Ribonucleic Acid from Aerobically and Anaerobically Grown Rhodopseudomonas spheroides: Comparison by Hybridization to Chromosomal and Satellite Deoxyribonucleic Acid

Ribonucleic acid (RNA) species from aerobically and anaerobically grown Rhodopseudomonas spheroides were compared via hybridization to deoxyribonucleic acid (DNA). Both long-labeled and stable RNA bound to chromosomal DNA to the same extent, regardless of derivation. About 4% of the chromosomal DNA hybridized with total cell RNA and about 0.08% with stable RNA. About 4% of the mixed satellite DNA could be hybridized to total cell RNA from aerobic or anaerobic cultures, whereas essentially no stable RNA formed a hybrid with this DNA. Hybridization competition experiments with aerobic and anaerobic pulse-labeled RNA and chromosomal or satellite DNA demonstrated that no qualitative differences existed between the RNA species. It is concluded that identical species of RNA in the same relative amounts are synthesized by R. spheroides during aerobic or anaerobic growth on the same medium.     

Myxococcus xanthus synthesizes a stabilized messenger RNA during fruiting body formation

Initial characterization of the unstable 5S-to-16S RNA fraction from developingMyxococcus xanthus cells reveals that it is rapidly labeled with radioactive RNA precursor and is associated with polyribosomes and released by puromycin from polyribosomes. The total unstable RNA fraction from 10-min pulse-labeled developing cells has a half-life of 13 min, compared with a 4-min half-life for unstable RNA (presumptive mRNA) from vegetative cells pulse-labeled for 2 min. We conclude that this developmental 5S-to-16S RNA contains messenger RNA and that this mRNA is stabilized compared with that in vegetative cells.     

Regulation of Ribonucleic Acid Synthesis in Escherichia coli During Diauxie Lag: Accumulation of Heterogeneous Ribonucleic Acid

The synthesis of ribonucleic acid (RNA) and of protein in Escherichia coli during glucose-lactose diauxie lag have been examined. The rate of RNA synthesis is about 7%, of the corresponding rate during exponential growth and the rate of protein synthesis 10 to 15%. Inhibition of RNA synthesis occurs to the same extent in both rel and rel(+) strains. The RNA which accumulates during 20 min in diauxie lag is composed of about 50% ribosomal and transfer RNA species and about 50% of a fraction which resembles messenger RNA (mRNA) in its heterogeneous sedimentation properties. Decay of the heterogeneous fraction occurs in the presence of glucose and actinomycin D with a half-life of 3 min, the same as that of pulse-labeled mRNA; however, during the diauxie lag, the half-life of this RNA is about 25 min. Accumulation of the heterogeneous RNA is further increased when protein synthesis is blocked by chloramphenicol. The data suggest that the disproportionate accumulation of mRNA during diauxie lag and energy source shift-down may be attributed at least in part to increased stability of mRNA, but do not rule out a preferential synthesis of mRNA.     

Dynamics of denitrification activity of Paracoccus denitrificans in continuous culture during aerobic-anaerobic changes.

Induction and repression of denitrification activity were studied in a continuous culture of Paracoccus denitrificans during changes from aerobic to anaerobic growth conditions and vice versa. The denitrification activity of the cells was monitored by measuring the formation of denitrification products (nitrite, nitric oxide, nitrous oxide, and dinitrogen), individual mRNA levels for the nitrate, nitrite, and nitrous oxide reductases, and the concentration of the nitrite reductase enzyme with polyclonal antibodies against the cd1-type nitrite reductase. On a change from aerobic to anaerobic respiration, the culture entered an unstable transition phase during which the denitrification pathway became induced. The onset of this phase was formed by a 15- to 45-fold increase of the mRNA levels for the individual denitrification enzymes. All mRNAs accumulated during a short period, after which their overall concentration declined to reach a stable value slightly higher than that observed under aerobic steady-state conditions. Interestingly, the first mRNAs to be formed were those for nitrate and nitrous oxide reductase. The nitrite reductase mRNA appeared significantly later, suggesting different modes of regulation for the three genes. Unlike the mRNA levels, the level of the nitrite reductase protein increased slowly during the anaerobic period, reaching a stable value about 30 h after the switch. All denitrification intermediates could be observed transiently, but when the new anaerobic steady state was reached, dinitrogen was the main product. When the anaerobic cultures were switched back to aerobic respiration, denitrification of the cells stopped at once, although sufficient nitrite reductase was still present. We could observe that the mRNA levels for the individual denitrification enzymes decreased slightly to their aerobic, uninduced levels. The nitrite reductase protein was not actively degraded during the aerobic period.     

