Effect of nalidixic acid and novobiocin on pBR322 genetic expression in Escherichia coli minicells

Plasmid DNA supercoiling and gyrase activity in Escherichia coli wild-type and rpoS stationary-phase cells

Stationary-phase cells displayed a distribution of relaxed plasmids and had the ability to recover plasmid supercoiling as soon as nutrients became available. Preexisting gyrase molecules in these cells were responsible for this recovery. Stationary-phase rpoS cells showed a bimodal distribution of plasmids and failed to supercoil plasmids after the addition of nutrients, suggesting that rpoS plays a role in the regulation of plasmid topology during the stationary phase.

LuxArray, a high-density, genomewide transcription analysis of Escherichia coli using bioluminescent reporter strains

A sequenced collection of plasmid-borne random fusions of Escherichia coli DNA to a Photorhabdus luminescens luxCDABE reporter was used as a starting point to select a set of 689 nonredundant functional gene fusions. This group, called LuxArray 1.0, represented 27% of the predicted transcriptional units in E. coli. High-density printing of the LuxArray 1.0 reporter strains to membranes on agar plates was used for simultaneous reporter gene assays of gene expression. The cellular response to nalidixic acid perturbation was analyzed using this format. As expected, fusions to promoters of LexA-controlled SOS-responsive genes dinG, dinB, uvrA, and ydjM were found to be upregulated in the presence of nalidixic acid. In addition, six fusions to genes not previously known to be induced by nalidixic acid were also reproducibly upregulated. The responses of two of these, fusions to oraA and yigN, were induced in a LexA-dependent manner by both nalidixic acid and mitomycin C, identifying these as members of the LexA regulon. The responses of the other four were neither induced by mitomycin C nor dependent on lexA function. Thus, the promoters of ycgH, intG, rihC, and a putative operon consisting of lpxA, lpxB, rnhB, and dnaE were not generally DNA damage responsive and represent a more specific response to nalidixic acid. These results demonstrate that cellular arrays of reporter gene fusions are an important alternative to DNA arrays for genomewide transcriptional analyses.

Plasmid curing effect of trovafloxacin

The effect of sub-inhibitory concentrations of trovafloxacin, a recently developed fluoroquinolone molecule, on the capability of Escherichia coli cells to maintain three different types of plasmids has been investigated by a number of approaches, including the quantification of the loss of plasmid-borne functions and of plasmid DNA by quantitative PCR. The results obtained demonstrate that at concentrations ranging from the MIC to 1/8 of the MIC, trovafloxacin induces a clear, albeit incomplete, 'episome-curing' effect which was observed with plasmids differing in copy number, size and nature of the replication origin of the episome. This effect was most likely not due to an alteration of DNA supercoiling.

Topoisomerase activity during the heat shock response in Escherichia coli K-12

During the upshift of temperature from 30 to 42, 45, 47, or 50 degrees C, an increase in the level of supercoiling of a reporter plasmid was observed. This increase was present in groE and dnaK mutants but was inhibited in cells treated with chloramphenicol and novobiocin. The intracellular [ATP]/[ADP] ratio increased rapidly after an upshift in temperature from 30 to 47 degrees C and then decreased to reach a level above that observed at 30 degrees C. These results suggest that gyrase and proteins synthesized during heat shock are responsible for the changes seen in plasmid supercoiling. Proteins GroE and DnaK are probably not involved in this phenomenon.

Supercoil-induced unusual DNA structures as transcriptional block

The transcriptional activity of pBR322 form V DNA template, a topologically unlinked, highly supercoiled molecule having unusual structures around or within coding regions was studied. Significant transcription was observed in vitro from this template despite high levels of supercoiling. An attenuated transcript, initiated accurately from the P4 promoter of rep gene, was observed which indicated pausing of E. coli RNA polymerase within the gene. This pausing could be removed by relieving the torsional stress implying that a supercoil induced structural alteration within the gene was acting as a transcriptional block. A stabilized unusual structure, most likely a cruciform, was found to be responsible for the elongation block. Absence of initiation from the tetR gene was correlated with the unusual structure present within its promoter region in form V DNA. These in vitro studies show that structural alterations within natural DNA could act as transcriptional blocks both at the level of initiation and elongation.

