Crystal structure of polysaccharide lyase family 20 endo-β-1,4-glucuronan lyase from the filamentous fungus Trichoderma reesei

The crystal structure of endo-β-(1→4)-glucuronan lyase from Trichoderma reesei (TrGL) has been determined at 1.8 Å resolution as the first three-dimensional structure of polysaccharide lyase (PL) family 20. TrGL has a typical β-jelly roll fold, which is similar to glycoside hydrolase family 16 and PL7 enzymes. A calcium ion is bound to the site far from the cleft and appears to contribute to the stability. There are several completely conserved residues in the cleft. Possible catalytic residues are predicted based on structural comparison with PL7 alginate lyase A1-II′.     

A method of purification, identification and characterization of β-glucosidase from Trichoderma koningii AS3.2774

In this study, we used native gradient-polyacrylamide gel electrophoresis and electroelution (NGGEE) to purify enzymatic proteins from Trichoderma koningii AS3.2774. With this method, we purified eight enzymatic proteins and classified them to the cellulase system by comparing secretions of T. koningii in inductive medium and in repressive medium. It resulted in 24-fold β-glucosidase (BG) purification with a recovery rate of 5.5%, and a specific activity of 994.6 IU mg^− 1 protein. The final yield of BG reached 8 μg under purifying procedure of NGGEE. We also identified BG using the enzyme assay with thin-layer chromatography and MALDI-TOFMS. This BG had one subunit with a molecular mass of 69.1 kDa as determined by sodium dodecylsulfate-polyacrylamide gel electrophoresis. The hydrolytic activity of the BG had an optimal pH of 5.0, an optimal temperature of 50 °C, an isoelectric point of 5.68 and a K_m for p-nitrophenyl-β-d-glucopyranoside of 2.67 mM. Taken together, we show that NGGEE is a reliable method through which μg grade of active proteins can be purified.     

Computational simulations of the Trichoderma reesei cellobiohydrolase I acting on microcrystalline cellulose Iβ: the enzyme-substrate complex

Cellobiohydrolases are the dominant components of the commercially relevant Trichoderma reesei cellulase system. Although natural cellulases can totally hydrolyze crystalline cellulose to soluble sugars, the current enzyme loadings and long digestion times required render these enzymes less than cost effective for biomass conversion processes. It is clear that cellobiohydrolases must be improved via protein engineering to reduce processing costs. To better understand cellobiohydrolase function, new simulations have been conducted using charmm of cellobiohydrolase I (CBH I) from T.reesei interacting with a model segment (cellodextrin) of a cellulose microfibril in which one chain from the substrate has been placed into the active site tunnel mimicking the hypothesized configuration prior to final substrate docking (i.e., the +1 and +2 sites are unoccupied), which is also the structure following a catalytic bond scission. No tendency was found for the protein to dissociate from or translate along the substrate surface during this initial simulation, nor to align with the direction of the cellulose chains. However, a tendency for the decrystallized cellodextrin to partially re-anneal into the cellulose surface hints that the arbitrary starting configuration selected was not ideal.     

Transgalactosylation and hydrolytic activities of commercial preparations of β-galactosidase for the synthesis of prebiotic carbohydrates

β-Galactosidases exhibit both hydrolytic and transgalactosylation activities; the former has been used traditionally for the production of delactosed milk and dairies, while the latter is being increasingly used for the synthesis of lactose-derived oligosaccharides: balance between both activities was highly dependent on the enzyme origin: β-galactosidases from Aspegillus oryzae and Bacillus circulans exhibited high transgalactosylation activity, while those from one from Kluyveromyces exhibited high hydrolytic activity but quite low transgalactosylation activity. Also the affinity for the donors (lactose or lactulose) and the acceptors (lactose, lactulose or fructose) of transgalactosylated galactose was dependent on the enzyme origin, as reflected by the Michaelis constants obtained in the synthesis of galacto-oligosaccharides, fructosyl-galacto-oligosaccharides and lactulose. Finally, the balance between transgalactosylation and hydrolytic activities of β-galactosidases could be tuned by changing the concentration of galactose donor.     

