Escherichia coli DNA topoisomerase I mutants have compensatory mutations in DNA gyrase genes

acrB mutation located at carboxyl-terminal region of gyrase B subunit reduces DNA binding of DNA gyrase

Mutations that exhibit susceptibility to acriflavine have been isolated and classified as acr mutations in Escherichia coli. We cloned the acrB gene, which has been identified as a mutation of the gyrB gene, and found a double point mutation altering two consecutive amino acids (S759R/R760C) in the COOH-terminal region of the gyrase B subunit. The mutant B subunit was found to associate with the A subunit to make the quaternary structure, and the reconstituted gyrase showed an 80-fold reduction of specific activity in DNA supercoiling assay; the sensitivity to acriflavine was not different in the same unit of wild-type and mutant gyrases. The mutant enzyme retained intrinsic ATPase activity, but DNA-dependent stimulation was observed infrequently. A gel shift assay showed that acriflavine inhibited the DNA binding of gyrase. The acrB mutation also reduced significantly the DNA binding of gyrase but did not change the sensitivity to acriflavine. These results revealed that the acrB mutation is related to the inhibitory mechanism of acriflavine; and the acriflavine sensitivity of the mutant, at least in vitro, is caused mainly by reduction of the enzyme activity. Further, our findings suggest that the COOH-terminal region of the B subunit is essential for the initial binding of gyrase to the substrate DNA.

DNA topoisomerases regulate R-loop formation during transcription of the rrnB operon in Escherichia coli

Recent in vivo and in vitro studies have suggested an important role for DNA topoisomerases in regulating R-loop formation during transcription in Escherichia coli. In the present report we present genetic and biochemical evidence strongly suggesting that R-loop formation can occur during transcription of a portion of the rrnB operon and that it is regulated by DNA topoisomerase activity. We found that a multicopy plasmid (pBR322) carrying an heavily transcribed portion of the rrnB operon cannot be transformed in topA mutants unless RNase H is overproduced. Transcription of the 567-base pair HindIII fragment from the rrnB operon allows the extraction of large amount of R-looped plasmid DNAs from a topA mutant, in a manner that depends on the intracellular level of RNase H activity. When DNA gyrase is sufficiently active, hypernegatively supercoiled plasmid DNA is produced if the same DNA fragment is transcribed in a topA mutant. The formation of such topoisomers most likely reflect the presence of extensive R-loops since it is sensitive to the intracellular level of RNase H activity. Finally, the formation of R-looped plasmid DNAs in an in vitro transcription system using phage RNA polymerases is also detected when the 567-base pair HindIII fragment is transcribed on a negatively supercoiled DNA template.

Discoordinate gene expression of gyrA and gyrB in response to DNA gyrase inhibition in Escherichia coli

The intracellular level of DNA supercoiling is regulated in Escherichia coli by a homeostatic control mechanism that includes DNA gyrase and topoisomerase I gene expression. Despite several biochemical and genetical evidence that supports the existence of a homeostatic regulation mechanism, there are only few studies focusing gyrA and gyrB gene expression in connection to the mechanism involved in the regulation of DNA supercoiling in vivo. To study DNA gyrase gene expression and to be able to isolate mutants with altered expression of DNA gyrase, we constructed a new chromosomal reporter system based on two translational fusions of gyrA and gyrB to lacZ Using this stable monitor system in a robust wild type, we simultaneously studied the influence of several inhibitors of DNA gyrase (quinolones and coumarins) on gyrA and gyrB gene expression as well as on the intracellular level of DNA supercoiling. Surprisingly, we found a delayed and differential response of gyrA and gyrB gene expression following inhibition of DNA gyrase by quinolones or coumarins. Whereas both groups of drugs were able to increase the expression of gyrA, the gyrB gene expression was only induced by the coumarins. Although the action of the quinolones was able to alter DNA supercoiling, we never observed any induction of gyrB from the chromosome. These results revealed that the gene expressio of gyrA appears to be more sensitive to alterations in DNA supercoiling than the gyrB gene expression and suggest that probably additional regulatory mechanisms on the post-translational level might be involved in the regulation of DNA supercoiling and DNA gyrase gene expression.

Targeted disruption of the mouse topoisomerase I gene by camptothecin selection

Topoisomerase I has ubiquitous roles in important cellular functions such as replication, transcription, and recombination. In order to further characterize this enzyme in vivo, we have used gene targeting to inactivate the mouse Top-1 gene. A selection protocol using the topoisomerase I inhibitor camptothecin facilitated isolation of embryonic stem cell clones containing an inactivated allele; isolation of correctly targeted clones was enhanced 75-fold over that achieved by normal selection procedures. The disrupted Top-1 allele is embryonic lethal when homozygous, and development of such embryos fails between the 4- and 16-cell stages. Both sperm and oocytes containing the inactive allele maintain viability through the fertilization point, and thus gene expression of topoisomerase I is not required for gamete viability. These studies demonstrate that topoisomerase I is essential for cell growth and division in vivo. The Top-1 gene was also shown to be linked to the agouti locus.

Heat shock-induced DNA relaxation in vitro by DNA gyrase of Escherichia coli in the presence of ATP

Genetic studies revealed that DNA gyrase seems to catalyze immediate and transient DNA relaxation after Escherichia coli cells are exposed to heat shock (Ogata, Y., Mizushima, T., Kataoka, K., Miki, T., and Sekimizu, K. (1994) Mol. Gen. Genet. 244, 451-455). We have now obtained biochemical evidence to support this hypothesis. DNA gyrase catalyzed an increase in the linking number of DNA and relaxation of negatively supercoiled DNA, under physiological concentrations of ATP. Analyses by gel filtration chromatography of each subunit revealed that DNA relaxation activity co-migrated with each subunit. The linking number of DNA increased as the temperature increased. Further, the reaction was inhibited by nalidixic acid or by oxolinic acid. Based on these results, we propose that DNA gyrase participates in a concerted reaction with DNA topoisomerases in the immediate relaxation of DNA in cells exposed to heat shock.

