Enzyme-Triggered Chromogenic and Fluorogenic Probes for Myrosinase Activity Detection

Myrosinase, a thioglucosidase, is a key enzyme in the mechanism of defense of plants that hydrolyzes glucosinolates (GSLs) into isothiocyanates. These isothiocyanates are the main bioactive molecules exerting protective effect in Brassicales plants. These plants that contain this specific enzyme-substrate couple belong to our daily human diet and have demonstrated health benefits, such as chemopreventive effects. Thus, the detection of myrosinase activity is a key aspect of the production of isothiocyanates from glucosinolates. Two novel chromogenic and fluorogenic GSLs, GSL p-nitrophenoxy (GSL-pNP) and GSL-4-methylumbelliferone (GSL-4MU), were designed and synthesized to be used as simple and reliable molecular tools to spectrophotometrically detect myrosinase activity in simple and complex mixtures. Notably, the chromogenic GSL enabled the UV-vis detection and quantification of isolated myrosinase activity, while fluorogenic GSL could be used for in vitro activity monitoring of more complex plant materials, such as seeds.

A Versatile β-Glycosidase from Petroclostridium xylanilyticum Prefers the Conversion of Ginsenoside Rb3 over Rb1, Rb2, and Rc to Rd by Its Specific Cleavage Activity toward 1,6-Glycosidic Linkages

To convert ginsenosides Rb1, Rb2, Rb3, and Rc into Rd by a single enzyme, a putative β-glycosidase (Pxbgl) from the xylan-degrading bacterium Petroclostridium xylanilyticum was identified and used. The kcat/Km value of Pxbgl for Rb3 was 18.18 ± 0.07 mM-1/s, which was significantly higher than those of Pxbgl for other ginsenosides. Pxbgl converted almost all Rb3 to Rd with a productivity of 5884 μM/h, which was 346-fold higher than that of only β-xylosidase from Thermoascus aurantiacus. The productivity of Rd from the Panax ginseng root and Panax notoginseng leaf was 146 and 995 μM/h, respectively. Mutants N293 K and I447L from site-directed mutagenesis based on bioinformatics analysis showed an increase in specific activity of 29 and 7% toward Rb3, respectively. This is the first report of a β-glycosidase that can simultaneously remove four different glycosyls at the C-20 position of natural PPD-type ginsenosides and produce Rd as the sole product from P. notoginseng leaf extracts with the highest productivity.

Preparation of fern root resistant starch by pullulanase and glucoamylase combined with autoclaving-enzymatic method: physicochemical properties and structural characterization

BACKGROUND

Fern root starch has a high percentage of amylose and has great potential for application in the field of slow-digesting foods. Clarifying the effect of treatment conditions on fern root starch is key to achieving industrialized production of fern root resistant starch. In the present study, fern root starch was treated by the autoclave-enzymatic method with pullulanase, glucoamylase and mixed enzyme.

RESULTS

The content of resistant starch in fern roots treated with mixed enzyme was the highest (24.07 ± 1.11%), which was approximately 320% times that of the native starch, had the best water-holding capacity (151.08%), vital transparency and freeze-thaw stability. By contrast, the solubility, swelling and viscosity were lower than natural starch. In addition, mixed enzyme shows a denser structure, and the crystal form changes from C-type to V-type, with a high relative crystallinity and significantly enhanced thermal stability.

CONCLUSION

After mixed enzyme combined with autoclave treatment, the content of resistant starch in fern root was greatly increased. The modified starch molecules did not produce new functional groups, which made the crystal structure of starch molecules more compact, and resistance to enzymatic hydrolysis and high temperature thermal stability were significantly enhanced. This provides a positive reference for further in-depth study of fern root starch, improvement of utilization value, development and innovation of new food health products, and diabetes treatment. © 2024 Society of Chemical Industry.

The structure investigation of GH174 endo-1,3-fucanase revealed an unusual glycoside hydrolase fold

Sulfated fucan has attracted increasing research interest due to its various biological activities. Endo-1,3-fucanases are favorable tools for structure investigation and structure-activity relationships establishment of sulfated fucan. However, the three-dimensional structure of enzymes from the GH174 family has not been disclosed, which hinders the understanding of the action mechanism. This study reports the first crystal structure of endo-1,3-fucanase from GH174 family (Fun174A) at a resolution of 1.60 Å. Notably, Fun174A exhibited an unusual distorted β-sandwich fold, which is distinct from other known glycoside hydrolase folds. The conserved amino acid residues D119 and H154 were proposed as the catalytic residues in the family. Molecular docking suggested that Fun174A primarily recognized sulfated fucan through a series of polar amino acid residues around the substrate binding pocket. Furthermore, structural bioinformatics analysis suggested that the structural analogs of Fun174A may be extensively implicated in the bacterial metabolism of polysaccharides, which provided opportunities for the discovery of novel glycoside hydrolases. This study offers new insights into the structural diversity of glycoside hydrolases and will contribute to the establishment of a novel clan of glycoside hydrolases.