β-d-glucosidase-catalysed transfer of the glycosyl group from aryl β-d-gluco- and β-d-xylo-pyranosides to phenols

The effect of phenols on the hydrolysis of substituted phenyl β-d-gluco- and β-d-xylo-pyranosides by β-d-glucosidase from Stachybotrys atra has been investigated. Depending on the glycon part of the substrate and on the phenol substituent, the hydrolysis is either inhibited or activated. With aryl β-d-xylopyranosides, transfer of the xylosyl residue to the phenol, with the formation of new phenyl β-d-xylopyranosides, is observed. With aryl β-d-glucopyranosides, such transfer does not occur when phenols are used as acceptors, but it does occur with anilines. A two-step mechanism, in which the first step is partially reversible, is proposed to explain these observations. A qualitative analysis of the various factors determining the overall effect of the phenol is given.     

PEP-1–metallothionein-III protein ameliorates the oxidative stress-induced neuronal cell death and brain ischemic insults

Background

Oxidative stress is considered to be involved in a number of human diseases including ischemia. Metallothioneins (MT)-III can protect neuronal cells from the cytotoxicity of reactive oxygen species (ROS). However, MT-III proteins biological function is unclear in ischemia. Thus, we examined the protective effects of MT-III proteins on oxidative stress-induced neuronal cell death and brain ischemic insult.

Methods

A human MT-III gene was fused with a protein transduction domain, PEP-1 peptide, to construct a cell permeable PEP-1–MT-III protein. PEP-1–MT-III protein was purified using affinity chromatograph. Transduced PEP-1–MT-III proteins were detected by Western blotting and immunoflourescence. Cell viability and DNA fragmentation were analyzed by 3-(4,5-dimethylthiazol-2-yl)-2,5-dipheyltetrazolium bromide (MTT) assay and terminal dexoynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) staining, respectively. Brain ischemic injury was detected with immunohistochemistry.

Results

Purified PEP-1–MT-III proteins transduced into astrocytes in a time- and dose-dependent manner and protected against oxidative stress-induced cell death. Also, transduced PEP-1–MT-III proteins efficiently protected cells against DNA fragmentation. Furthermore, immunohistochemical analysis revealed that PEP-1–MT-III prevented neuronal cell death in the CA1 region of the hippocampus induced by transient forebrain ischemia. We demonstrated that transduced PEP-1–MT-III protein protects against oxidative stress induced cell death in vitro and in vivo.

General significance

Transduced PEP-1–MT-III protein has neuroprotective roles as an antioxidant in vitro and in vivo. PEP-1–MT-III protein is a potential therapeutic agent for various human brain diseases such as stroke, Alzheimer's disease, and Parkinson's disease.     

Structure and chain conformation of five water-soluble derivatives of a β-d-glucan isolated from Ganoderma lucidum

A linear water-insoluble (1→3)-β-d-glucan, coded as GL-IV-I, was isolated from the fruit body of Ganoderma lucidum by extracting with NaOH solution. Its derivatives were prepared by using sulfation, carboxymethylation, hydroxyethylation, hydroxypropylation, and methylation, respectively, and these were labeled as S-GL, CM-GL, HE-GL, HP-GL and M-GL. Five derivatives exhibited good water solubility. Their structures and chain conformations were investigated with infrared spectroscopy, elemental analysis (EA), one- and two-dimensional NMR spectroscopy, laser light scattering (LLS), and size-exclusion chromatography combined with LLS (SEC-LLS). The reactivity of the hydroxyl group of GL-IV-I was ordered as C-6 > C-4 > C-2 for the five derivatives. The degree of substitution (DS) of the derivatives was calculated from EA and NMR spectroscopy to be from 0.32 to 1.18. The weight-average molecular mass (M_w) of GL-IV-I, S-GL, CM-GL, HE-GL, HP-GL, and M-GL was 13.3 × 10⁴, 10.1 × 10⁴, 6.3 × 10⁴, 7.2 × 10⁴, 5.1 × 10⁴, and 14.1 × 10⁴, respectively. The conformation analysis studies revealed that GL-IV-I exists as a compact coil in dimethyl sulfoxide, whereas the five derivatives are slightly expanded flexible chains in 0.9% aqueous NaCl solution.     

