Gene expression in Escherichia coli B/r during partial rifampicin-mediated restrictions of transcription initiation

Linking system-wide impacts of RNA polymerase mutations to the fitness cost of rifampin resistance in Pseudomonas aeruginosa

Fitness costs play a key role in the evolutionary dynamics of antibiotic resistance in bacteria by generating selection against resistance in the absence of antibiotics. Although the genetic basis of antibiotic resistance is well understood, the precise molecular mechanisms linking the genetic basis of resistance to its fitness cost remain poorly characterized. Here, we examine how the system-wide impacts of mutations in the RNA polymerase (RNAP) gene rpoB shape the fitness cost of rifampin resistance in Pseudomonas aeruginosa. Rifampin resistance mutations reduce transcriptional efficiency, and this explains 76% of the variation in fitness among rpoB mutants. The pleiotropic consequence of rpoB mutations is that mutants show altered relative transcript levels of essential genes. We find no evidence that global transcriptional responses have an impact on the fitness cost of rifampin resistance as revealed by transcriptome sequencing (RNA-Seq). Global changes in the transcriptional profiles of rpoB mutants compared to the transcriptional profile of the rifampin-sensitive ancestral strain are subtle, demonstrating that the transcriptional regulatory network of P. aeruginosa is robust to the decreased transcriptional efficiency associated with rpoB mutations. On a smaller scale, we find that rifampin resistance mutations increase the expression of RNAP due to decreased termination at an attenuator upstream from rpoB, and we argue that this helps to minimize the cost of rifampin resistance by buffering against reduced RNAP activity. In summary, our study shows that it is possible to dissect the molecular mechanisms underpinning variation in the cost of rifampin resistance and highlights the importance of genome-wide buffering of relative transcript levels in providing robustness against resistance mutations.

Antibiotic resistance mutations carry fitness costs. Relative to the characteristics of their antibiotic-sensitive ancestors, resistant mutants show reduced growth rates and competitive abilities. Fitness cost plays an important role in the evolution of antibiotic resistance in the absence of antibiotics; however, the molecular mechanisms underlying these fitness costs is not well understood. We applied a systems-level approach to dissect the molecular underpinnings of the fitness costs associated with rifampin resistance in P. aeruginosa and showed that most of the variation in fitness cost can be explained by the direct effect of resistance mutations on the enzymatic activity of the mutated gene. Pleiotropic changes in transcriptional profiles are subtle at a genome-wide scale, suggesting that the gene regulatory network of P. aeruginosa is robust in the face of the direct effects of resistance mutations.

Free RNA polymerase and modeling global transcription in Escherichia coli

Growth rate-dependent changes in the cytoplasmic concentration of free functional RNA polymerase, [R(f)], affect the activity of all bacterial genes. Since [R(f)] is not accessible to direct experimental quantitation, it can only be found indirectly from an evaluation of promoter activity data. Here, a theory has been derived to calculate [R(f)] from the concentrations of total RNA polymerase and promoters in a model system with known Michaelis-Menten constants for the polymerase-promoter interactions. The theory takes transcript lengths and elongation rates into account and predicts how [R(f)] changes with varying gene dosages. From experimental data on total concentrations of RNA polymerase and kinetic properties of different classes of promoters, the theory was developed into a mathematical model that reproduces the global transcriptional control in Escherichia coli growing at different rates. The model allows an estimation of the concentrations of free and DNA-bound RNA polymerase, as well as the partitioning of RNA polymerase into mRNA and stable RNA synthesizing fractions. According to this model, [R(f)] is about 0.4 and 1.2 microM at growth rates corresponding to 1.0 and 2.5 doublings/h, respectively. The model accurately reflects a number of further experimental observations and suggests that the free RNA polymerase concentration increases with increasing growth rate.

Expression of cloned rpoB gene of Escherichia coli: a genetic system for the isolation of dominant negative mutations and overproduction of defective beta subunit of RNA polymerase

