Participation of stress-inducible systems and enzymes involved in BER and NER in the protection of Escherichia coli against cumene hydroperoxide

Characterization of two Lactococcus lactis zinc membrane proteins, Llmg_0524 and Llmg_0526, and role of Llmg_0524 in cell wall integrity

BACKGROUND

Due to its extraordinary chemical properties, the cysteine amino acid residue is often involved in protein folding, electron driving, sensing stress, and binding metals such as iron or zinc. Lactococcus lactis, a Gram-positive bacterium, houses around one hundred cysteine-rich proteins (with the CX2C motif) in the cytoplasm, but only a few in the membrane.

RESULTS

In order to understand the role played by this motif we focused our work on two membrane proteins of unknown function: Llmg_0524 and Llmg_0526. Each of these proteins has two CX2C motifs separated by ten amino-acid residues (CX2CX10CX2C). Together with a short intervening gene (llmg_0525), the genes of these two proteins form an operon, which is induced only during the early log growth phase. In both proteins, we found that the CX2CX10CX2C motif chelated a zinc ion via its cysteine residues, but the sphere of coordination was remarkably different in each case. In the case of Llmg_0524, two of the four cysteines were ligands of a zinc ion whereas in Llmg_0526, all four residues were involved in binding zinc. In both proteins, the cysteine-zinc complex was very stable at 37 °C or in the presence of oxidative agents, suggesting a probable role in protein stability. We found that the complete deletion of llmg_0524 increased the sensitivity of the mutant to cumene hydroperoxide whereas the deletion of the cysteine motif in Llmg_0524 resulted in a growth defect. The latter mutant was much more resistant to lysozyme than other strains.

CONCLUSIONS

Our data suggest that the CX2CX10CX2C motif is used to chelate a zinc ion but we cannot predict the number of cysteine residue involved as ligand of metal. Although no other motif is present in sequence to identify roles played by these proteins, our results indicate that Llmg_0524 contributes to the cell wall integrity.

A new approach utilizing real-time qPCR to detect in vitro base excision repair

DNA lesions in mammalian cells may be induced by reactive oxygen species, alkylation, and ionizing radiation. This damage can then be repaired via the base excision repair (BER) pathway, which includes single strand break repair (SSBR). Thus, the BER (SSBR) pathway plays a critical role in maintaining genomic integrity, and may help us to better understand the mechanisms of aging, tumor formation, and degenerative diseases. AP site (apurinic/apyrimidinic site) or damaged base excision, nucleotide insertion and ligation are included in the BER (SSBR) pathway, which are facilitated by different enzymes at each step. Most previous in vitro BER studies have used modified radiolabeled (32)P oligonucleotide substrates. Which is a very conventional method for in vitro BER assay. However, the use of radioactive isotope material was limited in various laboratories which are unable to handle radioactive hazard. In this study, we developed a novel technique using real-time quantitative PCR (qPCR) to quantify BER activity in in vitro assays. Single strand breaks, DNA ligase activity, and glycosylase activity were detected to establish the feasibility and advantages of this qPCR technique for in vitro BER profiling.

Nucleotide excision repair genes are expressed at low levels and are not detectably inducible in Caenorhabditis elegans somatic tissues, but their function is required for normal adult life after UVC exposure

We performed experiments to characterize the inducibility of nucleotide excision repair (NER) in Caenorhabditis elegans, and to examine global gene expression in NER-deficient and -proficient strains as well as germline vs. somatic tissues, with and without genotoxic stress. We also carried out experiments to elucidate the importance of NER in the adult life of C. elegans under genotoxin-stressed and control conditions. Adult lifespan was not detectably different between wild-type and NER-deficient xpa-1 nematodes under control conditions. However, exposure to 6J/m(2)/day of ultraviolet C radiation (UVC) decreased lifespan in xpa-1 nematodes more than a dose of 100 J/m(2)/day in wild-type. Similar differential sensitivities were observed for adult size and feeding. Remarkably, global gene expression was nearly identical in young adult wild-type and xpa-1 nematodes, both in control conditions and 3h after exposure to 50 J/m(2) UVC. Neither NER genes nor repair activity were detectably inducible in young adults that lacked germ cells and developing embryos (glp-1 strain). However, expression levels of dozens of NER and other DNA damage response genes were much (5-30-fold) lower in adults lacking germ cells and developing embryos, suggesting that somatic and post-mitotic cells have a much lower DNA repair ability. Finally, we describe a refinement of our DNA damage assay that allows damage measurement in single nematodes.

