1 ORF. Three different E6-E7 exons were identified in mRNAs containing the 880/2708 and the 880/2581 splice junctions, namely, E6-E7, E6I-E7, E6II-E7. The E6I-E7 mRNAs are the most abundant. Expression of the various E2 mRNAs was detected in human keratinocytes immortalized by HPV16, in cervical tumors, and in carcinoma cell lines.
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PMID:Human papillomavirus type 16 expresses a variety of alternatively spliced mRNAs putatively encoding the E2 protein. 133 30

The 10.7-kb BamHI "C" restriction fragment of malignant rabbit fibroma virus (MV) contains genes that are important for its immunosuppressive activity. When this fragment is transferred to a related avirulent leporipoxvirus, Shope fibroma virus (SFV), recombinant viruses show clinical features characteristic of MV: they replicate in lymphocytes and alter immune function in vitro, induce disseminated tumors in recipient rabbits, and are immunosuppressive in vivo. The 10.7-kb BamHI "C" restriction fragment of MV was sequenced in its entirety. Its DNA sequence and the 14 ORF's derived from analyzing this sequence are discussed. Analysis of known open reading frames to which the ORF's from MV's Bam "C" fragment show homology permits us to identify some MV ORF's showing high degrees of similarity to known and postulated proteins produced by vaccinia virus. Functions for some of these vaccinia proteins are known, while functions for others are hypothetical or unknown. Further analysis of genetic determinants of MV's virulence has indicated that two overlapping restriction subfragments of the BamHI "C" fragment can transfer MV's virulent behavior to SFV. The 0.7-kb region in which these two subfragments overlap includes the C-terminus of MV orf C-7 and the N terminus of MV orf C-8. These correspond to the C- and N-termini, respectively, of SFV orf's D-9 and D-10 and to vaccinia orf's D-6 (early transcription factor) and D-7 (subunit of RNA polymerase). We sequenced the region of SFV's BamHI "D" fragment in this area and illustrate here the comparative sequences of this portion of SFV's genome and orf's. On the basis of comparisons between MV, SFV, and vaccinia in this area we discuss the potential significance of these observations.
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PMID:Sequence and analysis of a portion of the genomes of Shope fibroma virus and malignant rabbit fibroma virus that is important for viral replication in lymphocytes. 166 Jan 96

The sequences of two previously known tail genes, R and S, of the temperate bacteriophage P2 and the sequence of an additional open reading frame (orf-30) located between S and V, were determined. Amber mutations mapping within R and S, Ram3, Ram42, Ram23, Sam75, and Sam89 were sequenced and found to be within their corresponding open reading frames. We constructed overproducing plasmids for R and S and identified these proteins by SDS-PAGE of whole-cell lysates and Coomassie blue staining. The predicted molecular masses of proteins R and S were M(r) 17,400 and 17,300, respectively, although both polypeptides migrated more slowly during gel electrophoresis than would be expected from the sequence data. orf-30 occupies the strand opposite from RS and V and is preceded by several weak potential sigma 70-RNA polymerase promoters, some of which overlap with the V promoter. A construct that had the putative orf-30 promoter region upstream of the lacZ gene produced low levels of beta-galactosidase activity in vivo. Expression from the orf-30 promoter was not stimulated by the phage P4 transcriptional activator protein, delta, which acts at all the known P2 and P4 late promoters. Insertion mutagenesis showed that orf-30 was not an essential gene for P2 growth in Escherichia coli. None of the gene or protein sequences exhibited extensive homology to sequences in the nucleic acid and protein databases. However, the R protein contains a small region homologous to one in the phage T4 tail protein gp15, which is required for T4 tails to bind heads. We propose that R and S are tail completion proteins that are essential for stable head joining.
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PMID:Molecular cloning and characterization of bacteriophage P2 genes R and S involved in tail completion. 817 26

The beta protein encoded by the Streptococcus pyogenes plasmid pSM19035 is a site-specific recombinase involved in both resolution of plasmid multimers into monomers and DNA inversion. It has been proposed that the DNA region to which the beta recombinase binds to mediate recombination includes a promoter from which orf alpha and the beta gene are transcribed. We have determined the sites at which transcription of the orf alpha and the beta gene initiates in vitro and we have demonstrated that highly purified beta recombinase acts as a repressor of its own synthesis. The promoters are located within the beta recombinase binding site, which we have defined previously. The binding of the beta recombinase to its target site does not seem to exclude RNA polymerase from the promoter, despite the overlapping of their binding sites. Therefore, it is likely that the beta recombinase does not repress transcription by a mere steric hindrance on RNA polymerase binding.
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PMID:The beta recombinase from the Streptococcal plasmid pSM 19035 represses its own transcription by holding the RNA polymerase at the promoter region. 820 10

