Reducing methylmercury accumulation in fish using Escherichia coli with surface-displayed methylmercury-binding peptides

Replacing manual operation with bio-automation: A high-throughput evolution strategy to construct an integrated whole-cell biosensor for the simultaneous detection of methylmercury and mercury ions without manual sample digestion

Methylmercury is primarily responsible for most food mercury pollution cases. However, most biosensors developed for mercury pollution analysis can only detect mercury ions. Although oxidative strong-acid digestion or microwave-assisted digestion can convert methylmercury into mercury ions, it is unsuitable for on-site detection. This study designed a bio-digestion gene circuit and integrated it into a mercury ion whole-cell biosensor，creating a novel on-site methylmercury detection method. Five alkyl mercury lyases from different bacterial genomes were screened via bioinformatics analysis, of which goMerB from Gordonia otitis showed the highest catalytic biological digestion efficiency. The goMerB site-specific saturation and random mutation libraries were constructed. After two rounds of high-throughput visualization screening, the catalytic activity of the mutant increased 2.5-fold. The distance between the three crucial amino acid sites and methylmercury changed in the mutant, which likely contributed to the enhanced catalytic efficiency. The optimized whole-cell biosensor showed a linear dynamic concentration range of 100 nM to 100 μM (R2 =0.991), satisfactory specificity, and interference resistance. The detection limit of the goMerBt6-MerR-RFP biosensor was 0.015 μM, while the limit of quantitation was 0.049 μM. This study demonstrated the application of synthetic biology for food safety detection and highlighted the future potential of "Lab in a Cell" for hazard analysis.

A novel antimony metallochaperone AntC in Comamonas testosteroni JL40 and its application in antimony immobilization

The microbial metabolism of toxic antimony (Sb) and the bioremediation of Sb-contaminated environments have attracted significant attention recently. This study identified an Sb(III) metallochaperone AntC in the Sb(III) efflux operon antRCA of Comamonas testosteroni JL40. The deletion of AntC significantly increased the intracellular Sb content in strain JL40 and concomitantly diminished resistance to Sb(III). By contrast, the complementary expression of AntC in the knockout strain resulted in a substantial recovery of Sb(III) resistance. The site-directed mutagenesis assay demonstrated the three conserved cysteine (Cys) residues (Cys30, Cys34, and Cys36) play an essential role in the binding of Sb(III) to AntC and its transfer. The function of the metallochaperone AntC was further investigated in an Sb(III) sensitive bacterium Escherichia coli AW3110 (Δars). The co-expression of AntC and AntA in AW3110 cells resulted in a four-fold increase in minimum inhibitory concentrations (MICs) toward Sb(III), while the intracellular Sb content decreased five-fold compared to cells expressing AntA alone. In addition, a genetically modified E. coli strain was engineered to co-express AntC and the Sb uptake protein GlpF, showing an eight-fold increase in Sb absorption and achieving a remarkable 90% removal of Sb from the solution. This engineered strain was also applied in a hydroponic experiment, displaying a significant 80% reduction in Sb uptake by rice seedlings. This finding provides new insights into the mechanisms of bacterial Sb detoxification and a potential bioremediation strategy for Sb pollution.

Reducing cadmium accumulation in shrimp using Escherichia coli with surface-displayed peptide

Cadmium (Cd) is a hazardous metal that can accumulate in aquatic organisms and endanger human health via the food chain. In this study, genetic engineering was used to display a peptide with Cd-binding potential on the surface of Escherichia coli cells. This whole-cell adsorbent exhibited high affinity for Cd ions (Cd²⁺) in the solution. The Cd²⁺ adsorption capacity of the whole-cell adsorbent was three-fold that of the control cells in a 20 μM Cd²⁺ solution, and 97.2% ± 2.38% of the Cd²⁺ was removed. The whole-cell adsorbent was fed to shrimp (Neocaridina denticulata), and the surface-engineered E. coli successfully colonized the shrimp intestine, which showed significantly less Cd accumulation than the group not fed surface-engineered E. coli. The whole-cell adsorbent evidently protected shrimp from the toxicity of Cd²⁺ by adsorbing it. Moreover, the whole-cell adsorbent mitigated the changes in microbial community structure in the shrimp gut caused by the exposure of Cd²⁺. These findings suggest that this strategy is effective for controlling the contamination of Cd²⁺ in shrimp.

