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DNA-Directed RNA Polymerases (5):
Recent article
DNA-Directed RNA Polymerases
PLoS Genetics (7)6 2011
Abstract
We show through chromatin immunoprecipitation (ChIP) that SPT5L/KTF1, a silencing factor and a homolog of SPT5 elongation factors, binds chromatin at loci subject to transcriptional silencing. Chromatin binding of SPT5L/KTF1 occurs downstream of RNA Polymerase V, but independently from the presence...
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PMID: 21738482
PDF is available here.
PDF is available here.
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Journal of Molecular Biology (405)3 2011
Abstract
We report a fluorescence-based assay for measuring the real-time kinetics of single-nucleotide incorporation during transcription elongation. The fluorescent adenine analogue 2-aminopurine was incorporated at various single positions in the template or the nontemplate strand of the promoter-free elo...
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PMID: 21035457
PDF is available here.
PDF is available here.
Abstract
An efficient synthesis of new cap analogs containing 7-deazaguanosine moiety such as m(7)G[5']ppp[5'](7-deaza)G and m₂(7,3'O)G[5']ppp[5'](7-deaza)G is described. The biological substrate validation of these new cap analogs is evaluated with respect to its capping efficiency and in...
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PMID: 21128169
PDF is available here.
PDF is available here.
Abstract
We confirm that promoter regions are strongly depleted of nucleosomes, but find that terminator regions are much less depleted than expected. Unlike at promoter regions, nucleosome occupancy at terminators is strongly correlated with the orientation of and distance to adjacent genes. In addition, nu...
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PMID: 20921369
PDF is available here.
PDF is available here.
Abstract
Three housekeeping genes (dnaK, groEL and rpoB) of strains belonging to the genus Gluconacetobacter (37 strains) or related taxa (38 strains) were sequenced. Reference strains of the 15 species of the genus Gluconacetobacter were included. Phylogenetic trees generated using these gene sequences conf...
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PMID: 19915110
PDF is available here.
PDF is available here.
Abstract
We propose the previously deposited reference strain ATCC 12670(T) =DSM 44181(T) =NCIMB 10420(T), located in collections worldwide, as the type strain....
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PMID: 19915104
PDF is available here.
PDF is available here.
Abstract
A considerable number of species of the Halobacteriaceae possess multiple copies of the 16S rRNA gene that exhibit more than 5 % divergence, complicating phylogenetic interpretations. Two additional problems have been pointed out: (i) the genera Haloterrigena and Natrinema show a very close relati...
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PMID: 19946058
PDF is available here.
PDF is available here.
Abstract
We analyzed four amino acid residues within domain VI of the Sendai virus L protein and our data indicated that there could be differences in L protein sequence requirements for cap methylation in two different families of Mononegavirales - rhabdoviruses and paramyxoviruses. In this study, we conduc...
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PMID: 20609457
PDF is available here.
PDF is available here.
Abstract
Against pandemic influenza A (H1N1) 2009, anti-influenza drugs were useful to save the disease aggravation and reduce the mortality. In addition to the existing anti-influenza drugs, novel drugs, including neuraminidase inhibitors (peramivir and laninamivir) and RNA polymerase inhibitors (favipiravi...
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PMID: 20845748
PDF is available here.
PDF is available here.
Biophysical Journal (99)4 2010
Abstract
We hypothesize that tightly looping DNA is alone sufficient to repress transcription. To test this hypothesis, we have developed an assay to quantify transcription elongation by bacteriophage T7 RNAP on small, circular DNA templates approximately 100 bp in size. From these highly bent transcription...
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PMID: 20712997
PDF is available here.
PDF is available here.
EMBO Journal (29)15 2010
Abstract
We show that Lpm targets the sigma(70) subunit region 3.2 and the RNAP beta' subunit switch-2 element, which controls the clamping of promoter DNA in the RNAP active-site cleft. Lpm abolishes isomerization of the 'closed'-promoter complex to the transcriptionally competent 'open' complex and blocks...
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PMID: 20562828
PDF is available here.
PDF is available here.
Journal of Bacteriology (192)15 2010
Abstract
We found a ternary complex for the repressed purA promoter also. These findings, together with the backwards orientation of repressed marboxes, suggested a unique interaction of MarA with RNAP in repression. However, no repression-specific residues of MarA could be found among 38 single-alanine repl...
