Biosensing Vibrio cholerae with Genetically Engineered Escherichia coli

Engineering two-component systems for advanced biosensing: From architecture to applications in biotechnology

Two-component systems (TCSs) are prevalent signaling pathways in bacteria. These systems mediate phosphotransfer between histidine kinase and a response regulator, facilitating responses to diverse physical, chemical, and biological stimuli. Advancements in synthetic and structural biology have repurposed TCSs for applications in monitoring heavy metals, disease-associated biomarkers, and the production of bioproducts. However, the utility of many TCS biosensors is hindered by undesired performance due to the lack of effective engineering methods. Here, we briefly discuss the architectures and regulatory mechanisms of TCSs. We also summarize the recent advancements in TCS engineering by experimental or computational-based methods to fine-tune the biosensor functional parameters, such as response curve and specificity. Engineered TCSs have great potential in the medical, environmental, and biorefinery fields, demonstrating a crucial role in a wide area of biotechnology.

Titanium nitride-based hyperbolic metamaterial for near-infrared ultrasensitive sensing of microbes

We demonstrate an ultrasensitive microbe sensor for the first time using a titanium nitride (TiN) nanowire-based hyperbolic metamaterial (HMM) structure. We detected the change in the resonance wavelength shift due to the inclusion of microbes in a freshwater environment employing the finite-difference time-domain (FDTD) method. Our proposed HMM sensor exhibits strong bulk plasmon polariton (BPP) modes in the anisotropic hyperbolic regime (λ ≥ 590 nm) and operates in the near-infrared (NIR) wavelength region. We studied the impact of structural parameters on the resonance wavelength shift, where our proposed HMM sensor structure exhibited an outstanding sensing capability of 11 nm per bacteria. A limit of detection of 0.00008 RIU was achieved for our proposed HMM sensor structure. Additionally, we verified our results theoretically to calculate mode frequency shift by solving the effective medium theory (EMT). Our study revealed that HMM is the origin of highly sensitive BPP modes. We obtained two BPP modes, where the BPP mode at a longer wavelength (q = 1) exhibited the highest resonance wavelength shift compared to the BPP mode at a shorter wavelength (q = 2). More importantly, we demonstrated numerically the point-detection capability of our proposed HMM microbe sensor structure, which was unattainable in previously reported sensor work. Moreover, this sensor can be adapted to detect different viruses and bacteria. Our proposed TiN-based HMM structure can potentially be an ultrasensitive and straightforward microbe sensor for label-free detection.

Targeting microbial quorum sensing: the next frontier to hinder bacterial driven gastrointestinal infections

Bacteria synchronize social behaviors via a cell-cell communication and interaction mechanism termed as quorum sensing (QS). QS has been extensively studied in monocultures and proved to be intensively involved in bacterial virulence and infection. Despite the role QS plays in pathogens during laboratory engineered infections has been proved, the potential functions of QS related to pathogenesis in context of microbial consortia remain poorly understood. In this review, we summarize the basic molecular mechanisms of QS, primarily focusing on pathogenic microbes driving gastrointestinal (GI) infections. We further discuss how GI pathogens disequilibrate the homeostasis of the indigenous microbial consortia, rebuild a realm dominated by pathogens, and interact with host under worsening infectious conditions via pathogen-biased QS signaling. Additionally, we present recent applications and main challenges of manipulating QS network in microbial consortia with the goal of better understanding GI bacterial sociality and facilitating novel therapies targeting bacterial infections.

