Enhancing the copper-sensing capability of Escherichia coli-based whole-cell bioreporters by genetic engineering

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.

Challenges and opportunities in commercializing whole-cell bioreporters in environmental application

Since the initial introduction of whole-cell bioreporters (WCBs) nearly 30 years ago, their high sensitivity, selectivity, and suitability for on-site detection have rendered them highly promising for environmental monitoring, medical diagnosis, food safety, biomanufacturing, and other fields. Especially in the environmental field, the technology provides a fast and efficient way to assess the bioavailability of pollutants in the environment. Despite these advantages, the technology has not been commercialized. This lack of commercialization is confusing, given the broad application prospects of WCBs. Over the years, numerous research papers have focused primarily on enhancing the sensitivity and selectivity of WCBs, with little attention paid to their wider commercial applications. So far, there is no a critical review has been published yet on this topic. Therefore, in this article we critically reviewed the research progress of WCBs over the past three decades, assessing the performance and limitations of current systems to understand the barriers to commercial deployment. By identifying these obstacles, this article provided researchers and industry stakeholders with deeper insights into the challenges hindering market entry and inspire further research toward overcoming these barriers, thereby facilitating the commercialization of WCBs as a promising technology for environmental monitoring.

Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology

Living cells are exquisitely tuned to sense and respond to changes in their environment. Repurposing these systems to create engineered biosensors has seen growing interest in the field of synthetic biology and provides a foundation for many innovative applications spanning environmental monitoring to improved biobased production. In this review, we present a detailed overview of currently available biosensors and the methods that have supported their development, scale-up, and deployment. We focus on genetic sensors in living cells whose outputs affect gene expression. We find that emerging high-throughput experimental assays and evolutionary approaches combined with advanced bioinformatics and machine learning are establishing pipelines to produce genetic sensors for virtually any small molecule, protein, or nucleic acid. However, more complex sensing tasks based on classifying compositions of many stimuli and the reliable deployment of these systems into real-world settings remain challenges. We suggest that recent advances in our ability to precisely modify nonmodel organisms and the integration of proven control engineering principles (e.g., feedback) into the broader design of genetic sensing systems will be necessary to overcome these hurdles and realize the immense potential of the field.

A low-cost and eco-friendly recombinant protein expression system using copper-containing industrial wastewater

The development of innovative methods for highly efficient production of recombinant proteins remains a prominent focus of research in the biotechnology field, primarily due to the fact that current commercial protein expression systems rely on expensive chemical inducers, such as isopropyl β-D-thiogalactoside (IPTG). In our study, we designed a novel approach for protein expression by creating a plasmid that responds to copper. This specialized plasmid was engineered through the fusion of a copper-sensing element with an optimized multiple cloning site (MCS) sequence. This MCS sequence can be easily customized by inserting the coding sequences of target recombinant proteins. Once the plasmid was generated, it was introduced into an engineered Escherichia coli strain lacking copA and cueO. With this modified E. coli strain, we demonstrated that the presence of copper ions can efficiently trigger the induction of recombinant protein expression, resulting in the production of active proteins. Most importantly, this expression system can directly utilize copper-containing industrial wastewater as an inducer for protein expression while simultaneously removing copper from the wastewater. Thus, this study provides a low-cost and eco-friendly strategy for the large-scale recombinant protein production. To the best of our knowledge, this is the first report on the induction of recombinant proteins using industrial wastewater.

Engineered Bacillus subtilis Biofilm@Biochar living materials for in-situ sensing and bioremediation of heavy metal ions pollution

The simultaneous sensing and remediation of multiple heavy metal ions in wastewater or soil with microorganisms is currently a significant challenge. In this study, the microorganism Bacillus subtilis was used as a chassis organism to construct two genetic circuits for sensing and adsorbing heavy-metal ions. The engineered biosensor can sense three heavy metal ions (0.1-75 μM of Pb2+ and Cu2+, 0.01-3.5 μM of Hg2+) in situ real-time with high sensitivity. The engineered B. subtilis TasA-metallothionein (TasA-MT) biofilm can specifically adsorb metal ions from the environment, exhibiting remarkable removal efficiencies of 99.5% for Pb2+, 99.9% for Hg2+and 99.5% for Cu2+ in water. Furthermore, this engineered strain (as a biosensor and absorber of Pb2+, Cu2+, and Hg2+) was incubated with biochar to form a hybrid biofilm@biochar (BBC) material that could be applied in the bioremediation of heavy metal ions. The results showed that BBC material not only significantly reduced exchangeable Pb2+ in the soil but also reduced Pb2+ accumulation in maize plants. In addition, it enhanced maize growth and biomass. In conclusion, this study examined the potential applications of biosensors and hybrid living materials constructed using sensing and adsorption circuits in B. subtilis, providing rapid and cost-effective tools for sensing and remediating multiple heavy metal ions (Pb2+, Hg2+, and Cu2+).