DNA supercoiling and transcription: topological coupling of promoters

DNA supercoiling is a consequence of the double-stranded nature of DNA. When a linear DNA molecule is ligated into a covalently closed circle, the two strands become intertwined like the links of a chain, and will remain so unless one of the strands is broken. The number of times one strand is linked with the other is described by a fundamental property of DNA supercoiling, the linking number (Lk).

Silencing of the Escherichia coli bgl promoter: effects of template supercoiling and cell extracts on promoter activity in vitro

Regulation of the Escherichia coli bgl promoter involves the catabolite gene activator protein (CAP) and silencer elements that are located upstream and downstream of the promoter and its CAP binding site. The promoter is kept in a repressed state by the silencer elements and other normally active CAP-dependent or -independent promoters are repressed as well when flanked by these elements. To assess the mechanism of promoter repression, single round in vitro transcription was carried out with plasmids bearing either the wild-type bgl promoter or one of two derivatives that escape repression in vivo by different mechanisms: C234 by improving the CAP binding site of the promoter and delta1 by a deletion within the upstream silencer sequence. Repression of the bgl promoter in vitro was shown to depend on template topology and the presence of cellular factors. With negatively supercoiled templates, all three promoters are transcribed to similar extents by purified E. coli RNA polymerase and no CAP dependence is apparent; with relaxed templates, transcription is CAP dependent, but the levels of transcription of the three promoters are comparable. Addition of crude cell extract to the simple transcription system leads to repression of all three promoter alleles in the absence of CAP. Repression of the mutant alleles but not of the wild-type promoter is completely relieved in the presence of the CAP-cAMP complex. The topology of the DNA template is also important in the differential regulation of these promoters. In the case of C234, repression by cell extract is completely relieved by CAP-cAMP on relaxed or negatively supercoiled templates, while complete derepression of delta1 by CAP-cAMP occurs on negatively supercoiled templates only. Repression by cell extract requires the presence of the histone-like protein H-NS. However, H-NS alone does not appear to be sufficient for specific silencing of the wild-type promoter, since repression of all three promoter alleles caused by purified H-NS protein is completely relieved by the CAP-cAMP complex. These data suggest that template topology, H-NS and other cellular factors are involved in the formation of a specific nucleoprotein structure in the bgl promoter-silencer region; the formation of this nucleoprotein structure keeps an otherwise active promoter in an inactive state.

How is osmotic regulation of transcription of the Escherichia coli proU operon achieved? A review and a model

The proU operon in enterobacteria encodes a binding-protein-dependent transporter for the active uptake of glycine betaine and L-proline, and serves an adaptive role during growth of cells in hyperosmolar environments. Transcription of proU is induced 400-fold under these conditions, but the underlying signal transduction mechanisms are incompletely understood. Increased DNA supercoiling and activation by potassium glutamate have each been proposed in alternative models as mediators of proU osmoresponsivity. We review here the available experimental data on proU regulation, and in particular the roles for DNA supercoiling, potassium glutamate, histone-like proteins of the bacterial nucleoid, and alternative sigma factors of RNA polymerase in such regulation. We also propose a new unifying model, in which the pronounced osmotic regulation of proU expression is achieved through the additive effects of at least three separate mechanisms, each comprised of a cis element [two promoters P1 and P2, and negative-regulatory-element (NRE) downstream of both promoters] and distinct trans-acting factors that interact with it: stationary-phase sigma factor RpoS with P1, nucleoid proteins HU and IHF with P2, and nucleoid protein H-NS with the NRE. In this model, potassium glutamate may activate proU expression through each of the three mechanisms whereas DNA supercoiling has a very limited role, if any, in the osmotic induction of proU transcription. We also suggest that proU may be a virulence gene in the pathogenic enterobacteria.

Suppression of the Bgl+ phenotype of a delta hns strain of Escherichia coli by a Bacillus subtilis antiterminator binding site

Bacillus subtilis, like Escherichia coli, possesses several sets of genes involved in the utilization of beta-glucosides. In E. coli, all these genes are cryptic, including the genes forming the bgl operon, thus leading to a Bgl- phenotype. We screened for B. subtilis chromosomal DNA fragments capable of reverting the Bgl+ phenotype associated with an E. coli hns mutant to the Bgl- wild-type phenotype. One B. subtilis chromosomal fragment having this property was selected. It contained a putative Ribonucleic AntiTerminator binding site (RAT sequence) upstream from the bgl gene. Deletion studies as well as subcloning experiments allowed us to prove that the putative B. subtilis of the E. coli bgl operon. We propose that this repression results from the titration of the BglG antiterminator protein of E. coli bgl operon by our putative B. subtilis bglP RAT sequence. Thus, we report evidence for a new cross interaction between heterologous RAT-antiterminator protein pairs.

Characterization of the Haemophilus influenzae topA locus: DNA topoisomerase I is required for genetic competence

A gene essential for the development of genetic competence in Haemophilus influenzae (Hi) was identified as a homolog of the Escherichia coli (Ec) topA gene, which encodes DNA topoisomerase I (TopI). The Hi topA locus was initially identified by mini-Tn10kan mutagenesis. Three independent insertion events within 500 bp of each other resulted in mutant strains that shared a similar phenotype. Each was deficient in competence-induced DNA binding, showed increased sensitivity to UV irradiation, and had an increased doubling time as compared to the wild-type (wt) strain. The nucleotide sequence of a 6.6-kb fragment containing the wt allele was determined. The sequence contained an open reading frame (ORF) of 868 amino acids (aa) that was interrupted by each of the mini-Tn10kan mutations. The deduced aa sequence had a molecular mass of 98 155 Da, a pI of 8.59 and showed strong similarity to Ec TopI. Examination of the topoisomer distribution of a test plasmid in an Hi mutant carrying an insertion in this ORF showed an increase in the level of supercoiling, indicating that TopI is necessary to relax supercoiled DNA in Hi. Complementation studies and insertional inactivation of genes downstream from topA indicated that TopI and not some downstream gene product was essential for competence. Four other ORFs were identified and two of these had homology to known genes. ORF1, which was truncated at one end of the sequenced region, shared strong sequence similarity to the C-terminal end of Ec pyridine nucleotide transhydrogenase beta subunit. ORF4, which was also truncated, showed strong sequence similarity to the N-terminal end of the Ec threonyl-tRNA synthetase.

