Sensitive fluorescent microplate bioassay using recombinant Escherichia coli with multiple promoter-reporter units in tandem for detection of arsenic

Biosensing of arsenic by whole-cell bacterial bioreporter immobilized on polycaprolactone (PCL) electrospun fiber

In recent years, heavy metals derived from several anthropogenic sources have both direct and indirect detrimental effects on the health of the environment and living organisms. Whole-cell bioreporters (WCBs) that can be used to monitor the levels of heavy metals in drinking and natural spring waters are important. In this study, whole-cell arsenic bacterial bioreporters were immobilized using polycaprolactone (PCL) electrospun fibers as the support material. The aim is to determine the properties of this immobilized bioreporter system by evaluating its performance in arsenic detection. Within the scope of the study, different growth media and fiber immobilization times were tested to determine the parameters affecting the fluorescent signals emitted by the immobilized bioreporter system in the presence of two dominant forms of arsenic, namely arsenite (As(III)) and arsenate (As(V)). In addition, the sensitivity, selectivity, response time, and shelf-life of the developed bioreporter system were evaluated. As far as the literature is concerned, this is the first study to investigate the potential of using PCL-electrospun fiber-immobilized fluorescent bacterial bioreporter for arsenic detection. This study will open new avenues in environmental arsenic monitoring.

Imparting As(III) Responsiveness to the Choline Response Transcriptional Regulator BetI

The development of a low-cost and user-friendly sensor using microorganisms to monitor the presence of As(III) on earth has garnered significant attention. In conventional research on microbial As(III) sensors, the focus has been on transcription factor ArsR, which plays a role in As(III) metabolism. However, we recently discovered that LuxR, a quorum-sensing control factor in Vibrio fischeri that contains multiple cysteine residues, acted as an As(III) sensor despite having no role in As(III) metabolism. This finding suggested that any protein could be an As(III) sensor if cysteine residues were incorporated. In this study, we aimed to confer As(III) responsiveness to BetI, a transcriptional repressor of the TetR family involved in osmotic regulation of the choline response, unrelated to As(III) metabolism. Based on the BetI structure constructed using molecular dynamics calculations, we generated a series of mutants in which each of the three amino acids not critical for function was substituted with cysteine. Subsequent examination of their response to As(III) revealed that the cysteine-substituted mutant, incorporating all three substitutions, demonstrated As(III) responsiveness. This was evidenced by the fluorescence intensity of the downstream reporter superfolder green fluorescent protein expression regulated by the operator region. Intriguingly, the BetI cysteine mutant maintained its binding responsiveness to the natural ligand choline. We successfully engineered an OR logic gate capable of responding to two orthogonal ligands using a single protein.

Effective Cryopreservation of a Bioluminescent Auxotrophic Escherichia coli-Based Amino Acid Array to Enable Long-Term Ready-to-Use Applications

Amino acid arrays comprising bioluminescent amino acid auxotrophic Escherichia coli are effective systems to quantitatively determine multiple amino acids. However, there is a need to develop a method for convenient long-term preservation of the array to enable its practical applications. Here, we reported a potential strategy to efficiently maintain cell viability within the portable array. The method involves immobilization of cells within agarose gel supplemented with an appropriate cryoprotectant in individual wells of a 96-well plate, followed by storage under freezing conditions. Six cryoprotectants, namely dimethyl sulfoxide, glycerol, ethylene glycol, polyethylene glycol, sucrose, and trehalose, were tested in the methionine (Met) auxotroph-based array. Carbohydrate-type cryoprotectants (glycerol, sucrose, and trehalose) efficiently preserved the linearity of determination of Met concentration. In particular, the array with 5% trehalose exhibited the best performance. The Met array with 5% trehalose could determine Met concentration with high linearity (R² value = approximately 0.99) even after storage at −20 °C for up to 3 months. The clinical utilities of the Met and Leu array, preserved at −20 °C for 3 months, were also verified by successfully quantifying Met and Leu in spiked blood serum samples for the diagnosis of the corresponding metabolic diseases. This long-term preservation protocol enables the development of a ready-to-use bioluminescent E. coli-based amino acid array to quantify multiple amino acids and can replace the currently used laborious analytical methods.

