Chlorocatechol detection based on a clc operon/reporter gene system

A navigation guide of synthetic biology tools for Pseudomonas putida

Pseudomonas putida is a microbial chassis of huge potential for industrial and environmental biotechnology, owing to its remarkable metabolic versatility and ability to sustain difficult redox reactions and operational stresses, among other attractive characteristics. A wealth of genetic and in silico tools have been developed to enable the unravelling of its physiology and improvement of its performance. However, the rise of this microbe as a promising platform for biotechnological applications has resulted in diversification of tools and methods rather than standardization and convergence. As a consequence, multiple tools for the same purpose have been generated, whilst most of them have not been embraced by the scientific community, which has led to compartmentalization and inefficient use of resources. Inspired by this and by the substantial increase in popularity of P. putida, we aim herein to bring together and assess all currently available (wet and dry) synthetic biology tools specific for this microbe, focusing on the last 5 years. We provide information on the principles, functionality, advantages and limitations, with special focus on their use in metabolic engineering. Additionally, we compare the tool portfolio for P. putida with those for other bacterial chassis and discuss potential future directions for tool development. Therefore, this review is intended as a reference guide for experts and new 'users' of this promising chassis.

Engineering Rugged Field Assays to Detect Hazardous Chemicals Using Spore-Based Bacterial Biosensors

Bacterial whole cell-based biosensors have been genetically engineered to achieve selective and reliable detection of a wide range of hazardous chemicals. Although whole-cell biosensors demonstrate many advantages for field-based detection of target analytes, there are still some challenges that need to be addressed. Most notably, their often modest shelf life and need for special handling and storage make them challenging to use in situations where access to reagents, instrumentation, and expertise are limited. These problems can be circumvented by developing biosensors in Bacillus spores, which can be engineered to address all of these concerns. In its sporulated state, a whole cell-based biosensor has a remarkably long life span and is exceptionally resistant to environmental insult. When these spores are germinated for use in analytical techniques, they show no loss in performance, even after long periods of storage under harsh conditions. In this chapter, we will discuss the development and use of whole cell-based sensors, their adaptation to spore-based biosensors, their current applications, and future directions in the field.

Fluorescent and bioluminescent cell-based sensors: strategies for their preservation

Luminescent whole-cell biosensing systems have been developed for a variety of analytes of environmental, clinical, and biological interest. These analytical tools allow for sensitive, rapid, simple, and inexpensive quantitative detection of target analytes. Furthermore, they can be designed to be nonspecific, semispecific, or highly specific/selective. A notable feature of such sensing systems employing living cells is that they provide information on the analyte bioavailability and activity. These characteristics, along with their suitability to miniaturization, make cell-based sensors ideal for field applications. However, a major limitation to on-site use is their "shelf-life." To address this problem, various methods for preservation of sensing cells have been reported, including freeze-drying, immobilization in different types of matrices, and formation of spores. Among these, the use of spores emerged as a promising strategy for long-term storage of whole-cell sensing systems at room temperature as well as in extreme environmental conditions.

Integration of spore-based genetically engineered whole-cell sensing systems into portable centrifugal microfluidic platforms

Bacterial whole-cell biosensing systems provide important information about the bioavailable amount of target analytes. They are characterized by high sensitivity and specificity/selectivity along with rapid response times and amenability to miniaturization as well as high-throughput analysis. Accordingly, they have been employed in various environmental and clinical applications. The use of spore-based sensing systems offers the unique advantage of long-term preservation of the sensing cells by taking advantage of the environmental resistance and ruggedness of bacterial spores. In this work, we have incorporated spore-based whole-cell sensing systems into centrifugal compact disk (CD) microfluidic platforms in order to develop a portable sensing system, which should enable the use of these hardy sensors for fast on-field analysis of compounds of interest. For that, we have employed two spore-based sensing systems for the detection of arsenite and zinc, respectively, and evaluated their analytical performance in the miniaturized microfluidic format. Furthermore, we have tested environmental and clinical samples on the CD microfluidic platforms using the spore-based sensors. Germination of spores and quantitative response to the analyte could be obtained in 2.5-3 h, depending on the sensing system, with detection limits of 1 x 10(-7) M for arsenite and 1 x 10(-6) M for zinc in both serum and fresh water samples. Incorporation of spore-based whole-cell biosensing systems on microfluidic platforms enabled the rapid and sensitive detection of the analytes and is expected to facilitate the on-site use of such sensing systems.

Applications of whole-cell bacterial sensors in biotechnology and environmental science

Biosensors have major advantages over chemical or physical analyses with regard to specificity, sensitivity, and portability. Recently, many types of whole-cell bacterial biosensors have been developed using recombinant DNA technology. The bacteria are genetically engineered to respond to the presence of chemicals or physiological stresses by synthesizing a reporter protein, such as luciferase, beta-galactosidase, or green fluorescent protein. In addition to an overview of conventional biosensors, this minireview discusses a novel type of biosensor using a photosynthetic bacterium as the sensor strain and the crtA gene, which is responsible for carotenoid synthesis, as the reporter. Since bacteria possess a wide variety of stress-response mechanisms, including antioxidation, heat-shock responses, nutrient-starvation, and membrane-damage responses, DNA response elements for several stress-response proteins can be fused with various reporter genes to construct a versatile set of bacterial biosensors for a variety of analytes. Portable biosensors for on-site monitoring have been developed using a freeze-dried biosensing strain, and cell array biosensors have been designed for high-throughput analysis. Moreover, in the future, the use of single-cell biosensors will permit detailed analyses of samples. Signals from such sensors could be detected with digital imaging, epifluorescence microscopy, and/or flow cytometry.

