Directed evolution of the fluorescent protein CGP with in situ biosynthesized noncanonical amino acids.

The incorporation of noncanonical amino acids (ncAAs) into proteins can enhance their function beyond the abilities of canonical amino acids and even generate new functions. However, the ncAAs used for such research are usually chemically synthesized, which is expensive and hinders their application on large industrial scales. We believe that the biosynthesis of ncAAs using metabolic engineering and their employment in situ in target protein engineering with genetic code expansion could overcome these limitations. As a proof of principle, we biosynthesized four ncAAs, O-L-methyltyrosine, 3,4-dihydroxy-L-phenylalanine, 5-hydroxytryptophan, and 5-chloro-L-tryptophan using metabolic engineering and directly evolved the fluorescent consensus green protein (CGP) by combination with nine other exogenous ncAAs in Escherichia coli. After screening a TAG scanning library expressing 13 ncAAs, several variants with enhanced fluorescence and stability were identified. The variants CGPV3pMeoF/K190pMeoF and CGPG20pMeoF/K190pMeoF expressed with biosynthetic O-L-methyltyrosine showed an approximately 1.4-fold improvement in fluorescence compared to the original level, and a 2.5-fold improvement in residual fluorescence after heat treatment. Our results demonstrated the feasibility of integrating metabolic engineering, genetic code expansion, and directed evolution in engineered cells to employ biosynthetic ncAAs in protein engineering. These results could further promote the application of ncAAs in protein engineering and enzyme evolution. IMPORTANCE: Noncanonical amino acids (ncAAs) have shown great potential in protein engineering and enzyme evolution through genetic code expansion. However, in most cases, ncAAs must be provided exogenously during protein expression, which hinders their application, especially when they are expensive or have poor cell membrane penetration. Engineering cells with artificial metabolic pathways to biosynthesize ncAAs and employing them in situ for protein engineering and enzyme evolution could facilitate their application and reduce costs. Here, we attempted to evolve the fluorescent consensus green protein (CGP) with biosynthesized ncAAs. Our results demonstrated the feasibility of using biosynthesized ncAAs in protein engineering, which could further stimulate the application of ncAAs in bioengineering and biomedicine.

Fabrication of highly crystalline covalent organic framework for solid-phase extraction of three dyes from food and water samples.

Herein, a covalent organic framework, which was fabricated at room temperature by using 1,3,5-tris(p-formylphenyl) benzene and 1,3,5-tris(4-aminophenyl)benzene as building blocks, was employed as an adsorbent for solid-phase extraction of dyes including congo red, methyl blue and direct red 80 for the first time. The prepared covalent organic framework was properly characterized by different techniques and the results revealed that it had a uniform spherical structure, high crystallinity, satisfactory surface area, and good thermal stability. Moreover, the adsorption performance of the material was explored by using static and dynamic adsorption experiments and the results indicated that the material showed good adsorption capacities for three dyes with adsorption capacities in the range of 55.25-284.10 mg/g and the adsorption equilibrium can be achieved in 15 min. Further, to achieve the best adsorption effects of the material, the influence parameters such as pH, ionic strength, type of desorption solvent, and the material dosage in the solid-phase extraction column, were optimized in turn. Finally, under optimal conditions, the solid-phase extraction coupled with HPLC was applied to the analysis of dyes in food and water samples. The recoveries of dyes in actual samples were satisfactory, revealing the unique applicability of the material in the sample pretreatment field.

Identification and characterization of a versatile keratinase, KerZJ, from Stenotrophomonas sp. LMY.

Keratinases have drawn increasing attention in recent decades owing to their catalytic versatility and broad applications from agriculture to medicine. In the present study, we isolated a highly keratinolytic and fibrinolytic bacterium from the campus soil and named it Stenotrophomonas sp. LMY based on genetic information. To identify the potential keratinase genes, the genome sequence of the strain was obtained and analyzed. Sequence alignment and comparison revealed that the protein 1_737 (KerZJ) had the highest sequence homology to a reported keratinase KerBL. We recombinantly expressed KerZJ in Escherichia coli Origami™ (DE) pLysS and purified it to homogeneity. KerZJ showed the highest activity at 40 °C and pH 9.0, and metal ions exhibited no significant effects on its activity. Although reducing agents would break the disulfide bonds in KerZJ and reduce its activity, KerZJ still exhibited the ability to hydrolyze feather keratin in the presence of ß-ME. KerZJ could efficiently digest human prion proteins. In addition, KerZJ showed fibrinolytic activity on fibrin plates and effectively eliminated blood clots in a thrombosis mouse model without side effects. Our results suggest that KerZJ is a versatile keratinase with significant potential for keratin treatment, decontamination of prions, and fibrinolytic therapy.

