Rate Of mRNA Synthesis Research Articles

Analysis of the association between codon optimality and mRNA stability in Schizosaccharomyces pombe.

BackgroundRecent experiments have shown that codon optimality is a major determinant of mRNA stability in Saccharomyces cerevisiae and that this phenomenon may be conserved in Escherichia coli and some metazoans, although work in Neurospora crassa is not consistent with this model.ResultsWe examined the association between codon optimality and mRNA stability in the fission yeast Schizosaccharomyces pombe. Our analysis revealed the following points. First, we observe a genome-wide association between codon optimality and mRNA stability also in S. pombe, suggesting evolutionary conservation of the phenomenon. Second, in both S. pombe and S. cerevisiae, mRNA synthesis rates are also correlated at the genome-wide analysis with codon optimality, suggesting that the long-appreciated association between codon optimality and mRNA abundance is due to regulation of both mRNA synthesis and degradation. However, when we examined correlation of codon optimality and either mRNA half-lives or synthesis rates controlling for mRNA abundance, codon optimality was still positively correlated with mRNA half-lives in S. cerevisiae, but the association was no longer significant for mRNA half-lives in S. pombe or for synthesis rates in either organism. This illustrates how only the pairwise analysis of multiple correlating variables may limit these types of analyses. Finally, in S. pombe, codon optimality is associated with known DNA/RNA sequence motifs that are associated with mRNA production/stability, suggesting these two features have been under similar selective pressures for optimal gene expression.ConclusionsConsistent with the emerging body of studies, this study suggests that the association between codon optimality and mRNA stability may be a broadly conserved phenomenon. It also suggests that the association can be explained at least in part by independent adaptations of codon optimality and other transcript features for elevated expression during evolution.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3237-6) contains supplementary material, which is available to authorized users.

Inference of gene regulation functions from dynamic transcriptome data.

To quantify gene regulation, a function is required that relates transcription factor binding to DNA (input) to the rate of mRNA synthesis from a target gene (output). Such a 'gene regulation function' (GRF) generally cannot be measured because the experimental titration of inputs and simultaneous readout of outputs is difficult. Here we show that GRFs may instead be inferred from natural changes in cellular gene expression, as exemplified for the cell cycle in the yeast S. cerevisiae. We develop this inference approach based on a time series of mRNA synthesis rates from a synchronized population of cells observed over three cell cycles. We first estimate the functional form of how input transcription factors determine mRNA output and then derive GRFs for target genes in the CLB2 gene cluster that are expressed during G2/M phase. Systematic analysis of additional GRFs suggests a network architecture that rationalizes transcriptional cell cycle oscillations. We find that a transcription factor network alone can produce oscillations in mRNA expression, but that additional input from cyclin oscillations is required to arrive at the native behaviour of the cell cycle oscillator.

Matrix metalloproteinases-3 gene-promoter polymorphism as a risk factor in oral submucous fibrosis in an Indian population: a pilot study.

Host-related factors could be important to the fundamental understanding of oral diseases. One such factor is matrix metalloproteinases (MMP). MMP3 (stromelysin 1) is crucial in connective tissue remodeling. Promoter regions are specific segments of DNA that control the rate of mRNA synthesis. Thus, polymorphism in the (5A/6A) promoter region of the MMP3 gene results in different transcriptional activities and is related to susceptibility in diseases. The aim of the present study was to detect polymorphism in the MMP3 gene-promoter region in oral submucous fibrosis patients (OSF), oral squamous cell carcinoma patients (OSCC), and normal individuals with tobacco and areca nut habit and without lesions, and to correlate the genotype as a risk factor in these diseases. Genomic DNA from blood of OSF (n = 5), OSCC (n = 5), and normal individuals with tobacco and areca nut habit (n = 5) and without (n = 5) were subjected to polymerase chain reaction of the MMP3 gene-promoter region and DNA sequencing. The 5A allele in the MMP3 gene-promoter region was observed more frequently in the OSF group than the control groups. No significant difference was noted between OSCC and the control groups on the 5A allele. The results indicated that the 5A allele of the MMP3 gene-promoter region could be associated with OSF risk factor, but not OSCC, in an Indian population.

