Amplification of lambda plasmids in Escherichia coli relA mutants

Dynamic modulation of DNA replication and gene transcription in deep-sea filamentous phage SW1 in response to changes of host growth and temperature

Little is known about the response of deep-sea virus and their relationship with their host towards environmental change. Although viruses are thought to play key roles in the deep-sea ecological evolution and biogeochemical cycling, these roles are yet to be defined. This study aims to delineate the relationship between a deep-sea filamentous phage SW1 and its host Shewanella piezotolerans (S. piezotolerans) WP3, and their response towards temperature change. The copy number of SW1’s replicative form (RF-) DNA and single-stranded (ss-) DNA along the different growth phases of WP3 were quantified at 20°C and 4°C, respectively. The copy number of SW1 RF-DNA was found to be temperature and growth phase-dependent, while the ssDNA of SW1 was only produced at 4°C. This is the first report showing low-temperature dependence of phage DNA replication. The transcription of SW1 key genes fpsA and fpsR were also found to be induced at low temperature during all the monitored growth periods of WP3. Additionally, the transcription of SW1 was found to be induced by cold-shock while its DNA replication was not changed. Our data demonstrates a dynamic change of virus DNA replication and transcription in accordance with host growth, and the low temperature adapted mechanisms for SW1 activities in the deep sea. This low temperature adapted deep-sea virus-bacterium system could serve as an ideal model to further study the mechanism and relationship of deep-sea virus-bacteria ecosystems.

The effect of heat stress on the antibacterial resistance and plasmid profile in Escherichia coli isolates

In order to study the effect of heat stress on the antibacterial resistance and plasmid profile in Escherichia coli, thirty E. coli were isolated from sheep liver. Antibiotic susceptibility test were done by antibiotic disc diffusion method using filter paper disc on two 24 h cultures of each isolate which grown at 37 and 43 degrees C simultaneously in BHI Broth (Merck VM460193 531). The isolates which grown at 43 degrees C were under heat stress during their growth. Ten commonly used antibiotics, viz., ampicillin, erythromycin, neomycin, trimethoprim-sulfamethoxazol, lincospectine, tetracycline, gentamycin, flumequine, vancomycin and Tiamulin (Padtan Teb). The resistance level of all E. coli isolates against 10 antibacterial drugs compared statistically in 37 and 43 degrees C using MINITAB Version 14 program. Plasmid DNAs were extracted from each of the E. coli isolates which were grown at 37 and 43 degrees C overnight using alkali lysis method. In this study *lambdaDNA (EcoR1+Hind III digested) was used as marker DNA. According to the results of this study, the resistance rate of E. coli isolates have decreased against trimethoprim-sulfamethazol, lincospectine, tiamaulin, tetracyclin and gentamycin at 43 degrees C but only the difference between the resistance rate against gentamycin in 37 degrees C (83.3%) and 43 degrees C (60%) was significant Characterization of Plasmid DNAs by agarose gel electrophoresis showed that each of the thirty drug resistant E. coli harbored a single plasmid. There was no difference among the plasmid profiles of the thirty isolates in 37 and 43 degrees C. As the plasmid profile did not change in 43 degrees C (heat stress) so the resistance differences against antibacterial drugs were not significant except for gentamycine that its resistance may is chromosomal. According to the results of this study, In conclusion it can be said that heat stress could not be effective on antibacterial resistance and plasmid profile if the duration of the stress is short. The long duration of the heat stress plus other stress factors such as starvation will effect the plasmid replication and finally plasmid copy number of bacteria. Mechanism of this phenomenon remains unknown, though one might speculate that some bacterial addiction modules that are activated upon amino acid starvation, like mazEF could be involved.