Construction of cadmium whole-cell biosensors and circuit amplification

Owing to the prevalence of cadmium contamination and its serious hazards, it is important to establish an efficient and low-cost monitoring technique for the detection of the heavy metal cadmium. In this study, we first designed 30 cadmium whole-cell biosensors (WCBs) using different combinations of detection elements, reporting elements, and the host. The best performing WCB KT-5-R with Pseudomonas putida KT2440 as the host and composed of CadR and mCherry was selected for further analysis and engineering. In order to enhance its sensitivity, a positive feedback amplifier was added or the gene dosage of the reporter gene was increased. The WCB with the T7RNAP amplification module, p2T7RNAPmut-68, had the best performance and improved tolerance to cadmium with a detection limit of 0.01 μM, which is the WHO standard. It also showed excellent specificity toward cadmium when assayed with mixed metal ions. This study demonstrated the power of circuit engineering in WCB design and provided valuable insights for the development of other WCBs. KEY POINTS: • KT-5-R was selected after prescreening and engineered for better performance. • Using multi-copy reporters and the T7RNAP amplifier greatly improved the performance. • p2T7RNAPmut-68 had a detection limit of 0.01 μM and improved tolerance to cadmium.

In-situ monitoring of xenobiotics using genetically engineered whole-cell-based microbial biosensors: recent advances and outlook

Industrialisation, directly or indirectly, exposes humans to various xenobiotics. The increased magnitude of chemical pesticides and toxic heavy metals in the environment, as well as their intrusion into the food chain, seriously threatens human health. Therefore, the surveillance of xenobiotics is crucial for social safety and security. Online investigation by traditional methods is not sufficient for the detection and identification of such compounds because of the high costs and their complexity. Advancement in the field of genetic engineering provides a potential opportunity to use genetically modified microorganisms. In this regard, whole-cell-based microbial biosensors (WCBMB) represent an essential tool that couples genetically engineered organisms with an operator/promoter derived from a heavy metal-resistant operon combined with a regulatory protein in the gene circuit. The plasmid controls the expression of the reporter gene, such as gfp, luc, lux and lacZ, to an inducible gene promoter and has been widely applied to assay toxicity and bioavailability. This review summarises the recent trends in the development and application of microbial biosensors and the use of mobile genes for biomedical and environmental safety concerns.

Fluorescent bacterial biosensor E. coli/pTdcR-TurboYFP sensitive to terahertz radiation

A fluorescent biosensor E. coli/pTdcR-TurboYFP sensitive to terahertz (THz) radiation was developed via transformation of Escherichia coli (E. coli) cells with plasmid, in which the promotor of the tdcR gene controls the expression of yellow fluorescent protein TurboYFP. The biosensor was exposed to THz radiation in various vessels and nutrient media. The threshold and dynamics of fluorescence were found to depend on irradiation conditions. Heat shock or chemical stress yielded the absence of fluorescence induction. The biosensor is applicable to studying influence of THz radiation on the activity of tdcR promotor that is involved in the transport and metabolism of threonine and serine in E. coli.

Sensitive and Specific Whole-Cell Biosensor for Arsenic Detection

Whole-cell biosensors (WCBs) have been designed to detect As(III), but most suffer from poor sensitivity and specificity. In this paper, we developed an arsenic WCB with a positive feedback amplifier in Escherichia coli DH5α. The output signal from the reporter mCherry was significantly enhanced by the positive feedback amplifier. The sensitivity of the WCB with positive feedback is about 1 order of magnitude higher than that without positive feedback when evaluated using a half-saturation As(III) concentration. The minimum detection limit for As(III) was reduced by 1 order of magnitude to 0.1 µM, lower than the World Health Organization standard for the arsenic level in drinking water, 0.01 mg/liter or 0.13 µM. Due to the amplification of the output signal, the WCB was able to give detectable signals within a shorter period, and a fast response is essential for in situ operations. Moreover, the WCB with the positive feedback amplifier showed exceptionally high specificity toward As(III) when compared with other metal ions. Collectively, the designed positive feedback amplifier WCB meets the requirements for As(III) detection with high sensitivity and specificity. This work also demonstrates the importance of genetic circuit engineering in designing WCBs, and the use of genetic positive feedback amplifiers is a good strategy to improve the performance of WCBs.IMPORTANCE Arsenic poisoning is a severe public health issue. Rapid and simple methods for the sensitive and specific monitoring of arsenic concentration in drinking water are needed. In this study, we designed an arsenic WCB with a positive feedback amplifier. It is highly sensitive and able to detect arsenic below the WHO limit level. In addition, it also significantly improves the specificity of the biosensor toward arsenic, giving a signal that is about 10 to 20 times stronger in response to As(III) than to other metals. This work not only provides simple but effective arsenic biosensors but also demonstrates the importance of genetic engineering, particularly the use of positive feedback amplifiers, in designing WCBs.