The rifampin resistance rifD18 allele of rpoB, carried on the expression plasmid pXT7 beta, is controlled by a strong bacteriophage T7 late promoter and two weak Escherichia coli promoters. Depending on the host strain, pXT7 beta specifies different levels of Rifr beta subunit, providing a system for the isolation, maintenance, and overexpression of dominant lethal alleles of rpoB. In rpoB+ hosts, pXT7 beta confers the Rifr phenotype on the Rifs host. Negative rpoB mutations in the plasmid DNA can thus be scored by screening transformants for Rifs. In an rpoB(Am) supD(Ts) host in which chromosomal rpoB expression is decreased as the temperature goes up, some of the negative plasmid-borne rpoB mutations displayed a dominant phenotype. In a host harboring inducible T7 RNA polymerase, the defective beta subunits could be overexpressed independently of the E. coli transcriptional machinery. With this system, we isolated several negative rpoB mutations induced in vitro by hydroxylamine. Seven of the mutant rpoB alleles, when overexpressed, were found to specify normal-size beta polypeptides. Two of them displayed the dominant lethal phenotype in the rpoB(Am) supD(Ts) background. We also constructed a mutation (rpoB1800) in which 24 carboxy-terminal amino acids were substituted with a random 19-amino-acid sequence. The nonfunctional rpoB1800 beta polypeptide was isolated and assembled in vitro into the core enzyme molecule.

Direct evidence for rifampicin-promoted readthrough of the partial terminator tL7 in the rpoBC operon of Escherichia coli

The RNA polymerase subunits beta and beta' of Escherichia coli, encoded by the genes rpoB and rpoC, are co-transcribed with four 50 S ribosomal protein genes, rplKAJL. After treatment with the antibiotic rifampicin a partial uncoupling of rpoBC from rplKAJL transcription occurs. We have been investigating the role played in uncoupling by tL7, an 80% efficient terminator of transcription present in the 319 bp intercistronic space between rplL and rpoB, using S1 nuclease mapping of transcripts produced in vivo in normal (rpoBC haploid) strains. Our results show directly that rifampicin stimulates readthrough of tL7 on the chromosome by approximately twofold, an effect sufficient to explain the observed increase in beta beta' protein synthesis. We also provide preliminary evidence for the map position of PL7, and show that both this and P beta, two very weak promoters which might in principle be activated by rifampicin, are not in fact stimulated by the drug.

Overexpression of the dnaA gene in Escherichia coli B/r: chromosome and minichromosome replication in the presence of rifampin

The replication of chromosomes and minichromosomes in Escherichia coli B/r was examined under conditions in which the dnaA gene product was overproduced. Increased levels of the DnaA protein were achieved by thermoinduction of the dnaA gene, under the control of the lambda pL promoter, or by cellular maintenance of multicopy plasmids carrying the dnaA gene under the control of its own promoters. Previous work has shown that overproduction of DnaA protein stimulates replication of the chromosomal origin, oriC, but that the newly initiated forks do not progress along the length of the chromosome (T. Atlung, K. V. Rasmussen, E. Clausen, and F. G. Hansen, p. 282-297, in M. Schaechter, F. C. Neidhardt, J. L. Ingraham, and N. O. Kjeldgaard, ed., The Molecular Biology of Bacterial Growth, 1985). In the present study, it was found that overproduction of DnaA protein caused both a two- to threefold increase in the amount of residual chromosome replication and an extended synthesis of minichromosome DNA in the presence of rifampin. The amount of residual chromosome replication was consistent with the appearance of functional replication forks on the majority of the chromosomes. Since the rate of DNA accumulation and the cellular DNA/mass ratios were not increased significantly by overexpression of the dnaA gene, we concluded that the addition of rifampin either enabled stalled replication forks to proceed beyond oriC or enabled new forks to initiate on both chromosomes and minichromosomes, or both.

Direct evidence for autogenous regulation of the Escherichia coli genes rpoBC in vivo

We have fused the rpoBC genes to the strong controllable promoter PL in phage lambda while deleting most of the intercistronic regulatory DNA and ribosomal protein genes upstream of rpoB. Induction of a lysogen carrying the recombinant prophage gave rise to a 2-3-fold oversynthesis of beta beta' in the cell whereas rpoBC-mRNA levels rose by at least 10-fold. Similar observations were made when these sequences were present in the prophage, indicating that the removal of DNA sequences up to 26 base pairs before rpoB does not affect post-transcriptional autogenous regulation of beta beta' synthesis. Overexpression of beta beta' also autogenously regulated the synthesis of the beta polypeptide from the chromosome in two strains carrying electrophoretic mobility mutations in rpoB. S1 nuclease mapping experiments indicated that this regulation was also post-transcriptional, and confirmed that phage beta-mRNA synthesis exceeded chromosomal beta-mRNA synthesis by 20-fold. The provision of excess beta alone in the cell caused autoregulation of chromosomal beta, but not beta' synthesis, indicating that beta and beta' are regulated independently.

