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1. Acinetobacter nectaris sp. nov. and Acinetobacter boissieri sp. nov., isolated from floral nectar of wild Mediterranean insect-pollinated plants

Author:
Álvarez-Pérez, Sergio; Lievens, Bart; Jacquemyn, Hans; Herrera, Carlos M.
Source:
International journal of systematic and evolutionary microbiology 2013 v.63 no.Pt 4 pp. 1532-1539
ISSN:
1466-5034
Subject:
DNA-directed RNA polymerase,   etc   ; Acinetobacter; DNA; genes; microbiology; nectar; ribosomal RNA;     Show all 7 Subjects
Abstract:
... The taxonomic status of 14 strains of members of the genus Acinetobacter isolated from floral nectar of wild Mediterranean insect-pollinated plants, which did not belong to any previously described species within this genus, was investigated following a polyphasic approach. Confirmation that these strains formed two separate lineages within the genus Acinetobacter was obtained from comparative ana ...
DOI:
10.1099/ijs.0.043489-0

2. Activation of Chromatin-Bound DNA-Dependent RNA Polymerase (E.C. 2.7.7.6.) in Plant Storage Tissue Slices

Author:
Kahl, Günter; Wechselberger, Manfred
Source:
Zeitschrift für Naturforschung 2014 v.32 no.3-4 pp. 229-235
ISSN:
1865-7125
Subject:
DNA-directed RNA polymerase,   etc   ; DNA; Escherichia coli; RNA; Solanum tuberosum; actinomycin D; adenosine triphosphate; alpha-amanitin; chromatin; divalent metals; guanosine triphosphate; magnesium; manganese; potatoes; slicing; tubers; uridine triphosphate;     Show all 17 Subjects
Abstract:
... Chromatin, RNA Polymerase, Potato Tuber Tissue, Aging Phenomenon The synthesis of RNA by chromatin-bound RNA polymerase (E.C. 2.7.7.6.) from white potato tubers proceeds at a low rate, which is enhanced after slicing the tissue, however. Concomitantly DNA template availability as measured with saturating amounts of Escherichia coli polymerase is diminished drastically. Nearest neighbor frequency a ...
DOI:
10.1515/znc-1977-3-413

3. A Culture-Independent PCR-Based Assay to Detect the Root Rot Pathogen Fusarium solani Species Complex 11 from Soybean Roots and Soil

Author:
Chitrampalam, Periasamy; Abraham, Nivi; Nelson, Berlin D.
Source:
Plant disease 2018 v.102 no.2 pp. 327-333
ISSN:
0191-2917
Subject:
DNA-directed RNA polymerase,   etc   ; DNA; Fusarium solani; Pythium; genes; oligodeoxyribonucleotides; pathogens; phylogeny; polymerase chain reaction; root rot; roots; soil; soybeans; North Dakota;     Show all 14 Subjects
Abstract:
... Fusarium solani species complex (FSSC) 11 is the primary phylogenetic species of FSSC causing root rot in soybean in the north-central United States. A polymerase chain reaction (PCR)-based assay was developed to identify and differentiate FSSC 11 from the less aggressive FSSC 5 and other Fusarium and Pythium spp. associated with soybean roots. The primer set FSSC11-F and FSSC11-R designed from th ...
DOI:
10.1094/PDIS-03-17-0447-RE

4. Acute disseminated mycobacteriosis in captive Atlantic guitarfish (Rhinobatos lentiginosus)

Author:
Tuxbury, Kathryn A.; Young, Samuel A.; Bradway, Daniel S.; Marola, Jamie L.; Salfinger, Max; Garner, Michael M.
ISSN:
1943-4936
Subject:
DNA-directed RNA polymerase,   etc   ; DNA; Mycobacterium chelonae; Rhinobatos lentiginosus; adults; bacterial culture; blood; body condition; erythema; females; fish; genes; histology; immunosuppression; inflammation; liver; males; mineralization; mycobacterial diseases; necropsy; ovarian follicles; polymerase chain reaction; reproductive disorders; septicemia; tail;     Show all 25 Subjects
Abstract:
... An adult female captive-born Atlantic guitarfish (Rhinobatos lentiginosus) was found acutely moribund on exhibit and died soon after presentation. Abnormalities on autopsy were focal cutaneous erythema on the tail, a small liver, many variably sized friable ovarian follicles, and coelomic effusion. Histologic examination revealed systemic bacterial embolization, and yolk coelomitis with minimal as ...
DOI:
10.1177/1040638717721731

