Decay of rplN and lacZ mRNA in Escherichia coli

Capturing of extracellular vesicles derived from single cells of Escherichia coli

Bacteria secrete extracellular vesicles (EVs), also referred to as bacterial membrane vesicles, which carry, among other compounds, lipids, nucleic acids and virulence factors. Recent studies highlight the role of EVs in the emergence of antibiotic resistance, e.g. as carrier and absorbent particles of the drug to protect the cells, or as a pathway to disseminate resistance elements. In this study, we are interested in characterizing the secretion of EVs at the single bacterial level to ultimately understand how cells respond to antibiotic treatment. We introduce a microfluidic device that enables culture of single bacterial cells and capture of EVs secreted from these individuals. The device incorporates parallel, narrow winding channels to trap single rod-shaped E. coli cells at their entrances. The daughter cells are immediately removed by continuous flow on the open side of the trap, so that the trap contains always only a single cell. Cells grew in these traps over 24 h with a doubling time of 25 minutes. Under antibiotic treatment, the doubling time did not change, but we observed small changes in the cell length of the trapped cells (decrease from 4.0 μm to 3.6 μm for 0 and 250 ng mL-1 polymyxin B, respectively), and cells stopped growing within hours, depending on the drug concentration. Compared to bulk culture, the results indicate a higher susceptibility of on-chip-cultured cells (250 ng mL-1vs. >500 ng mL-1 in bulk), which may be caused, among other reasons, by the space limitation in the cell trap and shear forces. During the culture, EVs secreted by the trapped cells entered the winding channel. We developed a procedure to selectively coat these channels with poly-L-lysine resulting in a positively charged surface, which enabled electrostatic capture of negatively charged EVs. Subsequently, the immobilized EVs were stained with a lipophilic dye and detected by fluorescence microscopy. Our findings confirm large variations of EV secretion among individual bacteria and indicate a relative high rate of EV secretion under antibiotic treatment. The proposed method can be extended to the detection of other secreted substances of interest and may facilitate the elucidation of unknown heterogeneities in bacteria.

Effects of cell cycle variability on lineage and population measurements of messenger RNA abundance

Many models of gene expression do not explicitly incorporate a cell cycle description. Here, we derive a theory describing how messenger RNA (mRNA) fluctuations for constitutive and bursty gene expression are influenced by stochasticity in the duration of the cell cycle and the timing of DNA replication. Analytical expressions for the moments show that omitting cell cycle duration introduces an error in the predicted mean number of mRNAs that is a monotonically decreasing function of η, which is proportional to the ratio of the mean cell cycle duration and the mRNA lifetime. By contrast, the error in the variance of the mRNA distribution is highest for intermediate values of η consistent with genome-wide measurements in many organisms. Using eukaryotic cell data, we estimate the errors in the mean and variance to be at most 3% and 25%, respectively. Furthermore, we derive an accurate negative binomial mixture approximation to the mRNA distribution. This indicates that stochasticity in the cell cycle can introduce fluctuations in mRNA numbers that are similar to the effect of bursty transcription. Finally, we show that for real experimental data, disregarding cell cycle stochasticity can introduce errors in the inference of transcription rates larger than 10%.

Slowdown of Translational Elongation in Escherichia coli under Hyperosmotic Stress

In nature, bacteria frequently experience many adverse conditions, including heat, oxidation, acidity, and hyperosmolarity, which all tend to slow down if not outright stop cell growth. Previous work on bacterial stress mainly focused on understanding gene regulatory responses. Much less is known about how stresses compromise protein synthesis, which is the major driver of cell growth. Here, we quantitatively characterize the translational capacity of Escherichia coli cells growing exponentially under hyperosmotic stress. We found that hyperosmotic stress affects bacterial protein synthesis through reduction of the translational elongation rate, which is largely compensated for by an increase in the cellular ribosome content compared with nutrient limitation at a similar growth rate. The slowdown of translational elongation is attributed to a reduction in the rate of binding of tRNA ternary complexes to the ribosomes.

Hyperosmotic stress is a common stress condition confronted by E. coli during infection of the urinary tract. It can significantly compromise the bacterial growth rate. Protein translation capacity is a critical component of bacterial growth. In this study, we find for the first time that hyperosmotic stress causes substantial slowdown in bacterial ribosome translation elongation. The slowdown of translation elongation originates from a reduced binding rate of tRNA ternary complex to the ribosomes.