A Novel In Vitro System for Comparative Analyses of Bone Cells and Bacteria under Electrical Stimulation

Electrical stimulation is a promising approach to enhance bone regeneration while having potential to inhibit bacterial growth. To investigate effects of alternating electric field stimulation on both human osteoblasts and bacteria, a novel in vitro system was designed. Electric field distribution was simulated numerically and proved by experimental validation. Cells were stimulated on Ti6Al4V electrodes and in short distance to electrodes. Bacterial growth was enumerated in supernatant and on the electrode surface and biofilm formation was quantified. Electrical stimulation modulated gene expression of osteoblastic differentiation markers in a voltage-dependent manner, resulting in significantly enhanced osteocalcin mRNA synthesis rate on electrodes after stimulation with 1.4V RMS. While collagen type I synthesis increased when stimulated with 0.2V RMS, it decreased after stimulation with 1.4V RMS. Only slight and infrequent influence on bacterial growth was observed following stimulations with 0.2V RMS and 1.4V RMS after 48 and 72 h, respectively. In summary this novel test system is applicable for extended in vitro studies concerning definition of appropriate stimulation parameters for bone cell growth and differentiation, bacterial growth suppression, and investigation of general effects of electrical stimulation.

Abstract 2098: Histone deacetylation underlying hMAPK-induced ER mRNA repression

Abstract Estrogen receptor (ER)-negative breast cancer is more aggressive and associated with both shorter disease-free and overall survival than ER+ breast cancer. While anti-estrogen therapies have greatly improved treatment for ER+ breast cancer, both de-novo and acquired resistance occurs. Anti-estrogen therapies are not effective in ER- breast cancers, thus identifying mechanisms underlying lack of ER expression in ER- breast cancers is imperative. Hypermethylation of the ER promoter has been demonstrated to repress ER, and is found in ∼ 25% of ER- breast cancers. Previously we demonstrated that hyperactivation of MAPK (hMAPK) downstream of overexpressed EGFR or overexpression/amplification of Her2 represses ER protein and mRNA expression. Abrogation of hMAPK in ER- breast cancer cell lines and primary cultures causes re-expression of ER and restoration of anti-estrogen responses. hMAPK-mediated ER mRNA repression involves repression of transcription. We found that the ER mRNA synthesis rate and ER promoter activity, assessed with run-on assays and ER promoter reporter constructs, respectively, were significantly reduced in hMAPK-MCF-7 cell line models, with little to no ER expression, compared to control-transfected MCF-7 (coMCF-7) cells with high ER expression. Co-transfection of dnERK1/2 abrogated this repression restoring promoter activity to levels comparable with coMCF-7s but promoter bashing did not identify specific sequences responsible for this hMAPK repression. Thus we hypothesized that epigenetic mechanisms may be involved in hMAPK mediated repression of ER transcription; however, we could not detect ER promoter methylation in our hMAPK-MCF-7 models, nor in several breast cancer cell lines with hMAPK. In this study, we performed an epigenetic compound screen in the ER- SUM 149 breast cancer cell line, which presents hMAPK, and had been previously demonstrated to re-express ER with MAPK inhibition. Three candidate compounds, all HDAC inhibitors, were identified, validated in individual luciferase assays, and evaluated with rtPCR and Western blotting to verify their ability to modulate ER expression and estrogen signaling. They have been validated in additional ER- cell lines and clinical tumor samples lacking ER promoter methylation, as well. Finally, they have been used in our hMAPK-MCF-7 cells to demonstrate the role of hMAPK in histone deacetylation of the ER promoter. While HDAC inhibitors have been evaluated previously for their ability to sensitize anti-estrogen resistant ER+ breast cancers and re-express ER in ER- breast cancer cell lines exhibiting ER promoter methylation, histone deacetylation of ER in ER- breast cancers lacking ER promoter methylation has not been previously identified. Collectively, these data link histone deacetylation as an underlying mechanism in hMAPK-repression of ER mRNA suggesting this is may be a common epigenetic mechanism in the generation of ER-negative breast cancer. Citation Format: Amy J. Plotkin, Claude-Henry Volmar, Nagi Ayad, Dorraya El-Ashry. Histone deacetylation underlying hMAPK-induced ER mRNA repression. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2098. doi:10.1158/1538-7445.AM2014-2098

An efficient method of exploring simulation models by assimilating literature and biological observational data.