5. A deep phylogeny of viral and cellular right-hand polymerases

Author:
Černý, Jiří; Černá Bolfíková, Barbora; de A. Zanotto, Paolo M.; Grubhoffer, Libor; Růžek, Daniel
Source:
Infection, genetics, and evolution 2015 v.36 pp. 275-286
ISSN:
1567-1348
Subject:
DNA-directed RNA polymerase,   etc   ; DNA; DNA-directed DNA polymerase; RNA; RNA replication; RNA viruses; RNA-directed RNA polymerase; Retroviridae; bacteriophages; genetic variation; genome; monophyly; protein structure; proteins; sequence homology; viral morphology;     Show all 16 Subjects
Abstract:
... Right-hand polymerases are important players in genome replication and repair in cellular organisms as well as in viruses. All right-hand polymerases are grouped into seven related protein families: viral RNA-dependent RNA polymerases, reverse transcriptases, single-subunit RNA polymerases, and DNA polymerase families A, B, D, and Y. Although the evolutionary relationships of right-hand polymerase ...
DOI:
10.1016/j.meegid.2015.09.026

6. A distinct tymovirus infecting Cassia hoffmannseggii in Brazil

Author:
Nicolini, C.; Pio-Ribeiro, G.; Andrade, G. P.; Melo, F. L.; Oliveira, V. C.; Guimarães, F. C.; Resende, R. O.; Kitajima, E. W.; Rezende, J. A. M.; Nagata, Tatsuya
Source:
Virus genes 2012 v.45 no.1 pp. 190-194
ISSN:
0920-8569
Subject:
DNA-directed RNA polymerase,   etc   ; Cassia; Cowpea aphid-borne mosaic virus; DNA; Kennedya yellow mosaic virus; Passion fruit yellow mosaic virus; amino acids; antiserum; chloroplasts; forests; genes; leaves; transmission electron microscopy; viruses; Brazil;     Show all 15 Subjects
Abstract:
... Leaves of Cassia hoffmannseggii, a wild fabaceous species found in the Atlantic Forest, with a severe mosaic symptom were collected in Pernambuco State, Brazil. By transmission electron microscopy, two types of virus particles were found: the first was recognized as particles of a potyvirus, which was later identified as Cowpea aphid-borne mosaic virus; and the second was isometric and present in ...
DOI:
10.1007/s11262-012-0750-9
PubMed:
22528644

7. A DNA clone encoding the full-length infectious genome of odontoglossum ringspot tobamovirus and mutagenesis of its coat protein gene

Author:
Yu, H. H.; Wong, S. M.
Source:
Archives of virology 1998 v.143 no.1 pp. 163-171
ISSN:
0304-8608
Subject:
DNA-directed RNA polymerase,   etc   ; DNA; Nicotiana benthamiana; Northern blotting; Odontoglossum ringspot virus; Oncidium; RNA; Western blotting; electron microscopy; enzyme-linked immunosorbent assay; genes; mutagenesis; mutants; pathogenicity; phenotype; seedlings; start codon;     Show all 17 Subjects
Abstract:
... A full-length DNA clone encoding the genome of odontoglossum ringspot tobamovirus (ORSV) was synthesized and placed adjacent to a bacteriophage T7 RNA polymerase promoter. Capped-RNA transcripts produced in vitro were highly infectious when mechanically inoculated onto seedlings of Nicotiana benthamiana and Oncidium Gower Ramsey. A representative clone, designated pOT2, caused a disease phenotype ...
DOI:
10.1007/s007050050276
PubMed:
9505974

8. African swine fever virus replication and genomics

Author:
Dixon, Linda K.; Chapman, David A.G.; Netherton, Christopher L.; Upton, Chris
Source:
Virus research 2013 v.173 no.1 pp. 3-14
ISSN:
0168-1702
Subject:
DNA-directed RNA polymerase,   etc   ; African swine fever virus; DNA; DNA repair; DNA replication; Poxviridae; cytoplasm; genomics; macrophages; multigene family; nuclear genome; open reading frames; structural proteins; tandem repeat sequences; transcription (genetics); virion; virus replication; viruses;     Show all 18 Subjects
Abstract:
... African swine fever virus (ASFV) is a large icosahedral DNA virus which replicates predominantly in the cytoplasm of infected cells. The ASFV double-stranded DNA genome varies in length from about 170 to 193kbp depending on the isolate and contains between 150 and 167 open reading frames. These are closely spaced and read from both DNA strands. The virus genome termini are covalently closed by imp ...
DOI:
10.1016/j.virusres.2012.10.020