Cellular Biosensors with Engineered Genetic Circuits

An increasing interest in building novel biological devices with designed cellular functionalities has triggered the search of innovative tools for biocomputation. Utilizing the tools of synthetic biology, numerous genetic circuits have been implemented such as engineered logic operation in analog and digital circuits. Whole cell biosensors are widely used biological devices that employ several biocomputation tools to program cells for desired functions. Up to the present date, a wide range of whole-cell biosensors have been designed and implemented for disease theranostics, biomedical applications, and environmental monitoring. In this review, we investigated the recent developments in biocomputation tools such as analog, digital, and mix circuits, logic gates, switches, and state machines. Additionally, we stated the novel applications of biological devices with computing functionalities for diagnosis and therapy of various diseases such as infections, cancer, or metabolic diseases, as well as the detection of environmental pollutants such as heavy metals or organic toxic compounds. Current whole-cell biosensors are innovative alternatives to classical biosensors; however, there is still a need to advance decision making capabilities by developing novel biocomputing devices.

Paralogous Regulators ArsR1 and ArsR2 of Pseudomonas putida KT2440 as a Basis for Arsenic Biosensor Development

The remarkable metal resistance of many microorganisms is related to the presence of multiple metal resistance operons. Pseudomonas putida KT2440 can be considered a model for these microorganisms since its arsenic resistance is due to the action of proteins encoded by the two paralogous arsenic resistance operons ARS1 and ARS2. Both operons contain the genes encoding the transcriptional regulators ArsR1 and ArsR2 that control operon expression. We show here that purified ArsR1 and ArsR2 bind the trivalent salt of arsenic (arsenite) with similar affinities (~30 μM), whereas no binding is observed for the pentavalent salt (arsenate). Furthermore, trivalent salts of bismuth and antimony showed binding to both paralogues. The positions of cysteines, found to bind arsenic in other homologues, indicate that ArsR1 and ArsR2 employ different modes of arsenite recognition. Both paralogues are dimeric and possess significant thermal stability. Both proteins were used to construct whole-cell, lacZ-based biosensors. Whereas responses to bismuth were negligible, significant responses were observed for arsenite, arsenate, and antimony. Biosensors based on the P. putida arsB1 arsB2 arsenic efflux pump double mutant were significantly more sensitive than biosensors based on the wild-type strain. This sensitivity enhancement by pump mutation may be a convenient strategy for the construction of other biosensors. A frequent limitation found for other arsenic biosensors was their elevated background signal and interference by inorganic phosphate. The constructed biosensors show no interference by inorganic phosphate, are characterized by a very low background signal, and were found to be suitable to analyze environmental samples.

IMPORTANCE

Arsenic is at the top of the priority list of hazardous compounds issued by the U.S. Agency for Toxic Substances and Disease. The reason for the stunning arsenic resistance of many microorganisms is the existence of paralogous arsenic resistance operons. Pseudomonas putida KT2440 is a model organism for such bacteria, and their duplicated ars operons and in particular their ArsR transcription regulators have been studied in depth by in vivo approaches. Here we present an analysis of both purified ArsR paralogues by different biophysical techniques, and data obtained provide valuable insight into their structure and function. Particularly insightful was the comparison of ArsR effector profiles determined by in vitro and in vivo experimentation. We also report the use of both paralogues to construct robust and highly sensitive arsenic biosensors. Our finding that the deletion of both arsenic efflux pumps significantly increases biosensor sensitivity is of general relevance in the biosensor field.

