Yeast-based biosensors: design and applications

Engineered Biosensors in an Encapsulated and Deployable System for Environmental Chemical Detection

The long-term exposure of low levels of the fungicide, 2-phenylphenol (2-PP), to the environment presents a hazard to human and aquatic health. The cost and difficulty in large-scale production limit the use of existing sensors to detect 2-PP for applications such as personal protection and persistent environmental monitoring of large areas. While advances have been made in using whole cells as biosensors for specific chemical detection, a whole-cell biosensor system with robust biocontainment for field deployment and a strong visual reporter for readouts in the deployed environment has yet to be realized. Here, engineered biosensors in an encapsulated and deployable system (eBEADS) were created to demonstrate a portable, no-power living sensor for detection of 2-PP in the environment. A whole-cell living sensor to detect 2-PP was developed in Escherichia coli by utilizing the 2-PP degradation pathway with an agenetic amplification circuit to produce a visual colorimetric output. To enable field deployment, a physical biocontainment system comprising polyacrylamide alginate beads was designed to encapsulate sensor strains, support long-term viability without supplemental nutrients, and allow permeability of the target analyte. Integration of materials and sensing strains has led to the development of a potential deployable end-to-end living sensor that, with the addition of an amplification circuit, has up to a 66-fold increase in β-galactosidase reporter output over non-amplified strains, responding to as little as 1 μM 2-PP while unencapsulated and 10 μM 2-PP while encapsulated. eBEADS enable sensitive and specific in-field detection of environmental perturbations and chemical threats without electronics.

The Use of Yeast in Biosensing

Yeast has been used as a model for several diseases as it is the simplest unicellular eukaryote, safe and easy to culture and harbors most of the fundamental processes that are present in almost all higher eukaryotes, including humans. From understanding the pathogenesis of disease to drug discovery studies, yeast has served as an important biosensor. It is not only due to the conservation of genetics, amenable modification of its genome and easily accessible analytical methods, but also some characteristic features such as its ability to survive with defective mitochondria, making it a highly flexible microbe for designing whole-cell biosensing systems. The aim of this review is to report on how yeasts have been utilized as biosensors, reporting on responses to various stimuli.

Theoretical and Experimental Assay of Shock Experienced by Yeast Cells during Laser Bioprinting

Laser-induced forward transfer (LIFT) is a useful technique for bioprinting using gel-embedded cells. However, little is known about the stresses experienced by cells during LIFT. This paper theoretically and experimentally explores the levels of laser pulse irradiation and pulsed heating experienced by yeast cells during LIFT. It has been found that only 5% of the cells in the gel layer adjacent to the absorbing Ti film should be significantly heated for fractions of microseconds, which was confirmed by the fact that a corresponding population of cells died during LIFT. This was accompanied by the near-complete dimming of intracellular green fluorescent protein, also observed in response to heat shock. It is shown that microorganisms in the gel layer experience laser irradiation with an energy density of ~0.1–6 J/cm². This level of irradiation had no effect on yeast on its own. We conclude that in a wide range of laser fluences, bioprinting kills only a minority of the cell population. Importantly, we detected a previously unobserved change in membrane permeability in viable cells. Our data provide a wider perspective on the effects of LIFT-based bioprinting on living organisms and might provide new uses for the procedure based on its effects on cell permeability.

Engineering of Synthetic Transcriptional Switches in Yeast

Transcriptional switches can be utilized for many purposes in synthetic biology, including the assembly of complex genetic circuits to achieve sophisticated cellular systems and the construction of biosensors for real-time monitoring of intracellular metabolite concentrations. Although to date such switches have mainly been developed in prokaryotes, those for eukaryotes are increasingly being reported as both rational and random engineering technologies mature. In this review, we describe yeast transcriptional switches with different modes of action and how to alter their properties. We also discuss directed evolution technologies for the rapid and robust construction of yeast transcriptional switches.

