Precursor Ribosomal Ribonucleic Acid and Ribosome Accumulation In Vivo During the Recovery of Salmonella typhimurium from Thermal Injury

When cells of S. typhimurium were heated at 48 C for 30 min in phosphate buffer (pH 6.0), they became sensitive to Levine Eosin Methylene Blue Agar containing 2% NaCl (EMB-NaCl). The inoculation of injured cells into fresh growth medium supported the return of their normal tolerance to EMB-NaCl within 6 hr. The fractionation of ribosomal ribonucleic acid (rRNA) from unheated and heat-injured cells by polyacrylamide gel electrophoresis demonstrated that after injury the 16S RNA species was totally degraded and the 23S RNA was partially degraded. Sucrose gradient analysis demonstrated that after injury the 30S ribosomal subunit was totally destroyed and the sedimentation coefficient of the 50S particle was decreased to 47S. During the recovery of cells from thermal injury, four species of rRNA accumulated which were demonstrated to have the following sedimentation coefficients: 16, 17, 23, and 24S. Under identical recovery conditions, 22, 26, and 28S precursors of the 30S ribosomal subunit and 31 and 48S precursors of the 50S ribosomal subunit accumulated along with both the 30 and 50S mature particles. The addition of chloramphenicol to the recovery medium inhibited both the maturation of 17S RNA and the production of mature 30S ribosomal subunits, but permitted the accumulation of a single 22S precursor particle. Chloramphenicol did not affect either the maturation of 24S RNA or the mechanism of formation of 50S ribosomal subunits during recovery. Very little old ribosomal protein was associated with the new rRNA synthesized during recovery. New ribosomal proteins were synthesized during recovery and they were found associated with the new rRNA in ribosomal particles. The rate-limiting step in the recovery of S. typhimurium from thermal injury was in the maturation of the newly synthesized rRNA.     

Physiological Studies on the Recovery of Salt Tolerance by Staphylococcus aureus After Sublethal Heating

Cultures of S. aureus in 100 mM potassium phosphate buffer heated at 52 C for 15 min lost their tolerance to 7.5% NaCl. After incubation in a complex growth medium or in a diluted dialyzed medium in which unheated cells were unable to grow, salt tolerance was regained. Heat injury caused 30% loss of lipid. During recovery, the concentration of C(15) and C(17) fatty acids returned to normal, and there appeared to be an oversynthesis of C(16) and C(18) unsaturated acids. Penicillin abolished the latter reaction without affecting recovery; chloramphenicol did not affect fatty acid oversynthesis but reduced recovery. The K/Na ratio was 12.6 in control cells and 3.4 in injured cells, where it remained during the recovery of salt tolerance. Aspartate uptake was about 10% of the control level after injury and about 35% at recovery. Control cells grew without a lag on subculture, but injured cells which had regained their salt tolerance needed about 2 more h of incubation. Cells recovering with penicillin needed 6 more h, and cells recovering with chloramphenicol did not grow without a prolonged lag. Cells of S. aureus, therefore, may recover their salt tolerance while various membrane functions are still damaged.     

Ribosome Synthesis in Thermally Shocked Cells of Staphylococcus aureus

Thermally shocked cells of Staphylococcus aureus rapidly synthesized ribonucleic acid (RNA) during the early stages of recovery. During this period, protein synthesis was not observed and occurred only after RNA had reached a maximum level. Even in the absence of coordinated protein synthesis, a large portion of the RNA appeared in newly synthesized ribosomes. Although the 30S subunit was specifically destroyed by the heating process, both ribosomal particles were reassembled during recovery. The addition of chloramphenicol did not inhibit the formation of the ribosomal subunits, nor was the presence of immature chloramphenicol particles detected. Extended recovery with highly prelabeled cells showed that the original ribosomal proteins present before heating are conserved and recycled. Furthermore, the data indicate that the 50S subunit is turned over and used as a source of protein for new ribosome assembly. Kinetic studies of the assembly process by pulse labeling have not revealed the presence of the normally reported precursor particles. Rather, the data suggest that assembly may occur, in this system, in a manner similar to that reported for in vitro assembly of Escherichia coli subunits.     

On the interpretation of small-angle x-ray solution scattering from spherical viruses.

