Recombinant luminescent bacteria for measuring bioavailable arsenite and antimonite

Bacterial Metallostasis: Metal Sensing, Metalloproteome Remodeling, and Metal Trafficking

Transition metals function as structural and catalytic cofactors for a large diversity of proteins and enzymes that collectively comprise the metalloproteome. Metallostasis considers all cellular processes, notably metal sensing, metalloproteome remodeling, and trafficking (or allocation) of metals that collectively ensure the functional integrity and adaptability of the metalloproteome. Bacteria employ both protein and RNA-based mechanisms that sense intracellular transition metal bioavailability and orchestrate systems-level outputs that maintain metallostasis. In this review, we contextualize metallostasis by briefly discussing the metalloproteome and specialized roles that metals play in biology. We then offer a comprehensive perspective on the diversity of metalloregulatory proteins and metal-sensing riboswitches, defining general principles within each sensor superfamily that capture how specificity is encoded in the sequence, and how selectivity can be leveraged in downstream synthetic biology and biotechnology applications. This is followed by a discussion of recent work that highlights selected metalloregulatory outputs, including metalloproteome remodeling and metal allocation by metallochaperones to both client proteins and compartments. We close by briefly discussing places where more work is needed to fill in gaps in our understanding of metallostasis.

Surface display provides an efficient expression system for production of recombinant proteins and bacterial whole cell biosensor in E. coli

A novel bacterial display vector based on Escherichia coli has been engineered for recombinant protein production and purification. Accordingly, a construct harboring the enhanced green fluorescent protein (EGFP) and the ice nucleation protein (INP) was designed to produce EGFP via the surface display in E. coli cells. The fusion EGFP-expressed cells were then investigated using fluorescence measurement, SDS- and native-PAGE before and after TEV protease digestion. The displayed EGFP was obtained with a recovery of 57.7 % as a single band on SDS-PAGE. Next, the efficiency of the cell surface display for mutant EGFP (EGFP S202H/Q204H) was examined in sensing copper ions. Under optimal conditions, a satisfactorily linear range for copper ions concentrations up to 10 nM with a detection limit of 0.073 nM was obtained for cell-displayed mutant EGFP (mEGFP). In the presence of bacterial cell lysates and purified mEGFP, response to copper was linear in the 2-10 nM and 0.1-2 μM concentration range, respectively, with a 1.3 nM and 0.14 μM limit of detection. The sensitivity of bacterial cell lysates and surface-displayed mEGFP in the detection of copper ions is higher than the purified mEGFP.

AsIII Selectively Induces a Disorder-to-Order Transition in the Metalloid Binding Region of the AfArsR Protein

Arsenic is highly toxic and a significant threat to human health, but certain bacteria have developed defense mechanisms initiated by AsIII binding to AsIII-sensing proteins of the ArsR family. The transcriptional regulator AfArsR responds to AsIII and SbIII by coordinating the metalloids with three cysteines, located in a short sequence of the same monomer chain. Here, we characterize the binding of AsIII and HgII to a model peptide encompassing this fragment of the protein via solution equilibrium and spectroscopic/spectrometric techniques (pH potentiometry, UV, CD, NMR, PAC, EXAFS, and ESI-MS) combined with DFT calculations and MD simulations. Coordination of AsIII changes the peptide structure from a random-coil to a well-defined structure of the complex. A trigonal pyramidal AsS3 binding site is formed with almost exactly the same structure as observed in the crystal structure of the native protein, implying that the peptide possesses all of the features required to mimic the AsIII recognition and response selectivity of AfArsR. Contrary to this, binding of HgII to the peptide does not lead to a well-defined structure of the peptide, and the atoms near the metal binding site are displaced and reoriented in the HgII model. Our model study suggests that structural organization of the metal site by the inducer ion is a key element in the mechanism of the metalloid-selective recognition of this protein.

Design of a Whole-Cell Biosensor Based on Bacillus subtilis Spores and the Green Fluorescent Protein To Monitor Arsenic

A green fluorescent protein (GFP)-based whole-cell biosensor (WCB-GFP) for monitoring arsenic (As) was developed in Bacillus subtilis. To this end, we designed a reporter gene fusion carrying the gfpmut3a gene under the control of the promoter/operator region of the arsenic operon (Pars::gfpmut3a) in the extrachromosomal plasmid pAD123. This construct was transformed into B. subtilis 168, and the resultant strain was used as a whole-cell biosensor (BsWCB-GFP) for the detection of As. The BsWCB-GFP was specifically activated by inorganic As(III) and As(V), but not by dimethylarsinic acid [DMA(V)], and exhibited high tolerance to the noxious effects of arsenic. Accordingly, after 12 h exposure, B. subtilis cells carrying the Pars::gfpmut3a fusion exhibited 50 and 90% lethal doses (LD50 and LD90) to As(III) of 0.89 mM and As 1.71 mM, respectively. Notably, dormant spores from the BsWCB-GFP were able to report the presence of As(III) in a concentration range from 0.1 to 1,000 μM 4 h after the onset of germination. In summary, the specificity and high sensitivity for As, as well as its ability to proliferate under concentrations of the metal that are considered toxic in water and soil, makes the B. subtilis biosensor developed here a potentially important tool for monitoring environmental samples contaminated with this pollutant. IMPORTANCE Arsenic (As) contamination of groundwater is associated with serious worldwide health risks. Detection of this pollutant at concentrations that are established as permissible for water consumption by WHO is a matter of significant interest. Here, we report the generation of a whole-cell biosensor for As detection in the Gram-positive spore former B. subtilis. This biosensor reports the presence of inorganic As, activating the expression of the green fluorescent protein (GFP) under the control of the promoter/operator of the ars operon. The biosensor can proliferate under concentrations of As(III) that are considered toxic in water and soil and detect this ion at concentrations as low as 0.1 μM. Of note, spores of the Pars-GFP biosensor exhibited the ability to detect As(III) following germination and outgrowth. Therefore, this novel tool has the potential to be directly applied to monitor As contamination in environmental samples.

