Ribonucleic acid synthesis in bacteria treated with toluene

Characterization of YafO, an Escherichia coli toxin

YafO is a toxin encoded by the yafN-yafO antitoxin-toxin operon in the Escherichia coli genome. Our results show that YafO inhibits protein synthesis but not DNA or RNA synthesis. The in vivo [35S]methionine incorporation was inhibited within 5 min after YafO induction. In in vivo primer extension experiments with two different mRNAs, the specific cleavage bands appeared 11-13 bases downstream of the initiation codon, AUG, 2.5 min after the induction of YafO. An identical band was also detected in in vitro toeprinting experiments when YafO was added to the reaction mixture containing 70 S ribosomes and the same mRNAs even in the absence of tRNA(f)(Met). Notably, this band was not detected in the presence of YafO alone, indicating that YafO by itself does not have endoribonuclease activity under the conditions used. The full-length mRNAs almost completely disappeared 30 min after YafO induction in in vivo primer extension experiments, consistent with Northern blotting analysis. Over 84% of [35S]methionine-tRNA(f)(Met) was released from the translation initiation complex at 5.43 microM YafO in vitro. We demonstrated that the 70 S ribosome peak significantly increased upon YafO induction, and when the 70 S ribosomes dissociated into 50 and 30 S subunits, YafO was found to be associated with 50 S subunits. These results demonstrate that YafO is a ribosome-dependent mRNA interferase inhibiting protein synthesis.

The inhibitory mechanism of protein synthesis by YoeB, an Escherichia coli toxin

YoeB is a toxin encoded by the yefM-yoeB antitoxin-toxin operon in the Escherichia coli genome. Here we show that YoeB, a highly potent protein synthesis inhibitor, specifically blocks translation initiation. In in vivo primer extension experiments using two different mRNAs, a major band was detected after YoeB induction at three bases downstream of the initiation codon at 2.5 min. An identical band was also detected in in vitro toeprinting experiments after the addition of YoeB to the reaction mixtures containing 70 S ribosomes and the same mRNAs, even in the absence of tRNA(f)(Met). Notably, this band was not detected in the presence of YoeB alone, indicating that YoeB by itself does not have endoribonuclease activity under the conditions used. The 70 S ribosomes increased upon YoeB induction, and YoeB was found to be specifically associated with 50 S subunits. Using tetracycline and hygromycin B, we demonstrated that YoeB binds to the 50 S ribosomal subunit in 70 S ribosomes and interacts with the A site leading to mRNA cleavage at this site. As a result, the 3'-end portion of the mRNA was released from ribosomes, and translation initiation was effectively inhibited. These results demonstrate that YoeB primarily inhibits translation initiation.

Bacterial addiction module toxin Doc inhibits translation elongation through its association with the 30S ribosomal subunit

Bacterial toxin-antitoxin (TA) systems (or "addiction modules") typically facilitate cell survival during intervals of stress by inducing a state of reversible growth arrest. However, upon prolonged stress, TA toxin action leads to cell death. TA systems have also been implicated in several clinically important phenomena: biofilm formation, bacterial persistence during antibiotic treatment, and bacterial pathogenesis. TA systems harbored by pathogens also serve as attractive antibiotic targets. To date, the mechanism of action of the majority of known TA toxins has not yet been elucidated. We determined the mode of action of the Doc toxin of the Phd-Doc TA system. Doc expression resulted in rapid cell growth arrest and marked inhibition of translation without significant perturbation of transcription or replication. However, Doc did not cleave mRNA as do other addiction-module toxins whose activities result in translation inhibition. Instead, Doc induction mimicked the effects of treatment with the aminoglycoside antibiotic hygromycin B (HygB): Both Doc and HygB interacted with 30S ribosomal subunits, stabilized polysomes, and resulted in a significant increase in mRNA half-life. HygB also competed with ribosome-bound Doc, whereas HygB-resistant mutants suppressed Doc toxicity, suggesting that the Doc-binding site includes that of HygB (i.e., helix 44 region of 16S rRNA containing the A, P, and E sites). Overall, our results illuminate an intracellular target and mechanism of TA toxin action drawn from aminoglycoside antibiotics: Doc toxicity is the result of inhibition of translation elongation, possibly at the translocation step, through its interaction with the 30S ribosomal subunit.

