Analytical strategies for improving the robustness and reproducibility of bioluminescent microbial bioreporters

Novel yeast-based biosensor for environmental monitoring of tebuconazole

Due to increasing demand for high and stable crop production, human populations are highly dependent on pesticide use for growing and storing food. Environmental monitoring of these agrochemicals is therefore of utmost importance, because of their collateral effects on ecosystem and human health. Even though most current-use analytical methods achieve low detection limits, they require procedures that are too complex and costly for routine monitoring. As such, there has been an increased interest in biosensors as alternative or complementary tools to streamline detection and quantification of environmental contaminants. In this work, we developed a biosensor for environmental monitoring of tebuconazole (TEB), a common agrochemical fungicide. For that purpose, we engineered S. cerevisiae cells with a reporter gene downstream of specific promoters that are expressed after exposure to TEB and characterized the sensitivity and specificity of this model system. After optimization, we found that this easy-to-use biosensor consistently detects TEB at concentrations above 5 μg L-1 and does not respond to realistic environmental concentrations of other tested azoles, suggesting it is specific. We propose the use of this system as a complementary tool in environmental monitoring programs, namely, in high throughput scenarios requiring screening of numerous samples. KEY POINTS: • A yeast-based biosensor was developed for environmental monitoring of tebuconazole. •The biosensor offers a rapid and easy method for tebuconazole detection ≥ 5 μg L-1. •The biosensor is specific to tebuconazole at environmentally relevant concentrations.

Current advances in the use of bioluminescence assays for drug discovery: an update of the last ten years

INTRODUCTION

Bioluminescence is a well-established optical detection technique widely used in several bioanalytical applications, including high-throughput and high-content screenings. Thanks to advances in synthetic biology techniques and deep learning, a wide portfolio of luciferases is now available with tuned emission wavelengths, kinetics, and high stability. These luciferases can be implemented in the drug discovery and development pipeline, allowing high sensitivity and multiplexing capability.

AREAS COVERED

This review summarizes the latest advancements of bioluminescent systems as toolsets in drug discovery programs for in vitro applications. Particular attention is paid to the most advanced bioluminescence-based technologies for drug screening over the past 10 years (from 2013 to 2023) such as cell-free assays, cell-based assays based on genetically modified cells, bioluminescence resonance energy transfer, and protein complementation assays in 2D and 3D cell models.

EXPERT OPINION

The availability of tuned bioluminescent proteins with improved emission and stability properties is vital for the development of bioluminescence assays for drug discovery, spanning from reporter gene technology to protein-protein techniques. Further studies, combining machine learning with synthetic biology, will be necessary to obtain new tools for sustainable and highly predictive bioluminescent drug discovery platforms.

Biological and technical challenges for implementation of yeast-based biosensors

Biosensors are low-cost and low-maintenance alternatives to conventional analytical techniques for biomedical, industrial and environmental applications. Biosensors based on whole microorganisms can be genetically engineered to attain high sensitivity and specificity for the detection of selected analytes. While bacteria-based biosensors have been extensively reported, there is a recent interest in yeast-based biosensors, combining the microbial with the eukaryotic advantages, including possession of specific receptors, stability and high robustness. Here, we describe recently reported yeast-based biosensors highlighting their biological and technical features together with their status of development, that is, laboratory or prototype. Notably, most yeast-based biosensors are still in the early developmental stage, with only a few prototypes tested for real applications. Open challenges, including systematic use of advanced molecular and biotechnological tools, bioprospecting, and implementation of yeast-based biosensors in electrochemical setup, are discussed to find possible solutions for overcoming bottlenecks and promote real-world application of yeast-based biosensors.