MXene/ZnS/chitosan-cellulose composite with Schottky heterostructure for efficient removal of anionic dyes by synergistic effect of adsorption and photocatalytic degradation.

Nowadays, dye water pollution is becoming increasingly severe. Composite of MXene, ZnS, and chitosan-cellulose material (MX/ZnS/CC) was developed to remove anionic dyes through the synergistic effect of adsorption and photocatalytic degradation. MXene was introduced as the cocatalyst to form Schottky heterostructure with ZnS for improving the separation efficiency of photocarriers and photocatalytic performance. Chitosan-cellulose material mainly served as the dye adsorbent, while also could improve material stability and assist in generation of free radicals for dye degradation. The physics and chemistry properties of MX/ZnS/CC composite were systematically inspected through various characterizations. MX/ZnS/CC composite exhibited good adsorption ability to anionic dyes with adsorption capacity up to 1.29 g/g, and excellent synergistic effects of adsorption and photodegradation with synergistic removal capacity up to 5.63 g/g. MX/ZnS/CC composite performed higher synergistic removal ability and better optical and electrical properties than pure MXene, ZnS, chitosan-cellulose material, and MXene/ZnS. After compounding, the synergistic removal percentage of dyes increased by a maximum of 309 %. MX/ZnS/CC composite mainly adsorbs anionic dyes through electrostatic interactions and catalyzes the generation of •O2-, h+, and •OH to degrade dyes, which has been successfully used to remove anionic dyes from environmental water, achieving a 100 % removal of 50 mg/L dye.

Chitosan-alginate sponge with multiple cross-linking networks for adsorption of anionic dyes: Preparation, property evaluation, mechanism exploration, and application.

A chitosan-alginate sponge (CAS) with multiple cross-linking networks was developed using chitosan, sodium alginate, polyvinyl alcohol, and glutaraldehyde to adsorb and enrich the anionic dyes form the food samples. The multiple networks in CAS refer to the electrostatic cross-linking network, hydrogen bonding cross-linking network, and covalent cross-linking network. Compared with pure chitosan and alginate sponges, the CAS showed better three-dimensional network structure, mechanical behavior, and stability, which is benefit by multiple cross-linking networks. The physical and chemical properties of CAS were systematically studied by a series of characterizations. The adsorption performance of CAS on anionic dyes was inspected with different dye concentration, time, temperature, and pH conditions. CAS exhibited a good and stable adsorption property to amaranth, carmine, and sunset yellow with the saturation adsorption capacity of 94.34, 111.5, and 80.05 mg∙g-1, respectively. Furthermore, CAS performed outstanding selectivity to anionic dyes with the selectivity factor up to 16.99. Through electrostatic potential analysis, it is inferred that CAS mainly adsorbs anionic dyes through electrostatic interactions. CAS showed satisfactory reusability, maintaining 97 %-99 % of adsorption performance after six cycles of recycling. Finally, CAS was combined with high-performance liquid chromatography for the enrichment and detection of anionic dyes in candy and cocktail samples, achieving the enrichment factor up to 84.77.

Mannan-conjugated adenovirus enhanced gene therapy effects on murine hepatocellular carcinoma cells in vitro and in vivo.

