U.S. flag

An official website of the United States government

PubAg

Main content area

You searched for: Subject messenger RNA Remove constraint Subject: messenger RNA Subject Escherichia coli Remove constraint Subject: Escherichia coli Subject DNA-directed RNA polymerase Remove constraint Subject: DNA-directed RNA polymerase Text Availability Citation in PubAg Remove constraint Text Availability: Citation in PubAg
Start Over

Search

16  Search Results

1 - 16 of 16
Number of results to display per page

Search Results

1. Novel Escherichia coli RNA Polymerase Binding Protein Encoded by Bacteriophage T5

Author:
Klimuk, Evgeny; Mekler, Vladimir; Lavysh, Darya; Serebryakova, Marina; Akulenko, Natalia; Severinov, Konstantin
Source:
Viruses 2020 v.12 no.8
ISSN:
1999-4915
Subject:
DNA-directed RNA polymerase; Escherichia coli; bacteriophages; binding proteins; genes; messenger RNA; mutants; transcription (genetics); virion
Abstract:
... The Escherichia coli bacteriophage T5 has three temporal classes of genes (pre-early, early, and late). All three classes are transcribed by host RNA polymerase (RNAP) containing the σ⁷⁰ promoter specificity subunit. Molecular mechanisms responsible for the switching of viral transcription from one class to another remain unknown. Here, we find the product of T5 gene 026 (gpT5.026) in RNAP prepara ...
DOI:
10.3390/v12080807

2. RNA Polymerase's Relationship with the Ribosome: Not So Physical, Most of the Time

Author:
Chen, Menglin; Fredrick, Kurt
Source:
Journal of molecular biology 2020 v.432 no.14 pp. 3981-3986
ISSN:
0022-2836
Subject:
DNA-directed RNA polymerase; Escherichia coli; bacteria; messenger RNA; ribosomes; transcription termination; translation (genetics)
Abstract:
... In bacteria, the rates of transcription elongation and translation elongation are coordinated, changing together in response to growth conditions. It has been proposed that this is due to physical coupling of RNA polymerase and the lead ribosome on nascent mRNA, an interaction important for preventing premature transcription termination by Rho factor. Recent studies challenge this view and provide ...
DOI:
10.1016/j.jmb.2020.03.018

3. Mycobacterial transcript cleavage factor Gre, exhibits chaperone-like activity

Author:
Joseph, Abyson; Nagaraja, Valakunja; Natesh, Ramanathan
Source:
Biochimica et biophysica acta 2019 v.1867 no.9 pp. 757-764
ISSN:
1570-9639
Subject:
DNA-directed RNA polymerase; Escherichia coli; Mycobacterium smegmatis; Mycobacterium tuberculosis; circular dichroism spectroscopy; enzyme activity; heat; heat stress; hydrophobicity; messenger RNA; oligomerization; oxidative stress; proteins; stress response; sulfonates; transcription (genetics)
Abstract:
... Gre factors reactivate stalled elongation complexes by enhancing the intrinsic transcript cleavage activity of RNA polymerase. Previous work by us has shown that unlike in Escherichia coli (E.coli), Mycobacterium tuberculosis Gre factor is essential for its survival. Apart from their role in transcription regulation Gre factors have been implicated in stress response. A recent study has shown the ...
DOI:
10.1016/j.bbapap.2019.05.008

4. Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation

Author:
Abdelkareem, Mo’men; Saint-André, Charlotte; Takacs, Maria; Papai, Gabor; Crucifix, Corinne; Guo, Xieyang; Ortiz, Julio; Weixlbaumer, Albert
Source:
Molecular cell 2019 v.75 no.2 pp. 298-309.e4
ISSN:
1097-2765
Subject:
DNA; DNA-directed RNA polymerase; Escherichia coli; active sites; catalytic activity; eukaryotic cells; messenger RNA; regulatory sequences; transcription (genetics); transcription factors
Abstract:
... Regulatory sequences or erroneous incorporations during DNA transcription cause RNA polymerase backtracking and inactivation in all kingdoms of life. Reactivation requires RNA transcript cleavage. Essential transcription factors (GreA and GreB, or TFIIS) accelerate this reaction. We report four cryo-EM reconstructions of Escherichia coli RNA polymerase representing the entire reaction pathway: (1) ...
DOI:
10.1016/j.molcel.2019.04.029

