PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “RNA, BACTERIAL”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 199 records · Page 11Linked to original sources
PubMed2006

[The stringent response--bacterial mechanism of an adaptive stress response].

The stringent response is a key regulatory reaction exhibited by bacteria in response to amino acid deprivation or carbon, nitrogen and phosphate limitation. In E. coli, the products of the relA and spoT genes regulate accumulation of the effector molecules of the stringent response--guanosine tetra- and pentaphosphates (ppGpp and pppGpp respectively). These unusual hyperphosphorylated nucleotides bind directly to the bacterial RNA polymerase and change transcriptional activity of some genes--transcription repression of genes associated with the translational apparatus and the simultaneous upregulation of genes encoding metabolic enzymes, especially those involved in amino acid biosynthesis, protein hydrolysis and coding for the sigma S factor. Sigma S factor binds to the core of the bacterial RNA polymerase and induce stationary-phase-specific and stress-response-specific genes expression.

Adaptation, Physiological↗
PubMed2005

Translational autocontrol of the Escherichia coli hfq RNA chaperone gene.

The conserved bacterial RNA chaperone Hfq has been shown to play an important role in post-transcriptional regulation. Here, we demonstrate that Hfq synthesis is autoregulated at the translational level. We have mapped two Hfq binding sites in the 5'-untranslated region of hfq mRNA and show that Hfq binding inhibits formation of the translation initiation complex. In vitro translation and in vivo studies further revealed that Hfq binding to both sites is required for efficient translational repression of hfq mRNA.

5' Untranslated Regions↗
PubMed1989

Aromatic dienoyl tetramic acids. Novel antibacterial agents with activity against anaerobes and staphylococci.

Streptolydigin (1) and tirandamycin A (2) are typical members of the naturally occurring class of 3-dienoyl tetramic acids. These compounds, which possess potent antibacterial activity particularly against anaerobes, have been shown to inhibit bacterial RNA polymerase. In contrast, tenuazonic acid (5), which lacks a complex dioxabicyclononane moiety and diene chromophore present in 1 and 2, exhibits essentially no antimicrobial activity and has no effect on bacterial RNA polymerase, suggesting that one or both of these structural features may be critical for antibacterial activity. In this paper, we report on a novel series of synthetic dienoyl tetramic acids that lack a complex dioxabicyclononane unit. Several of these compounds, particularly 8T-W, exhibit potent antimicrobial activity against Gram-positive and Gram-negative anaerobes as well as staphylococci. We will discuss the structure-activity relationship for this series of compounds which, in contrast to their natural counterparts, do not inhibit significantly RNA polymerase. We will also discuss preliminary results on the biochemical and microbiological properties of this series of compounds, several of which moderately inhibit supercoiling by DNA gyrase isolated from E. coli H560, although this enzyme has not been established as their target in whole cells. Compound 8W, which is not cross-resistant with DNA gyrase subunit A or B inhibitors or tirandamycin, has also been demonstrated to be rapidly bactericidal.

Anti-Bacterial Agents↗
PubMed1971

Kinetics of RNA synthesis in toad bladder epithelium: action of aldosterone during the latent period.

Processing of RNA in the toad bladder was analyzed by polyacrylamide-gel electrophoresis to determine whether aldosterone causes any changes in the 1 hr before it potentiates transport of sodium ion. No change was found in the quantity or in the specific activity of bulk RNA labeled with uridine-5-(3)H. In vivo and in vitro with either uridine-5-(3)H or with methionine-(methyl)-(3)H as precursors, processing of RNA was extremely slow. Heterodisperse RNA was obvious after 30 min of continuous labeling, but labeling of the 40S precursor of ribosomal RNA was not apparent for 60 min. Labeling of mature 28S and 18S RNA first became apparent after 8 hr. approximately 7S RNA was the principal fastmigrating species labeled at 30 min, and 4S RNA was not heavily labeled until 1 hr. Aldosterone (5 x 10(-7) mole/liter) produced no changes. If care were not taken to inhibit metabolism of native bacteria colonizing the bladder, bacterial RNA of high specific activity predominated. We conclude that RNA metabolism in the toad bladder is extraordinarily slow, that a major acceleration of de novo synthesis in response to physiologic doses of aldosterone was not demonstrable, and that some reports to the contrary may have been influenced by artifacts from bacterial RNA metabolism. Earlier evidence for obligatory alterations in RNA metabolism during the latent period is not strong.

Aldosterone↗
PubMed2004

Crystal structure of the Mor protein of bacteriophage Mu, a member of the Mor/C family of transcription activators.