Plasmids derived from Gifsy-1/Gifsy-2, lambdoid prophages contributing to the virulence of Salmonella enterica serovar Typhimurium: implications for the evolution of replication initiation proteins of lambdoid phages and enterobacteria

Gifsy-1 and Gifsy-2 are lambdoid prophages which contribute to the virulence of Salmonella enterica serovar Typhimurium. The nucleotide sequence of the replication region of both prophages is identical, and similar in organization to the replication region of bacteriophage lambda. To investigate the replication of the Gifsy phages and the relationship between Gifsy and host chromosome replication, a plasmid which contained all the genes and regulatory sequences required for autonomous replication in bacterial cells was constructed. This plasmid, pGifsy, was stably maintained in Escherichia coli cells. The helicase loader of the Gifsy phages is very similar to the DnaC protein of the host, a feature characteristic of a large group of prophages common in the sequenced genomes of pathogenic enterobacteria. This DnaC-like protein showed no similarity to the helicase loader of bacteriophage lambda and closely related phages. Interestingly, unlike plasmids derived from bacteriophage lambda (lambda plasmids), pGifsy did not require a gene encoding the putative helicase loader for replication, although deletion of this gene resulted in a decrease in plasmid copy number. Under these conditions, it was shown that the plasmid utilized the helicase loader coded by the host. On the other hand, the viral protein could not substitute for DnaC in bacterial chromosome replication. The results of the current study support the hypothesis that the enterobacterial helicase loader is of viral origin. This hypothesis explains why the gene for DnaC, the protein central to both replication initiation and replication restart in E. coli, is present in the genomes of Escherichia, Shigella, Salmonella and Buchnera, but not in the genomes of related enterobacteria.

Isolation of chromosomal mutations that affect carotenoid production in Escherichia coli: mutations alter copy number of ColE1-type plasmids

Chromosomal mutants were isolated in Escherichia coli that altered carotenoid production from transformed carotenoid biosynthesis genes on a pACYC-derived plasmid (pPCB15). The mutations were mapped by sequencing. One group of mutations appeared to affect the cell metabolism without changing the copy number of the carotenoid synthesis plasmid. The other group of mutations either increased or decreased the copy number of the pPCB15 plasmid as determined by real-time PCR. The copy number change in most mutants was likely specific for ColE1-type plasmids for which copy number is controlled by a small antisense RNA. This collection of host strains would be useful for fine tuning expression of proteins and adjusting production of desired molecules without recloning to different vectors.

Stress responses and replication of plasmids in bacterial cells

Plasmids, DNA (or rarely RNA) molecules which replicate in cells autonomously (independently of chromosomes) as non-essential genetic elements, play important roles for microbes grown under specific environmental conditions as well as in scientific laboratories and in biotechnology. For example, bacterial plasmids are excellent models in studies on regulation of DNA replication, and their derivatives are the most commonly used vectors in genetic engineering. Detailed mechanisms of replication initiation, which is the crucial process for efficient maintenance of plasmids in cells, have been elucidated for several plasmids. However, to understand plasmid biology, it is necessary to understand regulation of plasmid DNA replication in response to different environmental conditions in which host cells exist. Knowledge of such regulatory processes is also very important for those who use plasmids as expression vectors to produce large amounts of recombinant proteins. Variable conditions in large-scale fermentations must influence replication of plasmid DNA in cells, thus affecting the efficiency of recombinant gene expression significantly. Contrary to extensively investigated biochemistry of plasmid replication, molecular mechanisms of regulation of plasmid DNA replication in response to various environmental stress conditions are relatively poorly understood. There are, however, recently published studies that add significant data to our knowledge on relations between cellular stress responses and control of plasmid DNA replication. In this review we focus on plasmids derived from bacteriophage lambda that are among the best investigated replicons. Nevertheless, recent results of studies on other plasmids are also discussed shortly.