Applications of Material-Binding Peptides: A Review

Material-binding peptides (MBPs) are functionalized adhesive materials consisting of a few to several dozen amino acids. This affinity between MBPs and materials is regulated by multiple interactions, including hydrogen bonding, electrostatic, hydrophobic interactions, and π-π stacking. They show selective binding and high affinity to a diverse range of inorganic and organic materials, such as silicon-based materials, metals, metal compounds, carbon materials, and polymers. They are used to improve the biocompatibility of materials, increase the efficiency of material synthesis, and guide the controlled synthesis of nanomaterials. In addition, these can be used for precise targeting of proteins by conjugating to target biomolecules. In this review, we summarize the main designs and applications of MBPs in recent years. The discussions focus on more efficient and functional peptides, including evolution and overall design of MBPs. We have also highlighted the recent applications of MBPs, such as functionalization of material surfaces, synthesis of nanomaterials, drug delivery, cancer therapy, and plastic degradation. Besides, we also discussed the development trend of MBPs. This interpretation will accelerate future investigations to bottleneck the drawbacks of available MBPs, promoting their commercial applications.

Potential Application of Living Microorganisms in the Detoxification of Heavy Metals

Heavy metal (HM) exposure remains a global occupational and environmental problem that creates a hazard to general health. Even low-level exposure to toxic metals contributes to the pathogenesis of various metabolic and immunological diseases, whereas, in this process, the gut microbiota serves as a major target and mediator of HM bioavailability and toxicity. Specifically, a picture is emerging from recent investigations identifying specific probiotic species to counteract the noxious effect of HM within the intestinal tract via a series of HM-resistant mechanisms. More encouragingly, aided by genetic engineering techniques, novel HM-bioremediation strategies using recombinant microorganisms have been fruitful and may provide access to promising biological medicines for HM poisoning. In this review, we summarized the pivotal mutualistic relationship between HM exposure and the gut microbiota, the probiotic-based protective strategies against HM-induced gut dysbiosis, with reference to recent advancements in developing engineered microorganisms for medically alleviating HM toxicity.

Improving selenium accumulation in broilers using Escherichia coli Nissle 1917 with surface-displayed selenite reductase SerV01

Selenium levels have a critical impact on livestock and poultry, and selenium nanoparticles (SeNPs) have shown significant efficiency in supplementation. This study identified a high-efficiency selenite reductase, SerV01, in Staphylococcus aureus LZ-01, which can convert Se₂O₃^2- to SeNPs. Subsequently, SerV01 was introduced into the intestines of the broilers using the surface display-engineered E. coli Nissle 1917 (EcN). The results showed that the engineered bacteria (EcN-IS) significantly increased the selenium content by 0.87 mg kg^-1, 0.52 mg kg^-1, and 6.10 mg L^-1 in the liver, breast muscle, and serum, respectively. With SeNPs + EcN-IS treatment, glutathione peroxidase and thioredoxin reductase levels reached 0.7536 ± 0.03176 U μL^-1 protein and 2.463 ± 0.1685 U μL^-1 protein, respectively. With the modified probiotics, the proportion of beneficial intestinal flora increased, with Lactobacillus and Propionibacterium accounting for 75.85% and 0.19%. This technology provides a novel idea to facilitate the exploitation of selenium in broiler diets and improve antioxidant capability.

Engineered Bacteria EcN-MT Alleviate Liver Injury in Cadmium-Exposed Mice via its Probiotics Characteristics and Expressing of Metallothionein

Cadmium (Cd) exposure is a widespread problem in many parts of the world, but effective means to treat Cd exposure is still lacking. Hence, an engineered strain expressing metallothionein (MT) named Escherichia coli Nissle 1917 (EcN)-MT was constructed, and its potential in the treatment of Cd exposure was evaluated. The in vitro studies showed that metallothionein expressed by EcN-MT could significantly bind Cd. Further, the in vivo results indicated that EcN-MT strain could reduce 26.3% Cd in the liver and increase 24.7% Cd in the feces, which greatly decreased malondialdehyde (MDA) levels and increased catalase (CAT), glutathione (GSH), and superoxide dismutase (SOD) levels in liver, and reduced the expression of toll-like receptor4 (TLR4), nuclear factor-κB (NF-κB), the myeloid differentiation factor 88 (Myd88) andincreased B-cell lymphoma 2 (Bcl-2)/Bcl-2-Associated X (Bax). Moreover, high throughput sequencing results indicated that EcN-MT strain greatly enhanced the beneficial bacteria of Ruminococcaceae, Lactobacillaceae, Akkermansia, Muribaculaceae, Lachnospiraceae, Dubosiella and restored the disturbed microbial ecology to the normal level. Therefore, the high Cd binding capacity of the expressed metallothionein, together with the beneficial characteristics of the host bacteria EcN, makes EcN-MT a sound reagent for the treatment of subchronic Cd exposure-induced liver injury.