Genetic engineering of Francisella tularensis LVS for use as a novel live vaccine platform against Pseudomonas aeruginosa infections

Francisella tularensis LVS (Live Vaccine Strain) is an attenuated bacterium that has been used as a live vaccine. Patients immunized with this organism show a very long-term memory response (over 30 years post vaccination) evidenced by the presence of indicators of robust cell-mediated immunity. Because F. tularensis LVS is such a potent vaccine, we hypothesized that this organism would be an effective vaccine platform. First, we sought to determine if we could genetically modify this strain to produce protective antigens of a heterologous pathogen. Currently, there is not a licensed vaccine against the important opportunistic bacterial pathogen, Pseudomonas aeruginosa. Because many P. aeruginosa strains are also drug resistant, the need for effective vaccines is magnified. Here, F. tularensis LVS was genetically modified to express surface proteins PilA_Pa, OprF_Pa, and FliC_Pa of P. aeruginosa. Immunization of mice with LVS expressing the recombinant FliC_Pa led to a significant production of antibodies specific for P. aeruginosa. However, mice that had been immunized with LVS expressing PilA_Pa or OprF_Pa did not produce high levels of antibodies specific for P. aerugionsa. Therefore, the recombinant LVS strain engineered to produce FliC_Pa may be able to provide immune protection against a P. aeruginosa challenge. However for future use of this vaccine platform, selection of the appropriate recombinant antigen is critical as not all recombinant antigens expressed in this strain were immunogenic.

Therapeutic and analytical applications of arsenic binding to proteins

Knowledge of arsenic binding to proteins advances the development of bioanalytical techniques and therapeutic drugs.

Biosensors for inorganic and organic arsenicals

Arsenic is a natural environmental contaminant to which humans are routinely exposed and is strongly associated with human health problems, including cancer, cardiovascular and neurological diseases. To date, a number of biosensors for the detection of arsenic involving the coupling of biological engineering and electrochemical techniques has been developed. The properties of whole-cell bacterial or cell-free biosensors are summarized in the present review with emphasis on their sensitivity and selectivity. Their limitations and future challenges are highlighted.

Advances in arsenic biosensor development--a comprehensive review

Biosensors are analytical devices having high sensitivity, portability, small sample requirement and ease of use for qualitative and quantitative monitoring of various analytes of human importance. Arsenic (As), owing to its widespread presence in nature and high toxicity to living creatures, requires frequent determination in water, soil, agricultural and food samples. The present review is an effort to highlight the various advancements made so far in the development of arsenic biosensors based either on recombinant whole cells or on certain arsenic-binding oligonucleotides or proteins. The role of futuristic approaches like surface plasmon resonance (SPR) and aptamer technology has also been discussed. The biomethods employed and their general mechanisms, advantages and limitations in relevance to arsenic biosensors developed so far are intended to be discussed in this review.

Molecular manipulations for enhancing luminescent bioreporters performance in the detection of toxic chemicals

Microbial whole-cell bioreporters are genetically modified microorganisms that produce a quantifiable output in response to the presence of toxic chemicals or other stress factors. These bioreporters harbor a genetic fusion between a sensing element (usually a gene regulatory element responsive to the target) and a reporter element, the product of which may be quantitatively monitored either by its presence or by its activity. In this chapter we review genetic manipulations undertaken in order to improve bioluminescent bioreporter performance by increasing luminescent output, lowering the limit of detection, and shortening the response time. We describe molecular manipulations applied to all aspects of whole-cell bioreporters: the host strain, the expression system, the sensing element, and the reporter element. The molecular construction of whole-cell luminescent bioreporters, harboring fusions of gene promoter elements to reporter genes, has been around for over three decades; in most cases, these two genetic elements are combined "as is." This chapter outlines diverse molecular manipulations for enhancing the performance of such sensors.

Microbial biosensors: engineered microorganisms as the sensing machinery

Whole-cell biosensors are a good alternative to enzyme-based biosensors since they offer the benefits of low cost and improved stability. In recent years, live cells have been employed as biosensors for a wide range of targets. In this review, we will focus on the use of microorganisms that are genetically modified with the desirable outputs in order to improve the biosensor performance. Different methodologies based on genetic/protein engineering and synthetic biology to construct microorganisms with the required signal outputs, sensitivity, and selectivity will be discussed.