Lambdap(o), a promoter for oop RNA synthesis, has a role in replication of plasmids derived from bacteriophage lambda

Transcription initiated at the bacteriophage lambdap(o) promoter gives a short RNA, called oop RNA. Early studies led to a proposal that this transcript plays a role in the initiation of lambda DNA replication. In fact, the p(o) promoter is located in the lambda replication region and it was suggested that oop RNA may be a primer for replication proceeding leftward from orilambda. However, since in vitro experiments demonstrated that primers for lambda DNA replication are produced by the dnaG gene product (DnaG primase) and subsequent in vivo studies indicated that oop RNA is an antisense RNA for the lambda cII gene expression, the above-mentioned hypothesis has fallen into oblivion. Nevertheless, here we demonstrate that the p(o) promoter plays a role in lambda DNA replication, indeed. We found that lambda plasmids bearing a mutation that inactivates p(o) occur in Escherichia coli cells in a copy number significantly lower than wild-type lambda plasmids. Amplification of lambdap(o)(-) plasmids during the relaxed response was less efficient relative to lambdap(o)(+) plasmids suggesting less frequent initiation of replication from orilambda in the absence of transcription from p(o). This suggestion was confirmed by measurement of incorporation of [(3)H]thymidine into lambda plasmid DNA during pulse-labeling experiments. Therefore, we propose that transcription from the p(o) promoter stimulates replication initiation at orilambda as suggested a long time ago, however, contrary to that suggestion, we assume that the process of p(o)-initiated transcription per se but not the transcription product (oop RNA) might play a role at early steps of lambda DNA replication.

Replication of plasmids during bacterial response to amino acid starvation

Amino acid starvation of bacterial cells leads to expression of the stringent (in wild-type strains) or relaxed (in relA mutants) response (also called the stringent or relaxed control, respectively). The stringent control is a pleiotropic response which changes drastically almost the entire cell physiology. Although starvation is a rule rather than an exception in natural environments of bacteria, and DNA replication is a fundamental cell process, until recently our knowledge about regulation of DNA replication in amino acid-starved cells has been unexpectedly poor. Within recent years the stringent control of DNA replication has been investigated mainly on plasmid models. Several plasmid replicons have been studied, including oriC plasmids, ColE1-like replicons, pSC101, F, R1, RK2, and R6K, and plasmids derived from bacteriophages lambda and P1. However, molecular models of replication regulation in amino acid-starved cells have been proposed to date only for lambda plasmids and ColE1-like replicons. Although further extensive studies are necessary in the understanding of molecular mechanisms of the stringent and relaxed control of replication of other plasmids, the results obtained to date (summarized and discussed in this review) show that studies on DNA replication in amino acid-starved cells may provide new insights into the regulatory mechanisms and lead to more general conclusions.

Replication and maintenance of lambda plasmids devoid of the Cro repressor autoregulatory loop in Escherichia coli

Plasmids derived from bacteriophage lambda are known as lambda plasmids. These plasmids contain the ori lambda region and lambda replication genes O and P. Typical lambda plasmids also contain the cro gene, the product of which is a repressor of the pR promoter when present at relatively high concentrations. These genes stably maintain the plasmid in Escherichia coli at copy numbers of 20 to 50 per cell. According to a generally accepted model, stable maintenance of lambda plasmids is possible due to the Cro repressor autoregulatory loop (the cro gene is under control of pR). Here we demonstrate that lambda plasmids devoid of the Cro autoregulatory loop can also be stably maintained in E. coli strains. We present data for two such plasmids: pTC lambda 1 in which the pR-cro region has been replaced by the ptetA promoter and the tetR gene (coding for the TetR repressor), and a standard lambda plasmid with inactivated cro gene (lambda cro-null plasmid). Thus, the presence of the Cro repressor autoregulatory loop does not appear to be essential to the maintenance of lambda plasmids in vivo.