A Portable, Encapsulated Microbial Whole-Cell Biosensing System for the Detection of Bioavailable Copper (II) in Soil

A portable, field deployable whole-cell biosensor was developed that can withstand the complex matrices of soil and requires minimal to no sample preparation to monitor bioavailable concentrations of the essential micronutrient copper (II). Conventional measurement of micronutrients is often complex, laboratory-based, and not suitable for monitoring their bioavailable concentration. To address this need, we developed a fluorescence based microbial whole-cell biosensing (MWCB) system encoding for a Cu2+-responsive protein capable of generating a signal upon binding to Cu2+. The sensing-reporting protein was designed by performing circular permutation on the green fluorescent protein (GFP) followed by insertion of a Cu2+ binding motif into the structure of GFP. The design included insertion of several binding motifs and creating plasmids that encoded the corresponding sensing proteins. The signal generated by the sensing-reporting protein is directly proportional to the concentration of Cu2+ in the sample. Evaluation of the resulting biosensing systems carrying these plasmids was performed prior to selection of the optimal fluorescence emitting Cu2+-binding protein. The resulting optimized biosensing system was encapsulated in polyacrylate-alginate beads and embedded in soil for detection of the analyte. Once exposed to the soil, the beads were interrogated to measure the fluorescence signal emitted by the sensing-reporting protein using a portable imaging device. The biosensor was optimized for detection of Cu2+ in terms of selectivity, sensitivity, matrix effects, detection limits, and reproducibility in both liquid and soil matrices. The limit of detection (LoD) of the optimized encapsulated biosensor was calculated as 0.27 mg/L and 1.26 mg/kg of Cu2+ for Cu2+ in solution and soil, respectively. Validation of the portable imaging tools as a potential biosensing device in the field was performed.

Engineered bacterial swarm patterns as spatial records of environmental inputs

A diverse array of bacteria species naturally self-organize into durable macroscale patterns on solid surfaces via swarming motility-a highly coordinated and rapid movement of bacteria powered by flagella. Engineering swarming is an untapped opportunity to increase the scale and robustness of coordinated synthetic microbial systems. Here we engineer Proteus mirabilis, which natively forms centimeter-scale bullseye swarm patterns, to 'write' external inputs into visible spatial records. Specifically, we engineer tunable expression of swarming-related genes that modify pattern features, and we develop quantitative approaches to decoding. Next, we develop a dual-input system that modulates two swarming-related genes simultaneously, and we separately show that growing colonies can record dynamic environmental changes. We decode the resulting multicondition patterns with deep classification and segmentation models. Finally, we engineer a strain that records the presence of aqueous copper. This work creates an approach for building macroscale bacterial recorders, expanding the framework for engineering emergent microbial behaviors.

Development of novel Escherichia coli cell-based biosensors to monitor Mn(II) in environmental systems

Escherichia coli uses manganese [Mn(II)] as an essential trace element; thus, it has a genetic system that regulates cellular Mn(II) levels. Several genes in the mnt-operon of E. coli respond to intercellular Mn(II) levels, and transcription is regulated by a transcription factor (MntR) that interacts with Mn(II). This study aimed to develop Mn(II)-sensing biosensors based on mnt-operon genetic systems. Additionally, the properties of biosensors developed based on the promoter regions of mntS, mntH, and mntP were investigated. MntR represses the transcription of MntS and MntH after binding with Mn(II), while it induces MntP transcription. Thus, Mn(II) biosensors that decrease and increase signals could be obtained by fusing the promoter regions of mntS/mntH and mntP, with egfp encoding an enhanced green fluorescent protein. However, only the biosensor-based mntS:egfp responded to Mn(II) exposure. Further, E. coli harboring P mntS :egfp showed a concentration-dependent decrease in fluorescence signals. To enhance the sensitivity of the biosensor toward Mn(II), E. coli containing a deleted MntP gene that encodes Mn(II) exporter, was used as a host cell for biosensor development. The sensitivity toward Mn(II) increased by two times on using E. coli-mntP, and the biosensor could quantify 0.01-10 μM of Mn(II). Further, the applicability of Mn(II) in artificially contaminated water samples was quantified and showed >95% accuracy. The newly developed Mn(II) biosensors could detect and quantify the residual Mn(II) from mancozeb in soil samples, with the quantification accuracy being approximately 90%. To the best of our knowledge, this is the first Mn (II)-specific bacterial cell-based biosensor that serves as a valuable tool for monitoring and assessing the risks of Mn(II) in environmental systems.