The creation of a camptothecin-sensitive Escherichia coli based on the expression of the human topoisomerase I

The synthesis of the human topoisomerase I (Topo I) in Escherichia coli (Ec) results in phenotypes consistent with the appearance of a DNA-relaxing activity. High-level expression was problematic and recloning the gene in a reduced-copy-number plasmid under more stringently regulated control produced a stable plasmid. An Ec strain with an inducible sensitivity to the eukaryotic Topo I poison, camptothecin (CPT), was constructed by introducing a mutation (imp4312) known to enhance the permeability of Ec to a wide variety of compounds. We are able to infer that CPT sensitivity in Ec involves DNA damage by noting elevated sensitivity in a repair-deficient recA strain and by observing the induction of a sulA::lac fusion following exposure to the drug.

Roles of topoisomerase IV and DNA gyrase in DNA unlinking during replication in Escherichia coli

For a cell to complete DNA replication, every link between the Watson-Crick strands must be removed by topoisomerases. Previously, we reported that the inhibition of topoisomerase IV (topo IV) leads to the accumulation of catenated plasmid replicons to a steady-state level of approximately 10%. Using pulse labeling with [3H]thymidine in Escherichia coli, we have found that in the absence of topo IV activity, nearly all newly synthesized plasmid DNA is catenated. Pulse-chase protocols revealed that catenanes are metabolized even in the absence of topo IV and that the residual turnover is carried out by DNA gyrase at a rate of approximately 0.01/sec. Using extremely short pulse-labeling times, we identified significant amounts of replication catenanes in wild-type cells. The rate of catenane unlinking in wild-type cells by the combined activities of topo IV and DNA gyrase was approximately 1/sec. Therefore, gyrase is 100-fold less efficient than topo IV in plasmid replicon decatenation in vivo. This may explain why a fully functional gyrase cannot prevent the catenation of newly synthesized plasmid DNA and the partition phenotype of topo IV mutants. We conclude that catenanes are kinetic intermediates in DNA replication and that the essential role of topo IV is to unlink daughter replicons.

Influence of DNA supercoiling on cisplatin toxicity in Escherichia coli K-12

DNA supercoiling is known to modulate the activity of numerous promoters in vitro and in vivo. Moreover, it has been reported to modulate the rate of formation of cisplatin/DNA crosslinks in vitro. In order to address the question of how the topology influences CDDP toxicity in E. coli, three mutants with altered gyrase activity which led to a decrease of about 25% in superhelical density were studied. Mutant strains gyrA224 and gyrB225 showed similar sensitivity to CDDP as the parental strain while the gyrB226 mutant was resistant. This resistance was abolished in uvrA (excision-repair) and recA (recombination and SOS processes) mutant derivatives. Thus supercoiling might play a role as an indirect modulator of CDDP toxicity in bacteria by interfering with repair processes.

Long-range interaction between two promoters: activation of the leu-500 promoter by a distant upstream promoter

The leu-500 mutation can be suppressed in S. typhimurium topA. Previous studies have demonstrated that the plasmid-borne leu-500 minimal promoter cannot be activated in topA mutants unless adjacent (< 250 bp) transcription occurs away from the leu-500 promoter (short-range promoter interaction). To search for a potential upstream promoter responsible for activation of leu-500 in the chromosomal context, we have identified the ilvlH promoter, located 1.9 kb upstream of leu-500 (long-range promoter interaction). Different from short-range promoter interaction, which is abolished by DNA sequence insertions, the long-range promoter interaction is mediated by the intervening DNA sequence. These studies suggest that the long-range interaction between a pair of divergently arrayed promoters is probably mediated by a complex process involving relay of DNA supercoiling by the DNA sequence located between the two promoters.

Overexpression of RNase H partially complements the growth defect of an Escherichia coli delta topA mutant: R-loop formation is a major problem in the absence of DNA topoisomerase I

Previous biochemical studies have suggested a role for bacterial DNA topoisomerase (TOPO) I in the suppression of R-loop formation during transcription. In this report, we present several pieces of genetic evidence to support a model in which R-loop formation is dynamically regulated during transcription by activities of multiple DNA TOPOs and RNase H. In addition, our results suggest that events leading to the serious growth problems in the absence of DNA TOPO I are linked to R-loop formation. We show that the overexpression of RNase H, an enzyme that degrades the RNA moiety of an R loop, can partially compensate for the absence of DNA TOPO I. We also note that a defect in DNA gyrase can correct several phenotypes associated with a mutation in the rnhA gene, which encodes the major RNase H activity. In addition, we found that a combination of topA and rnhA mutations is lethal.

The twisted 'life' of DNA in the cell: bacterial topoisomerases

DNA topoisomerases are essential to the cell for the regulation of DNA supercoiling levels and for chromosome decatenation. The proposed mechanisms for these reactions are essentially the same, except that a change in supercoiling is due to an intramolecular event, while decatenation requires an intermolecular event. The characterized bacterial topoisomerases appear capable of both types of reaction in vitro. Four DNA topoisomerases have been identified in Escherichia coli. Topoisomerase I, gyrase, and topoisomerase IV normally appear to have distinct essential functions within the cell. Gyrase and topoisomerase I are responsible for the regulation of DNA supercoiling. Both gyrase and topoisomerase IV are necessary for chromosomal decatenation. Multiple topoisomerases with distinct functions may give the cell more precise control over DNA topology by allowing tighter regulation of the principal enzymatic activities of these different proteins.

