Detection of 2,4-dinitrotoluene and 2,4,6-trinitrotoluene by an Escherichia coli bioreporter: performance enhancement by directed evolution

A sensitive PnpR-based biosensor for p-nitrophenol detection

A common aromatic and phenolic pollutant, p-nitrophenol (PNP), is widely used in various industry and has serious risk to the environmental health. Biosensors have been extensively employed as an alternative technology for pollutants monitoring. By mining the new sensing elements, more specific biosensors could be characterized for highly sensitive detection. Herein, the PnpR transcription factor was identified to activate the transcription of pnpC1 by binding to PpnpC1 promoter region in P. putida DLL-E4, and PNP was recognized as its specific inducer. The PnpR-based biosensor for detection of PNP was developed, demonstrating adequate sensitivity in a liquid solution with satisfactory specificity. The biosensor was optimized by adopting a transcriptional amplifier, which increased the maximum output by 149-fold, and improved the detection limit by 100-fold, from 1 mg/L to 10 μg/L. These biosensors had a linear range of 5-80 mg/L and 0.01-1.0 mg/L for PNP determination, respectively. Then, the agarose gel entrapment-based biosensor was constructed and allowed a good of PNP detection in the range of 5-60 mg/L in M9 solid agar within 70 min, and a detection sensitive of 16.8 mg/kg in soil. The good performance of the biosensor suggested its potential application of high-efficient and on-site detection in environmental matrices.

A Microbial Cocaine Bioreporter

The continuous emergence of new illegal compounds, particularly psychoactive chemicals, poses significant challenges for current drug detection methods. Developing new protocols and kits for each new drug requires substantial time, effort, and dedicated manpower. Whole-cell bacterial bioreporters have been proven capable of detecting diverse hazardous compounds in both laboratory and field settings, identifying not only single compounds but also chemical families. We present the development of a microbial bioreporter for the detection of cocaine, the nervous system stimulant that is the second-most widely used illegal drug in the US. Escherichia coli was transformed with a plasmid containing a bacterial luxCDABEG bioluminescence gene cassette, activated by a cocaine-responsive signaling cascade. The engineered bioreporter is demonstrated to be a sensitive and specific first-generation detection system for cocaine, with detection thresholds of 17 ± 8 μg/L and 130 ± 50 μg/L in a buffer solution and in urine, respectively. Further improvement of the sensor's performance was achieved by altering the nucleotide sequence of the PBen gene promoter, the construct's sensing element, using accelerated site-directed evolution. The applicability of ready-to-use paper strips with immobilized bioreporter cells was demonstrated for cocaine detection in aqueous solutions.

Development of lycopene-based whole-cell biosensors for the visual detection of trace explosives and heavy metals

Residual explosives in conflicting zones have caused irreversible damage to human safety and the environment. Whole-cell biosensors can to detect remnants of buried explosives, such as 2,4-dinitrotoluene (DNT), a stable and highly volatile compound in explosives. However, all the reported whole-cell biosensors utilize fluorescence or luminescence as the biological markers, making their detection difficult in real minefields. Here, we presented a lycopene-based whole-cell biosensor in Escherichia coli to output visible signals in response to DNT, which can help in the visual detection of buried explosives. To construct the whole-cell biosensor, the DNT-responsive promoter yqjF was used as the sensing element, and the lycopene synthetic gene cassette crtEBI was served as the reporting element. Then, the metabolic flux for lycopene production was enhanced to improve the output signal of the whole-cell biosensor, and a terminator was utilized to reduce the background interference. The optimized biosensor LSZ05 could perceive at least 1 mg/L DNT. The DNT-specificity and robust performance of the biosensor under different environmental factors were confirmed. Our results showed that converting the biosensor into a lyophilized powder was an effective storage method. The biosensor LSZ05 could effectively detect DNT in two kinds of soil samples. The lycopene-based whole-cell biosensor could also be used to visually detect heavy metals. Our findings laid the foundation for visually detecting buried explosives in minefields, which was a valuable supplement to the reported biosensors. The methods used for optimizing the lycopene-based whole-cell biosensor, including the improvement of the output signal and reduction of background interference, were quite effective.

Structural basis of transcription factor YhaJ for DNT detection

Detection of landmines without harming personnel is a global issue. The bacterial transcription factor YhaJ selectively detects metabolites of explosives, and it can be used as a key component of DNT biosensors. However, the wild-type YhaJ has a binding affinity that is not sufficient for the detection of trace amounts of explosives leaked from landmines buried in the soil. Here, we report crystal structures of the effector-binding domain of YhaJ in both the apo- and effector-bound forms. A structural comparison of the two forms revealed that the loop above the primary effector-binding site significantly switches its conformation upon effector binding. The primary effector-binding site involves hydrophobic and polar interactions, having specificity to hydroxyl-substituted benzene compounds. The structures explain the mechanism of activity-enhancing mutations and provide information for the rational engineering of YhaJ biosensors for the sensitive detection of explosives.

