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PubMed2000

The aprE leader is a determinant of extreme mRNA stability in Bacillus subtilis.

The Bacillus subtilis aprE gene encodes subtilisin, an extracellular proteolytic enzyme produced in stationary phase. The authors examined the stability of aprE mRNA and aprE leader-lacZ fusion mRNA. Both mRNAs were found to be unusually stable, with half-lives longer than 25 min, demonstrating that the aprE leader contains a determinant for extreme mRNA stability. The half-lives were the same in growing and stationary-phase cells. This contrasts with the findings of O. Resnekov et al. (1990) [Proc Natl Acad Sci USA 87, 8355-8359], which suggested a growth-phase-dependent mechanism for decay of aprE mRNA. The discrepancy is explained by the techniques used. Substitution of two bases or deletion of 25 nucleotides in the aprE leader led to a major difference in its predicted secondary structure and resulted in a fivefold reduction of the half-life of aprE mRNA. The authors also determined the half-life of amyE mRNA, which encodes alpha-amylase, another stationary-phase, excreted enzyme and found it to be around 5 min. This shows that extreme stability is not a general property of stationary-phase mRNAs encoding excreted enzymes.

5' Untranslated Regions↗

PubMed1981

Thiomethylation of tyrosine transfer ribonucleic acid is associated with initiation of sporulation in Bacillus subtilis: effect of phosphate concentration.

The thiomethylation of Bacillus subtilis tyrosine transfer ribonucleic acid (tRNATyr) (i6A) has been shown to occur during the slowing-down of growth. The extent of this modification in stationary-phase cells grown in defined medium has been determined in parallel with the sporulation frequency. We observed that the presence of phosphate repressed sporulation and also inhibited the thiomethylation of tRNATyr (i6A) of B. subtilis W168. These effects were partially eliminated by decreasing the glucose concentration until it was growth limiting. In the case of strain W23S, in which sporulation is insensitive to glucose repression, sporulation and tRNATyr thiomethylation were not inhibited by nonlimiting concentrations of phosphate. These results suggest that both sporulation and tRNATyr hyper-modification share some common regulatory process.

Bacillus subtilis↗

PubMed1987

RPC40, a unique gene for a subunit shared between yeast RNA polymerases A and C.

Yeast RNA polymerases A and C share an approximately equal to 40 kd subunit. We have identified, sequenced, and mutagenized in vitro the AC40 subunit gene. The RPC40 gene is unique in the yeast genome and is required for cell viability. This gene contains an open reading frame encoding a 37.6 kd protein having no significant homology with bacterial RNA polymerase subunits. The promoter region contains a 19 bp sequence also present in the largest subunit of RNA polymerase C. It also contains a well-conserved RPG box, a sequence found in the promoter region of many genes encoding the translational apparatus. A novel, plasmid-shuffling method was developed to isolate a large number of RPC40 ts mutants. One of these, ts4, was shown to be defective in the synthesis of RNA polymerases A and C at the restrictive temperature. In contrast, RNA polymerase B was made normally.

Amino Acid Sequence↗

PubMed1990

Interferon production by Shigella flexneri-infected fibroblasts depends upon intracellular bacterial metabolism.

The role of bacterial invasion and subsequent intracellular metabolism or replication, or both, in the induction of interferon (IFN) production in primary cultures of murine embryo fibroblasts (MEFs) was examined. IFN production appeared to be dependent upon bacterial invasion. MEFs that were challenged with Shigella flexneri cultured at 30 degrees C to inhibit the temperature-dependent virulence gene expression that is essential for invasion failed to produce IFN. Furthermore, inhibition of S. flexneri invasion by pretreatment of MEFs with cytochalasin B resulted in a reduction in IFN production. Intracellular bacterial residence alone, however, was not sufficient for the induction of IFN production since an avirulent isogenic variant of S. flexneri which invades but fails to grow intracellularly did not induce IFN production. In fact, the blocking of bacterial RNA synthesis immediately after cellular uptake of S. flexneri by rifampin inhibited IFN production by MEFs. Transfer of the invasion-encoding plasmid to a noninvasive Escherichia coli strain conferred upon the bacteria the ability to invade MEFs and induce IFN production. These results suggest that the induction of IFN production in S. flexneri-infected fibroblasts requires bacterial invasion and intracellular bacterial metabolism or replication, or both.