ClcR-based biosensing system in the detection of cis-dihydroxylated (chloro-)biphenyls

Polychlorinated biphenyls (PCBs) are a group of organic pollutants that are persistent when released into the environment. Among the metabolites of PCBs, dihydroxylated PCBs are also considered as toxic compounds. Various studies have shown that dihydroxylated PCBs affect the reproductive, immune, nervous, and endocrine systems. Detection of these chemicals in environmental and biological samples could provide first-hand information about their levels and lead to a better understanding of their role in toxicity. To that end, we developed a sensing system for the detection of dihydroxylated PCBs based on the clc operon. The Pseudomonas putida clc operon encodes a catabolic pathway for degradation of chlorocatechols, which are major metabolites of a large number of chlorinated compounds. In P. putida, the expression of these genes is regulated by a protein encoded by the gene clcR located upstream from the clcABD genes. We demonstrate here for the first time that dihydroxy PCBs can also induce the clc operon. Our sensing system employs P. putida bacteria harboring a plasmid in which the reporter gene, lacZ, is under the control of the regulatory protein ClcR. Consequently, when exposed to dihydroxy PCBs, the bacteria express beta-galactosidase in an amount related to the concentration of the corresponding dihydroxy PCB. Various dihydroxylated PCBs, differing in the number and position of chlorines and in the position of hydroxyls, were tested for their ability to induce expression of beta-galactosidase. Detection limits as low as 1 x 10(-6) mol L(-1) were obtained for various dihydroxylated PCBs.

Fluorescence-based sensing system for copper using genetically engineered living yeast cells

A whole cell-based optical sensing system for copper was developed based on Saccharomyces cerevisiae cells harboring plasmid pYEX-GFPuv. The basis of this system was the ability of the transcriptional activator protein Ace1 present in S. cerevisiae to control the expression of the reporter protein, GFPuv. When copper ions are present in the sample, the Ace1 protein activates the cup1 promoter located upstream from the gfpuv gene in plasmid pYEX-GFPuv, thus inducing the production of GFPuv. The concentration of copper ions in the sample can then be related to the GFPuv expressed in the yeast. The amount of GFPuv produced in the system was determined by monitoring the fluorescence emitted at 507 nm after excitation at 397 nm. This system can detect copper at concentrations as low as 5 x 10(-7) M, and is selective for copper over a variety of metal ions, with the exception of silver. The applicability of this sensing system to different analytical platforms and in real samples is demonstrated.

Microbial genes and enzymes in the degradation of chlorinated compounds

Microorganisms are well known for degrading numerous natural compounds. The synthesis of a multitude of chlorinated compounds by the chemical industry and their release into the natural environment have created major pollution problems. Part of the cause of such pollution is the inability of natural microorganisms to efficiently degrade synthetic chlorinated compounds. Microorganisms are, however, highly adaptable to changes in the environment and have consequently evolved the genes that specify the degradation of chlorinated compounds to varying degrees. Highly selective laboratory techniques have also enabled the isolation of microbial strains capable of utilizing normally recalcitrant highly chlorinated compounds as their sole source of carbon and energy. The evolution and role of microbial genes and enzymes, as well as their mode of regulation and genetic interrelationships, have therefore been the subjects of intense study. This review emphasizes the genetic organization and the regulation of gene expression, as well as evolutionary considerations, regarding the microbial degradation of chlorobenzoates, chlorocatechols, and chlorophenoxyacetic acids.

Luminescence-based whole-cell-sensing systems for cadmium and lead using genetically engineered bacteria

Whole-cell-based sensing systems that respond to cadmium and lead ions have been designed and developed using genetically engineered bacteria. These systems take advantage of the ability of certain bacteria to survive in environments polluted with cadmium and lead ions. The bacteria used in this investigation have been genetically engineered to produce reporter proteins in response to the toxic ions. This was achieved by modifying a strain of Escherichia colito harbor plasmids pYSC1 and pYS2/pYSG1. In these dual-plasmid-based sensing systems, the expression of the reporters beta-galactosidase and red-shifted green fluorescent protein (rs-GFP) was controlled by CadC, the regulatory protein of the cad operon. Regulation of the expression of the reporter proteins is related to the amount of cadmium and lead ions employed to induce the bacteria. The bacterial sensing systems were found to respond to cadmium, lead, and zinc ions, and had no significant response to nickel, copper, manganese, and cobalt.

Exposing culprit organic pollutants: a review

There is a continuing need for monitoring the health of the environment due to the presence of pollutants. Here, we review the development and attributes of biosensors by which bacteria have been genetically modified to express the luminescence genes, i.e. to glow, in a quantified manner, in response to pollutants. We have concentrated on the detection of organic hydrocarbon pollutants and discussed the molecular mechanisms by which some of these chemicals act as effector molecules on the respective regulatory systems. The future of environmental biosensors is predictably bright. As more knowledge is gathered on the sensing regulatory component, the possibility of developing targeted or pollutant-specific biosensors is promising. Moreover, the repertoire of biosensors for culprit organic pollutants is expected to be enlarged through advances in genomics technology and identification of new sensory or receptor molecules. The need for pollutant detection at concentrations in the parts per trillion range or biosensors configured in a nanoscale is anticipated.