GPCR-FEX: A Fluoride-Based Selection System for Rapid GPCR Screening and Engineering

The directed evolution of proteins comprises a search of sequence space for variants that improve a target phenotype, yet identification of desirable variants is inherently limited by library size and screening ability. Selections that couple protein phenotype to cell viability accelerate identification of promising variants by depleting libraries of undesirable variants en masse. Here, we introduce GPCR-FEX, a stringent selection platform that couples G-protein coupled receptor (GPCR) signaling to expression of a fluoride ion exporter (FEX)-GFP fusion gene and concomitant cellular fluoride tolerance in yeast. The GPCR-FEX platform works to deplete inactive GPCR variants from the library prior to high-throughput fluorescence-based cell sorting for rapid, inexpensive screening of receptor libraries that sample an expanded sequence space. Using this system, FEX1 was placed under the control of either P_FUS1 or P_FIG1, promoters activated upon agonist binding by the native yeast GPCRs, Ste2p or Ste3p. Addition of a C-terminal degron to FEX1p enhanced the dynamic range of cell growth between agonist-treated and untreated cells. Using deep sequencing to enumerate population members, we show rapid selection of a previously engineered Ste2p receptor mutant strain over wild-type Ste2p in a model library enrichment experiment. Overall, the GPCR-FEX platform provides a mechanism to rapidly engineer GPCRs, which are important cellular sensors for synthetic biology.

High-Throughput Screening of an Octanoic Acid Producer Strain Library Enables Detection of New Targets for Increasing Titers in Saccharomyces cerevisiae

Octanoic acid is an industrially relevant compound with applications in antimicrobials or as a precursor for biofuels. Microbial biosynthesis through yeast is a promising alternative to current unsustainable production methods. To increase octanoic acid titers in Saccharomyces cerevisiae, we use a previously developed biosensor that is based on the octanoic acid responsive pPDR12 promotor coupled to GFP. We establish a biosensor strain amenable for high-throughput screening of an octanoic acid producer strain library. Through development, optimization, and execution of a high-throughput screening approach, we were able to detect two new genetic targets, KCS1 and FSH2, which increased octanoic acid titers through combined overexpression by about 55% compared to the parental strain. Neither target has yet been reported to be involved in fatty acid biosynthesis. The presented methodology can be employed to screen any genetic library and thereby more genes involved in improving octanoic acid production can be detected in the future.

A fluorescence-based yeast sensor for monitoring acetic acid

Accumulation of acetic acid indicates an imbalance of the process due to a disturbed composition of the microorganisms. Hence, monitoring the acetic acid concentration is an important parameter to control the biogas process. Here, we describe the generation and validation of a fluorescence-based whole cell sensor for the detection of acetic acid based on the yeast Saccharomyces cerevisiae. Acetic acid induces the transcription of a subset of genes. The 5´-regulatory sequences (5´ URS) of these genes were cloned into a multicopy plasmid to drive the expression of a red fluorescent reporter gene. The 5´ URS of YGP1, encoding a cell wall-related glycoprotein, led to a 20-fold increase of fluorescence upon addition of 30 mM acetic acid to the media. We show that the system allows estimating the approximate concentration of acetic acid in condensation samples from a biogas plant. To avoid plasmid loss and increase the long-term stability of the sensor, we integrated the reporter construct into the yeast genome and tested the suitability of spores for long-term storage of sensor cells. Lowering the reporter gene's copy number resulted in a significant drop of the fluorescence, which can be compensated by applying a yeast pheromone-based signal amplification system.

Yeast grown in continuous culture systems can detect mutagens with improved sensitivity relative to the Ames test

Continuous culture systems allow for the controlled growth of microorganisms over a long period of time. Here, we develop a novel test for mutagenicity that involves growing yeast in continuous culture systems exposed to low levels of mutagen for a period of approximately 20 days. In contrast, most microorganism-based tests for mutagenicity expose the potential mutagen to the biological reporter at a high concentration of mutagen for a short period of time. Our test improves upon the sensitivity of the well-established Ames test by at least 20-fold for each of two mutagens that act by different mechanisms (the intercalator ethidium bromide and alkylating agent methyl methanesulfonate). To conduct the tests, cultures were grown in small, inexpensive continuous culture systems in media containing (potential) mutagen, and the resulting mutagenicity of the added compound was assessed via two methods: a canavanine-based plate assay and whole genome sequencing. In the canavanine-based plate assay, we were able to detect a clear relationship between the amount of mutagen and the number of canavanine-resistant mutant colonies over a period of one to three weeks of exposure. Whole genome sequencing of yeast grown in continuous culture systems exposed to methyl methanesulfonate demonstrated that quantification of mutations is possible by identifying the number of unique variants across each strain. However, this method had lower sensitivity than the plate-based assay and failed to distinguish the different concentrations of mutagen. In conclusion, we propose that yeast grown in continuous culture systems can provide an improved and more sensitive test for mutagenicity.