A critical review of on-site inorganic arsenic screening methods

Approximately 94 to 220 million people worldwide are at risk of drinking well water containing arsenic > 10 µg/L, the WHO guideline value. To identify non-compliant domestic wells, assess health risks and reduce exposure, accurate and rapid on-site inorganic arsenic screening methods are desirable because all domestic wells worldwide need to be tested. Here, the principles, advantages and limitations of commonly used colorimetry, electrochemistry, and biosensing methods are critically reviewed, with the performance compared with laboratory-based benchmark methods. Most commercial kits are based on the classic Gutzeit reaction. Despite being semi-quantitative, the more recent and more expensive products display improved and acceptable accuracy and shorter testing time (∼10 min). Carried out by trained professionals, electrochemical methods are also feasible for on-site analysis, although miniaturization is desirable yet challenging. Biosensing using whole bacterial cells or bio-engineered materials such as aptamers is promising, if incorporated with function specific nanomaterials and biomaterials. Since arsenic is frequently found as arsenite in reducing groundwater and subject to oxidation during sampling, transportation and storage, on-site separation and sample preservation are feasible but the specific methods should be chosen based on sample matrix and tested before use. To eliminate arsenic exposure among hundreds of millions of mostly rural residents worldwide, we call for concerted efforts in research community and regulatory authority to develop accurate, rapid, and affordable tests for on-site screening and monitoring of arsenic in drinking water. Access to affordable testing will benefit people who are socioeconomically disadvantaged.

Bioluminescence Color-Tuning Firefly Luciferases: Engineering and Prospects for Real-Time Intracellular pH Imaging and Heavy Metal Biosensing

Firefly luciferases catalyze the efficient production of yellow-green light under normal physiological conditions, having been extensively used for bioanalytical purposes for over 5 decades. Under acidic conditions, high temperatures and the presence of heavy metals, they produce red light, a property that is called pH-sensitivity or pH-dependency. Despite the demand for physiological intracellular biosensors for pH and heavy metals, firefly luciferase pH and metal sensitivities were considered drawbacks in analytical assays. We first demonstrated that firefly luciferases and their pH and metal sensitivities can be harnessed to estimate intracellular pH variations and toxic metal concentrations through ratiometric analysis. Using Macrolampis sp2 firefly luciferase, the intracellular pH could be ratiometrically estimated in bacteria and then in mammalian cells. The luciferases of Macrolampis sp2 and Cratomorphus distinctus fireflies were also harnessed to ratiometrically estimate zinc, mercury and other toxic metal concentrations in the micromolar range. The temperature was also ratiometrically estimated using firefly luciferases. The identification and engineering of metal-binding sites have allowed the development of novel luciferases that are more specific to certain metals. The luciferase of the Amydetes viviani firefly was selected for its special sensitivity to cadmium and mercury, and for its stability at higher temperatures. These color-tuning luciferases can potentially be used with smartphones for hands-on field analysis of water contamination and biochemistry teaching assays. Thus, firefly luciferases are novel color-tuning sensors for intracellular pH and toxic metals. Furthermore, a single luciferase gene is potentially useful as a dual bioluminescent reporter to simultaneously report intracellular ATP and/or luciferase concentrations luminometrically, and pH or metal concentrations ratiometrically, providing a useful tool for real-time imaging of intracellular dynamics and stress.

Optimization of Heavy Metal Sensors Based on Transcription Factors and Cell-Free Expression Systems

Many bacterial mechanisms for highly specific and sensitive detection of heavy metals and other hazards have been reengineered to serve as sensors. In some cases, these sensors have been implemented in cell-free expression systems, enabling easier design optimization and deployment in low-resource settings through lyophilization. Here, we apply the advantages of cell-free expression systems to optimize sensors based on three separate bacterial response mechanisms for arsenic, cadmium, and mercury. We achieved detection limits below the World Health Organization-recommended levels for arsenic and mercury and below the short-term US Military Exposure Guideline levels for all three. The optimization of each sensor was approached differently, leading to observations useful for the development of future sensors: (1) there can be a strong dependence of specificity on the particular cell-free expression system used, (2) tuning of relative concentrations of the sensing and reporter elements improves sensitivity, and (3) sensor performance can vary significantly with linear vs plasmid DNA. In addition, we show that simply combining DNA for the three sensors into a single reaction enables detection of each target heavy metal without any further optimization. This combined approach could lead to sensors that detect a range of hazards at once, such as a panel of water contaminants or all known variants of a target virus. For low-resource settings, such "all-hazard" sensors in a cheap, easy-to-use format could have high utility.