Model-based genome-wide determination of RNA chain elongation rates in Escherichia coli

Dynamics in the process of transcription are often simplified, yet they play an important role in transcript folding, translation into functional protein and DNA supercoiling. While the modulation of the speed of transcription of individual genes and its role in regulation and proper protein folding has been analyzed in depth, the functional relevance of differences in transcription speeds as well as the factors influencing it have not yet been determined on a genome-wide scale. Here we determined transcription speeds for the majority of E. coli genes based on experimental data. We find large differences in transcription speed between individual genes and a strong influence of both cellular location as well as the relative importance of genes for cellular function on transcription speeds. Investigating factors influencing transcription speeds we observe both codon composition as well as factors associated to DNA topology as most important factors influencing transcription speeds. Moreover, we show that differences in transcription speeds are sufficient to explain the timing of regulatory responses during environmental shifts and highlight the importance of the consideration of transcription speeds in the design of experiments measuring transcriptomic responses to perturbations.

Medium-dependent control of the bacterial growth rate

By combining results from previous studies of nutritional up-shifts we here re-investigate how bacteria adapt to different nutritional environments by adjusting their macromolecular composition for optimal growth. We demonstrate that, in contrast to a commonly held view the macromolecular composition of bacteria does not depend on the growth rate as an independent variable, but on three factors: (i) the genetic background (i.e. the strain used), (ii) the physiological history of the bacteria used for inoculation of a given growth medium, and (iii) the kind of nutrients in the growth medium. These factors determine the ribosome concentration and the average rate of protein synthesis per ribosome, and thus the growth rate. Immediately after a nutritional up-shift, the average number of ribosomes in the bacterial population increases exponentially with time at a rate which eventually is attained as the final post-shift growth rate of all cell components. After a nutritional up-shift from one minimal medium to another minimal medium of higher nutritional quality, ribosome and RNA polymerase syntheses are co-regulated and immediately increase by the same factor equal to the increase in the final growth rate. However, after an up-shift from a minimal medium to a medium containing all 20 amino acids, RNA polymerase and ribosome syntheses are no longer coregulated; a smaller rate of synthesis of RNA polymerase is compensated by a gradual increase in the fraction of free RNA polymerase, possibly due to a gradual saturation of mRNA promoters. We have also analyzed data from a recent publication, in which it was concluded that the macromolecular composition in terms of RNA/protein and RNA/DNA ratios is solely determined by the effector molecule ppGpp. Our analysis indicates that this is true only in special cases and that, in general, medium adaptation also depends on factors other than ppGpp.

Growth rate-dependent global effects on gene expression in bacteria

Bacterial gene expression depends not only on specific regulatory mechanisms, but also on bacterial growth, because important global parameters such as the abundance of RNA polymerases and ribosomes are all growth-rate dependent. Understanding of these global effects is necessary for a quantitative understanding of gene regulation and for the design of synthetic genetic circuits. We find that the observed growth-rate dependence of constitutive gene expression can be explained by a simple model using the measured growth-rate dependence of the relevant cellular parameters. More complex growth dependencies for genetic circuits involving activators, repressors, and feedback control were analyzed and verified experimentally with synthetic circuits. Additional results suggest a feedback mechanism mediated by general growth-dependent effects that does not require explicit gene regulation if the expressed protein affects cell growth. This mechanism can lead to growth bistability and promote the acquisition of important physiological functions such as antibiotic resistance and tolerance (persistence).

Maximum rrn promoter activity in Escherichia coli at saturating concentrations of free RNA polymerase

During fast growth, the rrn P1 promoters of Escherichia coli operate at their maximum strength, but below their maximum activity (V(max)), since they are not saturated with RNA polymerase. Since higher concentrations of free RNA polymerase are expected to be found in strains carrying rrn deletions, we have analyzed reported electron micrographs of rrn operons from rrn deletion strains growing at maximal rates (at 37 degrees C) in LB medium [1]. We conclude that, in a strain with four of the seven rrn operons inactivated by partial deletions, transcripts are initiated at rrn P1 promoters 1.6-fold more rapidly than in the wild-type strain and the entirety of the rrn operon is transcribed at a 1.5-fold higher average elongation rate due to shortened pauses in the 16S and 23S regions. Under this condition, traffic congestion occurs in front of a pause site in the 5' leader region of the rrn operon near the beginning of the 16S gene; the congestion extends all the way back to the promoter, impedes promoter clearance and limits the promoter activity to one initiation per 0.56 s. This corresponds to a promoter activity of 107 transcripts/min and is assumed to be close to the V(max) of rrn P1 promoters.