The Model System Saccharomyces cerevisiae Versus Emerging Non-Model Yeasts for the Production of Biofuels

Microorganisms are effective platforms for the production of a variety of chemicals including biofuels, commodity chemicals, polymers and other natural products. However, deep cellular understanding is required for improvement of current biofuel cell factories to truly transform the Bioeconomy. Modifications in microbial metabolic pathways and increased resistance to various types of stress caused by the production of these chemicals are crucial in the generation of robust and efficient production hosts. Recent advances in systems and synthetic biology provide new tools for metabolic engineering to design strategies and construct optimal biocatalysts for the sustainable production of desired chemicals, especially in the case of ethanol and fatty acid production. Yeast is an efficient producer of bioethanol and most of the available synthetic biology tools have been developed for the industrial yeast Saccharomyces cerevisiae. Non-conventional yeast systems have several advantageous characteristics that are not easily engineered such as ethanol tolerance, low pH tolerance, thermotolerance, inhibitor tolerance, genetic diversity and so forth. Currently, synthetic biology is still in its initial steps for studies in non-conventional yeasts such as Yarrowia lipolytica, Kluyveromyces marxianus, Issatchenkia orientalis and Pichia pastoris. Therefore, the development and application of advanced synthetic engineering tools must also focus on these underexploited, non-conventional yeast species. Herein, we review the basic synthetic biology tools that can be applied to the standard S. cerevisiae model strain, as well as those that have been developed for non-conventional yeasts. In addition, we will discuss the recent advances employed to develop non-conventional yeast strains that are efficient for the production of a variety of chemicals through the use of metabolic engineering and synthetic biology.

Yeast-Based Fluorescent Sensors for the Simultaneous Detection of Estrogenic and Androgenic Compounds, Coupled with High-Performance Thin Layer Chromatography

The persistence of endocrine disrupting compounds (EDCs) throughout wastewater treatment processes poses a significant health threat to humans and to the environment. The analysis of EDCs in wastewater remains a challenge for several reasons, including (a) the multitude of bioactive but partially unknown compounds, (b) the complexity of the wastewater matrix, and (c) the required analytical sensitivity. By coupling biological assays with high-performance thin-layer chromatography (HPTLC), different samples can be screened simultaneously, highlighting their active components; these may then be identified by chemical analysis. To allow the multiparallel detection of diverse endocrine disruption activities, we have constructed Saccharomyces cerevisiae-based bioreporter strains, responding to compounds with either estrogenic or androgenic activity, by the expression of green (EGFP), red (mRuby), or blue (mTagBFP2) fluorescent proteins. We demonstrate the analytical potential inherent in combining chromatographic compound separation with a direct fluorescent signal detection of EDC activities. The applicability of the system is further demonstrated by separating influent samples of wastewater treatment plants, and simultaneously quantifying estrogenic and androgenic activities of their components. The combination of a chemical separation technique with an optical yeast-based bioassay presents a potentially valuable addition to our arsenal of environmental pollution monitoring tools.

Recent advances in synthetic biology-enabled and natural whole-cell optical biosensing of heavy metals

A large number of scientific works have been published on whole-cell heavy metal biosensing based on optical transduction. The advances in the application of biotechnological tools not only have continuously improved the sensitivity, selectivity, and detection range for biosensors but also have simultaneously unveiled new challenges and restrictions for further improvements. This review highlights selected aspects of whole-cell biosensing of heavy metals using optical transducers. We have focused on the progress in genetic modulation in regulatory and reporter modules of recombinant plasmids that has enabled improvement of biosensor performance. Simultaneously, an attempt has been made to present newer platforms such as microfluidics that have generated promising results and might give a new turn to the optical biosensing field.