Development of a novel heterologous β-lactam-specific whole-cell biosensor in Bacillus subtilis

Background

Whole-cell biosensors are a powerful and easy-to-use screening tool for the fast and sensitive detection of chemical compounds, such as antibiotics. β-Lactams still represent one of the most important antibiotic groups in therapeutic use. They interfere with late stages of the bacterial cell wall biosynthesis and result in irreversible perturbations of cell division and growth, ultimately leading to cell lysis. In order to simplify the detection of these antibiotics from solutions, solid media or directly from producing organisms, we aimed at developing a novel heterologous whole-cell biosensor in Bacillus subtilis, based on the β-lactam-induced regulatory system BlaR1/BlaI from Staphylococcus aureus.

Results

The BlaR1/BlaI system was heterologously expressed in B. subtilis and combined with the luxABCDE operon of Photorhabdus luminescens under control of the BlaR1/BlaI target promoter to measure the output of the biosensor. A combination of codon adaptation, constitutive expression of blaR1 and blaI and the allelic replacement of penP increased the inducer spectrum and dynamic range of the biosensor. β-Lactams from all four classes induced the target promoter P_blaZ in a concentration-dependent manner, with a dynamic range of 7- to 53-fold. We applied our biosensor to a set of Streptomycetes soil isolates and demonstrated its potential to screen for the production of β-lactams. In addition to the successful implementation of a highly sensitive β-lactam biosensor, our results also provide the first experimental evidence to support previous suggestions that PenP functions as a β-lactamase in B. subtilis.

Conclusion

We have successfully established a novel heterologous whole-cell biosensor in B. subtilis that is highly sensitive for a broad spectrum of β-lactams from all four chemical classes. Therefore, it increases the detectable spectrum of compounds with respect to previous biosensor designs. Our biosensor can readily be applied for identifying β-lactams in liquid or on solid media, as well as for identifying potential β-lactam producers.

Antimony sensing whole-cell bioreporters derived from ArsR genetic engineering

Despite the known hazardous effects of antimony (Sb) on human health, Sb monitoring biosensors have not been as actively investigated as arsenic (As) biosensors. Whole-cell bioreporters (WCBs) employing an arsenic-responsive operon and a regulatory protein (ArsR) are reportedly capable of monitoring arsenite, arsenate, and antimonite. However, the potential of WCBs as Sb biosensors has been largely ignored. Here, the metal-binding site of ArsR (sequenced as ELCVCDLCTA from amino acid number 30 to 39) was modified via genetic engineering to enhance Sb specificity. By relocating cysteine residues and introducing point mutations, nine ArsR mutants were generated and tested for metal(loid) ion specificity. The Sb specificity of WCBs was enhanced by the C37S/A39C and L36C/C37S mutations on the As binding site of ArsR. Additionally, WCBs with other ArsR mutants exhibited new target sensing capabilities toward Cd and Pb. Although further research is required to enhance the specificity and sensitivity of WCBs and to broaden their practical applications, our proposed strategy based on genetic engineering of regulatory proteins provides a valuable basis to generate WCBs to monitor novel targets.

Bacterial Heavy-Metal and Antibiotic Resistance Genes in a Copper Tailing Dam Area in Northern China

Heavy metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) in bacteria can respond to the inducement of heavy metals. However, the co-occurrence of MRGs and ARGs in the long-term heavy metal contaminated area is still poorly understood. Here, we investigated the relationship between the abundance of soil bacteria MRGs, ARGs and heavy metal pollution in a copper tailing dam area of northern China. We found that arsC and ereA genes coding for resistance mechanisms to arsenic and to macrolides, respectively, are the most abundant MRG and ARG in the study area. The abundance of MRGs is positively correlated with cadmium (Cd) concentration, and this indicates the importance of Cd in the selection of MRGs. The network analysis results show that sulII and MRGs co-occur and copB occur with ARGs, which suggests that MRGs and ARGs can be co-selected in the soil contaminated by heavy metal. The network analysis also reveals the co-occurrence of Cd and MRGs, and thus heavy metal with a high 'toxic-response' factor can be used as the indicator of MRGs. This study improves the understanding of the relationship between bacterial resistance and multi-metal contamination, and underlies the exploration of the adaptive mechanism of microbes in the multi-metal contaminated environment.

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.