Engineered live bacteria as disease detection and diagnosis tools

Sensitive and minimally invasive medical diagnostics are essential to the early detection of diseases, monitoring their progression and response to treatment. Engineered bacteria as live sensors are being developed as a new class of biosensors for sensitive, robust, noninvasive, and in situ detection of disease onset at low cost. Akin to microrobotic systems, a combination of simple genetic rules, basic logic gates, and complex synthetic bioengineering principles are used to program bacterial vectors as living machines for detecting biomarkers of diseases, some of which cannot be detected with other sensing technologies. Bacterial whole-cell biosensors (BWCBs) can have wide-ranging functions from detection only, to detection and recording, to closed-loop detection-regulated treatment. In this review article, we first summarize the unique benefits of bacteria as living sensors. We then describe the different bacteria-based diagnosis approaches and provide examples of diagnosing various diseases and disorders. We also discuss the use of bacteria as imaging vectors for disease detection and image-guided surgery. We conclude by highlighting current challenges and opportunities for further exploration toward clinical translation of these bacteria-based systems.

Synthetic biology-inspired cell engineering in diagnosis, treatment, and drug development

The fast-developing synthetic biology (SB) has provided many genetic tools to reprogram and engineer cells for improved performance, novel functions, and diverse applications. Such cell engineering resources can play a critical role in the research and development of novel therapeutics. However, there are certain limitations and challenges in applying genetically engineered cells in clinical practice. This literature review updates the recent advances in biomedical applications, including diagnosis, treatment, and drug development, of SB-inspired cell engineering. It describes technologies and relevant examples in a clinical and experimental setup that may significantly impact the biomedicine field. At last, this review concludes the results with future directions to optimize the performances of synthetic gene circuits to regulate the therapeutic activities of cell-based tools in specific diseases.

Prebiotics-Controlled Disposable Engineered Bacteria for Intestinal Diseases

As a new method of diagnosis and treatment for intestinal diseases, intelligent engineered bacteria based on synthetic biology have been developed vigorously in recent years. However, how to deal with the engineered bacteria in vivo after completing the tasks is an urgent problem to be resolved. In this study, we constructed a thiosulfate (a biomarker of inflammatory bowel disease)-responsive engineered bacteria to generate two signals, sfGFP (monitoring) and gain-of-function (translation activation) mutation (ACG to ATG), in the initiation codon of lysisE (recording) via the CRISPR/Cas9-mediated base editing system. Once these two signals were detected, xylose could be added to induce lysis E expression, resulting in the destruction of the edited bacteria and the release of AvCystain simultaneously. Overall, our innovative engineered bacteria can record instant and historical information of the disease, and especially, the edited bacteria can be artificially attenuated and release drug in situ when needed, ultimately serving as a disposable and recyclable candidate for more types of diseases.

BMSS2: A Unified Database-Driven Modeling Tool for Systematic Biomodel Selection

Modeling in synthetic biology constitutes a powerful means in our continuous search for improved performance with a rational Design-Build-Test-Learn approach. Particularly, kinetic models unravel system dynamics and enable system analysis for guiding experimental design. However, a systematic yet modular pipeline that allows one to identify the appropriate model and guide the experimental designs while tracing the entire model development and analysis is still lacking. Here, we develop BMSS2, a unified tool that streamlines and automates model selection by combining information criterion ranking with upstream and parallel analysis algorithms. These include Bayesian parameter inference, a priori and a posteriori identifiability analysis, and global sensitivity analysis. In addition, the database-driven design supports interactive model storage/retrieval to encourage reusability and facilitate automated model selection. This allows ease of model manipulation and deposition for the selection and analysis, thus enabling better utilization of models in guiding experimental design.

Bioengineered Probiotics: Synthetic Biology Can Provide Live Cell Therapeutics for the Treatment of Foodborne Diseases