Animals↗

PubMed1999

Recombination during reverse transcription: an evaluation of the role of the nucleocapsid protein.

The human immuno deficiency virus type 1 nucleocapsid protein 7 (HIV-1 NCp7) is a major component of the reverse transcription complex. Its effect on reverse transcription and homologous recombination has been studied in vitro under strictly identical experimental conditions. For high enzyme concentrations, NCp7 did not stimulate DNA synthesis. The time-course for completion of reverse transcription as well as the processivity and the pattern of pausing were similar in the presence or absence of NCp7. However, the addition of NCp7 significantly affected the yield of the reaction, a decrease exacerbated as the length of the copied RNA increased. We attribute this phenomenon to a destabilization of the RNA/DNA duplex at intermediate stages of reverse transcription.In contrast, NCp7 enhanced homologous recombination during synthesis mediated by HIV-1 RT (reverse transcriptase), as it did for Moloney murine leukemia virus RT. On naked RNA the process of recombination was dependent on the concentration of RT, suggesting that binding of RT to an intermediate of strand transfer was the limiting step. This dependence was relieved in the presence of NCp7. This effect does not imply a direct interaction between RT and NCp7, since similar results were obtained when NCp7 was substituted by the bacterial RNA chaperon StpA. The dominant effect of NCp7 is therefore most probably exerted at the level of condensation of the RNA templates, leading to the formation of productive interactions between the nascent DNA and the acceptor template.

Capsid↗

PubMed1990

Complex character of senS, a novel gene regulating expression of extracellular-protein genes of Bacillus subtilis.

The senS gene of Bacillus subtilis, which in high copy number stimulates the expression of several extracellular-protein genes, has been cloned, genetically mapped, and sequenced. The gene codes for a highly charged basic protein containing 65 amino acid residues. The gene is characterized by the presence of a transcription terminator (attenuator) located between the promoter and open reading frame, a strong ribosome-binding site, and a strong transcription terminator at the 3' end of this monocistronic gene. The amino acid sequence of SenS showed partial homology with the N-terminal core binding domain region of bacterial RNA polymerase sigma factors and a helix-turn-helix motif found in DNA-binding proteins. The gene can be deleted without any effect on growth or sporulation.

Amino Acid Sequence↗

PubMed2003

The role of transcription initiation factor IIIB subunits in promoter opening probed by photochemical cross-linking.

The core transcription initiation factor (TF) IIIB recruits its conjugate RNA polymerase (pol) III to the promoter and also plays an essential role in promoter opening. TFIIIB assembled with certain deletion mutants of its Brf1 and Bdp1 subunits is competent in pol III recruitment, but the resulting preinitiation complex does not open the promoter. Whether Brf1 and Bdp1 participate in opening the promoter by direct DNA interaction (as sigma subunits of bacterial RNA polymerases do) or indirectly by their action on pol III has been approached by site-specific photochemical protein-DNA cross-linking of TFIIIB-pol III-U6 RNA gene promoter complexes. Brf1, Bdp1, and several pol III subunits can be cross-linked to the nontranscribed strand of the U6 promoter at base pair -9/-8 and +2/+3 (relative to the transcriptional start as +1), respectively the upstream and downstream ends of the DNA segment that opens up into the transcription bubble. Cross-linking of Bdp1 and Brf1 is detected at 0 degrees C in closed preinitiation complexes and at 30 degrees C in complexes that are partly open, but also it is detected in mutant TFIIIB-pol III-DNA complexes that are unable to open the promoter. In contrast, promoter opening-defective TFIIIB mutants generate significant changes of cross-linking of polymerase subunits. The weight of this evidence argues in favor of an indirect mode of action of TFIIIB in promoter opening.

Base Sequence↗

PubMed2002

DNA-PCR and RT-PCR for the 18-kDa gene of Mycobacterium leprae to assess the efficacy of multi-drug therapy for leprosy.