Feed-additive Limosilactobacillus fermentum GR-3 reduces arsenic accumulation in Procambarus clarkii

Procambarus clarkii (crayfish) accumulates a high concentration of Arsenic (As) from the aquatic environment and causes considerable human health risks. In this study, Limosilactobacillus fermentum GR-3 strain was isolated from "Jiangshui" and applied for As(III) adsorption and antioxidant abilities. Strain GR-3 removed 50.67% of 50 mg/L As(III) and exhibited the high antioxidant potential of DPPH (1,1-Diphenyl-2-picrylhydrazyl) (87.63%) and hydroxyl radical (74.51%) scavenging rate in vitro. P. clarkii was feed with strain GR-3, the results showed that As(III) concentration reduced, and residual level in hepatopancreas was decreased by 36%, compared to As(III)-exposed group (control). Gut microbial sequencing showed that strain GR-3 restores gut microbiota dysbiosis caused by As(III) exposure. Further application in the field scale was performed and revealed a decrease in As(III) accumulation and increasing 50% aquaculture production of the total output. In summary, feed-additive probiotic is recommended as a novel strategy to minimize aquaculture foods toxicity and safe human health.

Chitooligosaccharides production from shrimp chaff in chitosanase cell surface display system

Chitin refers to a natural biopolymer, which is economically significant to next-generation biorefineries. In this study, a novel high-yield method with cell surface-display chitosanase (CHI-1) was built to produce chitooligosaccharides (COS) from shrimp chaff through the co-fermentation in the presence of Bacillus subtilis and Acetobacter sp. Under the optimized co-fermentation conditions (5 g/L yeast extracts, 10 g/L KH₂PO₄, 6% ethanol, 50 g/L glucose), the final deproteinization (DP) and demineralization (DM) efficiency and the chitin yield were achieved as 94, 92 and 18%, respectively. The engineered E. coli BL21-pET23b(+)-NICHI maintained 81% of the initial enzyme activity after 40 days at room temperature. The crude CHI-1 was inactivated after one-day interacting with prepared chitosan. Moreover, E. coli BL21-pET23b(+)-NICHI still maintained excellent hydrolysis ability in 7 days, and the COS yield reached 41%. Accordingly, the proposed method exhibited excellent stability and a high hydrolysis efficiency to produce COS with whole engineered cells.

Limosilactobacillus fermentum JL-3 isolated from "Jiangshui" ameliorates hyperuricemia by degrading uric acid

Recent studies into the beneficial effects of fermented foods have shown that this class of foods are effective in managing hyperuricemia and gout. In this study, the uric acid (UA) degradation ability of Limosilactobacillus fermentum JL-3 strain, isolated from "Jiangshui" (a fermented Chinese food), was investigated. In vitro results showed that JL-3 strain exhibited high degradation capacity and selectivity toward UA. After oral administration to mice for 15 days, JL-3 colonization was continuously detected in the feces of mice. The UA level in urine of mice fed with JL-3 was similar with the control group mice. And the serum UA level of the former was significantly lower (31.3%) than in the control, further confirmed the UA-lowering effect of JL-3 strain. Limosilactobacillus fermentum JL-3 strain also restored some of the inflammatory markers and oxidative stress indicators (IL-1β, MDA, CRE, blood urea nitrogen) related to hyperuricemia, while the gut microbial diversity results showed that JL-3 could regulate gut microbiota dysbiosis caused by hyperuricemia. Therefore, the probiotic Limosilactobacillus fermentum JL-3 strain is effective in lowering UA levels in mice and could be used as a therapeutic adjunct agent in treating hyperuricemia.

Genetically engineered microbial remediation of soils co-contaminated by heavy metals and polycyclic aromatic hydrocarbons: Advances and ecological risk assessment

