Directed assembly of a bacterial quorum

Engineered bacteria as drug delivery vehicles: Principles and prospects

The development of drug delivery vehicles is in significant demand in the context of precision medicine. With the development of synthetic biology, the use of genetically engineered bacteria as drug delivery vectors has attracted more and more attention. Herein, we reviewed the research advances in bioengineered bacteria as drug carriers, with emphasis on the synthetic biology strategies for modifying these bacteria, including the targeted realization method of engineered bacteria, the designing scheme of genetic circuits, and the release pathways of therapeutic compounds. Based on this, the essential components, design principles, and health concerns of engineering bacteria as drug carriers and the development prospects in this field have been discussed.

Exploring the Function of Quorum Sensing Regulated Biofilms in Biological Wastewater Treatment: A Review

Quorum sensing (QS), a type of bacterial cell–cell communication, produces autoinducers which help in biofilm formation in response to cell population density. In this review, biofilm formation, the role of QS in biofilm formation and development with reference to biological wastewater treatment are discussed. Autoinducers, for example, acyl-homoserine lactones (AHLs), auto-inducing oligo-peptides (AIPs) and autoinducer 2, present in both Gram-negative and Gram-positive bacteria, with their mechanism, are also explained. Over the years, wastewater treatment (WWT) by QS-regulated biofilms and their optimization for WWT have gained much attention. This article gives a comprehensive review of QS regulation methods, QS enrichment methods and QS inhibition methods in biological waste treatment systems. Typical QS enrichment methods comprise adding QS molecules, adding QS accelerants and cultivating QS bacteria, while typical QS inhibition methods consist of additions of quorum quenching (QQ) bacteria, QS-degrading enzymes, QS-degrading oxidants, and QS inhibitors. Potential applications of QS regulated biofilms for WWT have also been summarized. At last, the knowledge gaps present in current researches are analyzed, and future study requirements are proposed.

Enzyme directed evolution using genetically encodable biosensors

Directed evolution has been remarkably successful in identifying enzyme variants with new or improved properties, such as altered substrate scope or novel reactivity. Genetically encodable biosensors (GEBs), which convert the concentration of a small molecule ligand into an easily detectable output signal, have seen increasing application to enzyme directed evolution in the last decade. GEBs enable the use of high-throughput methods to assess enzyme activity of very large libraries, which can accelerate the search for variants with desirable activity. Here, we review different classes of GEBs and their properties in the context of enzyme evolution, how GEBs have been integrated into directed evolution workflows, and recent examples of enzyme evolution efforts utilizing GEBs. Finally, we discuss the advantages, challenges, and opportunities for using GEBs in the directed evolution of enzymes.

Reprogramming of phytopathogen transcriptome by a non-bactericidal pesticide residue alleviates its virulence in rice

Bacteria equipped with virulence systems based on highly bioactive small molecules can circumvent their host's defense mechanisms. Pathogens employing this strategy are currently threatening global rice production. In the present study, variations in the virulence of the highly destructive Burkholderia plantarii were observed in different rice-producing regions. The environment-linked variation was not attributable to any known host-related or external factors. Co-occurrence analyses indicated a connection between reduced virulence and 5-Amino-1,3,4-thiadiazole-2-thiol (ATT), a non-bactericidal organic compound. ATT, which accumulates in rice plants during metabolization of specific agrochemicals, was found to reduce virulence factor secretion by B. plantarii up to 88.8% and inhibit pathogen virulence by hijacking an upstream signaling cascade. Detailed assessment of the newly discovered virulence inhibitor resulted in mechanistic insights into positive effects of ATT accumulation in plant tissues. Mechanisms of virulence alleviation were deciphered by integrating high-throughput data, gene knockout mutants, and molecular interaction assays. TroK, a histidine protein kinase in a two-component system that regulates virulence factor secretion, is likely the molecular target antagonized by ATT. Our findings provide novel insights into virulence modulation in an important plant-pathogen system that relies on the host's metabolic activity and subsequent signaling interference.

Electrogenetic Signal Transmission and Propagation in Coculture to Guide Production of a Small Molecule, Tyrosine

There are many strategies to actuate and control genetic circuits, including providing stimuli like exogenous chemical inducers, light, magnetic fields, and even applied voltage, that are orthogonal to metabolic activity. Their use enables actuation of gene expression for the production of small molecules and proteins in many contexts. Additionally, there are a growing number of reports wherein cocultures, consortia, or even complex microbiomes are employed for the production of biologics, taking advantage of an expanded array of biological function. Combining stimuli-responsive engineered cell populations enhances design space but increases complexity. In this work, we co-opt nature's redox networks and electrogenetically route control signals into a consortium of microbial cells engineered to produce a model small molecule, tyrosine. In particular, we show how electronically programmed short-lived signals (i.e., hydrogen peroxide) can be transformed by one population and propagated into sustained longer-distance signals that, in turn, guide tyrosine production in a second population building on bacterial quorum sensing that coordinates their collective behavior. Two design methodologies are demonstrated. First, we use electrogenetics to transform redox signals into the quorum sensing autoinducer, AI-1, that, in turn, induces a tyrosine biosynthesis pathway transformed into a second population. Second, we use the electrogenetically stimulated AI-1 to actuate expression of ptsH, boosting the growth rate of tyrosine-producing cells, augmenting both their number and metabolic activity. In both cases, we show how signal propagation within the coculture helps to ensure tyrosine production. We suggest that this work lays a foundation for employing electrochemical stimuli and engineered cocultures for production of molecular products in biomanufacturing environments.