MazF Cleaves Cellular mRNAs Specifically at ACA to Block Protein Synthesis in Escherichia coli

Escherichia coli contains operons called "addiction modules," encoding toxin and antitoxin, which are responsible for growth arrest and cell death. Here, we demonstrate that MazF toxin encoded by "mazEF addiction module" is a sequence-specific (ACA) endoribonuclease functional only for single-stranded RNA. MazF works as a ribonuclease independent of ribosomes, and is, therefore, functionally distinct from RelE, another E. coli toxin, which assists mRNA cleavage at the A site on ribosomes. Upon induction, MazF cleaves whole cellular mRNAs to efficiently block protein synthesis. Purified MazF inhibited protein synthesis in both prokaryotic and eukaryotic cell-free systems. This inhibition was released by MazE, the labile antitoxin against MazF. Thus, MazF functions as a toxic endoribonuclease to interfere with the function of cellular mRNAs by cleaving them at specific sequences leading to rapid cell growth arrest and cell death. The role of such endoribonucleases may have broad implication in cell physiology under various growth conditions.

Reverse transcriptase with concomitant ribonuclease H activity in the cell-free synthesis of branched RNA-linked msDNA of Myxococcus xanthus

msDNA is a peculiar molecule consisting of a branched RNA linked to single-stranded DNA via a 2',5' phosphodiester bond. A cell-free system, utilizing cells permeabilized with phenethyl alcohol, was established to study the synthesis of msDNA in M. xanthus. Permeablized cells labeled with [alpha-32P]dCTP in the presence of ddGTP, ddATP, or ddTTP produce a band that migrates at the same position as the full-sized msDNA in an polyacrylamide gel. However, when this band is treated with ribonuclease A prior to gel electrophoresis, it results in many different-sized bands. This indicates that during the labeling, intermediates are produced in which single-stranded DNAs of various lengths are associated with a compensatory length of RNA such that the total length for each intermediate is identical. These results provide evidence for the previously proposed model in which msDNA is synthesized by reverse transcriptase using a folded RNA precursor as a primer as well as a template. Furthermore, we found that there is a precise coupling mechanism of reverse transcriptase and ribonuclease H.

Inhibition of exogenous 3-deoxy-D-manno-octulosonate incorporation into lipid A precursor of toluene-treated Salmonella typhimurium cells

Analogs of 3-deoxy-D-manno-octulosonate (KDO) were designed to inhibit CTP:CMP-KDO cytidylyltransferase (CMP-KDO synthetase). Since these analogs lacked whole-cell antibacterial activity, a permeabilized-cell method was developed to measure intracellular compound activity directly. The method employed a mutant of Salmonella typhimurium defective in KDO-8-phosphate synthetase (kdsA), which accumulated lipid A precursor at 42 degrees C. Cells permeabilized with 1% toluene were used to evaluate inhibitor effect on [3H]KDO incorporation into preformed lipid A precursor. KDO incorporation proceeded through the enzymes CMP-KDO synthetase and CMP-KDO:lipid A KDO transferase. Optimum KDO incorporation occurred between pH 8 and 9 and required CTP, prior lipid A precursor accumulation, and a functional kdsB gene product, CMP-KDO synthetase. The apparent Km for KDO in this coupled system at pH 7.6 was 1.38 mM. The reaction products isolated and characterized contained 1 and 2 KDO residues per lipid A precursor molecule. Several KDO analogs produced concentration-related reductions of KDO incorporation in toluenized cells with 50% inhibitory concentrations comparable to those obtained in purified CMP-KDO synthetase systems. Two compounds, 8-amino-2-deoxy-KDO (A-60478) and 8-aminomethyl-2-deoxy-KDO (A-60821), competitively inhibited KDO incorporation, displaying Kis of 4.2 microM for A-60478 and 2.5 microM for A-60821. These data indicated that the inactivity of the KDO analogs on intact bacteria was the result of poor permeation into cells rather than intracellular inactivation.