The intermediates in the ribosome assembly in exponentially growing Escherichia coli have been identified by centrifuging a crude lysate, pulse-labeled with a radioactive RNA base, through a sucrose gradient and analyzing for precursor rRNA in the gradient fractions by gel electrophoresis. The major intermediate in the assembly of the 50 S subunit cosediments with the mature subunit, whereas two minor precursor species sediment between the 30 S and 50 S peaks. The assembly of the 30 S subunit proceeds via a minor intermediate sedimenting slightly behind the mature subunit and a major precursor particle that cosediments with the mature 30 S subunit.The fraction of the rRNA contained in these precursor particles was determined by direct determination of the amount of rRNA in the precursor particles, and from the labeling kinetics of their rRNA. The direct estimation indicated that about 2% of the total 23 S type RNA, and 3 to 5% of the total 16 S type RNA is harboured in precursor particles. In the kinetic experiments the specific activity of the nucleoside triphosphates and of the different ribosomal particles was followed after addition of a radioactive RNA precursor to the growth medium. The results were compared with a digital simulation of the flow of isotopes through the assembly pathways. This method indicated that approximately 2% of the total 23 S type RNA, as well as 2% of the total 16 S type RNA, is contained in the precursor particles.     

Putrescine-mediated Degradation of Ribonucleic Acid in Chloramphenicol-treated Escherichia coli

Escherichia coli treated with chloramphenicol (CM) accumulated ribonucleic acid (RNA) in the absence of protein synthesis. The accumulated RNA (CM-RNA) was largely ribosomal (23S and 16S) and soluble (4S). The stability of CM-RNA depended upon the incubation conditions following the removal of CM. Thus, conditions which allowed the complete recovery of cultures from CM inhibition resulted in only a 30% loss of CM-RNA. The addition of proflavine to recovering cultures, which prevented further RNA synthesis, also resulted in about 30 to 35% degradation of CM-RNA. However, when RNA synthesis was inhibited by starving the recovering cultures for the required amino acid, histidine, 55% of the CM-RNA was degraded. The decreased stability of CM-RNA in histidine-starved cultures appeared to be due specifically to the intracellular buildup of putrescine. Under the above conditions of incubation, that RNA which was stable sedimented in sucrose gradients as 23S, 16S, and 4S RNA. It is suggested that intracellular putrescine plays a role in the stability of ribosomal RNA accumulated during CM treatment.     

Ribosome assembly during recovery of heat-injured Staphylococcus aureus cells.

The process of ribosome formation during repair of sublethal heat injury was examined in Staphylococcus aureus. Sublethal heating of this organism results in the degradation of the 30S ribosomal subunit and alteration of the 50S subunit. Cells recovering from sublethal injury were examined for changes with time in the sedimentation and electrophoretic properties of ribonucleoprotein particles and ribonucleic acid, respectively. When cells were allowed to recover in [3H]uridine, the label could be followed into ribonucleic acid species that coelectrophoresed with 23S and 16S ribonucleic acid. Three ribonucleoprotein particles (49S, 36S, and 30S) were isolated from repairing cells by sedimentation through sucrose gradients. Polyacrylamide gel electrophoresis showed that the 49S particle contained 23S ribonucleic acid, the 36S particle contained both 23S ribonucleic acid and 16S precursor and mature ribonucleic acid, and the 30S particle contained 16S and precursor 16S ribonucleic acid. Particles with similar sedimentation properties were found in unheated cells.     

Characterization of Mild Thermal Stress in Pseudomonas fluorescens and Its Repair

The exposure of exponentially growing Pseudomonas fluorescens P7 cells to heating at 36 C for 2 h in a defined medium, followed by cooling to 25 C and further incubation at this, the optimal growth temperature, resulted in the apparent death of approximately 99% of the cells, as determined by their inability to form colonies on Trypticase soy agar. Continued incubation at 25 C resulted in an extremely rapid increase in the Trypticase soy agar count, demonstrating that the phenomenon observed was not death but rather injury. Presumptive evidence of heat-stimulated ribonucleic acid (RNA) degradation and membrane damage was provided by the observed loss of 260-nm absorbing materials. Confirmation of RNA degradation was obtained by colorimetric analysis. Ribosomal RNA from normal and injured cells, which was electrophoretically separated on polyacrylamide gels, revealed that the 23S and 16S species were only partially destroyed. Inhibitor studies demonstrated, however, that RNA synthesis was necessary for recovery. The unusual accumulation of 17S RNA during recovery pointed to the presence of a heat-induced lesion in the RNA maturation process. A thermally induced membrane lesion is also discussed.     

Sublethal heat stress of Vibrio parahaemolyticus.

When Vibrio parahaemolyticsu ATCC 17802 was heated at 41 degrees C for 30 min in 100 mM phosphate-3% NaCl buffer (pH 7.0), the plate counts obtained when using Trypticase soy agar containing 0.25% added NaCl (0.25 TSAS) were nearly 99.9% higher than plate counts using Trypticase soy agar containing 5.5% added NaCl (5.5 TSAS). A similar result was obtained when cells of V. parahaemolyticus were grown in a glucose salts medium (GSM) and heated at 45 degrees C. The injured cells recovered salt tolerance within 3 h when placed in either 2.5 TSBS or GSM at 30 degrees C. The addition of chloramphenicol, actinomycin D, or nalidixic acid to 2.5 TSBS during recovery of cells grown in 2.5 TSBS indicated that recovery was dependent upon protein, ribonucleic acid (RNA, and deoxyribonucleic acid (DNA) synthesis. Penicillin did not inhibit the recovery process. Heat-injured, GSM-grown cells required RNA synthesis but not DNA synthesis during recovery in GSM. Chemical analyses showed that total cellular RNA decreased and total cellular DNA remained constant during heat injury. The addition of [6-3H]uracil, L-[U-14C]leucine, and [methyl-3H]thymidine to the recovery media confirmed the results of the antibiotic experiments.     