Overexpression of the Shigella flexneri genes coding for DNA topoisomerase IV compensates for loss of DNA topoisomerase I: effect on virulence gene expression

Introducing the Escherichia coli topA20::Tn10 allele to Shigella flexneri results in osmotic sensitivity, a reduced growth rate, an increase in reporter plasmid supercoiling (all common to the E. coli mutants), an inability to grow on MacConkey agar and a loss of virulence gene expression. E. coli mutants harbouring this topA allele often compensate for the loss of DNA topoisomerase I by amplifying the genes coding for topoisomerase IV. Unlike the E. coli topA mutants, derivatives of S. flexneri harbouring this topA allele did not appear to acquire any compensatory mutations. We investigated the possibility that this was due in part to an inability of the S. flexneri topoisomerase IV genes to compensate for loss of DNA topoisomerase I when overexpressed. The S. flexneri genes encoding the alpha- and beta subunits of topoisomerase IV were detected and cloned in separate multicopy plasmids. These plasmids complemented well-characterized Salmonella typhimurium temperature-sensitive topoisomerase IV mutations, showing that the S. flexneri and S. typhimurium proteins are capable of combining to form active complexes. When the S. flexneri topoisomerase IV genes were cloned in the same multicopy plasmid and introduced into a S. flexneri topA mutant, the plasmid restored osmotic tolerance, improved the growth rate, allowed growth on MacConkey indicator plates and resulted in a relaxation of reporter plasmid supercoiling. The same plasmid also partially restored S. flexneri virulence gene transcription. These data show that overexpression of the S. flexneri topoisomerase IV genes can compensate for the loss of topoisomerase I in terms of general viability of the cell, DNA supercoiling, and (partially) virulence gene expression. The fact that S. flexneri does not exploit topoisomerase IV gene amplification as E. coli does points to a significant difference in the abilities of these species to adapt to the loss of topoisomerase I.

Genetics of selection-induced mutations: I. uvrA, uvrB, uvrC, and uvrD are selection-induced specific mutator loci

Selection-induced mutations, sometimes called "directed," "adaptive," or "Cairnsian" mutations, are spontaneous mutations that occur as specific responses to environmental challenges, usually during periods of prolonged stress, and that occur more often when they are selectively advantageous than when they are selectively neutral. In this study I show that lesions in uvrA, uvrB, uvrC, or uvrD increase the mutation rate from trpA46 to trpA+ by 10(2)- to 10(4)-fold during tryptophan starvation, but those same lesions do not affect random mutation rates in growing cells when tryptophan is present. The increased selection-induced mutation rates remain specific to the gene that is under selection in that no increase in the mutation rate from trpA46 to trpA+ is detected during proline starvation. Evidence is presented showing that proline starvation produces a state of cellular stress which results in a burst of mutations from trpA46 to trpA+ when proline-starved cells are plated onto medium lacking tryptophan but containing proline. These results are consistent with the hypermutable state model for selection-induced mutagenesis.

Structure and function of type II DNA topoisomerases

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Comparison of inhibition of Escherichia coli topoisomerase IV by quinolones with DNA gyrase inhibition

In order to examine the inhibitory activities of quinolones against topoisomerase IV, both subunits of this enzyme, ParC and ParE, were purified from Escherichia coli. The specific activity of topoisomerase IV decatenation was found to be more than five times greater than that of topoisomerase IV relaxation. Thus, the decatenation activity of topoisomerase IV seems the most relevant activity for use in studies of drug inhibition of this enzyme. Although topoisomerase IV was less sensitive to quinolones than DNA gyrase, the 50% inhibitory concentrations for decatenation were significantly lower than those for type I topoisomerases. Moreover, there was a positive correlation between the inhibitory activity against topoisomerase IV decatenation and that for DNA gyrase supercoiling. These results imply that topoisomerase IV could be a target for the quinolones in intact bacteria and that quinolones could inhibit not only supercoiling of DNA gyrase but also decatenation of topoisomerase IV when high concentrations of drug exist in bacterial cells.

Escherichia coli tyrT gene transcription is sensitive to DNA supercoiling in its native chromosomal context: effect of DNA topoisomerase IV overexpression on tyrT promoter function

We have investigated the in vivo DNA supercoiling sensitivity of the Escherichia coli tRNA(1tyr) gene (tyrT) promoter in its normal chromosomal location. Here, the native tyrT promoter is found to be exquisitely sensitive to mutations and to drugs which alter the level of DNA supercoiling. We show that the response of the tyrT promoter to supercoiling is qualitatively similar to that of a known supercoiling-sensitive tRNA gene promoter, hisR. Specifically, treatments which increase in vivo DNA supercoiling levels enhance transcription of these tRNA genes. Particularly striking is the strong enhancement of expression from both promoters by a transposon insertion mutation in the topA gene encoding DNA toposisomerase I. This phenotypic effect can be complemented by providing active topoisomerase I in trans from a recombinant plasmid. Interestingly, it can also be complemented by overexpression of the genes encoding the subunits of DNA topoisomerase IV. We believe that this is the first demonstration that DNA topoisomerase IV can influence gene expression and it suggests that DNA topoisomerase I is partially redundant, at least in E. coli.