Insights Into Arsenite and Arsenate Uptake Pathways Using a Whole Cell Biosensor

Despite its high toxicity and widespread occurrence in many parts of the world, arsenic (As) concentrations in decentralized water supplies such as domestic wells remain often unquantified. One limitation to effective monitoring is the high cost and lack of portability of current arsenic speciation techniques. Here, we present an arsenic biosensor assay capable of quantifying and determining the bioavailable fraction of arsenic species at environmentally relevant concentrations. First, we found that inorganic phosphate, a buffering agent and nutrient commonly found in most bioassay exposure media, was in fact limiting As(V) uptake, possibly explaining the variability in As(V) detection reported so far. Second, we show that the nature of the carbon source used in the bioassay differentially affects the response of the biosensor to As(III). Finally, our data support the existence of non-specific reduction pathways (non-ars encoded) that are responsible for the reduction of As(V) to As(III), allowing its detection by the biosensor. To validate our laboratory approach using field samples, we performed As(III) and As(V) standard additions on natural water samples collected from 17 lakes surrounding Giant Mine in Yellowknife (NWT), Canada. We found that legacy arsenic contamination in these lake water samples was accurately quantified by the biosensor. Interestingly, bioavailability of freshly added standards showed signs of matrix interference, indicative of dynamic interactions between As(III), As(V) and environmental constituents that have yet to be identified. Our results point toward dissolved organic carbon as possibly controlling these interactions, thus altering As bioavailability.

Copy number of ArsR reporter plasmid determines its arsenite response and metal specificity

The key component in bacteria-based biosensors is a transcriptional reporter employed to monitor induction or repression of a reporter gene corresponding to environmental change. In this study, we made a series of reporters in order to achieve highly sensitive detection of arsenite. From these reporters, two biosensors were developed by transformation of Escherichia coli DH5α with pLHPars9 and pLLPars9, consisting of either a high or low copy number plasmid, along with common elements of ArsR-luciferase fusion and addition of two binding sequences, one each from E. coli and Acidithiobacillus ferrooxidans chromosome, in front of the R773 ArsR operon. Both of them were highly sensitive to arsenite, with a low detection limit of 0.04 μM arsenite (~ 5 μg/L). They showed a wide dynamic range of detection up to 50 μM using high copy number pLHPars9 and 100 μM using low copy number pLLPars9. Significantly, they differ in metal specificity, pLLPars9 more specific to arsenite, while pLHPars9 to both arsenite and antimonite. The only difference between pLHPars9 and pLLPars9 is their copy numbers of plasmid and corresponding ratios of ArsR to its binding promoter/operator sequence. Therefore, we propose a working model in which DNA bound-ArsR is different from its free form in metal specificity.

Miniaturized Sample Preparation and Rapid Detection of Arsenite in Contaminated Soil Using a Smartphone

Conventional methods for analyzing heavy metal contamination in soil and water generally require laboratory equipped instruments, complex procedures, skilled personnel and a significant amount of time. With the advancement in computing and multitasking performances, smartphone-based sensors potentially allow the transition of the laboratory-based analytical processes to field applicable, simple methods. In the present work, we demonstrate the novel miniaturized setup for simultaneous sample preparation and smartphone-based optical sensing of arsenic As(III) in the contaminated soil. Colorimetric detection protocol utilizing aptamers, gold nanoparticles and NaCl have been optimized and tested on the PDMS-chip to obtain the high sensitivity with the limit of detection of 0.71 ppm (in the sample) and a correlation coefficient of 0.98. The performance of the device is further demonstrated through the comparative analysis of arsenic-spiked soil samples with standard laboratory method, and a good agreement with a correlation coefficient of 0.9917 and the average difference of 0.37 ppm, are experimentally achieved. With the android application on the device to run the experiment, the whole process from sample preparation to detection is completed within 3 hours without the necessity of skilled personnel. The approximate cost of setup is estimated around 1 USD, weight 55 g. Therefore, the presented method offers the simple, rapid, portable and cost-effective means for onsite sensing of arsenic in soil. Combined with the geometric information inside the smartphones, the system will allow the monitoring of the contamination status of soils in a nation-wide manner.

The Application of Whole Cell-Based Biosensors for Use in Environmental Analysis and in Medical Diagnostics

Various whole cell-based biosensors have been reported in the literature for the last 20 years and these reports have shown great potential for their use in the areas of pollution detection in environmental and in biomedical diagnostics. Unlike other reviews of this growing field, this mini-review argues that: (1) the selection of reporter genes and their regulatory proteins are directly linked to the performance of celllular biosensors; (2) broad enhancements in microelectronics and information technologies have also led to improvements in the performance of these sensors; (3) their future potential is most apparent in their use in the areas of medical diagnostics and in environmental monitoring; and (4) currently the most promising work is focused on the better integration of cellular sensors with nano and micro scaled integrated chips. With better integration it may become practical to see these cells used as (5) real-time portable devices for diagnostics at the bedside and for remote environmental toxin detection and this in situ application will make the technology commonplace and thus as unremarkable as other ubiquitous technologies.

A protease-based biosensor for the detection of schistosome cercariae

Parasitic diseases affect millions of people worldwide, causing debilitating illnesses and death. Rapid and cost-effective approaches to detect parasites are needed, especially in resource-limited settings. A common signature of parasitic diseases is the release of specific proteases by the parasites at multiple stages during their life cycles. To this end, we engineered several modular Escherichia coli and Bacillus subtilis whole-cell-based biosensors which incorporate an interchangeable protease recognition motif into their designs. Herein, we describe how several of our engineered biosensors have been applied to detect the presence and activity of elastase, an enzyme released by the cercarial larvae stage of Schistosoma mansoni. Collectively, S. mansoni and several other schistosomes are responsible for the infection of an estimated 200 million people worldwide. Since our biosensors are maintained in lyophilised cells, they could be applied for the detection of S. mansoni and other parasites in settings without reliable cold chain access.