Engineering Saccharomyces cerevisiae cells for production of fatty acid-derived biofuels and chemicals

The yeast Saccharomyces cerevisiae is a widely used cell factory for the production of fuels and chemicals, in particular ethanol, a biofuel produced in large quantities. With a need for high-energy-density fuels for jets and heavy trucks, there is, however, much interest in the biobased production of hydrocarbons that can be derived from fatty acids. Fatty acids also serve as precursors to a number of oleochemicals and hence provide interesting platform chemicals. Here, we review the recent strategies applied to metabolic engineering of S. cerevisiae for the production of fatty acid-derived biofuels and for improvement of the titre, rate and yield (TRY). This includes, for instance, redirection of the flux towards fatty acids through engineering of the central carbon metabolism, balancing the redox power and varying the chain length of fatty acids by enzyme engineering. We also discuss the challenges that currently hinder further TRY improvements and the potential solutions in order to meet the requirements for commercial application.

Bridging non-overlapping reads illuminates high-order epistasis between distal protein sites in a GPCR

Epistasis emerges when the effects of an amino acid depend on the identities of interacting residues. This phenomenon shapes fitness landscapes, which have the power to reveal evolutionary paths and inform evolution of desired functions. However, there is a need for easily implemented, high-throughput methods to capture epistasis particularly at distal sites. Here, we combine deep mutational scanning (DMS) with a straightforward data processing step to bridge reads in distal sites within genes (BRIDGE). We use BRIDGE, which matches non-overlapping reads to their cognate templates, to uncover prevalent epistasis within the binding pocket of a human G protein-coupled receptor (GPCR) yielding variants with 4-fold greater affinity to a target ligand. The greatest functional improvements in our screen result from distal substitutions and substitutions that are deleterious alone. Our results corroborate findings of mutational tolerance in GPCRs, even in conserved motifs, but reveal inherent constraints restricting tolerated substitutions due to epistasis.

Epistasis effects among amino acids at distal sites within binding pockets can have important impacts on protein fitness landscapes. Here the authors present BRIDGE, which matches non-overlapping sequence reads with their cognate DNA templates.

Engineering a Model Cell for Rational Tuning of GPCR Signaling

G protein-coupled receptor (GPCR) signaling is the primary method eukaryotes use to respond to specific cues in their environment. However, the relationship between stimulus and response for each GPCR is difficult to predict due to diversity in natural signal transduction architecture and expression. Using genome engineering in yeast, we constructed an insulated, modular GPCR signal transduction system to study how the response to stimuli can be predictably tuned using synthetic tools. We delineated the contributions of a minimal set of key components via computational and experimental refactoring, identifying simple design principles for rationally tuning the dose response. Using five different GPCRs, we demonstrate how this enables cells and consortia to be engineered to respond to desired concentrations of peptides, metabolites, and hormones relevant to human health. This work enables rational tuning of cell sensing while providing a framework to guide reprogramming of GPCR-based signaling in other systems.

Rapid Self-Assembly of Au Nanoparticles on Rigid Mesoporous Yeast-Based Microspheres for Sensitive Immunoassay

A simple, rapid, inexpensive, eco-friendly, and high-throughput biological strategy for the preparation of functional microspheres on a yeast-cell platform was introduced. Microspheres prepared through the treatment of yeast cells with formaldehyde and decoating buffer exhibited excellent characteristics, such as superior mechanical strength, high sulfhydryl group content, and mesoporous structure. Au nanoparticles (NPs) easily and rapidly self-assembled onto the surfaces of the yeast-based microspheres within 5 min to form rigid yeast@Au microspheres with high monodispersity and uniformity. The rapid formation of yeast@Au microspheres mainly involved the enhancement of sulfhydryl groups and mesoporosity. The yeast@Au microspheres were successfully used in a flow cytometry immunoassay to detect Pseudorabies viral infection events. Signal-to-noise ratio was enhanced by approximately 49.4-fold. The presence of Au NPs on the yeast-based microspheres greatly improved sensitivity by decreasing noise through reducing nonspecific adsorption, highly enhancing the fluorescence signal caused by the surface plasmon resonance effect, and increasing the coupling efficiency of the capture protein. The presented method was used to analyze 81 clinical swine serum specimens. The results obtained by this developed method were compared to those of commercial diagnostic kits. The sensitivity, specificity, and efficiency of the developed method were 92.31, 88.24, and 88.89%, respectively. The excellent characteristics of the yeast@Au microspheres illustrate its great potential for high-throughput immunoassay applications in the fields of disease diagnosis, environmental analysis, and food safety.