RNA Synthesis in Yersinia pestis During Growth Restriction in Calcium-Deficient Medium

Yersinia pestis requires 2.5 mM Ca(2+) for growth at 37 degrees C but not at 26 degrees C. After a shift from 26 to 37 degrees C in a Ca(2+)-deficient medium, an ordered series of metabolic alterations occur which result in transition from a growing cell to a viable but non-proliferating cell. The earliest known alteration in normal metabolism associated with this transition is a termination of net RNA synthesis. Competitive RNA/DNA hybridizations with uniformly labeled RNA and stable RNA competitor indicated identical mRNA to stable RNA ratios in growing cells and non-proliferating Ca(2+)-deprived cells. Similar hybridizations with pulse-labeled RNA demonstrated that growing cells synthesized 57% mRNA, 37% rRNA, and 5% tRNA, whereas Ca(2+)-deprived cells synthesized 95% mRNA, 4.7% rRNA, and 0.7% tRNA. After addition of radioactive uracil and rifampin to growing and Ca(2+)-deprived cells, decay of approximately 40 and 90% of the newly synthesized RNA was found for growing and Ca(2+)-deprived cells, respectively. The half-life of the mRNA was found to be 1.5 min for growing cells and 4.5 min for Ca(2+)-deprived cells. Y. pestis elicited increases in the levels of guanosine tetraphosphate and guanosine pentaphosphate in response to amino acid deprivation and yielded transient increases in the levels of these phosphorylated nucleotides after a shift from 26 to 37 degrees C. These increases were independent of Ca(2+) availability and preceded the alteration in RNA synthesis by more than 1 h. The levels of these phosphorylated nucleotides then stabilized at about 80 and 40 pmol for Ca(2+)-deprived and Ca(2+)-supplemented cultures, respectively, and did not increase further in the Ca(2+)-deprived culture at the time corresponding to the reduction in stable RNA synthesis. These findings indicate that the early lesion in RNA synthesis associated with the growth restriction of Ca(2+)-deprived Y. pestis reflects a block in stable RNA synthesis and that this effect is not mediated by guanosine tetraphosphate or guanosine pentaphosphate.     

Messenger Ribonucleic Acid Stability in Relaxed and Stringent Escherichia coli Starved for Methionine

During starvation for each of four amino acids, relaxed and stringent strains of Escherichia coli showed exponential decay of pulse-labeled unstable messenger ribonucleic acid (mRNA), with RNA degraded more slowly in the relaxed strain. An additional unique difference was observed during starvation for methionine: the relaxed strain showed non-exponential decay of mRNA, with a survival curve similar to that of an aging process.     

Changes in RNA in relation to growth of the fibroblast: II. The lifetime of mRNA,rRNA, and tRNA in resting and growing cells

The stabilities of the principal classes of RNA have been studied in resting and exponentially growing mouse fibroblast lines 3T6 and 3T3. Cytoplasmic mRNA, labeled with tritiated uridine and isolated by virtue of its poly A content, is equally stable in resting and growing cells, displaying a half-life of about 9 hr. We conclude that the accumulation of poly A(+) mRNA during transition from resting to growing state is due not to an increase in its stability, but to an increase in its rate of formation.The stability of cytoplasmic rRNA was measured after labeling with ³H-methyl-methionine. In agreement with the results of previous studies, we found that rRNA is stable in growing cells and unstable in resting cells. Quite unexpectedly, the 18S and 28S rRNA of resting cultures were found to differ appreciably in turnover rate. In both 3T6 and 3T3, the half-life of 28S RNA is about 50 hr, and that of 18S RNA about 72 hr. For this reason, though growing cells should synthesize the two ribosomal subunits in equal numbers, resting cells should synthesize more of the larger subunits than of the smaller. tRNA is unstable under all conditions. Its half-life is 36 hr in resting cells and about 60 hr in growing cells.     