DNA-PCR and reverse transcription (RT)-PCR for the 18-kDa protein of Mycobacterium leprae were used to examine the efficacy of multi-drug therapy (MDT) in leprosy. MDT was administered for 0-24 months. Fourteen (63.6%) of 22 patients showed positive PCR results after treatment for 12 months and the positive results decreased to 30% after 24 months of MDT. These results did not correlate with the bacterial index (BI) or the IgM antibody titre for the phenolic glycolipid (PGL)-1. One-dimensional densitometric analysis of agarose gels from PCR from the longitudinal study showed a gradual reduction of the 360-bp band after 12-24 months of MDT. RT-PCR for mRNA of the 18-kDa protein successfully tracked bacterial RNA changes in the biopsies and confirmed a decrease in the RNA of M. leprae in patients after MDT for 12 months. Thus, DNA- and RT-PCR for the 18-kDa protein of M. leprae are effective in assessing the efficacy of MDT for leprosy.

Animals↗

PubMed1989

Bacterial blight of soybean: regulation of a pathogen gene determining host cultivar specificity.

Soybean cultivars resistant to Pseudomonas syringae pathovar glycinea (Psg), the causal agent of bacterial blight, exhibit a hypersensitive (necrosis) reaction (HR) to infection. Psg strains carrying the avrB gene elicit the HR in soybean cultivars carrying the resistance gene Rpg1. Psg expressing avrB at a high level and capable of eliciting the HR in the absence of de novo bacterial RNA synthesis have been obtained in in vitro culture. Nutritional signals and regions within the Psg hrp gene cluster, an approximately 20-kilobase genomic region also necessary for pathogenicity, control avrB transcription.

Cloning, Molecular↗

PubMed2002

The A14-A43 heterodimer subunit in yeast RNA pol I and their relationship to Rpb4-Rpb7 pol II subunits.

A43, an essential subunit of yeast RNA polymerase I (pol I), interacts with Rrn3, a class I general transcription factor required for rDNA transcription. The pol I-Rrn3 complex is the only form of enzyme competent for promoter-dependent transcription initiation. In this paper, using biochemical and genetic approaches, we demonstrate that the A43 polypeptide forms a stable heterodimer with the A14 pol I subunit and interacts with the common ABC23 subunit, the yeast counterpart of the omega subunit of bacterial RNA polymerase. We show by immunoelectronic microscopy that A43, ABC23, and A14 colocalize in the three-dimensional structure of the pol I, and we demonstrate that the presence of A43 is required for the stabilization of both A14 and ABC23 within the pol I. Because the N-terminal half of A43 is clearly related to the pol II Rpb7 subunit, we propose that the A43-A14 pair is likely the pol I counterpart of the Rpb7-Rpb4 heterodimer, although A14 distinguishes from Rpb4 by specific sequence and structure features. This hypothesis, combined with our structural data, suggests a new localization of Rpb7-Rpb4 subunits in the three-dimensional structure of yeast pol II.

Amino Acid Sequence↗

PubMed1999

A minimal RNA polymerase III transcription system.

Transcription factor (TF) IIIB recruits RNA polymerase (pol) III for specific initiation of transcription. All three subunits of TFIIIB, TBP, Brf (the TFIIB-related subunit) and B", are required for transcription of supercoiled and linear duplex DNA, but we show here that B" is non-essential on a promoter that has been partly pre-opened by unpairing a short segment of the transcription bubble. These findings expose a striking similarity between transcriptional initiation by pol II, pol III and bacterial RNA polymerases: a preformed single-stranded DNA bubble upstream of the transcriptional start removes the dependence of pol II on TFIIE, TFIIH and ATP hydrolysis, and the dependence of pol III on B"; the favored placement of the transcription bubble for B"-independent transcription by pol III overlaps a DNA segment that interacts sequence specifically as single-stranded DNA with the sigma(70 )initiation subunit of Escherichia coli RNA polymerase holoenzyme.

Adenosine Triphosphate↗

PubMed2001

DNA melting within a binary sigma(54)-promoter DNA complex.