The rising prevalence of antibiotic resistant microbial pathogens presents an ominous health and economic challenge to modern society. The discovery and large-scale development of antibiotic drugs in previous decades was transformational, providing cheap, effective treatment for what would previously have been a lethal infection. As microbial strains resistant to many or even all antibiotic drug treatments have evolved, there is an urgent need for new drugs or antimicrobial treatments to control these pathogens. The ability to sequence and mine the genomes of an increasing number of microbial strains from previously unexplored environments has the potential to identify new natural product antibiotic biosynthesis pathways. This coupled with the power of synthetic biology to generate new production chassis, biosensors and “weaponized” live cell therapeutics may provide new means to combat the rapidly evolving threat of drug resistant microbial pathogens. This review focuses on the application of synthetic biology to construct probiotic strains that have been endowed with functionalities allowing them to identify, compete with and in some cases kill microbial pathogens as well as stimulate host immunity. Weaponized probiotics may have the greatest potential for use against pathogens that infect the gastrointestinal tract: Vibrio cholerae, Staphylococcus aureus, Clostridium perfringens and Clostridioides difficile. The potential benefits of engineered probiotics are highlighted along with the challenges that must still be met before these intriguing and exciting new therapeutic tools can be widely deployed.

Synthetic Biology Tools for Engineering Microbial Cells to Fight Superbugs

With the increase in clinical cases of bacterial infections with multiple antibiotic resistance, the world has entered a health crisis. Overuse, inappropriate prescribing, and lack of innovation of antibiotics have contributed to the surge of microorganisms that can overcome traditional antimicrobial treatments. In 2017, the World Health Organization published a list of pathogenic bacteria, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli (ESKAPE). These bacteria can adapt to multiple antibiotics and transfer their resistance to other organisms; therefore, studies to find new therapeutic strategies are needed. One of these strategies is synthetic biology geared toward developing new antimicrobial therapies. Synthetic biology is founded on a solid and well-established theoretical framework that provides tools for conceptualizing, designing, and constructing synthetic biological systems. Recent developments in synthetic biology provide tools for engineering synthetic control systems in microbial cells. Applying protein engineering, DNA synthesis, and in silico design allows building metabolic pathways and biological circuits to control cellular behavior. Thus, synthetic biology advances have permitted the construction of communication systems between microorganisms where exogenous molecules can control specific population behaviors, induce intracellular signaling, and establish co-dependent networks of microorganisms.

Combating Infectious Diseases with Synthetic Biology

Over the past decades, there have been numerous outbreaks, including parasitic, fungal, bacterial, and viral infections, worldwide. The rate at which infectious diseases are emerging is disproportionate to the rate of development for new strategies that could combat them. Therefore, there is an increasing demand to develop novel, specific, sensitive, and effective methods for infectious disease diagnosis and treatment. Designed synthetic systems and devices are becoming powerful tools to treat human diseases. The advancement in synthetic biology offers efficient, accurate, and cost-effective platforms for detecting and preventing infectious diseases. Herein we focus on the latest state of living theranostics and its implications.

Microbiome therapeutics: exploring the present scenario and challenges

Human gut-microbiome explorations have enriched our understanding of microbial colonization, maturation, and dysbiosis in health-and-disease subsets. The enormous metabolic potential of gut microbes and their role in the maintenance of human health is emerging, with new avenues to use them as therapeutic agents to overcome human disorders. Microbiome therapeutics are aimed at engineering the gut microbiome using additive, subtractive, or modulatory therapy with an application of native or engineered microbes, antibiotics, bacteriophages, and bacteriocins. This approach could overcome the limitation of conventional therapeutics by providing personalized, harmonized, reliable, and sustainable treatment. Its huge economic potential has been shown in the global therapeutics market. Despite the therapeutic and economical potential, microbiome therapeutics is still in the developing stage and is facing various technical and administrative issues that require research attention. This review aims to address the current knowledge and landscape of microbiome therapeutics, provides an overview of existing health-and-disease applications, and discusses the potential future directions of microbiome modulations.