Excess production of phage lambda delayed early proteins under conditions supporting high Escherichia coli growth rates

Bacteriophage lambda is unable to lysogenize Escherichia coli hosts harbouring the rpoA341 mutation due to a drastic reduction in transcription from CII-activated lysogenic promoters (pE, pI and paQ). In addition, the level of early transcripts involved in the lytic pathway of lambda development is also decreased in this genetic background due to impaired N-dependent antitermination. Here, it is demonstrated that despite the reduced level of early lytic pL- and pR-derived transcripts, lytic growth of bacteriophage lambda is not affected in rich media. The level of the late lytic, pR-derived transcripts also remains unaffected by the rpoA341 mutation under these conditions. However, it was found that whilst there is no significant difference in the phage burst size in rpoA+ and rpoA341 hosts growing in rich media, phage lambda is not able to produce progeny in the rpoA341 mutant growing in minimal medium, in contrast to otherwise isogenic rpoA+ bacteria. Provision of an excess of the phage replication proteins O and P in trans or overproduction of the antitermination protein N restore the ability of phage lambda to produce progeny in the rpoA341 mutant under the latter conditions. These results suggest that in rich media phage lambda produces some early proteins in excess of that needed for its effective propagation and indicate that replication proteins may be limiting factors for phage lytic growth in poor media.

Molecular mechanism of heat shock-provoked disassembly of the coliphage lambda replication complex

We have found previously that, in contrast to the free O initiator protein of lambda phage or plasmid rapidly degraded by the Escherichia coli ClpP/ClpX protease, the lambdaO present in the replication complex (RC) is protected from proteolysis. However, in cells growing in a complete medium, a temperature shift from 30 to 43 degrees C resulted in the decay of the lambdaO fraction, which indicated disassembly of RC. This process occurred due to heat shock induction of the groE operon, coding for molecular chaperones of the Hsp60 system. Here we demonstrate that an increase in the cellular concentration of GroEL and GroES proteins is not in itself sufficient to cause RC disassembly. Another requirement is a DNA gyrase-mediated negative resupercoiling of lambda plasmid DNA, which counteracts DNA relaxation and starts to dominate 10 min after the temperature upshift. We presume that RC dissociates from lambda DNA during the negative resupercoiling, becoming susceptible to the subsequent action of GroELS and ClpP/ClpX proteins. In contrast to lambda cro+, in lambda cro- plasmid-harboring cells, the RC reveals heat shock resistance. After temperature upshift of the lambda crots plasmid-harboring cells, a Cro repressor-independent control of lambda DNA replication and heat shock resistance of RC are established before the period of DNA gyrase-mediated negative supercoiling. We suggest that the tight binding of RC to lambda DNA is due to interaction of RC with other DNA-bound proteins, and is related to the molecular basis of the lambda cro- plasmid replication control.

Replication of plasmids derived from P1, F, R1, R6K and RK2 replicons in amino acid-starved Escherichia coli stringent and relaxed strains

Replication of mini-plasmids derived from bacteriophage P1 and naturally existing plasmids F, R1, R6K and RK2 in otherwise isogenic relA+ and relA- Escherichia coli strains during amino acid starvation and limitation was investigated. Since it was previously demonstrated that inhibition of DNA synthesis or amplification of plasmid DNA may depend on the nature of deprived amino acid, we starved bacteria for five different amino acids. We found differential replication of all these plasmids but RK2 (which did not replicate at all in amino acid-starved bacteria) during the stringent and relaxed response. While in almost all cases plasmid DNA replication was inhibited during the stringent response irrespective of the nature of deprived amino acid, wild-type or copy-up mini-P1, mini-F and mini-R1 plasmids replicated in relA- bacteria depending on the kind of starvation. R6K-derived plasmids harbouring ori beta and gamma (but not those containing ori alpha, beta and gamma or only ori gamma) were able to replicate in relA- bacteria starved for all tested amino acids. Possible explanations for the mechanisms of regulation of replication of plasmids derived from P1, F, R1, R6K and RK2 during amino acid starvation are discussed. Our results also indicate that, like in the case of some other replicons, appropriate amino acid starvation or limitation may be used as a method for efficient amplification of plasmids derived from P1, F, R1 and R6K.