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PMID: 20453091
PDF is available here.
PDF is available here.
Abstract
We performed Brownian dynamics simulations of the R.P(c) --> R.P(o) transition. In the fast trajectories, unwinding of the promoter DNA begins by local melting around the -10 element, which is followed by sequential unzipping of DNA till the +2 site. The R.P(c) --> R.P(o) transition occurs in three...
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PMID: 20615963
PDF is available here.
PDF is available here.
Journal of Bacteriology (192)14 2010
Abstract
We demonstrate that the putative -35 hexamer is dispensable for ExsA-independent transcription from the P(exsC) promoter and that deletion of sigma(70) region 4.2, which contacts the -35 hexamer, has no effect on ExsA-independent transcription from P(exsC). Region 4.2 of sigma(70), however, is requi...
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PMID: 20453093
PDF is available here.
PDF is available here.
Abstract
We describe examples of influenza A virus-derived small viral RNAs (svRNAs). svRNAs are 22-27 nt in length and correspond to the 5' end of each of the viral genomic RNA (vRNA) segments. Expression of svRNA correlates with the accumulation of vRNA and a bias in RNA-dependent RNA polymerase (RdRp) act...
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PMID: 20534471
PDF is available here.
PDF is available here.
Abstract
We have adopted a practical approach to successfully improve avermectin production in an industrial overproducer. Transcriptional levels of the wild-type strain and industrial overproducer in production cultures were monitored using microarray analysis. The avermectin biosynthetic genes, especially...
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PMID: 20534557
PDF is available here.
PDF is available here.
Abstract
We show that the reaction also requires the flexible domain of the active center, the trigger loop (TL). We show that the invariant histidine (beta' His1242) of the TL is essential for hydrolysis/proofreading and participates in the reaction in two distinct ways: by positioning the 3' end nucleotide...
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PMID: 20534498
PDF is available here.
PDF is available here.
Abstract
We create a burst of I(2) by rapidly destabilizing open complexes (RP(o)) with 1.1 M NaCl. Fast footprinting reveals that thymines at positions from -11 to +2 in I(2) are permanganate-reactive, demonstrating that RNAP opens the entire initiation bubble in the cleft in a single step. Rates of decay o...
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PMID: 20483995
PDF is available here.
PDF is available here.
Abstract
We have identified 56-kDa DNA primases defective in primer delivery by screening for their ability to support growth of T7Delta4 phage in the presence of this suppressor. Trp69 is critical for primer delivery. Replacement of Trp69 with lysine in either the 56- or 63-kDa gp4 results in defective prim...
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PMID: 20439755
PDF is available here.
PDF is available here.
Abstract
We focused on the RNAP-F/E subcomplex, which forms a stable heterodimer that binds the nascent RNA and thereby stimulates the processivity of elongation complexes. We used the pulsed-EPR method DEER and fluorescence spectroscopy to probe for conformational changes within the F/E dimer. Our results d...
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PMID: 20384325
PDF is available here.
PDF is available here.
Abstract
We have investigated the processing of site-specific Pt-DNA cross-links in live mammalian cells to enhance our understanding of the mechanism of action of platinum-based anticancer drugs. The activity of platinum drugs against cancer is mediated by a combination of processes including cell entry, dr...
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PMID: 20443565
PDF is available here.
PDF is available here.
Abstract
Our results demonstrate that memory CD4(+) T cells responding to C. pneumoniae stimulation can be detected in the circulation of healthy donors. Furthermore, among seropositive individuals, the presence or the absence of dual IFN-gamma- and IL-2-producing T-cell responses was associated with distinc...
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PMID: 20219874
PDF is available here.
PDF is available here.
Metabolic Engineering (12)3 2010
Abstract
We propose a new approach for predicting kinetic parameters from DNA-binding site sequences by correlating the protein-DNA-binding affinities with nucleotide sequence conservation. We present the dynamic modeling of the cra modulon transcription in Escherichia coli during glucose-limited fed-batch c...
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PMID: 19895901
PDF is available here.
PDF is available here.
Microbiology (156)Pt 5 2010
Abstract
We isolated M. smegmatis strains harbouring either an insertion (6 aa) or a deletion (10 aa) in their RpoB proteins. Although these strains showed a compromised fitness for growth in 7H9 Middlebrook medium, their resistance to Rif was remarkably high. The attenuated growth of the strains correlated...