5. Fast Translation within the First 45 Codons Decreases mRNA Stability and Increases Premature Transcription Termination in E. coli

Author:
Pedersen, Steen; Terkelsen, Thilde Bagger; Eriksen, Mette; Hauge, Magnus Krarup; Lund, Casper Carstens; Sneppen, Kim; Mitarai, Namiko
Source:
Journal of molecular biology 2019 v.431 no.6 pp. 1088-1097
ISSN:
0022-2836
Subject:
DNA-directed RNA polymerase; Escherichia coli; amino acids; codons; messenger RNA; models; ribosomal proteins; ribosomes; transcription termination; translation (genetics)
Abstract:
... We show here that the specific use of fast or slowly translated codons in the early coding region of a gene may influence both the mRNA stability and premature transcription termination. We first inserted a pair of nearly identical 42-base-pair (bp)-long sequences into codon 3 of the Escherichia coli lacZ gene. The only difference between the two inserts was that the first base in one was moved to ...
DOI:
10.1016/j.jmb.2019.01.026

6. Interactions in the active site of Deinococcus radiodurans RNA polymerase during RNA proofreading

Author:
Esyunina, Daria; Kulbachinskiy, Andrey
Source:
Biochemical and biophysical research communications 2019 v.509 no.1 pp. 161-166
ISSN:
0006-291X
Subject:
DNA-directed RNA polymerase; Deinococcus radiodurans; Escherichia coli; active sites; bacteria; genome; hydrolysis; messenger RNA; metal ions; nucleotides; transcription (genetics)
Abstract:
... Co-transcriptional RNA proofreading by RNA polymerase (RNAP) is essential for accurate mRNA synthesis and reactivation of stalled transcription complexes, which can otherwise compromise genome integrity. RNAP from the stress-resistant bacterium Deinococcus radiodurans exhibits high levels of RNA cleavage in comparison with RNAP from Escherichia coli, which allows it to remove misincorporated nucle ...
DOI:
10.1016/j.bbrc.2018.12.095

7. Deletion of an architectural unit, leucyl aminopeptidase (SCO2179), in Streptomyces coelicolor increases actinorhodin production and sporulation

Author:
Song, Eunjung; Rajesh, Thangamani; Lee, Bo-Rahm; Kim, Eun-jung; Jeon, Jong-Min; Park, Sung-Hee; Park, Hyung-Yeon; Choi, Kwon-Young; Kim, Yun-Gon; Yang, Yung-Hun; Kim, Byung-Gee
Source:
Applied microbiology and biotechnology 2013 v.97 no.15 pp. 6823-6833
ISSN:
0175-7598
Subject:
DNA-directed RNA polymerase; Escherichia coli; N-acetylglucosamine; Streptomyces coelicolor; antibiotics; gels; genes; hosts; leucyl aminopeptidase; messenger RNA; mutants; proteins; reverse transcriptase polymerase chain reaction; spores; sporulation; transcription (genetics)
Abstract:
... Several reports state that three architectural units, including integration host factor, leucyl aminopeptidase (PepA), and purine regulator, are involved in transcriptional process with RNA polymerase in Escherichia coli. Similarly, Streptomyces species possess the same structural units. We previously identified a protein, Streptomyces integration host factor (sIHF), involved in antibiotic product ...
DOI:
10.1007/s00253-013-4847-4
PubMed:
23525887

8. Enhanced in vitro translation at reduced temperatures using a cold-shock RNA motif

Author:
Freischmidt, Axel; Hiltl, Johannes; Kalbitzer, Hans Robert; Horn-Katting, Gudrun
Source:
Biotechnology letters 2013 v.35 no.3 pp. 389-395
ISSN:
0141-5492
Subject:
DNA-directed RNA polymerase; Escherichia coli; messenger RNA; protein synthesis; recombinant proteins; temperature; translation (genetics)
Abstract:
... Cell-free synthesis of recombinant proteins has emerged as an alternative method of protein production although protein yields still cannot compete with in vivo expression techniques. In systems based on S30 extracts of Escherichia coli unfavorable side-reactions are involved in limiting protein yields. Therefore, carrying out cell-free reactions at lower temperatures might be beneficial as side r ...
DOI:
10.1007/s10529-012-1091-4
PubMed:
23143178