Characterization of a nalidixic-acid-resistant mutant of Escherichia coli as a strict aerobe

An Escherichia coli mutant, C18, which plates at an efficiency of 5.0 x 10(-4) under anaerobic condition, was isolated among spontaneous nalidixic-acid-resistant mutants. This strict aerobic mutation was mapped by P1 cotransduction with a gyrA linked transposon Tn10 and found to be at the gyrA gene. A low degree of superhelicity of pBR322 DNA isolated from C18 was demonstrated by agarose gel electrophoresis with various concentrations of ethidium bromide. The superhelical density of pBR322 isolated from C18 was 80% of the value of pBR322 isolated from wild-type bacteria cultured under aerobic condition, and 50% cultured under anaerobic condition. These results lead us to conclude that a certain mutation of the gyrA gene causes a decrease in DNA superhelicity and prevents anaerobic growth.

Promoters and transcription of the plasmid-mediated citrate-utilization system in Escherichia coli

The nucleotide sequence of an 878-bp BamHI-BglII restriction endonuclease fragment from citrate utilization transposon Tn3411 was determined, and was compared with that from plasmid pMS185 [Sasatsu et al., J. Bacteriol. 164 (1985) 983-993]. A long open reading frame for a 379-amino acid (aa) polypeptide (citB) was found 5' to the citA gene (431-aa membrane protein) in Tn3411 as well as in pMS185. Promoter regions were identified by RNA polymerase filter-binding assays, S1 nuclease mapping and cit-lac fusion experiments. The results indicated that two genes (citA and citB) have separate promoters, and the location of the promoter for the citB gene in the Tn3411 nucleotide sequence was different from that in pMS185. The regulation of transcription of the two genes (citA and citB) was characterized by the use of cit-lacZ fusions. The level of the citB promoter activity was about five-fold higher than that of the citA gene promoter, and transcription from both was not induced by citrate. Synthesis of the mRNA for the citB gene (especially with the wild-type Cit+ determinant) was suppressed by citrate, accompanying growth suppression of Escherichia coli. The citB gene expressed in E. coli minicells produced a membrane-associated 37.5-kDa polypeptide.

Far upstream sequences of the bla promoter from TN3 are involved in complexation with E. coli RNA-polymerase

The structure of the final initiation complex between E. coli RNA polymerase (RNAP) and the bla promoter from the transposon TN3 has been probed by footprinting experiments and base accessibility to dimethyl sulfate at 37 degrees C. At RNAP/promoter molar ratios "standard" for these experiments (greater than or equal to 10), the contacts on bla extend from -100 to +20, i.e. a length exceeding twice the dimension of the RNAP major axis [33]. Since footprinting at about equimolar amounts of RNAP and bla extends to the usual (-55 to +20) promoter domain, it is very likely that at least two RNAP's participate in the complex observed at tenfold higher RNAP/bla ratios. Under the latter conditions, the extended footprint (-100 to +20) is observed above 30 degrees C, whereas at 15 degrees C, only the -55 to +20 promoter area is contacted. Furthermore, gel retardation experiments show the presence of two complexes of different migration rates. We have reported earlier [21] that at the "standard" RNAP/bla ratio, transcription initiation from the bla promoter is inhibited. The correlation of this inhibition with the postulated two RNAP/bla complex suggests a regulation of bla gene expression by RNAP availability controlled for instance by growth rate. These results can be correlated with those reported in [14, 15] for the tyrT promoter. Interestingly, both promoter share significant sequence homologies.

Heterogeneity in the level of ampicillin resistance conferred by pBR322 derivatives with different DNA supercoiling

Cloning of an EcoRI restriction fragment, containing the 900 bp gamma-terminal sequence of transposon Tn1000, into pBR322, resulted in two plasmids, pICV63 and pICV64, which differed in the orientation of the cloned fragment within the replicon and in the level of ampicillin resistance conferred on the host cell. The DNAs of these plasmids differ in superhelicity and we suggest that a change in supercoiling of pICV63 DNA leads to this plasmid conferring resistance to only low levels of ampicillin, probably by reducing the expression of the bla gene. This hypothesis is supported by the fact that topA or supX mutations, which abolish topoisomerase I, reduce still further the level of resistance to ampicillin of pICV63-containing cells, whereas the gyrB226 compensatory mutation renders these cells more ampicillin resistant. Plasmid pICV63, therefore, enables mutant alleles of genes governing DNA topology to be recognized.