Recently, several biological simulation models of, e.g., gene regulatory networks and metabolic pathways, have been constructed based on existing knowledge of biomolecular reactions, e.g., DNA-protein and protein-protein interactions. However, since these do not always contain all necessary molecules and reactions, their simulation results can be inconsistent with observational data. Therefore, improvements in such simulation models are urgently required. A previously reported method created multiple candidate simulation models by partially modifying existing models. However, this approach was computationally costly and could not handle a large number of candidates that are required to find models whose simulation results are highly consistent with the data. In order to overcome the problem, we focused on the fact that the qualitative dynamics of simulation models are highly similar if they share a certain amount of regulatory structures. This indicates that better fitting candidates tend to share the basic regulatory structure of the best fitting candidate, which can best predict the data among candidates. Thus, instead of evaluating all candidates, we propose an efficient explorative method that can selectively and sequentially evaluate candidates based on the similarity of their regulatory structures. Furthermore, in estimating the parameter values of a candidate, e.g., synthesis and degradation rates of mRNA, for the data, those of the previously evaluated candidates can be utilized. The method is applied here to the pharmacogenomic pathways for corticosteroids in rats, using time-series microarray expression data. In the performance test, we succeeded in obtaining more than 80% of consistent solutions within 15% of the computational time as compared to the comprehensive evaluation. Then, we applied this approach to 142 literature-recorded simulation models of corticosteroid-induced genes, and consequently selected 134 newly constructed better models. The method described here was found to be capable of efficiently exploring candidate simulation models and obtaining better models within a short span of time. Furthermore, the results suggest that there may be room for improvement in literature recorded pathways and that they can be systematically updated using biological observational data.

High fat diet and in utero exposure to maternal obesity disrupts circadian rhythm and leads to metabolic programming of liver in rat offspring.

The risk of obesity in adulthood is subject to programming beginning at conception. In animal models, exposure to maternal obesity and high fat diets influences the risk of obesity in the offspring. Among other long-term changes, offspring from obese rats develop hyperinsulinemia, hepatic steatosis, and lipogenic gene expression in the liver at weaning. However, the precise underlying mechanisms leading to metabolic dysregulation in the offspring remains unclear. Using a rat model of overfeeding-induced obesity, we previously demonstrated that exposure to maternal obesity from pre-conception to birth, is sufficient to program increased obesity risk in the offspring. Offspring of obese rat dams gain greater body weight and fat mass when fed high fat diet (HFD) as compared to lean dam. Since, disruptions of diurnal circadian rhythm are known to detrimentally impact metabolically active tissues such as liver, we examined the hypothesis that maternal obesity leads to perturbations of core clock components and thus energy metabolism in offspring liver. Offspring from lean and obese dams were examined at post-natal day 35, following a short (2 wk) HFD challenge. Hepatic mRNA expression of circadian (CLOCK, BMAL1, REV-ERBα, CRY, PER) and metabolic (PPARα, SIRT1) genes were strongly suppressed in offspring exposed to both maternal obesity and HFD. Using a mathematical model, we identified two distinct biological mechanisms that modulate PPARα mRNA expression: i) decreased mRNA synthesis rates; and ii) increased non-specific mRNA degradation rate. Moreover, our findings demonstrate that changes in PPARα transcription were associated with epigenomic alterations in H3K4me3 and H3K27me3 histone marks near the PPARα transcription start site. Our findings indicated that offspring from obese rat dams have detrimental alternations to circadian machinery that may contribute to impaired liver metabolism in response to HFD, specifically via reduced PPARα expression prior to obesity development.

Periodic mRNA synthesis and degradation co‐operate during cell cycle gene expression

During the cell cycle, the levels of hundreds of mRNAs change in a periodic manner, but how this is achieved by alterations in the rates of mRNA synthesis and degradation has not been studied systematically. Here, we used metabolic RNA labeling and comparative dynamic transcriptome analysis (cDTA) to derive mRNA synthesis and degradation rates every 5min during three cell cycle periods of the yeast Saccharomyces cerevisiae. A novel statistical model identified 479 genes that show periodic changes in mRNA synthesis and generally also periodic changes in their mRNA degradation rates. Peaks of mRNA degradation generally follow peaks of mRNA synthesis, resulting in sharp and high peaks of mRNA levels at defined times during the cell cycle. Whereas the timing of mRNA synthesis is set by upstream DNA motifs and their associated transcription factors (TFs), the synthesis rate of a periodically expressed gene is apparently set by its core promoter.