Preparation and Assay of Simple Light off Biosensor Based on Immobilized Bioluminescent Bacteria for General Toxicity Assays

We describe a simple light off bioluminescent biosensor for general environmental toxicity assays based on immobilized bioluminescent bacteria engineered with beetle luciferases.

A low cost color-based bacterial biosensor for measuring arsenic in groundwater

Using arsenic (As) contaminated groundwater for drinking or irrigation has caused major health problems for humans around the world, raising a need to monitor As level efficiently and economically. This study developed a color-based bacterial biosensor which is easy-to-use and inexpensive for measuring As and could be complementary to current As detecting techniques. The arsR-lacZ recombinant gene cassette in nonpathogenic strain Escherichia coli DH5α was used in the color-based biosensor which could be observed by eyes or measured by spectrometer. The developed bacterial biosensor demonstrates a quantitative range from 10 to 500μgL(-1) of As in 3-h reaction time. Furthermore, the biosensor was able to successfully detect and estimate As concentration in groundwater sample by measuring optical density at 595nm (OD595). Among different storage methods used in this study, biosensor in liquid at 4°C showed the longest shelf life about 9d, and liquid storage at RT and cell pellet could also be stored for about 3-5d. In conclusion, this study showed that the As biosensor with reliable color signal and economical preservation methods is useful for rapid screening of As pollutant, providing the potential for large scale screening and better management strategies for environmental quality control.

Detection of bioavailable cadmium, lead, and arsenic in polluted soil by tailored multiple Escherichia coli whole-cell sensor set

Microbial whole-cell sensor has been widely used to assess bioavailability and risk of toxic elements, but their environmental use is still limited due to the presence of other interfering pollutants and the nonspecific binding in cells, which leads to inaccurate results. Here, we proposed a strategy combining Escherichia coli sensor set with binary regression models for the specific detection of bioavailable cadmium (Cd), lead (Pb), and arsenic (As) in a co-polluted environment. Initial tests suggested that the sensor set respectively termed pcadCluc, pzntRluc, and parsRluc could be classified into two groups according to their specific response to Cd, Pb, and As: group 1 (pcadCluc and pzntRluc) induced by a Cd-Pb mix and group 2 (parsRluc) induced by a Cd-As mix. Based on the variance in responses of each sensor to mixtures of target elements, three binary linear equations for two sensor groups were set up to calculate the individual concentrations in the mixture solutions. This method was then used to quantify the bioavailable Cd, Pb, and As in soils from a co-polluted mining region and to compare the results with other methods. Results showed that the conventional single target sensor method overestimated the bioavailability of each element, while sensor set was credible for accurate bioavailable Cd, Pb, and As quantification and comparable with the results from inductively coupled plasma mass spectrometry (ICP-MS) analysis. Our method can potentially be extended to cover the specific detection of other bioavailable toxic elements in different environmental settings.

Development of a set of bacterial biosensors for simultaneously detecting arsenic and mercury in groundwater

There is a growing need for effective and inexpensive environmental monitoring strategies for assessing heavy metal contamination levels. We developed a set of bacterial biosensors to simultaneously detect multiple bioavailable heavy metals (As(III) and Hg(II)). The biosensors provide a choice of the two reporter systems, luxCDABE and gfp, combined with metal responsive regulatory elements (ars and mer for As(III) and Hg(II), respectively). The results showed that the induction of the luxCDABE-based constructs was more sensitive than that of the gfp-based constructs for the detection of As(III) and Hg(II). In addition, both the luminescent and fluorescent biosensors readily distinguished As and Hg concentrations in groundwater samples to meet the groundwater quality standards. Due to the potentially complicated chemicals present in environmental samples, using a set of bacterial biosensors with different reporter genes to simultaneously determine the bioavailable proportions of heavy metals is desirable.

Integrated phytobial remediation for sustainable management of arsenic in soil and water

Arsenic (As), cited as the most hazardous substance by the U.S. Agency for Toxic Substance and Disease Registry (ATSDR, 2005), is an ubiquitous metalloid which when ingested for prolonged periods cause extensive health effects leading to ultimate untimely death. Plants and microbes can help mitigate soil and groundwater As problem since they have evolved elaborate detoxification machineries against this toxic metalloid as a result of their coexistence with this since the origin of life on earth. Utilization of the phytoremediation and bioremediation potential of the plants and microbes, respectively, is now regarded as two innovative tools that encompass biology, geology, biotechnology and allied sciences with cutting edge applications for sustainable mitigation of As epidemic. Discovery of As hyperaccumulating plants that uptake and concentrate large amounts of this toxic metalloid in their shoots or roots offered new hope to As phytoremediation, solar power based nature's own green remediation. This review focuses on how phytoremediation and bioremediation can be merged together to form an integrated phytobial remediation which could synergistically achieve the goal of large scale removal of As from soil, sediment and groundwater and overcome the drawbacks of the either processes alone. The review also points to the feasibility of the introduction of transgenic plants and microbes that bring new hope for more efficient treatment of As. The review identifies one critical research gap on the importance of remediation of As contaminated groundwater not only for drinking purpose but also for irrigation purpose and stresses that more research should be conducted on the use of constructed wetland, one of the most suitable areas of application of phytobial remediation. Finally the review has narrowed down on different phytoinvestigation and phytodisposal methods, which constitute the most essential and the most difficult part of pilot scale and field scale applications of phytoremediation programs.