In vivo and in vitro effect of mutations in tetA promoter from pSC101: insertion of poly(dA.dT) stretch in the spacer region does not inactivate the promoter

Two mutants, mapping at the HindIII site (between the consensus sequences) of the pSC101 tetA promoter, were studied: MA2 corresponds to a 4 bp deletion between positions -12 and -15; B30 bears a 44 bp insertion C(TA)21 G at the HindIII site. Both mutants were assayed in vivo (ability of the plasmid to confer resistance to tetracycline, plasmid-directed protein synthesis, S1-mapping of mRNA) and in vitro (abortive initiation assay). Compared to w.t., MA2 is a poor promoter in vivo; RNA polymerase binding, complex activation and rate of initial oligonucleotide synthesis are strongly reduced in vitro; this is in keeping with the known effects of altering the consensus elements in E. coli promoters. In contrast, B30 shows in vivo a promoter activity only slightly reduced in comparison to that of the w.t. tetA promoter; both in vivo and in vitro, the transcription start site is outside and downstream the (TA)21 stretch, 5-7 bp upstream that found in the w.t. To adjust the behaviour of B30 and the claimed consensus distance between the E. coli promoter consensus sequences, some structural modification in the (TA)21 stretch -either spontaneous or induced by RNA polymerase- can be hypothesized. Unless the (TA)21 stretch itself plays the role of a relatively good promoter, the results suggest that promoter-specific elements may be distributed along the DNA sequences over distances longer, but seldom less, than the 17 +/- 2 bp consensus distance.

Genetic expression and gyrase dependence of methylated and undermethylated DNA in Escherichia coli

The genetic expression and dependence on gyrase of plasmid pBR322 were studied in dam-3, dcm-6, and dam-3 dcm-6 derivatives of a minicell-producing Escherichia coli strain. The results obtained with both methylated and undermethylated plasmid DNA were similar.

In vitro transcription initiation from three different Escherichia coli promoters. Effect of supercoiling

Transcription initiation from beta-lactamase, tetracycline resistance and RNA 1 promoters, present in plasmid pAT153, were studied employing the abortive initiation technique. Assays appear to be promoter-specific with supercoiled and linear templates. Supercoiling enhances the isomerization rate constant of the open RNA-polymerase--promoter complex formation. Results agree with the in vivo behaviour of the corresponding promoters, and allow us to propose a hypothesis about the effect of supercoiling on transcription initiation.

Polypeptide involved in the Escherichia coli plasmid-mediated citrate transport system

A genetic determinant conferring on Escherichia coli the ability to utilize citrate as a sole source of carbon and energy was subcloned into pBR322 from a naturally occurring, citrate utilization (Cit+) plasmid, pOH30221, and was localized to a 1.6-kilobase region by cloning and subsequent deletion analysis. Genetic expression of the Cit+ determinant in E. coli minicells revealed that the Cit+ determinant encoded a single, membrane-associated polypeptide with an apparent molecular weight of 35,000, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. This polypeptide seemed not to be synthesized as a precursor with an amino-terminal signal sequence.