A 3.3-kb BamHI fragment from the center of the orf virus (OV) NZ2 genome has been sequenced, revealing three major open reading frames (ORFs) with homology to vaccinia virus (VAC) genes. These ORFs have been designated F2L, F3R, and F4R and the proteins they encode were found to be homologous to VAC genes H4L (RNA polymerase-associated protein RAP94), H5R (35-kDa virion envelope antigen) and H6R (topoisomerase), respectively. The OV ORFs are arranged on the genome in an almost identical manner to their VAC counterparts revealing the common evolutionary origin of the two viruses despite the extreme difference in their G+C content. Like its VAC counterpart, F3R was shown to be transcribed early and late during infection. S1 and primer extension analysis located the 5' ends of F3R early transcripts to a position 15-16 nt and 5-10 nt, respectively, downstream from an AT-rich sequence resembling a VAC early promoter. The 5' ends of F3R late transcripts were located to an A within the sequence 5'-TAAAG, 41 nt downstream from the early promoter and 17 nt upstream from the initiation codon. S1 analysis of F2L, which is transcribed only late in infection, revealed transcripts initiating from within the sequence 5'-TAAATG. No transcriptional start point could be detected for F4R but the VAC late transcriptional initiation sequence TAAAT was found close to the predicted translational start point. Another late promoter-like sequence, 5'-TAAATG, was found at the 3' end of F2L. This preceded a short ORF tentatively designated as F1L and predicted to be the beginning of a homologue of VAC H3L.
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PMID:Conservation of gene structure and arrangement between vaccinia virus and orf virus. 831 94

Human T cell leukemia/lymphotropic virus (HTLV) is a complex 9 kb human retrovirus with at least eight alternatively spliced mRNAs expressed from the 3' or pX region of the genome. These mRNAs allow for the expression of novel proteins from the previously recognized pX open reading frames I and II in addition to Tax, Rex and p21rex encoded from orf III and IV. These alternatively spliced messages have been detected using reverse-transcriptase polymerase chain reaction (RT/PCR) amplification in HTLV-I-transformed T cell lines as well as in peripheral blood mononuclear cells (PBMC) from infected patients with and without disease. To gain insight into the role of these alternatively spliced mRNAs in pathogenesis, we developed a semi-quantitative non-PCR-based RNase protection assay to detect and quantitate their presence in HTLV-I-infected cells. Analysis of RNA from HTLV-I-infected cells established from patients with adult T cell leukemia (ATL) as well as tropical spastic paraparesis/HTLV-I-associated myelopathy (TSP/HAM) and both IL-2-dependent and IL-2-independent HTLV-I-infected cell lines by RNase protection has confirmed the existence of all of the alternatively spliced messages in each cell line analyzed. However, the relative quantity of each message was significantly different among these lines suggesting that splice site utilization is an important viral regulatory pathway.
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PMID:Differential expression of alternatively spliced pX mRNAs in HTLV-I-infected cell lines. 917 42

A genetic screen was devised to obtain plasmid-borne rpoA alleles exhibiting partial or no complementation of the chromosomal Escherichia coli rpoA341 allele responsible for a pleiotropic phenotype. Nine of the ten mutants obtained carried single base pair deletions within the 3' end of rpoA resulting in frameshifting into a 72 codon +1 orf extending from within codon L262 and terminating 16 bp downstream of the rpoA reading frame. These frameshifts give rise to a set of substituted alpha deletions that are all of the same size (334 aa) and carry segments of the Orf sequence replacing the alpha region from the C-terminus (residue 329) to various points between 272 > 319. The in vivo properties of this nested set of nine C-terminal-substituted derivatives of the alpha subunit of RNA polymerase have been assessed in terms of their assembly and transcriptional proficiency. The results indicate: (i) replacement of as much as 42 C-terminal residues of the alpha subunit does not prevent formation of a transcriptionally proficient holoenzyme form of RNA polymerase capable of complementing rpoA112(Ts); (ii) the extreme C-terminal Orf region, like that of alpha itself, is exposed in holoenzyme; (iii) these substituted deletions are not commonly functional at class I activated promoters.
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PMID:The effect of a nested set of C-terminal substituted deletions on the function of the alpha subunit of Escherichia coli RNA polymerase. 957 Jan 42