A Simple Biosensor-Based Assay for Quantitative Autoinducer-2 Analysis

Bacteria produce and react to interspecies signaling molecules in order to control the expression of genes that are particularly beneficial when they are expressed by a bacterial community. In addition to intraspecies communication, the signaling molecule autoinducer-2 (AI-2) can also serve for interspecies communication between Gram-positive and Gram-negative bacteria and is therefore of particular interest. The analysis and quantification of AI-2 are essential for understanding population density-dependent changes in bacterial behavior and pathogenicity. However, currently available bioassays for AI-2 quantification are rather complex, have narrow detection ranges, and are very sensitive to trace components of, for example, growth media. To facilitate and improve the detection of AI-2, we have developed an Escherichia coli biosensor-based assay that is sensitive, cheap, fast, robust, and reliable in the quantification of biologically active AI-2. The bioassay is based on an lsr promoter-fluorescent reporter gene fusion cassette that we chromosomally integrated in a biosensor strain, but the cassette can also be used in a low-copy number plasmid for the application in other Gram-negative bacterial species. We show here that AI-2 quantification was possible in a concentration range from 400 nM to 100 μM and that a critical interpretation of the kinetics of the measurements can reveal sugar interference. With the help of our biosensor strain, coculture experiments were done to test the capability and kinetics of AI-2 secretion by various Gram-negative bacteria in real time. Finally, calibration curves were used to calculate the absolute AI-2 concentration in cell-free bacterial samples.

A Redox-Based Autoinduction Strategy to Facilitate Expression of 5xCys-Tagged Proteins for Electrobiofabrication

Biofabrication utilizes biological materials and biological means, or mimics thereof, for assembly. When interfaced with microelectronics, electrobiofabricated assemblies enable exquisite sensing and reporting capabilities. We recently demonstrated that thiolated polyethylene glycol (PEG-SH) could be oxidatively assembled into a thin disulfide crosslinked hydrogel at an electrode surface; with sufficient oxidation, extra sulfenic acid groups are made available for covalent, disulfide coupling to sulfhydryl groups of proteins or peptides. We intentionally introduced a polycysteine tag (5xCys-tag) consisting of five consecutive cysteine residues at the C-terminus of a Streptococcal protein G to enable its covalent coupling to an electroassembled PEG-SH film. We found, however, that its expression and purification from E. coli was difficult, owing to the extra cysteine residues. We developed a redox-based autoinduction methodology that greatly enhanced the yield, especially in the soluble fraction of E. coli extracts. The redox component involved the deletion of oxyRS, a global regulator of the oxidative stress response and the autoinduction component integrated a quorum sensing (QS) switch that keys the secreted QS autoinducer-2 to induction. Interestingly, both methods helped when independently employed and further, when used in combination (i.e., autodinduced oxyRS mutant) the results were best—we found the highest total yield and highest yield in the soluble fraction. We hypothesize that the production host was less prone to severe metabolic perturbations that might reduce yield or drive sequestration of the -tagged protein into inclusion bodies. We expect this methodology will be useful for the expression of many such Cys-tagged proteins, ultimately enabling a diverse array of functionalized devices.

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

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

Bioelectronic control of a microbial community using surface-assembled electrogenetic cells to route signals

We developed a bioelectronic communication system that is enabled by a redox signal transduction modality to exchange information between a living cell-embedded bioelectronics interface and an engineered microbial network. A naturally communicating three-member microbial network is 'plugged into' an external electronic system that interrogates and controls biological function in real time. First, electrode-generated redox molecules are programmed to activate gene expression in an engineered population of electrode-attached bacterial cells, effectively creating a living transducer electrode. These cells interpret and translate electronic signals and then transmit this information biologically by producing quorum sensing molecules that are, in turn, interpreted by a planktonic coculture. The propagated molecular communication drives expression and secretion of a therapeutic peptide from one strain and simultaneously enables direct electronic feedback from the second strain, thus enabling real-time electronic verification of biological signal propagation. Overall, we show how this multifunctional bioelectronic platform, termed a BioLAN, reliably facilitates on-demand bioelectronic communication and concurrently performs programmed tasks.

Function of quorum sensing and cell signaling in wastewater treatment systems

Quorum sensing (QS) is a communication mode between microorganisms to regulate bacteria ecological relations and physiological behaviors, thus achieve the physiological function that single bacteria cannot complete. This phenomenon plays important roles in the formation of biofilm and granular sludge, and may be related to enhancement of some functional bacteria activity in wastewater treatment systems. There is a need to better understand bacterial QS in engineered reactors, and to assess how designs and operations might improve the removal efficiency. This article reviewed the recent advances of QS in several environmental systems and mainly analyzed the regulation mechanism of QS-based strategies for biofilm, granular sludge, functional bacteria, and biofouling control. The co-existences of multiple signal molecules in wastewater treatment (WWT) processes were also summarized, which provide basis for the future research on the QS mechanism of multiple signal molecules' interaction in WWT. This review would present some prospects and suggestions which are of practical significance for further application.