A comparison of the β-d-glucosidase and β-d-galactosidase activities from eleven enzyme sources

• 1.1. Eleven enzyme sources have been examined for their β-glucosidase and β-galactosidase content using 4-methylumbelliferyl β-glycosides as substrates.
• 2.2. Inhibition studies, starch-gel electrophoresis and DEAE-cellulose chromatography indicate that multiple forms of these two enzymes are common.
• 3.3. Specific β-glucosidases and β-galactosidases and Emulsin-type enzymes with activity towards both substrates may occur in the same crude source.

     

The ineffectiveness of analogs of d-galactal as competitive inhibitors of,and substrates for, β-d-galactosidase from Escherichia coli

2,6-Anhydro-3-deoxy-aldehydo-d-lyxo-hept-2-enose (7) 2,6-anhydro-3-deoxy-d-lyxo-hept-2-enitol (8) were synthesized as half-chair analogs of d-galactal (1). As 1 is a strong inhibitor of, as well as a substrate for, β-d-galactosidase from Escherichia coli, the same properties were expected for 7 and 8; however, both were ineffective. This result, together with those of other authors, allows speculative conclusions on the tight binding of 1 to the enzyme only, when water or an alcohol is bound as a co-substrate.     

Crystal structure of glycoside hydrolase family 127 β-l-arabinofuranosidase from Bifidobacterium longum

Enzymes acting on β-linked arabinofuranosides have been unknown until recently, in spite of wide distribution of β-l-arabinofuranosyl oligosaccharides in plant cells. Recently, a β-l-arabinofuranosidase from the glycoside hydrolase family 127 (HypBA1) was discovered in the newly characterized degradation system of hydroxyproline-linked β-l-arabinooligosaccharides in the bacterium Bifidobacterium longum. Here, we report the crystal structure of HypBA1 in the ligand-free and β-l-arabinofuranose complex forms. The structure of HypBA1 consists of a catalytic barrel domain and two additional β-sandwich domains, with one β-sandwich domain involved in the formation of a dimer. Interestingly, there is an unprecedented metal-binding motif with Zn²⁺ coordinated by glutamate and three cysteines in the active site. The glutamate residue is located far from the anomeric carbon of the β-l-arabinofuranose ligand, but one cysteine residue is appropriately located for nucleophilic attack for glycosidic bond cleavage. The residues around the active site are highly conserved among GH127 members. Based on biochemical experiments and quantum mechanical calculations, a possible reaction mechanism involving cysteine as the nucleophile is proposed.     

Biochemical characterization of a 27 kDa 1,3-β-d-glucanase from Trichoderma asperellum induced by cell wall of Rhizoctonia solani

Trichoderma asperellum produces two extracellular 1,3-β-d-glucanase upon induction with cell walls from Rhizoctonia solani. A minor 1,3-β-d-glucanase was purified to homogeneity by ion exchange chromatography on Q-Sepharose and gel filtration on Sephacryl S-100. A typical procedure provided 13.8-fold purification with 70% yield. SDS-PAGE of the purified enzyme showed a single protein band of molecular weight 27 kDa. The enzyme exhibited optimum catalytic activity at pH 3.6 and 45 °C. It was thermostable at 40 °C, and retained 75% activity after 60 min at 45 °C. The K_m and V_max values for 1,3-β-d-glucanase, using laminarin as substrate, were 0.323 mg ml⁻¹ and 0.315 U min⁻¹, respectively. The enzyme was strongly inhibited by Hg²⁺ and SDS. The enzyme was only active toward glucans containing β-1,3-linkages. Peptide sequences showed similarity with two endo-1,3(4)-β-d-glucanases from Aspergillus fumigatus Af293when compared against GenBank non-redundant database.     

