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At least 559 records · Page 31Linked to original sources
PubMed2006

Mode of action of microbial bioactive metabolites.

Pathogenic microorganisms can be suppressed by cell wall destruction. Biosynthesis of peptidoglycans forming bacterial cell wall is interrupted by glycopeptides which inhibit polymerization of a disaccharide formed by N-acetylglucosamine and N-acetylmuramic acid, beta-lactams and their derivatives inhibit peptidoglycan cross-linking. Antibiotics inhibiting protein synthesis bind to different sites on the rRNA and interfere with the formation of the polypeptide chain. Tumor cells resistant to chemotherapeutic drugs overproduce proteins transporting the drugs out of cells; these proteins eliminate substances which inhibit transcription of transport proteins. Some antitumor drugs (anthracyclines, fluoroquinolones, acridines etc.) act at topoisomerases which irreversibly bind to DNA and inhibit DNA synthesis. Immunosuppressants affect various components of the immune system such as T-helper, T-effector cell function, antigen presentation and B-cell function. Antiparasitics--avermectins--bind to a receptor of this Gab-gated chlorine channel in the nerve fiber of nematodes and anthropodes, increasing the permeability of the membrane for chloride ions; the increased transport of chloride ions into the cell causes the death of the parasite. Ionophores dissolve in phospholipid bilayers and enormously increase their ionic permeability. Respiration inhibitors block the transport of electrons at several places of the respiratory chain. Rifamycin binds to the beta subunit of bacterial RNA polymerase, thereby blocking mRNA synthesis. Antiviral compounds inhibit the transcription of DNA by several mechnisms or by inhibition of viral entry into host cells.

Anti-Bacterial Agents↗
PubMed2003

RNA polymerase II/TFIIF structure and conserved organization of the initiation complex.

The structure of an RNA polymerase II/general transcription factor TFIIF complex was determined by cryo-electron microscopy and single particle analysis. Density due to TFIIF was not concentrated in one area but rather was widely distributed across the surface of the polymerase. The largest subunit of TFIIF interacted with the dissociable Rpb4/Rpb7 polymerase subunit complex and with the mobile "clamp." The distribution of the second largest subunit of TFIIF was very similar to that previously reported for the sigma subunit in the bacterial RNA polymerase holoenzyme, consisting of a series of globular domains extending along the polymerase active site cleft. This result indicates that the second TFIIF subunit is a true structural homolog of the bacterial sigma factor and reveals an important similarity of the transcription initiation mechanism between bacteria and eukaryotes. The structure of the RNAPII/TFIIF complex suggests a model for the organization of a minimal transcription initiation complex.

Animals↗
PubMed1997

Unusual oligomerization required for activity of NtrC, a bacterial enhancer-binding protein.

Nitrogen regulatory protein C (NtrC) contacts a bacterial RNA polymerase from distant enhancers by means of DNA loops and activates transcription by allowing polymerase to gain access to the template DNA strand. It was shown that NtrC from Salmonella typhimurium must build large oligomers to activate transcription. In contrast to eukaryotic enhancer-binding proteins, most of which must bind directly to DNA, some NtrC dimers were bound solely by protein-protein interactions. NtrC oligomers were visualized with scanning force microscopy. Evidence of their functional importance was provided by showing that some inactive non-DNA-binding and DNA-binding mutant forms of NtrC can cooperate to activate transcription.

Adenosine Triphosphatases↗
PubMed1981

Transcription of the major Drosophila heat-shock genes in vitro.

Active eukaryotic genes are more accessible to some proteins than bind DNA than are inactive genes. In order to probe the accessibility of the Drosophila heat-shock genes we have isolated nuclei from Drosophila tissue culture cells and have used these nuclei as templates for Escherichia coli RNA polymerase. With nuclei isolated from cells that had not been heat shocked, the synthesis of heat-shock RNA was not detected by hybridization to a DNA clone containing sequences from the major heat-shock region. In contrast, approximately 0.22% of the RNA synthesized in nuclei isolated from cells that had been previously heat shocked hybridized to the heat-shock clone. The synthesis of heat-shock RNA was DNA dependent, was sensitive to rifampicin and to actinomycin D, and represented a 70-fold enrichment over random transcription of the Drosophila genome. Transcription showed an extraordinary preference for a region 5' distal to the structural gene. These results demonstrate that preferential transcription by the bacterial RNA polymerase is indicative of the active state of Drosophila genes.

Animals↗
PubMed1995

A novel bacterial transcription cycle involving sigma 54.

sigma 54 is the promoter recognition subunit of the form of bacterial RNA polymerase that transcribes from promoters with enhancer elements. DNase footprinting experiments show that sigma 54 is attached selectively to the template strand, which must be single-stranded for transcription initiation. sigma 54 remains bound at the promoter after core polymerase begins elongation, in contrast to the well-established sigma 70-holoenzyme transcription cycle. Permanganate footprinting experiments show that the bound sigma 54 and the elongating core RNA polymerase downstream of it are each associated with a single-strand DNA region. Template commitment assays show that the promoter-bound sigma 54 must be reconfigured before reinitiation of transcription can occur. This unexpected pathway raises interesting possibilities for transcriptional regulation, especially with regard to control at the level of reinitiation.