Synthesis of pigment-binding protein in toluene-treated Rhodopseudomonas capsulata and in cell-free systems

Pigment-binding protein of the facultatively phototrophic bacterium Rhodospeudomonas capsulata could be selectively synthesized in toluene-treated cells as well as in homologous and heterologous cell-free translation systems by isolated polysomes. It is shown that the pigment-binding polypeptides of the light-harvesting complexes are encoded by messenger RNA of extreme longevity. The dependence of their synthesis on the concomitant synthesis of tetrapyrroles was demonstrated in the toluene-treated cells. The large Mr-28 000 polypeptide of the reaction center and the Mr-10 000 pigment-binding polypeptide of the light-harvesting complex II were found to be synthesized by free (water-soluble) polysomes without a cleavable 'leader' or 'signal' peptide [reviewed by W. Wickner (1979) Annu. Rev. Biochem. 48, 23-45]. The Mr-10 000 polypeptide, as synthesized in vitro, was studied in more detail. Unlike the membrane-assembled polypeptide in vivo it was insoluble in an organic solvent mixture (chloroform/methanol 1:1, v/v). After detergent denaturation in the presence of membrane isolated from the organism it became organic-solvent-soluble. Obviously the polypeptide could be induced to assume alternative conformations in which its apolar residues were either exposed to the solvent or buried within. These findings, in agreement with Wickner's hypothesis, indicate that the Mr-10 000 polypeptide may enter the lipid bilayer by a 'membrane-triggered' conformational change.

Synthesis of polyadenylate-containing RNA in vitro in permeable cells of Escherichia coli B

As a starting point for the study of the biosynthesis of polyadenylated RNA in bacteria, the characteristics of RNA synthesis by cells of Escherichia coli B made permeable to small molecules by treatment with toluene were examined. Such cells mediated the incorporation of radiolabeled ribonucleoside triphosphates into RNA in a reaction that was sensitive to inhibitors of RNA polymerase and required the simultaneous presence of the four ribonucleoside triphosphates. Between 10 to 15% of the RNA synthesized under these conditions was polyadenylated as shown by affinity chromatography on oligo(dT)-cellulose. The presence of orthophosphate or dADP, inhibitors of polynucleotide phosphorylase, had no effect on the reaction and the rate of RNA synthesis was indistinguishable in the polynucleotide phosphorylase-deficient strain PR-7 and in its otherwise isogenic parent strain PR-100. The poly(A) tracts associated with the newly synthesized RNA could be isolated after exhaustive digestion with pancreatic and T1 ribonucleases and accounted for 14% of the poly(A)-RNA. At least 74% of the poly(A) sequences were located at the 3' ends of RNA molecules and their weight-average length was 48 nucleotide residues. The size distribution of total RNA and poly(A)-RNA synthesized in the toluenized cell system was similar to that of the corresponding pulse-labeled fractions derived from growing cultures. The sequence complexity of poly(A)-RNA and unadenylated RNA synthesized in toluenized cells with [alpha-32P]CTP as the labeled substrate was analyzed by hybridization to fragments of Escherichia coli B DNA generated by digestion with EcoRI restriction endonuclease and immobilized on nitrocellulose sheets. Both RNA fractions hybridized with many DNA fractions, the hybridization patterns being similar with poly(A)-RNA and unadenylated RNA. This indicated that many different types of RNA transcripts synthesized in toluenized cells were subject to polyadenylation, but that polyadenylation was incomplete so that each transcript was present in both an adenylated and an unadenylated state.