The incidence of advanced hepatocellular carcinoma (HCC) is increasing worldwide, and its prognosis is extremely poor. For some patients for whom surgical treatments are not appropriate, one can only rely on chemotherapy. In the conventional chemotherapy, side effects usually occurred in most cases due to high toxicity levels. Moreover, the development of drug resistance toward chemotherapeutic agents often prevents the successful long-term use of chemotherapy for HCC. Gene therapy represents the exciting biotechnological advance that may revolutionize the conventional fashion of cancer treatment. Overexpression of phosphatase and tensin homologue (PTEN) in cancer cells carrying deletion/mutant type of it can induce the apoptosis of cancer cells and inhibit cell proliferation. In this work, in order to make full use of the high transfectivity of adenovirus, we managed to conjugate the polysaccharide mannan (polymannose) to the surface of the adenovirus chemically under appropriate oxidizing conditions to prepare the mannan-modified adenovirus (Man-Ad5-PTEN). The cytotoxicity and anticancer activity of Man-Ad5-PTEN were assessed in vitro. Reporter gene expression of LacZ transferred by Man-Ad5-LacZ was verified on mannose receptor-deficient NIH/3T3 cells versus mannose receptor-efficient macrophages. Hepatocellular carcinoma cell lines transduced by mannan-modified adenovirus were assayed for cell cycle, apoptosis, invasion, and migration. Further, we detected the antitumor effect on intraperitoneal H22 tumor-bearing mice treated by Man-Ad5-PTEN alone or combined with chemotherapeutic agent of doxorubicin. The results demonstrated that cell growth suppression was not observed in Chang normal hepatocyte cells and the cell killing by Man-Ad5-PTEN is tumor selective. Further, the results showed that the strategy of mannan conjugation could enhance adenovirus-mediated PTEN gene therapy effects on murine hepatocellular carcinoma cells in vitro and in vivo.

Carbonized human hair derived carbon dots for detection of clozapine.

Clozapine (CLZ) is known as the most effective antipsychotic medication for schizophrenia. However, low dosage or over dosage of CLZ is adverse to the treatment of Schizophrenia. Thus, it is necessary to develop effective detection method for CLZ. Recently, due to the advantages such as excellent optical properties, good photobleachability and sensitivity, carbon dots (CDs)-based fluorescent sensors for the detection of target analytes have drawn a great deal of attention. In this work, blue fluorescent CDs (Named as B-CDs) with quantum yield (QY) as high as 38% were obtained by using carbonized human hair as source material through one-step dialysis method for the first time. B-CDs showed obvious graphite-like structure with an average of 1.76 nm, containing abundant functional groups such as -C=O, amino N and C-N on the surface of carbon cores. Optical analysis showed that the B-CDs exhibited excitation-dependent emission property with maximum emission wavelength of 450 nm. Moreover, B-CDs were further applied as a fluorescence sensor to the detection of CLZ. The B-CDs based sensor exhibited a good quenching response by CLZ through the inner filter effect and static quenching mechanism with a limit of detection of 67 ng/mL, which was much lower than the minimal effective concentration in blood (0.35 µg/mL). Finally, to test the practical application value of the developed fluorescence method, the determination of the content of CLZ in tablets and the concentration in blood was carried out. Compared with the results of high-performance liquid chromatography (HPLC) method, it can be found that the constructed fluorescence detection method showed high accuracy and had great application potential in the detection of CLZ. Additionally, the results of cytotoxicity experiment showed that B-CDs had low cytotoxicity, which laid the foundation for the subsequent application of B-CDs in biological systems.

Oral Administration of 5-Hydroxytryptophan Restores Gut Microbiota Dysbiosis in a Mouse Model of Depression.

5-Hydroxytryptophan (5-HTP) has positive clinical effects on various neuropsychiatric and metabiotic disorders, especially depression. Although it increases serotonin levels in the brain and gastrointestinal tract, its pharmacology remains largely unknown. Our goal was to determine the effects of 5-HTP on the mouse gut microbiome, which has a close relationship with depression through the "microbiota-gut-brain axis." We confirmed that depressive disorder restructures the gut microbial community, and 5-HTP efficiently improves depressive symptoms in mice. Oral administration of 5-HTP significantly restored gut microbiota dysbiosis in mice with depression-like behaviors. The diversity and richness of gut microbial communities and relative abundance of specific microbial taxa at both phylum and genus levels were partially recovered. 5-HTP exhibited some positive effects on restoring the alterations in the concentrations of short-chain fatty acids and brain-derived neurotrophic factors caused by depression in mice. Our results may provide new insights into the pharmacology of 5-HTP in treating depression and other disorders.

Preparation of sulphuric acid-mediated N,S-codoped red emissive carbon dots: Applications in food dyes detection, solid-state luminescence and cell imaging.