A hemicellulosic β-glucan from the hypocotyls of Phaseolus aureus

A glucan of $\text{DP}$_nca 80 has been isolated from the hypocotyls of mung bean plants (Phaseolus aureus). Methylation analysis and periodate oxidation studies showed that the glucan has (1 → 3) and (1 → 4) linked d-glucopyranosyl residues in the molar ratio 1·0:1·7. Oligosaccharides containing both β(1 → 3) and β(1 → 4) linked residues were isolated from partial hydrolysates.     

Purification and characterisation of β-N-acetylhexosaminidase from the butter clam, saxidomus purpuratus

A β-N-acetylhexosaminidase [EC 3.2.1.30] has been purified ～98-fold from an extract of the digestive organs of Saxidomus purpuratus by using ammonium sulfate fractionation, and chromatography on Toyopearl HW-50, CM-cellulose, and Sepharose 4B. The purified enzyme, the molecular weight of which was estimated to be ～66,000 by gel filtration, was composed of two sub-units of molecular weight 30,000 as determined by sodium dodecyl sulphate-polyacrylamide gel electrophoresis. The purified enzyme had a pH optimum of 3.8 and an optimum temperature of 55°, and its activity was enhanced ～2-fold in the presence of 0.1m sodium chloride. The Michaelis constants toward p-nitrophenyl 2-acetamido-2-deoxy-β-d-glucoside and -galactoside were 1.2 × 10^?4 and 1.3 × 10^?4m, respectively.     

On the active site of β-hexosaminidase from latex of Ficus glabrata

N-Acetyl-β-d-hexosaminidase (EC 3.2.1.52), active against both p-nitrophenyl-N-acetyl-β-d-glucosaminide and p-nitrophenyl-N-acetyl-β-d-galactosaminide, is present in latex of Ficus glabrata. The final specific activity was increased 150-fold from crude extract after ammonium sulphate fractionation and affinity chromatography on Concanavalin A-Sepharose. The activity ratio β-N-acetylglucosaminidase-β-N-acetylgalactosaminidase remained constant. Substrate competition, competitive inhibition studies and Arrhenius plots confirm that, in the hexosamidase, only one kind of active site is responsible for both activities. Acetate and acetamide are more effective competitive inhibitors than iodoacetamide, N-acetylglucosamine and N-acetylgalactosamine more than glucosamine and galactosamine, and α-methylmannoside more than mannose, suggesting that the active site binds the N-acetyl moiety of the substrate and a hydrophobic interaction of the methyl group is involved. The difference between the strength of the inhibition by mannosamine with respect to glucosamine and galactosamine, that do not inhibit, seems to be due to the position at C-2 of the amino group in the pyranose ring.     

Phospholipase C and sphingomyelinase activities of the Clostridium perfringens α-toxin

α-Toxin is a major pathogenic determinant of Clostridium perfringens, the causative agent of gas gangrene. α-Toxin has been known for long to be a phospholipase C, but up to now its hydrolytic properties have been studied only through indirect methods, e.g. release of cell contents, or under non-physiological conditions, e.g., in micelles, or with soluble substrates. In this report we characterize the phospholipase C and sphingomyelinase activities of α-toxin using a direct assay method (water-soluble phosphorous assay) with phospholipids in bilayer form (large unilamellar vesicles) in the absence of detergents. The simplest bilayer compositions allowing measurable activities under these conditions were DOPC:Chol (2:1 mol ratio) and SM:PE:Chol (2:1:1 mol ratio) for the PLC and SMase activities respectively. PLC activity was five times higher than SMase activity. Both activities gave rise to vesicle aggregation, after a lag time during which ca. 10% of the substrate was hydrolyzed. Vesicle aggregation, measured as an increase in light scattering, was a convenient semi-quantitative method for estimating the enzyme activities. The optimum pH for the combined PLC and SMase activities was in the 5-7 range, in agreement with the proposed role of α-toxin in aiding the bacterium to escape the fagosome and survive within the cytosol.     