Performance upgrade of a microbial explosives' sensor strain by screening a high throughput saturation library of a transcriptional regulator

We present a methodology for a high-throughput screening (HTS) of transcription factor libraries, based on bacterial cells and GFP fluorescence. The method is demonstrated on the Escherichia coli LysR-type transcriptional regulator YhaJ, a key element in 2,4-dinitrotuluene (DNT) detection by bacterial explosives' sensor strains. Enhancing the performance characteristics of the YhaJ transcription factor is essential for future standoff detection of buried landmines. However, conventional directed evolution methods for modifying YhaJ are limited in scope, due to the vast sequence space and the absence of efficient screening methods to select optimal transcription factor mutants. To overcome this limitation, we have constructed a focused saturation library of ca. 6.4 × 107 yhaJ variants, and have screened over 70 % of its sequence space using fluorescence-activated cell sorting (FACS). Through this screening process, we have identified YhaJ mutants exhibiting superior fluorescence responses to DNT, which were then effectively transformed into a bioluminescence-based DNT detection system. The best modified DNT reporter strain demonstrated a 7-fold lower DNT detection threshold, a 45-fold increased signal intensity, and a 40 % shorter response time compared to the parental bioreporter. The FACS-based HTS approach presented here may hold a potential for future molecular enhancement of other sensing and catalytic bioreactions.

Design and optimization of E. coli artificial genetic circuits for detection of explosive composition 2,4-dinitrotoluene

The detection of mine-based explosives poses a serious threat to the lives of deminers, and carcinogenic residues may cause severe environmental pollution. Whole-cell biosensors that can detect on-site in dangerous or inaccessible environments have great potential to replace conventional methods. Synthetic biology based on engineering modularity serves as a new tool that could be used to engineer microbes to acquire desired functions through artificial design and precise regulation. In this study, we designed artificial genetic circuits in Escherichia coli MG1655 by reconstructing the transcription factor YhaJ-based system to detect explosive composition 2,4-dinitrotoluene (2,4-DNT). These genetic circuits were optimized at the transcriptional, translational, and post-translational levels. The binding affinity of the transcription factor YhaJ with inducer 2,4-DNT metabolites was enhanced via directed evolution, and several activator binding sites were inserted in sensing yqjF promoter (P_yqjF) to further improve the output level. The optimized biosensor P_yqjF×2-TEV-(mYhaJ + GFP)-Ssr had a maximum induction ratio of 189 with green fluorescent signal output, and it could perceive at least 1 μg/mL 2,4-DNT. Its effective and robust performance was verified in different water samples. Our results demonstrate the use of synthetic biology tools to systematically optimize the performance of sensors for 2,4-DNT detection, that lay the foundation for practical applications.

Introduction of quorum sensing elements into bacterial bioreporter circuits enhances explosives' detection capabilities

A possible solution for the standoff detection of buried landmines is based on the use of microbial bioreporters, genetically engineered to emit a remotely detectable optical signal in response to trace amounts of explosives' signature chemicals, mostly 2,4-dinitrotoluene (DNT). Previously developed DNT sensor strains were based on the fusion of a DNT-inducible gene promoter to a reporting element, either a fluorescent protein gene or a bacterial bioluminescence gene cassette. In the present study, a different approach was used: the DNT-inducible promoter activates, in Escherichia coli, the quorum-sensing luxI and luxR genes of Aliivibrio fischeri. N-Acyl homoserine lactone (AHL), synthesized by LuxI, combines with LuxR and activates the bioluminescence reporter genes. The resulting bioreporter displayed a dose-dependent luminescent signal in the presence of DNT. Performance of the sensor strain was further enhanced by manipulation of the sensing element (combining the E. coli DNT-inducible azoR and yqjF gene promoters), by replacing the luminescence gene cassette of Photorhabdus luminescens luxCDABE with A. fischeri luxCDABEG, and by introducing two mutations, eutE and ygdD, into the host strain. DNT detection sensitivity of the final bioreporter was over 340-fold higher than the original construct.