Direct measurement of transcription rates reveals multiple mechanisms for configuration of the Arabidopsisambient temperature response

BackgroundSensing and responding to ambient temperature is important for controlling growth and development of many organisms, in part by regulating mRNA levels. mRNA abundance can change with temperature, but it is unclear whether this results from changes in transcription or decay rates, and whether passive or active temperature regulation is involved.ResultsUsing a base analog labelling method, we directly measured the temperature coefficient, Q10, of mRNA synthesis and degradation rates of the Arabidopsis transcriptome. We show that for most genes, transcript levels are buffered against passive increases in transcription rates by balancing passive increases in the rate of decay. Strikingly, for temperature-responsive transcripts, increasing temperature raises transcript abundance primarily by promoting faster transcription relative to decay and not vice versa, suggesting a global transcriptional process exists that controls mRNA abundance by temperature. This is partly accounted for by gene body H2A.Z which is associated with low transcription rate Q10, but is also influenced by other marks and transcription factor activities.ConclusionsOur data show that less frequent chromatin states can produce temperature responses simply by virtue of their rarity and the difference between their thermal properties and those of the most common states, and underline the advantages of directly measuring transcription rate changes in dynamic systems, rather than inferring rates from changes in mRNA abundance.

Global Analysis of Eukaryotic mRNA Degradation Reveals Xrn1-Dependent Buffering of Transcript Levels

The rates of mRNA synthesis and degradation determine cellular mRNA levels and can be monitored by comparative dynamic transcriptome analysis (cDTA) that uses nonperturbing metabolic RNA labeling. Here we present cDTA data for 46 yeast strains lacking genes involved in mRNA degradation and metabolism. In these strains, changes in mRNA degradation rates are generally compensated by changes in mRNA synthesis rates, resulting in a buffering of mRNA levels. We show that buffering of mRNA levels requires the RNA exonuclease Xrn1. The buffering is rapidly established when mRNA synthesis is impaired, but is delayed when mRNA degradation is impaired, apparently due to Xrn1-dependent transcription repressor induction. Cluster analysis of the data defines the general mRNA degradation machinery, reveals different substrate preferences for the two mRNA deadenylase complexes Ccr4-Not and Pan2-Pan3, and unveils an interwoven cellular mRNA surveillance network.

What do you mean by transcription rate?

mRNA synthesis in all organisms is performed by RNA polymerases, which work as nanomachines on DNA templates. The rate at which their product is made is an important parameter in gene expression. Transcription rate encompasses two related, yet different, concepts: the nascent transcription rate, which measures the in situ mRNA production by RNA polymerase, and the rate of synthesis of mature mRNA, which measures the contribution of transcription to the mRNA concentration. Both parameters are useful for molecular biologists, but they are not interchangeable and they are expressed in different units. It is important to distinguish when and where each one should be used. We propose that for functional genomics the use of nascent transcription rates should be restricted to the evaluation of the transcriptional process itself, whereas mature mRNA synthesis rates should be employed to address the transcriptional input to mRNA concentration balance leading to variation of gene expression.

Real-Time mRNA Measurement during an in Vitro Transcription and Translation Reaction Using Binary Probes

In vitro transcription and translation reactions have become popular for a bottom-up approach to synthetic biology. Concentrations of the mRNA intermediate are rarely determined, although knowledge of synthesis and degradation rates could facilitate rational engineering of in vitro systems. We designed binary probes to measure mRNA dynamics during cell-free protein synthesis by fluorescence resonance energy transfer. We tested different mRNA variants and show that the location and sequence environment of the probe target sites are important parameters for probe association kinetics and output signal. Best suited for sensitive real-time quantitation of mRNA was a target site located in the 3' untranslated region, which we designed to reduce secondary structure. We used this probe-target pair to refine our knowledge of mRNA dynamics in the commercially available PURE cell-free protein synthesis system and characterized the effect of TetR repressor on mRNA synthesis rates from a T7 promoter.

