DNA degradation at elevated temperatures after plasmid amplification in amino acid-starved Escherichia coli cells

The role of amino acids in the amplification and quality of DNA vectors for industrial applications

In this study, we have demonstrated that the type and feeding regimen of amino acids have a significant impact on the quality as well as the quantity of DNA vectors produced. Nutrient pool and factorial design experiments were carried out in order to identify the amino acids involved in increased biomass and induction of plasmid amplification. Leucine, glycine, and histidine were responsible for increased biomass and leucine starvation in the presence of histidine was implicated in plasmid amplification. Supercoiling of the plasmid was optimized using a dual feeding strategy. As a result of this, a fed-batch fermentation strategy for the production of a 6.9 kb plasmid, pSVß, in Escherichia coli DH5α was developed. In batch fermentation, a maximum plasmid yield of 39.4 mg/L equivalent to 11.3 mg/g dry cell weight (DCW) was achieved with casein hydrolysate limitation. About 90% of plasmid was in the supercoiled (SC) form after 31 hr of fermentation but only remained so for a short period, leading to a very brief window for harvesting cells at scale. Subsequently, a fed-batch fermentation using a dual feeding strategy was employed. A mean maximum plasmid yield of 44 mg/L equivalent to 9.1 mg plasmid/g DCW was achieved. After 25 hr, 90% of plasmid was in the SC form and remained at this level for the remaining 10 hr of the fermentation, allowing adequate time for the harvesting of cells without the loss of supercoiling of product. This study emphasized that optimizing fermentation strategy and identifying the essential nutrients are beneficial for bioprocessing of plasmid DNA for therapeutic applications.

Composting: A Potentially Safe Process for Disposal of Genetically Modified Organisms

The widespread use of genetically modified organisms (GMOs) may result in the release of GMOs into the environment. The potential risks regarding their use and implementation of disposal methods, especially the possibility of novel genes from GMOs being transferred to natural organisms, need to be evaluated and better understood. There is an increasingly accepted public view that GMO products introduced into the environment should be degradable and should disappear after a limited period of time. Due to the risk of possible horizontal gene transfer, disposal methods for GMOs need to address destruction of both the organism and the genetic material. During the last two decades, we have developed a greater understanding of the biochemical, microbiological and molecular concepts of the composting process, such that maximum decomposition may be achieved in the shortest time with minimal negative impacts to the environment. The conditions created in a properly managed composting process environment may help in destroying GMOs and their genes, thereby reducing the risk of the spread of genetic material. When considering composting as a potential method for the disposal of GMOs, the establishment of controlled conditions providing an essentially homogenous environment appears to be an important requirement. An evaluation of composting as a safe option for disposal of GMOs is provided in this review.

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.

A model for regulation of ColE1-like plasmid replication by uncharged tRNAs in amino acid-starved Escherichia coli cells

It has been previously observed that various ColE1-like plasmids replicate differentially in Escherichia coli cells during the relaxed response to amino acid starvation. Here we develop a kinetic model to explain these observations based on the possibility of interaction of the 3' CCA-OH sequence with the UGG triplets in loops of RNA I and RNA II encoded by ColE1-like plasmids. According to our model, when the interaction of uncharged CCA with RNA I is possible, the replication of the ColE1-like plasmid is affected by differences in the concentration of various tRNAs in the starved cell, but it is not affected by the tRNA concentration if the hypothetical pairing occurs between the CCA-OH and RNA II. Using the previously determined parameters for the pBR322 plasmid, the concentration of uncharged tRNAs in the amino acid starved relaxed strains and the assumed efficiency of binding of tRNA and RNA I, we show that our model explains the differences in pBR322 copy number in the relaxed strain starved for several amino acids.

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.

Amplification of ColE1 related plasmids in recombinant cultures of Escherichia coli after IPTG induction

ColE1-derived plasmids containing different recombinant genes which are controlled by the tac promoter were amplified following induction with IPTG, but no amplification occurred if product formation was not induced. The plasmid copy number of recombinant E. coli increased three- to sixfold within a period of about 6 h in shake flask experiments, batch cultures, and glucose-limited fed-batch cultivations. Plasmid amplification occurred in E. coli B strains as well as in K-12 strains with different plasmids (rop+ and rop-) coding for various heterologous proteins. The amplification was not caused by a toxic effect of IPTG, but was related to a strong inhibition of translation and chromosomal replication after the induction of heterologous gene expression. Similar to the amplification after chloramphenicol addition, plasmid replication proceeded even if oriC replication and translation were inhibited following strong induction of a recombinant gene. In accordance with the effect of chloramphenicol, the level of ppGpp, which is a negative regulator of ColE1 derived plasmid replication, decreased after induction.

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.

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.