What limits the efficiency of double-strand break-dependent stress-induced mutation in Escherichia coli?

Stress-induced mutation is a collection of molecular mechanisms in bacterial, yeast and human cells that promote mutagenesis specifically when cells are maladapted to their environment, i.e. when they are stressed. Here, we review one molecular mechanism: double-strand break (DSB)-dependent stress-induced mutagenesis described in starving Escherichia coli. In it, the otherwise high-fidelity process of DSB repair by homologous recombination is switched to an error-prone mode under the control of the RpoS general stress response, which licenses the use of error-prone DNA polymerase, DinB, in DSB repair. This mechanism requires DSB repair proteins, RpoS, the SOS response and DinB. This pathway underlies half of spontaneous chromosomal frameshift and base substitution mutations in starving E. coli [Proc Natl Acad Sci USA 2011;108:13659-13664], yet appeared less efficient in chromosomal than F' plasmid-borne genes. Here, we demonstrate and quantify DSB-dependent stress-induced reversion of a chromosomal lac allele with DSBs supplied by I-SceI double-strand endonuclease. I-SceI-induced reversion of this allele was previously studied in an F'. We compare the efficiencies of mutagenesis in the two locations. When we account for contributions of an F'-borne extra dinB gene, strain background differences, and bypass considerations of rates of spontaneous DNA breakage by providing I-SceI cuts, the chromosome is still ～100 times less active than F. We suggest that availability of a homologous partner molecule for recombinational break repair may be limiting. That partner could be a duplicated chromosomal segment or sister chromosome.     

Relevance of Fatty Acid Covalently Bound to Escherichia coli ��-Hemolysin and Membrane Microdomains in the Oligomerization Process

α-Hemolysin (HlyA) is an exotoxin secreted by some pathogenic strains of Escherichia coli that causes lysis of several mammalian cells, including erythrocytes of different species. HlyA is synthesized as a protoxin, pro-HlyA, which is activated by acylation at two internal lysines Lys-563 and Lys-689. It has been proposed that pore formation is the mechanism of cytolytic activity for this toxin, as shown in experiments with whole cells, planar lipid membranes, and liposomes, but these experiments have yielded conflicting results about the structure of the pore. In this study, HlyA cysteine replacement mutant proteins of amino acids have been labeled with Alexa-488 and Alexa-546. Fluorescence resonance energy transfer measurements, employing labeled toxin bound to sheep ghost erythrocytes, have demonstrated that HlyA oligomerizes on erythrocyte membranes. As the cytotoxic activity is absolutely dependent on acylation, we have studied the role of acylation in the oligomerization, demonstrating that fatty acids are essential in this process. On the other hand, fluorescence resonance energy transfer and the hemolytic activity decrease when the erythrocyte ghosts are cholesterol-depleted, hence indicating the role of membrane microdomains in the clustering of HlyA. Simultaneously, HlyA was found in detergent-resistant membranes. Pro-HlyA has also been found in detergent-resistant membranes, thus demonstrating that the importance of acyl chains in toxin oligomerization is the promotion of protein-protein interaction. These results change the concept of the main role assigned to acyl chain in the targeting of proteins to membrane microdomains.Escherichia coli α-hemolysin, HlyA,⁴ is an exotoxin that elicits a number of responses from mammalian target cells and also alters the membrane permeability of host cells, causing lysis and death (1, 2). Synthesis, maturation, and secretion of E. coli HlyA are determined by the hlyCABD operon (3). The gene A product is a 110-kDa polypeptide corresponding to protoxin (Pro-HlyA), which is matured in bacterial cytosol to the active form (HlyA) by HlyC-directed acylation. This post-translational modification involves a covalent amide linkage of fatty acids at two internal lysine residues (Lys-563 and Lys-689) for activation (4). HlyA activated in vivo consists of a heterogeneous family of up to nine different covalent structures (two acylation sites and three possible modifying groups in each site, C14:0 (68%), C15:0 (26%) and C17:0 (6%) (5)). Although these fatty acids are not required for the binding of the toxin to membranes, they are essential for the hemolytic process, inducing a molten globule conformation and promoting the irreversibility of the binding (6, 7).It has been proposed that pore formation is the mechanism of cytolytic activity for this toxin, as shown in experiments with whole cells, planar lipid membranes, and liposomes. However, these experiments have yielded conflicting results. Although a group of researchers is in favor of a monomer as the active species of the toxin in membranes, other groups postulate that an oligomerization process is involved. Based on experiments with lipid bilayers, Menestrina et al. (8) have suggested that one single HlyA molecule is responsible for the formation of the channel. HlyA has also been recovered from deoxycholate-solubilized erythrocyte membranes as a monomer, indicating either that oligomerization is not required for pore formation or that oligomers are dissociated in the detergent (1).On the other hand, Benz et al. (9) have found that small variations of toxin concentration have had a considerable effect on the specific membrane conductance. An increase in HlyA concentration, by a factor of 5, results in about 40–100-fold higher membrane conductance. This means that several HlyA molecules could be involved in channel formation (9). Besides, they have found that the active channel-forming oligomer and inactive monomer are in an association-dissociation equilibrium (10). In addition, the complementation of inactive deleted mutant proteins of HlyA with the corresponding wild type toxin produces hemolytic activity, suggesting that two or more toxin molecules aggregate before pore formation (11). All of the evidence suggests the formation of an oligomer.Experiments employing erythrocytes and model membranes have shown that the lesion created by HlyA is perhaps a more complicated event than the creation of a simple, static protein-lined pore. We have recently found that addition of nanomolar concentrations of toxin to planar lipid membranes have resulted in a decrease in membrane lifetime up to 3 orders of magnitude in a voltage-dependent manner, a typical behavior of proteolipidic pores (12). Moayeri and Welch (13) have previously demonstrated that osmotic protection of erythrocytes by sugars of different sizes is a function of toxin concentration and assay time. It appears that HlyA induces heterogeneous erythrocyte lesions that increase in size over time and that the rate of the putative growth in the size of HlyA-mediated lesions is temperature-dependent (13).On the other hand, it has been recognized that a variety of pathogens and toxins interacts with microdomains in the plasma membrane. These microdomains are enriched in cholesterol and sphingolipids and probably exist in a liquid-ordered phase, in which lipid acyl chains are extended and ordered (14). Many proteins are targeted to these membrane microdomains by their favorable association with ordered lipids. Interestingly, these proteins are linked to saturated acyl chains, which partition well into these domains (15).In this context, and in view of the fact that acyl chains covalently bound to proteins are determinant of specific protein-protein interactions, this research presents a study of HlyA oligomerization on sheep erythrocytes, as well as the implication of fatty acids and cholesterol-enriched microdomains in this process.     