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.

Novel application of pH-sensitive firefly luciferases as dual reporter genes for simultaneous ratiometric analysis of intracellular pH and gene expression/location

Firefly luciferases are widely used as bioluminescent reporter genes for bioimaging and biosensors. Aiming at simultaneous analyses of different gene expression and cellular events, luciferases and GFPs that exhibit distinct bioluminescence and fluorescence colors have been coupled with each promoter, making dual and multicolor reporter systems. Despite their wide use, firefly luciferase bioluminescence spectra are pH-sensitive, resulting in a typical large red shift at acidic pH, a side-effect that may affect some bioanalytical purposes. Although some intracellular pH-indicators employ dual color and fluorescent dyes, none has been considered to benefit from the characteristic spectral pH-sensitivity of firefly luciferases to monitor intracellular pH-associated stress, an important indicator of cell homeostasis. Here we demonstrate a linear relationship between the ratio of intensities in the green and red regions of the bioluminescence spectra and pH using firefly luciferases cloned in our laboratory (Macrolampis sp2 and Cratomorphus distinctus), allowing estimation of E. coli intracellular pH, thus providing a new analytical method for ratiometric intracellular pH-sensing. This is the first dual reporter system that employs a single luciferase gene to simultaneously monitor intracellular pH using spectral changes, and gene expression and/or ATP concentration using the bioluminescence intensity, showing great potential for real time bioanalysis of intracellular processes associated with metabolic changes such as apoptosis, cell death, inflammation and tissue acidification, among the other physiological changes.

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.

Whole-cell bioreporters for the detection of bioavailable metals

Whole-cell bioreporters are living microorganisms that produce a specific, quantifiable output in response to target chemicals. Typically, whole-cell bioreporters combine a sensor element for the substance of interest and a reporter element coding for an easily detectable protein. The sensor element is responsible for recognizing the presence of an analyte. In the case of metal bioreporters, the sensor element consists of a DNA promoter region for a metal-binding transcription factor fused to a promoterless reporter gene that encodes a signal-producing protein. In this review, we provide an overview of specific whole-cell bioreporters for heavy metals. Because the sensing of metals by bioreporter microorganisms is usually based on heavy metal resistance/homeostasis mechanisms, the basis of these mechanisms will also be discussed. The goal here is not to present a comprehensive summary of individual metal-specific bioreporters that have been constructed, but rather to express views on the theory and applications of metal-specific bioreporters and identify some directions for future research and development.

Fiber-optic based cell sensors

Different whole cell fiber optic based biosensors have been developed to detect the total effect of a wide range of environmental pollutants, providing results within a very short period. These biosensors are usually built from three major components, the biorecognition element (whole-cells) intimately attached to a transducer (optic fiber) using a variety of techniques (adsorption, covalent binding, polymer trapping, etc). Even with a great progress in the field of biosensors, there is still a serious lack of commercial applications, capable of competing with traditional analytical tools.

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.

Microbial interactions in the arsenic cycle: adoptive strategies and applications in environmental management

Arsenic (As) is a nonessential element that is often present in plants and in other organisms. However, it is one of the most hazardous of toxic elements globally. In many parts of the world, arsenic contamination in groundwater is a serious and continuing threat to human health. Microbes play an important role in regulating the environmental fate of arsenic. Different microbial processes influence the biogeochemical cycling of arsenic in ways that affect the accumulation of different arsenic species in various ecosystem compartments. For example, in soil, there are bacteria that methylate arsenite to trimethylarsine gas, thereby releasing arsenic to the atmosphere.In marine ecosystems, microbes exist that can convert inorganic arsenicals to organic arsenicals (e.g., di- and tri-methylated arsenic derivatives, arsenocholine,arsenobetaine, arsenosugars, arsenolipids). The organo arsenicals are further metabolized to complete the arsenic cycle.Microbes have developed various strategies that enable them to tolerate arsenic and to survive in arsenic-rich environments. Such strategies include As exclusion from cells by establishing permeability barrier, intra- and extracellular sequestration,active efflux pumps, enzymatic reduction, and reduction in the sensitivity of cellular targets. These strategies are used either singly or in combination. In bacteria,the genes for arsenic resistance/detoxification are encoded by the arsenic resistance operons (ars operon).In this review, we have addressed and emphasized the impact of different microbial processes (e.g., arsenite oxidation, cytoplasmic arsenate reduction, respiratory arsenate reduction, arsenite methylation) on the arsenic cycle. Microbes are the only life forms reported to exist in heavy arsenic-contaminated environments. Therefore,an understanding of the strategies adopted by microbes to cope with arsenic stress is important in managing such arsenic-contaminated sites. Further future insights into the different microbial genes/proteins that are involved in arsenic resistance may also be useful for developing arsenic resistant crop plants.

