DNA supercoiling and transcription in Escherichia coli: influence of RNA polymerase mutations

Ciprofloxacin selects for RNA polymerase mutations with pleiotropic antibiotic resistance effects

OBJECTIVES

Resistance to the fluoroquinolone drug ciprofloxacin is commonly linked to mutations that alter the drug target or increase drug efflux via the major AcrAB-TolC transporter. Very little is known about other mutations that might also reduce susceptibility to ciprofloxacin. We discovered that an Escherichia coli strain experimentally evolved for resistance to ciprofloxacin had acquired a mutation in rpoB, the gene coding for the β-subunit of RNA polymerase. The aim of this work was to determine whether this mutation, and other mutations in rpoB, contribute to ciprofloxacin resistance and, if so, by which mechanism.

METHODS

Independent lineages of E. coli were evolved in the presence of ciprofloxacin and clones from endpoint cultures were screened for mutations in rpoB. Ciprofloxacin-selected rpoB mutations were identified and characterized in terms of effects on susceptibility and mode of action.

RESULTS

Mutations in rpoB were selected at a high frequency in 3 out of 10 evolved lineages, in each case arising after the occurrence of mutations affecting topoisomerases and drug efflux. All ciprofloxacin-selected rpoB mutations had a high fitness cost in the absence of drug, but conferred a competitive advantage in the presence of ciprofloxacin. RNA sequencing and quantitative RT-PCR analysis showed that expression of mdtK, encoding a multidrug efflux transporter, was significantly increased by the ciprofloxacin-selected rpoB mutations. The susceptibility phenotype was shown to depend on the presence of an active mdtK and a mutant rpoB allele.

CONCLUSIONS

These data identify mutations in RNA polymerase as novel contributors to the evolution of resistance to ciprofloxacin and show that the phenotype is mediated by increased MdtK-dependent drug efflux.

Bending the rules of transcriptional repression: tightly looped DNA directly represses T7 RNA polymerase

From supercoiled DNA to the tight loops of DNA formed by some gene repressors, DNA in cells is often highly bent. Despite evidence that transcription by RNA polymerase (RNAP) is affected in systems where DNA is deformed significantly, the mechanistic details underlying the relationship between polymerase function and mechanically stressed DNA remain unclear. Seeking to gain additional insight into the regulatory consequences of highly bent DNA, we hypothesize that tightly looping DNA is alone sufficient to repress transcription. To test this hypothesis, we have developed an assay to quantify transcription elongation by bacteriophage T7 RNAP on small, circular DNA templates approximately 100 bp in size. From these highly bent transcription templates, we observe that the elongation velocity and processivity can be repressed by at least two orders of magnitude. Further, we show that minicircle templates sustaining variable levels of twist yield only moderate differences in repression efficiency. We therefore conclude that the bending mechanics within the minicircle templates dominate the observed repression. Our results support a model in which RNAP function is highly dependent on the bending mechanics of DNA and are suggestive of a direct, regulatory role played by the template itself in regulatory systems where DNA is known to be highly bent.

DNA supercoiling — a global transcriptional regulator for enterobacterial growth?

A fundamental principle of exponential bacterial growth is that no more ribosomes are produced than are necessary to support the balance between nutrient availability and protein synthesis. Although this conclusion was first expressed more than 40 years ago, a full understanding of the molecular mechanisms involved remains elusive and the issue is still controversial. There is currently agreement that, although many different systems are undoubtedly involved in fine-tuning this balance, an important control, and in our opinion perhaps the main control, is regulation of the rate of transcription initiation of the stable (ribosomal and transfer) RNA transcriptons. In this review, we argue that regulation of DNA supercoiling provides a coherent explanation for the main modes of transcriptional control - stringent control, growth-rate control and growth-phase control - during the normal growth of Escherichia coli.