Synthesis and properties of arsenic(III)-reactive coumarin-appended benzothiazolines: a new approach for inorganic arsenic detection

The EPA has established a maximum contaminant level (MCL) of 10 ppb for arsenic (As) in drinking water requiring sensitive and selective detection methodologies. To tackle this challenge, we have been active in constructing small molecules that react specifically with As(3+) to furnish a new fluorescent species (termed a chemodosimeter). We report in this contribution, the synthesis and spectroscopy of two small-molecule fluorescent probes that we term ArsenoFluors (or AFs) as As-specific chemodosimeters. The AFs (AF1 and AF2) incorporate a coumarin fluorescent reporter coupled with an As-reactive benzothiazoline functional group. AFs react with As(3+) to yield the highly fluorescent coumarin-6 dye (C6) resulting in a 20-25-fold fluorescence enhancement at λem ∼ 500 nm with detection limits of 0.14-0.23 ppb in tetrahydrofuran (THF) at 298 K. The AFs also react with common environmental As(3+) sources such as sodium arsenite in a THF/CHES (N-cyclohexyl-2-aminoethanesulfonic acid) (1:1, pH 9, 298 K) mixture resulting in a modest fluorescence turn-ON (1.5- to 3-fold) due to the quenched nature of coumarin-6 derivatives in high polarity solvents. Bulk analysis of the reaction of the AFs with As(3+) revealed that the C6 derivatives and the Schiff-base disulfide of the AFs (SB1 and SB2) are the ultimate end-products of this chemistry with the formation of C6 being the principle photoproduct responsible for the As(3+)-specific turn-ON. It appears that a likely species that is traversed in the reaction path is an As-hydride-ligand complex that is a putative intermediate in the proposed reaction path.

Tunable reporter signal production in feedback-uncoupled arsenic bioreporters

Escherichia coli-based bioreporters for arsenic detection are typically based on the natural feedback loop that controls ars operon transcription. Feedback loops are known to show a wide range linear response to the detriment of the overall amplification of the incoming signal. While being a favourable feature in controlling arsenic detoxification for the cell, a feedback loop is not necessarily the most optimal for obtaining highest sensitivity and response in a designed cellular reporter for arsenic detection. Here we systematically explore the effects of uncoupling the topology of arsenic sensing circuitry on the developed reporter signal as a function of arsenite concentration input. A model was developed to describe relative ArsR and GFP levels in feedback and uncoupled circuitry, which was used to explore new ArsR-based synthetic circuits. The expression of arsR was then placed under the control of a series of constitutive promoters, which differed in promoter strength, and which could be further modulated by TetR repression. Expression of the reporter gene was maintained under the ArsR-controlled Pars promoter. ArsR expression in the systems was measured by using ArsR-mCherry fusion proteins. We find that stronger constitutive ArsR production decreases arsenite-dependent EGFP output from Pars and vice versa. This leads to a tunable series of arsenite-dependent EGFP outputs in a variety of systematically characterized circuitries. The higher expression levels and sensitivities of the response curves in the uncoupled circuits may be useful for improving field-test assays using arsenic bioreporters.

Surface-scribed transparency-based microplates

Transparency sheets, which are normally associated with use on overhead projectors, offer lowered costs and high amenability for optical diagnostics in microplate instrumentation. An alternative microplate design in which circles are scribed on the surface of the transparency to create the boundaries to hold the drop in place is investigated here. The 3D profile of the scribed regions obtained optically showed strong likelihood of affecting three-phase contact line interactions. During dispensation, the contact angle (≈95°) was larger than the drop advancing state (≈80°) due to a period of nonadhesion, where the contact angle later reduced to the drop advancing state followed by increase in the liquid area coverage on the substrate. It was established that 50 μL was needed to fill the well fully, and the maximum volume retainable before breaching was 190 μL. While the tilt angle needed for displacement reduced significantly from 50 to 95 μL, this was markedly better than nonscribed surfaces, where tilt angles always had to be kept to within 30°. It was found that there was greater ability to fill the well with smaller volumes with dispensation at the center. This was attributed to the growing contact line not meeting the scribed edge in parallel if liquid was dispensed closer to it, wherein pinning reduction in some directions permitted liquid travel along the scribed edge to undergo contact angle hysteresis. Fluorescence measurements conducted showed no performance compromise when using scribed transparency microplates over standard microplates.