Recent advances in the analytical strategies of microbial biosensor for detection of pollutants

Microbial biosensor which integrates different types of microorganisms, such as bacteria, microalgae, fungi, and virus have become suitable technologies to address limitations of conventional analytical methods. The main applications of biosensors include the detection of environmental pollutants, pathogenic bacteria and compounds related to illness, and food quality. Each type of microorganisms possesses advantages and disadvantages with different mechanisms to detect the analytes of interest. Furthermore, there is an increasing trend in genetic modifications for the development of microbial biosensors due to potential for high-throughput analysis and portability. Many review articles have discussed the applications of microbial biosensor, but many of them focusing only about bacterial-based biosensor although other microbes also possess many advantages. Additionally, reviews on the applications of all microbes as biosensor especially viral and microbial fuel cell biosensors are also still limited. Therefore, this review summarizes all the current applications of bacterial-, microalgal-, fungal-, viral-based biosensor in regard to environmental, food, and medical-related applications. The underlying mechanism of each microbes to detect the analytes are also discussed. Additionally, microbial fuel cell biosensors which have great potential in the future are also discussed. Although many advantageous microbial-based biosensors have been discovered, other areas such as forensic detection, early detection of bacteria or virus species that can lead to pandemics, and others still need further investigation. With that said, microbial-based biosensors have promising potential for vast applications where the biosensing performance of various microorganisms are presented in this review along with future perspectives to resolve problems related on microbial biosensors.

Transcription Factor-Based Biosensors for Detecting Pathogens

Microorganisms are omnipresent and inseparable from our life. Many of them are beneficial to humans, while some are not. Importantly, foods and beverages are susceptible to microbial contamination, with their toxins causing illnesses and even death in some cases. Therefore, monitoring and detecting harmful microorganisms are critical to ensuring human health and safety. For several decades, many methods have been developed to detect and monitor microorganisms and their toxicants. Conventionally, nucleic acid analysis and antibody-based analysis were used to detect pathogens. Additionally, diverse chromatographic methods were employed to detect toxins based on their chemical and structural properties. However, conventional techniques have several disadvantages concerning analysis time, sensitivity, and expense. With the advances in biotechnology, new approaches to detect pathogens and toxins have been reported to compensate for the disadvantages of conventional analysis from different research fields, including electrochemistry, nanotechnology, and molecular biology. Among them, we focused on the recent studies of transcription factor (TF)-based biosensors to detect microorganisms and discuss their perspectives and applications. Additionally, the other biosensors for detecting microorganisms reported in recent studies were also introduced in this review.

Enriching intracellular macrolides in Escherichia coli improved the sensitivity of bioluminescent sensing systems

A repressor protein MphR and an enhanced green fluorescent protein (eGFP) were used to construct a bioluminescent sensing system for macrolide analysis in Escherichia coli host cells. We deleted TolC, an efflux pump for macrolides in E. coli, to promote the intracellular accumulation of macrolides. The binding constant (K_1/2) of the sensing system constructed in an E. coli strain was decreased up to 33-fold with deleted TolC, and its sensitivity to the macrolides erythromycin, azithromycin, roxithromycin, and pikromycin was increased. The limit of detection of the bioluminescent sensing system for serum azithromycin was 4.1 nM. The ability to detect serum azithromycin concentrations was confirmed by analyzing photographs using ImageJ software. We also developed a novel sensing system for the immune suppressor FK506, another macrolide that is frequently prescribed. Deleting TolC also significantly improved the sensitivity of this sensing system. Bioluminescent sensing systems constructed in TolC mutants were sensitive to various macrolides, indicating their potential for clinical application with hand-held devices.

Design of Pb(II)-Specific E. coli-Based Biosensors by Engineering Regulatory Proteins and Host Cells

Bacterial cell-based biosensors have been widely developed for detecting environmental toxic materials. The znt-operon in Escherichia coli is a Zn(II)-responsive genetic system and is employed in Zn(II), Cd(II), and Hg(II)-sensing biosensors. In this study, point mutations were introduced in the regulatory protein ZntR to modulate its target selectivity, and metal ion-exporting genes, such as copA and zntA, in host cells were deleted to increase cellular metal ion levels and enhance specificity. Thus, the overall responses of the E. coli cell-based biosensors toward metal(loid) ions were increased, and their selectivity, which was originally for Cd(II) and Hg(II), was shifted to Pb(II). The gene encoding ZntA, known as the Zn(II)-translocating P-type ATPase, showed an impact on the ability of E. coli to export Pb(II), whereas copA deletion showed no significant impact. Noteworthily, the newly generated biosensors employing ZntR Cys115Ile showed the capacity to detect under 5 nM Pb(II) in solution, without response to other tested metal ions within 0–100 nM. To understand the marked effect of single point mutations on ZntR, computational modeling was employed. Although it did not provide clear answers, changes in the sequences of the metal-binding loops of ZntR modulated its transcriptional strength and target selectivity. In summary, the approaches proposed in this study can be valuable to generate new target-sensing biosensors with superior selectivity and specificity, which can in turn broaden the applicability of cell-based biosensors to monitor Pb(II) in environmental systems.