On the Existence of a Possible A2A-D2-β-Arrestin2 Complex: A2A Agonist Modulation of D2 Agonist-Induced β-Arrestin2 Recruitment

Given that coactivation of adenosine A_2A (A_2AR) and dopamine D₂ (D₂R) receptors results in the coaggregation, cointernalization, and codesensitization of the A_2AR and D₂R and the role of scaffolding protein β-arrestin2 in the desensitization, internalization, and signaling of G-protein-coupled receptors, in this study we explored the ability of the A_2AR agonist CGS21680 in A_2AR-D₂R-coexpressing cells to modulate the D₂R agonist-induced recruitment of β-arrestin2 to the D₂R by means of proximity-based bioluminescence resonance energy transfer (BRET²) and co-trafficking analysis. We found evidence that CGS21680 can increase the maximal BRET² signal between β-arrestin2^RLuc and D_2LR^GFP2 upon D₂R activation, by increasing the potency of the D₂R agonist to exert this action. In addition, this change was associated with an increased formation of cytoplasmic clusters containing β-arrestin2^GFP2 and D_2LR^YFP as seen from the co-trafficking analysis. Furthermore, the A_2AR agonist advanced the time for the increase in Akt phosphorylation obtained with the D₂R agonist. Finally, using a novel bioinformatics approach to predict the protein-protein interface, we have also found that amino acid pro-triplets TNY, LLS, RAF, and VSR may be crucial for the -induced β-arrestin2 recruitment by A_2AR-D₂R heteromers. Taken together, the results indicate that the antagonistic A_2AR-D₂R allosteric receptor-receptor interaction in A_2AR-D₂R heteromers favors β-arrestin2 recruitment to the D_2LR protomer with subsequent cointernalization associated with a reduced time onset of Akt phosphorylation followed by a rapid dephosphorylation. Thus, β-arrestin2 action becomes more rapid and short-lasting and, in this way, mimics G-protein-mediated signaling.     

Characterization of β-galactosidase and α-galactosidase activities from the halophilic bacterium Gracilibacillus dipsosauri

Purpose

Higher alcohol is a by-product of the fermentation of wine, and its content is one of the most important parameters that affect and are used to appraise the final quality of Chinese rice wine. Ammonium compensation is an efficient and convenient method to reduce the content of higher alcohols, but the molecule mechanism is poorly understood. Therefore, an iTRAQ-based proteomic analysis was designed to reveal the proteomic changes of Saccharomyces cerevisiae to elucidate the molecular mechanism of ammonium compensation in reducing the content of higher alcohols.

Methods

The iTRAQ proteomic analysis method was used to analyze a blank group and an experimental group with an exogenous addition of 200 mg/L (NH₄)₂HPO₄ during inoculation. The extracted intracellular proteins were processed by liquid chromatography-mass spectrometry and identified using bioinformatics tools. Real-time quantitative polymerase chain reaction was used to verify the gene expression of differentially expressed proteins.

Results

About 4062 proteins, including 123 upregulated and 88 downregulated proteins, were identified by iTRAQ-based proteomic analysis. GO and KEGG analysis uncovered that significant proteins were concentrated during carbohydrate metabolism, such as carbon metabolism, glyoxylate, and dicarboxylate metabolism, pyruvate metabolism, and the nitrogen metabolism, such as amino acid synthesis and catabolism pathway. In accordance with the trend of differential protein regulation in the central carbon metabolism pathway and the analysis of carbon metabolic flux, a possible regulatory model was proposed and verified, in which ammonium compensation facilitated glucose consumption, regulated metabolic flow direction into tricarboxylic acid, and further led to a decrease in higher alcohols. The results of RT-qPCR confirmed the authenticity of the proteomic analysis results at the level of gene.

Conclusion

Ammonium assimilation promoted by ammonium compensation regulated the intracellular carbon metabolism of S. cerevisiae and affected the distribution of metabolic flux. The carbon flow that should have gone to the synthesis pathway of higher alcohols was reversed to the TCA cycle, thereby decreasing the content of higher alcohols. These findings may contribute to an improved understanding of the molecular mechanism for the decrease in higher alcohol content through ammonium compensation.