Theranostic cells: emerging clinical applications of synthetic biology

Synthetic biology seeks to redesign biological systems to perform novel functions in a predictable manner. Recent advances in bacterial and mammalian cell engineering include the development of cells that function in biological samples or within the body as minimally invasive diagnostics or theranostics for the real-time regulation of complex diseased states. Ex vivo and in vivo cell-based biosensors and therapeutics have been developed to target a wide range of diseases including cancer, microbiome dysbiosis and autoimmune and metabolic diseases. While probiotic therapies have advanced to clinical trials, chimeric antigen receptor (CAR) T cell therapies have received regulatory approval, exemplifying the clinical potential of cellular therapies. This Review discusses preclinical and clinical applications of bacterial and mammalian sensing and drug delivery platforms as well as the underlying biological designs that could enable new classes of cell diagnostics and therapeutics. Additionally, we describe challenges that must be overcome for more rapid and safer clinical use of engineered systems.

Design and in silico analysis of a whole-cell biosensor able to kill methicillin-resistant Staphylococcus aureus

The rise of methicillin-resistant Staphylococcus aureus (MRSA) infections has gained concern throughout the world over the past decades. Alternative therapeutic agents to antibiotics are rapidly growing to impede the proliferation of MRSA-caused infections. Lately, synthetic biology techniques have developed whole-cell biosensors by designing gene circuitry capable of sensing quorum-sensing (QS) molecules of pathogens and triggering expression of an antimicrobial moiety that kills MRSA and therefore prevents its further proliferation. Here, an E. coli was engineered in silico to act as a whole-cell biosensor that senses QS molecules from MRSA and triggers the expression of a bacteriocin that kills MRSA. To achieve this functionality, biosensor and bacteriocin modules were constructed and assembled into a vector. Both modules were codon-optimized to increase the yield production of the recombinant proteins. We then demonstrate in silico that the construction of a dual biosensor-killer plasmid, which holds two genetical modules known as biosensor and bacteriocin modules, enables the recombinant host to sense QS molecules from MRSA. Our designed whole-cell biosensor demonstrates in silico its ability to produce and secrete the bacteriocin as a function of the external concentration of autoinducer peptide from MRSA. These in silico results unravel the possibility of designing antimicrobial smarter therapeutics against resistant pathogens.

A Whole-Cell Biosensor for Point-of-Care Detection of Waterborne Bacterial Pathogens

Water contamination by pathogenic bacteria is a major public health concern globally. Monitoring bacterial contamination in water is critically important to protect human health, but this remains a critical challenge. Engineered whole-cell biosensors created through synthetic biology hold great promise for rapid and cost-effective detection of waterborne pathogens. In this study, we created a novel whole-cell biosensor to detect water contamination by Pseudomonas aeruginosa and Burkholderia pseudomallei, which are two critical bacterial pathogens and are recognized as common causative agents for waterborne diseases. The biosensor detects the target bacterial pathogens by responding to the relevant quorum sensing signal molecules. Particularly, this study constructed and characterized the biosensor on the basis of the QscR quorum sensing signal system for the first time. We first designed and constructed a QscR on the basis of the sensing module in the E. coli host cell and integrated the QscR sensing module with a reporting module that expressed an enhanced green fluorescent protein (EGFP). The results demonstrated that the biosensor had high sensitivity in response to the quorum sensing signals of the target bacterial pathogens. We further engineered a biosensor that expressed a red pigment lycopene in the reporting module to produce a visible signal readout for the pathogen detection. Additionally, we investigated the feasibility of a paper-based assay by immobilizing the lycopene-based whole-cell biosensor on paper with the aim to build a prototype for developing portable detection devices. The biosensor would provide a simple and inexpensive alternative for timely and point-of-care detection of water contamination and protect human health.