Development of Colorimetric Whole-Cell Biosensor for Detection of Heavy Metals in Environment for Public Health

Heavy metals cause various fetal diseases in humans. Heavy metals from factory wastewater can contaminate drinking water, fish, and crops. Inductively coupled plasma-mass spectrometry (ICP-MS) and atomic absorption spectrometry (AAS) are commonly used to analyze heavy metal contents; however, these methods require pre-treatment processes and are expensive and complex. To overcome these limitations, three metal-sensing materials using a whole-cell biosensor in Escherichia coli (E. coli) were developed. Strains were engineered to harbor three kinds of plasmids containing the copA, zntA, and mer promoters for sensing copper, cadmium, and mercury, respectively. The luciferase (lux) gene was inserted as a reporter into the plasmid, which was later replaced with a fused protein sequence containing OmpA (1–159) and mCherry for optical detection. The constructed strains could detect mercury, cadmium, and copper at 0.1–0.75 ppm, 0.2–0.75 ppm, and 2–7.5 ppm, respectively, with linearity values of 0.99030, 0.99676, and 0.95933, respectively. The immobilization linearity value was 0.99765. Notably, these three heavy metals could be detected by visual analysis of the strains. Overall, these findings establish this novel sensor as a potential approach for heavy metal detection in biological samples and foods.

Transport Across Two Membrane Bilayers in E. coli by Efflux Pumps of Different Dimensions

AcrAB-TolC and CusBAC are two of the most well-studied Resistance-Nodulation-Division (RND) family tripartite efflux pumps in E. coli. AcrAB-TolC is a multidrug efflux system, while CusBAC transports Cu(I), Cu(II) and Ag(I). The RND pump complexes span both the inner membrane (IM) and the outer membrane (OM). The long axis dimension of the fully assembled AcrAB-TolC is ∼3 nm longer than that of CusBAC. To probe if these two efflux systems with different dimensions affect each other when they need to work simultaneously in the same cell, two real-time assays were used to monitor the efflux activities of these two pumps and their impact on each other. The results showed that the presence of AcrAB-TolC substrates accelerated the accumulation of Cu(I) in BW25113 but not in BW25113ΔcusBA or BW25113ΔtolC strains. Similarly, the presence of Ag(I) slowed down the Nile red efflux in the parent strain more significantly than in the CusBA deficient mutant. To further investigate the impact of the OM/IM distance on the function of these tripartite complexes, we experimented with strains lacking the lipoprotein Lpp or containing Lpp mutant of different lengths. Data from efflux/accumulation assays and susceptibility tests revealed that mutation of Lpp resulted in functional deficiency of both AcrAB-TolC and CusBAC. In conclusion, this study demonstrated that when AcrAB-TolC and CusBAC functioned simultaneously, it took the cell a few minutes to adjust. Furthermore, the presence of Lpp of proper length is important to support full efflux activity of transporters spanning both membrane layers in E. coli.

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.

Electronic signals are electrogenetically relayed to control cell growth and co-culture composition

There is much to be gained by enabling electronic interrogation and control of biological function. While the benefits of bioelectronics that rely on potential-driven ionic flows are well known (electrocardiograms, defibrillators, neural prostheses, etc) there are relatively few advances targeting nonionic molecular networks, including genetic circuits. Redox activities combine connectivity to electronics with the potential for specific genetic control in cells. Here, electrode-generated hydrogen peroxide is used to actuate an electrogenetic "relay" cell population, which interprets the redox cue and synthesizes a bacterial signaling molecule (quorum sensing autoinducer AI-1) that, in turn, signals increased growth rate in a second population. The dramatically increased growth rate of the second population is enabled by expression of a phosphotransferase system protein, HPr, which is important for glucose transport. The potential to electronically modulate cell growth via direct genetic control will enable new opportunities in the treatment of disease and manufacture of biological therapeutics and other molecules.

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.