Intracistronic transcriptional polarity enhances translational repression: a new role for Rho

Transcriptional polarity in Escherichia coli occurs when cryptic Rho-dependent transcription terminators become activated as a consequence of reduced translation. Whether this is due to an increased spacing between the RNA polymerase and the leading ribosome or to prior functional inactivation of a subpopulation of the mRNAs has been a matter of discussion. Transcriptional polarity results in decreased synthesis of inefficiently translated mRNAs and therefore in decreased expression of downstream genes in the same operon (intercistronic polarity). By analogy, expression of the gene in which the conditional termination occurs is also expected to decrease, but this has so far not been demonstrated experimentally. To study the relevance of this intracistronic polarity for expression regulation in vivo, the polarity-prone IacZ reporter gene was fused to a range of mutated ribosome binding sites, repressed to different degrees by local RNA structure. Quantitative analysis of protein and mRNA synthesis shows that polarity occurs on functionally active mRNA molecules and that it indeed affects expression of the cistron carrying the terminator, thus enhancing the effect of translational repression. These findings point to a novel regulatory function of transcriptional polarity, reminiscent of transcriptional attenuation but opposite in effect.

Killer and protective ribosomes

In prokaryotes, translation influences mRNA decay. The breakdown of most Escherichia coli mRNAs is initiated by RNase E, a 5'-dependent endonuclease. Some mRNAs are protected by ribosomes even if these are located far upstream of cleavage sites ("protection at a distance"), whereas others require direct shielding of these sites. I argue that these situations reflect different modes of interaction of RNase E with mRNAs. Protection at a distance is most impressive in Bacilli, where ribosomes can protect kilobases of unstable downstream sequences. I propose that this protection reflects the role in mRNA decay of RNase J1, a 5'-->3' exonuclease with no E. coli equivalent. Finally, recent years have shown that besides their protective role, ribosomes can also cleave their mRNA under circumstances that cause ribosome stalling. The endonuclease associated with this "killing" activity, which has a eukaryotic counterpart ("no-go decay"), is not characterized; it may be borne by the distressed ribosome itself.

A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function

Riboswitches are RNA-based genetic control elements that regulate gene expression in a ligand-dependent fashion without the need for proteins. The ability to create synthetic riboswitches that control gene expression in response to any desired small-molecule ligand will enable the development of sensitive genetic screens that can detect the presence of small molecules, as well as designer genetic control elements to conditionally modulate cellular behavior. Herein, we present an automated high-throughput screening method that identifies synthetic riboswitches that display extremely low background levels of gene expression in the absence of the desired ligand and robust increases in expression in its presence. Mechanistic studies reveal how these riboswitches function and suggest design principles for creating new synthetic riboswitches. We anticipate that the screening method and design principles will be generally useful for creating functional synthetic riboswitches.

Feedback control of ribosome synthesis in Escherichia coli is dependent on eight critical amino acids

When bacteria growing in minimal medium are supplied with exogenous amino acids, they respond by increasing the synthesis of ribosomes; this leads to more protein synthesis capacity and faster growth. To examine how amino acids control the synthesis of ribosomes, two strategies were used. First, single amino acids were added to bacteria growing in minimal medium and their effect on the relative strength of the rrnB P1 promoter was determined. The addition of any one of eight amino acids (alanine, glutamine, and glutamic acid, isoleucine, leucine, methionine, serine, valine) increased the strength of the P1 promoter by 1.25- to 2.0-fold with no appreciable effect on transcription from an isolated rrn P2 promoter or on the bacterial growth rate. The effects of adding combinations of these critical amino acids were partially additive. When any one of the other amino acids was added, no discernable stimulation in relative P1 expression or growth was observed. In the second strategy, all amino acids were present in the growth medium, but the carbon source was altered to change the growth rate. In this case the relative strength of the P1 promoter was always constant and maximal. We suggest that addition of any of the eight critical amino acids reduces the ppGpp synthesis activity of the spoT gene product; the lower ppGpp levels, in turn, increase the strength of the rrn P1 promoters. It is suggested that these amino acids are involved in a feedback chain of reactions that control the rate of ribosome function by adjusting the rate of ribosome synthesis.