Synthetic Biology Approaches in The Development of Engineered Therapeutic Microbes

Since the intimate relationship between microbes and human health has been uncovered, microbes have been in the spotlight as therapeutic targets for several diseases. Microbes contribute to a wide range of diseases, such as gastrointestinal disorders, diabetes and cancer. However, as host-microbiome interactions have not been fully elucidated, treatments such as probiotic administration and fecal transplantations that are used to modulate the microbial community often cause nonspecific results with serious safety concerns. As an alternative, synthetic biology can be used to rewire microbial networks such that the microbes can function as therapeutic agents. Genetic sensors can be transformed to detect biomarkers associated with disease occurrence and progression. Moreover, microbes can be reprogrammed to produce various therapeutic molecules from the host and bacterial proteins, such as cytokines, enzymes and signaling molecules, in response to a disturbed physiological state of the host. These therapeutic treatment systems are composed of several genetic parts, either identified in bacterial endogenous regulation systems or developed through synthetic design. Such genetic components are connected to form complex genetic logic circuits for sophisticated therapy. In this review, we discussed the synthetic biology strategies that can be used to construct engineered therapeutic microbes for improved microbiome-based treatment.

Crosstalks Between Gut Microbiota and Vibrio Cholerae

Vibrio cholerae, the causative agent of cholera, could proliferate in aquatic environment and infect humans through contaminated food and water. Enormous microorganisms residing in human gastrointestinal tract establish a special microecological system, which immediately responds to the invasion of V. cholerae, through “colonization resistance” mechanisms, such as antimicrobial peptide production, nutrients competition, and intestinal barrier maintenances. Meanwhile, V. cholerae could quickly sense those signals and modulate the expression of relevant genes to circumvent those stresses during infection, leading to successful colonization on the surface of small intestinal epithelial cells. In this review, we summarized the crosstalks profiles between gut microbiota and V. cholerae in the terms of Type VI Secretion System (T6SS), Quorum Sensing (QS), Reactive Oxygen Species (ROS)/pH stress, and Bioactive metabolites. These mechanisms can also be applied to molecular bacterial pathogenesis of other pathogens in host.

Engineered bacteria to report gut function: technologies and implementation

Advances in synthetic biology and microbiology have enabled the creation of engineered bacteria which can sense and report on intracellular and extracellular signals. When deployed in vivo these whole-cell bacterial biosensors can act as sentinels to monitor biomolecules of interest in human health and disease settings. This is particularly interesting in the context of the gut microbiota, which interacts extensively with the human host throughout time and transit of the gut and can be accessed from feces without requiring invasive collection. Leveraging rational engineering approaches for genetic circuits as well as an expanding catalog of disease-associated biomarkers, bacterial biosensors can act as non-invasive and easy-to-monitor reporters of the gut. Here, we summarize recent engineering approaches applied in vivo in animal models and then highlight promising technologies for designing the next generation of bacterial biosensors.

Dynamic Cell Programming with Quorum Sensing-Controlled CRISPRi Circuit

Synthetic biology is enabling rapid advances in the areas of biomanufacturing and live therapeutics. Dynamic circuits that can be used to regulate cellular resources and microbial community behavior represent a defining focus of synthetic biology, and have attracted tremendous interest. However, the existing dynamic circuits are mostly gene editing-dependent or cell lysis-based, which limits their broad and convenient application, and in some cases, such lysis-based circuits can suffer from genetic instability due to evolution. There is limited research in quorum sensing-assisted CRISPRi, which can function in a gene editing-independent manner. Here, we constructed a series of quorum sensing controlled CRISPRi systems (Q-CRISPRi), which can dynamically program bacteria by using customized sgRNA without introducing cell lysis. We successfully applied Q-CRISPRi circuits to dynamically program gene expression, population density, phenotype, physical property, and community composition of microbial consortia. The strategies reported here represent methods for dynamic cell programming and could be effective in programming industrially and medically important microorganisms to offer better control of their metabolism and behavior.