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PMID: 20150242
PDF is available here.
PDF is available here.
Bing du xue bao = Chinese journal of virology / [bian ji, Bing du xue bao bian ji wei yuan hui] (26)3 2010
Abstract
We collected fecal and anal swabs specimens from 24 outbreaks of acute gastroenteritis from 2005 to 2008 to detect norovirus. Specimens were detected by RT-PCR and then sequenced. The descriptive data were also collected. According to our research, 19 of 24 outbreaks of gastroenteritis were positive...
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PMID: 20572341
PDF is available here.
PDF is available here.
Abstract
Streptomyces lydicus NRRL2433 and S. spectabilis NRRL2494 produce two inhibitors of bacterial RNA polymerase: the 3-acyltetramic acid streptolydigin and the naphthalenic ansamycin streptovaricin, respectively. Both strains are highly resistant to their own antibiotics. Independent expression of the...
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PMID: 20176899
PDF is available here.
PDF is available here.
Veterinary Parasitology (169)1-2 2010
Abstract
Sarcocystis neurona is an apicomplexan parasite identified as a cause of fatal neurological disease in the threatened southern sea otter (Enhydra lutris nereis). In an effort to characterize virulent S. neurona strains circulating in the marine ecosystem, this study developed a range of markers rele...
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PMID: 20071081
PDF is available here.
PDF is available here.
Methods in Molecular Biology (629)629 2010
Abstract
We recently demonstrated that the activation of RIG-1 by siRNA-bearing 5'-triphosphate can be used to enhance dendritic cell maturation and function. Indeed, immature DCs that had been transfected with siRNA-bearing 5'-triphosphate activated T cells, indicating that, even in the absence of external...
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PMID: 20387164
PDF is available here.
PDF is available here.
Abstract
A retrospective nationwide study including all culture-verified multidrug-resistant (MDR) tuberculosis (TB) cases was performed in Denmark. The aim was to examine the long-term treatment outcome of MDR-TB, to assess if MDR-TB transmission occurs, and to evaluate a rapid mutation analysis detecting r...
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PMID: 20082573
PDF is available here.
PDF is available here.
Abstract
We report the characterization of novel mutations in the A. thaliana RPOTm gene. The mutations did not affect pollen formation, but significantly retarded the growth of the rpoTm mutant pollen tubes and had an impact on the fusion of the polar nuclei in the rpoTm mutant embryo sacs. Moreover, develo...
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PMID: 20231244
PDF is available here.
PDF is available here.
Abstract
We recently unraveled a high-density interaction network formed by nuclear RNAP subunits from the soluble fraction of human cell extracts. Validation of the dataset using a machine learning approach trained to minimize the rate of false positives and false negatives yielded a high-confidence dataset...
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PMID: 20453924
PDF is available here.
PDF is available here.
Abstract
We have therefore implemented a robotic high-throughput structure-function experimental system based on the automatic generation and assaying of hundreds of site-directed mutants in the archaeal RNAP from Methanocaldococcus jannaschii. In the present paper, I focus on recent insights obtained from a...
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PMID: 20298196
PDF is available here.
PDF is available here.
Biotechnology Letters (32)4 2010
Abstract
We obtained T7 RNA polymerase (RNAP) substitution mutants in Burkholderia cepacia. To test the expression abilities of the T7 mutants, four different lipase expression vectors were transformed and the lipase activity of these recombinants was evaluated. Our results suggest that 500 nt homology betwe...
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PMID: 20033831
PDF is available here.
PDF is available here.
Abstract
We have demonstrated that it exits as a monomer in solution, possesses multiple domains, harbors primarily alpha-helix and efficiently binds to a S. aureus promoter DNA in the presence of core RNA polymerase. While both N- and C-terminal ends of His- sigma(A) are flexible in nature, two Trp residues...
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PMID: 20356457
PDF is available here.
PDF is available here.
Abstract
We have mapped the structural organization of the mtRNAP using site-specific protein-DNA photo-cross-linking studies. Both Mtf1 and Rpo41 cross-linked to distinct sites on the promoter DNA, but the dominant cross-links were those of the Mtf1, which indicates a direct role of Mtf1 in promoter-specifi...