Cloning of the thermostable α-amylase gene from Pyrococcus woesei in Escherichia coli

Pyrococcus woesei (DSM 3773) α-amylase gene was cloned into pET21d(+) and pYTB2 plasmids, and the pET21d(+)α-amyl and pYTB2α-amyl vectors obtained were used for expression of thermostable α-amylase or fusion of α-amylase and intein in Escherichia coli BL21(DE3) or BL21(DE3)pLysS cells, respectively. As compared with other expression systems, the synthesis of α-amylase in fusion with intein in E. coli BL21(DE3)pLysS strain led to a lower level of inclusion bodies formation—they exhibit only 35% of total cell activity—and high productivity of the soluble enzyme form (195,000 U/L of the growth medium). The thermostable α-amylase can be purified free of most of the bacterial protein and released from fusion with intein by heat treatment at about 75°C in the presence of thiol compounds. The recombinant enzyme has maximal activity at pH 5.6 and 95°C. The half-life of this preparation in 0.05 M acetate buffer (pH 5.6) at 90°C and 110°C was 11 h and 3.5 h, respectively, and retained 24% of residual activity following incubation for 2 h at 120°C. Maltose was the main end product of starch hydrolysis catalyzed by this α-amylase. However, small amounts of glucose and some residual unconverted oligosaccharides were also detected. Furthermore, this enzyme shows remarkable activity toward glycogen (49.9% of the value determined for starch hydrolysis) but not toward pullulan.     

Bacterial diversity of Escherichia coli in the gut: a reason to re-evaluate probiotic formulations?

Humans and animals are increasingly being subjected to various probiotic formulations with the claim of providing a number of health benefits to the consumer. These formulations usually incorporate bacterial consortia comprising of mostly lactic acid bacteria (LAB). Recent studies have shown that strains found in different regions of the gut are genetically different from each other and may therefore have different abilities to interact with bacteria that they come into contact with. Even LAB show differences in their ability to interact, and further, inhibit growth of pathogenic bacteria in vitro due to individual strain differences. If these results are repeatedly shown to be true in future assessments, an evaluation of bacterial consortia used in probiotic formulations may now be necessary. This may have an impact in the way future probiotic formulations are prepared.     