Enhancing DNT Detection by a Bacterial Bioreporter: Directed Evolution of the Transcriptional Activator YhaJ

Detection of buried landmines is a dangerous and complicated task that consumes large financial resources and poses significant risks to the personnel involved. A potential alternative to conventional detection methodologies is the use of microbial bioreporters, capable of emitting an optical signal upon exposure to explosives, thus revealing to a remote detector the location of buried explosive devices. We have previously reported the design, construction, and optimization of an Escherichia coli-based bioreporter for the detection of 2,4,6-trinitrotoluene (TNT) and its accompanying impurity 2,4-dinitrotoluene (DNT). Here we describe the further enhancement of this bioreporter by the directed evolution of YhaJ, the transcriptional activator of the yqjF gene promoter, the sensing element of the bioreporter's molecular circuit. This process resulted in a 37-fold reduction of the detection threshold, as well as significant enhancements to signal intensity and response time, rendering this sensor strain more suitable for detecting the minute concentrations of DNT in the soil above buried landmines. The capability of this enhanced bioreporter to detect DNT buried in sand is demonstrated.

Microbial whole-cell biosensors: Current applications, challenges, and future perspectives

Microbial Whole-Cell Biosensors (MWCBs) have seen rapid development with the arrival of 21st century biological and technological capabilities. They consist of microbial species which produce, or limit the production of, a reporter protein in the presence of a target analyte. The quantifiable signal from the reporter protein can be used to determine the bioavailable levels of the target analyte in a variety of sample types at a significantly lower cost than most widely used and well-established analytical instrumentation. Furthermore, the versatile and robust nature of MWCBs shows great potential for their use in otherwise unavailable settings and environments. While MWCBs have been developed for use in biomedical, environmental, and agricultural monitoring, they still face various challenges before they can transition from the laboratory into industrialized settings like their enzyme-based counterparts. In this comprehensive and critical review, we describe the underlying working principles of MWCBs, highlight developments for their use in a variety of fields, detail challenges and current efforts to address them, and discuss exciting implementations of MWCBs helping redefine what is thought to be possible with this expeditiously evolving technology.

A bacterial bioreporter for the detection of 1,3,5-trinitro-1,3,5-triazinane (RDX)

We report the design, construction, and testing of Escherichia coli-based bioluminescent bioreporters for the detection of 1,3,5-trinitro-1,3,5-triazinane (RDX), one of the most prevalent military-grade explosives in use today. These sensor strains are based on a fusion between the promoter of either the hmp (nitric oxide dioxygenase) or the hcp (a high-affinity nitric oxide reductase) E. coli gene, to the microbial bioluminescence luxCDABEG gene cassette. Signal intensity was enhanced in ∆hmp and ∆hcp mutants, and detection sensitivity was improved when the two gene promoters were cloned in tandem. The Photobacterium leiognathi luxCDABEG reporter genes were superior to those of Aliivibrio fischeri in terms of signal intensity, but in most cases inferior in terms of detection sensitivity, due to a higher background signal. Both sensor strains were also induced by additional nitro-organic explosives, as well as by nitrate salts. Sensitive detection of RDX in a solid matrix (either LB agar or sand) was also demonstrated, with the bioreporters encapsulated in 1.5-mm calcium alginate beads. Lowest RDX concentration detected in sand was 1.67 mg/kg sand. The bioreporter strains described herein may serve as a basis for a standoff detection technology of RDX-based explosive devices, including buried landmines.

A chemical genetic approach using genetically encoded reporters to detect and assess the toxicity of plant secondary metabolites against bacterial pathogens

Plant secondary metabolites are emerging as attractive alternatives in the development of therapeutics against infectious and chronic diseases. Due to the present pandemic, therapeutics showing toxicity against bacterial pathogens and viruses are gaining interest. Plant metabolites of terpenoid and phenylpropanoid categories have known antibacterial and antiviral properties. These metabolites have also been associated with toxicity to eukaryotic cells in terms of carcinogenicity, hepatotoxicity, and neurotoxicity. Sensing methods that can report the exact antibacterial dosage, formation, and accumulation of these antibacterial compounds are needed. The whole-cell reporters for such antibacterial metabolites are cost-effective and easy to maintain. In the present study, battery of toxicity sensors containing fluorescent transcriptional bioreporters was constructed, followed by fine-tuning the response using gene-debilitated E. coli mutants. This study shows that by combining regulatory switches with chemical genetics strategy, it may be possible to detect and elucidate the mode of action of effective antibacterial plant secondary metabolites - thymol, cinnamaldehyde, eugenol, and carvacrol in both pure and complex formats. Apart from the detection of adulteration of pure compounds present in complex mixture of essential oils, this approach will be useful to detect authenticity of essential oils and thus reduce unintended harmful effects on human and animal health.

