Construction of a ColD cda promoter-based SOS-green fluorescent protein whole-cell biosensor with higher sensitivity toward genotoxic compounds than constructs based on recA, umuDC, or sulA promoters

Cell-based genotoxicity testing : genetically modified and genetically engineered bacteria in environmental genotoxicology

Genotoxicity test systems that are based on bacteria display an important role in the detection and assessment of DNA damaging chemicals. They belong to the basic line of test systems due to their easy realization, rapidness, broad applicability, high sensitivity and good reproducibility. Since the development of the Salmonella microsomal mutagenicity assay by Ames and coworkers in the early 1970s, significant development in bacterial genotoxicity assays was achieved and is still a subject matter of research. The basic principle of the mutagenicity assay is a reversion of a growth inhibited bacterial strain, e.g., due to auxotrophy, back to a fast growing phenotype (regain of prototrophy). Deeper knowledge of the -mutation events allows a mechanistic understanding of the induced DNA-damage by the utilization of base specific tester strains. Collections of such specific tester strains were extended by genetic engineering. Beside the reversion assays, test systems utilizing the bacterial SOS-response were invented. These methods are based on the fusion of various SOS-responsive promoters with a broad variety of reporter genes facilitating numerous methods of signal detection. A very important aspect of genotoxicity testing is the bioactivation of -xenobiotics to DNA-damaging compounds. Most widely used is the extracellular metabolic activation by making use of rodent liver homogenates. Again, genetic engineering allows the construction of highly sophisticated bacterial tester strains with significantly enhanced sensitivity due to overexpression of enzymes that are involved in the metabolism of xenobiotics. This provides mechanistic insights into the toxification and detoxification pathways of xenobiotics and helps explaining the chemical nature of hazardous substances in unknown mixtures. In summary, beginning with "natural" tester strains the rational design of bacteria led to highly specific and sensitive tools for a rapid, reliable and cost effective -genotoxicity testing that is of outstanding importance in the risk assessment of compounds (REACH) and in ecotoxicology.

The role of SOS boxes in enteric bacteriocin regulation

Bacteriocins are a large and functionally diverse family of toxins found in all major lineages of Bacteria. Colicins, those bacteriocins produced by Escherichia coli, serve as a model system for investigations of bacteriocin structure-function relationships, genetic organization, and their ecological role and evolutionary history. Colicin expression is often dependent on host regulatory pathways (such as the SOS system), is usually confined to times of stress, and results in death of the producing cells. This study investigates the role of the SOS system in mediating this unique form of toxin expression. A comparison of all the sequenced enteric bacteriocin promoters reveals that over 75 % are regulated by dual, overlapping SOS boxes, which serve to bind two LexA repressor proteins. Furthermore, a highly conserved poly-A motif is present in both of the binding sites examined, indicating enhanced affinity of the LexA protein for the binding site. The use of gene expression analysis and deletion mutations further demonstrates that these unique LexA cooperative binding regions result in a fine tuning of bacteriocin production, limiting it to times of stress. These results suggest that the evolution of dual SOS boxes elegantly accomplishes the task of increasing the amount of toxin produced by a cell while decreasing the rate of uninduced production, effectively reducing the cost of colicin production. This hypothesis may explain why such a promoter motif is present at such high frequencies in natural populations of bacteriocin-producing enteric bacteria.

Construction of a nrdA::luxCDABE Fusion and Its Use in Escherichia coli as a DNA Damage Biosensor

The promoter of nrdA gene which is related with DNA synthesis was used to construct a DNA damage sensitive biosensor. A recombinant bioluminescent E. coli strain, BBTNrdA, harboring a plasmid with the nrdA promoter fused to the luxCDABE operon, was successfully constructed. Its response to various chemicals including genotoxic chemicals substantiates it as a DNA damage biosensor. In characterization, three different classes of toxicants were used: DNA damaging chemicals, oxidative stress chemicals, and phenolics. BBTNrdA only responded strongly to DNA damaging chemicals, such as nalidixic acid (NDA), mitomycin C (MMC), 1-methyl-1-nitroso-N-methylguanidine (MNNG), and 4-nitroquinoline N-oxide (4-NQO). In contrast, there were no responses from the oxidative stress chemicals and phenolics, except from hydrogen peroxide (H₂O₂) which is known to cause DNA damage indirectly. Therefore, the results of the study demonstrate that BBTNrdA can be used as a DNA damage biosensor.