Homologous Quorum Sensing Regulatory Circuit: A Dual-Input Genetic Controller for Modulating Quorum Sensing-Mediated Protein Expression in E. coli

We developed a hybrid synthetic circuit that co-opts the genetic regulation of the native bacterial quorum sensing autoinducer-2 and imposes an extra external controller for maintaining tightly controlled gene expression. This dual-input genetic controller was mathematically modeled and, by design, can be operated in three modes: a constitutive mode that enables consistent and high levels of expression; a tightly repressed mode in which there is very little background expression; and an inducible mode in which concentrations of two signals (arabinose and autoinducer-2) determine the net amplification of the gene(s)-of-interest. We demonstrate the utility of the circuit for the controlled expression of human granulocyte macrophage colony stimulating factor in an engineered probiotic E. coli. This dual-input genetic controller is the first homologous AI-2 quorum sensing circuit that has the ability to be operated in three different modes. We believe it has the potential for wide-ranging biotechnological applications due its versatile features.

Redox Electrochemistry to Interrogate and Control Biomolecular Communication

Cells often communicate by the secretion, transport, and perception of molecules. Information conveyed by molecules is encoded, transmitted, and decoded by cells within the context of the prevailing microenvironments. Conversely, in electronics, transmission reliability and message validation are predictable, robust, and less context dependent. In turn, many transformative advances have resulted by the formal consideration of information transfer. One way to explore this potential for biological systems is to create bio-device interfaces that facilitate bidirectional information transfer between biology and electronics. Redox reactions enable this linkage because reduction and oxidation mediate communication within biology and can be coupled with electronics. By manipulating redox reactions, one is able to combine the programmable features of electronics with the ability to interrogate and modulate biological function. In this review, we examine methods to electrochemically interrogate the various components of molecular communication using redox chemistry and to electronically control cell communication using redox electrogenetics.

Enhancement of specific T-lymphocyte responses by monocyte-derived dendritic cells pulsed with E2 protein of human papillomavirus 16 and human p16INK4A

Introduction

Prophylactic vaccines are already available for prevention of human papillomavirus (HPV) infection. However, we still await development of therapeutic vaccines with high efficiency for stimulating specific T lymphocytes to clear HPV infection.

Objective

This study investigates the potential for subunits of human p16INK4a protein and E2 protein of HPV16 to stimulate dendritic cells and enhance the specific response of T lymphocytes against HPV-infected cells.

Methodology

Immunogenic epitopes of HPV16 E2 and p16INK4a proteins were predicted through the common HLA class I and II alleles present in the Thai population. Then, monocyte-derived dendritic cells (MDCs) were pulsed with HPV16 E2 and/or p16INK4a protein s and their maturity assessed. MDCs pulsed with either or both of these proteins at optimal concentrations were used for activation of autologous T lymphocytes and IFN-γ production was measured for specific response function.

Results

HPV16 E2 and p16INK4a proteins contain various immunogenic epitopes which can be presented by antigen-presenting cells via both HLA class I and II molecules. The stimulation of MDCs with either HPV16 E2 or p16INK4a proteins increased percentages and mean fluorescence intensity (MFI) of CD83⁺ MDCs in a dose-dependent manner. An optimum concentration of 250 ng/mL and 150 ng/mL of HPV16 E2 and p16INK4a proteins, respectively, stimulated MDCs via the MAPK pathway (confirmed by use of MAPK inhibitors). T lymphocytes could be activated by MDCs pulsed with these proteins, leading to high percentages of both CD4⁺ IFN-γ⁺ T lymphocytes and CD8⁺ IFN-γ⁺ T lymphocytes. The production of IFN-γ was higher in co-cultures containing MDCs pulsed with HPV16 E2 protein than those pulsed with p16INK4a. Interestingly, MDCs pulsed with a combination of HPV16 E2 and p16INK4a significantly increased IFN-γ production of T lymphocytes. The IFN-γ production was inhibited by both HLA class I and II blockade, particularly in co-cultures with MDCs pulsed with a combination of HPV16 E2 and p16INK4a.

Conclusions

This suggests that MDCs pulsed with both proteins enhances specific response of both CD4⁺ and CD8⁺ T lymphocytes. This study might provide a strategy for further in vivo study of stimulation of T lymphocytes for therapy of HPV-associated cancer.

Quorum Sensing Communication: Molecularly Connecting Cells, Their Neighbors, and Even Devices

Quorum sensing (QS) is a molecular signaling modality that mediates molecular-based cell–cell communication. Prevalent in nature, QS networks provide bacteria with a method to gather information from the environment and make decisions based on the intel. With its ability to autonomously facilitate both inter- and intraspecies gene regulation, this process can be rewired to enable autonomously actuated, but molecularly programmed, genetic control. On the one hand, novel QS-based genetic circuits endow cells with smart functions that can be used in many fields of engineering, and on the other, repurposed QS circuitry promotes communication and aids in the development of synthetic microbial consortia. Furthermore, engineered QS systems can probe and intervene in interkingdom signaling between bacteria and their hosts. Lastly, QS is demonstrated to establish conversation with abiotic materials, especially by taking advantage of biological and even electronically induced assembly processes; such QS-incorporated biohybrid devices offer innovative ways to program cell behavior and biological function.

The role of quorum sensing in granular sludge: Impact and future application: A review

Quorum sensing (QS) is a process widely exist in bacteria, which refers to the cell-cell communication through secretion and sensing the specific chemical signal molecules named autoinducers. This review demonstrated recent research progresses on the specific impacts of signal molecules in the granular sludge reactors, such corresponding exogenous strategies contained the addition of QS signal molecules, QS-related enzymes and bacteria associated with QS process. Accordingly, the correlation between QS signaling molecule content and sludge granulation (including the formation and stability) was assumed, the comprehensive conclusion elucidated that some QS signals (acyl-homoserine lactone and Autoinducer 2) can accelerate the growth of particle diameter, the production of extracellular polymeric substance (EPS), microbial adhesion and change the microbiome structure. But diffusable signal factor (DSF) acted as a significant disincentive to the formation and stability of GS. As a result, it deserved serious attention on the value and role of QS signals in the GS. This review attempts to illuminate the potential method for addressing the main bottleneck: to accelerate the formation of granules and keep the high stability of GS for a long-term reactor. Therefore, review discussed the possible trends of GS: QS and intercellular/intracellular signaling which can lay a theoretical foundation for mechanism of GS formation and stability, would be of practical significance for further application in the future.