9. Vector-initiated transitive RNA interference in the filamentous fungus Aspergillus oryzae

Author:
Fernandez, Evee Q.; Moyer, Donna L.; Maiyuran, Suchindra; Labaro, Anna; Brody, Howard
Source:
Fungal genetics and biology 2012 v.49 no.4 pp. 294-301
ISSN:
1087-1845
Subject:
Arabidopsis thaliana; Aspergillus oryzae; Caenorhabditis elegans; DNA-directed RNA polymerase; Escherichia coli; RNA interference; color; double-stranded RNA; fungi; gene expression; genes; messenger RNA; small interfering RNA; spores
Abstract:
... RNA interference (RNAi), modulates gene expression via cleavage of double-stranded RNA (dsRNA) by Dicer, producing 21–25 nucleotide silence-inducing RNAs (siRNAs). In association with Argonaute containing complexes, these siRNAs target sequence-specific degradation of the homologous single-stranded messenger RNA. In the majority of eukaryotes, degradation occurs within the boundaries of the dsRNA ...
DOI:
10.1016/j.fgb.2012.01.011
PubMed:
22366516

10. Increase in cell viability by polyamines through stimulation of the synthesis of ppGpp regulatory protein and ω protein of RNA polymerase in Escherichia coli

Author:
Terui, Yusuke; Akiyama, Mariko; Sakamoto, Akihiko; Tomitori, Hideyuki; Yamamoto, Kaneyoshi; Ishihama, Akira; Igarashi, Kazuei; Kashiwagi, Keiko
Source:
international journal of biochemistry & cell biology 2012 v.44 no.2 pp. 412-422
ISSN:
1357-2725
Subject:
polyamines; messenger RNA; translation (genetics); cell growth; cell viability; regulatory proteins; ribosomes; start codon; DNA-directed RNA polymerase; Escherichia coli
Abstract:
... It is known that polyamines increase cell growth through stimulation of the synthesis of several kinds of proteins encoded by the so-called “polyamine modulon”. We recently reported that polyamines also increase cell viability at the stationary phase of cell growth through stimulation of the synthesis of ribosome modulation factor, a component of the polyamine modulon. Accordingly, we looked for o ...
DOI:
10.1016/j.biocel.2011.11.017

11. Antisense inhibition of gene expression and growth in gram-negative bacteria by cell-penetrating peptide conjugates of peptide nucleic acids targeted to rpoD gene

Author:
Bai, Hui; You, Yu; Yan, Hua; Meng, Jingru; Xue, Xiaoyan; Hou, Zheng; Zhou, Ying; Ma, Xue; Sang, Guojun; Luo, Xiaoxing
Source:
Biomaterials 2012 v.33 no.2 pp. 659-667
ISSN:
0142-9612
Subject:
DNA-directed RNA polymerase; Escherichia coli; Gram-negative bacteria; Klebsiella pneumoniae; Salmonella enterica; Shigella flexneri; anti-infective properties; antibiotic resistance; antibiotics; epithelial cells; gene expression; genes; human growth; humans; messenger RNA; microbial growth; models; mortality; multiple drug resistance; nucleotide sequences
Abstract:
... Gram-negative bacteria (GNB) cause common and severe hospital- and community-acquired infections with a high incidence of multidrug resistance (MDR) and mortality. The emergence and spread of MDR-GNB strains limit therapeutic options and highlight the need to develop new therapeutic strategies. In this study, the peptide (RXR)₄XB- and (KFF)₃K-conjugated peptide nucleic acids (PPNAs) were developed ...
DOI:
10.1016/j.biomaterials.2011.09.075

12. E. coli 6S RNA: A universal transcriptional regulator within the centre of growth adaptation

Author:
Geißen, René; Steuten, Benedikt; Polen, Tino; Wagner, Rolf
Source:
RNA biology 2010 v.7 no.5 pp. 564-568
ISSN:
1555-8584
Subject:
DNA-directed RNA polymerase; Escherichia coli; gene expression regulation; genes; messenger RNA; metabolism; ribosomal proteins; sigma factors; transcription (genetics); translation (genetics); transporters
Abstract:
... Bacterial 6S RNA has been shown to bind with high affinity to σ⁷⁰-containing RNA polymerase, suppressing σ⁷⁰-dependent transcription during stationary phase, when 6S RNA concentrations are highest. We recently reported a genome-wide transcriptional comparison of wild-type and 6S RNA deficient E. coli strains. Contrary to the expected σ⁷⁰- and stationary phase-specific regulatory effect of 6S RNA i ...
DOI:
10.4161/rna.7.5.12969