Structure and function of the class C tetracycline/H+ antiporter: three independent groups of phenotypes are conferred by TetA (C)

The class C tetracycline/H+ antiporter, TetA(C), confers nine distinct phenotypes in Escherichia coli: resistance to tetracycline, reduced culture density at stationary phase (growth yield), increased supercoiling of plasmid DNA, delayed growth in succinate minimal medium, complementation of potassium uptake defects, increased susceptibility to cadmium, increased susceptibility to fusaric acid, increased susceptibility to bleomycin and increased susceptibility to several classes of cationic aminoglycoside antibiotics. These nine phenotypes were resolved into three 'linkage' groups based on their patterns of suppression by mutations of the tetA(C) gene of plasmid pBR322. Group I includes resistance to tetracycline, increased susceptibility to cadmium and reduced growth yield. Group II includes delayed growth in succinate minimal medium and complementation of potassium uptake defects. Group III includes increased supercoiling of plasmid DNA and increased susceptibilities to fusaric acid, bleomycin and cationic aminoglycosides. Phenotypes of Groups II and III, but not Group I, also were conferred by a chimeric gene encoding a fusion between the N-terminal 34 residues of TetA(C) and the C-terminal 429 residues of a structurally-similar protein, the E. coli galactose/H+ symporter, GalP. In contrast, none of these phenotypes was conferred by a chimeric gene encoding a fusion between the N-terminal 34 residues of TetA(C) and a structurally-dissimilar protein, TEM beta-lactamase. These results demonstrate that the three groups of linked phenotypes are dependent on different elements of the TetA(C) amino acid sequence, implying that TetA(C) confers these phenotypes by at least three independent mechanisms.

Identification of DNA topoisomerases involved in immediate and transient DNA relaxation induced by heat shock in Escherichia coli

The linking number of plasmid DNA in exponentially growing Escherichia coli increases immediately and transiently after heat shock. The purpose of this study was to search for DNA topoisomerases that catalyze this relaxation of DNA. Neither introduction of a topA deletion mutation nor treatment of cells with DNA gyrase inhibitors affected the DNA relaxation induced by heat shock. Thus, DNA topoisomerase I and DNA gyrase are apparently not involved in the process. However, the reaction was inhibited by nalidixic acid or by oxolinic acid in the topA mutant and the reaction was resistant to nalidixic acid in a topA mutant carrying, in addition, the nalA26 mutation. These results are interpreted as indicating that both DNA topoisomerase I and DNA gyrase are involved in the DNA relaxation induced by heat shock.

Elevated unconstrained supercoiling of plasmid DNA generated by transcription and translation of the tetracycline resistance gene in eubacteria

Our previous studies have indicated that the leu-500 promoter of Salmonella typhimurium is activated by local supercoiling arising from the transcription of a divergent promoter (Chen et al., 1992). For this to occur on a plasmid, we have shown that the transcribing RNA polymerase must be anchored to the cell membrane by transcription, translation, and export of the tetA gene and that the cell background must be topA. In this study we have used (AT)n reporter sequences to analyze changes in unconstrained supercoiling of plasmid DNA under the circumstances in which the leu-500 promoter becomes activated. (AT)n sequences undergo a structural transition to a cruciform at a threshold level of negative supercoiling that is determined by the length of the tract, and this can be detected in the cellular DNA by in situ chemical probing. These studies have shown that there is elevated unconstrained supercoiling in tetA-carrying plasmids in either Escherichia coli or S. typhimurium cells in exponential growth. This oversupercoiling depends on the function of the tetA gene in cis and the delta topA cell background. These are exactly the conditions that lead to the activation of the leu-500 promoter, supporting the proposed mechanism for the suppression of the leu-500 mutation by topA. Use of (AT)n sequences of different lengths has permitted us to estimate the extent of oversupercoiling. When the tetA gene was initiated using the strong tac promoter, we were able to detect increased unconstrained DNA supercoiling even in topA+ E. coli cells.

Topological promoter coupling in Escherichia coli: delta topA-dependent activation of the leu-500 promoter on a plasmid

The leu-500 promoter of Salmonella typhimurium is activated in topA mutants. We have previously shown that this promoter can be activated on circular plasmids in a manner that depends on transcription and translation of the tetracycline resistance gene tetA and insertion of its product into the cell membrane. We have suggested that in the absence of enzymatic relaxation by topoisomerase I, the local domain of transcription-induced DNA supercoiling reaches a steady-state level that leads to the activation of the leu-500 promoter. In the present paper, we have shown that the leu-500 promoter may also be activated in Escherichia coli. Comparison of the closely related pair of E. coli strains DM800 (delta topA) and SD108 (topA+) shows that the activation is dependent on the presence of a null mutation in topA. We have also shown that activation of the plasmid-borne leu-500 promoter depends, as in S. typhimurium, on the function of an adjacent tetA gene, suggesting that membrane anchorage of the TetA peptide prevents dissipation of transcription-induced supercoiling by superhelical diffusion. The activity of the leu-500 promoter is boosted by placing a divergent tac promoter on the side opposite to tetA. The topoisomer distributions of these plasmids extracted from the cell have been analyzed. We find that when the parent plasmid pLEU500Tc, containing the leu-500 promoter upstream of the complete tetA gene, is extracted from E. coli DM800 (delta topA), the distribution of linking numbers is bimodal. There is a fraction with a lower level of supercoiling (mean linking difference approximately -0.05) that is constant for all plasmids extracted from either delta topA or topA+ cells. In addition, we observe a second fraction with highly negatively supercoiled DNA (mean linking difference approximately -0.09) only in DNA extracted from delta topA cells. The proportion of the oversupercoiled fraction correlates with the activity of the leu-500 promoter: it is strongly reduced when the tetA promoter is deleted or when translation of TetA is prematurely terminated, while it is increased when the strong tac promoter is present in cis. We suggest that this oversupercoiled fraction represents the proportion of plasmid molecules active in tetA transcription and that it is this supercoiling that activates the leu-500 promoter.