A pH-based biosensor for detection of arsenic in drinking water

Arsenic contaminated groundwater is estimated to affect over 100 million people worldwide, with Bangladesh and West Bengal being among the worst affected regions. A simple, cheap, accurate and disposable device is required for arsenic field testing. We have previously described a novel biosensor for arsenic in which the output is a change in pH, which can be detected visually as a colour change by the use of a pH indicator. Here, we present an improved formulation allowing sensitive and accurate detection of less than 10 ppb arsenate with static overnight incubation. Furthermore, we describe a cheap and simple high-throughput system for simultaneous monitoring of pH in multiple assays over time. Up to 50 samples can be monitored continuously over the desired time period. Cells can be stored and distributed in either air-dried or freeze-dried form. This system was successfully tested on arsenic-contaminated groundwater samples from the South East region of Hungary. We hope to continue to develop this sensor to produce a device suitable for field trials.

Escherichia coli as a bioreporter in ecotoxicology

Ecotoxicological assessment relies to a large extent on the information gathered with surrogate species and the extrapolation of test results across species and different levels of biological organisation. Bacteria have long been used as a bioreporter for genotoxic testing and general toxicity. Today, it is clear that bacteria have the potential for screening of other toxicological endpoints. Escherichia coli has been studied for years; in-depth knowledge of its biochemistry and genetics makes it the most proficient prokaryote for the development of new toxicological assays. Several assays have been designed with E. coli as a bioreporter, and the recent trend to develop novel, better advanced reporters makes bioreporter development one of the most dynamic in ecotoxicology. Based on in-depth knowledge of E. coli, new assays are being developed or existing ones redesigned, thanks to the availability of new reporter genes and new or improved substrates. The technological evolution towards easier and more sensitive detection of different gene products is another important aspect. Often, this requires the redesign of the bacterium to make it compatible with the novel measuring tests. Recent advances in surface chemistry and nanoelectronics open the perspective for advanced reporter based on novel measuring platforms and with an online potential. In this article, we will discuss the use of E. coli-based bioreporters in ecotoxicological applications as well as some innovative sensors awaited for the future.

Application of fluorescent protein-tagged trans factors and immobilized cis elements to monitoring of toxic metals based on in vitro protein-DNA interactions

Environmental toxic metals cause serious global public health problems. On-site monitoring protects people from exposure to such harmful elements. In this study, the bacterial transcriptional switches were applied to monitoring of toxic metals. ArsR and CadC, trans factors of Escherichia coli and Staphylococcus aureus, were fused to GFP. The fusion proteins, ArsR-GFP and CadC-GFP, associated with cis elements, P(ars)-O(ars) and P(cad)-O(cad), respectively and dissociated from those upon recognition of As(III) or Pb/Cd. Cell lysates containing ArsR-GFP were pre-incubated with As(III) standard solutions for 15 min and loaded into P(ars)-O(ars)-immobilized microplate wells. Cell lysates containing CadC-GFP were pre-incubated with Pb or Cd solutions and loaded into P(cad)-O(cad)-immobilized wells. The cell lysates were incubated for 15 min and removed from the wells. Fluorescence intensity in the wells dose-dependently decreased in response to As(III) up to 200 μg/l or Pb/Cd up to 100 μg/l. Detection limits were 10 μg/l for As(III) 10 μg/l for Cd, and 20 μg/l for Pb with a microplate fluororeader, whereas 5.0 μg/l for As(III), 1.0 μg/l for Cd, and 10 μg/l for Pb with a handheld fluorometer. This method was available to detect Pb/Cd or As(III) in water containing soil extracts. This is the first demonstration of a simple and rapid fluorometry to detect analytes based on in vitro interaction between a cis element and a trans factor.