RNA polymerase (rpoB) mutants selected for increased resistance to gyrase inhibitors in Salmonella typhimurium

Some rifampicin-resistance (RifR) mutations make bacteria slightly resistant to the gyrase inhibitors novobiocin (Nov) and nalidixic acid (Nal). This suggested that it might be possible to isolate rpoB mutants using either drug for positive selection. In an initial test, we confirmed the presence of Rif-resistant isolates among clones selected for Nov resistance. These mutants are also more resistant to Nal. In a subsequent experiment, we found that mutants selected for low-level resistance to Nal include isolates harboring mutations genetically linked to the rpoB locus; of two such mutants studied, one is temperature-sensitive for growth. These two mutants, which are only marginally affected in their response to Nov, are normally sensitive to Rif and thus might be representative of a new class of rpoB alleles. The Rif-resistant and Rif-sensitive rpoB alleles that increase resistance to gyrase inhibitors have one property in common: they all suppress, to varying degrees, the defect in his operon regulation (transcriptional deattenuation) caused by a gyrase defect or inhibition by novobiocin. To further analyse the transcription-supercoiling relationships in these mutants, we examined the ability of RNA polymerase to recruit gyrase activity during transcription. This was done by two independent approaches: (i) observing transcription-induced accumulation of hyper-negatively supercoiled plasmid DNA in a topA mutant background and (ii) measuring transcription-induced plasmid DNA cleavage in the presence of oxolinic acid. Results indicate that the rpoB alleles described in this study diminish the recruitment of gyrase activity by the transcription process. This property correlates with a decrease in the rate of transcription initiation.(ABSTRACT TRUNCATED AT 250 WORDS)

Regulation of DNA superhelicity by rpoB mutations that suppress defective Rho-mediated transcription termination in Escherichia coli

The highly defective rho-15 mutant of Escherichia coli produces plasmid DNA that is 22% less negatively supercoiled than DNA from an isogenic wild-type strain (J. S. Fassler, G. F. Arnold, and I. Tessman, Mol. Gen. Genet. 204:424-429, 1986). We extended our measurements of plasmid superhelicity to additional rho mutants and to strains containing mutations that suppress rho transcription termination defects; the suppressor mutations were in the rpoB and the rho genes. The superhelicity of plasmid DNA was reduced by 11 and 10%, respectively, in the rho-702 and rho-201 mutants, both of which are less defective in Rho-mediated transcription termination than rho-15. Plasmid superhelicity was restored in all the suppressed rho mutants; in one rpoB mutant, plasmid DNA was even more negatively supercoiled than in rpoB+ cells, whether in a rho+ or rho mutant background. Suppression of rho mutants enabled them to maintain plasmids that could not be maintained in the mutants in the absence of the suppressor mutations. The results indicate that in addition to DNA gyrase, topoisomerase I, and Rho, RNA polymerase is also a determinant of DNA superhelicity, and its effect is modified by the Rho protein. We propose that Rho may increase the degree of DNA unwinding by the transcription complex, possibly at transcription termination sites.

Estimation of the effect of coumermycin A1 on Salmonella typhimurium promoters by using random operon fusions

We have estimated the extent to which relaxation of supercoiling by the DNA gyrase inhibitor coumermycin A1 affects gene expression in vivo in Salmonella typhimurium. We isolated a set of Mu d1-8 Lac+ operon fusions to random promoters and measured the effect of coumermycin A1 on the expression of 67 fusions. The differential rate of synthesis was increased for 70% of the fusions and decreased for 16%, and 13% of the fusions had less than a 25% change in expression. The coumermycin A1 response was found to correlate well (P = 0.067) with the basal level of expression such that coumermycin A1 tended to stimulate fusions with low expression and inhibit those with high expression. Since the vast majority of the fusions were sensitive to coumermycin A1 addition and, therefore, to the level of supercoiling, these results indicate that if the level of supercoiling were to vary under physiological conditions, then major readjustments in the cellular economy would occur.