An enhanced fluorescence detection of a nitroaromatic compound using bacteria embedded in porous poly lactic-co-glycolic acid microbeads

The detection of explosive nitroaromatic compounds has caused worldwide concern for human safety. In this study, we introduce a fluorescent biosensor based on porous biocompatible microspheres loaded with a bioreporter for the detection of nitroaromatic compounds. Poly(lactic-co-glycolic acid) microbeads were designed as biosensors embedded with the bacterial bioreporters. The genetically engineered bacterial bioreporter can express a green fluorescent protein in response to nitroaromatic compounds (e.g., trinitrotoluene and dinitrotoluene). The modified surface structure in microbeads provides a large surface area, as well as easy penetration, and increases the number of attached bioreporters for enhanced fluorescent signals of biosensors. Moreover, the addition of the M13 bacteriophage in open porous microbeads significantly amplified the fluorescence signal for detection by the π-π interaction between peptides in the M13 bacteriophage and nitroaromatic compounds. The modification of the surface morphology, as well as the genetically engineered M13 phage, significantly amplifies the fluorescence signal, which makes the detection of explosives easier, and has great potential for the stand-off remote sensing of TNT buried in the field.

Bacterial bioreporters for the detection of trace explosives: performance enhancement by DNA shuffling and random mutagenesis

Landmines and other explosive remnants of war pose a global humanitarian problem that claims numerous casualties long after the conflict has ended. As there are no acceptable methodologies for the remote discovery of such devices, current detection practices still require the risky presence of personnel in the minefield. We have recently described bacterial sensor strains capable of reporting the existence of 2,4-dinitrotoluene (DNT) vapors in the soil above 2,4,6-trinitrotoluene (TNT)-based landmines, by generating a bioluminescent or a fluorescent signal. This may allow the identification of landmine location by remote imaging of an area over which the bacteria have been spread. In the study reported herein, we have improved the DNT-detection capabilities of these sensor strains by combining two DNT-responsive Escherichia coli gene promoters, yqjF and azoR, and subjecting them to three cycles of random mutagenesis by error-prone PCR, combined with segmentation and rearrangement ("DNA shuffling"). The activity of selected modified promoters was evaluated with the Aliivibrio fischeri and Photobacterium leiognathi luxCDABEG gene cassettes as the bioluminescent reporters, exhibiting a ten-fold background reduction that has led to a three-fold decrease in detection threshold. Signal intensity was further enhanced by modifying the ribosomal binding site of the yqjF gene promoter. The superior DNT detection capabilities on a solid matrix by the improved sensor strain were demonstrated. KEY POINTS: • Performance of microbial sensor strains for buried explosives was molecularly enhanced. • Manipulations included random mutagenesis, "DNA shuffling," and RBS reprogramming. • The re-engineered constructs exhibited superior detection of trace explosives.

An autonomous bioluminescent bacterial biosensor module for outdoor sensor networks, and its application for the detection of buried explosives

We describe a miniaturized field-deployable biosensor module, designed to function as an element in a sensor network for standoff monitoring and mapping of environmental hazards. The module harbors live bacterial sensor cells, genetically engineered to emit a bioluminescent signal in the presence of preselected target materials, which act as its core sensing elements. The module, which detects and processes the biological signal, composes a digital record that describes its findings, and can be transmitted to a remote receiver. The module is an autonomous self-contained unit that can function either as a standalone sensor, or as a node in a sensor network. The biosensor module can potentially be used for detecting any target material to which the sensor cells were engineered to respond. The module described herein was constructed to detect the presence of buried landmines underneath its footprint. The demonstrated detection sensitivity was 0.25 mg 2,4-dinitrotoluene per Kg soil.

Detection of buried explosives with immobilized bacterial bioreporters

The unchecked dispersal of antipersonnel landmines since the late 19th century has resulted in large areas contaminated with these explosive devices, creating a substantial worldwide humanitarian safety risk. The main obstacle to safe and effective landmine removal is the identification of their exact location, an activity that currently requires entry of personnel into the minefields; to date, there is no commercialized technology for an efficient stand-off detection of buried landmines. In this article, we describe the optimization of a microbial sensor strain, genetically engineered for the remote detection of 2,4,6-trinitrotoloune (TNT)-based mines. This bioreporter, designed to bioluminescence in response to minute concentrations of either TNT or 2,4-dinitotoluene (DNT), was immobilized in hydrogel beads and optimized for dispersion over the minefield. Following modifications of the hydrogel matrix in which the sensor bacteria are encapsulated, as well as their genetic reporting elements, these sensor bacteria sensitively detected buried 2,4-dinitrotoluene in laboratory experiments. Encapsulated in 1.5 mm 2% alginate beads containing 1% polyacrylic acid, they also detected the location of a real metallic antipersonnel landmine under field conditions. To the best of our knowledge, this is the first report demonstrating the detection of a buried landmine with a luminescent microbial bioreporter.

