Synthesis and turnover of ribosomal ribonucleic acid in guanine-starved cells of Escherichia coli

rRNA regulation during growth and under stringent conditions in Staphylococcus aureus

The control of rRNA synthesis and, thereby, translation is vital for adapting to changing environmental conditions. The decrease of rRNA is a common feature of the stringent response, which is elicited by the rapid synthesis of (p)ppGpp. Here we analysed the properties and regulation of one representative rRNA operon of Staphylococcus aureus under stringent conditions and during growth. The promoters, P1 and P2, are severely downregulated at low intracellular guanosine triphosphate (GTP) concentrations either imposed by stringent conditions or in a guanine auxotroph guaBA mutant. In a (p)ppGpp(0) strain, the GTP level increased under stringent conditions, and rRNA transcription was upregulated. The correlation of the intracellular GTP levels and rRNA promoter activity could be linked to GTP nucleotides in the initiation region of both promoters at positions between +1 and +4. This indicates that not only transcriptional initiation, but also the first steps of elongation, requires high concentrations of free nucleotides. However, the severe downregulation of rRNA in post-exponential growth phase is independent of (p)ppGpp, the composition of the initiation region and the intracellular nucleotide pool. In summary, rRNA transcription in S. aureus is only partially and presumably indirectly controlled by (p)ppGpp.

Invariance of the nucleoside triphosphate pools of Escherichia coli with growth rate

The ATP and GTP pools of Escherichia coli have recently been reported to increase approximately 10-fold with increasing growth rates in the range from 0.4 to 1.4 generations/hour (Gaal, T., Bartlett, M. S., Ross, W., Turnbough, C. L., and Gourse, R. L. (1997) Science 278, 2092-2097). Moreover, it was proposed that this variation of the nucleotide pools, particularly the ATP pool, might be responsible for the well known growth rate-dependent regulation of rRNA synthesis in E. coli. To test this hypothesis we have measured the nucleoside triphosphate pools as a function of growth rate for several E. coli strains. We found that the size of all four RNA precursor pools are essentially invariant with growth rate, in the range from 0.5 to 2.3 generations/hour. Nevertheless we observed the expected growth rate-dependent increase of RNA accumulation in these strains. In light of these results, it seems unlikely that nucleotide pool variations should be responsible for the growth rate-dependent regulation of rRNA synthesis.

Effect of purine and pyrimidine limitations on RNA synthesis in Bacillus subtilis

The effects of varying the intracellular levels of GTP or UTP on the rate of RNA synthesis in Bacillus subtilis were studied. The levels of these nucleotides were manipulated by pyrimidine limitation in a pyr auxotroph, by purine limitation in a pur auxotroph, or by the addition of decoyinine , which specifically inhibits GMP synthesis. Decreased levels of UTP and GTP were accompanied by dramatically decreased synthesis and accumulation of stable RNAs (tRNA and rRNA), but mRNA synthesis was less affected. However, sporulation was initiated only when the intracellular level of GTP decreased.

GTP pool expansion is necessary for the growth rate increase occurring in Bacillus subtilis after amino acids shift-up

After addition of amino acids to a Bacillus subtilis glucose culture the intracellular guanosine triphosphate (GTP) concentration increased. The growth rate and the rate of RNA accumulation increased too. With mycophenolic acid, an inhibitor of inosinate dehydrogenase, it was possible to adjust the intracellular GTP concentration to values ranging between that of the glucose culture and that of the culture which had received amino acids. This led to intermediate growth rate values. Guanosine abolished the mycophenolic acid inhibition of GTP synthesis. It also counteracted the drug effects on growth rate and RNA accumulation. In cultures growing on Nutrient Sporulation Medium, in which the growth rate decreases as cell density increases, the GTP concentration did correlate with the growth rate.

RNA synthesis and degradation during preferential inhibition of protein synthesis by cobalt chloride in Escherichia coli K-12

It has been observed that growth of Escherichia coli cells are inhibited when treated with cobalt chloride (300 microM). It has also been shown that CoCl2 preferentially inhibits translation without inhibiting the process of transcription (1, 2, 8). We report here, that during treatment of E. coli cells with CoCl2, both messenger RNA and stable RNA synthesis is slowed down about 2.5 folds. The rate of degradation of mRNA also decreases and both chemical and functional half-life of mRNA increases about 2.5 folds in Co-treated cells. This clearly shows that the process of transcription is also affected while translation is preferentially inhibited during CoCl2 treatment.