Characterization of fluoroquinolone-resistant mutants of escherichia coli selected in vitro

Wild-type mutants highly resistant to fluoroquinolones were selected in vitro from a quinolone-susceptible Escherichia coli isolate by stepwise exposure to increasing concentrations of nalidixic acid and ciprofloxacin (CIP) either in liquid medium or on solid medium. Mutant R17 was selected by serial passage in liquid medium; the MIC of CIP for mutant R17 was 256 micrograms/ml. On solid medium, consecutive mutants MI, MII, MIII, MIVa, and MIVb were selected in four steps. The frequencies of mutations were between 10(-9) and 10(-11), and the MICs of CIP ranged from 0.5 microgram/ml (for mutant MI) to 256 micrograms/ml (for mutant MIVb). From the results of a dominance test with the gyrB+ plasmid (pBP547), no gyrB mutations were detectable. In the first step, mutant MI, a mutation from a Ser to a Leu residue at position 83 (a Ser-83-->Leu mutation), was detected in the quinolone resistance-determining region of the gyrA gene. In addition, the second-step mutation was associated with a reduced uptake of CIP and an altered outer membrane protein profile. The third mutation was identified as an Asp-87-->Gly mutation in the quinolone resistance-determining region of the gyrA gene. Concomitantly, a slight increase in the doubling time was detected. For two different four-step mutants, mutants MIVa and MIVb, the MICs of only some quinolones, including CIP, increased. The accumulation of CIP in the mutants was comparable to that in their parent MIII. The doubling time of mutant MIVa was similar to that of mutant MIII, but differed by a factor of 3 from that of the very slow growing mutant MIVb. In contrast, a clinical isolate of E.coli (isolate 205096) described previously (P. Heisig, H. Schedletzky, and H. Falkenstein-Paul, Antimicrob. Agents Chemother. 37:696-701, 1993) which has the same double mutation in gyrA had a doubling time comparable to that of the wild-type isolate.

Neighboring plasmid sequences can affect Mini-Mu DNA transposition in the absence of expression of the bacteriophage Mu semi-essential early region

Bacteriophage Mu DNA, like other transposable elements, requires DNA sequences at both extremities to transpose. It has been previously demonstrated that the transposition activity of various transposons can be influenced by sequences outside their ends. We have found that alterations in the neighboring plasmid sequences near the right extremity of a Mini-Mu, inserted in the plasmid pSC101, can exert an influence on the efficiency of Mini-Mu DNA transposition when an induced helper Mu prophage contains a polar insertion in its semi-essential early region (SEER). The SEER of Mu is known to contain several genes that can affect DNA transposition, and our results suggest that some function(s), located in the SEER of Mu, may be required for optimizing transposition (and thus, replication) of Mu genomes from restrictive locations during the lytic cycle.

Phenotypic suppression of DNA gyrase deficiencies by a deletion lowering the gene dosage of a major tRNA in Salmonella typhimurium

One of the pleiotropic phenotypes of mutations affecting DNA gyrase activity in Salmonella typhimurium is the constitutive deattenuation of the histidine operon. In the present work, we isolated and characterized a suppressor mutation which restores his attenuation in the presence of a defective gyrase. Such a suppressor, initially named sgdA1 (for suppressor gyrase deficiency), was found to correct additional phenotypes associated with defective gyrase function. These include the aberrant nucleoid partitioning of a gyrB mutant and the conditional lethality of a gyrA mutation. Furthermore, the sgdA1 mutation was found to confer low-level resistance to nalidixic acid. The last phenotype permitted isolation of a number of additional sgdA mutants. Genetic analysis established the recessive character of these alleles as well as the position of the sgdA locus at 57 U on the Salmonella genetic map. All of the sgdA mutants result from the same molecular event: a deletion removing three of the four tandemly repeated copies of argV, the gene which specifies tRNA(2Arg), the major arginine isoacceptor tRNA. These findings, combined with the observation of some Sgd-like phenotypes in a tRNA modification mutant (hisT mutant), lead us to propose that protein synthesis contributes, directly or indirectly, to the pathology of gyrase alterations in growing bacteria. We discuss plausible mechanisms which may be responsible for these effects.

Activation of the leu-500 promoter by adjacent transcription

The leu-500 mutation is an A-to-G point mutation in the -10 region of the promoter controlling the leuABCD operon of Salmonella typhimurium. Suppression of the leu-500 mutation in an S. typhimurium topA mutant has demonstrated the functional dependency of this mutated promoter on negative supercoiling. A plasmid bearing a minimal leu-500 promoter region (positions -80 to +87) failed to restore its expression in the S. typhimurium topA mutant. We showed that transcription-mediated local negative supercoiling can activate the leu-500 promoter on a plasmid. The coupled transcription and translation process is required for this activation, but peptide-mediated membrane anchorage may not be involved in this activation. Although the effect of negative supercoiling generated during transcription away from the promoter is limited to a short distance of 250 bp, it can activate the negative-supercoiling-dependent leu-500 promoter from positions either 5' or 3' of the leu-500 promoter. In the presence of a parallel-oriented lac promoter which transcribed away from the 3' end of the leu-500 promoter, transcriptional activation of the leu-500 promoter is a strong indication of cooperativity during the transcriptional initiation process.

The relative contributions of transcription and translation to plasmid DNA supercoiling in Salmonella typhimurium

Mutations affecting DNA topoisomerase I (topA) in Salmonella typhimurium were isolated and graded on the basis of their ability to reverse the effects of gyrB mutations on his operon expression. Different topA and gyrB alleles (in otherwise isogenic strains) were used to gather insights into the transcription-dependent variability of plasmid DNA-linking deficit in growing bacteria. This study showed that modulation of DNA supercoiling by transcription results from the action of two components: one is highly dependent on the coupling of translation to RNA-chain elongation; and the other is unrelated to protein synthesis and entirely dependent on promoter determinants. The former greatly predominates in DNA topoisomerase I mutants (topA and topA gyrB) while the latter is the sole contributor to plasmid DNA-linking deficit in wild-type cells. Altogether, these data suggest that whereas translation acts by enhancing the formation of twin supercoiled domains during elongation, the promoter-dependent effects bear no relation to the twin-supercoiled-domain model and are better explained by a mechanism which responds to the binding/unwinding of template DNA by RNA polymerase.