The effect of parabens on DNA, RNA and protein synthesis in Escherichia coli and Bacillus subtilis

The effect of methyl, propyl and butyl esters of p-hydroxybenzoic acid on DNA and RNA synthesis has been tested in toluenized cells of Escherichia coli and Bacillus subtilis. Both RNA and DNA synthesis of these bacteria were inhibited. The inhibitory concentrations were higher than those previously reported for growth inhibition. Protein synthesis in cell-free extracts (S-30 fraction) of B. subtilis was even more sensitive to parabens than DNA and RNA synthesis, while protein synthesis in Esch. coli was largely unaffected.

Transcription of exogenous and endogenous deoxyribonucleic acid templates in cold-shocked Bacillus subtilis

Ribonucleic acid (RNA) synthesis was examined in cold-shocked Bacillus subtilis cells. The cells were grown to mid-log stage, harvested, and cold shocked. RNA synthesis was monitored by the incorporation of [3H]uridine triphosphate or [alpha 32P]adenosine triphosphate into trichloroacetic acid-precipitable material in the presence of all four nucleoside triphosphates. The inhibition of RNA synthesis in cold-shocked cells by lipiarmycin, ethidium bromide, rifampin. or streptolydigin was analyzed using mutant or wild-type cells. Also examined were the effects of temperature, salt concentration, and the addition of polyamines or highly phosphorylated nucleotides. In ultraviolet-irradiated and cold-shocked cells, RNA wynthesis decreased to low levels. The addition of exogenous phi 29 or TSP-1 template to these cells caused a 13- to 20-fold increase in RNA synthesis, as monitored by trichloroacetic acid-precipitable counts. RNA synthesized in the presence of phi 29 deoxyribonucleic acid (DNA) hybridizes mainly to EcoRI fragments A and C of phi 29 DBA, These two fragments direct transcription by purified RNA polymerase in vitro and hybridize to early phi 29 DNA produced in vivo. Our results with TSP-1 DNA in this system indicated that the RNA produced hybridizes to the same fragments as early RNA produced in vivo. Plasmic pUB110 DNA was not transcribed in this system.

Secretion and membrane localization of proteins in Escherichia coli

The envelope of Escherichia coli consists of two distinct membranes, the outer membrane and the cytoplasmic membrane. The space between the two membranes is called the periplasmic space, and each fraction contains its own specific proteins. In this review, it is discussed how proteins are localized in their final locations in the envelope. Proteins localized in the outer membrane and the periplasmic space as well as transmembranous proteins in the cytoplasmic membranes appear to be produced from their precursors which have peptide extensions of about 20 amino acid residues at the amino terminal ends. General features for the peptide extension are deduced from the known sequences of the peptide extensions, and, based on their known properties, a hypothesis (loop model) is proposed to explain the possible functions of the peptide extension during the mechanism of secretion across the cytoplasmic membrane.

Permeabilization of cells for studies on the biochemistry of bacterial chemotaxis

The cell membranes of Salmonella typhimurium and Escherichia coli have been made permeable in order to introduce S-adenosylmethionine into the cell for study of the course of methylation. A series of protein bands in the Mr 60,000 region were methylated, the specific bands and the extent of methylation depending on the attractant used. The change in levels of methylation was essentially the same as the in vivo responses, indicating that the permeabilization procedure maintains the relative relationships of the cellular proteins. A shift in intensity of the methylated bands occurred over time, indicating that a sequential process is involved in the methylation of these proteins. The permeabilization technique appears to offer major advantages in tracing the biochemical processes of the behavioral system.

Synthesis of chloroplast ribonucleic acid in Chlamydomonas reinhardtii toluene-treated cells

Chlamydomonas reinhardtii cells treated with toluene at 0 degrees C and 25 degrees C incorporate ribonucleoside triphosphates (NTPs) into chloroplast RNA at 25 degrees C and also at 35 degrees C. The incorporation requires all four NTPs and Mg2+, and is completely inhibited by DNase, RNase, actinomycin D (40 microgram/ml) and rifampicin (350 microgram/ml). However, the incorporation is almost totally insensitive to both alpha-amanitin and streptolydigin at 200 microgram/ml.