Focusing quorum sensing signalling by nano-magnetic assembly

Quorum sensing (QS) exists widely among bacteria, enabling a transition to multicellular behaviour after bacterial populations reach a particular density. The coordination of multicellularity enables biotechnological application, dissolution of biofilms, coordination of virulence, and so forth. Here, a method to elicit and subsequently disperse multicellular behaviour among QS-negative cells is developed using magnetic nanoparticle assembly. We fabricated magnetic nanoparticles (MNPs, ∼5 nm) that electrostatically collect wild-type (WT) Escherichia coli BL21 cells and brings them into proximity of bioengineered E. coli [CT104 (W3110 lsrFG^- luxS^- pCT6 + pET-DsRed)] reporter cells that exhibit a QS response after receiving autoinducer-2 (AI-2). By shortening the distance between WT and reporter cells (e.g., increasing local available AI-2 concentrations), the QS response signalling was amplified four-fold compared to that in native conditions without assembly. This study suggests potential applications in facilitating intercellular communication and modulating multicellular behaviours based on user-specified designs.

Bacterial co-culture with cell signaling translator and growth controller modules for autonomously regulated culture composition

Synthetic biology and metabolic engineering have expanded the possibilities for engineered cell-based systems. The addition of non-native biosynthetic and regulatory components can, however, overburden the reprogrammed cells. In order to avoid metabolic overload, an emerging area of focus is on engineering consortia, wherein cell subpopulations work together to carry out a desired function. This strategy requires regulation of the cell populations. Here, we design a synthetic co-culture controller consisting of cell-based signal translator and growth-controller modules that, when implemented, provide for autonomous regulation of the consortia composition. The system co-opts the orthogonal autoinducer AI-1 and AI-2 cell-cell signaling mechanisms of bacterial quorum sensing (QS) to enable cross-talk between strains and a QS signal-controlled growth rate controller to modulate relative population densities. We further develop a simple mathematical model that enables cell and system design for autonomous closed-loop control of population trajectories.

To avoid metabolic overload and divide tasks, synthetic biologists are turning to microbial consortia engineering. Here the authors design a co-culture controller that autonomously regulates population composition.

Engineering Escherichia coli for enhanced sensitivity to the autoinducer-2 quorum sensing signal

The autoinducer-2 (AI-2) quorum sensing system is involved in a range of population-based bacterial behaviors and has been engineered for cell-cell communication in synthetic biology systems. Investigation into the cellular mechanisms of AI-2 processing has determined that overexpression of uptake genes increases AI-2 uptake rate, and genomic deletions of degradation genes lowers the AI-2 level required for activation of reporter genes. Here, we combine these two strategies to engineer an Escherichia coli strain with enhanced ability to detect and respond to AI-2. In an E. coli strain that does not produce AI-2, we monitored AI-2 uptake and reporter protein expression in a strain that overproduced the AI-2 uptake or phosphorylation units LsrACDB or LsrK, a strain with the deletion of AI-2 degradation units LsrF and LsrG, and an "enhanced" strain with both overproduction of AI-2 uptake and deletion of AI-2 degradation elements. By adding up to 40 μM AI-2 to growing cell cultures, we determine that this "enhanced" AI-2 sensitive strain both uptakes AI-2 more rapidly and responds with increased reporter protein expression than the others. This work expands the toolbox for manipulating AI-2 quorum sensing processes both in native environments and for synthetic biology applications.

Bacteria Floc, but Do They Flock? Insights from Population Interaction Models of Quorum Sensing

Quorum sensing (QS) enables coordinated, population-wide behavior. QS-active bacteria "communicate" their number density using autoinducers which they synthesize, collect, and interpret. Tangentially, chemotactic bacteria migrate, seeking out nutrients and other molecules. It has long been hypothesized that bacterial behaviors, such as chemotaxis, were the primordial progenitors of complex behaviors of higher-order organisms. Recently, QS was linked to chemotaxis, yet the notion that these behaviors can together contribute to higher-order behaviors has not been shown. Here, we mathematically link flocking behavior, commonly observed in fish and birds, to bacterial chemotaxis and QS by constructing a phenomenological model of population-scale QS-mediated phenomena. Specifically, we recast a previously developed mathematical model of flocking and found that simulated bacterial behaviors aligned well with well-known QS behaviors. This relatively simple system of ordinary differential equations affords analytical analysis of asymptotic behavior and describes cell position and velocity, QS-mediated protein expression, and the surrounding concentrations of an autoinducer. Further, heuristic explorations of the model revealed that the emergence of "migratory" subpopulations occurs only when chemotaxis is directly linked to QS. That is, behaviors were simulated when chemotaxis was coupled to QS and when not. When coupled, the bacterial flocking model predicts the formation of two distinct groups of cells migrating at different speeds in their journey toward an attractant. This is qualitatively similar to phenomena spotted in our Escherichiacoli chemotaxis experiments as well as in analogous work observed over 50 years ago.IMPORTANCE Our modeling efforts show how cell density can affect chemotaxis; they help to explain the roots of subgroup formation in bacterial populations. Our work also reinforces the notion that bacterial mechanisms are at times exhibited in higher-order organisms.