Bacterial Proteins↗
PubMed1984

Hybrid 5 S ribosomal RNA encoded by a multicopy plasmid is incorporated into ribosomes of Escherichia coli.

The recombinant plasmid pJR3 delta contains a tandem pair of promoters from rrnA followed by a hybrid 5 S rRNA gene, derived from the two 5 S rRNA genes of the rrnD transcription unit, and a terminator. Escherichia coli cells transformed with this plasmid produce 2-3-times more 5 S rRNA compared to untransformed cells. The growth of cells containing this plasmid is not affected significantly. Although the sequence and the secondary structure of the plasmid-specific 5 S rRNA differ from those of its counterparts (e.g., from 5 S rRNA species encoded by chromosomal genes), it is processed properly and is incorporated into ribosomes.

Base Sequence↗
PubMed1988

Ribosomal-RNA patterns of Escherichia coli, Salmonella typhimurium and related Enterobacteriaceae.

rRNA sequences are usually highly conserved among species. In Enterobacteriaceae we have shown that Salmonella typhimurium does not have an equivalent to the 23S rRNA of Escherichia coli but its 23S rRNA is cleaved in vivo into two smaller species. This cleavage appears to be a result of a difference between the S. typhimurium and E. coli rRNA sequences rather than to differences in ribonuclease activity. We have surveyed a wide range of Enterobacteriaceae for the presence or absence of 23S rRNA and found this rRNA species to be present in all strains of E. coli, Shigella and Citrobacter and all salmonellae examined except S. typhimurium. All S. typhimurium cultures, isolated at different times and from several different countries, lack an intact 23S rRNA. Thus, the presence or absence of this rRNA species is an excellent diagnostic characteristic for S. typhimurium.

Animals↗
PubMed1976

The binding site of Escherichia coli ribosomal protein S4 on 16-S ribosomal RNA from different bacterial species.

Ribosomal protein S4 of Escherichia coli was bound to 16-S ribosomal RNAs from several bacterial species and the complexes digested with pancreatic ribonuclease in an effort to isolate heterologous RNA binding sites for protein S4. 16-S RNAs from Aeromonas punctata, Pseudomonas fluorescens and Vibrio cuneatus each gave rise to protected fragments whose electrophoretic mobility was 7S, i.e. similar to that of the fragment generated from E. coli 16-S RNA using the same conditions. No comparable fragment was obtained from 16-S RNA of either Bacillus subtilis or Bacillus stearothermophilus, if E. coli protein S4 was present prior to digestion. The protected 7-S RNA fragment from A. punctata and the subfragments obtained from it by gel electrophoresis under denaturing conditions were characterized further by fingerprinting and nucleotide sequence analysis. The sequence of many of the T1 ribonuclease oligonucleotides was obtained and compared to those from the E. coli 7-S fragment. This has permitted a tentative identification of the sequences of A. punctata 16-S RNA which are protected by E. coli protein S4, namely, the regions homologous to the E. coli sequence from section M through C''. The fingerprints of the protected 7-S fragments from both P. fluorescens and V. cuneatus were sufficiently different from that of the E. coli 7-S fragment that no conclusions regarding sequence homologies could be drawn.

Aeromonas↗
PubMed1994

Mutations in sigma factor that affect the temperature dependence of transcription from a promoter, but not from a mismatch bubble in double-stranded DNA.

Specificity of promoter utilization in bacterial RNA polymerases is imparted by a class of proteins referred to as sigma factors. Conserved region 2.3 of these proteins is thought to play a role in the strand separation process that occurs during the formation of an initiation-competent RNA polymerase-promoter complex. We have used a heterologous system consisting of Escherichia coli core RNA polymerase and Bacillus subtilis sigma A to probe the effects of amino acid substitutions in region 2.3. In agreement with previous work [Juang & Helmann (1994) J. Mol. Biol. 235, 1470-1488] we observe that several amino acid substitutions exacerbate the deleterious effect of low temperature on promoter-dependent initiation. On the other hand, no such enhanced cold sensitivity is found with double-stranded templates that contain short "bubbles" of single-stranded DNA, indicating that the DNA-melting defect imposed by these mutant sigma factors can be suppressed by the use of such bubble templates. These results support the involvement of region 2.3 in the strand separation process that accompanies open complex formation at promoters.

Amino Acid Sequence↗
PubMed2004

Incidence and function of sigma factors in Ralstonia metallidurans and other bacteria.