As diseases such as cardiovascular disease and cancer caused by food problems are more and more frequent, food safety has received great attention. Among them, the safety problem caused by food dyes is more prominent. Thus, it is of great value to develop sensitive detection methods for food dyes. In present study, sulphuric acid-mediated N,S-codoped red emissive carbon dots (namely as R-CDs) had been manufactured by using N-phenyl-o-phenylenediamine as precursor, sulfuric acid as additive for the first time. The structural and fluorescence properties of R-CDs had been systematically studied. The results demonstrated that R-CDs showed uniform spherical morphology and had a graphite-like structure, for which the average diameters size was 5.05 nm. Due to the various functional groups such as hydroxyl, pyridinic N, pyrrolic N and -C-SO4, R-CDs emitted bright red fluorescence. Importantly, because of the interactions between the functional groups of R-CDs with the selected food dyes, three dyes including amaranth, brilliant blue FCF and methylene blue can sensitively quench the fluorescence of R-CDs through IFE and static quenching effects. The linearity ranges of them were separately detected as 0.20 µM -20 µM, 10 nM-1 µM and 60 nM-8 µM. The limits of detection (LODs) of them were 70 nM, 4 nM and 20 nM, respectively. Further, R-CDs was successfully applied to the sensitive detection of three dyes from various food samples. To maximize the fluorescence properties of R-CDs, a R-CDs/PVA composite gel was fabricated to make R-CDs fluoresce in solid state condition. The potential of R-CDs/PVA composite gel for preliminary visualization analysis of three dyes was studied. Finally, ascribed to the low toxicity and good biocompatibility, the potential of R-CDs as probe for cell imaging was explored preliminarily.

Comparative Analyses of the Transcriptome and Proteome of Escherichia coli C321.△A and Further Improving Its Noncanonical Amino Acids Containing Protein Expression Ability by Integration of T7 RNA Polymerase.

Incorporation of noncanonical amino acids (ncAAs) into proteins has been proven to be a powerful tool to manipulate protein structure and function, and to investigate many biological processes. Improving the yields of ncAA-containing proteins is of great significance in industrial-scale applications. Escherichia coli C321.ΔA was generated by the replacement of all known amber codons and the deletion of RF1 in the genome and has been proven to be an ideal host for ncAA-containing protein expression using genetic code expansion. In this study, we investigated the transcriptome and proteome profiles of this first codon reassignment strain and found that some functions and metabolic pathways were differentially expressed when compared with those of its parent strain. Genes involved in carbohydrate and energy metabolism were remarkably downregulated. Our results may provide important clues about the growth defects in E. coli C321.ΔA. Furthermore, we improved the yields of ncAA-containing proteins in E. coli C321.ΔA by integrating the T7 RNA polymerase system.

Effects of Nisin, Cecropin, and Penthorum chinense Pursh on the Intestinal Microbiome of Common Carp (Cyprinus carpio).

Following a ban on antibiotic use in the feed industry, trials on the effects of various immunostimulants (prebiotics, probiotics, antimicrobial peptides [AMPs], and herbs) on the survival, growth, immunity, and disease control of farmed fish in aquaculture are being rapidly conducted. The wide variety of microbes with roles in nutrition, metabolism, and immunity in the fish intestine is the primary factor affecting the fermentability and functionality of dietary immunostimulants. For this reason, the dynamic interactions between immunostimulants and the intestinal microbiome may influence fish health. In this study, the effects of two agriculturally important AMPs (nisin and cecropin) and one herb (Penthorum chinense) on the gut microbiome of common carp were investigated, using 16S rDNA high-throughput sequencing. The results suggest that all three substances can alter the richness, diversity, and composition of the intestinal microbiota of common carp. P. chinense had a similar effect on the gut microbiota of common carp to that of nisin, and both promoted more striking changes in the gut microbiota community than did cecropin. The relative abundance of Proteobacteria was lower in the nisin and P. chinense groups than in the control and cecropin groups. The relative abundance of Bacteroidetes in the nisin, cecropin, and P. chinense groups was markedly increased, compared with that of the control group. Additionally, nisin, cecropin, and P. chinense showed obvious anti-inflammatory effects on the fish intestine, which was reflected by significantly increasing the expression levels of two anti-inflammatory cytokines IL-10 and TGF-ß. Some digestive enzyme activities in the fish intestine were also significantly enhanced by supplementing these three substances in feeds.