Plasmid-encoded protein attenuates Escherichia coli swimming velocity and cell growth, not reprogrammed regulatory functions

In addition to engineering new pathways for synthesis, synthetic biologists rewire cells to carry out "programmable" functions, an example being the creation of wound-healing probiotics. Engineering regulatory circuits and synthetic machinery, however, can be deleterious to cell function, particularly if the "metabolic burden" is significant. Here, a synthetic regulatory circuit previously constructed to direct Escherichia coli to swim toward hydrogen peroxide, a signal of wound generation, was shown to work even with coexpression of antibiotic resistance genes and genes associated with lactose utilization. We found, however, that cotransformation with a second vector constitutively expressing GFP (as a marker) and additionally conferring resistance to kanamycin and tetracycline resulted in slower velocity (Δ~6 μm/s) and dramatically reduced growth rate (Δ > 50%). The additional vector did not, however, alter the run-and-tumble ratio or directional characteristics of H2 O2 -dependent motility. The main impact of this additional burden was limited to slowing cell velocity and growth, suggesting that reprogrammed cell motility by minimally altering native regulatory circuits can be maintained even when extraneous burden is placed on the host cell. © 2019 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2778, 2019.

An immune magnetic nano-assembly for specifically amplifying intercellular quorum sensing signals

Quorum sensing (QS) enables intercellular communication after bacterial cells sense the autoinducers have reached or exceeded a critical concentration. Selectively amplifying specific bacterial "quorum" activity at a lower cell density is still a challenge. Here, we propose a novel platform of immune magnetic nano-assembly to amplify specific bacterial QS signaling via improving the bioavailability of autoinducers-2 (AI-2, furanosyl borate) from sender (wide-type, WT cells) to receiver (reporter cells). Antibody coated magnetic nanoparticle (MNPAB) was fabricated with an average diameter of 12 nm and a specific surface area of 96.5 m²/g. The distribution efficiency of the antibody on the surface was 25.8 μg/m² of magnetic nanoparticles. It was found that more than 3 × 10⁸ of K12 serotype Escherichia coli (E. coli) reporter or WT cells were collected using 1 mg fabricated MNPAB at a saturated condition. The MNPAB not only captured E. coli WT cells but also brought them into proximity of E. coli (CT104, pCT6+pET-DsRed) reporter cells via magnetic attraction. The amplified QS signaling of the reporter cells by this immune magnetic nano-assembly was approximately 3 times higher than the nature QS signaling in cell suspension at optical density (OD) 0.08. This study foresees potential applications in amplifying specific biological QS signals based on a preprogrammed design.

Quorum sensing inhibitors: a patent review (2014-2018)

Introduction: Quorum sensing (QS) is a cell density-dependent phenomenon in which specific pathways are activated after autoinducers (AIs) outside the microorganism reach a threshold concentration. QS creates a positive feedback loop that induces a cascade of gene expression and causes biofilm formation, virulence and sporulation. QS signals are diverse, acyl-homoserine lactone (AHL), AI peptide (AIP) and AI-2 are three major categories of QS signals. QS inhibitors (QSIs) can disrupt or prevent the formation of biofilm and reduce virulence while exerting less selective pressure on the bacteria, suggesting that QSIs are potential alternatives for antibiotics. Areas covered: This review summarized the pertinent patents on QS inhibition available from 2014 to 2018. The authors analyze these patents and provided an overview of them and their potential applications. Expert opinion: The main strategy for QS inhibition is to use the analogues of various QS signals to block downstream signal transducers. The inactivation of signal molecules or the stimulation of the immune response is also attractive strategies to inhibit QS. However, additional clinical trials are needed to assess their efficacy in mammals. In sum, QS inhibition can reduce the virulence of bacteria without affecting their growth or killing them and the reduced pressure may minimize the increasingly resistance.

A Genetically Encoded Biosensor for Monitoring Isoprene Production in Engineered Escherichia coli

Isoprene is a valuable precursor for synthetic rubber and a signature product of terpenoid pathways. Here, we developed an isoprene biosensor by employing a TbuT transcriptional regulator of Ralstonia pickettii to express a fluorescent reporter gene in response to intracellular isoprene in engineered Escherichia coli. The TbuT regulator recognizes isoprene as its less-preferred effector molecule; thus, we amplified the reporter gene expression using a T7 RNA polymerase-mediated transcriptional cascade and iteratively tuned the promoter transcribing tbuT to improve the sensitivity for detecting isoprene. When the engineered E. coli cells expressed heterologous genes for isoprene biosynthesis, the intracellular isoprene was expelled and the tbuT transcription factor was subsequently activated, leading to gfp expression. The chromosomal isoprene biosensor showed a linear correlation between GFP fluorescence and intracellular isoprene concentration. Using this chromosomal isoprene biosensor, we successfully identified the highest isoprene producer among four different E. coli strains producing different amounts of isoprene. The isoprene biosensor presented here can enable high-throughput screening of isoprene synthases and metabolic pathways for efficient and sustainable production of bioisoprene in engineered microbes.