Amplification of pSC101 replicons in Escherichia coli during amino acid limitation

Amino acid starvation of Escherichia coli relA mutants was previously proposed as a method for efficient amplification of plasmids bearing origin of replication derived from ColE1-type plasmids and bacteriophage lambda. Here we demonstrate that plasmids derived from pSC101 replicon can be amplified in E. col relA+ and relA- strains during amino acid limitation but not during amino acid starvation. The amplification efficiency is dependent on temperature (37 degrees C was found to be the optimal temperature). Under optimal conditions, up to 13-fold amplification of a pSC101-derived plasmid may be achieved.

Differential amplification efficiency of pMB1 and p15A (ColE1-type) replicons in Escherichia coli stringent and relaxed strains starved for particular amino acids

It was demonstrated previously that ColE1-type plasmids, the most commonly used vectors in molecular cloning, can be amplified in amino acid-starved relA mutants of Escherichia coli. Subsequent studies demonstrated that replication of at least some plasmids during amino acid starvation depends not only on the host relA allele but also on temperature and on the nature of deprived amino acid. Therefore, we investigated efficiency of amplification of two types of ColE1 plasmids (pMB1- and p15A-derived replicons) in E. coli relA+ and relA- hosts starved for different amino acids at 30 degrees C, 37 degrees C and 43 degrees C. We found differential amplification efficiency of plasmids pBR328 (pMB1-derived replicon) and pACYC184 (p15A-derived replicon) in the relA mutant during starvation for particular amino acids. Although amplification of pBR328 was negligible in the relA+ host, significant increase in pACYC184 content was observed in this strain starved for some (but not all) amino acids. The amplification efficiency of pBR328 and pACYC184 was found to be dependent on temperature. These results indicate that for maximal amplification of particular plasmid appropriate amino acid starvation and optimal temperature should be chosen. Our findings are in agreement with recently proposed model of the regulation of ColE1-type plasmid replication in amino acid-starved E. coli cells.

Replication and amplification of lambda plasmids in Escherichia coli during amino acid starvation and limitation

It was demonstrated previously that replication of plasmids derived from bacteriophage lambda (so-called lambda plasmids) is inhibited in wild-type Escherichia coli cells starved for isoleucine and arginine whereas it proceeds under the same conditions in relA mutants. Since replication of other replicons during the stringent or relaxed response depends on the nature of the deprived amino acid, we investigated replication of lambda plasmids in E. coli relA+ and relA- strains starved for different amino acids. We found that replication of lambda plasmids is generally inhibited during the stringent, but not relaxed, response. Differences between cells starved for different amino acids, although reproducible, were not dramatic. Amino acid starvation was previously proposed as a method for amplification of lambda plasmid DNA in vivo. We found that during amino acid limitation lambda plasmids replicate more extensively in the relA mutants than during amino acid starvation. The efficiency of plasmid DNA amplification was found to be dependent on the kind of limited amino acid; in relA- bacteria limited for leucine we observed about 10-fold plasmid amplification. Some lambda plasmid replication was also found under these conditions in the relA+ host. The mechanism of the stringent control of lambda plasmid DNA replication has already been proposed. Here the possible mechanism of the regulation of lambda plasmid replication during amino acid limitation is presented.

Allele specificity of the Escherichia coli dnaA gene function in the replication of plasmids derived from phage lambda

We demonstrate a variation in the effects of seven alleles of the Escherichia coli dnaA gene, which cause temperature sensitivity of initiation of chromosomal replication, on the replication of lambda phage-derived plasmids at 30 degrees C. These mutants showed no allele specificity of dnaA function in replication of either of two lambda pi plasmids studied. On the other hand, the inability of the lambda P+ plasmid to replicate in dnaA508, 46 and 204 cells, in dnaB (groP A15) or in cells that are temperature sensitive for the chaperone genes dnaK756, dnaJ259 and grpE280 at 30 degrees C was suppressible by a single pi mutatation. This suggests that it is a common property of the pi protein, probably its weaker interaction with DnaB helicase, that is responsible for the suppression. One can also conclude that the DnaA-regulated transcriptional activation of ori lambda acts at the step, in which all these gene products cooperate, i.e. during preprimosome loading and chaperone-mediated release of DnaB from P protein inhibition.