Engineered Saccharomyces cerevisiae strain BioS-1, for the detection of water-borne toxic metal contaminants

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.

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.

Temporal and spatial properties of a yeast multi-cellular amplification system based on signal molecule diffusion

We report on the spatial and temporal signaling properties of a yeast pheromone-based cell communication and amplifier system. It utilizes the Saccharomyces cerevisiae mating response pathway and relies on diffusion of the pheromone α-factor as key signaling molecule between two cell types. One cell type represents the α-factor secreting sensor part and the other the reporter part emitting fluorescence upon activation. Although multi-cellular signaling systems promise higher specificity and modularity, the complex interaction of the cells makes prediction of sensor performance difficult. To test the maximum distance and response time between sensor and reporter cells, the two cell types were spatially separated in defined compartments of agarose hydrogel (5 x 5 mm) and reconnected by diffusion of the yeast pheromone. Different ratios of sensor to reporter cells were tested to evaluate the minimum amount of sensor cells required for signal transduction. Even the smallest ratio, one α-factor-secreting cell to twenty reporter cells, generated a distinct fluorescence signal. When using a 1:1 ratio, the secreted pheromone induced fluorescence in a distance of up to four millimeters after six hours. We conclude from both our experimental results and a mathematical diffusion model that in our approach: (1) the maximum dimension of separated compartments should not exceed five millimeters in gradient direction; and (2) the time-limiting step is not diffusion of the signaling molecule but production of the reporter protein.

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

Genetically modified bacterial biosensors can detect specific environmental compounds. Here, we attempted to establish a fluorescent microplate method to detect arsenic using recombinant Escherichia coli cells transformed with plasmids harboring three tandem copies of the ars promoter/operator-the gene for green fluorescent protein (gfp). In the biosensors, one copy of arsR, whose transcription is autoregulated by the ars promoter/operator and ArsR in the genome of E. coli, was placed in trans in another plasmid under the control of isopropyl-1-thio-beta-D-galactopyranoside-inducible promoter. First, this manipulation enabled regulation of the arsR expression at an adequate level. Second, the copy number of reporter unit also affected signal and noise. When the plasmid harboring three copies of the reporter unit was used, the signal-to-noise ratio doubled and the detection limit decreased from 20 to 7.5 microg L(-1) As(III), compared to the use of the plasmid harboring one copy of the ars promoter/operator-arsR-gfp. Thus, segregation of arsR from the ars promoter/operator-gfp using two plasmids is effective in regulating the signal-to-noise ratio and the detection limit with the different functions.

Development of a yeast biosensor–biocatalyst for the detection and biodegradation of the organophosphate paraoxon

Organophosphate (OP) poisoning can occur through unintentional exposure to OP pesticides, or by the deliberate release of OP nerve agents. Consequently, there is considerable interest in the development of systems that can detect and/or biodegrade these agents. The aim of this study was to generate a prototype fluorescent reporter yeast biosensor that could detect and biodegrade the model OP pesticide, paraoxon, and subsequently detect paraoxon hydrolysis. Saccharomyces cerevisiae was engineered to hydrolyze paraoxon through the heterologous expression of the Flavobacterium species opd (organophosphate degrading) gene. Global transcription profiling was subsequently used to identify yeast genes, which were induced in the presence of paraoxon, and genes, which were associated with paraoxon hydrolysis. Paraoxon-inducible genes and genes associated with paraoxon hydrolysis were identified. Candidate paraoxon-inducible promoters were cloned and fused to the yeast-enhanced green fluorescent protein (yEGFP), and candidate promoters associated with paraoxon hydrolysis were fused to the red fluorescent protein (yDsRed). The ability of the yeast biosensor to detect paraoxon and paraoxon hydrolysis was demonstrated by the specific induction of the fluorescent reporter (yEGFP and yDsRed, respectively). Biosensors responded to paraoxon in a dose- and time-dependent manner, and detection was rapid (15 to 30 min). yDsRed induction occurred only in the recombinant opd(+) strains suggesting that yDsRed induction was strictly associated with paraoxon hydrolysis. Together, these results indicate that the yeast biocatalyst-biosensor can detect and degrade paraoxon and potentially also monitor the decontamination process.

Chemical sensing of DNT by engineered olfactory yeast strain

With the increasing threat of environmental toxicants including biological and chemical warfare agents, fabricating innovative biomimetic systems to detect these harmful agents is critically important. With the broad objective of developing such a biosensor, here we report the construction of a Saccharomyces cerevisiae strain containing the primary components of the mammalian olfactory signaling pathway. In this engineered yeast strain, WIF-1alpha, olfactory receptor signaling is coupled to green fluorescent protein expression. Using this 'olfactory yeast', we screened for olfactory receptors that could report the presence of the odorant 2,4-dinitrotoluene, an explosive residue mimic. With this approach, we have identified the novel rat olfactory receptor Olfr226, which is closely related to the mouse olfactory receptors Olfr2 and MOR226-1, as a 2,4-dinitrotoluene-responsive receptor.