Unfolding the Bridge between Transcription and Translation

Transcription antiterminator RfaH alternates between closed (inactive) and open (activated) conformation. In this issue of Cell, Burmann et al. show that opening is accompanied by dramatic all-α to all-β refolding of its C-terminal domain. Each of the folds has a distinct function: all-α-fold acts as a specificity determinant, directing RfaH to a small subset of operons, whereas the all-β-fold recruits ribosome, thereby coupling RfaH-stimulated transcription to translation.

Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation

To monitor eukaryotic mRNA metabolism, we developed comparative dynamic transcriptome analysis (cDTA). cDTA provides absolute rates of mRNA synthesis and decay in Saccharomyces cerevisiae (Sc) cells with the use of Schizosaccharomyces pombe (Sp) as an internal standard. cDTA uses nonperturbing metabolic labeling that supersedes conventional methods for mRNA turnover analysis. cDTA reveals that Sc and Sp transcripts that encode orthologous proteins have similar synthesis rates, whereas decay rates are fivefold lower in Sp, resulting in similar mRNA concentrations despite the larger Sp cell volume. cDTA of Sc mutants reveals that a eukaryote can buffer mRNA levels. Impairing transcription with a point mutation in RNA polymerase (Pol) II causes decreased mRNA synthesis rates as expected, but also decreased decay rates. Impairing mRNA degradation by deleting deadenylase subunits of the Ccr4–Not complex causes decreased decay rates as expected, but also decreased synthesis rates. Extended kinetic modeling reveals mutual feedback between mRNA synthesis and degradation that may be achieved by a factor that inhibits synthesis and enhances degradation.

Promoter Elements Regulate Cytoplasmic mRNA Decay

Promoters are DNA elements that enable transcription and its regulation by trans-acting factors. Here, we demonstrate that yeast promoters can also regulate mRNA decay after the mRNA leaves the nucleus. A conventional yeast promoter consists of a core element and an upstream activating sequence (UAS). We find that changing UASs of a reporter gene without altering the transcript sequence affects the transcript's decay kinetics. A short cis element, comprising two Rap1p-binding sites, and Rap1p itself, are necessary and sufficient to induce enhanced decay of the reporter mRNA. Furthermore, Rap1p stimulates both the synthesis and the decay of a specific population of endogenous mRNAs. We propose that Rap1p association with target promoter in the nucleus affects the composition of the exported mRNP, which in turn regulates mRNA decay in the cytoplasm. Thus, promoters can play key roles in determining mRNA levels and have the capacity to coordinate rates of mRNA synthesis and decay.

Quantitative transcript analysis of the inducible expression system pSIP: comparison of the overexpression of Lactobacillus spp. β-galactosidases in Lactobacillus plantarum

BackgroundTwo sets of overlapping genes, lacLMReu and lacLMAci, encoding heterodimeric β-galactosidases from Lactobacillus reuteri and Lactobacillus acidophilus, respectively, have previously been cloned and expressed using the pSIP vector system and Lactobacillus plantarum WCSF1 as host. Despite the high similarity between these lacLM genes and the use of identical cloning and expression strategies, strains harboring lacLMReu produced about twenty-fold more β-galactosidase than strains containing lacLMAci.ResultsIn this study, the plasmid copy numbers (PCN) of expression vectors pEH9R (lacLMReu) and pEH9A (lacLMAci) as well as the transcription levels of both lacLM genes were compared using quantitative PCR methods. Analyses of parallel fermentations of L. plantarum harboring either pEH9R or pEH9A showed that the expression plasmids were present in similar copy numbers. However, transcript levels of lacLM from L. reuteri (pEH9R) were up to 18 times higher than those of lacLM from L. acidophilus (pEH9A). As a control, it was shown that the expression levels of regulatory genes involved in pheromone-induced promoter activation were similar in both strains.ConclusionThe use of identical expression strategies for highly similar genes led to very different mRNA levels. The data indicate that this difference is primarily caused by translational effects that are likely to affect both mRNA synthesis rates and mRNA stability. These translational effects thus seem to be a dominant determinant for the success of gene expression efforts in lactobacilli.