Engineering probiotics as living diagnostics and therapeutics for improving human health

The gut microbiota that inhabit our gastrointestinal tract are well known to play an important role in maintaining human health in many aspects, including facilitating the digestion and absorption of nutrients, protecting against pathogens and regulating immune system. Gut microbiota dysbiosis is associated with a lot of diseases, such as inflammatory bowel disease, allergy, obesity, cardiovascular and neurodegenerative diseases and cancers. With the increasing knowledge of the microbiome, utilization of probiotic bacteria in modulating gut microbiota to prevent and treat a large number of disorders and diseases has gained much interest. In recent years, aided by the continuous development of tools and techniques, engineering probiotic microbes with desired characteristics and functionalities to benefit human health has made significant progress. In this paper, we summarize the recent advances in design and construction of probiotics as living diagnostics and therapeutics for probing and treating a series of diseases including metabolic disorders, inflammation and pathogenic bacteria infections. We also discuss the current challenges and future perspectives in expanding the application of probiotics for disease treatment and detection. We intend to provide insights and ideas for engineering of probiotics to better serve disease therapy and human health.

Emerging Frontiers in Microbiome Engineering

The gut microbiome has a significant impact on health and disease and can actively contribute to obesity, diabetes, inflammatory bowel disease, cardiovascular disease, and neurological disorders. We do not yet have the necessary tools to fine-tune the microbial communities that constitute the microbiome, though such tools could unlock extensive benefits to human health. Here, we provide an overview of the current state of technological tools that may be used for microbiome engineering. These tools can enable investigators to define the parameters of a healthy microbiome and to determine how gut bacteria may contribute to the etiology of a variety of diseases. These tools may also allow us to explore the exciting prospect of developing targeted therapies and personalized treatments for microbiome-linked diseases.

Probiotic strains detect and suppress cholera in mice

Microbiota-modulating interventions are an emerging strategy to promote gastrointestinal homeostasis. Yet, their use in the detection, prevention, and treatment of acute infections remains underexplored. We report the basis of a probiotic-based strategy to promote colonization resistance and point-of-need diagnosis of cholera, an acute diarrheal disease caused by the pathogen Vibrio cholerae. Oral administration of Lactococcus lactis, a common dietary fermentative bacterium, reduced intestinal V. cholerae burden and improved survival in infected infant mice through the production of lactic acid. Furthermore, we engineered an L. lactis strain that specifically detects quorum-sensing signals of V. cholerae in the gut and triggers expression of an enzymatic reporter that is readily detected in fecal samples. We postulate that preventive dietary interventions with fermented foods containing natural and engineered L. lactis strains may hinder cholera progression and improve disease surveillance in populations at risk of cholera outbreaks.

An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs

Constructing a complex functional gene circuit composed of different modular biological parts to achieve the desired performance remains challenging without a proper understanding of how the individual module behaves. To address this, mathematical models serve as an important tool toward better interpretation by quantifying the performance of the overall gene circuit, providing insights, and guiding the experimental designs. As different gene circuits might require exclusively different mathematical representations in the form of ordinary differential equations to capture their transient dynamic behaviors, a recurring challenge in model development is the selection of the appropriate model. Here, we developed an automated biomodel selection system (BMSS) which includes a library of pre-established models with intuitive or unintuitive features derived from a vast array of expression profiles. Selection of models is built upon the Akaike information criteria (AIC). We tested the automated platform using characterization data of routinely used inducible systems, constitutive expression systems, and several different logic gate systems (NOT, AND, and OR gates). The BMSS achieved a good agreement for all the different characterization data sets and managed to select the most appropriate model accordingly. To enable exchange and reproducibility of gene circuit design models, the BMSS platform also generates Synthetic Biology Open Language (SBOL)-compliant gene circuit diagrams and Systems Biology Markup Language (SBML) output files. All aspects of the algorithm were programmed in a modular manner to ease the efforts on model extensions or customizations by users. Taken together, the BMSS which is implemented in Python supports users in deriving the best mathematical model candidate in a fast, efficient, and automated way using part/circuit characterization data.