Model-based inference of gene expression dynamics from sequence information

A dynamic model of prokaryotic gene expression is developed that makes considerable use of gene sequence information. The main contribution arises from the fact that the combined gene expression model allows us to access the impact of altering a nucleotide sequence on the dynamics of gene expression rates mechanistically. The high level of detail of the mathematical model is considered as an important step towards bringing together the tremendous amount of biological in-depth knowledge that has been accumulated at the molecular level, using a systems level analysis (in the sense of a bottom-up, inductive approach). This enables to the model to provide highly detailed insights into the various steps of the protein expression process and it allows us to access possible targets for model-based design. Taken as a whole, the mathematical gene expression model presented in this study provides a comprehensive framework for a thorough analysis of sequence-related effects on the stages of mRNA synthesis, mRNA degradation and ribosomal translation, as well as their nonlinear interconnectedness. Therefore, it may be useful in the rational design of recombinant bacterial protein synthesis systems, the modulation of enzyme activities in pathway design, in vitro protein biosynthesis, and RNA-based vaccination.

Tolerance of the Rieske-type [2Fe-2S] cluster in recombinant ferredoxin BphA3 from Pseudomonas sp. KKS102 to histidine ligand mutations

BphA3 from Pseudomonas sp. KKS102 is a Rieske-type [2Fe-2S] ferredoxin that transfers electrons from an NADH-dependent oxidoreductase, BphA4, to a biphenyl dioxygenase complex. A high-level expression and purification system for the recombinant BphA3 in Escherichia coli was constructed. Two histidine ligands of the Rieske-type cluster in BphA3, were each replaced with serine, cysteine, asparagine and tyrosine. The single mutants, in which either His44 or His65 was replaced with a cysteine residue (CH and HC mutants respectively), and the double mutant, in which both histidine residues were replaced with cysteine residue (CC mutant), accumulated to high levels in the E. coli cells, while the other single mutants did not. The purified WT (wild-type) protein showed characteristic near-UV and visible absorption and CD spectra of Rieske-type clusters. The X-ray absorption spectra were suggestive of the existence of [2Fe-2S] clusters, with one histidine and three cysteine ligands in the CH and HC mutants, and an [2Fe-2S] cluster with four cysteine ligands in the CC mutant. The BphA4-dependent cytochrome c reductase activities of the mutants were less than 0.3% of that of the WT protein. The redox potential of the WT protein determined by cyclic voltammetry was -180+/-5 mV compared with the standard hydrogen electrode, and that of the CH mutant was approx. 175 mV lower. The changes in the near-UV and visible absorption spectra of the mutants showed that the reduced iron-sulphur clusters in the mutants were unstable. His44 and His65 in BphA3 can be replaced with cysteine residues, but are required for the stabilization of the reduced form of the cluster.

Control of rRNA synthesis in Escherichia coli: a systems biology approach

The first part of this review contains an overview of the various contributions and models relating to the control of rRNA synthesis reported over the last 45 years. The second part describes a systems biology approach to identify the factors and effectors that control the interactions between RNA polymerase and rRNA (rrn) promoters of Escherichia coli bacteria during exponential growth in different media. This analysis is based on measurements of absolute rrn promoter activities as transcripts per minute per promoter in bacterial strains either deficient or proficient in the synthesis of the factor Fis and/or the effector ppGpp. These absolute promoter activities are evaluated in terms of rrn promoter strength (V(max)/K(m)) and free RNA polymerase concentrations. Three major conclusions emerge from this evaluation. First, the rrn promoters are not saturated with RNA polymerase. As a consequence, changes in the concentration of free RNA polymerase contribute to changes in rrn promoter activities. Second, rrn P2 promoter strength is not specifically regulated during exponential growth at different rates; its activity changes only when the concentration of free RNA polymerase changes. Third, the effector ppGpp reduces the strength of the rrn P1 promoter both directly and indirectly by reducing synthesis of the stimulating factor Fis. This control of rrn P1 promoter strength forms part of a larger feedback loop that adjusts the synthesis of ribosomes to the availability of amino acids via amino acid-dependent control of ppGpp accumulation.

Authentic precursors to ribosomal subunits accumulate in Escherichia coli in the absence of functional DnaK chaperone

Escherichia coli dnaK-ts mutants are defective in the late stages of ribosome biogenesis at high temperature. Here, we show that the 21S, 32S and 45S ribosomal particles that accumulate in the dnaK756-ts mutant at 44 degrees C contain unprocessed forms of their 16S and 23S rRNAs (partially processed in the case of 45S particles). Their 5S rRNA stoichiometry and ribosomal protein composition are typical of the genuine ribosomal precursors found in a wild-type (dnaK+) strain. Despite the lack of a functional DnaK, a very slow maturation of these 21S, 32S and 45S particles to structurally and functionally normal 30S and 50S ribosomal subunits still occurs at high temperature. This conversion is accompanied by the processing of p16S and p23S rRNAs to their mature forms. We conclude that: (i) 21S, 32S and 45S particles are not dead-end particles, but true precursors to active ribosomes (21S particles are converted to 30S subunits, and 32S and 45S to 50S subunits); (ii) DnaK is not absolutely necessary for ribosome biogenesis, but accelerates the late steps of this process considerably at high temperature; and (iii) 23S rRNA processing depends on the stage reached in the stepwise assembly of the 50S subunit, not directly on DnaK.