Different bacterial host-based lux reporter array for fast identification and toxicity indication of multiple metal ions

Although luminescent bacteria-based bioluminescence inhibition assay has been widely used in the toxicity assessment of environmental pollutants, the response of a luminescent bacterium usually lacks specificity to a target analyte. Recently, some specific analyte inductive promoters were fused to the lux genes for the purpose of selective bioluminescent sensing, and suits of specific promoters were fused to lux genes to compose a bioluminescent array sensor for simultaneous identification of multiple analytes. However, specific promoter-based methods still suffer from drawbacks including limited selectivity, slow responding time, expensive to construct different promoters involved plasmids, and laborious to find new promoters. Herein, we proposed a novel strategy to construct a lux reporter array sensor by directly transforming the natural lux genes in different bacterial hosts without the involvement of any specific promoters. Due to the distinct pathways of signal production, the responding time of the current different bacterial host (DBH)-based lux reporter array has nearly an order of magnitude faster than with specific promoter-based methods. The DBH-based lux reporter array was successfully used for simultaneous identification, quantification, and toxicity/bioactivity assessment of multiple metal ions. Obviously, all the chemical synthetic material-based metal ion sensing methods cannot simultaneously achieve analysis and toxicity evaluation. This approach possessed additional advantages of facile construction, easy operation, high selectivity, fast response, and strong adaptability to other analytes. A different bacterial host-based lux reporter array was established for simultaneous analysis and toxicity assessment of multiple metal ions.

Genome-wide gene-deletion screening identifies mutations that significantly enhance explosives vapor detection by a microbial sensor

Genetically engineered microbial biosensors, capable of detecting traces of explosives residues above buried military ordnance and emitting an optical signal in response, may potentially serve for the standoff detection of buried landmines. A promising candidate for such an application is a previously reported Escherichia coli-based reporter strain that employs the yqjF gene promoter as its sensing element; however, for this sensor to be able to detect actual landmines reliably, it was necessary for its detection sensitivity and signal intensity to be enhanced. In this study, a high-throughput approach was employed to screen the effects of individual gene deletions on yqjF activation by 2,4-dinitrotoluene (DNT). Several genes were identified, the deletion of which elicited a significant enhancement of yqjF induction by DNT. The most promising of these mutations were introduced into the sensor strain, individually or in pairs, yielding a considerable increase in signal intensity and a lowering of the detection threshold. A strain harboring two of the identified mutations, ygdD and eutE, appears to be the most sensitive microbial biosensor currently described for the detection of traces of landmine explosives.

A Minimized Chemoenzymatic Cascade for Bacterial Luciferase in Bioreporter Applications

Bacterial luciferase (Lux) catalyzes a bioluminescence reaction by using long-chain aldehyde, reduced flavin and molecular oxygen as substrates. The reaction can be applied in reporter gene systems for biomolecular detection in both prokaryotic and eukaryotic organisms. Because reduced flavin is unstable under aerobic conditions, another enzyme, flavin reductase, is needed to supply reduced flavin to the Lux-catalyzed reaction. To create a minimized cascade for Lux that would have greater ease of use, a chemoenzymatic reaction with a biomimetic nicotinamide (BNAH) was used in place of the flavin reductase reaction in the Lux system. The results showed that the minimized cascade reaction can be applied to monitor bioluminescence of the Lux reporter in eukaryotic cells effectively, and that it can achieve higher efficiencies than the system with flavin reductase. This development is useful for future applications as high-throughput detection tools for drug screening applications.

Synthetic Biology Enables Programmable Cell-Based Biosensors

Cell-based biosensors offer cheap, portable and simple methods of detecting molecules of interest but have yet to be truly adopted commercially. Issues with their performance and specificity initially slowed the development of cell-based biosensors. With the development of rational approaches to tune response curves, the performance of biosensors has rapidly improved and there are now many biosensors capable of sensing with the required performance. This has stimulated an increased interest in biosensors and their commercial potential. However the reliability, long term stability and biosecurity of these sensors are still barriers to commercial application and public acceptance. Research into overcoming these issues remains active. Here we present the state-of-the-art tools offered by synthetic biology to allow construction of cell-based biosensors with customisable performance to meet the real world requirements in terms of sensitivity and dynamic range and discuss the research progress to overcome the challenges in terms of the sensor stability and biosecurity fears.

A flower-like ZnO–Ag2O nanocomposite for label and mediator free direct sensing of dinitrotoluene

2,4-Dinitrotoluene (2,4-DNT) is a nitro aromatic compound used as a raw material for trinitrotoluene (TNT) explosive synthesis along with several other industrial applications. Easy, rapid, cost-effective, and selective detection of 2,4-DNT is becoming essential due to its hepato carcinogenic nature and presence in surface as well as ground water as a contaminant. Keeping this in view, this research, for the first-time, reports the synthesis of novel ZnO–Ag₂O composite nanoflowers on a gold (Au) substrate, to fabricate an electrochemical sensor for label-free, direct sensing of 2,4-DNT selectively. The proposed ZnO–Ag₂O/Au sensor exhibits a sensitivity of 5 μA μM⁻¹ cm⁻² with a low limit of detection (LOD) of 13 nM, in a linear dynamic range (LDR) of 0.4 μM to 40 μM. The sensor showed reasonably high re-usability and reproducibility, with reliable results for laboratory and real-world samples.