Mutant of Escherichia coli with unusual patterns of rpoB,C expression in response to rifampicin and acridine orange

A mutation located near rpoB (89') in E. coli is responsible for unusual patterns of beta and beta ' (but not L7/L12) synthesis in response to the drugs rifampicin and acridine orange.

Autogenous posttranscriptional regulation of RNA polymerase beta and beta' subunit synthesis in Escherichia coli

Bacterial strains carrying poorly suppressed amber mutations in the RNA polymerase beta subunit gene (rpoB) exhibit regulatory compensation. This compensation allows these strains to produce an adequate content of RNA polymerase to support a near normal rate of growth despite the poorly suppressed amber mutation. The primary compensatory mechanism permitting the elevated expression functions by permitting a much more efficient (up to threefold) loading of ribosomes at the beta cistron translation initiation site on the mRNA. This result supports the concept that the production of beta and beta' RNA polymerase subunits are autogenously regulated at the level of mRNA translation; this translational mechanism is clearly distinct from the transcriptional mechanism regulating beta and beta' expression described previously (P. P. Dennis, Proc. Natl. Acad. Sci. U.S.A. 74:5416-5420, 1977).

Effect of rifampicin on expression of lacZ fused to promoters or terminators of the E.coli rpoBC operon

The genes encoding the beta and beta' subunits of RNA polymerase in E.coli lie downstream of at least two ribosomal protein genes in a single unit of transcription. Treatment of E.coli with rifampicin, under conditions producing partial inhibition of general RNA synthesis, can strongly stimulate transcription of the polymerase genes, while activating the neighbouring ribosomal genes only slightly. We have investigated the mechanism of this effect by fusing strong promoters, a weak internal promoter, and an attenuator of the polymerase operon to the lacZ gene, in derivatives of plasmid pMC81. Studies of these fusions confirm our conclusion, based on similar fusions to galK, that rifampicin can foster readthrough of transcriptional terminators. They also suggest the existence of extra terminators and anti-termination elements in the above transcription unit.

Evidence that rifampicin can stimulate readthrough of transcriptional terminators in Escherichia coli, including the attenuator of the rpoBC operon

The genes encoding the beta and beta' subunits of RNA polymerase in E.coli, rpoB and rpoC, lie downstream of at least two ribosomal protein genes, rplJ (encoding L10) and rplL (L7/12), in a common operon. All four genes are served by promoter PL10, and an attenuator (partial terminator) of transcription, t1, lies between rplJL and rpoBC. Treatment of E.coli with rifampicin, under conditions producing partial inhibition of general RNA synthesis, can stimulate transcription of rpoBC. We have investigated the locus of this effect by fusing PL10 and t1 separately to galK, in suitable plasmids. Our studies of these fusions, and similar fusions involving transcriptional terminators derived from coliphage T7, indicate that low concentrations of rifampicin cause increased readthrough of several different transcriptional terminators in E.coli in vivo, including rpo t1. We discuss whether or not this unspecific mechanism is solely responsible for the observed stimulatory effects of the drug on rpoBC transcription.

RNA polymerase subunit biosynthesis in Bacillus subtilis

The relative rates of RNA polymerase biosynthesis in Bacillus subtilis has been examined under steady-state growth conditions. The synthesis of RNA polymerase subunits (alpha, beta, beta', omega) has been followed by subunit fractionation of immunoprecipitated [3H]-labelled samples on SDS-polyacrylamide gels. The stoichiometries of alpha:beta:beta':omega subunits have been determined from cultures pulse-labelled during steady-state growth. The results suggest that an unassembled pool of the alpha-subunit exists from which the holoenzyme is formed. Upon shift-up from acetate to glycerol containing medium, a rapid rise in the differential rate of core enzyme synthesis was observed, while the rate of synthesis of the alpha-subunit was not stimulated. During shift-down, a concomitant reduction in the rate of synthesis of all subunits occurred for the first 20 min after the shift; thereafter, a rate of synthesis characteristic of the new growth rate was established. As cultures enter sporulation, an immediate reduction in the rate of beta beta'-subunit synthesis was demonstrated.

Induction of prophage lambda does not require full induction of RecA protein synthesis

In mitomycin C-treated lambda lysogens, even though the rate of synthesis of RecA protein was greatly reduced by a low concentration of rifampicin (4 microgram/ml), induction of prophage lambda occurred readily as assessed by (i) cell lysis of the lysogens, (ii) production of progeny phage, and (iii) extensive cleavage of lambda repressor. The extent and the rate of cleavage of lambda repressor were not significantly affected by the low rate of synthesis of RecA protein resulting from rifampicin action. However, the yield of phage progeny was reduced and lysis of the cells was slightly delayed. We conclude that in RecA+ bacteria, induction of prophage lambda does not require full induction of RecA protein synthesis.