Temperature-sensitive Yeast Mutant Defective in Ribonucleic Acid Production

A single, recessive mutation in a nuclear gene confers a temperature-sensitive growth response in a mutant of Saccharomyces cerevisiae, ts(-) 136. The mutant grows normally at 23 C, but exhibits a rapid and preferential inhibition of ribonucleic acid (RNA) accumulation after a shift to 36 C, demonstrating a defect in stable RNA production. Cultures of the mutant which were shifted from 23 to 36 C display the following phenomena which indicate that messenger RNA (mRNA), as well as stable RNA production, is defective. The entrance of pulse-labeled RNA into cytoplasmic polyribosomes is even more strongly inhibited than is net RNA accumulation. The rate of protein synthesis, at first unaffected, decreases slowly; this decrease is paralleled by the decay of polyribosomes to monoribosomes with a half-time of 23 min. The polyribosomes which remain after a 30-min preincubation of the mutant at 36 C are active in polypeptide synthesis in vivo, whereas the monoribosomes which accumulate are not. Furthermore, ribosomes isolated from a culture of the mutant preincubated for 1 hr at 36 C are inactive in polypeptide synthesis in vitro, but can be restored to full activity by the addition of polyuridylic acid as mRNA. We conclude that mutant ts(-) 136 is defective either in the synthesis of all types of cytoplasmic RNA, or in the transport of newly synthesized RNA from the nucleus to the cytoplasm, and that the mRNA of a eucaryotic organism (yeast) is metabolically unstable, having a half-life of approximately 23 min at 36 C.     

Selective Degradation of Newly Synthesized Nonmessenger Simian Virus 40 Transcripts

By pretreating simian virus 40-infected BSC-1 cells with glucosamine, [(3)H]uridine labeling of both cellular and viral RNA can be halted instantaneously by addition of cold uridine. We have studied the fate of pulse-labeled viral RNA from cells at 45 h postinfection under these conditions. During a 5-min period of labeling, both the messenger and nonmessenger regions of the late strand were transcribed. After various chase periods, nuclear viral species which sediment at 19, 17.5, and 16S were observed. Nuclear viral RNA decays in a multiphasic manner. Of the material present at the beginning of the chase period, 50% was degraded rapidly with a half-life of 8 min (initial processing). This rapidly degraded material was that fraction of the late strand which did not give rise to stable late mRNA species. Forty percent was transported to the cytoplasm, and 10% remained in the nucleus as material which sedimented in the 2 to 4S region. These 2 to 4S viral RNAs had a half-life of 3 h, and hybridization studies suggest that they are in part coded for by the late-strand nonmessenger region and are derived from the initial nuclear processing step. Another part is coded for by the late-strand messenger region and may be generated by some subsequent nuclear cleavages of 19S RNA into 17.5 and 16S RNAs. Transport of nuclear viral RNA into the cytoplasm was detected after a 5-min pulse and a 7-min chase. The maximum amount of labeled viral RNA was accumulated in the cytoplasm after a 30-min to 1-h chase. At least two viral cytoplasmic species were observed. Kinetic data suggest that 19S RNA is transported directly from the nucleus. Whether cytoplasmic 16S is formed by cleavage of 19S RNA in the cytoplasm is not clear. The half-lives of cytoplasmic 19 and 16S RNAs can be approximated as 2 and 5 h, respectively.     