2,4-Dinitrotoluene (2,4-DNT) is a nitro aromatic compound used as a raw material for trinitrotoluene (TNT) explosive synthesis along with several other industrial applications.

Implementation of Combinatorial Genetic and Microenvironmental Engineering to Microbial-Based Field-Deployable Microbead Biosensors for Highly Sensitive and Remote Chemical Detection

Bioreporters, microbial species genetically engineered to provide measurable signals in response to specific chemicals, have been widely investigated as sensors for biomedical and environmental monitoring. More specifically, the bioreporter encapsulated within a biocompatible material, such as a hydrogel that can provide a suitable microenvironment for its prolonged activity as well as efficient scalable production, has been viewed as a more broadly applicable mode of biosensors. In this study, alginate-based microbeads encapsulated with the bacterial bioreporter capable of expressing green fluorescence protein in response to nitro compounds (e.g., trinitrotoluene and dinitrotoluene) are developed as biosensors. To significantly enhance the sensitivity of the microbial-based microbead biosensors, "multifaceted" modification strategies are simultaneously employed: (1) multiple genetic modifications of the bioreporter, (2) tuning the physicomechanical properties of the encapsulating microbeads, (3) controlling the initial cell density within the microbeads, and (4) enrichment of nitro compounds inside microbeads via functional nanomaterials. These microbial and microenvironmental engineering approaches combine to significantly enhance the sensing capability, even allowing highly sensitive remote detection under a low-vapor phase. Thus, the strategy developed herein is expected to contribute to various cell-based biosensors.

Development of a Highly Sensitive Whole-Cell Biosensor for Arsenite Detection through Engineered Promoter Modifications

Whole-cell biosensors have attracted considerable interests because they are robust, eco-friendly, and cost-effective. However, most of the biosensors harness the naturally occurring wild-type promoter, which often suffers from high background noise and low sensitivity. In this study, we demonstrate how to design the core elements (i.e., RNA polymerase binding site and transcription factor binding site) of the promoters to obtain a significant gain in the signal-to-noise output ratio of the whole-cell biosensor circuits. As a proof of concept, we modified the arsenite-regulated promoter from Escherichia coli K-12 genome, such that it has a lower background and higher expression. This was achieved by balancing the relationship between the number of ArsR binding sites (ABS) and the activity of the promoter and adjusting the location of the auxiliary ABS. A promoter variant ParsD-ABS-8 was obtained with an induction ratio of 179 (11-fold increase over the wild-type promoter) when induced with 1 μM arsenite. Importantly, the developed biosensor exhibited good dose-response in the range of 0.1 to 4 μM (R² = 0.9928) of arsenite with a detection limit of ca. 10 nM. These results indicated that the engineered promoter modification approach could be used to improve the performance of whole-cell biosensors, thereby facilitating their practical application.

Fluorescence Enhancement from Nitro-Compound-Sensitive Bacteria within Spherical Hydrogel Scaffolds

For the safety of both production and life, it is a very significant issue to detect explosive nitro compounds in a remote way or over a long distance. Here, we report that nitro compounds were detected by the bacterial sensor based on hydrogel microbeads as a platform. Green fluorescent protein-producing Escherichia coli, which was genetically engineered to be sensitive to nitro compounds, was loaded within poly(2-hydroxyethyl methacrylate) [poly(HEMA)]-based hydrogel beads, in which fluorescent signals from bacteria were concentrated and strong enough to be easily detected. For efficient loading of negatively charged bacteria, the surface charge of poly(HEMA)-based beads was controlled by copolymerization with 2-(methacryloyloxy)ethyltrimethylammonium chloride (MAETC) as a cationic monomer. With the addition of MAETC, the cell affinity was nine times enhanced by the interaction between the positively charged poly(HEMA- co-MAETC) beads and negatively charged bacteria. The increased cell affinity resulted in an enhancement of a sensing signal. After exposure to 2,4,6-trinitrotoluene, a typical explosive nitro compound, the fluorescence intensity of bacterial sensors using poly(HEMA- co-MAETC) beads having 80 wt % MAETC was five times increased compared to those based on poly(HEMA) beads. This amplification of the fluorescent signal enables easier detection of explosives efficiently by a remote detection, even over a long distance.