Effect of gene location, mRNA secondary structures, and RNase sites on expression of two genes in an engineered operon

The effects of endoribonuclease sites, secondary structures in mRNA, and gene placement on protein production and mRNA stability and steady-state levels were tested in a dual-gene operon containing the genes encoding beta-galactosidase (lacZ) from Escherichia coli and green fluorescent protein (gfp) from Aequorea victoria. Two previously identified RNase E sites were placed separately between the coding regions to direct cleavage in this area and produce two secondary transcripts, each containing a single-gene coding region. Novel secondary structures were engineered into the 3' and 5' ends of each of the coding regions to protect the transcript from inactivation by endoribonucleases (5' hairpins) and degradation by exoribonucleases (3' hairpins). In addition, the effects of relative gene placement were examined by switching the locations of the two coding regions. Depending on the particular secondary structures and RNase E sites placed between the genes the relative steady-state transcript and protein levels encoded by the two reporter genes could be changed up to 2.5-fold and 4-fold, respectively. By changing gene location and incorporating secondary structures and RNase E sites the relative steady-state transcript and protein levels encoded by the two reporter genes could be changed up to 100-fold and 750-fold, respectively.

Kinetic properties of rrn promoters in Escherichia coli

How do bacteria adapt and optimize their growth in response to different environments? The answer to this question is intimately related to the control of ribosome bio-synthesis. During the last decades numerous proposals have been made to explain this control but none has been definitive. To readdress the problem, we have used measurements of rRNA synthesis rates and rrn gene dosages in E. coli to find the absolute transcription rates of the average rrn operon (transcripts per min per operon) at different growth rates. By combining these rates with lacZ expression data from rRNA promoter-lacZ fusions, the abolute activities of the isolated rrnB P1 and P2 promoters were determined as functions of the growth rate in the presence and absence of Fis and of the effector ppGpp. The promoter activity data were analyzed to obtain the relative concentrations of free RNA polymerase, [R(f)], and the ratio of the Michaelis-Menten parameters, V(max)/K(m) (promoter strength), that characterize the promoter-RNA polymerase interaction. The results indicate that changes in the basal concentration of ppGpp can account for all growth-medium dependent regulation of the rrn P1 promoter strength. The P1 promoter strength was maximal when Fis was present and the level of ppGpp was undetectable during growth in rich media or in ppGpp-deficient strains; this maximal strength was 3-fold reduced when Fis was removed and the level of ppGpp remained undetectable. At ppGpp levels above 55 pmol per cell mass unit (OD(460)) during growth in poor media, the P1 promoter strength was minimal and not affected by the presence or absence of fis. The half-maximal value occurred at 20 pmol ppGpp/OD(460) and corresponds to an intracellular concentration of about 50 microM. In connection with previously published data, the results suggest that ppGpp reduces the P1 promoter strength directly, by binding RNA polymerase, and indirectly, by inhibiting the synthesis of Fis.

mRNA composition and control of bacterial gene expression

The expression of any given bacterial protein is predicted to depend on (i) the transcriptional regulation of the promoter and the translational regulation of its mRNA and (ii) the synthesis and translation of total (bulk) mRNA. This is because total mRNA acts as a competitor to the specific mRNA for the binding of initiation-ready free ribosomes. To characterize the effects of mRNA competition on gene expression, the specific activity of beta-galactosidase expressed from three different promoter-lacZ fusions (P(spc)-lacZ, P(RNAI)-lacZ, and P(RNAII)-lacZ) was measured (i) in a relA(+) background during exponential growth at different rates and (ii) in relA(+) and DeltarelA derivatives of Escherichia coli B/r after induction of a mild stringent or a relaxed response to raise or lower, respectively, the level of ppGpp. Expression from all three promoters was stimulated during slow exponential growth or at elevated levels of ppGpp and was reduced during fast exponential growth or at lower levels of ppGpp. From these observations and from other considerations, we propose (i) that the concentration of free, initiation-ready ribosomes is approximately constant and independent of the growth rate and (ii) that bulk mRNA made during slow growth and at elevated levels of ppGpp is less efficiently translated than bulk mRNA made during fast growth and at reduced levels of ppGpp. These features lead to an indirect enhancement in the expression of LacZ (or of any other protein) during growth in media of poor nutritional quality and at increased levels of ppGpp.