Sensitive and Specific Cadmium Biosensor Developed by Reconfiguring Metal Transport and Leveraging Natural Gene Repositories

Whole-cell biosensors are useful for monitoring heavy metal toxicity in public health and ecosystems, but their development has been hindered by intrinsic trade-offs between sensitivity and specificity. Here, we demonstrated an effective engineering solution by building a sensitive, specific, and high-response biosensor for carcinogenic cadmium ions. We genetically programmed the metal transport system of Escherichia coli to enrich intracellular cadmium ions and deprive interfering metal species. We then selected 16 cadmium-sensing transcription factors from the GenBank database and tested their reactivity to 14 metal ions in the engineered E. coli using the expression of the green fluorescent protein as the readout. The resulting cadmium biosensor was highly specific and showed a detection limit of 3 nM, a linear increase in fluorescent intensities from 0 to 200 nM, and a maximal 777-fold signal change. Using this whole-cell biosensor, a smartphone, and low-tech equipment, we developed a simple assay capable of measuring cadmium ions at the same concentration range in irrigation water and human urine. This method is user-friendly and cost-effective, making it affordable to screen large amounts of samples for cadmium toxicity in agriculture and medicine. Moreover, our work highlights natural gene repositories as a treasure chest for bioengineering.

Potential Whole-Cell Biosensors for Detection of Metal Using MerR Family Proteins from Enterobacter sp. YSU and Stenotrophomonas maltophilia OR02

Cell-based biosensors harness a cell's ability to respond to the environment by repurposing its sensing mechanisms. MerR family proteins are activator/repressor switches that regulate the expression of bacterial metal resistance genes and have been used in metal biosensors. Upon metal binding, a conformational change switches gene expression from off to on. The genomes of the multimetal resistant bacterial strains, Stenotrophomonas maltophilia Oak Ridge strain 02 (S. maltophilia 02) and Enterobacter sp. YSU, were recently sequenced. Sequence analysis and gene cloning identified three mercury resistance operons and three MerR switches in these strains. Transposon mutagenesis and sequence analysis identified Enterobacter sp. YSU zinc and copper resistance operons, which appear to be regulated by the protein switches, ZntR and CueR, respectively. Sequence analysis and reverse transcriptase polymerase chain reaction (RT-PCR) showed that a CueR switch appears to activate a S. maltophilia 02 copper transport gene in the presence of CuSO₄ and HAuCl₄·3H₂O. In previous studies, genetic engineering replaced metal resistance genes with the reporter genes for β-galactosidase, luciferase or the green fluorescence protein (GFP). These produce a color change of a reagent, produce light, or fluoresce in the presence of ultraviolet (UV) light, respectively. Coupling these discovered operons with reporter genes has the potential to create whole-cell biosensors for HgCl₂, ZnCl₂, CuSO₄ and HAuCl₄·3H₂O.

A copper-specific microbial fuel cell biosensor based on riboflavin biosynthesis of engineered Escherichia coli

Copper pollution poses a serious threat to the aquatic environment; however, in situ analytical methods for copper monitoring are still scarce. In the current study, Escherichia coli Rosetta was genetically modified to express OprF and ribB with promoter P_t7 and P_cusC , respectively, which could synthesize porin and senses Cu²⁺ to produce riboflavin. The cell membrane permeability of this engineered strain was increased and its riboflavin production (1.45-3.56 μM) was positively correlated to Cu²⁺ (0-0.5 mM). The biosynthetic strain was then employed in microbial fuel cell (MFC) based biosensor. Under optimal operating parameters of pH 7.1 and 37°C, the maximum voltage (248, 295, 333, 352, and 407 mV) of the constructed MFC biosensor showed a linear correlation with Cu²⁺ concentration (0.1, 0.2, 0.3, 0.4, 0.5 mM, respectively; R²  = 0.977). The continuous mode testing demonstrated that the MFC biosensor specifically senses Cu²⁺ with calculated detection limit of 28 μM, which conforms to the common Cu²⁺ safety standard (32 μM). The results obtained with the developed biosensor system were consistent with the existing analytical methods such as colorimetry, flame atomic absorption spectrometry, and inductively coupled plasma optical emission spectrometry. In conclusion, this MFC-based biosensor overcomes the signal conversion and transmission problems of conventional approaches, providing a fast and economic analytical alternative for in situ monitoring of Cu²⁺ in water.

Modulation of the Metal(loid) Specificity of Whole-Cell Bioreporters by Genetic Engineering of ZntR Metal-Binding Loops

Bacterial cell-based biosensors, or whole-cell bioreporters (WCBs), are an alternative tool for the quantification of hazardous materials. Most WCBs share similar working mechanisms. In brief, the recognition of a target by sensing domains induces a biological event, such as changes in protein conformation or gene expression, providing a basis for quantification. WCBs targeting heavy metal(loid)s employ metalloregulators as sensing domains and control the expression of genes in the presence of target metal(loid) ions, but the diversity of targets, specificity, and sensitivity of these WCBs are limited. In this study, we genetically engineered the metal-binding loop (MBL) of ZntR, which controls the znt-operon in Escherichia coli. In the MBL of ZntR, three Cys sites interact with metal ions. Based on the crystal structure of ZntR, MBL sequences were modified by sitedirected mutagenesis. As a result, the metal-sensing properties of WCBs differed depending on amino acid sequences and the new selectivity to Cr or Pb was observed. Although there is room for improvement, our results support the use of currently available WCBs as a platform to generate new WCBs to target other environmental pollutants including metal(loid)s.