Bacterial sigma factors are essential for directing the bacterial RNA polymerase to promoter regions during transcription initiation. Genomic sequencing of the highly heavy-metal-resistant beta-proteobacterium Ralstonia metallidurans strain CH34 revealed 17 candidate genes for sigma factors. This review compares the sigma factor machinery of R. metallidurans to that of other bacteria. The sigma factors of 105 bacterial genomes were assigned to sigma factor clusters and families formed around the factors from Escherichia coli, Bacillus subtilis, and R. metallidurans. Genes for between 1 and 65 sigma-factor-related proteins were found in these genomes. Although prediction of sigma factor function from sequence comparisons can be misleading, organization of the R. metallidurans sigma factors into clusters and protein families, together with a discussion of the physiological function of members of these clusters, might yield insight into the cellular roles of bacterial sigma factors and the genes that depend on them for their expression.

Genome, Bacterial↗
PubMed2000

Sequences within the DNA cross-linking patch of sigma 54 involved in promoter recognition, sigma isomerization, and open complex formation.

The bacterial RNA polymerase holoenzyme containing the final sigma(54) subunit functions in enhancer-dependent transcription. Mutagenesis has been used to probe the function of a sequence in the final sigma(54) DNA binding domain that includes residues that cross-link to promoter DNA. Several activities of the final sigma and holoenzyme are shown to depend on the cross-linking patch. The patch contributes to promoter binding by final sigma(54), and holoenzyme and is involved in activator-dependent final sigma isomerization. As part of the final sigma(54)-holoenzyme, some residues in the patch limit basal transcription. Other cross-linking patch sequences appear to limit activator-dependent open complex formation. Deletion of 19 residues adjacent to the cross-linking patch resulted in a holoenzyme unable to respond to activator but capable of activator-independent (bypass) transcription in vitro. Overall results are consistent with the cross-linking patch directing interactions to the -12 promoter region to set basal and activated levels of transcription.

Bacterial Proteins↗
PubMed1991

Plasmid RSF1010 DNA replication in vitro promoted by purified RSF1010 RepA, RepB and RepC proteins.

We have constructed and analyzed an in vitro system that will efficiently replicate plasmid RSF1010 and its derivatives. The system contains a partially purified extract from E.coli cells and three purified RSF1010-encoded proteins, the products of genes repA, repB (or mobA/repB), and repC. Replication in this system mimics the in vivo mechanism in that it (i) is initiated at oriV, the origin of vegetative DNA replication, (ii) proceeds in a population of plasmid molecules in both directions from this 396-base-pair origin region, and (iii) is absolutely dependent on the presence of each of the three rep gene products. In addition, we find that E.coli DNA gyrase, DnaZ protein (gamma subunit of poIIII holoenzyme) and SSB are required for in vitro plasmid synthesis. The bacterial RNA polymerase, the initiation protein DnaA, and the primosomal proteins DnaB, DnaC, DnaG and DnaT are not required. Furthermore, the replicative intermediates seen in the electron microscope suggest that replication in vitro begins with the simultaneous or non-simultaneous formation of two displacement loops that expand for a short stretch of DNA toward each other, and form a theta-type structure when the two displacing strands pass each other.

Bacterial Proteins↗
PubMed2002

Proteolytic DNA for mapping protein-DNA interactions.

We describe a technique to determine sites on proteins involved in protein-DNA interactions. DNA was synthesized via polymerase chain reaction (PCR) to produce four polynucleotide products with phosphorothioate nucleotides at the A, T, G, or C residues. Limited conjugation with the chemical protease FeBABE results in the surface of DNA being randomly labeled at the phosphorothioate sites with this protein-cleaving reagent. After formation of a protein-DNA complex, the proteolytic DNA can be activated to cleave the protein backbone at sites near the DNA. This technique was used to study the bacterial RNA polymerase/lacUV5 DNA open promoter complex, about which significant structural information is available. Cleavage sites on the two largest subunits of RNA polymerase, beta and beta', agree well with a recent model based on the crystal structure of the core enzyme alpha(2)betabeta' [Naryshkin, N., Revyakin, A., Kim, Y., Mekler, V., and Ebright, R. H. (2000) Cell 101, 601-611]. The cleavage site present on alpha supports previous studies regarding DNA binding regions of the alpha subunit. Cleavage sites identified throughout the sigma(70) subunit help to orient it with respect to the open promoter complex.

Bacterial Proteins↗
PubMed1988

Events during eucaryotic rRNA transcription initiation and elongation: conversion from the closed to the open promoter complex requires nucleotide substrates.

Chemical footprinting and topological analysis were carried out on the Acanthamoeba castellanii rRNA transcription initiation factor (TIF) and RNA polymerase I complexes with DNA during transcription initiation and elongation. The results show that the binding of TIF and polymerase to the promoter does not alter the supercoiling of the DNA template and the template does not become sensitive to modification by diethylpyrocarbonate, which can identify melted DNA regions. Thus, in contrast to bacterial RNA polymerase, the eucaryotic RNA polymerase I-promoter complex is in a closed configuration preceding addition of nucleotides in vitro. Initiation and 3'-O-methyl CTP-limited translocation by RNA polymerase I results in separation of the polymerase-TIF footprints, leaving the TIF footprint unaltered. In contrast, initiation and translocation result in a significant change in the conformation of the polymerase-DNA complex, culminating in an unwound DNA region of at least 10 base pairs.

Acanthamoeba↗