Topoisomerase mutations affect the relative abundance of many Escherichia coli proteins

The relative abundance of 88 proteins was measured in extracts from three strains of Escherichia coli K-12 that are isogenic except for the topA and gyrB genes. Mutations in these genes slightly raise or lower, respectively, steady-state DNA supercoiling levels but have little effect on growth rate. Altered protein abundances were observed in the mutant strains relative to wild type. Many proteins exhibited minimum abundance at wild-type supercoiling levels, and other proteins exhibited maximal abundance at relaxed levels. A smaller number showed maximal abundance at elevated levels of supercoiling. These data suggest that small, non-lethal changes in DNA supercoiling can have widespread effects on patterns of gene expression.

The influence of DNA topology on the environmental regulation of a pH-regulated locus in Salmonella typhimurium

Salmonella typhimurium is exposed to major shifts in H+ concentration both in its natural and pathogenic environments. The organism undergoes extensive changes in gene expression in response to these pH fluctuations. A current question of regulatory biology is how a change in external pH selectively modulates transcription. We have analysed the expression of one such pH-regulated locus, aniG, and found it is controlled by several additional environmental conditions including osmolarity and oxygen. For factors such as osmolarity and anaerobiosis, an environmentally triggered change in DNA supercoiling has been suggested as a means for controlling gene expression. Thus, environmentally induced changes in DNA topology were explored as a possible common means for establishing the multiple controls on aniG. The involvement of DNA supercoiling in the genetic response of S. typhimurium to external pH has not previously been defined. This report establishes that alkaline environments lower the linking number of reporter plasmids when compared to acidic environments. A consistent pattern was then established whereby conditions or mutations leading to either increased or decreased negative supercoiling were associated with altered expression of aniG. A similar relationship was observed for another environmentally regulated locus, proU. The DNA topology effects on aniG expression were dependent on the presence of EarA, the negative regulator of aniG. These data can be explained by a model in which repressor-operator interactions are very sensitive to changes in operator conformation. These environmentally induced topological influences on operator DNA structure contribute to the magnitude of pH control exerted upon aniG.

Molecular cloning and characterization of acrA and acrE genes of Escherichia coli

The DNA fragment containing the acrA locus of the Escherichia coli chromosome has been cloned by using a complementation test. The nucleotide sequence indicates the presence of two open reading frames (ORFs). Sequence analysis suggests that the first ORF encodes a 397-residue lipoprotein with a 24-amino-acid signal peptide at its N terminus. One inactive allele of acrA from strain N43 was shown to contain an IS2 element inserted into this ORF. Therefore, this ORF was designated acrA. The second downstream ORF is predicted to encode a transmembrane protein of 1,049 amino acids and is named acrE. Genes acrA and acrE are probably located on the same operon, and both of their products are likely to affect drug susceptibilities observed in wild-type cells. The cellular localizations of these polypeptides have been analyzed by making acrA::TnphoA and acrE::TnphoA fusion proteins. Interestingly, AcrA and AcrE share 65 and 77% amino acid identity with two other E. coli polypeptides, EnvC and EnvD, respectively. Drug susceptibilities in one acrA mutant (N43) and one envCD mutant (PM61) have been determined and compared. Finally, the possible functions of these proteins are discussed.

Physiological compensation in antisense transformants: specific induction of an "ersatz" glucan endo-1,3-beta-glucosidase in plants infected with necrotizing viruses

Plant class I glucan endo-1,3-beta-glucosidases (beta-1,3-glucanase; 1,3-beta-D-glucan glucanohydrolase, EC 3.2.1.39) have been implicated in development and defense against pathogen attack. Nevertheless, beta-1,3-glucanase deficiencies generated by antisense transformation of Nicotiana sylvestris and tobacco have little biological effect. We report here that another beta-1,3-glucanase activity is induced in these deficient mutants after infection with necrotizing viruses. Induction of class I beta-1,3-glucanase was markedly inhibited in leaves of N. sylvestris and tobacco antisense transformants infected with tobacco necrosis virus and tobacco mosaic virus, respectively. A serologically distinct beta-1,3-glucanase activity was present in the infected antisense transformants but was absent in both healthy and infected control plants and in antisense transformants treated with the stress hormone ethylene. Immunoblot analyses, localization studies, and measurements of antibody specificity indicate that this compensatory beta-1,3-glucanase activity is an intracellular enzyme different from known tobacco beta-1,3-glucanases. Therefore, plants can compensate for a deficiency in enzyme activity by producing a functionally equivalent replacement--i.e., "ersatz"--protein or proteins. The fact that compensation for beta-1,3-glucanase activity occurs in response to infection argues strongly for an important role of these enzymes in pathogenesis.

DNA topoisomerase I is essential in Drosophila melanogaster

Both biochemical and genetic experiments suggest that the type I DNA topoisomerase may participate in DNA replication, recombination, transcription, and other aspects of DNA metabolism. Despite its apparent importance, genetic studies in unicellular organisms including eubacteria and yeasts indicate that topoisomerase I is not essential for viability. We have previously isolated the cDNA clone encoding DNA topoisomerase I from Drosophila melanogaster. We report here the cytogenetic mapping of top1 to the X chromosome at 13C1 and isolation of top1 genomic DNA. Using P-element mutagenesis, we have isolated a mutant deficient in Drosophila topoisomerase I functions. Genetic studies of this mutant show that topoisomerase I is essential for the growth and development of the fruit fly, a multicellular organism. The biological functions of topoisomerase I are inferred from our analysis of the regulation of topoisomerase I expression during Drosophila development.

Multiple bacterial topoisomerases: specialization or redundancy?

In the past few years, two new DNA topoisomerases have been discovered in bacteria, bringing the total number of DNA topoisomerases in E. coli to four. Two classes of topoisomerases, type 1 and type 2, are distinguishable by their amino acid homology and their apparent reaction mechanism. Of the four E. coli topoisomerases, there are two type 1 and two type 2 enzymes. In eukaryotes, the existence of multiple type 1 and type 2 enzymes has also become apparent. The existence of these multiple enzymes provokes a question whose answer has both evolutionary and physiological implications: are these topoisomerases functionally redundant, or have they acquired sufficient specialization that they now perform unique biological reactions? In bacteria, there is evidence for both specialization and redundancy in the functions of topoisomerases.