Important role of the nucleotide excision repair pathway in Mycobacterium smegmatis in conferring protection against commonly encountered DNA-damaging agents

Mycobacteria are an important group of human pathogens. Although the DNA repair mechanisms in mycobacteria are not well understood, these are vital for the pathogen's persistence in the host macrophages. In this study, we generated a null mutation in the uvrB gene of Mycobacterium smegmatis to allow us to compare the significance of the nucleotide excision repair (NER) pathway with two important base excision repair pathways, initiated by uracil DNA glycosylase (Ung) and formamidopyrimidine DNA glycosylase (Fpg or MutM), in an isogenic strain background. The strain deficient in NER was the most sensitive to commonly encountered DNA-damaging agents such as UV, low pH, reactive oxygen species, hypoxia, and was also sensitive to acidified nitrite. Taken together with previous observations on NER-deficient M. tuberculosis, these results suggest that NER is an important DNA repair pathway in mycobacteria.

Dual role of NER in mutagenesis in Pseudomonas putida

Nucleotide excision repair (NER) is one of the most important repair systems which counteracts different forms of DNA damage either induced by various chemicals or irradiation. At the same time, less is known about the functions of NER in repair of DNA that is not exposed to exogenous DNA-damaging agents. We have investigated the role of NER in mutagenesis in Pseudomonas putida. The genome of this organism contains two uvrA genes, uvrA and uvrA2. Genetic studies on the effects of uvrA, uvrA2, uvrB and UvrC in mutagenic processes revealed that all of these genes are responsible for the repair of UV-induced DNA damage in P. putida. However, uvrA plays more important role in this process than uvrA2 since the deletion of uvrA2 gene had an effect on the UV-tolerance of bacteria only in the case when uvrA was also inactivated. Interestingly, the lack of functional uvrB, uvrC or uvrA2 gene reduced the frequency of stationary-phase mutations. The contribution of uvrA2, uvrB and uvrC to the mutagenesis appeared to be most significant in the case of 1-bp deletions whose emergence is dependent on error-prone DNA polymerase Pol IV. These data imply that NER has a dual role in mutagenesis in P. putida-besides functioning in repair of damaged DNA, NER is also important in generation of mutations. We hypothesize that NER enzymes may initiate gratuitous DNA repair and the following DNA repair synthesis might be mutagenic.

Effects of oxidative compounds on thermotolerance in escherichia coli O157:H7 strains EO139 and 380-94