Transcription from the middle promoter, Pm, of bacteriophage Mu requires the phage-encoded activator protein Mor and bacterial RNA polymerase. Mor is a sequence-specific DNA-binding protein that mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. Here we present the first structure for a member of the Mor/C family of transcription activators, the crystal structure of Mor to 2.2-A resolution. Each monomer of the Mor dimer is composed of two domains, the N-terminal dimerization domain and C-terminal DNA-binding domain, which are connected by a linker containing a beta strand. The N-terminal dimerization domain has an unusual mode of dimerization; helices alpha1 and alpha2 of both monomers are intertwined to form a four-helix bundle, generating a hydrophobic core that is further stabilized by antiparallel interactions between the two beta strands. Mutational analysis of key leucine residues in helix alpha1 demonstrated a role for this hydrophobic core in protein solubility and function. The C-terminal domain has a classical helix-turn-helix DNA-binding motif that is located at opposite ends of the elongated dimer. Since the distance between the two helix-turn-helix motifs is too great to allow binding to two adjacent major grooves of the 16-bp Mor-binding site, we propose that conformational changes in the protein and DNA will be required for Mor to interact with the DNA. The highly conserved glycines flanking the beta strand may act as pivot points, facilitating the conformational changes of Mor, and the DNA may be bent.

Amino Acid Sequence↗
PubMed1994

Mechanistic aspects of tagetitoxin inhibition of RNA polymerase from Escherichia coli.

Tagetitoxin inhibits RNA synthesis directed by bacterial RNA polymerase, and the current study explores several mechanistic aspects of this inhibition. Tagetitoxin inhibition of in vitro RNA synthesis directed by Escherichia coli RNA polymerase is independent of the template DNA concentration. The toxin can block Escherichia coli RNA polymerase during elongation of a nascent RNA chain. In abortive initiation assays, the rate of dinucleotide formation is inhibited by tagetitoxin when initiated with ATP or CpA but not when AMP is used to initiate. Formation of longer oligonucleotides is inhibited by the toxin regardless of the initiating nucleotide. These abortive initiation studies indicate that tagetitoxin does not affect nucleotide substrate binding or phosphodiester bond formation and suggest that the toxin may interfere with a subsequent step. It is suggested that tagetitoxin affects the stability of nascent oligonucleotide binding and/or the translocation of the catalytic center with respect to the 3'-OH of nascent oligonucleotides.

Adenosine Triphosphate↗
PubMed2005

An electrochemical RNA hybridization assay for detection of the fecal indicator bacterium Escherichia coli.

Monitoring waters for indicator bacteria is required to protect the public from exposure to fecal pollution. Our proof-of-concept study describes a method for detecting fecal coliforms. The coliform Escherichia coli was used as a model fecal indicator. DNA probe-coated magnetic beads in combination with the electrochemical monitoring of the oxidation state of guanine nucleotides should allow for direct detection of bacterial RNA. To demonstrate this concept, we used voltammetry in connection with pencil electrodes to detect isolated E. coli 16S rRNA. Using this approach, 10(7) cells of E. coli were detected in a quantitative, reproducible fashion in 4h. Detection was achieved without a nucleic acid amplification step. The specificity of the assay for coliforms was demonstrated by testing against a panel of bacterial RNA. We also show that E. coli RNA can be detected directly from cell extracts. The method could be used for on-site detection and shows promise for adaptation into automated biosensors for water-quality monitoring.

Biological Assay↗
PubMed1975

DNA-dependent RNA polymerase from Pseudomonas BAL-31. I. Purification and properties of the enzyme.