Genetic Engineering-Facilitated Coassembly of Synthetic Bacterial Cells and Magnetic Nanoparticles for Efficient Heavy Metal Removal

Heavy-metal pollution is becoming a worldwide problem severely threatening our health and ecosystem. In this study, we constructed a genetic-engineering-driven coassembly of synthetic bacterial cells and magnetic nanoparticles (MNPs) for capturing heavy metals. The Escherichia coli cells were genetically engineered by introducing a de novo synthetic heavy-metal-capturing gene (encoding a protein SynHMB containing a six-histidine tag, two cystine-rich peptides, and a metallothionein sequence) and a synthetic type VI secretory system (T6SS) cluster of Pseudomonas putida, endowing the synthetic cells (SynEc2) with high ability of displaying the heavy-metal-capturing SynHMB on cell surface. MNPs were synthesized by a coprecipitation method and further modified by polyethylenimine (PEI) and diethylenetriaminepentaacetic acid (DTPA). Owing to the surface exposure of six-histidine tag on the synthetic bacteria and carboxyl groups on the modified MNPs (MNP@SiO₂-PEI-DTPA), the synthetic bacterial cells and MNPs coassembled to form biotic/abiotic complex exhibiting a self-developing characteristic. In the culture medium containing both Cd²⁺ and Pb²⁺, the coassemblies captured these heavy metals with high removal efficiency (>90% even at 50 mg/L of Cd²⁺ and 50 mg/L of Pb²⁺) and were conveniently recycled by artificial magnetic fields. Moreover, the coassemblies realized coremoval of organic carbon pollutants with the removal efficiency of >80%. This study builds a novel biotic/abiotic coassembling platform facilitated by genetic engineering and sheds light on development of artificial magnetic biological systems for efficient treatment of environmental pollution.

Development of a Sensitive Escherichia coli Bioreporter Without Antibiotic Markers for Detecting Bioavailable Copper in Water Environments

The whole-cell bioreporters based on the cop-operon sensing elements have been proven specifically useful in the assessment of bioavailable copper ions in water environments. In this study, a series of experiments was conducted to further improve the sensitivity and robustness of bioreporters. First, an Escherichia coli △copA△cueO△cusA mutant with three copper transport genes knocked out was constructed. Then, the copAp::gfpmut2 sensing element was inserted into the chromosome of E. coli △copA△cueO△cusA by gene knock-in method to obtain the bioreporter strain E. coli WMC-007. In optimized assay conditions, the linear detection range of Cu²⁺ was 0.025–5 mg/L (0.39–78.68 μM) after incubating E. coli WMC-007 in Luria–Bertani medium for 5 h. The limit of detection of Cu²⁺ was 0.0157 mg/L (0.25 μM). Moreover, fluorescence spectrometry and flow cytometry experiments showed more environmental robustness and lower background fluorescence signal than those of the sensor element based on plasmids. In addition, we found that the expression of GFPmut2 in E. coli WMC-007 was induced by free copper ions, rather than complex-bound copper, in a dose-dependent manner. Particularly, the addition of 40 mM 3-(N-Morpholino)propanesulfonic acid buffer to E. coli WMC-007 culture enabled accurate quantification of bioavailable copper content in aqueous solution samples within a pH range from 0.87 to 12.84. The copper recovery rate was about 95.88–113.40%. These results demonstrate potential applications of E. coli WMC-007 as a bioreporter to monitor copper contamination in acidic mine drainage, industrial wastewater, and drinking water. Since whole-cell bioreporters are relatively inexpensive and easy to operate, the combination of this method with other physicochemical techniques will in turn provide more specific information on the degree of toxicity in water environments.

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.

Specific heavy metal/metalloid sensors: current state and perspectives

Heavy metal(loid)s play pivotal roles in regulating physiological and developmental aspects in living organisms depending on their concentration. For example, a trace amount of heavy metal(loid)s is essential for living organisms, but heavy metal(loid)s in high concentrations negatively affect their physiology and development. Because of rapid industrial developments, heavy metal(loid)s have been accumulating in environmental systems, thereby becoming a threat to human health and the earth's ecosystem. Thus, the development of tools to quantify and monitor heavy metal(loid)s in environmental systems has become essential. Typically, risk has been determined through instrument-based analysis, regardless of the shortcomings regarding expense and duration. Nowadays, the need for alternative tools, besides instrumental analysis, to detect heavy metals has prompted the development of new techniques, and many different methods have been reported from various research areas, including new techniques based on electrochemistry and biological systems. Nonetheless, it seems that the gap between laboratory and fieldwork is still greater than it should be when it comes to applying these systems. In this mini-review, we discuss the current status of heavy metals/metalloid detection techniques, with an emphasis on biosensors. Moreover, we discuss the advantages and disadvantages as well as the mechanisms behind newly developed sensors and make suggestions to improve applicability and to develop new objective targeting sensors. Although many different types of metal(loid) sensors are available, we focused on metal sensors based on biological systems. Additionally, we suggest potent approaches to developing new biosensor systems based on current metal sensor mechanisms.