An oxidative complex composed of ferric iron chloride hexahydrate, ADP, and ascorbic acid can generate hydrogen peroxide and hydroxyl radicals in fibroblasts. These compounds are naturally found in meat and meat-based products and may elicit oxidative stress on Escherichia coli O157:H7, thus conferring thermotolerance to the bacterium due to the phenomenon of the global stress response. The effect of the levels of the oxidative complex on the thermotolerance of E. coli O157:H7 was investigated. Cultures of E. coli O157:H7 strains EO139 and 380-94 were mixed in three different concentrations (10:10: 40, 15:15:60, and 20:20:80 microM) of the oxidative complex (iron III chloride, ADP, and ascorbic acid, respectively). The samples were inserted into capillary tubes and heated in a circulating water bath at 59 and 60 degrees C for EO139 and 380-94, respectively. Tubes were removed at intervals of 5 min for up to 1 h and contents spirally plated on plate count agar that was incubated for 48 h at 37 degrees C. The thermotolerance of both E. coli O157:H7 strains EO139 and 380-94 was influenced by the concentrations of the oxidative complex. The ratio of 10:10:40 microM enhanced thermotolerance of EO139 and 390-94 at 59 and 60 degrees C, respectively. However, exposure to the ratios of 15:15:60 and 20:20:80 microM rendered the pathogen more sensitive to the lethal effect and did not enhance the thermotolerance of the cells. The significance of this study is twofold. This experiment proves that oxidative stress can enhance thermotolerance of bacterial cells induced by an oxidative complex if only in a specific ratio and concentration. It is possible to speculate that if the chemical compounds are present in this ratio in meats, they may enhance the thermal resistance of E. coli O157:H7 and make the bacteria more difficult to eliminate, thus increasing the risk of foodborne illness in consumers.

Participation of BER and NER pathways in the repair of DNA lesions induced at low N-nitrosodiethylamine concentrations

In the present work, we evaluated (p < 0.05) the participation of base excision repair (BER) and nucleotide excision repair (NER) mechanisms in repairing DNA lesions induced by N-nitrosodiethylamine (NDEA) at 1.5 ng/mL-36.5 microg/mL, through cell survival, in different single and double Escherichia coli DNA repair mutants (uvrA, uvrB, uvrC, fpg, nth, xthA, fpg/nth, uvrA/fpg, fpg/xthA, mutY, and fpg/mutY), using pre-incubation periods of 90 min. Mutant strains BH20 (fpg) and AB1886 (uvrA) showed microsomal enzyme (S9 mix) independent NDEA cytotoxicity. Cytotoxicity was also detected at lowest NDEA concentrations, in the presence of S9 mix, with strains BH980 (mutY) and BH990 (fpg/mutY). NDEA cytotoxicity, without S9 mix, was detected for mutant strains AB1884 (uvrC) and AB1885 (uvrB). Through SOS chromotest with 90 min of pre-incubation for uvrA and nth strains, only NER was shown to be required for repairing NDEA-induced lesions with or without metabolic activation. PQ37 and PQ66 strains, both uvrA mutants, showed different levels of NDEA sensitivity. The findings suggest that, under the used conditions, and at low concentrations, NDEA-induced lesions require both repair pathways.

Genotoxic evaluation of a vinifera skin extract that present pharmacological activities

Toxicity of an alcohol-free hydro-alcoholic grape skin extract (GSE) obtained from red grapes Vitis labrusca (Isabel varietal) that present antihypertensive, vasodilator and antioxidant effects was estimated by different bioassays. Using the Salmonella/microsome assay for strains TA97, TA98, TA100 and TA102 no mutagenicity was detected for all tested concentrations (0.1-100 microg/ml), even with metabolization. Nevertheless, cytotoxicity was observed for TA97 and TA102 with and without metabolization and for TA100 with metabolization. The measurement of beta-galactosidase induction in the SOS-chromotest was positive only for Escherichia coli PQ37 when metabolization enzymes were present. Using Balb/c 3T3 fibroblasts, DNA strand breaks induction by GSE was also investigated by the comet assay and no significative difference was detected for treated and no treated DNA for 60 min. Our data suggest that GSE although no mutagenic presents cytotoxic activity.

N-Nitrosodiethylamine mutagenicity at low concentrations

N-Nitrosodiethylamine (NDEA) requires metabolic activation by cytochrome P450 enzymes, leading to electrophile species that react in DNA. Although, carcinogenicity is not an end point in genotoxicity assays, NDEA has been considered a weak carcinogen. In this study, we carried out an analysis of the mutagenicity at low concentrations of NDEA. Using SOS chromotest in the presence of metabolic activation, we detected positive mutagenicity response for NDEA doses between 0.75 and 36.46 microg/ml. In Ames test, using more sensitive strains in the presence of S9 metabolic activation mixture (S9 mix), positive results were also detected for NDEA doses between 1.01 x 10(-3) and 50.64 x 10(-3 microg per plate. Our results indicate that NDEA mutagenicity can be detected at low concentrations when more sensitive conditions are used.