Three genes (sspH, sspL, and tlp) encoding new, minor small, acid-soluble proteins (SASP) unique to spores of Bacillus subtilis are expressed only in the forespore compartment during sporulation of this organism. The sspH and sspL genes are monocistronic, whereas tlp is the second gene in an operon with a second small orf, which we have termed sspN. The sspH and sspL genes are recognized primarily by the forespore-specific sigma factor for RNA polymerase, sigmaG; the sspN-tlp operon is recognized equally well by sigmaG and the other forespore-specific sigma factor, sigmaF. Sequences centered 10 and 35nt upstream of the 5'-ends of sspH, sspL, and sspN mRNAs all show homology to -10 and -35 sequences recognized by sigmaF and sigmaG, which are generally quite similar. Mutations disrupting the sspH, sspL, sspN-tlp, or tlp loci cause a loss of the appropriate SASP from spores, but have no discernible effect on sporulation, spore properties, or spore germination.
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PMID:Regulation of four genes encoding small, acid-soluble spore proteins in Bacillus subtilis. 1033 16

The genus Parapoxvirus (PAPV) is comprised traditionally of orf virus (ORFV), pseudocowpox virus (PCPV) and bovine papular stomatitis virus (BPSV), which cause infections of ruminants and their handlers in the U.S. and worldwide. Unlike orthopoxvirus infections, which can cause systemic or localized infections, PAPV infections present normally as benign, self-limited and localized skin lesions; infections do not confer lifelong immunity. In recent years, related potentially to enhanced awareness and the availability of diagnostic methods, there has been an observed increase in reported cases of PAPV in animals and humans. This study describes TaqMan based real-time PCR assays for both generic and specific detection of PAPV species for surveillance and outbreak investigations. These assays target highly conserved PAPV RNA polymerase gene sequences and are capable of detecting three known species of PAPVs (ORFV, PCPV, and BPSV). The assays were evaluated using a panel of PAPV DNA derived from human infections or animal specimen remainders. The sensitivities of all four assays were determined using droplet digital PCR; fewer than 10 copies of clinical PAPV DNA can be detected consistently. These assays provide a reliable and sensitive method for rapid confirmation and characterization PAPV infections with varying clinical presentations.
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PMID:Specific qPCR assays for the detection of orf virus, pseudocowpox virus and bovine papular stomatitis virus. 2403 7

The impact of phage infection on the host cell is severe. In order to take over the cellular machinery, some phage proteins were produced to shut off the host biosynthesis early in the phage infection. The discovery and identification of these phage-derived inhibitors have a significant prospect of application in antibacterial treatment. This work presented a phage protein, gp70.1, with non-specific inhibitory effects on Pseudomonas aeruginosa and Escherichia coli. Gp70.1 was encoded by early gene - orf 70.1 from P. aeruginosa phage PaP3. The P. aeruginosa with a plasmid encoding gp70.1 showed with delayed growth and had the appearance of a small colony. The combination of multifaceted analysis including microarray-based transcriptomic analysis, RT-qPCR, nuclear magnetic resonance (NMR) spectroscopy-based metabolomics and phenotype experiments were performed to investigate the effects of gp70.1 on P. aeruginosa. A total of 178 genes of P. aeruginosa mainly involved in extracellular function and metabolism were differentially expressed in the presence of gp70.1 at three examined time points. Furthermore, our results indicated that gp70.1 had an extensive impact on the extracellular phenotype of P. aeruginosa, such as motility, pyocyanin, extracellular protease, polysaccharide, and cellulase. For the metabolism of P. aeruginosa, the main effect of gp70.1 was the reduction of amino acid consumption. Finally, the RNA polymerase sigma factor RpoS was identified as a potential cellular target of gp70.1. Gp70.1 was the first bacterial inhibitor identified from Pseudomonas aeruginosa phage PaP3. It was also the first phage protein that interacted with the global regulator RpoS of bacteria. Our results indicated the potential value of gp70.1 in antibacterial applications. This study preliminarily revealed the biological function of gp70.1 and provided a reference for the study of other phage genes sharing similarities with orf70.1.
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PMID:Transcriptomic and Metabolomic Analysis Revealed Multifaceted Effects of Phage Protein Gp70.1 on Pseudomonas aeruginosa. 2772 12


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