Control of dimorphism in Mucor rouxii

Haidle, C. W. (The University of Texas, Austin), and R. Storck. Control of dimorphism in Mucor rouxii. J. Bacteriol. 92:1236-1244. 1966.-Yeastlike cells of Mucor rouxii NRRL 1894 were converted to filaments in a medium containing glucose, mineral salts, casein hydrolysate, nicotinic acid, and thiamine when the gas phase was changed from CO(2)-N(2) or N(2) alone to air. Germ tubes began to appear 3 to 4 hr after exposure to air. Ribonucleic acid (RNA) precursors were incorporated into RNA in a discontinuous fashion during this conversion, but the incorporation was continuous during the anaerobic growth of yeastlike cells and during the aerobic germination of sporangiospores. The incorporation of labeled amino acids during the conversion was exponential. Labeling of ribosomal RNA occurred as shortly as 5 min after replacement of CO(2)-N(2) with air. However, P(32)-labeled RNA isolated 20 min after exposure to air had a guanine plus cytosine (GC) content of 41% (mole%) as compared with the 47% found for labeled and unlabeled RNA isolated at other stages of the life cycle of this organism or later during the conversion. In addition, the overall base composition of this 20-min pulse-labeled RNA resembled that of deoxyribonucleic acid (GC = 39%), suggesting that a significant proportion of this RNA is of the messenger type. Furthermore, the synthesis of cytochrome oxidase was induced upon exposure of yeastlike cells to air. Cyanide, acriflavine, and cycloheximide, which inhibited the action or synthesis of cytochrome oxidase, also inhibited the yeast to filament transition.     

Division Cycle of Myxococcus xanthus II. Kinetics of Stable and Unstable Ribonucleic Acid Synthesis

The kinetics of stable and unstable ribonucleic acid (RNA) synthesis during the division cycle of Myxococcus xanthus growing in a defined medium was determined. Under these conditions, M. xanthus contains one chromosome which is replicated during 80% of the cell cycle. Stable RNA synthesis was measured by pulselabeling an exponential-phase culture with radioactive uridine and then preparing the cells for quantitative autoradiography. By measuring the size of individual cells as well as the number of grains, the rate of stable RNA synthesis as a function of cell size was determined. Unstable RNA synthesis during the division cycle was determined by correlating the data for stable RNA synthesis with the relative amounts of stable and unstable RNA labeled during the short pulse. The data reported here demonstrate that: (i) cells synthesize both stable and unstable RNA throughout the division cycle; (ii) the rate of stable RNA synthesis increases in two discrete steps, corresponding to average ages of 0.15 and 0.75 generations; (iii) the rate of unstable RNA synthesis exhibits an initial rise, followed by a relatively constant rate of synthesis, and finally, a burst of unstable RNA synthesis prior to septum formation. The half-life of unstable RNA of M. xanthus, generation time of 390 min at 30 C, was 4 min. Comparison of the rates of stable and unstable RNA synthesis indicates noncoordinate RNA synthesis within the normal division cycle.     

Anaerobic and aerobic biodegradation of chlorophenols using UASB and ASG bioreactors

Chlorophenol degradation was studied by combined anaerobic–aerobic treatments as a single or multi-substrate system. 2,4-Dichlorophenol (2,4-DCP) was degraded to the extent of 52 and 78% in up-flow anaerobic sludge blanket (UASB) and aerobic suspended growth (ASG) reactors respectively, at organic loading rates of 0.18kg/m³/day and hydraulic retention time of 26.4h in the presence of glucose. The UASB represents the dominating facultative anaerobic microbial population. When the effluent from the anaerobic reactor (UASB) was subjected to aerobic treatment on the ASG reactor, 2,4-DCP and COD removals of 86 and 95% respectively were achieved. Aerobic degradation of chlorophenol by acclimated mixed bacterial isolates was found to be sequential: 2-Chlorophenol (2-CP) and 4-CP were degraded first, followed by 2,4-DCP and 2,4,6-Trichlorophenol (2,4,6-TCP) while the contrary was obtained in anaerobic degradation. In anaerobic degradation by acclimated mixed bacterial cells, 2,4-DCP and 2,4,6-TCP were degraded first followed by mono-chlorophenols. The anaerobic/aerobic bioreactors were most efficient when operated in sequence (series) rather than in parallel.     

Synthesis and turnover of hdRNA and mRNA in the salivary gland of the blowfly Calliphora erythrocephala.