Screening of target-specific stress-responsive genes for the development of cell-based biosensors using a DNA microarray

In this study, we describe a straightforward strategy to develop whole cell-based biosensors using fusions of the bacterial bioluminescence genes and the promoters from chemically responsive genes within Escherichia coli, in which chemical target-responsive genes were screened by using the information of gene expression data obtained from DNA microarray analysis. Paraquat was used as a model chemical to trigger gene expression changes of E. coli and to show the DNA microarray-assisted development of whole cell-based biosensors. Gene expression data from the DNA microarray were obtained by time course analysis (10, 30, and 60 min) after exposure to paraquat. After clustering gene expression data obtained by time course analysis, a group of highly expressed genes over the all time courses could be classified. Within this group, three genes expressed highly for overall time points were selected and promoters of these genes were used as fusion partners with reporter genes, lux CDABE, to construct whole cell-based biosensors. The constructed biosensors recognized the presence of model inducer, paraquat, and structural analogue chemicals of paraquat with a high specificity, and the results were reconfirmed by using DNA microarray experiments for those structural analogues. This strategy to develop whole cell-based biosensors assisted by DNA microarray information should be useful in general for constructing chemical-specific or stress-specific biosensors with a high-throughput manner.

The cda GenoTox assay: a new and sensitive method for detection of environmental genotoxins, including nitroarenes and aromatic amines

A new bacterial test system for detection of genotoxic compounds was developed, based on two new Salmonella typhimurium tester strains, TGO1 and TGO2. Both strains contain a gene fusion between a strong SOS-promotor, P(cda), and the gfp gene, which allows detection of genotoxic compounds that induce the SOS response. SOS induction was detected by means of flow cytometry. TGO1 showed an increased sensitivity to N-methyl-N'-nitro-N-nitrosoguanidine compared with a previously developed strain, which had an Escherichia coli strain as host instead of S. typhimurium. S9 mix was introduced into the assay, making the test system suitable for detection of indirect mutagens. Furthermore, the genes for bacterial nitro-reductase (NR) and o-acetyl transferase (o-AT) were inserted into TGO2, making it an NR- and o-AT-over-expressing strain. This resulted in an assay that was able to detect the nitroarene 1-nitropyrene and the aromatic amine 2-aminoanthracene with high sensitivity.

Colicin biology

Colicins are proteins produced by and toxic for some strains of Escherichia coli. They are produced by strains of E. coli carrying a colicinogenic plasmid that bears the genetic determinants for colicin synthesis, immunity, and release. Insights gained into each fundamental aspect of their biology are presented: their synthesis, which is under SOS regulation; their release into the extracellular medium, which involves the colicin lysis protein; and their uptake mechanisms and modes of action. Colicins are organized into three domains, each one involved in a different step of the process of killing sensitive bacteria. The structures of some colicins are known at the atomic level and are discussed. Colicins exert their lethal action by first binding to specific receptors, which are outer membrane proteins used for the entry of specific nutrients. They are then translocated through the outer membrane and transit through the periplasm by either the Tol or the TonB system. The components of each system are known, and their implication in the functioning of the system is described. Colicins then reach their lethal target and act either by forming a voltage-dependent channel into the inner membrane or by using their endonuclease activity on DNA, rRNA, or tRNA. The mechanisms of inhibition by specific and cognate immunity proteins are presented. Finally, the use of colicins as laboratory or biotechnological tools and their mode of evolution are discussed.

Genetically Engineered pfabA pfabR Bacteria: an Electrochemical Whole Cell Biosensor for Detection of Water Toxicity

We describe here a bacterial sensor for electrochemical detection of toxic chemicals. The sensor constitutes recombinant bacteria harboring plasmids encoding the fabA and fabR genes and has high-resolution amperometric response to membrane-damaging chemicals. For example, it can detect phenol at concentrations ranging between 1.6 and 16 ppm within 20 min. The high sensitivity is achieved by using the fabA promoter fused to a reporter gene-encoded beta-galactosidase on a low copy number plasmid, under the control of the FabR repressor. The use of electrochemical whole cell sensors enables sensitive, fast, easy to operate, and cost-effective detection of water toxicity threats.

