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.     

Synthesis and function of ribonucleic acid polymerase and ribosomes in Escherichia coli B/r after a nutritional shift-up.

The syntheses of stable ribosomal ribonucleic acid (RNA) and transfer RNA in bacteria depend on the concentration and activity of RNA polymerase and on the fraction of active RNA polymerase synthesizing stable RNA. These parameters were measured in Escherichia coli B/r after a nutritional shift-up from succinate-minimal to glucose-amino acids medium and were found to change in complex patterns during a 1- to 2-h period after the shift-up before reaching a final steady-state level characteristic for the postshift growth medium. The combined effect of these changes was an immediate, one-step increase in the exponential rate of stable RNA synthesis and thus of ribosome synthesis. This suggests that the distribution of transcribing RNA polymerase over ribosomal and nonribosomal genes and the polymerase activity are continuously adjusted during postshift growth to some growth-limiting reaction whose rate increases exponentially. It is proposed that this reaction is the production of amino-acylated transfer RNA and that is exponentially increasing rate results in part from a gradually increasing concentration of aminoacyl transfer RNA synthetases after a shift-up. This idea was tested and is supported by a computer simulation of a nutritional shift-up.     

Synthesis of individual ribosomal proteins in Escherichia coli B/r

The differential synthesis rates of individual ribosomal proteins (r-proteins) were measured in Escherichia coli B/r during the transition period following a nutritional shift-up from succinate minimal to glucose/ammo acids medium. These rates were observed to respond sequentially to the shift-up; the differential synthesis rate of protein L28 begins to increase within 0.1 of a minute following the shift-up, while the protein L29 synthesis rate begins to increase only after a lag of 2.5 minutes. The onset of induction of the remaining r-proteins occurs within this 2.5-minute interval. Furthermore, there was a twofold variation in the acceleration of the differential synthesis rates of individual r-proteins. Within the initial two to ten-minute period following the shift-up the differential synthesis rates of most r-proteins reached values ranging from 2.2 to 3.0-fold higher than the pre-shift rates, before declining to the post-shift steady-state values. It is suggested that the increases in the differential synthesis rates of r-proteins result in part from increases in the translational efficiency of messenger RNA in the post-shift growth medium and in part from increases in the amount of r-protein mRNA that is present.     

Macromolecular synthesis after a nutritional shift-up of Bacillus subtilis

Summary Effects of amino acids on macromolecular synthesis in Bacillus subtilis were studied. Two mutants, CRK4001 and NIG45, that were selected as slow growers in rich media were proved to be useful to analyse early events occurring after addition of amino acids to exponentially growing cells in a glucose-salts medium (nutritional shift-up). In a wild type strain, the rate of stable RNA (sRNA: essentially ribosomal RNA) synthesis increased 2.3 fold shortly after the shift-up to the rate characteristic of the post-shift steady state growth. In contrast, sRNA synthesis in the mutant strains responded to the shift-up in two steps. Thus, shortly after the shift the rate of sRNA synthesis increased 2.2 fold as in the wild type, but this increased level was maintained temporarily for 60 min and suddenly decreased to the post-shift steady state rate (1.4 fold increase). On the other hand, rates of DNA synthesis increased some 30 min after the shift directly to the post-shift steady state rates in all strains. Ratios of an origin to a terminus marker (purA/metB) began to increase exponentially to reach maximum values at 60 min after the shift, indicating that initiation of DNA replication occurred at frequencies characteristic of respective post-shift growth rates soon after the shift. These results revealed that the initial increase in the rate of sRNA synthesis and the frequency of initiation of DNA replication after nutritional shift are not related to each other and are independently affected by amino acids. In concert with these findings, the increase in sRNA synthesis was not affected by inhibition of DNA synthesis for the first 60 min after the shift, while it was completely prevented by puromycin and chloramphenicol. Protein synthesis for 10 min after the shift was sufficient to fully change the sRNA synthesis rate by amino acids.     

Levels of the ribonucleoside triphosphates and rate of RNA synthesis in Neurospora crassa.

The levels of the four ribonucleoside triphosphate (ATP, GTP, UTP and CTP) have been determined in Neurospora crassa in three conditions of exponential growth (on glucose, acetate and glycerol) as well as in the course of a shift-up and a shift-down transition of growth between two of them. Although in some cases the pools appear proportional to the rate of synthesis of ribosomal RNA, this seems not to be strictly dependent on the level of the nucleotides.     