A Luciferase Mutant with Improved Brightness and Stability for Whole-Cell Bioluminescent Biosensors and In Vitro Biosensing

The availability of new bioluminescent proteins with tuned properties, both in terms of emission wavelength, kinetics and protein stability, is highly valuable in the bioanalytical field, with the potential to improve the sensitivity and analytical performance of the currently used methods for ATP detection, whole-cell biosensors, and viability assays among others. We present a new luciferase mutant, called BgLuc, suitable for developing whole-cell biosensors and in vitro biosensors characterized by a bioluminescence maximum of 548 nm, narrow emission bandwidth, favorable kinetic properties, and excellent pH- and thermo-stabilities at 37 and 45 °C and pH from 5.0 to 8.0. We assessed the suitability of this new luciferase for whole-cell biosensing with a cell-based bioreporter assay for Nuclear Factor-kappa B (NF-kB) signal transduction pathway using 2D and 3D human embryonic kidney (HEK293T) cells, and for ATP detection with the purified enzyme. In both cases the luciferase showed suitable for sensitive detection of the target analytes, with better or similar performance than the commercial counterparts.

Engineering Saccharomyces cerevisiae-based biosensors for copper detection

Heavy metals, that is Cu(II), are harmful to the environment. There is an increasing demand to develop inexpensive detection methods for heavy metals. Here, we developed a yeast biosensor with reduced‐noise and improved signal output for potential on‐site copper ion detection. The copper‐sensing circuit was achieved by employing a secondary genetic layer to control the galactose‐inducible (GAL) system in Saccharomyces cerevisiae. The reciprocal control of the Gal4 activator and Gal80 repressor under copper‐responsive promoters resulted in a low‐noise and sensitive yeast biosensor for copper ion detection. Furthermore, we developed a betaxanthin‐based colorimetric assay, as well as 2‐phenylethanol and styrene‐based olfactory outputs for the copper ion detection. Notably, our engineered yeast sensor confers a narrow range switch‐like behaviour, which can give a ‘yes/no’ response when coupled with a betaxanthin‐based visual phenotype. Taken together, we envision that the design principle established here might be applicable to develop other sensing systems for various chemical detections.

A low‐noise yeast biosensor was developed for copper detection. The yeast biosensor confers a switch‐like behavior with a “yes/no” response. The olfactory outputs for copper detection were also developed.

Orthogonal paper biosensor for mercury(II) combining bioluminescence and colorimetric smartphone detection

Mercury contamination in the environment has reached alarming levels. Due to its persistence and bioaccumulation, mercury is one of the most widespread toxic heavy metals found in air, water and food. Thus, it is mandatory to monitor mercury and its compounds, and the availability of sensitive and rapid biosensors is highly valuable. We developed a low-cost biosensor for orthogonal detection of mercury(II) integrating three different biorecognition principles on a three-leaf paper: i) a mercury-specific bioluminescent Escherichia coli bioreporter strain expressing NanoLuc luciferase as reporter protein, ii) a purified β-galactosidase (β-gal) enzyme which is irreversibly inhibited by mercury and other metal ions, and iii) an Aliivibrio fischeri bioluminescent strain which is used to quantitatively assess sample toxicity and correct the analytical signal accordingly. Both sensory elements and substrates, Furimazine for the bioluminescent reporter strain and chlorophenol red-β-D-galactopyranoside for colorimetric detection of β-gal, were integrated in the paper sensor to provide a stable all-in-one disposable cartridge which can be easily snapped into a smartphone with a clover-shaped 3D printed housing. This is the first integration of bioluminescence and colorimetric detection on a smartphone-paper sensor, providing a readout within 15 and 60 min for the colorimetric and bioluminescent detection respectively. The biosensor was applied to water samples spiked with different concentrations of mercury, interferents and toxic chemicals providing a limit of detection for Hg(II) at the ppb levels.