Polypeptide synthesis in toluene-treated lymphocytes

Normal human lymphocytes stimulated by phytohemagglutinin P, and other mammalian cells were rendered permeable to macromolecules such as poly(U) and proteins, by treatment with a low concentration of toluene. Under this condition, poly(U) translation was more efficient in the permeabilized cells than in 10000 X g extracts. Such a process occurs inside the treated cells as demonstrated by the fact that [14C]uridine-labelled ribosomes remain associated with the toluene-treated lymphocytes even after incubation at 37 degrees C. A nuclease from Staphylococcus aureus was able to penetrate the permeabilized cells and to break the polysome-bound endogenous messenger RNA. However, the protein-synthesizing machinery inside the toluene-treated lymphocytes was unaffected by the nuclease, as demonstrated by the unimpairment of polyphenylalanine synthesis when poly(U) was added after the preincubation with the enzyme. These results suggest that the toluene treatment can be considered as an important tool for the study of the synthesis of macromolecules and its regulation in eukaryotic cells.

The effect of toluene on the structure and permeability of the outer and cytoplasmic membranes of Escherichia coli

The effect of toluene on Escherichia coli has been examined. In the presence of Mg2+, toluene removes very little protein, phospholipid, or lipopolysacharide from E. coli. In the absence of Mg2+, or in the presence of EDTA, toluene removes considerably more cell material, including several specific cytoplasmic proteins such as malate dehydrogenase (EC 1.1.1.37). In contrast, glucose-6-phosphate dehydrogenase (EC 1.1.1.49) and glutamate dehydrogenase (EC 1.4.1.4) are not released at all under the same conditions. Cells treated with toluene in the presence of Mg2+ remain relatively impermeable to pyridne nucleotides, while cells treated with toluene in the presence of EDTA become permeable to these compounds. Freeze-fracture electron microscopy shows that toluene causes considerable damage to the cytoplasmic membrane, while the outer membrane remains relatively intact. These results indicate that the permeability characteristics of toluene-treated cells depend at least partly on the state of the outer membrane after the toluene treatment.

Regulation of ribonucleic acid synthesis in spheroplasts, cold-shocked cells, and toluene-treated cells of Escherichia coli

The effects on the stringent control of ribosomal ribonculeic acid synthesis of the removal of cell wall, cold-shock treatment of cells, LiCl treatment of toluene-treated cells, and hypotonic treatment of spheroplasts were examined using Escherichia coli rel+ cells. Neither the removal of cell wall with penicillin or lysozyme nor the cold-shock treatment of the cells had an effect on the stringent control. The control mechanism, however, disappeared after the LiCl treatment of the toluene-treated cells, with the release of some protein component(s), possibly from the cytoplasmic membrane. The hypotonic and other treatments of spheroplasts, which disrupt the cytoplasmic membrane, also led to the abolishment of the control mechanism. These results suggested that the operation of the stringent control of ribosomal ribonucleic acid synthesis requires the cytoplasmic membrane, in which some proteins labile with LiCl treatment are embedded.

Coumerimycin A1: A preferential inhibitor of replicative DNA synthesis in Escherichia coli. II. In vivo characterization

In vitro inhibitions by coumermycin A1 of DNA and RNA synthesis in toluenized cells were studied. In a sensitive strain, 50% inhibitions of replication and transcription were observed at 0.035 and 0.600 mug/ml, respectively. DNA synthesis in a toluenized-resistant mutant was 50% inhibited at 0.140 mug/ml of coumermycin A1, whereas RNA synthesis was unaffected at all concentrations tested. Studies with a mixture of toluenized-sensitive and -resistant bacteria ruled out the presence of a diffusable activator or inhibitor of coumermycin A1 action. Density label studies with toluenized pol A+ and pol A- strains indicated that replicative DNA synthesis was specifically inhibited, in agreement with the in vivo studies in the preceding paper of this issue (Ryan, M. J. (1976), Biochemistry 15). Highly purified Escherichia coli DNA polymerase III and RNA polymerase both were inhibited by this antibiotic. However, the high concentrations necessary for these inhibitions suggest that they are not biologically relevant. No interaction between DNA and coumermycin A1 was observed with the following analytical procedures: ultraviolet difference spectra, DNA absorbance-temperature transitions, equilibrium buoyant density centrifugation, and DNA cross-linking determinations.