Reversion of Ribosomal Helix Formation in Escherichia coli

After transfer into fresh medium, Escherichia coli cells containing ribosomal helices resume growth without a lag period. The helices disappear within 15 min after transfer, the number of 70S ribosomes decreases, and a steady-state ribosomal profile appears within one cell generation time. Subunits isolated from the helices support in vitro protein synthesis, but efficiency is optimal only when supplemented with an undetermined factor that is contained in the S-100 fraction of log-phase cells. The data suggest a possible role of helices as ribosomal reserve units.     

The role of osmotic effects in haloadaptation of Vibrio costicola

Growth rates of Vibrio costicola showed a broad optimum between 0.8 and 1.5 M-NaCl, and there was no growth above 3.3 M-NaCl in a peptone-based medium. The minimum requirement of 0.5 M-NaCl for growth in NaCl alone was reduced to 0.3 M-NaCl when the total solute concentration was raised to 0.5 to 1.0 M equivalent with sucrose or glycerol. Compared with equivalent NaCl concentrations, higher concentrations of sucrose were more inhibitory to growth, whereas glycerol had less effect. Increasing the medium NaCl concentration suddenly by 2- or 3-fold with either a constant starting, or final, salt concentration showed that, after the shift-up, the lag in growth, the rate of growth, and the inhibition of phospholipid synthesis depended both on the final NaCl concentration and the magnitude of the shift in salinity. The time-courses of phospholipid synthesis following a 2- or 3-fold shift-up in NaCl or sucrose media were very similar and exhibited a relative increase in phosphatidylglycerol synthesis over that of phosphatidylethanolamine. This 'switch-over' was not seen following shift-up in glycerol media when there was also a stimulation, rather than inhibition, of phospholipid synthesis. It is concluded that during phenotypic haloadaptation of V. costicola, osmotic effects play a significant part in the sensing of and response to raised external salinity.     

Regulation of ribonucleic acid synthesis in Escherichia coli B-r: an analysis of a shift-up. 1. Ribosomal RNA chain growth rates

The chain growth rate for ribosomal RNA was determined for Escherichia coli$\text{B}\text{r}$ growing in succinate (μ = 0.69 doublings/h), glucose (μ = 1.36) and glucose/ amino acids (μ = 2.10) medium. With increasing bacterial growth rate the chain growth rate increases from 4400 to 6300 nucleotides/min. These values are almost twofold higher than the chain growth rate reported for messenger RNA; this implies that, following a nutritional shift-up, the transfer of a relatively small number of RNA polymerase molecules from unstable to stable RNA genes along with the increase in the stable RNA chain growth rate is sufficient to account for the abrupt increase in the net rate of RNA synthesis. Furthermore, our calculations indicate that the linear density of polymerase molecules on the ribosomal DNA template increases with the bacterial growth rate, such that in rapidly growing bacteria all ribosomal RNA genes (48 copies at μ = 3) are nearly saturated with RNA polymerase.     

Regulatory state of ribosomal genes and physiological changes in the concentration of free ribonucleic acid polymerase in Escherichia coli.

The concept of promoter efficiency is introduced as frequency of RNA chain initiation at a given promoter normalized to the intracellular concentration of free (but functional) RNA polymerase. Previous observations from this laboratory on the synthesis of ribosomes and beta-galactosidase are used to show that during a nutritional shift-up from succinate minimal to glucose-amino acids medium (3-fold increase in steady-state growth rate) the concentration of free (active) RNA polymerase decreases to one-quarter of the pre-shift value and the promoter efficiencies of the genes for ribosomal RNA and ribosomal proteins increase 9- and 6-fold respectively. This extent of control of ribosomal genes is much greater than expected on the basis of the increase in the rate of ribosome synthesis (3-fold).     

Macromolecular Synthesis in Saccharomyces cerevisiae in Different Growth Media

Synthesis of ribonucleic acid (RNA), deoxyribonucleic acid (DNA), and protein was determined in Saccharomyces cerevisiae during amino acid and pyrimidine starvation and during shift-up and shift-down conditions. During amino acid starvation, cell mass, cell number, and RNA continued to increase for varying periods. During amino acid and pyrimidine starvation, cell mass and RNA showed little increase, whereas total DNA increased 11 to 17%. After a shift from broth medium to a minimal defined medium, increase in RNA and protein remained at the preshift rate before assuming a lower rate. DNA increase remained at an intermediate rate during shift-down, and then dropped to a low rate. During shift-up from minimal to broth medium, increase in cell number, protein, and DNA showed varying lag periods before increasing to the new rate characteristic of broth medium; each of these quantities exhibited a step sometime in the first 2 hr after transfer to rich medium, suggesting a partial synchronous division. Immediately after shift-up, RNA synthesis assumed a high rate, and then dropped to a rate characteristic of growth in the rich medium after about 1 hr.     