Repetitive Detection of Aromatic Hydrocarbon Contaminants with Bioluminescent Bioreporters Attached on Tapered Optical Fiber Elements

In this study, we show the repetitive detection of toluene on a tapered optical fiber element (OFE) with an attached layer of Pseudomonas putida TVA8 bioluminescent bioreporters. The bioluminescent cell layer was attached on polished quartz modified with (3-aminopropyl)triethoxysilane (APTES). The repeatability of the preparation of the optical probe and its use was demonstrated with five differently shaped OFEs. The intensity of measured bioluminescence was minimally influenced by the OFE shape, possessing transmittances between 1.41% and 5.00%. OFE probes layered with P. putida TVA8 were used to monitor liquid toluene over a two-week period. It was demonstrated that OFE probes layered with positively induced P. putida TVA8 bioreporters were reliable detectors of toluene. A toluene concentration of 26.5 mg/L was detected after <30 min after immersion of the probe in the toluene solution. Additional experiments also immobilized constitutively bioluminescent cells of E. coli 652T7, on OFEs with polyethyleneimine (PEI). These OFEs were repetitively induced with Lauria-Bertani (LB) nutrient medium. Bioluminescence appeared 15 minutes after immersion of the OFE in LB. A change in pH from 7 to 6 resulted in a decrease in bioluminescence that was not restored following additional nutrient inductions at pH 7. The E. coli 652T7 OFE probe was therefore sensitive to negative influences but could not be repetitively used.

Yeast-Based Biosensors: Current Applications and New Developments

Biosensors are regarded as a powerful tool to detect and monitor environmental contaminants, toxins, and, more generally, organic or chemical markers of potential threats to human health. They are basically composed of a sensor part made up of either live cells or biological active molecules coupled to a transducer/reporter technological element. Whole-cells biosensors may be based on animal tissues, bacteria, or eukaryotic microorganisms such as yeasts and microalgae. Although very resistant to adverse environmental conditions, yeasts can sense and respond to a wide variety of stimuli. As eukaryotes, they also constitute excellent cellular models to detect chemicals and organic contaminants that are harmful to animals. For these reasons, combined with their ease of culture and genetic modification, yeasts have been commonly used as biological elements of biosensors since the 1970s. This review aims first at giving a survey on the different types of yeast-based biosensors developed for the environmental and medical domains. We then present the technological developments currently undertaken by academic and corporate scientists to further drive yeasts biosensors into a new era where the biological element is optimized in a tailor-made fashion by in silico design and where the output signals can be recorded or followed on a smartphone.

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.

Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments

Metatranscriptomics, a subset of metagenomics, provides valuable information about the whole gene expression profiling of complex microbial communities of an ecosystem. Metagenomic studies mainly focus on the genomic content and identification of microbes present within a community, while metatranscriptomics provides the diversity of the active genes within such community, their expression profile and how these levels change due to change in environmental conditions. Metatranscriptomics has been applied to different types of environments, from the study of human microbiomes, to those found in plants, animals, within soils and in aquatic systems. Metatranscriptomics, based on the utilization of mRNA isolated from environmental samples, is a suitable approach to mine the eukaryotic gene pool for genes of biotechnological relevance. Also, it is imperative to develop different bioinformatic pipelines to analyse the data obtained from metatranscriptomic analysis. In the present review, we summarise the metatranscriptomics applied to soil environments to study the functional diversity, and discuss approaches for isolating the genes involved in organic matter degradation and providing tolerance to toxic metals, role of metatranscriptomics in microbiome research, various bioinformatics pipelines used in data analysis and technical challenges for gaining biologically meaningful insight of this approach.

Luciferase Genes as Reporter Reactions: How to Use Them in Molecular Biology?

: The latest advances in molecular biology have made available several biotechnological tools that take advantage of the high detectability and quantum efficiency of bioluminescence (BL), with an ever-increasing number of novel applications in environmental, pharmaceutical, food, and forensic fields. Indeed, BL proteins are being used to develop ultrasensitive binding assays and cell-based assays, thanks to their high detectability and to the availability of highly sensitive BL instruments. The appealing aspect of molecular biology tools relying on BL reactions is their general applicability in both in vitro assays, such as cell cultures or purified proteins, and in vivo settings, such as in whole-animal BL imaging. The aim of this chapter is to provide the reader with an overview of state-of-the-art bioluminescent tools based on luciferase genes, highlighting molecular biology strategies that have been applied so far, together with some selected examples.