Ribonucleic acid synthesis dependent on exogenous triphosphates in nystatin-treated cells of of Kluyveromyces latis

Kluyveromyces lactis cells treated with nystatin became permeable to ribonucleoside triphosphates. Although not viable, nystatin-treated cells were capable of sustaining ribonucleic acid synthesis. The system depended on the presence of divalent ions and the four nucleoside triphosphates, and was strongly stimulated by ammonium sulfate. The system utilized endogenous deoxyribonucleic acid as template. Synthesis of ribonucleic acid was associated with the cells and probably occurred internally.

Puromycin-resistant biosynthesis of a specific outer-membrane lipoprotein of Escherichia coli

The reported puromycin resistance of the in vivo biosynthesis of a specific outer-membrane lipoprotein of Escherichia coli was further investigated. The biosynthetic machinery making the lipoprotein was made more accessible to puromycin by disruption of the cell structure using ethylenediaminetetracetate or toluene, and finally in an in vitro protein biosynthesis system using polyribosomes. Puromycin sensitivity of overall protein synthesis increased by about 10-fold for each method of disruption of the cell structure; 50% inhibitions were obtained at 330, 35, 2.7, and 0.22 mug of puromycin per ml for intact cells, ethylenediaminetetraacetate-treated cells, toluene-treated cells, and the polyribosome system, respectively. However, the lipoprotein biosynthesis remained more resistant to puromycin than the biosynthesis of other proteins in all systems tested. These results strongly suggest that puromycin resistance of the lipoprotein biosynthesis is due to an intrinsic property of the lipoprotein biosynthetic machinery.

Preparation of cells permeable to macromolecules by treatment with toluene: studies of transfer ribonucleic acid nucleotidyltransferase

Transfer ribonucleic acid (tRNA) nucleotidyltransferase was studied after making cells permeable to macromolecules by treatment with toluene. The conditions of toluene treatment necessary for obtaining maximal activity were defined. Toluene treatment was most efficient when carried out for 5 min at 37 C at pH 9.0 on log-phase cells. No activity could be detected if cells were treated at 0 C, or in the presence of MgCl(2), or if the cells were in the stationary phase of growth. However, inclusion of lysozyme and ethylenediaminetetraacetic acid during the toluene treatment did render stationary phase cells permeable. The properties of tRNA nucleotidyltransferase from toluene-treated cells were essentially identical to those of purified enzyme with regard to pH optimum, specificity for nucleoside triphosphates and tRNA, and apparent K(m) values for substrates. In addition to tRNA nucleotidyltransferase, a variety of other enzymes which incorporate adenosine 5'-triphosphate into acid-precipitable material could also be detected in toluene-treated cells. Centrifugation of cells treated with toluene revealed that tRNA nucleotidyltransferase leaked out of cells, whereas other activities remained associated with the cell pellets. Chromatography of the material extracted from toluene-treated cells on Sephadex G-100 indicated that toluene treatment selectively extracts lower molecular weight proteins. The usefulness of such a procedure as an initial step in purification of such enzymes, and its application to tRNA nucleotidyltransferase, is discussed.

Stimulation of unbalanced ribonucleic acid synthesis in Escherichia coli by methanol

Addition of methanol to a stringent strain of Escherichia coli, starving of methionine, stimulates unbalanced ribonucleic acid (RNA) synthesis. The newly formed RNA and ribonucleoprotein species sediment between 4S and 30S. As a result of methanol treatment, cells become permeable to actinomycin D. Damage to cellular membrane appears to influence the control for RNA synthesis.