Metabolic regulation of beta-galactosidase synthesis in Escherichia coli. A test for constitutive ribosome synthesis.

The rate of differential synthesis of beta-galactosidase (alphalac) was measured in maximally induced cultures of Escherichia coli B/r with 0.01 M-inducer and 0.01 M-cyclic AMP. The value of alphalac decreases with growth rate (60% between 0.67 and 2.1 doublings/h) and after a nutritional shift-up. This decrease is presumed to reflect a decrease in the intracellular concentration of free active RNA polymerase after a shift-up, which implies that the increase in ribosome synthesis after a shift-up is due to an active induction of the ribosomal components.     

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.     

Polyamine stimulation of ribosomal synthesis and activity in a polyamine-dependent mutant of Escherichia coli

A polyamine-dependent mutant of Escherichia coli KK101 was isolated by treatment of E. coli MA261 with N-methyl-N'-nitro-N-nitrosoguanidine. In the absence of putrescine, doubling time of the mutant was 496 min. The mutation was accompanied by a change in the nature of the 30 S ribosomal subunits. Addition of putrescine to the mutant stimulated the synthesis of proteins and subsequently, this led to stimulation of RNA and DNA synthesis. Under these conditions, we determined which proteins were preferentially synthesized. Putrescine stimulated the synthesis of ribosomal protein S1 markedly, but stimulated ribosomal proteins S4, L20, and X1, and RNA polymerase slightly. The amounts of initiation factors 2 and 3 synthesized were not influenced significantly by putrescine. The preferential stimulation of the synthesis of ribosomal protein S1 occurred as early as 20 min after the addition of putrescine, while stimulation of the synthesis of the other ribosomal proteins and RNA polymerase appeared at 40 min. The stimulation of the synthesis of ribosomal RNA also occurred at 40 min after addition of putrescine. Our results indicate that putrescine can stimulate both the synthesis and the activity of ribosomes. The increase in the activity of ribosomes was achieved by the association of S1 protein to S1-depleted ribosomes. The early stimulation of ribosomal protein S1 synthesis after addition of putrescine may be important for stimulation of cell growth by polyamines.     

Regulation of RNA synthesis in Neurospora crassa : An analysis of a shift-up

A shift-up transition of growth from acetate to glucose is analyzed in Neurospora crassa. The rates of DNA and of protein accumulations remain at the preshift values for about 2 h, afterwards they increase to the rate characteristic of the new medium. The rate of RNA accumulation increases markedly 30 min after glucose addition initially at a rate greater than that of the new exponential growth which is achieved later on. An increase of the level of ribosomal proteins accompanies the increase of the rRNA content of the shifting cells, and 2–2.5 h after the shift the ribosomal level has reached the value characteristic of the new steady state of growth. The rate of rRNA methylation, which is strictly proportional to rRNA synthesis, remains almost unchanged in the 30 min following the shift; thereafter it increases to values greater than the final rate. It is interesting that the rate of rRNA synthesis is enhanced above the value typical of the new steady state as long as the ribosome level in the cells is below that characteristic of the new steady state, as if a compensatory mechanism were active.     

Hierarchy of elements regulating synthesis of ribosomal proteins in Saccharomyces cerevisiae.

Saccharomyces cerevisiae cells respond to a heat shock by temporarily slowing the synthesis of ribosomal proteins (C. Gorenstein and J. R. Warner, Proc. Natl. Acad. Sci. U.S.A. 73:1574-1551, 1976). When cultures growing oxidatively on ethanol as the sole carbon source were shifted from 23 to 36 degrees C, the synthesis of ribosomal proteins was coordinately inhibited twice as rapidly and 45% more severely than in comparable cultures growing fermentatively on glucose. Within 15 min, the relative rates of synthesis of at least 30 ribosomal proteins declined to less than one-sixth their initial values, whereas the overall rate of protein synthesis increased at least threefold. We suggest that this is due primarily to controls at the level of synthesis of messenger ribonucleic acid for ribosomal proteins but may also involve changes in messenger ribonucleic acid stability. In contrast, a nutritional shift-up causes a stimulation of the synthesis of ribosomal proteins. Experiments designed to determine the hierarchy of stimuli affecting the synthesis of these proteins demonstrated that temperature shock was dominant to glucose stimulation. When a culture growing on ethanol was shifted from 23 to 36 degrees C and glucose was added shortly afterward, the decline in ribosomal protein synthesis continued unabated. However, in wild-type cells ribosomal protein synthesis began to recover within 15 min. In mutants temperature sensitive for ribosome synthesis, e.g., rna2, there was no recovery in the synthesis of most ribosomal proteins, suggesting that the product of rna2 is essential for the production of these proteins under all vegetative conditions.