We have measured the absolute molar rates of synthesis, accumulation, and turnover of blowfly salivary gland heterodisperse RNA. Twelve- and 84-hr-stage third-instar Calliphora erythrocephala larvae were injected with [³H]adenosine, and its flow into glandular ATP, heterodisperse RNA, and polyadenylated RNA was each quantitated over a 360-min time course. The results of these experiments indicate that at least 80% of the newly synthesized heterodisperse RNA mass is a >28 S nuclear species whose average first-order half-life is approximately 20 min. The remaining 20% of the heterodisperse RNA has a 6–28 S size distribution, accumulates in the cytoplasm, and is associated with functional polysomes. The average first-order half-life of this more stable species is 20–25 hr. In addition, we have independently quantitated by optical methods the developmental change in the content of polysome-associated mRNA. The mRNA in these studies also has an average first-order half-life of 25 hr and accounts for 25–55% of the mRNA mass predicted by the incorporation-kinetic analysis of the pulse-labeled heterodisperse RNA. Despite the increased polyteny of the older stage glands, the rates of synthesis and accumulation of each of the individual heterodisperse RNA classes are the same at the 12- and 84-hr stages. Collectively, these results demonstrate that salivary gland functional specialization results from the accumulation of long-lived mRNA and not from changes in the overall rate of mRNA synthesis.     

Determination of synthesis rate and lifetime of bacterial mRNAs

A method has been developed to determine the synthesis rate and lifetime of bacterial mRNAs, either bulk mRNA or specific mRNAs, with a minimum of physiological disturbance. The method uses hybridization of pulse-labeled RNA to specific probes followed by an evaluation based on a computer simulation of the labeling kinetics of different classes of RNA. The method was applied to the determination of bulk mRNA in Escherichia coli growing in glucose minimal medium: 60% of the instantaneous rate of RNA synthesis, or 2.3% of the total amount of RNA, was found to be mRNA with an average lifetime of 1.0 +/- 0.2 min (= 0.7 min half-life).     

Concentrations of 4.5S RNA and Ffh protein in Escherichia coli: the stability of Ffh protein is dependent on the concentration of 4.5S RNA.

We measured the concentrations of both 4.5S RNA and Ffh protein under a variety of growth conditions and found that there were 400 molecules of 4.5S RNA per 10,000 ribosomes in wild-type cells and that the concentration of Ffh protein was one-fourth of that. This difference in concentration is 1 order of magnitude less than that previously reported but still significant. Pulse-chase labeling experiments indicated that Ffh protein is unstable in cells carrying ffh on high-copy-number plasmids and that simultaneous overproduction of 4.5S RNA stabilizes Ffh protein. Our analyses show that free Ffh protein is degraded with a half-life of approximately 20 min. We also tested whether three previously isolated suppressors of 4.5S RNA deficiency could reduce the requirement for Ffh protein. Since the two sffE suppressors do not suppress the Ffh requirement, we suggest that 4.5S RNA either acts in a sequential reaction with Ffh or has two functions.     

Biodegradation of RDX in Unsaturated Soil

Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a military explosive that is a common soil and groundwater contaminant at facilities that manufacture, handle, and dispose of munitions. One such facility is the U.S. Department of Energy Pantex Plant, the focus of this research in which the feasibility of in situ bioremediation of contaminated soil in the vadose zone was assessed. A batch technique using ¹⁴C-RDX was developed to investigate the degradation of RDX under aerobic, microaerobic, and anaerobic conditions. In addition, the effect of nutrients (organic carbon and phosphorus) on biodegradation rates was studied. The extent of mineralization was quantified by monitoring the production of ¹⁴CO₂, and RDX biodegradation rates were estimated for each environmental condition. The results showed that RDX degraders were indigenous to the contaminated soil and degraded RDX to a significant extent under anaerobic conditions. Little biotransformation was observed under aerobic conditions. The addition of a biodegradable organic carbon source significantly increased the RDX biodegradation rate. Under appropriate environmental conditions, significant mineralization of RDX also was observed. The half-lives for the degradation of RDX under anaerobic conditions were approximately 60 days and decreased to approximately 40 days with nutrient addition. In contrast, the half-life for aerobic degradation was on the order of 1000 days, with an upper 95% confidence interval approaching infinity.