Subribosomal particle analysis reveals the stages of bacterial ribosome assembly at which rRNA nucleotides are modified

Modified nucleosides of ribosomal RNA are synthesized during ribosome assembly. In bacteria, each modification is made by a specialized enzyme. In vitro studies have shown that some enzymes need the presence of ribosomal proteins while other enzymes can modify only protein-free rRNA. We have analyzed the addition of modified nucleosides to rRNA during ribosome assembly. Accumulation of incompletely assembled ribosomal particles (25S, 35S, and 45S) was induced by chloramphenicol or erythromycin in an exponentially growing Escherichia coli culture. Incompletely assembled ribosomal particles were isolated from drug-treated and free 30S and 50S subunits and mature 70S ribosomes from untreated cells. Nucleosides of 16S and 23S rRNA were prepared and analyzed by reverse-phase, high-performance liquid chromatography (HPLC). Pseudouridines were identified by the chemical modification/primer extension method. Based on the results, the rRNA modifications were divided into three major groups: early, intermediate, and late assembly specific modifications. Seven out of 11 modified nucleosides of 16S rRNA were late assembly specific. In contrast, 16 out of 25 modified nucleosides of 23S rRNA were made during early steps of ribosome assembly. Free subunits of exponentially growing bacteria contain undermodified rRNA, indicating that a specific set of modifications is synthesized during very late steps of ribosome subunit assembly.     

Ribosomal proteins: XLIII. In vivo assembly of Escherichia coli ribosomal proteins

Isolation of ribosomal precursors from Escherichia coli K12 is described. The RNA and protein content of the precursor particles was determined.One physiologically stable precursor was found for the 30 S subunit. The assembly scheme is as follows: p16 S RNA + 9 proteins → p30 S (“21 S” precursor) p30 S + 12 proteins → 30 S subunit where p is precursor.Each of the two precursors for the 50 S subunit, P₁50 S and p₂50 S (“32 S” and “43 S” precursors, respectively), contains p5 S + p23 S RNA's in a 1:1 molar ratio. The assembly scheme is as follows: p23 S RNA + p5 S RNA + 16 or 17 proteins → p₁50 S

In contrast to the p₂50 S precursor the p₁50 S precursor is not similar to any core particles, which were obtained by treating 50 S subunits with different concentrations of LiCl or CsCl.The precursors p30 S and p₂50 S can be converted into active 30 S and 50 S sub-units, respectively, by incubation at 42 °C in the presence of ribosomal proteins and under RNA methylating conditions.     

ULTRASTRUCTURAL AND BIOCHEMICAL STUDIES ON THE PRECURSOR RIBOSOMAL PARTICLES ISOLATED FROM RAT LIVER NUCLEOLI

Sucrose density gradient analyses of pH 5.5 and pH 7.4 extracts from rat liver nucleoli revealed the presence of two broad peaks of approximately 60S and 80S, and 60S and 80–100S, respectively. Ribonucleoprotein (RNP) particles containing precursor ribosomal RNA in these peaks have been characterized by electron microscopy and RNA analyses. Spherical particles only were found in the 60S peak of the pH 5.5 extract, from which 28S RNA and smaller RNA (23S and 18S RNA) exclusively were extracted. In the broad 80S peak of the pH 5.5 extract, about 60% of the particles were spherical while 30% were rodlike. In the RNA species present there were 28S plus smaller RNA (80%) and 35S RNA (20%). The 60Speak of the pH 7.4 extract contained mainly spherical particles (84%), and the RNA species present was mostly 28S plus smaller RNA (89%). In addition to spherical particles (43%), a number of rodlike (31%) and filamentous molecules (26%) were observed in the heavier side of the 80–100S peak of the pH 7.4 extract, from which 45S (14%), 35S (26%), and 28S and smaller RNA (60%) were extracted. Thus the precursor ribosomal particles containing 45S RNA and 35S RNA appear to be filamentous and rodlike molecules, respectively. Folding of loose ribonucleoprotein filaments into compact, spherical, large subparticles may be part of the maturation process of ribosomal large subparticles, in addition to the so-called sequential cleavage of RNA.     

The composition of an unusual precursor of 50 S ribosomes in a mutant of Escherichia coli.