In vivo localization of DNA topoisomerase II cleavage sites on Drosophila heat shock chromatin

Similar to its inhibitory effect on mammalian DNA topoisomerase II, the cytotoxic drug VM26 (teniposide) also interferes with the breakage-reunion reaction of Drosophila melanogaster DNA topoisomerase II. VM26 induces topoisomerase II-mediated DNA breakage in vitro and in cultured D. melanogaster cells presumably by stabilizing an enzyme-DNA cleavable complex. The drug-induced DNA breaks on D. melanogaster hsp70 genes were mapped in cultured cells using the indirect end-labeling procedure. Multiple and specific cleavage sites occurred at both the 3' and 5' ends of the hsp70 genes. A number of these cellular topoisomerase II cleavage sites mapped close to the DNase I-hypersensitive regions of the hsp70 genes. The intensities of several topoisomerase II cleavage sites changed significantly on heat shock induction. Treatment of cultured D. melanogaster cells with VM26 at 25 degrees C resulted in the stimulation of transcription of the hsp70 genes. These results suggest that inhibition of DNA topoisomerase II may lead to heat shock transcription.

In vivo localization of DNA topoisomerase II cleavage sites on Drosophila heat shock chromatin

Similar to its inhibitory effect on mammalian DNA topoisomerase II, the cytotoxic drug VM26 (teniposide) also interferes with the breakage-reunion reaction of Drosophila melanogaster DNA topoisomerase II. VM26 induces topoisomerase II-mediated DNA breakage in vitro and in cultured D. melanogaster cells presumably by stabilizing an enzyme-DNA cleavable complex. The drug-induced DNA breaks on D. melanogaster hsp70 genes were mapped in cultured cells using the indirect end-labeling procedure. Multiple and specific cleavage sites occurred at both the 3' and 5' ends of the hsp70 genes. A number of these cellular topoisomerase II cleavage sites mapped close to the DNase I-hypersensitive regions of the hsp70 genes. The intensities of several topoisomerase II cleavage sites changed significantly on heat shock induction. Treatment of cultured D. melanogaster cells with VM26 at 25 degrees C resulted in the stimulation of transcription of the hsp70 genes. These results suggest that inhibition of DNA topoisomerase II may lead to heat shock transcription.

H1 histone, polylysine and spermine facilitate nucleosome assembly in vitro

Nucleosome formation has been studied in a system containing relaxed Col E1 DNA, core histones and an extract of Drosophila embryos. The formation of nucleosomes was established by the introduction of supercoils into DNA. The degree of DNA supercoiling was shown to be higher if nucleosomes were assembled in the presence of the H1 histone, polylysine (Mr 20 000) or spermine. These agents do not stimulate relaxation and are the more effective the earlier they are added to the reaction. Thus, the H1 histone, polylysine and spermine facilitate nucleosome assembly in vitro.

DNA replication and transcription in a temperature-sensitive mutant of E. coli with a defective DNA gyrase B subunit

A temperature-sensitive mutant of E. coli with a defective DNA gyrase B subunit has been obtained. The mutation is expressed in the thermolability of DNA gyrase in vitro and in DNA relaxation in vivo. DNA replication in the mutant does not stop under non-permissive conditions; its rate gradually falls by a factor of 2 to 3. The transcription rate also drops by a factor of 2 to 3, but before replication. Small concentrations of rifampicin, an inhibitor of bacterial RNA polymerase, make for a partial survival of the mutant cells under non-permissive conditions. The results suggest the conclusion that DNA supercoiling is mainly required to ensure the optimum transcription level in the cell.

Novel pleiotropic effect of rifampicin resistance mutation in a Micromonospora sp

Rifampicin-resistant mutants have been isolated from aMicromonosporasp. In one of these, rifampicin failed to inhibit [3H]UTP incorporation in osmotically shocked cells; consequently, resistance was probably not due to the alteration of rifampicin permeability. Parallel to the rifampicin resistance there was a substantial increase in the novobiocin sensitivity of the mutants. Rifampicin-sensitive revertants exhibited their original novobiocin sensitivity. At the same time there was no increase in their sensitivity towards coumermycin A1, an agent of related structure and activity. The possible mechanism for this pleiotropy is discussed.