A Portable Biosensor for 2,4-Dinitrotoluene Vapors

Buried explosive material, e.g., landmines, represent a severe issue for human safety all over the world. Most explosives consist of environmentally hazardous chemicals like 2,4,6-trinitrotoluene (TNT), carcinogenic 2,4-dinitrotoluene (2,4-DNT) and related compounds. Vapors leaking from buried landmines offer a detection marker for landmines, presenting an option to detect landmines without relying on metal detection. 2,4-Dinitrotoluene (DNT), an impurity and byproduct of common TNT synthesis, is a feasible detection marker since it is extremely volatile. We report on the construction of a wireless, handy and cost effective 2,4-dinitrotoluene biosensor combining recombinant bioluminescent bacterial cells and a compact, portable optical detection device. This biosensor could serve as a potential alternative to the current detection technique. The influence of temperature, oxygen and different immobilization procedures on bioluminescence were tested. Oxygen penetration depth in agarose gels was investigated, and showed that aeration with molecular oxygen is necessary to maintain bioluminescence activity at higher cell densities. Bioluminescence was low even at high cell densities and 2,4-DNT concentrations, hence optimization of different prototypes was carried out regarding radiation surface of the gels used for immobilization. These findings were applied to sensor construction, and 50 ppb gaseous 2,4-DNT was successfully detected.

Development of a 2-Nitrobenzoate-Sensing Bioreporter Based on an Inducible Gene Cluster

Based on the sole information of structural genes of the 2-nitrobenzoate (2NBA) utilizing catabolic gene cluster (onbX1X2FCAR1EHJIGDBX3), 2NBA-sensing bioreporters were constructed by incorporating egfp into the onb gene cluster of Cupriavidus sp. strain ST-14. Incorporation of reporter gene in proximal to the hypothesized promoter region in conjunction with the disruption of the gene encoding inducer-metabolizing enzyme was turned out to be advantageous in reporter gene expression at low inducer concentration. The bioreporter strain was capable of expressing EGFP from the very 1st hour of induction and could detect 2NBA at (sub) nanomolar level exhibiting a strict specificity toward 2NBA, displaying no response to EGFP expression from its meta- and para-isomers as well as from a number of structurally related compounds. The present study is a successful demonstration of the development of a 2NBA-sensing bioreporter with respect to ease of construction, inducer specificity, and sensitivity, without prior knowledge of the associated inducer-responsive promoter-regulator elements. The present approach can be used as a model for the development of bioreporters for other environmental pollutants.

Aerobic Transformation of 2,4-Dinitrotoluene by Escherichia coli and Its Implications for the Detection of Trace Explosives

DNT (2,4-dinitrotoluene), a volatile impurity in military-grade 2,4,6-trinitrotoluene (TNT)-based explosives, is a potential tracer for the detection of buried landmines and other explosive devices. We have previously described an Escherichia coli bioreporter strain engineered to detect traces of DNT and have demonstrated that the yqjF gene promoter, the sensing element of this bioreporter, is induced not by DNT but by at least one of its transformation products. In the present study, we have characterized the initial stages of DNT biotransformation in E. coli, have identified the key metabolic products in this reductive pathway, and demonstrate that the main DNT metabolite that induces yqjF is 2,4,5-trihydroxytoluene. We further show that E. coli cannot utilize DNT as a sole carbon or nitrogen source and propose that this compound is metabolized in order to neutralize its toxicity to the cells.IMPORTANCE The information provided in this article sheds new light both on the microbial biodegradability of nitroaromatic compounds and on the metabolic capabilities of E. coli By doing so, it also clarifies the pathway leading to the previously unexplained induction of the E. coli yqjF gene by 2,4-dinitrotoluene, an impurity that accompanies 2,4,6-trinitrotoluene (TNT)-based explosives. Our improved understanding of these processes will serve to molecularly enhance the performance of a previously described microbial bioreporter of buried landmines and other explosive devices, in which the yqjF gene promoter serves as the sensing element.

Microbial bioreporters of trace explosives

Since its introduction as an explosive in the late 19th century, 2,4,6-trinitrotoluene (TNT), along with other explosive compounds, has left numerous environmental marks. One of these is widespread soil and water pollution by trace explosives in military proving grounds, manufacturing facilities, or actual battlefields. Another dramatic impact is that exerted by the millions of landmines and other explosive devices buried in large parts of the world, causing extensive loss of life, injuries, and economical damage. In this review we highlight recent advances in the design and construction of microbial bioreporters, molecularly engineered to generate a quantifiable dose-dependent signal in the presence of trace amounts of explosives. Such sensor strains may be employed for monitoring environmental pollution as well as for the remote detection of buried landmines.