9. A Genome Comparison of T7-like Podoviruses That Infect Caulobacter crescentus

Author:
Nguyen, Doreen; Ely, Bert
Source:
Current microbiology 2018 v.75 no.6 pp. 760-765
ISSN:
0343-8651
Subject:
DNA-directed RNA polymerase,   etc   ; Caulobacter crescentus; DNA; DNA-directed DNA polymerase; Podoviridae; amino acid sequences; bacteria; bacterial communities; bacteriophages; genes; phylogeny; viral morphology;     Show all 12 Subjects
Abstract:
... Bacteriophages remain an understudied component of bacterial communities. Therefore, our laboratory has initiated an effort to isolate large numbers of bacteriophages that infect Caulobacter crescentus to provide an estimate of the diversity of bacteriophages that infect this common environmental bacterium. The majority of the new isolates are phicbkviruses, a genus of giant viruses that appear to ...
DOI:
10.1007/s00284-018-1445-9

10. Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity

Author:
Coyotzi, Sara; Doxey, Andrew C.; Clark, Ian D.; Lapen, David R.; Van Cappellen, Philippe; Neufeld, Josh D.
Source:
Environmental microbiology 2017 v.19 no.3 pp. 1189-1208
ISSN:
1462-2912
Subject:
DNA-directed RNA polymerase,   etc   ; Acidovorax; Azoarcus; DNA; Dechloromonas; Janthinobacterium; Pseudomonas; Rhizobium; Streptomycetaceae; agricultural soils; anaerobic conditions; denitrification; denitrifying microorganisms; fertilizers; genes; genetic variation; greenhouse gases; metagenomics; nitrates; nitric oxide; nitrite reductase; nitrogen; nitrous oxide; nitrous-oxide reductase; ribosomal RNA; stable isotopes;     Show all 26 Subjects
Abstract:
... Denitrification transforms nitrogen applied as fertilizer and emits N₂O, which is a potent greenhouse gas. Very little is known about the identities of abundant and active denitrifiers in agricultural soils. We coupled DNA stable‐isotope probing (DNA‐SIP) with flow‐through reactors (FTRs) to detect active agricultural soil denitrifiers. The FTRs were incubated with nitrate and ¹³C₆‐glucose under a ...
DOI:
10.1111/1462-2920.13643

11. A‐ kinase anchoring protein AKAP95 is a novel regulator of ribosomal RNA synthesis

Author:
Marstad, Anne; Landsverk, Ole Jørgen B.; Strømme, Olaf; Otterlei, Marit; Collas, Philippe; Sundan, Anders; Brede, Gaute
Source:
The FEBS journal 2016 v.283 no.4 pp. 757-770
ISSN:
1742-464X
Subject:
DNA-directed RNA polymerase,   etc   ; DNA; cell communication; cell growth; cell nucleolus; chromatin; evolution; fluorescence recovery after photobleaching; interphase; ligands; precipitin tests; regulatory proteins; ribosomal RNA; ribosomes; transcription factors;     Show all 15 Subjects
Abstract:
... The RNA polymerase I transcription apparatus acquires and integrates the combined information from multiple cellular signalling cascades to regulate ribosome production essential for cell growth and proliferation. In the present study, we show that a subpopulation of A‐kinase anchoring protein 95 (AKAP95) targets the nucleolus during interphase and is involved in regulating rRNA production. We sho ...
DOI:
10.1111/febs.13630

12. Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA

Author:
Molodtsov, Vadim; Sineva, Elena; Zhang, Lu; Huang, Xuhui; Cashel, Michael; Ades, Sarah E.; Murakami, Katsuhiko S.
Source:
Molecular cell 2018 v.69 no.5 pp. 828-839.e5
ISSN:
1097-2765
Subject:
DNA-directed RNA polymerase,   etc   ; DNA; Escherichia coli; active sites; binding sites; crystal structure; models; pleiotropy; ribosomal RNA; ribosomes; stress response; synergism; transcription (genetics); transcriptome;     Show all 14 Subjects
Abstract:
... DksA and ppGpp are the central players in the stringent response and mediate a complete reprogramming of the transcriptome. A major component of the response is a reduction in ribosome synthesis, which is accomplished by the synergistic action of DksA and ppGpp bound to RNA polymerase (RNAP) inhibiting transcription of rRNAs. Here, we report the X-ray crystal structures of Escherichia coli RNAP in ...
DOI:
10.1016/j.molcel.2018.01.035