Regulation of ribonucleic acid polymerase synthesis during restriction of an Escherichia coli mutant temperature sensitive for transcription factor sigma

An Escherichia coli mutant temperature sensitive for the sigma subunit of ribonucleic acid polymerase was shifted to restrictive temperatures. In response to these restrictions the transcription of rpoBC increased markedly, and the synthesis rates of the beta and beta' subunits of ribonucleic acid polymerase increased. The ratio of the beta and beta' synthesis rates (beta/beta') decreased.

Autogenous regulation of the synthesis of ribosomal proteins, L10 and L7/12, in Escherichia coli

The in vitro synthesis of Escherichia coli ribosomal proteins, L10 and L7/12, is specifically repressed by the addition of the L10-L7/12 complex, while that of other ribosomal proteins encoded by the neighboring operons is not affected. Thus the expression of the rpoBC operon is controlled by two autorepression systems, one for the two ribosomal proteins and the other for RNA polymerase beta and beta' subunits, both operating probably at the translational level.

Synthesis and activity of ribonucleic acid polymerase in Escherichia coli

The amounts of ribonucleic acid (RNA) polymerase (beta' subunits) and ribosomes (RNA), and the fraction of RNA polymerase actively engaged in transcription, were measured in Escherichia coli B/r as a function of growth rate. By an improved method of quantitating protein bands on electrophoresis gels, the systematic error and reproducibility of the RNA polymerase determination were estimated to be less than 15 and 6%, respectively. For a threefold increase in growth rate, the fractional synthesis of polymerase (relative to protein) increased 1.5-fold, whereas the fractional synthesis of ribosomal protein increased 2.2-fold. The decrease in the amount of RNA polymerase per ribosome with increasing growth rate is interpreted as an expression of the control of the transcriptional read-through from the genes for ribosomal protein, rplJ,L, to the adjacent genes for RNA polymerase subunits, rpoB,C. The number of active RNA polymerase molecules was determined from the synthesis rates of stable and messenger RNA and the known RNA chain growth rates. Comparison of active and total RNA polymerase indicates that the fraction of active enzyme increases from 20 to 30% in the range of growth rates between 0.6 and 2.0 doublings per hour. Possible causes for the inactive enzyme are discussed.

A kinetic analysis of cell division, and induction and stability of recA protein in U.V. Irradiated ion+ and ion-strains of Escherichia coli K12

Kinetic analysis of induction of recA protein synthesis after U.V. irradiation does not show correspondence with the kinetics of division inhibition in ion+ and ion- strains. When the induction of recA protein after U.V. is drastically reduced by rifampicin treatment, no effect on the kinetics of division inhibition is observed.

Expression of RNA polymerase and ribosome component genes in Escherichia coli mutants having conditionally defective RNA polymerases

The expression of the genes coding for the beta and beta' subunits of RNA polymerase, ribosomal RNA, ribosomal proteins, and beta-galactosidase was investigated in strains carrying conditionally lethal mutations affecting either RNA polymerase core assembly or RNA polymerase enzyme activity. The mutant strain XH56 produces a temperature-sensitive beta' subunit and at 42 degrees C is defective in RNA chain initiation; consequently, little or no transcription occurs at the restrictive temperature. A partial restriction, produced by shifting the strain to 39 degrees C, resulted in a rapid fivefold increase in the transcription of the rpoB and C genes and in the synthesis of the beta- and beta'-subunit proteins for which they code. The RNA polymerase assembly-defective strains A2R7 and TS4 exhibited a 1.5- to 2-fold increase in the transcription of the rpoB and C genes and in the synthesis of beta- and beta-subunit proteins after prolonged restriction. These results demonstrate (i) that regulation of the synthesis of the beta- and beta-RNA polymerase subunits is under these conditions primarily transcriptional rather than translational, and (ii) that a stimulation of rpoB and C gene expression results from a restriction on RNA synthesis caused by either RNA polymerase inactivation or inhibition of its assembly. During restriction of the mutant strains, the transcription of the ribosome component genes exhibited patterns which were similar to transcription of the rpoB and C genes, supporting the evidence that genes coding for RNA polymerase are cotranscribed with ribosomal protein genes; transcription of the lacZ gene was observed to decrease concomitant with the stimulation of the rpoB and C genes.