Involvement of the drug efflux protein TolC in mutagenicity induced by MNNG or Trp-P-2

In the development of mutation assay systems, a number of approaches have been performed with a particular view to improve sensitivity. The inhibition of mutagen-efflux from tester bacteria might lead to increased mutagenic activity as the concentration of mutagen increases inside the cell. In this study, we constructed a series of Escherichia coli CC strains lacking the TolC protein to determine if mutation is actually enhanced by the inhibition of mutagen reflux. TolC is an outer-membrane protein that forms part of an excretion system in E. coli. The frequency of induction of mutations by N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), N-ethyl-N'-nitro-N-nitrosoguanidine (ENNG) and ethyl methanesulfonate (EMS) were significantly higher in TolC-deficient strain KA796-1/CC102 than in TolC-proficient strains, especially that of MNNG was seven times higher and detected at lower doses than in the parent strain. In a KA796-1/CC108 TolC-deficient strain, mutation induced by Trp-P-2 was detected at significant levels, even at low doses that did not induce detectable levels of mutation in the parent strain KA796/CC108. When the wild-type E. coli tolC gene was introduced into a strain lacking the gene, TolC function was restored and the frequency of induction by MNNG became similar to that of the wild-type. In contrast, introduction of a mutant tolC gene did not complement the TolC deficiency and the frequency of MNNG-induced mutations remained high. These results suggest that some mutagens are excreted at least in part via the TolC system, and that the lack of functional TolC increases the susceptibility of bacteria to many mutagens.

Whole-cell living biosensors—are they ready for environmental application?

Since the development of the first whole-cell living biosensor or bioreporter about 15 years ago, construction and testing of new genetically modified microorganisms for environmental sensing and reporting has proceeded at an ever increasing rate. One and a half decades appear as a reasonable time span for a new technology to reach the maturity needed for application and commercial success. It seems, however, that the research into cellular biosensors is still mostly in a proof-of-principle or demonstration phase and not close to extensive or commercial use outside of academia. In this review, we consider the motivations for bioreporter developments and discuss the suitability of extant bioreporters for the proposed applications to stimulate complementary research and to help researchers to develop realistic objectives. This includes the identification of some popular misconceptions about the qualities and shortcomings of bioreporters.

A flow cytometry-optimized assay using an SOS–green fluorescent protein (SOS–GFP) whole-cell biosensor for the detection of genotoxins in complex environments

Whole-cell biosensors have become popular tools for detection of ecotoxic compounds in environmental samples. We have developed an assay optimized for flow cytometry with detection of genotoxic compounds in mind. The assay features extended pre-incubation and a cell density of only 10(6)-10(7) cells/mL, and proved far more sensitive than a previously published assay using the same biosensor strain. By applying the SOS-green fluorescent protein (GFP) whole-cell biosensor directly to soil microcosms we were also able to evaluate both the applicability and sensitivity of a biosensor based on SOS-induction in whole soil samples. Soil microcosms were spiked with a dilution-series of crude broth extract from the mitomycin C-producing streptomycete Streptomyces caespitosus. Biosensors extracted from these microcosms after 1 day of incubation at 30 degrees C were easily distinguished from extracts of non-contaminated soil particles when using flow cytometry, and induction of the biosensor by mitomycin C was detectable at concentrations as low as 2.5 ng/g of soil.

Making bio-sense of toxicity: new developments in whole-cell biosensors

Bacterial whole-cell biosensors are very useful for toxicity measurements of various samples. Semi-specific biosensors, containing fusions of stress-regulated promoters and reporter genes, have several advantages over the traditional, general biosensors that are based on constitutively expressed reporter genes. Furthermore, semi-specific biosensors are constantly being refined to lower their sensitivity and, in combination, are able to detect a wide range of toxic agents. However, the requirement for a positive response of these biosensors to toxicants can result in false-negative responses. The application of in situ inoculation and single-cell detection, combined with the introduction of new reporter genes and refined detection equipment, could lead to the extensive use of semi-specific, stress-responsive biosensors for toxicity estimations in the future.

Information from single-cell bacterial biosensors: what is it good for?

Bacterial reporter cells (i.e. strains engineered to produce easily measurable signals in response to one or more chemical targets) can principally be used to quantify chemical signals and analytes, physicochemical conditions and gradients on a microscale (i.e. micrometer to submillimeter distances), when the reporter signal is determined in individual cells. This makes sense, as bacterial life essentially thrives in microheterogenic environments and single-cell reporter information can help us to understand the microphysiology of bacterial cells and its importance for macroscale processes like pollutant biodegradation, beneficial bacteria-eukaryote interactions, and infection. Recent findings, however, showed that clonal bacterial populations are essentially always physiologically, phenotypically and genotypically heterogeneous, thus emphasizing the need for sound statistical approaches for the interpretation of reporter response in individual bacterial cells. Serious attempts have been made to measure and interpret single-cell reporter gene expression and to understand variability in reporter expression among individuals in a population.