13. Alteration in template recognition byEscherichia coli RNA polymerase lacking the ω subunit: A mechanistic analysis through gel retardation and foot-printing studies

Author:
Mukherjee, Kakoli; Chatterji, Dipankar
Source:
Journal of biosciences 1999 v.24 no.4 pp. 453-459
ISSN:
0250-5991
Subject:
DNA-directed RNA polymerase,   etc   ; DNA; amino acids; gel electrophoresis; gels; polypeptides; potassium permanganate; transcription (genetics);     Show all 8 Subjects
Abstract:
... The ω subunit ofEscherichia coli RNA polymerase is a 91 amino acid polypeptide which co-purifies with the enzyme and is thought to help in maturing the rest of the enzyme to its full functionality. Purified ω when added externally was found to inhibit general transcriptional activity of ω-less RNA polymerase as well as promoter-specific single-round transcriptional activity at all the promoters te ...
DOI:
10.1007/BF02942656

14. Alu‐DNA repeat‐binding protein p68 is a part of Alu‐RNA containing α‐RNP

Author:
Lukyanov, Dmitry V.; Urusova, Maria E.; Shcherba, Ksenia M.; Podgornaya, Olga I.
Source:
European journal of biochemistry 2000 v.267 no.8 pp. 2362-2371
ISSN:
0014-2956
Subject:
DNA-directed RNA polymerase,   etc   ; DNA; antibodies; binding properties; binding proteins; binding sites; cytoplasm; fluorescent antibody technique; humans; molecular weight; oligonucleotides; somatic cells;     Show all 12 Subjects
Abstract:
... An Alu‐DNA repeat‐binding protein with a molecular mass of 68 kDa (p68) is identified in the somatic human cell nucleoplasm. Gel mobility shift assay (GMSA), South‐western blotting and affinity purification on DNA attached to the carrier were used in the identification. GMSA revealed multiple complexes with the exponential dependence of their relative mobility. A narrow binding site of the ...
DOI:
10.1046/j.1432-1327.2000.01248.x

15. A molecular model of chromatin organisation and transcription: how a multi-RNA polymerase II machine transcribes and remodels the β-globin locus during development

Author:
Wong, Hua; Winn, Peter J.; Mozziconacci, Julien
Source:
BioEssays 2009 v.31 no.12 pp. 1357-1366
ISSN:
0265-9247
Subject:
DNA-directed RNA polymerase,   etc   ; DNA; chromatin; loci; models; regulator genes; transcription (genetics);     Show all 7 Subjects
Abstract:
... We present a molecular model of eukaryotic gene transcription. For the β-globin locus, we hypothesise that a transcription machine composed of multiple RNA polymerase II (PolII) assembles using the locus control region as a foundation. Transcription and locus remodelling can be achieved by pulling DNA through this multi-PolII 'reading head'. Once a transcription complex is formed, it may engage an ...
DOI:
10.1002/bies.200900062

16. Analysis of a 26 756 bp segment from the left arm of yeast chromosome IV

Author:
Wölfl, Stefan; Hanemann, Vera; Saluz, Hans Peter
Source:
Yeast 1996 v.12 no.15 pp. 1549-1554
ISSN:
0749-503X
Subject:
DNA-directed RNA polymerase,   etc   ; DNA; Saccharomyces cerevisiae; chromosomes; genes; introns; open reading frames; phosphoprotein phosphatase; sequence analysis; yeasts;     Show all 10 Subjects
Abstract:
... The nucleotide sequence of a 26·7 kb DNA segment from the left arm of Saccharomyces cerevisiae chromosome IV is presented. An analysis of this segment revealed 11 open reading frames (ORFs) longer than 300 bp and one split gene. These ORFs include the genes encoding the large subunit of RNA polymerase II, the biotin apo‐protein ligase, an ADP‐ribosylation factor (ARF 2), the ‘L35'‐ribosomal protei ...
DOI:
10.1002/(SICI)1097-0061(199612)12:15<1549::AID-YEA42>3.0.CO;2-S
PubMed:
8972577