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

To obtain rates of mRNA synthesis and decay in yeast, we established dynamic transcriptome analysis (DTA). DTA combines non-perturbing metabolic RNA labeling with dynamic kinetic modeling. DTA reveals that most mRNA synthesis rates are around several transcripts per cell and cell cycle, and most mRNA half-lives range around a median of 11 min. DTA can monitor the cellular response to osmotic stress with higher sensitivity and temporal resolution than standard transcriptomics. In contrast to monotonically increasing total mRNA levels, DTA reveals three phases of the stress response. During the initial shock phase, mRNA synthesis and decay rates decrease globally, resulting in mRNA storage. During the subsequent induction phase, both rates increase for a subset of genes, resulting in production and rapid removal of stress-responsive mRNAs. During the recovery phase, decay rates are largely restored, whereas synthesis rates remain altered, apparently enabling growth at high salt concentration. Stress-induced changes in mRNA synthesis rates are predicted from gene occupancy with RNA polymerase II. DTA-derived mRNA synthesis rates identified 16 stress-specific pairs/triples of cooperative transcription factors, of which seven were known. Thus, DTA realistically monitors the dynamics in mRNA metabolism that underlie gene regulatory systems.

Exogenous proline modifies differential expression of superoxide dismutase genes in UV-B-irradiated Salvia officinalis plants

Grown in water culture 6-week-old Salvia officinalis plants with 4–5 true leaves were exposed to irradiation with UV-B (10 min, 12.3 kJ/m2), subjected to 5 mM exogenous proline in the nutrient solution, and treated with a combination of both factors. The plants responded to short UV-B irradiation by the appearance of oxidative stress, which was manifested in elevated content of malondialdehyde in leaves. Exogenous proline added 24 h before the irradiation inhibited lipid peroxidation. The total activity of superoxide dismutase (SOD) was analyzed in plant leaves, and three SOD isoforms—Mn-SOD, Fe-SOD, and Cu/Zn-SOD—were identified. Activities of these isoforms were measured over time, and the expression of their respective genes was analyzed by reverse transcription polymerase chain reaction (RT-PCR). It is shown that the addition of proline, UV-B irradiation, or combination of both treatments regulated in a differential manner the activities of SOD isoforms localized in various cell compartments. The activity of the cytosolic Cu/Zn-SOD isoform was limited by the presence of its mRNA, the content of which was regulated by mRNA synthesis or decay rate. By contrast, the activity of plastidic Fe-SOD isoform was regulated on the substrate (allosteric) level, not on the level of FSD gene expression. The activity of mitochondrial Mn-SOD isoform was insensitive to UV-B irradiation, addition of proline, or combination of both treatments, even though the level of MSD gene transcripts increased significantly after UV-B irradiation. The results indicate that MSD gene transcripts induced by UV-B were not completely processed to produce mature mRNA or mature mRNA was not capable of translation. It cannot be excluded that the synthesized macromolecule, the Mn-SOD precursor did not undergo posttranslational maturation to produce biologically active enzyme molecules. It appears that proline is involved in the differentially regulated complex expression of various SOD isoforms. This regulation is largely based on various extents of oxidative stress in different cell compartments.

Quantifying mRNA Synthesis and Decay Rates Using Small RNAs

Regulation of mRNA decay is a critical component of global cellular adaptation to changing environments. The corresponding changes in mRNA lifetimes can be coordinated with changes in mRNA transcription rates to fine-tune gene expression. Current approaches for measuring mRNA lifetimes can give rise to secondary effects due to transcription inhibition and require separate experiments to estimate changes in mRNA transcription rates. Here, we propose an approach for simultaneous determination of changes in mRNA transcription rate and lifetime using regulatory small RNAs (sRNAs) to control mRNA decay. We analyze a stochastic model for coupled degradation of mRNAs and sRNAs and derive exact results connecting RNA lifetimes and transcription rates to mean abundances. The results obtained are then generalized to include nonstoichiometric coupled degradation of sRNAs. Our analysis suggests experimental protocols for determining parameters controlling the efficiency of stoichiometric regulation by small RNAs and for analyzing factors and processes regulating changes in mRNA transcription and decay.

Syntheses That Stay Together

The rate of mRNA translation determines the rate of mRNA synthesis in bacteria through direct coupling of the respective molecular machinery.