A Yeast-Based Biosensor for Screening of Short- and Medium-Chain Fatty Acid Production

Short- and medium-chain fatty acids (SMCFA) are important platform chemicals currently produced from nonsustainable resources. The engineering of microbial cells to produce SMCFA, however, lacks high-throughput methods to screen for best performing cells. Here, we present the development of a whole-cell biosensor for easy and rapid detection of SMCFA. The biosensor is based on a multicopy yeast plasmid containing the SMCFA-responsive PDR12 promoter coupled to GFP as the reporter gene. The sensor detected hexanoic, heptanoic and octanoic acid over a linear range up to 2, 1.5, and 0.75 mM, respectively, but did not show a linear response to decanoic and dodecanoic acid. We validated the functionality of the biosensor with culture supernatants of a previously engineered Saccharomyces cerevisiae octanoic acid producer strain and derivatives thereof. The biosensor signal correlated strongly with the octanoic acid concentrations as determined by gas chromatography. Thus, this biosensor enables the high-throughput screening of SMCFA producers and has the potential to drastically speed up the engineering of diverse SMCFA producing cell factories.

Tuning Vector Stability and Integration Frequency Elevates Functional GPCR Production and Homogeneity in Saccharomyces cerevisiae

Membrane proteins play a valuable role in biotechnology, yet the difficulty of producing high yields of functional membrane protein limits their use in synthetic biology. The practical application of G protein-coupled receptors in whole cell biosensors, for example, is restricted to those that are functionally produced at the cell surface in the chosen host, limiting the range of detectable molecules. Here, we present a facile approach to significantly improve the yield and homogeneity of functional membrane proteins in Saccharomyces cerevisiae by altering only the choice of expression vector. Expression of a model GPCR, the human adenosine A₂a receptor, from commonly used centromeric and episomal vectors leads to low yields and cellular heterogeneity due to plasmid loss in 20-90% of the cell population. In contrast, homogeneous production of GPCR is attained using a multisite integrating vector or a novel, modified high copy vector that does not require genomic integration or addition of any selection agents. Finally, we introduce a FACS-based screen, which enables rapid isolation of cells with 4- to 15-fold increases in gene dosage and up to a 9-fold increase in functional protein yield without loss of homogeneity compared to a strain isolated through conventional, low-throughput methods. These results can be extended to improve the cellular homogeneity and yield of other membrane proteins, expanding the repertoire of useful receptors for synthetic biology applications.

The Smell of Synthetic Biology: Engineering Strategies for Aroma Compound Production in Yeast

Yeast—especially Saccharomyces cerevisiae—have long been a preferred workhorse for the production of numerous recombinant proteins and other metabolites. S. cerevisiae is a noteworthy aroma compound producer and has also been exploited to produce foreign bioflavour compounds. In the past few years, important strides have been made in unlocking the key elements in the biochemical pathways involved in the production of many aroma compounds. The expression of these biochemical pathways in yeast often involves the manipulation of the host strain to direct the flux towards certain precursors needed for the production of the given aroma compound. This review highlights recent advances in the bioengineering of yeast—including S. cerevisiae—to produce aroma compounds and bioflavours. To capitalise on recent advances in synthetic yeast genomics, this review presents yeast as a significant producer of bioflavours in a fresh context and proposes new directions for combining engineering and biology principles to improve the yield of targeted aroma compounds.

Current status of water environment and their microbial biosensor techniques - Part II: Recent trends in microbial biosensor development

In Part I of the present review series, I presented the current state of the water environment by focusing on Japanese cases and discussed the need to further develop microbial biosensor technologies for the actual water environment. I comprehensively present trends after approximately 2010 in microbial biosensor development for the water environment. In the first section, after briefly summarizing historical studies, recent studies on microbial biosensor principles are introduced. In the second section, recent application studies for the water environment are also introduced. Finally, I conclude the present review series by describing the need to further develop microbial biosensor technologies. Graphical abstract Current water pollution indirectly occurs by anthropogenic eutrophication (Part I). Recent trends in microbial biosensor development for water environment are described in part II of the present review series.