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PMID: 20008320
PDF is available here.
PDF is available here.
Abstract
Fusobacterium nucleatum is classified into five subspecies that inhabit the human oral cavity (F. nucleatum subsp. nucleatum, F. nucleatum subsp. polymorphum, F. nucleatum subsp. fusiforme, F. nucleatum subsp. vincentii, and F. nucleatum subsp. animalis) based on several phenotypic characteristics a...
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PMID: 19955278
PDF is available here.
PDF is available here.
Abstract
We report on the incidence, genetic diversity, and molecular epidemiology of sapoviruses detected in domestic pigs in a comprehensive study conducted in six European countries (Denmark, Finland, Hungary, Italy, Slovenia, and Spain) between 2004 and 2007. A total of 1,050 swine fecal samples from 88...
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PMID: 19940055
PDF is available here.
PDF is available here.
YAKUGAKU ZASSHI (130)2 2010
Abstract
Antiviral therapy for chronic hepatitis C has advanced dramatically since the discovery of the hepatitis C virus and the introduction of interferon in early 1990's. An initial treatment regimen, 24 weeks of interferon monotherapy, achieved sustained virologic response, which is formally defined at 2...
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PMID: 20118636
PDF is available here.
PDF is available here.
Abstract
We describe the first atomic resolution structure of Gp2, which reveals a distinct run of surface-exposed negatively charged amino acid residues on one side of the molecule. Our comprehensive mutagenesis data reveal that two conserved arginine residues located on the opposite side of Gp2 are importa...
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PMID: 20133868
PDF is available here.
PDF is available here.
Journal of Virology (84)3 2010
Abstract
We systematically investigated the interactions between the polymerase subunits and their localization in living cells by fluorescence cross-correlation spectroscopy (FCCS) and quantitative confocal microscopy. We could show that PB1 and PA form a dimer in the cytoplasm, which is imported into the n...
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PMID: 19906916
PDF is available here.
PDF is available here.
Abstract
We discuss recent work on the plant-specific PolII variant enzymes and discuss the mechanistic convergences that have been observed in the role of these enzymes in their respective siRNA-mediated heterochromatin formation pathways....
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PMID: 20173420
PDF is available here.
PDF is available here.
Abstract
We report that neither intrinsic nor regulator-assisted transcript cleavage of backtracked RNA requires formation of the TH. We find that the principal contribution of TH formation to rapid nucleotidyl transfer is steric alignment of the reactants rather than acid-base catalysis, and that the TL/TH...
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PMID: 19966797
PDF is available here.
PDF is available here.
Acta Crystallographica Section F (66)Pt 1 2010
Abstract
RNA polymerase (RNAP) elongates RNA by iterative nucleotide-addition cycles (NAC). A specific structural state (or states) of RNAP may be the target of transcription elongation factors. Gfh1, a Thermus thermophilus Gre-family protein, inhibits NAC. To elucidate which RNAP structural state Gfh1 assoc...
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PMID: 20057074
PDF is available here.
PDF is available here.
Abstract
We find that the E. coli replisome stalls upon collision with a head-on transcription complex, but instead of collapsing, the replication fork remains highly stable and eventually resumes elongation after displacing the RNAP from DNA. We also find that the transcription-repair coupling factor, Mfd,...
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PMID: 20436399
PDF is available here.
PDF is available here.
BMC Molecular Biology (11)1 2010
Abstract
The most stable reference genes were Rpl32, Gapdh and Polr2a in mouse post-infarction heart failure, Polr2a, Rpl32 and Tbp in rat post-infarction heart failure and Rpl32 and Pgk1 in human heart failure (ischemic disease and cardiomyopathy). The overall most stable reference genes across all three sp...
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PMID: 20331858
PDF is available here.
PDF is available here.
Abstract
We use HeLa nuclear extracts to study two of these activities, poly(A) signal-dependent transcriptional pausing, which was originally proposed as a surveillance checkpoint, and poly(A) signal-dependent degradation (PDD) of unprocessed transcripts from weak poly(A) signals. We confirm directly, by me...
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PMID: 19926725
PDF is available here.
PDF is available here.
