Synthetic Biology: A New Era in Hydrocarbon Bioremediation

Crude oil is a viscous dark liquid resource composed by a mix of hydrocarbons which, after refining, is used for the elaboration of distinct products. A major concern is that many petroleum components are highly toxic due to their teratogenic, hemotoxic, and carcinogenic effects, becoming an environmental concern on a global scale, which must be solved through innovative, efficient, and sustainable techniques. One of the most widely used procedures to totally degrade contaminants are biological methods such as bioremediation. Synthetic biology is a scientific field based on biology and engineering principles, with the purpose of redesigning and restructuring microorganisms to optimize or create new biological systems with enhanced features. The use of this discipline offers improvement of bioremediation processes. This article will review some of the techniques that use synthetic biology as a platform to be used in the area of hydrocarbon bioremediation.

Synthetic Biology Approaches to Hydrocarbon Biosensors: A Review

Monooxygenases are a class of enzymes that facilitate the bacterial degradation of alkanes and alkenes. The regulatory components associated with monooxygenases are nature's own hydrocarbon sensors, and once functionally characterised, these components can be used to create rapid, inexpensive and sensitive biosensors for use in applications such as bioremediation and metabolic engineering. Many bacterial monooxygenases have been identified, yet the regulation of only a few of these have been investigated in detail. A wealth of genetic and functional diversity of regulatory enzymes and promoter elements still remains unexplored and unexploited, both in published genome sequences and in yet-to-be-cultured bacteria. In this review we examine in detail the current state of research on monooxygenase gene regulation, and on the development of transcription-factor-based microbial biosensors for detection of alkanes and alkenes. A new framework for the systematic characterisation of the underlying genetic components and for further development of biosensors is presented, and we identify focus areas that should be targeted to enable progression of more biosensor candidates to commercialisation and deployment in industry and in the environment.

Development of fluorescent protein-based biosensing strains: A new tool for the detection of aromatic hydrocarbon pollutants in the environment

The major sources for release of hydrocarbons into the environment include the effluents generated from chemical processing industries and ports. The introduction of such hazardous compounds into natural water bodies creates considerable disturbances in aquatic life and causes a threat to humans. Thus, it is essential to detect and quantify pollutants at various stages of the wastewater generation and treatment before they reach natural aquatic environments and contaminate them. This study reports the development of "biosensing strains" by cloning hydrocarbon recognizing promoter-operator and a reporter gene in bacterial strains for sensing the presence of pollutants at their lowest possible concentration. So far, various biosensing strains have been constructed with a fused promoter-operator region of the hydrocarbon degrading operons, but most of them use luxAB as a reporter gene. A novel approach in the present study aimed at constructing strains harboring two different fluorescent protein (FP)-based reporter genes for the quantification of multiple pollutants at a time. Two vectors were designed with a fusion of tbuT-gfp and phnR-cfp for the quantification of mono- and poly-aromatic hydrocarbons, respectively. The designed vectors were transformed into E. coli DH5α, and these strains were designated as E. coli DH5α 2296-gfp (containing pPROBE-Tbut-RBS-gfp-npt) and E. coli DH5α 2301-cfp (containing pPROBE-phn-RBS-cfp-npt). Both the developed recombinant strains were capable of successfully detecting mono- and poly-aromatic hydrocarbons in the range of 1-100 μM. The sensing capacity of recombinant strains was successfully validated with actual wastewater samples against available physico-chemical analytical techniques. The development of such recombinant microbial strains indicates the future for online contaminant detection, treatment quality monitoring and protection of aquatic flora and fauna.

Structure prediction and molecular docking studies of aromatic hydrocarbon sensing proteins TbuT, HbpR and PhnR to detect priority pollutants

On-line detection of aromatic hydrocarbon pollutants in aqueous environments can be achieved by biosensing strains having fusion of gene responsible for pollutant sensing protein with a reporter gene. Regulatory proteins TbuT, HbpR and PhnR are such proteins for recognizing one-, two-and three-ring aromatic hydrocarbon pollutants respectively, for which the structure is not known till date. Aim of the present study was to predict the structure of proteins and to determine their in-silico interaction with array of pollutants. Structure prediction of proteins was performed using I-TASSER and Phyre2 and refined with ModRefiner and 3DRefine. Total 14 models were obtained for each protein and the best model had more than 95% coverage in Ramachandran plot region. After successful structure prediction, molecular interaction of proteins with respective aromatic hydrocarbon pollutants categorized by United States Environmental Protection Agency was studied using AutoDockVina where the binding energy was found to fall in range of -4.6 to -8.4 kcal/mol. The types of protein-pollutant interaction were analyzed by LigPlus and Discovery Studio 2017 R2 Client which were found to be similar for standard and pollutant compounds. This study enables us to predict the range of pollutants possible to be detected using these regulatory protein-based biosensors.

Optical Biosensors for Label-Free Detection of Small Molecules

Label-free optical biosensors are an intriguing option for the analyses of many analytes, as they offer several advantages such as high sensitivity, direct and real-time measurement in addition to multiplexing capabilities. However, development of label-free optical biosensors for small molecules can be challenging as most of them are not naturally chromogenic or fluorescent, and in some cases, the sensor response is related to the size of the analyte. To overcome some of the limitations associated with the analysis of biologically, pharmacologically, or environmentally relevant compounds of low molecular weight, recent advances in the field have improved the detection of these analytes using outstanding methodology, instrumentation, recognition elements, or immobilization strategies. In this review, we aim to introduce some of the latest developments in the field of label-free optical biosensors with the focus on applications with novel innovations to overcome the challenges related to small molecule detection. Optical label-free methods with different transduction schemes, including evanescent wave and optical fiber sensors, surface plasmon resonance, surface-enhanced Raman spectroscopy, and interferometry, using various biorecognition elements, such as antibodies, aptamers, enzymes, and bioinspired molecularly imprinted polymers, are reviewed.

Encapsulation of Autoinducer Sensing Reporter Bacteria in Reinforced Alginate-Based Microbeads

Quorum sensing, in which bacteria communities use signaling molecules for inter- and intracellular communication, has been intensively studied in recent decades. In order to fabricate highly sensitive easy-to-handle point of care biosensors that detect quorum sensing molecules, we have developed, as is reported here, reporter bacteria loaded alginate-methacrylate (alginate-MA) hydrogel beads. The alginate-MA beads, which were obtained by electrostatic extrusion, were reinforced by photo-cross-linking to increase stability and thereby to reduce bacteria leaching. In these beads the genetically engineered fluorescent reporter bacterium Escherichia coli pTetR-LasR-pLuxR-GFP (E. coli pLuxR-GFP) was encapsulated, which responds to the autoinducer N-(3-oxododecanoyl)homoserine lactone secreted by Pseudomonas aeruginosa. After encapsulation in alginate-MA hydrogel beads with diameters in the range of 100-300 μm that were produced by an electrostatic extrusion method and rapid photo-cross-linking, the E. coli pLuxR-GFP were found to possess a high degree of viability and sensing activity. The encapsulated bacteria could proliferate inside the hydrogel beads, when exposed to bacteria culture medium. In media containing the autoinducer N-(3-oxododecanoyl)homoserine lactone, the encapsulated reporter bacteria responded with a strong fluorescence signal due to an increased green fluorescent protein (GFP) expression. A prototype dipstick type sensor developed here underlines the potential of encapsulation of viable and functional reporter bacteria inside reinforced alginate-methacrylate hydrogel beads for whole cell sensors for bacteria detection.