Ribonucleic acid synthesis during fruiting body formation in Myxococcus xanthus

A method has been devised that allowed us, for the first time, to pulse-label M. xanthus cells with precursors for ribonucleic acid biosynthesis while they were undergoing fruiting body formation. Using this method, we examined patterns of ribonucleic acid (RNA) accumulation throughout the process of fruiting body formation. As development proceeded, the rate of RNA accumulation increased at two periods of the developmental cycle: once just before aggregation and once late in the cycle, when sporulation was essentially completed. In contrast to vegetatively growing cells, in which only stable RNA species are labeled during a 30-min pulse, the majority of radioactivity found in RNA from 30-min pulse-labeled developing cells was found in an unstable heterodisperse fraction that migrated to the 5S to 16S region of sucrose density gradients and sodium dodecyl sulfate-polyacrylamide gels. This pattern of incorporation could not be induced (i) by a shift down of vegetatively growing cells to a nutritionally poor medium, in which the generation time was increased to that of developing cells during the growth phase, or (ii) by plating of vegetative cells onto the same solid-surface environment as that of developing cells, but which surface supported vegetative growth rather than fruiting body formation. Thus, the RNA synthesis pattern observed appeared to be related to development per se rather than to nutritional depletion or growth on a solid surface alone. The radioactivity incorporated into the unstable 5S to 16S RNA fraction accumulated as the pulse length was increased from 10 to 30 min; in contrast, an analogous unstable fraction from vegetative cells decreased as pulse length was increased. This suggested that developmental 5S to 16S RNA was more stable than vegetative cell 5S to 16S RNA (presumptive messenger RNA). However, during a 45-min chase period, radioactivity in 30-min-pulse-labeled developmental 5S to 16S RNA decayed to an extent twice that of developmental RNA located in 16S and 23S regions of sucrose density gradients and was considerably less stable than the 5S, 16S, and 23S RNA species labeled during a 30-min pulse of vegetative cells.

Noncoordinate control of the synthesis of different species of RNA in Escherichia coli K12 during uridine starvation

During uridine starvation in Escherichia coli K12, the rate of RNA accumulation comes down to about 7% of the nonstarved rate. This is achieved, in part, by an eight-fold increase in the assembly time of stable RNA molecules. However, the assembly time of mRNA molecules is not enhanced as much, being longer by a factor of 3 in starved cells compared to nonstarved ones. It, therefore, appears that the rate of synthesis of these two RNA species is noncoordinately controlled during uridine starvation. This control does not seem to be mediated by guanosine tetraphosphate.

Regulatory nucleotides involved in the Rel function of Bacillus subtilis

We have examined the accumulation of polyphosphorylated nucleotides in Bacillus subtilis in relation to the function of the rel gene. Our results are as follows. (i) During inhibition of isoleucine activation by O-methylthreonine, wildtype B. subtilis cells accumulate unusual nucleotides with the chromatographic and chemical properties of pppApp, ppApp, pppGpp, ppGpp, pGpp, and ppGp. (ii) During the carbon source downshift elicited by inhibiting glucose uptake, we observed accumulation of the polyphosphorylated guanosine but not adenosine nucleotides. (iii) At the end of long phase in sporulation medium, we observed a small transient accumulation of the polyphosphorylated guanosine but not adenosine nucleotides. (iv) We were unable to detect a nucleotide with chromatographic behavior expected for pppAppp under any conditions. (v) The rel mutant of Swanton and Edlin (Biochem. Biophys. Res. Commun. 46-583-588, 1972) did not accumulate any of these polyphosphorylated nucleotides under any of the conditions examined. (vi) the rel mutant is unimpaired in sporulation. We conclude that one or more of the nucleotides we have detected may be involved in controlling the specificity of transcription during the stringent response, but none of them are required for sporogenesis.

Enzyme induction in Streptomyces hydrogenas, VII. Short-term accumulation of guanosine polyphosphates

Cells of Streptomyces hydrogenans (ATCC 19631) synthesize guanosine 3'(2')-diphosphate 5'-triphosphate (pppGpp) and guanosine 3'(2')-diphosphate 5'-diphosphate (ppGpp). 10 to 20 min after addition of steroids to the culture medium, the amount of pppGpp and ppGpp increases 2- to 3-fold. At the same time, the cellular amount of both ATP and GTP has been found to increase. While "shift down" experiments arrest growth of the cells temporarily, steroids do not impair cell division of Streptomyces hydrogenans. It is suggested that ppGpp and pppGpp mediate the regulatory shut off of nucleic acid synthesis or control their increased turnover triggered by the steroids.