Online detection of metals in environmental samples: comparing two concepts of bioluminescent bacterial biosensors

In this study, we compared two bacterial biosensors designed for the environmental monitoring of metals: Lumisens III and Lumisens IV. These two biosensors are based on the same bacterial sensors (inducible or constitutive bacterial strains) but with a different conservation mode. The results showed that the biosensor Lumisens III using immobilized cells in agarose hydrogel, allowed to detect artificial mercury contaminations on the limited period of 7 days in laboratory conditions with a reproducibility of 40%. With environmental samples, bioluminescence of the immobilized bacteria inside the biosensor was strongly limited by the environmental microflora because of the lack of oxygen, limiting the use of the biosensor to 2 days. The biosensor of the last generation, Lumisens IV, using freeze-dried bacteria in a disposable card allowed a stable detection during 10 days with 3% of reproducibility of the bioluminescence signal both in laboratory conditions and environmental samples. One analysis was performed in only 90 min against 360 min for Lumisens III. Nevertheless, the lack of specificity of the promoter, which regulates the bioluminescent reporter genes, limits the metal detection. We addressed the problem by using Lumisens IV and a data analysis software namely Metalsoft, developed in previous works. Thanks to this analytical software, Lumisens IV was a reliable online biosensor for the multidetection of Cd, As, Hg, and Cu.

Development of a microfluidics biosensor for agarose-bead immobilized Escherichia coli bioreporter cells for arsenite detection in aqueous samples

Contamination with arsenic is a recurring problem in both industrialized and developing countries. Drinking water supplies for large populations can have concentrations much higher than the permissible levels (for most European countries and the United States, 10 μg As per L; elsewhere, 50 μg As per L). Arsenic analysis requires high-end instruments, which are largely unavailable in developing countries. Bioassays based on genetically engineered bacteria have been proposed as suitable alternatives but such tests would profit from better standardization and direct incorporation into sensing devices. The goal of this work was to develop and test microfluidic devices in which bacterial bioreporters could be embedded, exposed and reporter signals detected, as a further step towards a complete miniaturized bacterial biosensor. The signal element in the biosensor is a nonpathogenic laboratory strain of Escherichia coli, which produces a variant of the green fluorescent protein after contact to arsenite and arsenate. E. coli bioreporter cells were encapsulated in agarose beads and incorporated into a microfluidic device where they were captured in 500 × 500 μm(2) cages and exposed to aqueous samples containing arsenic. Cell-beads frozen at -20 °C in the microfluidic chip retained inducibility for up to a month and arsenic samples with 10 or 50 μg L(-1) could be reproducibly discriminated from the blank. In the 0-50 μg L(-1) range and with an exposure time of 200 minutes, the rate of signal increase was linearly proportional to the arsenic concentration. The time needed to reliably and reproducibly detect a concentration of 50 μg L(-1) was 75-120 minutes, and 120-180 minutes for a concentration of 10 μg L(-1).

Improved triacylglycerol production in Acinetobacter baylyi ADP1 by metabolic engineering

Background

Triacylglycerols are used in various purposes including food applications, cosmetics, oleochemicals and biofuels. Currently the main sources for triacylglycerol are vegetable oils, and microbial triacylglycerol has been suggested as an alternative for these. Due to the low production rates and yields of microbial processes, the role of metabolic engineering has become more significant. As a robust model organism for genetic and metabolic studies, and for the natural capability to produce triacylglycerol, Acinetobacter baylyi ADP1 serves as an excellent organism for modelling the effects of metabolic engineering for energy molecule biosynthesis.

Results

Beneficial gene deletions regarding triacylglycerol production were screened by computational means exploiting the metabolic model of ADP1. Four deletions, acr1, poxB, dgkA, and a triacylglycerol lipase were chosen to be studied experimentally both separately and concurrently by constructing a knock-out strain (MT) with three of the deletions. Improvements in triacylglycerol production were observed: the strain MT produced 5.6 fold more triacylglycerol (mg/g cell dry weight) compared to the wild type strain, and the proportion of triacylglycerol in total lipids was increased by 8-fold.

Conclusions

In silico predictions of beneficial gene deletions were verified experimentally. The chosen single and multiple gene deletions affected beneficially the natural triacylglycerol metabolism of A. baylyi ADP1. This study demonstrates the importance of single gene deletions in triacylglycerol metabolism, and proposes Acinetobacter sp. ADP1 as a model system for bioenergetic studies regarding metabolic engineering.