A turn-off fluorescence sensor for insensitive munition using anthraquinone-appended oxacalix[4]arene and its computational studies

Herein, a fluorescent oxacalix[4]arene-based receptor, DAQTNOC(5,17-di(N-(9,10-dioxo-9,10-dihydroanthracen-1-yl)acetamide) tetranitrooxacalix[4]arene), was described for the specific recognition of N-methyl-p-nitroaniline (MNA).

Immobilized Biocatalyst for Detection and Destruction of the Insensitive Explosive, 2,4-Dinitroanisole (DNAN)

Accurate and convenient detection of explosive components is vital for a wide spectrum of applications ranging from national security and demilitarization to environmental monitoring and restoration. With the increasing use of DNAN as a replacement for 2,4,6-trinitrotoluene (TNT) in insensitive explosive formulations, there has been a growing interest in strategies to minimize its release and to understand and predict its behavior in the environment. Consequently, a convenient tool for its detection and destruction could enable development of more effective decontamination and demilitarization strategies. Biosensors and biocatalysts have limited applicability to the more traditional explosives because of the inherent limitations of the relevant enzymes. Here, we report a highly specific, convenient and robust biocatalyst based on a novel ether hydrolase enzyme, DNAN demethylase (that requires no cofactors), from a Nocardioides strain that can mineralize DNAN. Biogenic silica encapsulation was used to stabilize the enzyme and enable it to be packed into a model microcolumn for application as a biosensor or as a bioreactor for continuous destruction of DNAN. The immobilized enzyme was stable and not inhibited by other insensitive munitions constituents. An alternative method for DNAN detection involved coating the encapsulated enzyme on cellulose filter paper. The hydrolase based biocatalyst could provide the basis for a wide spectrum of applications including detection, identification, destruction or inertion of explosives containing DNAN (demilitarization operations), and for environmental restorations.

The Highly Conserved Escherichia coli Transcription Factor YhaJ Regulates Aromatic Compound Degradation

The aromatic compound 2,4-dinitrotoluene (DNT), a common impurity in 2,4,6-trinitrotoluene (TNT) production, has been suggested as a tracer for the presence of TNT-based landmines due to its stability and high volatility. We have previously described an Escherichia coli bioreporter capable of detecting the presence of DNT vapors, harboring a fusion of the yqjF gene promoter to a reporter element. However, the DNT metabolite which is the direct inducer of yqjF, has not yet been identified, nor has the regulatory mechanism of the induction been clarified. We demonstrate here that the YhaJ protein, a member of the LysR type family, acts as a transcriptional regulator of yqjF activation, as well as of a panel of additional E. coli genes. This group of genes share a common sequence motif in their promoters, which is suggested here as a putative YhaJ-box. In addition, we have linked YhaJ to the regulation of quinol-like compound degradation in the cell, and identified yhaK as playing a role in the degradation of DNT.

Standoff detection of explosives and buried landmines using fluorescent bacterial sensor cells

A standoff detection scheme for buried landmines and concealed explosive charges is presented. The detection procedure consists of the following: Live bacterial sensor strains, genetically engineered to produce a dose-dependent amount of green fluorescent protein (GFP) in the presence of explosives' vapors, are encapsulated and spread on the suspected area. The fluorescence produced by the bacteria in response to traces of the explosive material in their microenvironment is remotely detected by a phase-locked optoelectronic sampling system. This scheme enables fast direct access to a large minefield area, while obviating the need to endanger personnel and equipment. Moreover, the employment of phase locking detection efficiently isolates the bacterial sensors' fluorescent output from the background optical signals. This facilitates the application of bacterial sensors in an outdoor environment, where control of background illumination is not possible. Using this system, we demonstrate standoff detection of 2,4-DNT both in aqueous solution and when buried in soil, by sensor bacteria either in liquid culture or agar-immobilized, respectively, at a distance of 50 m in a realistic optically noisy environment.

Genetically engineered microorganisms for the detection of explosives' residues

The manufacture and use of explosives throughout the past century has resulted in the extensive pollution of soils and groundwater, and the widespread interment of landmines imposes a major humanitarian risk and prevents civil development of large areas. As most current landmine detection technologies require actual presence at the surveyed areas, thus posing a significant risk to personnel, diverse research efforts are aimed at the development of remote detection solutions. One possible means proposed to fulfill this objective is the use of microbial bioreporters: genetically engineered microorganisms “tailored” to generate an optical signal in the presence of explosives’ vapors. The use of such sensor bacteria will allow to pinpoint the locations of explosive devices in a minefield. While no study has yet resulted in a commercially operational system, significant progress has been made in the design and construction of explosives-sensing bacterial strains. In this article we review the attempts to construct microbial bioreporters for the detection of explosives, and analyze the steps that need to be undertaken for this strategy to be applicable for landmine detection.