Development of Cell-Based Sentinels for Nitric Oxide: Ensuring Marker Expression and Unimodality

We generated "sentinel" bacteria that respond to the biomarker nitric oxide (NO) and produce a homogeneous and strong fluorescent response. Our dual-plasmid system consists of a signal "relay" vector that employs an NO-responsive promoter that amplifies the native signal (via expression of T7 Polymerase (T7Pol)) to a second vector responsible for GFP expression. Importantly, to achieve an optimal "sentinel" response, we developed strategies that balance the transcriptional load within cells by altering (i) translation and (ii) activity of the T7Pol. Our optimized genetic circuitry was then used to transform commensal E. coli Nissle, as a proof-of-concept toward an ingestible cell-based sensor for Crohn's disease (CD) that, in turn, is marked by elevated levels of intestinal NO. Thus, the "biosensors" demonstrated here may serve as a simple diagnostic tool, contrasting the standard of care including colonoscopies or biopsies.

An Engineered Device for Indoleacetic Acid Production under Quorum Sensing Signals Enables Cupriavidus pinatubonensis JMP134 To Stimulate Plant Growth

The environmental effects of chemical fertilizers and pesticides have encouraged the quest for new strategies to increase crop productivity with minimal impacts on the natural medium. Plant growth promoting rhizobacteria (PGPR) can contribute to this endeavor by improving fitness through better nutrition acquisition and stress tolerance. Using the neutral (non PGPR) rhizobacterium Cupriavidus pinatubonensis JMP134 as the host, we engineered a regulatory forward loop that triggered the synthesis of the phytohormone indole-3-acetic acid (IAA) in a manner dependent on quorum sensing (QS) signals. Implementation of the device in JMP134 yielded synthesis of IAA in an autoregulated manner, improving the growth of the roots of inoculated Arabidopsis thaliana. These results not only demonstrated the value of the designed genetic module, but also validated C. pinatubonensis JMP134 as a suitable vehicle for agricultural applications, as it is amenable to genetic manipulations.

Modification and Assembly of a Versatile Lactonase for Bacterial Quorum Quenching

This work sets out to provide a self-assembled biopolymer capsule activated with a multi-functional enzyme for localized delivery. This enzyme, SsoPox, which is a lactonase and phosphotriesterase, provides a means of interrupting bacterial communication pathways that have been shown to mediate pathogenicity. Here we demonstrate the capability to express, purify and attach SsoPox to the natural biopolymer chitosan, preserving its activity to "neutralize" long-chain autoinducer-1 (AI-1) communication molecules. Attachment is shown via non-specific binding and by engineering tyrosine and glutamine affinity 'tags' at the C-terminus for covalent linkage. Subsequent degradation of AI-1, in this case N-(3-oxododecanoyl)-l-homoserine lactone (OdDHL), serves to "quench" bacterial quorum sensing (QS), silencing intraspecies communication. By attaching enzymes to pH-responsive chitosan that, in turn, can be assembled into various forms, we demonstrate device-based flexibility for enzyme delivery. Specifically, we have assembled quorum-quenching capsules consisting of an alginate inner core and an enzyme "decorated" chitosan shell that are shown to preclude bacterial QS crosstalk, minimizing QS mediated behaviors.

Production, detection and application perspectives of quorum sensing autoinducer-2 in bacteria

Autoinducer-2 (AI-2) is a major signal molecule in bacterial quorum sensing (QS) besides N-acyl homoserine lactones (AHLs or AI-1). AI-2 mediated QS pathways have been proved to regulate gene expression and physiological behaviors of bacteria in either intraspecies or interspecies communication. Recent reviews have mainly summarized AI-2 structures, AI-2 mediated QS pathways and the role of AI-2 in gene regulation, etc. In this article, we present a comprehensive review of AI-2 production, detection and applications. Firstly, intracellular AI-2 synthetic routes were outlined and environmental influences on AI-2 production were focused. Furthermore, recent advances in AI-2 detection and quantification were elucidated from an overall perspective. An in-depth understanding of mechanisms and features of various detection methods may facilitate development of new technologies aimed at signal molecule detection. Finally, utilization of AI-2 mediated QS in health improvement, water treatment and drug production indicate promising and extensive application perspectives of QS strategies.

Incorporating LsrK AI-2 quorum quenching capability in a functionalized biopolymer capsule

Antibacterial resistance is an issue of increasing severity as current antibiotics are losing their effectiveness and fewer antibiotics are being developed. New methods for combating bacterial virulence are required. Modulating molecular communication among bacteria can alter phenotype, including attachment to epithelia, biofilm formation, and even toxin production. Intercepting and modulating communication networks provide a means to attenuate virulence without directly interacting with the bacteria of interest. In this work, we target communication mediated by the quorum sensing (QS) bacterial autoinducer-2, AI-2. We have assembled a capsule of biological polymers alginate and chitosan, attached an AI-2 processing kinase, LsrK, and provided substrate, ATP, for enzymatic alteration of AI-2 in culture fluids. Correspondingly, AI-2 mediated QS activity is diminished. All components of this system are "biofabricated"-they are biologically derived and their assembly is accomplished using biological means. Initially, component quantities and kinetics were tested as assembled in microtiter plates. Subsequently, the identical components and assembly means were used to create the "artificial cell" capsules. The functionalized capsules, when introduced into populations of bacteria, alter the dynamics of the AI-2 bacterial communication, attenuating QS activated phenotypes. We envision the assembly of these and other capsules or similar materials, as means to alter QS activity in a biologically compatible manner and in many environments, including in humans.