Microbial reporters of metal bioavailability

When attempting to assess the extent and the implications of environmental pollution, it is often essential to quantify not only the total concentration of the studied contaminant but also its bioavailable fraction: higher bioavailability, often correlated with increased mobility, signifies enhanced risk but may also facilitate bioremediation. Genetically engineered microorganisms, tailored to respond by a quantifiable signal to the presence of the target chemical(s), may serve as powerful tools for bioavailability assessment. This review summarizes the current knowledge on such microbial bioreporters designed to assay metal bioavailability. Numerous bacterial metal‐sensor strains have been developed over the past 15 years, displaying very high detection sensitivities for a broad spectrum of environmentally significant metal targets. These constructs are based on the use of a relatively small number of gene promoters as the sensing elements, and an even smaller selection of molecular reporter systems; they comprise a potentially useful panel of tools for simple and cost‐effective determination of the bioavailability of heavy metals in the environment, and for the quantification of the non‐bioavailable fraction of the pollutant. In spite of their inherent advantages, however, these tools have not yet been put to actual use in the evaluation of metal bioavailability in a real environmental remediation scheme. For this to happen, acceptance by regulatory authorities is essential, as is a standardization of assay conditions.

Improvement of the identification of four heavy metals in environmental samples by using predictive decision tree models coupled with a set of five bioluminescent bacteria

A primary statistical model based on the crossings between the different detection ranges of a set of five bioluminescent bacterial strains was developed to identify and quantify four metals which were at several concentrations in different mixtures: cadmium, arsenic III, mercury, and copper. Four specific decision trees based on the CHAID algorithm (CHi-squared Automatic Interaction Detector type) which compose this model were designed from a database of 576 experiments (192 different mixture conditions). A specific software, 'Metalsoft', helped us choose the best decision tree and a user-friendly way to identify the metal. To validate this innovative approach, 18 environmental samples containing a mixture of these metals were submitted to a bioassay and to standardized chemical methods. The results show on average a high correlation of 98.6% for the qualitative metal identification and 94.2% for the quantification. The results are particularly encouraging, and our model is able to provide semiquantitative information after only 60 min without pretreatments of samples.

Construction and characterization of Escherichia coli whole-cell biosensors for toluene and related compounds

The XylR regulatory protein is a transcriptional activator from the TOL plasmid of Pseudomonas putida mt-2 that is involved in the toluene and benzene degradation pathway. Here we describe the construction and laboratory characterization of recombinant biosensors (pGLPX plasmids) based on XylR and its cognate promoter (Pu). In the pGLPX plasmid, the reporter luc gene is under the control of the Pu promoter. We evaluated the ability of two distinct nucleotide sequences to function as SD elements and improve sensitivity of bioreporting. We also evaluated the effect of introducing the T₂rrnβ terminator on the specificity of the construct. E. coli transformed with pGLPX plasmids were used to sense toluene and its derivatives. The pattern of induction was different for each derivative. In general, more luciferase activity was induced by toluene and benzene than by TNT and DNT at most tested concentrations. The bioluminescence response of the reporter strains to the nitrotoluenes was significantly stronger at lower concentrations (≥ 50 μmol) than at higher concentrations. Our results show that the SD sequence (taaggagg) is crucially important for biosensor sensitivity. The presence of the T₂rrnβ terminator in the bioreporter plasmid prevents nonspecific responses and also reduces biosensor sensitivity upon exposure to inducers. These data suggest that pGLPX strains can be used as whole-cell biosensors to detect toluene and related compounds. Further investigation will be required to optimize the application of pGLPX biosensors.

Construction of WCB-11: a novel phiYFP arsenic-resistant whole-cell biosensor

The prediction and assessment of environmental pollution by arsenic are important preconditions of advocating environmental protection and human health risk assessment. A yellow fluorescent protein-based whole-cell biosensor for the detection of arsenite and arsenate was constructed and tested. An arsenic-resistant promoter and the regulatory gene arsR were obtained by PCR from the genome of Escherichia coli DH5alpha, and phiYFP was introduced into E. coli DH5alpha as a reporter gene to construct an arsenic-resistant whole-cell biosensor (WCB-11) in which phiYFP was expressed well for the first time. Experimental results demonstrated that the biosensor has a good response to arsenic and the expression of phiYFP. When strain WCB-11 was exposed to As3+ and As5+, the expression of yellow fluorescence was time-dependent and dose-dependent. This engineered construct is expected to become established as an inexpensive and convenient method for the detection of arsenic in the field.

Development of bacteria-based bioassays for arsenic detection in natural waters

Arsenic contamination of natural waters is a worldwide concern, as the drinking water supplies for large populations can have high concentrations of arsenic. Traditional techniques to detect arsenic in natural water samples can be costly and time-consuming; therefore, robust and inexpensive methods to detect arsenic in water are highly desirable. Additionally, methods for detecting arsenic in the field have been greatly sought after. This article focuses on the use of bacteria-based assays as an emerging method that is both robust and inexpensive for the detection of arsenic in groundwater both in the field and in the laboratory. The arsenic detection elements in bacteria-based bioassays are biosensor-reporter strains; genetically modified strains of, e.g., Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Rhodopseudomonas palustris. In response to the presence of arsenic, such bacteria produce a reporter protein, the amount or activity of which is measured in the bioassay. Some of these bacterial biosensor-reporters have been successfully utilized for comparative in-field analyses through the use of simple solution-based assays, but future methods may concentrate on miniaturization using fiberoptics or microfluidics platforms. Additionally, there are other potential emerging bioassays for the detection of arsenic in natural waters including nematodes and clams.