Molecular clocks reduce plasmid loss rates: the R1 case

Plasmids control their replication so that the replication frequency per plasmid copy responds to the number of plasmid copies per cell. High sensitivity amplification in replication response to copy number deviations generally reduces variation in copy numbers between different single cells, thereby reducing the plasmid loss rate in a cell population. However, experiments show that plasmid R1 has a gradual, insensitive replication control predicting considerable copy number variation between single cells. The critical step in R1 copy number control is regulation of synthesis of a rate-limiting cis-acting replication protein, RepA. De novo synthesis of a large number of RepA molecules is required for replication, suggesting that copy number control is exercised at multiple steps. In this theoretical kinetic study we analyse R1 multistep copy number control and show that it results in the insensitive replication response found experimentally but that it at the same time effectively prohibits the existence of only one plasmid copy in a dividing cell. In combination with the partition system of R1, this can lead to very high segregational stability. The R1 control mechanism is compared to the different multistep copy number control of plasmid ColE1 that is based on conventional sensitivity amplification. This implies that while copy number control for ColE1 efficiently corrects for fluctuations that have already occurred, R1 copy number control prevents their emergence in cells that by chance start their cycle with only one plasmid copy. We also discuss how regular, clock-like, behaviour of single plasmid copies becomes hidden in experiments probing collective properties of a population of plasmid copies because the individual copies are out of phase. The model is formulated using master equations, taking a stochastic approach to regulation, but the mathematical formalism is kept to a minimum and the model is simplified to its bare essence. This simplicity makes it possible to extend the analysis to other replicons with similar design principles.

Activities of constitutive promoters in Escherichia coli

The in vivo activities of seven constitutive promoters in Escherichia coli have been determined as functions of growth rate in wild-type relA+ spoT+ strains with normal levels of guanosine tetraphosphate (ppGpp) and in ppGpp-deficient DeltarelADeltaspoT derivatives. The promoters include (i) the spc ribosomal protein operon promotor Pspc; (ii) the beta-lactamase gene promotor Pblaof plasmid pBR322; (iii) the PLpromoter of phage lambda; (iv) and (v) the replication control promoters PRNAIand PRNAIIof plasmid pBR322; and (vi) and (vii) the P1 and P2 promoters of the rrnB ribosomal RNA operon. Each strain carried an operon fusion consisting of one of the respective promoter regions linked to lacZ and recombined into the chromosome at the mal locus of a lac deletion strain. The amount of 5'-terminal lacZ mRNA and of beta-galactosidase activity expressed from these promoters were determined by standard hybridization or enzyme activity assays, respectively. In addition, DNA, RNA and protein measurements were used to obtain information about gene dosage, rRNA synthesis and translation rates. By combining lacZ mRNA hybridization data with gene dosage and rRNA synthesis data, the absolute activity of the different promoters, in transcripts/minute per promoter, was determined. In ppGpp-proficient (relA+ spoT+) strains, the respective activities of rrnB P1 and P2 increased 40 and fivefold with increasing growth rate between 0.7 and 3.0 doublings/hour. The activities of Pspc, PL, Pbla, and PRNAIincreased two- to threefold and reached a maximum at growth rates above 2.0 doublings/hour. In contrast, PRNAIIactivity decreased threefold over this range of growth rates. In ppGpp-deficient (DeltarelA DeltaspoT) bacterial strains, the activities of rrnB P1 and P2 promoters both increased about twofold between 1.6 and 3.0 doublings/hour, whereas the activities of Pspc, PL, Pbla, and PRNAI, and PRNAIIwere about constant. To explain these observations, we suggest that the cellular concentration of free RNA polymerase increases with increasing growth rate; for saturation the P1 and P2 rRNA promoters require a high RNA polymerase concentration that is approached only at the highest growth rates, whereas the other promoters are saturated at lower polymerase concentrations achieved at intermediate growth rates. In addition, the data indicate that the respective rrnB P1 and PRNAIIpromoters were under negative and positive control by ppGpp. This caused a reduced activity of rrnB P1 and an increased activity of PRNAIIduring slow growth in wild-type (relA+ spoT+) relative to ppGpp-deficient (DeltarelA DeltaspoT) bacterial strains.