Regulation of bacteria population behaviors by AI-2 "consumer cells" and "supplier cells"

Background

Autoinducer-2 (AI-2) is a universal signal molecule and enables an individual bacteria to communicate with each other and ultimately control behaviors of the population. Harnessing the character of AI-2, two kinds of AI-2 “controller cells” (“consumer cells” and “supplier cells”) were designed to “reprogram” the behaviors of entire population.

Results

For the consumer cells, genes associated with the uptake and processing of AI-2, which includes LsrACDB, LsrFG, LsrK, were overexpressed in varying combinations. Four consumer cell strains were constructed: Escherichia coli MG1655 pLsrACDB (NK-C1), MG1655 pLsrACDBK (NK-C2), MG1655 pLsrACDBFG (NK-C3) and MG1655 pLsrACDBFGK (NK-C4). The key enzymes responsible for production of AI-2, LuxS and Mtn, were also overexpressed, yielding strains MG1655 pLuxS (NK-SU1), and MG1655 pLuxS-Mtn (NK-SU2). All the consumer cells could decrease the environmental AI-2 concentration. NK-C2 and NK-C4 were most effective in AI-2 uptake and inhibited biofilm formation. While suppliers can increase the environmental AI-2 concentration and NK-SU2 was most effective in supplying AI-2 and facilitated biofilm formation. Further, reporter strain, MG1655 pLGFP was constructed. The expression of green fluorescent protein (GFP) in reporter cells was initiated and guided by AI-2. Mixture of consumer cells and reporter cells suggest that consumer cells can decrease the AI-2 concentration. And the supplier cells were co-cultured with reporter cells, indicating that supplier cells can provide more AI-2 compared to the control.

Conclusions

The consumer cells and supplier cells could be used to regulate environmental AI-2 concentration and the biofilm formation. They can also modulate the AI-2 concentration when they were co-cultured with reporter cells. It can be envisioned that this system will become useful tools in synthetic biology and researching new antimicrobials.

Electronic supplementary material

The online version of this article (10.1186/s12866-017-1107-2) contains supplementary material, which is available to authorized users.

Signal Destruction Tunes the Zone of Activation in Spatially Distributed Signaling Networks

Diverse microbial communities coordinate group behaviors through signal exchange, such as the exchange of acyl-homoserine lactones (AHLs) by Gram-negative bacteria. Cellular communication is prone to interference by neighboring microbes. One mechanism of interference is signal destruction through the production of an enzyme that cleaves the signaling molecule. Here we examine the ability of one such interference enzyme, AiiA, to modulate signal propagation in a spatially distributed system of bacteria. We have developed an experimental assay to measure signal transduction and implement a theoretical model of signaling dynamics to predict how the system responds to interference. We show that titration of an interfering strain into a signaling network tunes the spatial range of activation over the centimeter length scale, quantifying the robustness of the signaling network to signal destruction and demonstrating the ability to program systems-level responses of spatially heterogeneous cellular networks.

Electronic control of gene expression and cell behaviour in Escherichia coli through redox signalling

The ability to interconvert information between electronic and ionic modalities has transformed our ability to record and actuate biological function. Synthetic biology offers the potential to expand communication ‘bandwidth' by using biomolecules and providing electrochemical access to redox-based cell signals and behaviours. While engineered cells have transmitted molecular information to electronic devices, the potential for bidirectional communication stands largely untapped. Here we present a simple electrogenetic device that uses redox biomolecules to carry electronic information to engineered bacterial cells in order to control transcription from a simple synthetic gene circuit. Electronic actuation of the native transcriptional regulator SoxR and transcription from the PsoxS promoter allows cell response that is quick, reversible and dependent on the amplitude and frequency of the imposed electronic signals. Further, induction of bacterial motility and population based cell-to-cell communication demonstrates the versatility of our approach and potential to drive intricate biological behaviours.

Synthetic biology offers the ability to explore new ways of manipulating gene expression and function. Here the authors demonstrate an electrogenetic device that allows control of transcription by an exogenous electrical signal.

TumbleScore: Run and tumble analysis for low frame-rate motility videos

Scientists often exploit the motility of peritrichously flagellated bacteria for various applications. A common alteration is modifying the frequency of mid-movement changes in direction, known as tumbles. Such differences in bacterial swimming patterns can prove difficult to quantify, especially for those without access to high-speed optical equipment. Traditionally, scientists have resorted to less accurate techniques, such as soft agar plate assays, or have been forced to invest in costly equipment. Here, we present TumbleScore, software designed to track and quantify bacterial movies with slow, as well as fast, frame-rates. Developed and fully contained within MATLAB, TumbleScore processes motility videos and returns pertinent tumbling metrics, including: (i) linear speed, (ii) rotational speed, (iii) percentage of angle changes below a given threshold, and (iv) ratio of total path length to Euclidian distance, or arc-chord ratio (ACR). In addition, TumbleScore produces a "rose graph" visualization of bacterial paths. The software was validated using both fabricated and experimental motility videos.