Enhancement of Activity and Thermostability of Keratinase From Pseudomonas aeruginosa CCTCC AB2013184 by Directed Evolution With Noncanonical Amino Acids.

A keratinase from Pseudomonas aeruginosa (KerPA), which belongs to the M4 family of metallopeptidases, was characterised in this study. This enzyme was engineered with non-canonical amino acids (ncAAs) using genetic code expansion. Several variants with enhanced activity and thermostability were identified and the most prominent, Y21pBpF/Y70pBpF/Y114pBpF, showed an increase in enzyme activity and half-life of approximately 1.3-fold and 8.2-fold, respectively. Considering that keratinases usually require reducing agents to efficiently degrade keratin, the Y21pBpF/Y70pBpF/Y114pBpF variant with enhanced activity and stability under reducing conditions may have great significance for practical applications. Molecular Dynamics (MD) was performed to identify the potential mechanisms underlying these improvements. The results showed that mutation with pBpF at specific sites of the enzyme could fill voids, form new interactions, and reshape the local structure of the active site of the enzyme.

Comparative analysis of the gut microbiota of grass carp fed with chicken faeces.

The gut microbiota is closely related to health and disease. Grass carp (Ctenopharyngodon idella) is an important food fish in China. We aimed to investigate the effect of a chicken faeces diet on the gut microbiota composition of grass carp reared in an integrated farming system in China. Gut microbiota compositions of grass carps fed chicken faeces, a commercial diet, and grass were compared based on 16S rRNA gene sequencing. The major intestinal phyla in grass carps fed chicken faeces were Firmicutes, Proteobacteria, and Actinobacteria. The untreated chicken faeces diet altered the gut microbiota composition and increased the number of potential pathogens and antibiotic-resistant bacteria in the gut to varying degrees. To reduce the risk of diseases, it is necessary to remove residual antibiotics and antibiotic-resistant bacteria in chicken faeces by fermentation or other techniques, before it can be used as a fish feed for grass carp.

Insight Into the Effects of Nisin and Cecropin on the Oral Microbial Community of Rats by High-Throughput Sequencing.

The oral microbiome has major impacts on oral health and disease. Antimicrobial peptides (AMPs), such as nisin and cecropin, have been widely used as food preservatives or feed additives, and are thus inevitably ingested by consumers through their oral cavity. However, as broad-spectrum antimicrobial reagents, the effect of AMPs on the oral microbiome of consumer's remains poorly characterized. In this study, we performed 16S rDNA high-throughput sequencing to investigate the effect of nisin and cecropin on the oral microbiomes of rats. Our results suggest that although nisin and cecropin have different effects on the oral microbiome of rats, both AMPs impact the composition of oral microbial communities at the phylum and genus levels. Cecropin significantly reduced the diversity and richness of rat oral microbial communities. Notably, the relative abundance of the pathogen Acinetobacter baumannii increased in the oral microbial community of rats fed cecropin-containing feed. In addition, nisin significantly reduced the amount of secretory immunoglobulin A in the saliva of rats.

Aptamer-mediated gene therapy enhanced antitumor activity against human hepatocellular carcinoma in vitro and in vivo.

A recombinant adenovirus carrying the tumor suppressor gene PTEN (Ad5-PTEN) is an effective antitumor agent against liver cancer. But the application of Ad5-PTEN has been greatly hindered by its auto-immunogenicity, non-specific toxicity to normal tissues, as well as poor stability in blood stream because of neutralizing antibody. Epithelial cell adhesion molecule (EpCAM) is over-expressed in most solid tumors and it has been identified to be a cancer stem cell surface marker in liver cancer. An RNA aptamer EpDT3 could specially bind with EpCAM and target EpCAM-positive cells. Therefore, we hypothesized that developing a novel gene delivery system of EpDT3-modified Ad5-PTEN could overcome the disadvantages of naked Ad5-PTEN and enhance the antitumor effect on hepatocellular carcinoma. We took polyethylene glycol (PEG) as a linker to conjugate EpDT3 with Ad5-PTEN to prepare EpDT3-PEG-Ad5-PTEN (EPAP) by simple chemical synthesis method. We found that the stability of this novel gene delivery system in human blood serum increased about 16-fold compared to the naked adenovirus. Meanwhile, EPAP enhanced gene expression and cellular uptake in HepG2 cells, and showed significant inhibition in cell proliferation and cell migration against hepatocellular carcinoma cells HepG2 while showing no cytotoxicity to normal liver cells L-02, compared with Ad5-PTEN. Importantly, EPAP could induce cell apoptosis and presented superior antitumor activity against aggressive HepG2 xenograft in nude mice but showed no obvious toxicity to the tested mice at the therapy concentration. In conclusion, EpCAM aptamer EpDT3 could significantly enhance the antitumor effect of Ad5-PTEN with high binding ability to EpCAM-positive cells HepG2.