Original sequence divergence among Pseudomonas putida CadRs drive specificity

Bacteria, especially those living in soils, are in constant contact with metals. Transition metals like Fe or Zn, are required for proper growth. Some other metals like Cd or Hg are only toxic. Several systems exist to detoxify cells when these metals are present in concentrations harmful to biological systems. The expression of these systems is under control of specialized regulatory proteins able to detect metals and to regulate cognate detoxifying systems. In this work we report on the characterisation of the metallo-regulator CadR from Pseudomonas putida KT2440. By using gene reporter assays, we investigated the repertoire of metals detected by CadR. We show that CadR is much more responsive to Hg than to Cd, as compared to CadR from P. putida 06909. CadR from P. putida KT2440 differs in only 3 amino-acids in its metal-binding domain with respect to CadR from P. putida 06909. We show that these residues are important determinants of metal selectivity by engineering a modified CadR.

Biodetection and bioremediation of copper ions in environmental water samples using a temperature-controlled, dual-functional Escherichia coli cell

Although a variety of whole-cell biosensors and biosorbents have been developed for detection and removal of heavy metal contaminants, few whole cells can be applied to both monitoring and remediation of copper pollution in water. In this study, a modified plasmid was constructed by incorporating a copper-sensing element and a copper-adsorbing element into a temperature-inducible plasmid, pBV220. This plasmid was subsequently transformed into an engineered Escherichia coli strain lacking copA and cueO. This dual-functional E. coli cell selectively responded to copper ions with a linear detection range of 0.01-25 μM at 37 °C and could express surface-displayed CueR when treated at 42 °C without any costly chemical inducers. The display of CueR on the cell surface specifically enhanced its copper adsorption capacity and rapidly removed copper ions from aqueous solutions. In addition, the CueR surface-displayed cells could be regenerated by adsorption-desorption cycles via pH regulation. Moreover, by simply using two different temperatures, the detection or adsorption of copper using this dual-functional whole cell was achieved without any cross-interference. Most importantly, it provided highly sensitive, accurate quantification, and effective removal of copper in real environmental water samples. Thus, this E. coli cell can be used for large-scale detection and remediation of copper pollutants.

Development of a Cell-Free Optical Biosensor for Detection of a Broad Range of Mercury Contaminants in Water: A Plasmid DNA-Based Approach

Mercury (Hg) is one of the main water contaminants worldwide. In this study, we have developed both whole-cell and cell-free biosensors to detect Hg. Genetically modified plasmids containing the merR gene were used to design biosensors. Firefly luciferase (LucFF) and emerald green fluorescent protein (EmGFP) genes were separately introduced as a reporter. Both constructs showed a detection limit of 1 ppb (Hg) in Escherichia coli and the cell-free system. We found that higher concentrations of Hg become detrimental to bacteria. This cytotoxic effect shows an anomalous result in high Hg concentrations. This was also observed in the cell-free system. We found that EmGFP fluorescence was decreased in the cell-free system because of a change in pH and quenching effect by Hg excess. Once the pH was adjusted to 7 and a chelating agent was used, the EmGFP fluorescence was partially restored. These adjustments can only be done in the cell-free system after the GFP expression and not in whole cells where their number has been decreased because of toxicity. Therefore, we suggest the use of the cell-free-system, which not only reduces the total experimental time but also allows us to perform these postexperimental adjustments to achieve higher sensitivity. We would also recommend to perform more measurements at a time with different dilution factors to bring down the Hg concentration within the measurable limits or to use some other chelating agents which can further reduce the excess Hg concentration.

Heavy metal(loid) biosensor based on split-enhanced green fluorescent protein: development and characterization

Heavy metal(loid)s such as Cd and Hg adversely affect human health and are therefore strictly regulated and monitored; however, their quantitation in the environment is usually performed by expensive and time-consuming instrumental analysis techniques, which necessitates the search for more practical alternatives. Herein, we prepare enhanced green fluorescent protein (eGFP)-based biomolecules for metal(loid) sensing by insertion of metal-binding loops (MBLs) into a loop region of eGFP to render this protein inactive and show that the binding of metal ions to MBLs induces a conformational change and restores the original activity. Specifically, eGFP with an MBL sequenced as CTTCGCG regains fluorescence upon exposure to Cd and Hg, which allows the above metals to be quantified in the concentration range of 0-5 μM. For practical applicability verification, the developed sensing platform is used to quantify Cd in artificially amended soil and water samples. Although the obtained results imply that sensor performance needs to be significantly improved, the presented design concept is believed to be of high value to researchers in the field of heavy metal sensing and facilitate the development of new biosensors.

