Microbial surface displaying formate dehydrogenase and its application in optical detection of formate

Enzymes encapsulated in organic-inorganic hybrid nanoflower with spatial localization for sensitive and colorimetric detection of formate

Formate is an important environmental pollutant, and meanwhile its concentration change is associated with a variety of diseases. Thus, rapid and sensitive detection of formate is critical for the biochemical analysis of complex samples and clinical diagnosis of multiple diseases. Herein, a colorimetric biosensor was constructed based on the cascade catalysis of formate oxidase (FOx) and horseradish peroxidase (HRP). These two enzymes were co-immobilized in Cu3(PO4)2-based hybrid nanoflower with spatial localization, in which FOx and HRP were located in the shell and core of nanoflower, respectively (FOx@HRP). In this system, FOx could catalyze the oxidation of formate to generate H2O2, which was then utilized by HRP to oxidize 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulphonic acid to yield blue product. Ideal linear correlation could be obtained between the absorbance at 420 nm and formate concentration. Meanwhile, FOx@HRP exhibited excellent detection performance with low limit of detection (6 μM), wide linear detection range (10-900 μM), and favorable specificity, stability and reusability. Moreover, it could be applied in the detection of formate in environmental, food and biological samples with high accuracy. Collectively, FOx@HRP provides a useful strategy for the simple and sensitive detection of formate and is potentially to be used in biochemical analysis and clinical diagnosis.

Hierarchical porous MoS2 particles: excellent multi-enzyme-like activities, mechanism and its sensitive phenol sensing based on inhibition of sulfite oxidase mimics

It is important to exploit highly efficient methods for detecting pollutants selectively and sensitively. Artificial enzymes are promising to replace natural enzymes with diverse functions for sustainable developments and various applications. However, it remains the challenge to develop novel mimic enzymes or multi-enzyme mimics for pollutant detection. Herein we report hierarchical porous MoS₂ particles prepared by a simple hydrothermal method, which demonstrated excellent sulfite oxidase (SuO_x)-, nicotinamide adenine dinucleotide (NADH) oxidase- and superoxide dismutase-mimicking activities. In addition, the catalytic conditions for SuO_x-like and NADH oxidase-like activities of MoS₂ were optimized. The catalytic mechanism of the NADH oxidase mimics is that O₂ involves in the oxidation of NADH, to generate O₂^.- intermediate and finally turn to H₂O₂, while SuO_x mimics comes from that MoS₂ particles can effectively catalyze sulfite to reduce [Fe(CN)₆]^3-. Based on the excellent SuO_x-like activity of MoS₂ particles, while phenol can inhibit the oxidation of sulfite, a phenol colorimetric sensor was explored with the dynamic range of 2-1000 μM and the limit of detection of 0.72 μM, applicable to detect phenol in effluents. Therefore, MoS₂ particles with the SuO_x-like, NADH oxidase-like and SOD-like activities has broad application prospects in environmental monitoring and bio-analysis.

Microbial whole-cell biosensors: Current applications, challenges, and future perspectives

Microbial Whole-Cell Biosensors (MWCBs) have seen rapid development with the arrival of 21st century biological and technological capabilities. They consist of microbial species which produce, or limit the production of, a reporter protein in the presence of a target analyte. The quantifiable signal from the reporter protein can be used to determine the bioavailable levels of the target analyte in a variety of sample types at a significantly lower cost than most widely used and well-established analytical instrumentation. Furthermore, the versatile and robust nature of MWCBs shows great potential for their use in otherwise unavailable settings and environments. While MWCBs have been developed for use in biomedical, environmental, and agricultural monitoring, they still face various challenges before they can transition from the laboratory into industrialized settings like their enzyme-based counterparts. In this comprehensive and critical review, we describe the underlying working principles of MWCBs, highlight developments for their use in a variety of fields, detail challenges and current efforts to address them, and discuss exciting implementations of MWCBs helping redefine what is thought to be possible with this expeditiously evolving technology.

Yeast cell surface display of bacterial PET hydrolase as a sustainable biocatalyst for the degradation of polyethylene terephthalate

Enzymatic hydrolysis of polyethylene terephthalate (PET) is considered to be an environmentally friendly method for the recycling of plastic waste. Recently, a bacterial enzyme named IsPETase was found in Ideonella sakaiensis with the ability to degrade amorphous PET at ambient temperature suggesting its possible use in recycling of PET. However, applying the purified IsPETase in large-scale PET recycling has limitations, i.e., a complicated production process, high cost of single-use, and instability of the enzyme. Yeast cell surface display has proven to be an effectual alternative for improving enzyme degradation efficiency and realizing industrial applications. This chapter deals with the construction and application of a whole-cell biocatalyst by displaying IsPETase on the surface of yeast (Pichia pastoris) cells.