The final sigma(54) subunit of the bacterial RNA polymerase requires the action of specialized enhancer-binding activators to initiate transcription. Here we show that final sigma(54) is able to melt promoter DNA when it is bound to a DNA structure representing the initial nucleation of DNA opening found in closed complexes. Melting occurs in response to activator in a nucleotide-hydrolyzing reaction and appears to spread downstream from the nucleation point toward the transcription start site. We show that final sigma(54) contains some weak determinants for DNA melting that are masked by the Region I sequences and some strong ones that require Region I. It seems that final sigma(54) binds to DNA in a self-inhibited state, and one function of the activator is therefore to promote a conformational change in final sigma(54) to reveal its DNA-melting activity. Results with the holoenzyme bound to early melted DNA suggest an ordered series of events in which changes in core to final sigma(54) interactions and final sigma(54)-DNA interactions occur in response to activator to allow final sigma(54) isomerization and the holoenzyme to progress from the closed complex to the open complex.

Bacterial Proteins↗

PubMed1982

DNA replication and transcription in a temperature-sensitive mutant of E. coli with a defective DNA gyrase B subunit.

A temperature-sensitive mutant of E. coli with a defective DNA gyrase B subunit has been obtained. The mutation is expressed in the thermolability of DNA gyrase in vitro and in DNA relaxation in vivo. DNA replication in the mutant does not stop under non-permissive conditions; its rate gradually falls by a factor of 2 to 3. The transcription rate also drops by a factor of 2 to 3, but before replication. Small concentrations of rifampicin, an inhibitor of bacterial RNA polymerase, make for a partial survival of the mutant cells under non-permissive conditions. The results suggest the conclusion that DNA supercoiling is mainly required to ensure the optimum transcription level in the cell.

Cell Division↗

PubMed2006

[Recurrent autoreactive pericardial effusion. Impact of an aetiological classification of pericarditis].

HISTORY: A 36 year-old man suffered from fever, fatigue, pleurodynia and precordial discomfort. His family physician suspected febrile tracheobronchitis and treated it with ampicillin for 5 days. Because symptoms persisted an ECG was done which suggested acute myocardial infarction. The patient underwent an emergency coronary angiography which excluded coronary artery disease and aortic dissection. Pericarditis was suspected and the patient put on aspirin, 500 mg/d. Because of persisting cardiac symptoms an echocardiography was performed which revealed systolic separation between epi- and pericardium, characteristic of a small pericardial effusion after acute pericarditis. The symptoms improved after one week of treatment with diclofenac and the ECG had become normal. Two months later the patient was seen at our cardiac outpatient clinic. He had night sweats, sporadic precordial pain and severe dyspnoe. INVESTIGATIONS: Further investigations revealed tachycardia (120/min), hypotension (95/70 mm Hg), pulsus paradoxus and jugular vein sustension. Echocardiography revealed a large pericardial effusion ("swinging heart"), which explained the low voltage and the electrical alternans in the ECG. TREATMENT AND COURSE: Pericardiocentesis was carried out the same day to relieve the tamponade. It was followed by pericardioscopy and epi- as well as pericardial biopsy. 485 ml of a serous effusion were drained. Cytology and histology demonstrated a lymphocytic fibrinous pericarditis. Polymerase chain reaction (PCR) on viral and bacterial RNA and DNA of potentially cardiotropic agents remained negative. The pigtail catheter was left in place and 80 mg of gentamycin were given intrapericardially on day 1 and 2, followed by 500 mg of crystalloid triamcinolone acetate after the PCR was found to be negative. Oral treatment with 0.5 mg colchicine three times a day (off-label use) was started and maintained for 6 months. After 9 months no effusion was detected and the patient was free of symptoms. CONCLUSIONS: After exclusion of bacterial and viral pericardial infection, a high single dose of intrapericardial triamcinolone combined with long-term oral colchicine has proven to be a highly efficacious treatment of autoreactive pericarditis which will avoid relapses in most cases.

Adult↗

PubMed1990

[Pleiotropic effect of the rpoC mutation in Escherichia coli K-12 reducing the frequency of lysogenization by phage lambda].