Simultaneous detection of bioavailable arsenic and cadmium in contaminated soils using dual-sensing bioreporters

Whole-cell bioreporters (WCBs) have attracted increasing attention during the last few decades because they allow fast determination of bioavailable heavy metals in contaminated sites. Various WCBs to monitor specific heavy metals such as arsenic and cadmium in diverse environmental systems are available. However, currently, no study on simultaneous analysis of arsenic and cadmium has been reported, even though soils are contaminated by diverse heavy metals and metalloids. We demonstrated herein the development of dual-sensing WCBs to simultaneously quantify bioavailable arsenic and cadmium in contaminated sites by employing the promoter regions of the ars and znt operons as separate metal-sensing domains, and egfp and mcherry as reporter genes. The dual-sensing WCBs were generated by inserting two sets of genes into E. coli DH5α. The capability of WCBs was successfully proved to simultaneously quantify bioavailable arsenic and cadmium in amended Landwirtschaftliche Untersuchungs und Forschungsanstalt (LUFA) soils, and then, it was applied to contaminated field soils collected from a smelter area in Korea. As a result, it was noticed that the bioavailable portion of cadmium was higher than that of arsenic while the absolute amount of bioavailable arsenic and cadmium level was opposite. Since both cadmium and arsenic were assessed from the same E. coli cells, the data obtained by using dual-sensing WCBs would be more efficient and convenient than that from comparative WCB assay. In spite of advantageous aspects, to our knowledge, this is the first report on a dual-sensing WCB for rapid and concurrent quantification of bioavailable arsenic and cadmium in contaminated soils.

Defining an additivity framework for mixture research in inducible whole-cell biosensors

A novel additivity framework for mixture effect modelling in the context of whole cell inducible biosensors has been mathematically developed and implemented in R. The proposed method is a multivariate extension of the effective dose (ED_p) concept. Specifically, the extension accounts for differential maximal effects among analytes and response inhibition beyond the maximum permissive concentrations. This allows a multivariate extension of Loewe additivity, enabling direct application in a biphasic dose-response framework. The proposed additivity definition was validated, and its applicability illustrated by studying the response of the cyanobacterial biosensor Synechococcus elongatus PCC 7942 pBG2120 to binary mixtures of Zn, Cu, Cd, Ag, Co and Hg. The novel method allowed by the first time to model complete dose-response profiles of an inducible whole cell biosensor to mixtures. In addition, the approach also allowed identification and quantification of departures from additivity (interactions) among analytes. The biosensor was found to respond in a near additive way to heavy metal mixtures except when Hg, Co and Ag were present, in which case strong interactions occurred. The method is a useful contribution for the whole cell biosensors discipline and related areas allowing to perform appropriate assessment of mixture effects in non-monotonic dose-response frameworks

Genetically engineered microorganisms for the detection of explosives' residues

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

Heavy metal whole-cell biosensors using eukaryotic microorganisms: an updated critical review

This review analyzes the advantages and disadvantages of using eukaryotic microorganisms to design whole-cell biosensors (WCBs) for monitoring environmental heavy metal pollution in soil or aquatic habitats. Basic considerations for designing a eukaryotic WCB are also shown. A comparative analysis of the promoter genes used to design WCBs is carried out, and the sensitivity and reproducibility of the main reporter genes used is also reviewed. Three main eukaryotic taxonomic groups are considered: yeasts, microalgae, and ciliated protozoa. Models that have been widely analyzed as potential WCBs are the Saccharomyces cerevisiae model among yeasts, the Tetrahymena thermophila model for ciliates and Chlamydomonas model for microalgae. The advantages and disadvantages of each microbial group are discussed, and a ranking of sensitivity to the same type of metal pollutant from reported eukaryotic WCBs is also shown. General conclusions and possible future developments of eukaryotic WCBs are reported.