Inhibition of DNA synthesis accompanied by stimulation of protein synthesis in novobiocin-treated developing sea urchins

Novobiocin, an inhibitor of bacterial DNA gyrase, induces abnormalities in developing embryo of the American sea urchin Arbacia punctulata. In addition this drug is also a specific inhibitor of DNA synthesis. This block in DNA synthesis is accompanied by a stimulation in protein synthesis. This effect appears to be characteristic of novobiocin, as hydroxyurea another inhibitor of DNA synthesis in the developing sea urchin, does not stimulate protein production. The present findings constitute the first report of a novobiocin-induced specific inhibition of DNA synthesis in a higher eukaryote.

Enhancement of ribosomal ribonucleic acid synthesis by deoxyribonucleic acid gyrase activity in Escherichia coli

The effect of the deoxyribonucleic acid (DNA) gyrase inhibitors coumermycin A1, novobiocin, and oxolinic acid on ribonucleic acid (RNA) synthesis in Escherichia coli was studied in vivo and in vitro. Preferential inhibition of ribosomal RNA (rRNA) synthesis was observed. No effect of oxolinic acid and coumermycin on rRNA synthesis was seen in mutants having a DNA gyrase which is resistant to these inhibitors. In a temperature-sensitive DNA gyrase mutant rRNA synthesis was decreased at nonpermissive temperatures. Thus, a functional DNA gyrase is required for rRNA synthesis. Purified DNA gyrase had no effect on rRNA synthesis in a purified system. However, DNA gyrase does show preferential stimulation of rRNA synthesis in a system supplemented with other proteins. Apparently, DNA gyrase stimulation of rRNA synthesis requires another protein.

Essential role of the gyrB gene product in the transcriptional event coupled to dnaA-dependent initiation of Escherichia coli chromosome replication

When a culture of the gyrB41-ts mutant is shifted to the nonpermissive temperature, DNA synthesis is arrested at the initiation phase of chromosome replication. After thermal inactivation of the gyrB gene product reinitiation occurs in the presence of chloramphenicol but not in the presence of rifampicin. This suggests that the B subunit of DNA gyrase may regulate synthesis of an "initiator RNA". An rpoB202 mutation has been isolated which suppresses both the DnaA-initiation phenotype and the inhibitory action of antibiotics which are known to result in relaxation of chromosomal DNA in vivo. We propose that DNA tertiary structure rather than DNA gyrase itself plays an essential regulatory function in the dnaA-dependent transcription which precedes the initiation of chromosome replication.

Cold-sensitive mutations in beta and beta' subunit gene affecting the interaction of RNA polymerase with promoters

RNA polymerases with a cold-sensitive activity were purified from seven mutants of Escherichia coli. Subunit reconstitution experiments have shown that RNA polymerases from three mutants (Rpob262, RpoB264, and RpoB265) owed their cold sensitivity to alterations in the beta subunit. Three mutants (RpoC3, RpoC263, and RpoC267) were shown to be defective in the beta' subunit and one (RpoBC266) in both beta and beta' subunits. Two mutations (rpoC3 and rpoC263) reduced the level of RNA polymerase reconstitution. RNA polymerases from RpoC3 and RpoBC266 mutants are defective in RNA chain elongation at 6 degree C, while all the other mutants are defective in RNA polymerase-promoter interaction. most mutant RNA polymerases differ from the wild-type enzyme in transcription selectivity. The results obtained in this study indicate that both beta and beta' subunits are involved in RNA chain elongation and promoter binding and selection.

Curing of Escherichia coli K12 plasmids by coumermycin

Low concentrations of the antibiotic coumermycin A1, the inhibitor of bacterial DNA gyrase, effectively eliminate pBR322, pMB9 and other ColE 1 related plasmids from E. coli K12 strains. The curing action of antibiotic seems to result from the plasmid degradation and not just from the inhibition of replication.