Developing a Genetically Encoded, Cross-Species Biosensor for Detecting Ammonium and Regulating Biosynthesis of Cyanophycin

Responding to nitrogen status is essential for all living organisms. Bacteria have evolved various complex and exquisite regulatory systems to control nitrogen metabolism. However, natural nitrogen regulatory systems, owing to their complexity, often function only in their original hosts and do not respond properly when transferred to another species. By harnessing the Lactococcus GlnRA system, we developed a genetically encoded, cross-species ammonium biosensor that displays a dynamic range up to 9-fold upon detection of ammonium ion. We demonstrated applications of this ammonium biosensor in three different species (Escherichia coli, Pseudomonas putida, and Synechocystis sp.) to detect different nitrogen sources. This ammonium sensor was further used to regulate the biosynthesis of a nitrogen-rich polymer, cyanophycin, based on ammonium concentration. Given the importance of nitrogen responses, the developed biosensor should be broadly applicable to synthetic biology and bioengineering.

Modulating and evaluating receptor promiscuity through directed evolution and modeling

The promiscuity of G-protein-coupled receptors (GPCRs) has broad implications in disease, pharmacology and biosensing. Promiscuity is a particularly crucial consideration for protein engineering, where the ability to modulate and model promiscuity is essential for developing desirable proteins. Here, we present methodologies for (i) modifying GPCR promiscuity using directed evolution and (ii) predicting receptor response and identifying important peptide features using quantitative structure-activity relationship models and grouping-exhaustive feature selection. We apply these methodologies to the yeast pheromone receptor Ste2 and its native ligand α-factor. Using directed evolution, we created Ste2 mutants with altered specificity toward a library of α-factor variants. We then used the  Vectors of Hydrophobic, Steric, and Electronic properties and partial least squares regression to characterize receptor-ligand interactions, identify important ligand positions and properties, and predict receptor response to novel ligands. Together, directed evolution and computational analysis enable the control and evaluation of GPCR promiscuity. These approaches should be broadly useful for the study and engineering of GPCRs and other protein-small molecule interactions.

Tuning the Sensitivity of the PDR5 Promoter-Based Detection of Diclofenac in Yeast Biosensors

The commonly used drug diclofenac is an important environmental anthropogenic pollutant. Currently, detection of diclofenac is mainly based on chemical and physical methods. Here we describe a yeast biosensor that drives the diclofenac-dependent expression of a recombinant fluorescent protein from the authentic promoter of the PDR5 gene. This key component of the pleiotropic drug response encodes a multidrug transporter that is involved in cellular detoxification. We analyse the effects on diclofenac sensitivity of artificial PDR5 promoter derivatives in wild-type and various yeast mutant strains. This approach enabled us to generate sensor strains with elevated drug sensitivity.

Hydrophobin-Based Surface Engineering for Sensitive and Robust Quantification of Yeast Pheromones

Detection and quantification of small peptides, such as yeast pheromones, are often challenging. We developed a highly sensitive and robust affinity-assay for the quantification of the α-factor pheromone of Saccharomyces cerevisiae based on recombinant hydrophobins. These small, amphipathic proteins self-assemble into highly stable monolayers at hydrophilic-hydrophobic interfaces. Upon functionalization of solid supports with a combination of hydrophobins either lacking or exposing the α-factor, pheromone-specific antibodies were bound to the surface. Increasing concentrations of the pheromone competitively detached the antibodies, thus allowing for quantification of the pheromone. By adjusting the percentage of pheromone-exposing hydrophobins, the sensitivity of the assay could be precisely predefined. The assay proved to be highly robust against changes in sample matrix composition. Due to the high stability of hydrophobin layers, the functionalized surfaces could be repeatedly used without affecting the sensitivity. Furthermore, by using an inverse setup, the sensitivity was increased by three orders of magnitude, yielding a novel kind of biosensor for the yeast pheromone with the lowest limit of detection reported so far. This assay was applied to study the pheromone secretion of diverse yeast strains including a whole-cell biosensor strain of Schizosaccharomyces pombe modulating α-factor secretion in response to an environmental signal.