Effect of Metal Ions on the Activity of Ten NAD-Dependent Formate Dehydrogenases

NAD-dependent formate dehydrogenase (FDH) enzymes are frequently used in industrial and scientific applications. FDH is a reversible enzyme that reduces the NAD molecule to NADH and produces CO₂ by oxidation of the formate ion, whereas it causes CO₂ reduction in the reverse reaction. Some transition metal elements - Fe³⁺, Mo⁶⁺ and W^{6 +} - can be found in the FDH structure of anaerobic and archaeal microorganisms, and these enzymes require cations and other redox-active cofactors for their FDH activity. While NAD-dependent FDHs do not necessarily require any metal cations, the presence of various metal cations can still affect FDH activities. To study the effect of 11 different metal ions, NAD-dependent FDH enzymes from ten different microorganisms were tested: Ancylobacter aquaticus (AaFDH), Candida boidinii (CboFDH), Candida methylica (CmFDH), Ceriporiopsis subvermispora (CsFDH), Chaetomium thermophilum (CtFDH), Moraxella sp. (MsFDH), Myceliophthora thermophila (MtFDH), Paracoccus sp. (PsFDH), Saccharomyces cerevisiae (ScFDH) and Thiobacillus sp. (TsFDH). It was found that metal ions (mainly Cu²⁺ and Zn²⁺) could have quite strong inhibition effects on several enzymes in the forward reaction, whereas several cations (Li⁺, Mg²⁺, Mn²⁺, Fe³⁺ and W⁶⁺) could increase the forward reaction of two FDHs. The highest activity increase (1.97 fold) was caused by Fe³⁺ in AaFDH. The effect on the reverse reaction was minimal. The modelled structures of ten FDHs showed that the active site is formed by 15 highly conserved amino acid residues spatially settling around the formate binding site in a conserved way. However, the residue differences at some of the sites close to the substrate do not explain the activity differences. The active site space is very tight, excluding water molecules, as observed in earlier studies. Structural examination indicated that smaller metal ions might be spaced close to the active site to affect the reaction. Metal ion size showed partial correlation to the effect on inhibition or activation. Affinity of the substrate may also affect the sensitivity to the metal's effect. In addition, amino acid differences on the protein surface may also be important for the metal ion effect.

Growth of E. coli on formate and methanol via the reductive glycine pathway

Engineering a biotechnological microorganism for growth on one-carbon intermediates, produced from the abiotic activation of CO₂, is a key synthetic biology step towards the valorization of this greenhouse gas to commodity chemicals. Here we redesign the central carbon metabolism of the model bacterium Escherichia coli for growth on one-carbon compounds using the reductive glycine pathway. Sequential genomic introduction of the four metabolic modules of the synthetic pathway resulted in a strain capable of growth on formate and CO₂ with a doubling time of ~70 h and growth yield of ~1.5 g cell dry weight (gCDW) per mol-formate. Short-term evolution decreased doubling time to less than 8 h and improved biomass yield to 2.3 gCDW per mol-formate. Growth on methanol and CO₂ was achieved by further expression of a methanol dehydrogenase. Establishing synthetic formatotrophy and methylotrophy, as demonstrated here, paves the way for sustainable bioproduction rooted in CO₂ and renewable energy.

Tackling the Challenges of Enzymatic (Bio)Fuel Cells

The ever-increasing demands for clean and sustainable energy sources combined with rapid advances in biointegrated portable or implantable electronic devices have stimulated intensive research activities in enzymatic (bio)fuel cells (EFCs). The use of renewable biocatalysts, the utilization of abundant green, safe, and high energy density fuels, together with the capability of working at modest and biocompatible conditions make EFCs promising as next generation alternative power sources. However, the main challenges (low energy density, relatively low power density, poor operational stability, and limited voltage output) hinder future applications of EFCs. This review aims at exploring the underlying mechanism of EFCs and providing possible practical strategies, methodologies and insights to tackle these issues. First, this review summarizes approaches in achieving high energy densities in EFCs, particularly, employing enzyme cascades for the deep/complete oxidation of fuels. Second, strategies for increasing power densities in EFCs, including increasing enzyme activities, facilitating electron transfers, employing nanomaterials, and designing more efficient enzyme-electrode interfaces, are described. The potential of EFCs/(super)capacitor combination is discussed. Third, the review evaluates a range of strategies for improving the stability of EFCs, including the use of different enzyme immobilization approaches, tuning enzyme properties, designing protective matrixes, and using microbial surface displaying enzymes. Fourth, approaches for the improvement of the cell voltage of EFCs are highlighted. Finally, future developments and a prospective on EFCs are envisioned.