The DNA-dependent RNA polymerase from Pseudomonas BAL-31, the host for bacteriophage PM2, has been purified 154-fold using differential centrifugation, chromatography on DEAE-cellulose, ammonium sulfate precipitation, and sucrose gradient centrifugations at low and high ionic strength. The resulting enzyme is free of enzyme activities which could interfere with transcription studies and is greater than 85% pure as judged by polyacrylamide gel electrophoresis. Like other bacterial RNA polymerases, its subunit structure is beta'beta sigma alpha2. From gel electrophoresis the beta', beta, and alpha subunits have approximately the same molecular weights as those from Escherichia coli, whereas the sigma subunit is 5% larger (89,000 vs. 85,000). A summation of the subunits yields a molecular weight of 485,000 for the holoenzyme. Like other bacterial RNA polymerases, it sediments as a monomer (15 S) at low ionic strength (0.065) and as a dimer (22 S) at high ionic strength (0.75). Its activity is stimulated three-fold by monovalent cations (K+,NH4+, NA+) with additional stimulation provided by divalent cations (Mg2plus, Mn2plus). The transcription of phage PM2 form I (supercoiled) DNA has an ionic strength optimum of 0.26 for continuous long-term synthesis, and over an ionic strength range of 0.09-0.46 "plateau-type" kinetics are not observed. The sigma subunit is required for optimal PM2 transcription. The enzyme is sensitive to the same inhibitors of transcription as the RNA polymerase from E. coli, it has a temperature optimum of 28 degrees, and it is 50% inactivated by heating 10 min at 41 degrees. It has template preference similar to E. coli polymerase and shows little preference for homologous templates. With various DNAs the order of template activities is T7 greater than PM2 I congruent to T4 greater than PM2 II (relaxed circular form) greater than lambda-c greater than calf thymus greater than BAL-31 DNA. Phage PM2 form I DNA is transcribed at a twofold greater rate than PM2 form II DNA by this enzyme.

Bacteriophages↗
PubMed2005

Transcription regulation by bacteriophage T4 AsiA.

Bacteriophage T4 AsiA, a strong inhibitor of bacterial RNA polymerase, was the first antisigma protein to be discovered. Recent advances that made it possible to purify large amounts of this highly toxic protein led to an increased understanding of AsiA function and structure. In this review, we discuss how the small 10-KDa AsiA protein plays a key role in T4 development through its ability to both inhibit and activate bacterial RNA polymerase transcription.

Bacteriophage T4↗
PubMed2006

Development of a quantitative real-time PCR method to enumerate total bacterial counts in ready-to-eat fruits and vegetables.

A newly developed real-time PCR assay rapidly quantifies the total bacterial numbers in contaminated ready-to-eat vegetables and fruits compared with the standard plate count method. Primers targeting the rpoB gene, which encodes for the beta subunit of the bacterial RNA polymerase and which is common to most bacterial species, was used instead of the 16S rRNA gene, which has multiple copies and varies among bacterial species. A primer pair specific for rpoB was confirmed to amplify rpoB in a wide range of bacterial species after we assessed 49 strains isolated from five kinds of fruits and vegetables. We purchased fruits and vegetables from retail shops and enumerated the bacteria associated with them by use of real-time PCR and compared this to the number found by the culture method. We found a high correlation between the threshold PCR cycle number when compared with the plate count culture number. The real-time PCR assay developed in this study can enumerate the dominant bacterial species in ready-to-eat fruits and vegetables.

Bacteria↗
PubMed1994

A Chlorella virus gene promoter functions as a strong promoter both in plants and bacteria.

An upstream region from an algal virus methyltransferase gene was tested for promoter function in transgenic plants, electroporated monocot protoplasts and bacteria. Fusion of the 851 bp upstream region to a reporter gene significantly enhanced the reporter gene expression in transgenic Arabidopsis and potato plants and in electroporated maize and Sorghum cells relative to the cauliflower mosaic virus 35S promoter. The promoter was also functional in several Escherichia coli strains and in three species of phytopathogenic bacteria, Erwinia, Pseudomonas, and Xanthomonas. These findings indicate that the upstream region is a strong promoter uniquely functional in both eukaryotes and prokaryotes and capable of using both eukaryotic RNA polymerase II and bacterial RNA polymerases.

Arabidopsis↗
PubMed2002

Identification and characterization of FTSJ2, a novel human nucleolar protein homologous to bacterial ribosomal RNA methyltransferase.

Cellular RNAs in eukaryotes undergo extensive posttranscriptional modifications, but as yet only a few RNA-modifying enzymes have been identified and characterized. Here we report on the cloning of FTSJ2, a novel human gene encoding a putative RNA methyltransferase. FTSJ2 shares significant sequence homology with FtsJ/RrmJ, a recently identified Escherichia coli 23S rRNA uridine-2'-O-methyltransferase. FTSJ2 belongs to a new family of evolutionarily conserved S-adenosylmethionine-binding proteins. The gene FTSJ2 is located on chromosome 7p22 between MAD1L1 and NUDT1. It is 8 kb in length, spanning three exons. Northern blot analysis revealed that the FTSJ2 transcripts are abundant in skeletal muscle, placenta, and heart, as well as in cancer cells. Immunofluorescence staining demonstrated that FTSJ2 protein localizes to the nucleolus. Our results suggest that FTSJ2 is likely a nucleolar RNA methyltransferase involved in eukaryotic RNA processing and modification.

Amino Acid Sequence↗