17. Analysis of PolA1 intron 19 and Ntag sequences reveals two ancestral lineages in the origin of the Brassica rapa complex and Chinese cabbage (B. rapa var. pekinensis)

Author:
Fareed, A.; Shindo, H.; Takahashi, H.; Nakamura, I.
Source:
Journal of horticultural science & biotechnology 2015 v.90 no.3 pp. 273-278
ISSN:
1462-0316
Subject:
DNA-directed RNA polymerase,   etc   ; Chinese cabbage; sequence analysis; hybrids; chromosome elimination; DNA; hybridization; biotechnology; horticulture; exons; meiosis; Brassica rapa subsp. oleifera; introns; single nucleotide polymorphism;     Show all 14 Subjects
Abstract:
... Brassica rapa L. used to be classified into two species, Brassica campestris and B. rapa. These two species can cross with each other, but no molecular marker exists to discriminate between them. Therefore, these two species are now combined into one species, B. rapa. Because nuclear genomes have been genetically recombined through repeated inter-specific hybridisation, most DNA sequences have los ...

18. Analysis of the domain structure and the DNA binding site of the transcriptional activator FhlA

Author:
Leonhartsberger, Susanne; Ehrenreich, Armin; Böck, August
Source:
European journal of biochemistry 2000 v.267 no.12 pp. 3672-3684
ISSN:
0014-2956
Subject:
DNA-directed RNA polymerase,   etc   ; sequence analysis; transcription factors; transcriptional activation; consensus sequence; DNA; models; adenosine triphosphate; amino acids; binding sites; genes; hydrogen; hydrolysis; screening; Escherichia coli;     Show all 15 Subjects
Abstract:
... FhlA is the transcriptional activator of the genes coding for the formate hydrogen lyase system in Escherichia coli. It is activated by the binding of formate and induces transcription by σ54 RNA polymerase after binding to specific upstream activating sequences (UAS). Sequence comparison had shown that FhlA exhibits a structure composed of three domains, which is typical for σ54‐dependent reg ...
DOI:
10.1046/j.1432-1327.2000.01399.x

19. A new multiplex PCR protocol to detect mixed trypanosomatid infections in species of Apis and Bombus

Author:
Bartolomé, Carolina; Buendía, María; Benito, María; De la Rúa, Pilar; Ornosa, Concepción; Martín-Hernández, Raquel; Higes, Mariano; Maside, Xulio
Source:
Journal of invertebrate pathology 2018 v.154 pp. 37-41
ISSN:
0022-2011
Subject:
DNA-directed RNA polymerase,   etc   ; Apis mellifera; Bombus terrestris; Crithidia bombi; DNA; DNA topoisomerase (ATP-hydrolysing); cell culture; epidemiology; glyceraldehyde-3-phosphate dehydrogenase; honey bees; parasites; pathogens; polymerase chain reaction; protocols;     Show all 14 Subjects
Abstract:
... Trypanosomatids are highly prevalent pathogens of Hymenoptera; however, most molecular methods used to detect them in Apis and Bombus spp. do not allow the identification of the infecting species, which then becomes expensive and time consuming. To overcome this drawback, we developed a multiplex PCR protocol to readily identify in a single reaction the main trypanosomatids present in these hymeno ...
DOI:
10.1016/j.jip.2018.03.015

20. An intron loss in the chloroplast gene rpoC1 supports a monophyletic origin for the subfamily Cactoideae of the Cactaceae

Author:
Wallace, R.S.; Cota, J.H.
Source:
Current genetics 1996 v.29 no.3 pp. 275-281
ISSN:
0172-8083
Subject:
DNA-directed RNA polymerase,   etc   ; nucleic acid hybridization; structural genes; Cactaceae; DNA; DNA probes; phylogeny; introns; chemotaxonomy; chloroplasts;     Show all 10 Subjects
Abstract:
... The deletion of an approximately 700-bp intron in the chloroplast-encoded gene rpoC1 was shown in 21 representative species of the subfamily Cactoideae of the angiosperm family Cactaceae. Members of the subfamilies Pereskioideae and Opuntioideae were found to possess the intron, as did members of the related families Aizoaceae, Basellaceae, Didiereaceae, Phytolaccaceae, and Portulacaceae. These re ...
DOI:
10.1007/BF02221558
PubMed:
8595674