Soils contaminated with heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) have been becoming a worldwide concerned environmental problem because of threatening public healthy via food chain exposure. Thus soils polluted by HMs and PAHs need to be remediated urgently. Physical and chemical remediation methods usually have some disadvantages, e.g., cost-expensiveness and incomplete removal, easily causing secondary pollution, which are hence not environmental-friendly. Conventional microbial approaches are mostly used to treat a single contaminant in soils and lack high efficiency and specificity for combined contaminants. Genetically engineered microorganisms (GEMs) have emerged as a desired requirement of higher bioremediation efficiency for soils polluted with HMs and PAHs and environmental sustainability, which can provide a more eco-friendly and cost-effective strategy in comparison with some conventional techniques. This review comments the recent advances about successful bioremediation techniques and approaches for soil contaminated with HMs and/or PAHs by GEMs, and discusses some challenges in the simultaneous removal of HMs and PAHs from soil by designing multi-functional genetic engineering microorganisms (MFGEMs), such as improvement of higher efficiency, strict environmental conditions, and possible ecological risks. Also, the modern biotechnological techniques and approaches in improving the ability of microbial enzymes to effectively degrade combined contaminants at a faster rate are introduced, such as reasonable gene editing, metabolic pathway modification, and protoplast fusion. Although MFGEMs are more potent than the native microbes and can quickly adapt to combined contaminants in soils, the ecological risk of MFGEMs needs to be evaluated under a regulatory, safety, or costs benefit-driving system in a way of stratified regulation. Nevertheless, the innovation of genetic engineering to produce MFGEMs should be inspired for the welfare of successful bioremediation for soils contaminated with HMs and PAHs but it must be supervised by the public, authorities, and laws.

Enhanced removal of trivalent chromium from leather wastewater using engineered bacteria immobilized on magnetic pellets

Leather wastewater contains various toxic contaminants, with trivalent chromium (Cr(III)) having high concentration and adversely affecting wastewater treatment. In this study, a Cr(III) adsorption protein (MerP) was displayed on the cell surface of Escherichia coli and then coupled with a magnetic pellet system to facilitate Cr(III) adsorption. The results showed the engineered strain M-BL21 achieved an in vitro Cr(III) adsorption capacity of 2.38 mmol/g. Next, the magnetic pellets were prepared as component ratios of sodium alginate (2.5%), polyvinyl alcohol (8%), Fe₃O₄ nanoparticles (3.5%), and M-BL21 at 3 g/L. The optimized system was capable of Cr(III) adsorption at an efficiency of 91.29%, which was substantially higher than that of the magnetic carrier alone (67%). Results of scanning electron microscopy with energy-dispersive X-ray analysis proved that Cr(III) was absorbed on the magnetic pellet. The recyclable performance of magnetic property (13.34185 emu/g) and high Cr(III) adsorption efficiency (68.75%) remained after five cycles of Cr(III) absorption. In the medium-scale experiment, 25 L of leather wastewater were treated with magnetic pellet and the Cr(III) removal efficiency reached 88.2%. Thus, our results present an advanced, fully operational, and eco-friendly method for in situ removal of Cr(III) from contaminated wastewater.

Probiotic Therapy (BIO-THREE) Mitigates Intestinal Microbial Imbalance and Intestinal Damage Caused by Oxaliplatin

Gastrointestinal mucositis associated with the use of chemotherapeutic drugs can seriously affect the quality of life of patients. In this study, a probiotic mixture, BIO-THREE, was used to alleviate intestinal damage caused by oxaliplatin in mice and human patients. Kunming mice were injected with 15 mg/kg of oxaliplatin twice, and BIO-THREE tablets were administered to mice for 12 days. Patients with gastric cancer undergoing oxaliplatin treatment took BIO-THREE tablets for 2 weeks. The changes in the composition of fecal microbiota both in patients and mice were analyzed using 16S rRNA high-throughput sequencing. In mice, oxaliplatin caused a drop in body weight and produced lesions in the liver and small intestines. Probiotic therapy successfully mitigated the damage caused by oxaliplatin to the intestinal tract, but it was not very effective for the liver damage and weight loss caused by oxaliplatin. The sequencing of the gut microflora indicated that oxaliplatin treatment increased the abundance of Bacteroidetes and decreased the abundance of Prevotella in mice. After taking probiotics, the feces of mice and human patients both had a higher abundance of Plovitella and a lower abundance of Bacteroides. The increase in Bacteroidetes and decrease in Prevotella in the gut community might be associated with oxaliplatin-induced intestinal damage. Probiotics appeared to be beneficial, decreasing intestinal damage by restoring the abundance of Bacteroidetes and Prevotella.

Gut Escherichia coli expressing Pb2+-adsorption protein reduces lead accumulation in grass carp, Ctenopharyngodon idellus

Lead (Pb²⁺) is easy to accumulate in fish which become a major source of Pb²⁺ exposure to humans. In this study, a recombinant Escherichia coli strain expressing Pb²⁺-specific surface-binding protein anchored by the ice nucleation protein was introduced into grass carp (Ctenopharyngodon idellus) gut to investigate its protective effect against dietary Pb²⁺ exposure. Pb²⁺ mostly precipitated on the surface of the engineered strain through Pb²⁺-specific surface-binding protein, with a maximum adsorption efficiency of 73% and an adsorption capacity of 163 μmol/g dry cells. The Pb²⁺ concentration in engineered bacteria-fed grass carp was reduced significantly, and the residual level of Pb²⁺ in feces was increased by 76%, compared with the control group. Meantime, the engineered bacteria were able to mitigate the oxidative stress and histological alterations of intestines and dysbiosis of gut microbiota induced by Pb²⁺exposure. Thus, the engineered bacterium that can effectively reduce Pb²⁺ residue in grass carp might be a useful tool for decontamintion of lead in aquatic organisms.