Biocatalytic Degradation of Parabens Mediated by Cell Surface Displayed Cutinase

Parabens are emerging environmental contaminants with known endocrine-disrupting effects. This study created a novel biocatalyst (named as SDFsC) by expressing the enzyme Fusarium solani pisi cutinase (FsC) on the cell surface of Baker's yeast Sacchromycese cerevisiae and demonstrated successful enzyme-mediated removal of parabens for the first time. Parabens with different side chain structures had different degradation rates by the SDFsC. The SDFsC preferentially degraded the parabens with relatively long alkyl or aromatic side chains. The structure-dependent degradability was in a good agreement with the binding energy between the active site of FsC and different parabens. In real wastewater effluent solution, the SDFsC effectively degraded 800 μg/L of propylparaben, butylparaben, and benzylparaben, either as a single compound or as a mixture, within 48 h. The estrogenic activity of parabens was considerably reduced as the parent parabens were degraded into 4-hydroxybenzoic acid via hydrolysis pathway by the SDFsC. The SDFsC showed superior reusability and maintained 93% of its initial catalytic activity after six rounds of paraben degradation reaction. Results from this study provide scientific basis for developing biocatalysis as a green chemistry alternative for advanced treatment of parabens in sustainable water reclamation.

Ionic Liquids as Bifunctional Cosolvents Enhanced CO2 Conversion Catalysed by NADH-Dependent Formate Dehydrogenase

Efficient CO2 conversion by formate dehydrogenase is limited by the low CO2 concentrations that can be reached in traditional buffers. The use of ionic liquids was proposed as a manner to increase CO2 concentration in the reaction system. It has been found, however, that the required cofactor (NADH) heavily degraded during the enzymatic reaction and that acidity was the main reason. Acidity, indeed, resulted in reduction of the conversion of CO2 into formic acid and contributed to overestimate the amount of formic acid produced when the progression of the reaction was followed by a decrease in NADH absorbance (method N). Stability of NADH and the mechanism of NADH degradation was investigated by UV, NMR and by DFT calculations. It was found that by selecting neutral–basic ionic liquids and by adjusting the concentration of the ionic liquid in the buffer, the concentration of NADH can be maintained in the reaction system with little loss. Conversion of CO2 to methanol in BmimBF4 (67.1%) was more than twice as compared with the conversion attained by the enzymatic reaction in phosphate buffer (24.3%).

Simultaneous hydrolysis of carbaryl and chlorpyrifos by Stenotrophomonas sp. strain YC-1 with surface-displayed carbaryl hydrolase

Many sites are often co-contaminated with multiple pesticides. To date, there are no reports on simultaneous degradation of different classes of pesticides by a natural microorganism. In this work, we aim at constructing a live biocatalyst able to simultaneously hydrolyze carbaryl and chlorpyrifos. For this purpose, carbaryl hydrolase (CH) was displayed on the cell surface of a chlorpyrifos-degrading bacterium Stenotrophomonas sp. strain YC-1 using N- and C-terminal domain of ice nucleation protein (INPNC) from Pseudomonas syringae INA5 as an anchoring motif. The localization of INPNC-CH fusion protein in the outer membrane fraction was demonstrated by cell fractionation followed by Western blot analysis. Surface display of INPNC-CH was further confirmed by proteinase accessibility experiment and immunofluorescence microscope. CH was present in an active form on cell surface without causing any growth inhibition, suggesting that the INP-based display system is a useful tool for surface expression of macromolecular heterologous proteins on the bacterial cell surface. Because surface-displayed CH has free access to pesticides, this bacterium can be used as a whole-cell biocatalyst for efficient hydrolysis of pesticides.

Novel Cell-Inorganic Hybrid Catalytic Interfaces with Enhanced Enzymatic Activity and Stability for Sensitive Biosensing of Paraoxon

To improve the biosensing performance of organophosphorus hydrolase (OPH), the novel bioinorganic hybrid catalysts were facilely explored by biomineralization and cell surface display technology. During biomineralization, cobalt phosphate crystals were deposited onto the surface of OPH-fused bacteria, and the inorganic crystals at middle of cell collapsed inwardly to form the final spindle morphology because of the lowest energy principle and the mechanics principle. OPH would show the allosteric effect from "inactive" form to "active" form, and the "active" form was "fixed" when OPH was embedded into cobalt phosphate. Therefore, the activity of mineralized OPH-fused cells was greatly enhanced about 3 times in comparison with original OPH-fused cells. Additionally, the stability of the novel hybrid catalysts was also significantly improved. Further, the as-synthesized bioinorganic hybrid catalysts were applied to sensitive paraoxon biosensing, which exhibited lower limit of detection than that of the original counterpart. Thus, this hybrid biocatalytic system would provide a model to develop a wide range of biocatalysts and find a wide range of applications in industrial catalysis, analytical chemistry, and environmental engineering.