Engineered dCas9 with reduced toxicity in bacteria: implications for genetic circuit design

Large synthetic genetic circuits require the simultaneous expression of many regulators. Deactivated Cas9 (dCas9) can serve as a repressor by having a small guide RNA (sgRNA) direct it to bind a promoter. The programmability and specificity of RNA:DNA basepairing simplifies the generation of many orthogonal sgRNAs that, in theory, could serve as a large set of regulators in a circuit. However, dCas9 is toxic in many bacteria, thus limiting how high it can be expressed, and low concentrations are quickly sequestered by multiple sgRNAs. Here, we construct a non-toxic version of dCas9 by eliminating PAM (protospacer adjacent motif) binding with a R1335K mutation (dCas9*) and recovering DNA binding by fusing it to the PhlF repressor (dCas9*_PhlF). Both the 30 bp PhlF operator and 20 bp sgRNA binding site are required to repress a promoter. The larger region required for recognition mitigates toxicity in Escherichia coli, allowing up to 9600 ± 800 molecules of dCas9*_PhlF per cell before growth or morphology are impacted, as compared to 530 ± 40 molecules of dCas9. Further, PhlF multimerization leads to an increase in average cooperativity from n = 0.9 (dCas9) to 1.6 (dCas9*_PhlF). A set of 30 orthogonal sgRNA-promoter pairs are characterized as NOT gates; however, the simultaneous use of multiple sgRNAs leads to a monotonic decline in repression and after 15 are co-expressed the dynamic range is <10-fold. This work introduces a non-toxic variant of dCas9, critical for its use in applications in metabolic engineering and synthetic biology, and exposes a limitation in the number of regulators that can be used in one cell when they rely on a shared resource.

Programming the Dynamic Control of Bacterial Gene Expression with a Chimeric Ligand- and Light-Based Promoter System

To program cells in a dynamic manner, synthetic biologists require precise control over the threshold levels and timing of gene expression. However, in practice, modulating gene expression is widely carried out using prototypical ligand-inducible promoters, which have limited tunability and spatiotemporal resolution. Here, we built two dual-input hybrid promoters, each retaining the function of the ligand-inducible promoter while being enhanced with a blue-light-switchable tuning knob. Using the new promoters, we show that both ligand and light inputs can be synchronously modulated to achieve desired amplitude or independently regulated to generate desired frequency at a specific amplitude. We exploit the versatile programmability and orthogonality of the two promoters to build the first reprogrammable logic gene circuit capable of reconfiguring into logic OR and N-IMPLY logic on the fly in both space and time without the need to modify the circuit. Overall, we demonstrate concentration- and time-based combinatorial regulation in live bacterial cells with potential applications in biotechnology and synthetic biology.

Synthetic gene circuits for the detection, elimination and prevention of disease

In living organisms, naturally evolved sensors that constantly monitor and process environmental cues trigger corrective actions that enable the organisms to cope with changing conditions. Such natural processes have inspired biologists to construct synthetic living sensors and signalling pathways, by repurposing naturally occurring proteins and by designing molecular building blocks de novo, for customized diagnostics and therapeutics. In particular, designer cells that employ user-defined synthetic gene circuits to survey disease biomarkers and to autonomously re-adjust unbalanced pathological states can coordinate the production of therapeutics, with controlled timing and dosage. Furthermore, tailored genetic networks operating in bacterial or human cells have led to cancer remission in experimental animal models, owing to the network's unprecedented specificity. Other applications of designer cells in infectious, metabolic and autoimmune diseases are also being explored. In this Review, we describe the biomedical applications of synthetic gene circuits in major disease areas, and discuss how the first genetically engineered devices developed on the basis of synthetic-biology principles made the leap from the laboratory to the clinic.