Escherichia coli strain 15--28 is a mutant which during exponential growth contains large amounts of a '47S' ribonucleoprotein precursor to 50S ribosomes. The '47S particles' are more sensitive to ribonuclease than are 50S ribosomes. The 23 S RNA of 47S particles may be slightly undermethylated, but cannot be distinguished from the 23S RNA of 50S ribosomes by sedimentation or electrophoresis. Isolated particles have 10--15% less protein than do 50S ribosomes; proteins L16, L28 and L33 are absent. Comparison with precursor particles studied by other workers in wild-type strains of E. coli suggests that the assembly of 50S ribosomes in strain 15--28 is atypical.     

Effect of low doses of chloramphenicol on ribosomal precursor formation in E. coli cells]

RNA synthesized in the cells of E. coli CP 78 (rel+) in the presence of chloramphenicol low concentrations (5 microgram/ml) was found in 30S and 50S subunits and monosomes. A significant part of it was alotted to ribonucleoproteid or chloramphenicol particles. The protein content of ribonucleoproteid amounted to 22-25% and the content of RNA in it was equal to 78-75%.     

Stability of ribosomal and transfer ribonucleic acid in Escherichia coli B/r after treatment with ethylenedinitrilotetraacetic acid and rifampicin.

A short treatment with ethylenedinitrilotetraacetic acid to permeabilize bacteria for various antibiotics or treatment with the ribonucleic acid (RNA) synthesis inhibitor rifampin causes a slow degradation of 50S and 30S ribosomal particles and of the corresponding 23S and 16S ribosomal RNA species (about 25 percent in 1 h). The effects are additive such that the decay is about 50 percent/h if rifampin is employed after permeabilization by ethylenedinitrilotetraacetic acid. The 5S ribosomal RNA and transfer RNA are essentially stable under these conditions.     

Comparative studies of the effects of galactosamine and actinomycin D on nuclear ribonucleoprotein particles from rat liver

Nuclear ribonucleoprotein particles of 75S were obtained from rat liver nuclei after mild sonication and isotonic salt extraction only when the preparation was carried out in the presence of a cytosolic ribonuclease inhibitor. Particles of 38S were isolated in the absence of inhibitor. The 38S nuclear ribonucleoprotein (nRNP) particles showed a protein/RNA ratio of 8, and a buoyant density of 1.39 g/ml in cesium chloride solution. They were further characterized by the pattern of their proteins on sodium dodecylsulfate (SDS)-acrylamide gel electrophoresis. Incorporation of [³H]cytidine into nuclear RNA was reduced to approx. 20% of controls 3 and 6 h after administration of galactosamine or actinomycin D. However, when [³H]cytidine was administered 30 min prior to the drugs a decrease of radioactivity in 38S nRNP particles to 43 and 81% of controls was found after 3 h. The yield of 38S particles 3 h after galactosamine or actinomycin D dropped to 41% and 78% of controls, and after 6 h to 43 and 70%, respectively. Six hours after galactosamine or actinomycin D treatment, the protein to RNA ratio increased to 13.3 and 9.1. No significant changes in protein patterns 3 h after treatment with galactosamine or actinomycin D were observed. Possible mechanisms, such as impaired transport of 38S nRNP particles after actinomycin D treatment or increased loss of particles due to a defective nuclear membrane after galactosamine administration are discussed.     

Accumulation of 70S Monoribosomes in Escherichia coli After Energy Source Shift-Down

When Escherichia coli is shifted from glucose-minimal to succinate-minimal medium, a transient inhibition of protein synthesis and a time-dependent redistribution of ribosomes from polysomes to 70S monosomes occurs. These processes are reversed by a shift-up with glucose. In a lysate made from a mixture of log-phase and down-shifted cells, the 70S monosomes are derived solely from the down-shifted cells and are therefore not produced by polysome breakage during preparation. This conclusion is supported by the absence of nascent proteins from the 70S peak. The monosomes are not dissociated by NaCl or by a crude ribosome dissociation factor, so they behave as "complexed" rather than "free" particles. When down-shifted cells are incubated with rifampin to block ribonucleic acid (RNA) synthesis, the 70S monosomes disappear with a half-life of 15 min. When glucose is also added this half-life decreases to 3 min. The 70S particles are stable in the presence of rifampin when chloramphenicol is added to block protein synthesis. We interpret these data to mean that the existence of the 70S monosomes depends on the continued synthesis of messenger RNA and their conversion to free ribosomes (which dissociate under our conditions) is a result of their participation in protein synthesis. Finally, a significant fraction of the RNA labeled during a brief pulse of (3)H-uracil is found associated with the 70S peak. These results are consistent with the hypothesis that the 70S monosomes are initiation complexes of single ribosomes and messenger RNA, which do not initiate polypeptide synthesis during a shift-down.