Delineating the requirements for spontaneous DNA damage resistance pathways in genome maintenance and viability in Saccharomyces cerevisiae

Cellular metabolic processes constantly generate reactive species that damage DNA. To counteract this relentless assault, cells have developed multiple pathways to resist damage. The base excision repair (BER) and nucleotide excision repair (NER) pathways remove damage whereas the recombination (REC) and postreplication repair (PRR) pathways bypass the damage, allowing deferred removal. Genetic studies in yeast indicate that these pathways can process a common spontaneous lesion(s), with mutational inactivation of any pathway increasing the burden on the remaining pathways. In this study, we examine the consequences of simultaneously compromising three or more of these pathways. Although the presence of a functional BER pathway alone is able to support haploid growth, retention of the NER, REC, or PRR pathway alone is not, indicating that BER is the key damage resistance pathway in yeast and may be responsible for the removal of the majority of either spontaneous DNA damage or specifically those lesions that are potentially lethal. In the diploid state, functional BER, NER, or REC alone can support growth, while PRR alone is insufficient for growth. In diploids, the presence of PRR alone may confer a lethal mutation load or, alternatively, PRR alone may be insufficient to deal with potentially lethal, replication-blocking lesions.

Effects of low iron conditions on the repair of DNA lesions induced by Cumene hydroperoxide in Escherichia coli cells

In the present study, we evaluated the sensitivity of different Escherichia coli strains to Cumene hydroperoxide (CHP) treatment under distinct conditions of Fe2+ availability. Our results showed that the pretreatment with an iron chelator (dipyridyl) protects all the tested strains against CHP toxic effects, but it was not sufficient to abolish the CHP induced mutagenesis. On the other hand, simultaneous pretreatment with both dipyridyl and neocuproine (copper chelator) leads to a complete protection against CHP mutagenic effects. Our data suggest the participation of copper ion in the CHP mutagenesis induced in E. coli.

Toxicological evaluation by in vitro and in vivo assays of an aqueous extract prepared from Echinodorus macrophyllus leaves

Toxicity of an aqueous extract prepared from Echinodorus macrophyllus dried leaves, a plant used in folk medicine to treat inflammation and kidney malfunctions, was estimated by different bioassays. Mutagenicity of the aqueous extract was evaluated in the Salmonella/microsome assay (TA97a, TA98, TA100 and TA102 strains), with or without metabolic activation. No mutagenic activity (lyophilized extract tested up to 50 mg/plate) could be detected to any of the tester strain. Furthermore, no cytotoxic effect has been observed when a crude extract of E. macrophyllus (up to 7.5 mg/ml) was tested on the exponential growth of hepatoma and normal kidney epithelial cells in culture. Toxicity of E. macrophyllus was also evaluated in male Swiss mice after 6 weeks of continuous ingestion of the aqueous extract in drinking water. Average daily ingested doses were 3, 23 and 297 mg/kg for a lyophilized extract, and 2200 mg/kg for a crude extract, with dose two being equivalent to the daily dose recommended to humans. At the end of the treatment, all animals revealed a deficit in final body weight ranging from 5 to 47%. Biochemical analysis of the plasma revealed some minor alterations indicating subclinical hepatic toxicity. Genotoxic effect on liver, kidney and blood cells has been also evaluated by the comet assay, being negative to liver and blood cells. However, DNA analyses of the kidney cells detected some genotoxic activity for the highest dose tested of E. macrophyllus extract, either lyophilized or crude. On the other hand, exposure dose of 23 mg/kg, equivalent to the daily dose recommended to humans, did not revealed any genotoxic effect and hence this herb seems to be safe to human organism.