Evaluation of the ecotoxicity of pollutants with bioluminescent microorganisms

This chapter deals with the use of bioluminescent microorganisms in environmental monitoring, particularly in the assessment of the ecotoxicity of pollutants. Toxicity bioassays based on bioluminescent microorganisms are an interesting complement to classical toxicity assays, providing easiness of use, rapid response, mass production, and cost effectiveness. A description of the characteristics and main environmental applications in ecotoxicity testing of naturally bioluminescent microorganisms, covering bacteria and eukaryotes such as fungi and dinoglagellates, is reported in this chapter. The main features and applications of a wide variety of recombinant bioluminescent microorganisms, both prokaryotic and eukaryotic, are also summarized and critically considered. Quantitative structure-activity relationship models and hormesis are two important concepts in ecotoxicology; bioluminescent microorganisms have played a pivotal role in their development. As pollutants usually occur in complex mixtures in the environment, the use of both natural and recombinant bioluminescent microorganisms to assess mixture toxicity has been discussed. The main information has been summarized in tables, allowing quick consultation of the variety of luminescent organisms, bioluminescence gene systems, commercially available bioluminescent tests, environmental applications, and relevant references.

Bioengineered bioluminescent magnetotactic bacteria as a powerful tool for chip-based whole-cell biosensors

This paper describes the generation of genetically engineered bioluminescent magnetotactic bacteria (BL-MTB) and their integration into a microfluidic analytical device to create a portable toxicity detection system. Magnetospirillum gryphiswaldense strain MSR-1 was bioengineered to constitutively express a red-emitting click beetle luciferase whose bioluminescent signal is directly proportional to bacterial viability. The magnetic properties of these bacteria have been exploited as "natural actuators" to transfer the cells in the chip from the reaction to the detection area, optimizing the chip's analytical performance. A robust and cost-effective biosensor for the evaluation of sample toxicity, named MAGNETOX, based on lens-free contact imaging detection, has been developed. A microfluidic chip has been fabricated using multilayered black and transparent polydimethyl siloxane (PDMS) in which BL-MTB are incubated for 30 min with the sample, then moved by microfluidics, trapped, and concentrated in detection chambers by an array of neodymium-iron-boron magnets. The chip is placed in contact with a cooled CCD via a fiber optic taper to perform quantitative bioluminescence imaging after addition of luciferin substrate. A model toxic compound (dimethyl sulfoxide, DMSO) and a bile acid (taurochenodeoxycholic acid, TCDCA) were used to investigate the analytical performance of the MAGNETOX. Incubation with DMSO and TCDCA drastically reduces the bioluminescent signal in a dose-related manner. The generation of bacteria that are both magnetic and bioluminescent combines the advantages of easy 2D cell handling with ultra sensitive detection, offering undoubted potential to develop cell-based biosensors integrated into microfluidic chips.

Testosterone challenge and androgen receptor activity in relation to UGT2B17 genotypes

BACKGROUND

We investigated the androgen receptor (AR) bioluminescense response in serum and urine before and after testosterone challenge in different genotypes of the UGT2B17 enzyme, which catalyses testosterone glucuronidation.

MATERIAL AND METHODS

The androgen receptor activity was determined using a yeast-based bioluminescence assay. The androgens were analysed using LC-MS/MS, and the individuals were genotyped for UGT2B17 deletion polymorphism using real-time polymerase chain reaction.

RESULTS

The serum concentrations of testosterone and dihydrotestosterone (DHT) were markedly elevated on days 2 and 4 and were still above baseline on day 15 after a dose of 500 mg testosterone enanthate. The androgenic activity in serum increased in parallel and correlated with the hormone concentrations and remained above baseline on day 15. The urinary androgenic activity increased 4-5-fold and was closely related to the unconjugated testosterone and independent of the UGT2B17 genotype.

CONCLUSIONS

The AR assay may serve as a complement to the urinary testosterone/epitestosterone (T/E) doping test, because this is profoundly influenced by the UGT2B17 deletion polymorphism. It may also be useful for detection of other illicit androgens in sports, or in the society, or for monitoring and diagnostics of androgen-related disorders.

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.