We described earlier the isolation of lfl25 mutation reducing the frequency of lysogenization of mutant cells by phage lambda (LycA phenotype). The mutation is mapped at present in the rpoC gene coding for the beta' subunit of bacterial RNA polymerase and named rpoC90. It is dominant and causes decrease in pools of some branched amino acids, pyrimidines and thiamine (vitamin B1) in mutant cells. Combination of rpoC90 mutation with some Rif-r mutations strengthens both the LycA phenotype and deficiency in metabolites mentioned above. Such combination was shown to also cause a defect in antitermination (or increases the efficiency of termination) of transcription on the DNA of lambdoid phage phi 434. This defect may indicate the possible mechanism of changes in the regulation of different bacterial operons induced by rpoC90 mutation.

Bacteriophage lambda↗

PubMed2006

Mapping ATP-dependent activation at a sigma54 promoter.

The sigma(54) promoter specificity factor is distinct from other bacterial RNA polymerase (RNAP) sigma factors in that it forms a transcriptionally silent closed complex upon promoter binding. Transcriptional activation occurs through a nucleotide-dependent isomerization of sigma(54), mediated via its interactions with an enhancer-binding activator protein that utilizes the energy released in ATP hydrolysis to effect structural changes in sigma(54) and core RNA polymerase. The organization of sigma(54)-promoter and sigma(54)-RNAP-promoter complexes was investigated by fluorescence resonance energy transfer assays using sigma(54) single cysteine-mutants labeled with an acceptor fluorophore and donor fluorophore-labeled DNA sequences containing mismatches that mimic nifH early- and late-melted promoters. The results show that sigma(54) undergoes spatial rearrangements of functionally important domains upon closed complex formation. sigma(54) and sigma(54)-RNAP promoter complexes reconstituted with the different mismatched DNA constructs were assayed by the addition of the activator phage shock protein F in the presence or absence of ATP and of non-hydrolysable analogues. Nucleotide-dependent alterations in fluorescence resonance energy transfer efficiencies identify different functional states of the activator-sigma(54)-RNAP-promoter complex that exist throughout the mechano-chemical transduction pathway of transcriptional activation, i.e. from closed to open promoter complexes. The results suggest that open complex formation only occurs efficiently on replacement of a repressive fork junction with down-stream melted DNA.

Adenosine Triphosphate↗

PubMed1988

RNA binding specificity of hnRNP proteins: a subset bind to the 3' end of introns.

The binding of hnRNP proteins to pre-mRNAs in nuclear extracts, and as isolated proteins, was studied by using monoclonal antibody immunopurification of hnRNP proteins bound to RNase T1-generated fragments. Several major hnRNP proteins, A1, C and D, bind specifically to the 3' end of introns within a region containing the conserved polypyrimidine stretch between the branch site and the 3' splice site. Mutations which alter the conserved 3' splice site dinucleotide AG strongly impair or abolish the binding of the A1 protein as well as of an anti-Sm reactive component(s) to this region. The A1, C and D proteins do not bind efficiently to fragments of either bacterial RNA or the intronless spliced product (mRNA). The binding of these proteins at the 3' end of the intron does not require addition to the extract of exogenous ATP, but remains after ATP addition. These findings demonstrate that several hnRNP proteins have RNA binding specificities on pre-mRNA, and suggest a model for hnRNP particle structure and assembly.

Binding Sites↗

PubMed1990

Mapping the active site of yeast RNA polymerase B (II).

Yeast RNA polymerase B (II) was incubated with a collection of 13 different nucleotide derivatives and affinity labeled by allowing DNA-directed phosphodiester bond formation. The 32P-labeled site was localized in the C-terminal part of the B150 subunit by microsequencing a proteolytic fragment, then further mapped by a combination of extensive or single-hit chemical cleavage reactions and analysis of the labeled peptide patterns. The affinity label was mapped to between Asn946 and Met999, within one of the nine regions that are conserved between B150 and the bacterial beta subunit. The results underscore the conservative evolution of the catalytic center of eukaryotic and bacterial RNA polymerases.

Amino Acid Sequence↗