Mutagenic SOS repair of site-specific psoralen damage in plasmid pBR322

The mutagenic repair of psoralen damage was examined by transforming Escherichia coli with psoralen-treated pBR322. Plasmid DNA randomly reacted with psoralen was repaired only when the E. coli was uvrA+ and recA+, and only when the cells were pre-irradiated with far-ultraviolet light. The recA dependence and requirement for pre-irradiation are characteristics of SOS repair. Psoralens were placed specifically near the BamHI site, in the tetracycline-resistance gene of pBR322, using a sulfhydryl-containing psoralen derivative. Repair of this damage also required pre-irradiation of the host cells. This repair was accompanied by a 4% frequency of mutagenesis to a tetracycline-sensitive phenotype. Sequence analysis of these mutant plasmids revealed that 75% had mutations within the targeted region, while 25% had no sequence changes within 100 bases of the BamHI site. In up to five independent isolates only one kind of mutation was observed at each site, suggesting that mutagenic SOS repair is influenced by DNA structure at the site of the psoralen. Most mutations were transitions, primarily G-C to A-T changes. Some transitions occurred at sites where psoralen crosslinks could not have formed, and these may have arisen from the repair of psoralen monoadducts.

Molecular cloning and characterisation of the gua regulatory region of Escherichia coli K12

The regulatory region of the gua operon of Escherichia coli is contained within a 2.1 kb EcoR1 restriction fragment isolated from a lambda pgua transducing phage. This DNA fragment was inserted into pPV33-II, a promoter-cloning vector, where it activated the gene(s) for tetracycline resistance. The level of tetracycline resistance conferred by the hybrid plasmid was reduced by the addition of guanine and increased by adenine, indicating the presence of the gua promoter. The cloned fragment codes for a polypeptide that complements in vivo the defective enzymes present in certain guaB mutants. This polypeptide was characterised using minicells and immunoprecipitation, and is presumed to correspond to the N-terminal region of IMP dehydrogenase.

Expression of human interferon genes using the recA promoter of Escherichia coli

Interferon beta 1 and three alpha-interferon genes were cloned on Eco RI fragments isolated from a human genomic library into the Eco RI site of a plasmid containing the recA promoter of E. coli. Expression of interferon activity from cells carrying these plasmids was nalidixic acid inducible. The alpha-interferon genes were expressed only when in the same transcriptional orientation as the recA promoter while the beta 1 interferon gene was expressed in either orientation. Interferon activity was also inducibly expressed from the recA promoter in cells containing a plasmid carrying a fusion of the recA gene with the beta 1 interferon gene. This interferon activity was thirty-fold less sensitive to neutralization by polyclonal antibodies than authentic interferon, implying that the change near the amino terminus affects either antibody recognition or specific activity or both.

The effect of gyrase inhibitors and cyclic AMP on induction and glucose repression of the 6-hydroxy-nicotine oxidases in Arthrobacter oxidans

The induction by D,L-nicotine of the enantiozymes 6-hydroxy-L-nicotine oxidase and 6-hydroxy-D-nicotine oxidase in Arthrobacter oxidans was differently affected by the inhibitors of Escherichia coli gyrase, novobiocin and nalidixic acid. These compounds inhibited 6-hydroxy-L-nicotine oxidase induction slightly, but led to an increase in the level of 6-hydroxy-D-nicotine oxidase activity. Furthermore, the specific repression by glucose of 6-hydroxy-D-nicotine oxidase synthesis was not abolished by the addition of cAMP but by that of novobiocin.

Elastic torsional strain in DNA within a fraction of SV40 minichromosomes: relation to transcriptionally active chromatin

After treatment of SV40 minichromosomes with DNA topoisomerase I, the superhelicity in the bulk of the DNA extracted from minichromosomes is known to remain unchanged. However, we found that the DNA extracted from a small fraction of SV40 minichromosomes (2-5%), was almost completely relaxed, and covalently closed as shown by agarose gel electrophoresis. Thus, the DNA in these 2-5% of SV40 minichromosomes was probably torsionally strained (TS). The proportion of such TS minichromosomes is close to the estimated proportion of transcriptionally active minichromosomes. The distribution of the TS minichromosomes in sucrose gradient coincided with the distribution of transcriptionally active complexes. Both sedimented faster than the majority of minichromosomes. Furthermore, after treatment with topoisomerase I the relaxed minichromosomes could be quantitatively separated from the bulk of material by recentrifugation in a sucrose gradient. A major part of the endogenous RNA polymerase activity was recovered in the relaxed fraction. These data suggest that TS-minichromosomes correspond to transcriptionally active chromatin. After relaxation with topoisomerase I the TS minichromosomes lacked histones.