Anchoring of DNA to the bacterial cytoplasmic membrane through cotranscriptional synthesis of polypeptides encoding membrane proteins or proteins for export: a mechanism of plasmid hypernegative supercoiling in mutants deficient in DNA topoisomerase I

A homologous set of plasmids expressing tet, lacY, and melB, genes encoding integral cytoplasmic membrane proteins, and tolC and ampC, genes encoding proteins for export through the cytoplasmic membrane, was constructed for studying the effects of transcription and translation of such genes on the hypernegative supercoiling of plasmids in Escherichia coli cells deficient in DNA topoisomerase I. The results support the view that intracellular bacterial DNA is anchored to the cytoplasmic membrane at many points through cotranscriptional synthesis of membrane proteins or proteins designated for export across the cytoplasmic membrane; in the latter case, the presence of the signal peptide appears to be unnecessary for cotranscriptional membrane association.

Isolation and characterization of a topA mutant of Shigella flexneri

Shigella flexneri was shown to possess a homologue of the Escherichia coli K-12 topA gene which encodes DNA topoisomerase I. The S. flexneri topA gene was replaced by a copy of the E. coli K-12 topA gene which has been insertionally inactivated by transposon Tn10. The topoisomer distribution of reporter plasmids showed that the presence of this topA lesion in S. flexneri correlated with an increase in the level of negative DNA supercoiling in the mutant, indicating that topoisomerase I is required to relax DNA in S. flexneri as it is in E. coli and Salmonella typhimurium. The introduction of the topA mutation also resulted in repression of transcription of a thermally regulated invasion gene located on the 230 kb virulence plasmid. In addition, the topA mutant was hypersensitive to growth medium osmolarity, was unable to grow on MacConkey indicator plates and exhibited an increased doubling time under all growth conditions tested. All of these phenotypes were fully complemented in trans by a cloned copy of the E. coli topA gene carried on a recombinant plasmid. Unlike E. coli topA mutants which acquire compensatory mutations at a high frequency, such compensatory mutations were not detected in the S. flexneri topA::Tn10 mutant.

A mutation in a new gene of Escherichia coli, psu, requires secondary mutations for survival: psu mutants express a pleiotropic suppressor phenotype

A mutation in an apparently new gene of Escherichia coli, psu, maps close to ara (1.3 min). psu mutants express a pleiotropic suppressor phenotype in which several auxotrophic requirements and some deletion mutations are suppressed. psu cloned in pBR322 can be maintained by the transformed cell only in the presence of several secondary mutations which accumulate in cultures of psu mutants and have an apparently compensatory role. The accumulation of secondary mutations is not due to mutator activity. The secondary mutations can each act as a suppressor of an auxotrophic requirement in the absence of psu, while suppression of deletions requires the presence of psu. Thus, the suppressor phenotype of psu mutants is due to both psu and the secondary mutations. The functions of psu and the secondary mutations are not known. However, two observations suggest an association with DNA gyrase and with DNA supercoiling. (i) psu mutants are highly resistant to oxolinic acid, the gyrase A inhibitor, while the secondary mutants vary from being very sensitive to more resistant than the wild-type strain. (ii) Novobiocin, which decreases the level of DNA supercoiling, significantly stimulates suppression of auxotrophy in some secondary mutants.

Histone-like proteins are required for cell growth and constraint of supercoils in DNA

The gene hns of Escherichia coli K-12, which encodes the histone-like protein H-NS, was inactivated by insertion of a DNA (gene hph) encoding hygromycin phosphotransferase. The growth rates of two mutants lacking either one or the other of the histone-like proteins, HU and IHF, were not affected by introduction of the hns mutation. However, cells depleted of HU, IHF and H-NS simultaneously, could not be constructed by P1 phage-mediated transduction. These results, together with our previous finding that cells deficient in both HU and IHF are viable at 30-37 degrees C [Kano and Imamoto, Gene 89 (1990) 133-137] showed that E. coli cells deficient in any two of these three histone-like proteins are viable at 30-37 degrees C, and suggested that simultaneous deficiency of all three of the proteins is lethal. There were no detectable differences in the levels of superhelicity of the reporter plasmids isolated from cells deficient in either IHF or H-NS, or from wild-type cells, but about 15% decrease in negative superhelicity was detected for the reporter plasmid isolated from cells lacking HU and lacking both HU and H-NS. However, the cryptic bgl operon, whose expression was reported to be regulated through topological changes of cellular DNA, could not be activated in cells depleted of HU or IHF. The bgl operon was expressed in cells depleted of both HU and H-NS as well as in cells depleted of H-NS.(ABSTRACT TRUNCATED AT 250 WORDS)

Dynamics of DNA supercoiling by transcription in Escherichia coli

The relative rotation between RNA polymerase and DNA during transcription elongation can lead to supercoiling of the DNA template. However, the variables that influence the efficiency of supercoiling by RNA polymerase in vivo are poorly understood, despite the importance of supercoiling for DNA metabolism. We describe a model system to measure the rate of supercoiling by transcription and to estimate the rates of topoisomerase turnover in Escherichia coli. Transcription in a strain lacking topoisomerase I can lead to optimal supercoiling, wherein nearly one positive and one negative superturn are produced for each 10.4 base pairs transcribed. This rapid efficient supercoiling is observed during transcription of membrane-associated gene products, encoded by tet (the gene for tetracycline resistance) and phoA (the gene for E. coli alkaline phosphatase), when the genes are oppositely oriented. Replacement of tet by cat, the gene from Tn9 encoding resistance to chloramphenicol, whose gene product is soluble in the cytosol, reduces the efficiency of supercoiling by RNA polymerase. In a wild-type topoisomerase background, both gyrase and topoisomerase I are kinetically competent to relieve superturns produced by transcription. These results suggest that the level of DNA supercoiling in vivo is probably determined by topoisomerase activity, not by transcription.