Redox-Based Synthetic Biology Enables Electrochemical Detection of the Herbicides Dicamba and Roundup via Rewired Escherichia coli

Synthetic biology is typically exploited to endow bacterial cells with new biosynthetic capabilities. It can also serve to create "smart" bacteria such as probiotics that detect and treat disease. Here, we show how minimally rewiring the genetic regulation of bacterial cells can enable their ability to recognize and report on chemical herbicides, including those routinely used to clear weeds from gardens and crops. In so doing, we demonstrate how constructs of synthetic biology, in this case redox-based synthetic biology, can serve as a vector for information flow mediating molecular communication between biochemical systems and microelectronics. We coupled the common genetic reporter, β-galactosidase, with the E. coli superoxide response regulon promoter pSoxS, for detection of the herbicides dicamba and Roundup. Both herbicides activated our genetic construct in a concentration dependent manner. Results indicate robust detection using spectrophotometry, via the Miller assay, and electrochemistry using the enzymatic cleavage of 4-aminophenyl β-d-galactopyranoside into the redox active molecule p-aminophenol. We found that environmental components, in particular, the availability of glucose, are important factors for the cellular detection of dicamba. Importantly, both herbicides were detected at concentrations relevant for aquatic toxicity.

A Biosensor Platform for Metal Detection Based on Enhanced Green Fluorescent Protein

Microbial cell-based biosensors, which mostly rely on stress-responsive operons, have been widely developed to monitor environmental pollutants. Biosensors are usually more convenient and inexpensive than traditional instrumental analyses of environmental pollutants. However, the targets of biosensors are restricted by the limited number of genetic operon systems available. In this study, we demonstrated a novel strategy to overcome this limitation by engineering an enhanced green fluorescent protein (eGFP). It has been reported that combining two fragments of split-eGFP can form a native structure. Thus, we engineered new biosensors by inserting metal-binding loops (MBLs) between β-strands 9 and 10 of the eGFP, which then undergoes conformational changes upon interaction between the MBLs and targets, thereby emitting fluorescence. The two designed MLBs based on our previous study were employed as linkers between two fragments of eGFP. As a result, an Escherichia coli biosensor exhibited a fluorescent signal only when interacting with cadmium ions, revealing the prospect of a new biosensor for cadmium detection. Although this study is a starting stage for further developing biosensors, we believe that the proposed strategy can serve as basis to develop new biosensors to target various environmental pollutants.

Engineering and characterization of copper and gold sensors in Escherichia coli and Synechococcus sp. PCC 7002

The anthropogenic release of toxic metals into the environment poses danger to the health of both humans and the local ecosystem. Biosensors for the detection of metals have been developed to improve our ability to monitor these environmental contaminants, yet most of these sensors use heterotrophic bacterial hosts, which require a fixed carbon source and do not typically grow in natural waterways. In this study, we constructed and characterized metal sensors for development of a photoautotrophic biosensor using Synechococcus sp. PCC 7002. We characterized gold and copper sensors based on modified MerR transcriptional activators: GolS^A113T, with improved gold binding, and GolSCL, containing the metal-binding loop from CueR which binds both gold and copper. The metal-sensing constructs were first optimized and characterized in Escherichia coli MG1655. The addition of a strong ribosome binding site to the optical reporter protein increased translation of the fluorescent reporter, and expression of golS^A113T from the rbc promoter of Synechococcus sp. PCC 7002 improved the response to gold in MG1655. In rich medium, the GolS^A113T-based E. coli sensor detected gold at concentrations as low as 100 nM, while the GolSCL-based E. coli sensor detected gold and copper at sensitivities of 100 nM and 10 μM, respectively. Both E. coli sensors responded to gold and copper yet showed no detectable response to other metals. Abiotic factors, such as medium complexity, were found to influence the response of the E. coli sensors, with minimal medium resulting in higher sensitivities of detection. Expression of the GolS^A113T- and GolSCL-based sensor constructs in the cyanobacterium Synechococcus sp. PCC 7002 resulted in photoautotrophic gold sensors, but these biosensors failed to produce a significant response to copper. Moreover, the fluorescence response of the cyanobacterial sensors to gold was significantly reduced compared to that of analogous E. coli sensors. While this effort demonstrates feasibility for the development of photoautotrophic biosensors, additional efforts to optimize sensor performance will be required.