13. Auto-assembly of E. coli DsrA small noncoding RNA: Molecular characteristics and functional consequences

Author:
Cayrol, Bastien; Geinguenaud, Frédéric; Lacoste, Jérôme; Busi, Florent; Le Dérout, Jacques; Piétrement, Olivier; Le Cam, Eric; Régnier, Philippe; Lavelle, Christophe; Arluison, Véronique
Source:
RNA biology 2009 v.6 no.4 pp. 434-445
ISSN:
1555-8584
Subject:
DNA; DNA-directed RNA polymerase; Escherichia coli; catalysts; genes; messenger RNA; models; non-coding RNA; nucleotides; polymerization; polymers; protein synthesis; proteins; quality control; stress response; translation (genetics)
Abstract:
... RNA molecules are important factors involved in different cellular processes and have a multitude of roles in the cell. These roles include serving as a temporary copy of genes used for protein synthesis or functions in translational machinery. Interestingly, RNA is so far the only biological molecule that serves both as a catalyst (like proteins) and as information storage (like DNA). However, in ...
DOI:
10.4161/rna.6.4.8949

14. The role of the omega subunit of RNA polymerase in expression of the relA gene in Escherichia coli

Author:
Chatterji, Dipankar; Ogawa, Yoshito; Shimada, Tomohiro; Ishihama, Akira
Source:
FEMS microbiology letters 2007 v.267 no.1 pp. 51-55
ISSN:
0378-1097
Subject:
messenger RNA; starvation; stress response; DNA microarrays; gene expression; ribosomal proteins; operon; DNA-directed RNA polymerase; Escherichia coli
Abstract:
... The rpoZ gene for the omega subunit of Escherichia coli RNA polymerase constitutes single operon with the spoT gene, which is responsible for the maintenance of stringent response under nutrient starvation conditions. To identify the physiological role of the omega subunit, we compared the gene expression profile of wild-type Escherichia coli with that of an rpoZ deleted strain by microarray analy ...
DOI:
10.1111/j.1574-6968.2006.00532.x

15. Identification of a putative mitochondrial RNA polymerase from Physarum polycephalum: characterization, expression, purification, and transcription in vitro

Author:
Miller, Mara L.; Antes, Travis J.; Qian, Fang; Miller, Dennis L.
Source:
Current genetics 2006 v.49 no.4 pp. 259-271
ISSN:
0172-8083
Subject:
DNA-directed RNA polymerase; Escherichia coli; Physarum polycephalum; RNA editing; affinity chromatography; amino acid sequences; binding proteins; biogenesis; cDNA libraries; complementary DNA; genes; in vitro studies; maltose; messenger RNA; mitochondria; mitochondrial DNA; mitochondrial RNA; open reading frames; polymerase chain reaction; ribosomal RNA; transfer RNA
Abstract:
... Mitochondrial RNA polymerases (mtRNAPs) are necessary for the biogenesis of mitochondria and for proper mitochondrial function since they transcribe genes on mtDNA for tRNAs, rRNAs, and mRNAs. The unique type of RNA editing identified in mitochondria of Physarum polycephalum is thought to be closely associated with transcription, and as such, RNA editing activity would be expected to be closely as ...
DOI:
10.1007/s00294-005-0053-y
PubMed:
16402203

16. ORF7 of yeast plasmid pGKL2: analysis of gene expression in vivo

Author:
Schaffrath, R.; Meinhardt, F.; Meacock, P.A.
Source:
Current genetics 1997 v.31 no.2 pp. 190-192
ISSN:
0172-8083
Subject:
Kluyveromyces marxianus var. lactis; plasmids; open reading frames; DNA-directed RNA polymerase; gene expression; gene transfer; genetic transformation; Escherichia coli; messenger RNA; mutagenesis; transcription (genetics)
Abstract:
... ORF7 of Kluyveromyces lactis killer plasmid pGKL2 (k2) is capable of encoding a putative RNA polymerase subunit of 16 kDa. RNA analysis detected a single, plasmid-dependent ORF7 transcript of 550 nt indicating that the gene is transcribed mono-cistronically. Attempted one-step gene disruption of ORF7 resulted in chromosomal integration of the marker gene rather than the formation of stable recombi ...
DOI:
10.1007/s002940050195
PubMed:
9021138