Constructing "quantized quorums" to guide emergent phenotypes through quorum quenching capsules

Microbial cells have for many years been engineered to facilitate efficient production of biologics, chemicals, and other compounds. As the "metabolic" burden of synthetic genetic components can impair cell performance, microbial consortia are being developed to piece together specialized subpopulations that collectively produce desired products. Their use, however, has been limited by the inability to control their composition and function. One approach to leverage advantages of the division of labor within consortia is to link microbial subpopulations together through quorum sensing (QS) molecules. Previously, we directed the assembly of "quantized quorums," microbial subpopulations that are parsed through QS activation, by the exogenous addition of QS signal molecules to QS synthase mutants. In this work, we develop a more facile and general platform for creating "quantized quorums." Moreover, the methodology is not restricted to QS-mutant populations. We constructed quorum quenching capsules that partition QS-mediated phenotypes into discrete subpopulations. This compartmentalization guides QS subpopulations in a dose-dependent manner, parsing cell populations into activated or deactivated groups. The capsular "devices" consist of polyelectrolyte alginate-chitosan beads that encapsulate high-efficiency (HE) "controller cells" that, in turn, provide rapid uptake of the QS signal molecule AI-2 from culture fluids. In this methodology, instead of adding AI-2 to parse QS-mutants into subpopulations, we engineered cells to encapsulate them into compartments, and they serve to deplete AI-2 from wild-type populations. These encapsulated bacteria therefore, provide orthogonal control of population composition while allowing only minimal interaction with the product-producing cell population or consortia. We envision that compartmentalized control of QS should have applications in both metabolic engineering and human disease. Biotechnol. Bioeng. 2017;114: 407-415. © 2016 Wiley Periodicals, Inc.

Enhancing Intercellular Coordination: Rewiring Quorum Sensing Networks for Increased Protein Expression through Autonomous Induction

While inducing agents are often used to redirect resources from growth and proliferation toward product outputs, they can be prohibitively expensive on the industrial scale. Previously, we developed an autonomously guided protein production system based on the rewiring of E. coli's native quorum sensing (QS) signal transduction cascade. Self-secreted autoinducer, AI-2, accumulated over time and actuated recombinant gene expression-its design, co-opting the collective nature of QS-mediated behavior. We recently demonstrated that desynchronization of autoinduced intercellular feedback leads to bimodality in QS activation. In this work, we developed a new QS-enabled system with enhanced feedback to reduce cell heterogeneity. This narrows the population distribution of protein expression, leading to significant per cell and overall increases in productivity. We believe directed engineering of cell populations and/or cell consortia will offer many such opportunities in future bioprocessing applications.

Quorum Sensing Desynchronization Leads to Bimodality and Patterned Behaviors

Quorum Sensing (QS) drives coordinated phenotypic outcomes among bacterial populations. Its role in mediating infectious disease has led to the elucidation of numerous autoinducers and their corresponding QS signaling pathways. Among them, the Lsr (LuxS-regulated) QS system is conserved in scores of bacteria, and its signal molecule, autoinducer-2 (AI-2), is synthesized as a product of 1-carbon metabolism. Lsr signal transduction processes, therefore, may help organize population scale activities in numerous bacterial consortia. Conceptions of how Lsr QS organizes population scale behaviors remain limited, however. Using mathematical simulations, we examined how desynchronized Lsr QS activation, arising from cell-to-cell population heterogeneity, could lead to bimodal Lsr signaling and fractional activation. This has been previously observed experimentally. Governing these processes are an asynchronous AI-2 uptake, where positive intracellular feedback in Lsr expression is combined with negative feedback between cells. The resulting activation patterns differ from that of the more widely studied LuxIR system, the topology of which consists of only positive feedback. To elucidate differences, both QS systems were simulated in 2D, where cell populations grow and signal each other via traditional growth and diffusion equations. Our results demonstrate that the LuxIR QS system produces an ‘outward wave’ of autoinduction, and the Lsr QS system yields dispersed autoinduction from spatially-localized secretion and uptake profiles. In both cases, our simulations mirror previously demonstrated experimental results. As a whole, these models inform QS observations and synthetic biology designs.

Bacterial behavior is responsive to a multitude of soluble molecular cues. Among them are self-secreted autoinducers that control quorum sensing (QS) processes. While new quorum sensing systems are constantly being discovered, several systems have been well defined in terms of their molecular and genetic topologies, each influencing a variety of resultant phenotypes. These quorum sensing systems include LuxIR homologs that use an array of species specific autoinducers and Lsr system homologs that share a single autoinducer among numerous species. Here we suggest that the regulatory topology of these two systems mark them as opposites of a sort. Whereas the LuxIR system bears a strong positive intercellular feedback mechanism, the Lsr system bears strong negative intercellular feedback. In our simulations these differences are manifested in distinct patterns of signaling. This was readily visualized in the outward spread of autogenous LuxIR expression in a growing bacterial 2D ‘colony’ whereas a dispersed activity was produced by autogenous Lsr expression in an otherwise identical colony. Here, this dispersed activity is a reflection of bimodal Lsr expression. We show that this bimodality could arise from desynchronized Lsr driven autoinducer import (intercellular negative feedback). This may have consequences on the arrangement of downstream phenotypes.

Nano-guided cell networks as conveyors of molecular communication

Advances in nanotechnology have provided unprecedented physical means to sample molecular space. Living cells provide additional capability in that they identify molecules within complex environments and actuate function. We have merged cells with nanotechnology for an integrated molecular processing network. Here we show that an engineered cell consortium autonomously generates feedback to chemical cues. Moreover, abiotic components are readily assembled onto cells, enabling amplified and 'binned' responses. Specifically, engineered cell populations are triggered by a quorum sensing (QS) signal molecule, autoinducer-2, to express surface-displayed fusions consisting of a fluorescent marker and an affinity peptide. The latter provides means for attaching magnetic nanoparticles to fluorescently activated subpopulations for coalescence into colour-indexed output. The resultant nano-guided cell network assesses QS activity and conveys molecular information as a 'bio-litmus' in a manner read by simple optical means.