Biological Chemistry (391)2-3 2010
Abstract
We analyzed the conditions of dnRNA synthesis and determined their effect on the 6S RNA-mediated inhibition of RNA polymerase in vitro and in vivo. Upon nutritional upshift the RNA polymerase/6S RNA complex induces the rapid synthesis of dnRNAs, which form stable hybrids with the 6S RNA template. Th...
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PMID: 20030589
PDF is available here.
PDF is available here.
Genome Biology (11)5 2010
Abstract
We hypothesize that the fast turnover relative to the slow generation time in Prochlorococcus may enable a swift response to environmental changes through rapid recycling of nucleotides, which could be advantageous in nutrient poor oceans. Our growing understanding of RNA half-lives will help us int...
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PMID: 20482874
PDF is available here.
PDF is available here.
Abstract
The phylogenetic relationships within Coronophorales have been debated because of uncertainty over the taxonomic usefulness of characteristics such as quellkörper, number of ascospores per ascus, presence of ascospore appendages, presence of subiculum and ascomatal vestiture. The phylogenetic relat...
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PMID: 20120241
PDF is available here.
PDF is available here.
Abstract
We showed that initiation of R-loop formation at an R-loop initiation zone (RIZ) is favored by G clusters. Here, using a purified in vitro system with T7 RNA polymerase, we show that increased distance between the promoter and the R-loop-supporting G-rich region reduces R-loop formation. When the G-...
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PMID: 19841062
PDF is available here.
PDF is available here.
Journal of Virology (84)1 2010
Abstract
We report changes in expression levels of host miRNAs upon ascovirus infection in an insect cell line and investigated the role of a host miRNA, Hz-miR24, in the host-virus system. We found that Hz-miR24 is differentially expressed following virus infection, with an increase in its expression levels...
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PMID: 19846520
PDF is available here.
PDF is available here.
Journal of Virology (84)1 2010
Abstract
We systematically assessed the effect that PB1-F2 expression has on viral polymerase activity, accumulation and localization of PB1, and replication in vitro and in mice. We used both the laboratory strain PR8 and a set of viruses engineered to study clinically relevant PB1-F2 proteins. PB1-F2 expre...
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PMID: 19828614
PDF is available here.
PDF is available here.
Journal of Virology (84)1 2010
Abstract
We report the successful development of efficient CCHFV helper virus-independent S, M, and L segment minigenome systems for analysis of virus RNA and protein features involved in replication. The virus RNA segment S, M, and L untranslated regions were found to be similar in support of replication of...
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PMID: 19864393
PDF is available here.
PDF is available here.
Abstract
Abstract
We present a generic kinetic model taking the latter steps into account and show analytically and by Monte Carlo simulations that it predicts transcriptional bursts even in the absence of explicit regulation of the transcription by master proteins....
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PMID: 20365024
PDF is available here.
PDF is available here.
Abstract
The first total synthesis of the potent RNA-polymerase inhibitor etnangien is described, which establishes unequivocally the relative and absolute configuration of this sensitive macrolide antibiotic. Key features of the expedient and modular synthesis include stereoselective substrate-controlled bo...
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PMID: 19645468
PDF is available here.
PDF is available here.
Abstract
We suggest that the "traffic viewpoint" provides a unique perspective towards understanding the control of ribosome synthesis in both bacterial and eukaryotic cells....
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PMID: 19502817
PDF is available here.
PDF is available here.
Biochemistry (Washington) (48)33 2009
Abstract
We show that mutations in the interface between RapA's SWI/SNF and double-stranded nucleic acid-binding domains significantly alter ATP hydrolysis in purified RapA. The effects of individual mutations on ATP hydrolysis loosely correlated with RapA's nucleic acid remodeling activity, indicating that...
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PMID: 19580329
PDF is available here.
PDF is available here.
Abstract
We validate the approach on a carbon-alpha representation of adenylate kinase and illustrate its use with electron microscopy maps of E. coli RNA polymerase, E. coli ribosome, and eukaryotic chaperonin containing T-complex polypeptide 1, which were difficult to model with traditional ENMs. For adeny...
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PMID: 19708737
PDF is available here.
PDF is available here.
Abstract
We have determined that the Pol II associated with the promoters of many genes has initiated transcription but paused in the region 20-50 nucleotides from the start. Here we describe the application of this method in Drosophila and human cells. The method should prove useful in assessing if promoter...
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PMID: 19272453
PDF is available here.
PDF is available here.