Carbondioxide affects the growth rate of “oxygen limited”Escherichia coli at low concentrations of oxygen

Summary It is shown that addition of 1% CO₂ in Argon, containing traces of oxygen (<30 ppm O₂) to a described mineral salts medium leads to deblockage of the normal oxygen limited growth pattern ofEscherichia coli (ATCC 1524).     

Sulphur islands in the Escherichia coli genome: markers of the cell's architecture?

Two highly contrasted images depict genomes: at first sight, genes appear to be distributed randomly along the chromosome. In contrast, their organisation into operons (or pathogenicity islands) suggests that, at least locally, related functions are in physical proximity. Analysis of the codon usage bias in orthologous genes in the genome of bacteria which diverged a long time ago suggested that some physical (architectural) selection pressure organised the distribution of genes along the chromosome. The metabolism of highly reactive species such as sulphur-containing molecules must be compartmentalised to escape the deleterious actions of diffusible reagents such as gases or radicals. We analysed the distribution of sulphur metabolism genes in the genome of Escherichia coli and found a number of them to be clustered into statistically significant islands. Another interesting feature of these genes is that the proteins they encode are significantly deprived of cysteine and methionine residues, as compared to the bulk proteins. We speculate that this clustering is associated to the organisation of sulphur metabolism proteins into islands where the sensitive sulphur-containing molecules are protected from reacting with elements in the environment such as dioxygen, nitric oxide or radicals.     

Cloning and expression of the insecticidal toxin gene “tccB” from Photorhabdus temperata M1021 in Escherichia coli expression system

Photorhabdus spp. has a high molecular weight Tc toxin with insecticidal activity. These toxins have been suggested as an alternative to BT toxin from Bacillus thuringiensis. Herein, we constructed a cosmid library with the genome of M1021 and screened the Escherichia coli clones showing insect toxicity by injecting each clone into Galleria mellonella larvae. In a total of 1020 clones, one clone with high insecticidal activity was selected and the nucleotide sequence of the cosmid of the clone was determined. In cosmid PtC28, a gene with 87% homology to the tccB gene of Photorhabdus temperata was found. Consequently, we have isolated the tccB gene cassette from the M1021 and expressed in E. coli expression vectors. The toxin was produced in the form of inclusion bodies but the denatured and refolded recombinant TccB showed strong mortality to the G. mellonella larvae.     

Secretion to the growth medium of an α-amylase by Escherichia coli clones carrying a Bacillus laterosporus gene

-Amylase gene from Bacillus laterosporus P₃ was cloned and expressed in Escherichia coli HB101 and DH5. Up to 92% of the cloned gene product was secreted into the medium by the recombinant E. coli. The recombinant crude enzyme showed improved functionality in terms of activity at a wider pH range and at higher temperature, as compared to the crude enzyme from the donor strain. The improved functionality of the cloned enzyme was due to the absence of a contaminating protease which was co-produced in the donor strain. Sub-cloning of the -amylase gene using the promoter-probe vector, pKT240 in E. coli DH5 indicated the presence of a promoter of B. laterosporus P₃ in the cloned fragment.     

Cultivation at 6-10°C is an effective strategy to overcome the insolubility of recombinant proteins in Escherichia coli

Protein expression in Escherichia coli at 15-25°C is widely used to increase the solubility of recombinant proteins. However, many recombinant proteins are insolubly expressed even at those low temperatures. Here, we show that recombinant proteins can be expressed as soluble forms by simply lowering temperature to 6-10°C without cold adapted chaperon systems. By using E. coli Rosetta-gami2(DE3), we obtained 1.8 and 0.9mg of Cryptopygus antarticus mannanase (CaMan) and cellulase (CaCel) from 1l culture grown at 6 and 10°C, respectively. Cultivation at 10°C also led to successful expression of EM3L7 (a lipase isolated from a metagenomic library) in a soluble form in E. coli BL21(DE3). Consequently, E. coli cultivation at 6-10°C is an effective strategy for overcoming a major hurdle of the inclusion body formation.