Feed-additive of bioengineering strain with surface-displayed laccase degrades sulfadiazine in broiler manure and maintains intestinal flora structure

Sulfonamide antibiotics (SAs) are excreted into the ecosystem unchanged through feces and urine because of their low adsorption and degradation in the guts of humans and animals. In this study, a novel whole-cell biocatalyst with fungal laccase on the cell surface of Escherichia coli Nissle 1917 was developed to degrade sulfadiazine (SDZ). Engineered strain EcN-IL showed laccase enzyme activity of 2 ± 1 U/mg dry weight of cell and degraded 37 ± 1% of SDZ at temperature 40 °C and pH 5 within 3 h in vitro. Strain EcN-IL with 500 mg/kg of SDZ was employed as a food supplement to feed chicken broilers, which can reduce the residue of SDZ in broiler manure by 58 ± 2% and also reduced dysbiosis of the gut microbiota due to overuse of antibiotics. The genetically engineered EcN-IL has laid a foundation for degrading SDZ in broilers and their manure.

Reducing residual antibiotic levels in animal feces using intestinal Escherichia coli with surface-displayed erythromycin esterase

Antibiotics are widely used in livestock and poultry industries, which results in large quantities of antibiotic residues in manure that influences subsequent treatments. In this study, an Escherichia coli strain was engineered to display erythromycin esterase on its cell surface. The engineered strain (E. coli ereA) efficiently degraded erythromycin by opening the macrocyclic 14-membered lactone ring in solution. Erythromycin (50 mg/L) was completely degraded in a solution by E. coli ereA (1 × 10⁹ CFU/mL) within 24 h. E. coli ereA retained over 86.7 % of the initial enzyme activity after 40 days of storage at 25 °C, and 78.5 % of the initial activity after seven repeated batch reactions in solution at 25 °C. Mice were fed with E. coli ereA and real-time quantitative PCR data showed that E. coli ereA colonized in the mice large intestine. The mice group fed E. coli ereA exhibited 83.13 % decrease in erythromycin levels in their feces compared with the mice group not fed E. coli ereA. E. coli ereA eliminated antibiotics from the source preventing its release into the environment. The surface-engineered strain therefore is an effective alternative agent for treating recalcitrant antibiotics, and has the potential to be applied in livestock and poultry industries.

Efficient biodegradation of highly crystallized polyethylene terephthalate through cell surface display of bacterial PETase

Polyethylene terephthalate (PET) is one of the most widely used plastics in the world. Accumulation of the discarded PET in the environment is creating a global environmental problem. Recently, a bacterial enzyme named PETase was found to have the novel ability to degrade the highly crystallized PET. However, the enzymatic activity of native PETase is still low limiting its possible use in recycling of PET. In this study, we developed a whole-cell biocatalyst by displaying PETase on the surface of yeast (Pichia pastoris) cell to improve its degradation efficiency. Our data shows that PETase could be functionally displayed on the yeast cell with enhanced pH and thermal stability. The turnover rate of the PETase-displaying yeast whole-cell biocatalyst towards highly crystallized PET dramatically increased about 36-fold compared with that of purified PETase. Furthermore, the whole-cell biocatalyst showed stable turnover rate after seven repeated use and under some chemical/solvent conditions, and its ability to degrade different commercial highly crystallized PET bottles. Our results reveal that PETase-displaying whole-cell biocatalyst affords a promising route for efficient biological recycling of PET.

Studies of advanced lignin valorization based on various types of lignolytic enzymes and microbes

Lignin is a robust material that is considered useless because it has an inhibitory effect on microbes and acts as a physical barrier for cellulose degradation. Therefore, it has been removed from cellulosic biomass to produce high-value materials. However, lignin monomers can be converted to value-added chemicals such as biodegradable plastics and food additives by appropriately engineered microbes. Lignin degradation through peroxidase, laccase and other proteins with auxiliary activity is the first step in lignin valorization. Metabolic engineering of microorganisms for increased tolerance and production yield is the second step for lignin valorization. Here, this review offers a summary of current biotechnologies using various enzymatic activities, synergistic enzyme mixtures and metabolic engineering for lignin valorization in biorefinery.