Reprogramming Probiotic Lactobacillus reuteri as a Biosensor for Staphylococcus aureus Derived AIP-I Detection

Gram-positive Staphylococcus aureus infection that results in pneumonia, urinary tract infection, and in severe cases, sepsis, has recently been classified as a serious threat to public health. Rapid and cost-effective detection of these infections are costly and time-consuming. Here, we present probiotic lactic acid bacteria engineered to detect autoinducer peptide-I (AIP-I), a quorum sensing molecule produced by Staphylococcus sp. during pathogenesis. We achieved this by adapting the well-characterized agr quorum sensing ( agrQS) from Staphylococcus aureus into Lactobacillus reuteri. The engineered biosensor is able to detect AIP-I levels in the nanomolar to micromolar range. We further investigated the function of the biosensor to detect real-time changes in AIP-I levels to understand the dynamics of Staphylococcus aureus under various strenuous conditions. The developed sensors would be useful for detection of Staphylococcus contamination in hospital settings and for high-throughput drug screening.

Engineered Probiotic for the Inhibition of Salmonella via Tetrathionate-Induced Production of Microcin H47

Complications arising from antibiotic-resistant bacteria are becoming one of the key issues in modern medicine. Members of drug-resistant Enterobacteriaceae spp. include opportunistic pathogens (e.g., Salmonella spp.) that are among the leading causes of morbidity and mortality worldwide. Overgrowth of these bacteria is considered a hallmark of intestinal dysbiosis. Microcins (small antimicrobial peptides) produced by some gut commensals can potentially cure these conditions by inhibiting these pathogens and have been proposed as a viable alternative to antibiotic treatment. In this proof-of-concept work, we leverage this idea to develop a genetically engineered prototype probiotic to inhibit Salmonella spp. upon exposure to tetrathionate, a molecule produced in the inflamed gut during the course of Salmonella infection. We developed a plasmid-based system capable of conferring the ability to detect and utilize tetrathionate, while at the same time producing microcin H47. We transferred this plasmid-based system to Escherichia coli and demonstrated the ability of the engineered strain to inhibit growth of Salmonella in anaerobic conditions while in the presence of tetrathionate, with no detectable inhibition in the absence of tetrathionate. In direct competition assays between the engineered E. coli and Salmonella, the engineered E. coli had a considerable increase in fitness advantage in the presence of 1 mM tetrathionate as compared to the absence of tetrathionate. In this work, we have demonstrated the ability to engineer a strain of E. coli capable of using an environmental signal indicative of intestinal inflammation as an inducing molecule, resulting in production of a microcin capable of inhibiting the organism responsible for the inflammation.

Designing and Assembling Plasmids for the Construction of Escherichia coli Biosensor for Vibrio cholerae Detection

In the process of constructing and characterizing the whole cell biosensor for Vibrio cholerae detection, two main techniques have been employed-DNA assembly using the Gibson isothermal assembly reaction was used for the assembly of the PCRed plasmid fragments (DNA parts), and microplate fluorescence readings were used for bacterial strain characterization. The general workflow can be summed up as: the in silico designed DNA fragments were assembled by isothermal assembly to be later transformed into Escherichia coli that, in turn, was characterized using the microplate reader. As fine-tuning of the sensor design was required, the process was repeated iteratively until the final strain was created with desired characteristics. This chapter describes in detail this workflow for different constructs which finally led to the creation of the first whole cell biosensor in E. coli for V. cholerae detection.

Repurposing a Two-Component System-Based Biosensor for the Killing of Vibrio cholerae

New strategies to control cholera are urgently needed. This study develops an in vitro proof-of-concept sense-and-kill system in a wild-type Escherichia coli strain to target the causative pathogen Vibrio cholerae using a synthetic biology approach. Our engineered E. coli specifically detects V. cholerae via its quorum-sensing molecule CAI-1 and responds by expressing the lysis protein YebF-Art-085, thereby self-lysing to release the killing protein Art-085 to kill V. cholerae. For this report, we individually characterized YebF-Art-085 and Art-085 expression and their activities when coupled to our previously developed V. cholerae biosensing circuit. We show that, in the presence of V. cholerae supernatant, the final integrated sense-and-kill system in our engineered E. coli can effectively inhibit the growth of V. cholerae cells. This work represents the first step toward a novel probiotic treatment modality that could potentially prevent and treat cholera in the future.