Enhanced growth inhibition of prostate cancer in vitro and in vivo by a recombinant adenovirus-mediated dual-aptamer modified drug delivery system.

The peptide aptamer DUP-1 targets prostate-specific membrane antigen (PSMA)-negative cells, while the RNA aptamer A10-3.2 targets PSMA-positive prostate cancer cells. Moreover, the tumor-suppressor gene phosphatase and tensin homolog (PTEN) and the chemotherapeutic agent doxorubicin (DOX) effectively inhibit prostate cancer, and a recombinant adenovirus (Ad5) mediates high gene transfer efficiency. Here, we design a dual-aptamer modified tumor targeting gene and DOX delivery system mediated by recombinant adenovirus (A10-3.2(DOX)/DUP-1-PEG-Ad5, ADDP-Ad5). DUP-1 and A10-3.2 are connected to the adenovirus through polyethylene glycol (PEG), PTEN is integrated into Ad5, and DOX is embedded into the double chain of aptamer A10-3.2. The PEG-modification rate of Ad5 is 98.70 ± 2.43%. The DUP-1 and A10-3.2 modified products yield 80.40 ± 1.36% and 82.20 ± 2.14%, respectively. The uptake of ADDP-Ad5 and the expression of the reporter gene are enhanced by the system in PSMA-positive LNCaP and PSMA-negative PC3 human prostate cancer cells. ADDP-Ad5 significantly inhibits the cell growth of both LNCaP and PC3 cells. More importantly, ADDP-Ad5 is active in vivo against LNCaP and PC3 tumor xenografts and exhibits no significant toxicity to the mice. Therefore, ADDP-Ad5 may have clinical potential in prostate cancer therapy.

Mannan-modified Ad5-PTEN treatment combined with docetaxel improves the therapeutic effect in H22 tumor-bearing mice.

BACKGROUND: It has been reported that the tumor suppressor gene, PTEN, which is inactivated in many malignant tumors, plays an important role in apoptosis, cell cycle arrest, cell migration, and cell spread. For cancer gene therapy, one of the most important problems is low gene transfection efficiency. METHODS: In the present study, to take full advantage of adenovirus in gene expression, we prepared mannan-modified recombinant adenovirus using the PTEN gene (Man-Ad5-PTEN) and investigated the effect of Man-Ad5-PTEN combined with docetaxel (Man-Ad5-PTEN-docetaxel) on tumor growth in a murine model of hepatocellular carcinoma. RESULTS: Man-Ad5-PTEN effectively suppressed tumor growth and induced significant apoptosis of murine H22 hepatoma in vivo. Apoptosis levels in tumor-bearing mice treated with Man-Ad5-PTEN-docetaxel were significantly higher than those in tumor-bearing mice treated with naked Ad5-PTEN, Man-Ad5-PTEN, or docetaxel alone. Treatment with Man-Ad5-PTEN-docetaxel resulted in a significant inhibitory effect in this tumor model. Compared with the controls treated with phosphate-buffered solution, the tumor inhibition rate with naked Ad5-PTEN, docetaxel, Man-Ad5-PTEN, and Man-Ad5-PTEN-docetaxel was 48.69%, 49.98%, 75.88%, and 96.93%, respectively. CONCLUSION: These results suggest that combined treatment with Man-Ad5-PTEN and other chemotherapeutic agents may be a potent adjuvant therapeutic approach for the treatment of hepatocellular carcinoma.