Glycosylium Ions in Superacid Mimic the Transition State of Enzyme Reactions

The hydrolysis of glycosides is a biochemical transformation that occurs in all living organisms, catalyzed by a broad group of enzymes, including glycoside hydrolases. These enzymes cleave the glycosidic bond via a transition state with substantial oxocarbenium ion character, resulting in short-lived oxocarbenium ion-like species. While such transient species have been inferred through theoretical studies and kinetic isotope effect measurements, their direct spectroscopic characterization remains challenging. In this study, we exploit a superacid environment to generate, accumulate, and fully characterize nonprotected 2-deoxy glycosyl cations in the d-glucopyranose, d-galactopyranose, and l-arabinofuranose series using low-temperature NMR spectroscopy, supported by DFT calculations. Additionally, QM/MM MD simulations reveal that the properties of these glycosyl cations in superacid closely resemble those within the active sites of glycosidase enzymes, particularly in terms of conformation and anomeric charge distribution. These findings highlight a parallel between the stabilizing effect of counterions in superacid media and the network of multidentate noncovalent interactions within glycosidase active sites, which stabilize transition states with pronounced oxocarbenium ion character.

Glucosinolates and Their Hydrolytic Products-A Love Story of Environmental, Biological, and Chemical Conditions

BACKGROUND

Glucosinolates (GSL) play an important role in providing defense to plants and helping them to cope with various biotic, as well as abiotic, stresses. Many living beings including humans and animals, including some herbivores, have adapted themselves to use this defense mechanism for their own use. More than 120 glucosinolates are distributed within a large number of plants. Many factors are known to influence the GSL composition in a plant. Among these, cofactors, myrosinase isozymes, heavy metals and the environmental conditions such as light, CO2 and temperature are important in regulation. These factors ensure that different glucosinolate compositions can be produced by the plants, thus impacting the defense mechanism.

OBJECTIVE

The objective of the current review is to highlight the importance of the factors responsible for affecting glucosinolate composition and concentration.

METHODS

The review has been compiled using accessible literature from Pubmed, Scopus, and Google scholar. Efforts have been made to restrict the literature to the last 5 years (2018-2023), with some exceptions.

RESULTS

The current critical review acts as a resource for all the researchers working on these essential compounds. It provides information on the factors that may influence glucosinolate production. It also gives them an opportunity to modify the glucosinolate composition of a plant using the given information.

CONCLUSIONS

Glucosinolates have long been an ignored class of biomolecule. The plethora of biological activities of the compounds can be useful. Though there are some harmful components such as goitrin and progoitrin, these can be easily removed by modulating some of the factors highlighted in the review.

HIGHLIGHTS

The current review has covered most of the factors that have the ability to modify glucosinolate composition and concentration. The mechanistic action of these factors has also been discussed using the current available literature.

PARG inhibition induces nuclear aggregation of PARylated PARP1

Poly (ADP-ribose) glycohydrolase (PARG) inhibitors are currently under clinical development for the treatment of DNA repair-deficient cancers; however, their precise mechanism of action is still unclear. Here, we report that PARG inhibition leads to excessive PARylated poly (ADP-ribose) polymerase 1 (PARP1) reducing the ability of PARP1 to properly localize to sites of DNA damage. Strikingly, the mis-localized PARP1 accumulates as aggregates throughout the nucleus. Abrogation of the catalytic activity of PARP1 prevents aggregate formation, indicating that PAR chains play a key role in this process. Finally, we find that PARP1 nuclear aggregates were highly persistent and were associated with cleaved cytoplasmic PARP1, ultimately leading to cell death. Overall, our data uncover an unexpected mechanism of PARG inhibitor cytotoxicity, which will shed light on the use of these drugs as anti-cancer therapeutics.

Crystal structure of β-d-galactofuranosidase from Streptomyces sp. JHA19 in complex with an inhibitor provides insights into substrate specificity

d-Galactofuranose (Galf) is widely distributed in glycoconjugates of pathogenic microbes. β-d-Galactofuranosidase (Galf-ase) from Streptomyces sp. JHA19 (ORF1110) belongs to glycoside hydrolase (GH) family 2 and is the first identified Galf-specific degradation enzyme. Here, the crystal structure of ORF1110 in complex with a mechanism-based potent inhibitor, d-iminogalactitol (Ki = 65 μm) was solved. ORF1110 binds to the C5-C6 hydroxy groups of d-iminogalactitol with an extensive and integral hydrogen bond network, a key interaction that discriminates the substrates. The active site structure of ORF1110 is largely different from those of β-glucuronidases and β-galactosidases in the same GH2 family. A C-terminal domain of ORF1110 is predicted to be a carbohydrate-binding module family 42 that may bind Galf. The structural insights into Galf-ase will contribute to the investigation of therapeutic tools against pathogens.

CAZac: an activity descriptor for carbohydrate-active enzymes

The Carbohydrate-Active enZYme database (CAZy; www.cazy.org) has been providing the reference classification of carbohydrate-active enzymes (CAZymes) for >30 years. Based on literature survey, the sequence-based families of CAZymes are enriched with functional data by using the International Union of Biochemistry and Molecular Biology Enzyme Commission (EC) number system. However, this system was not developed to search or compare functional information. To better harness functional information, we have developed CAZac (CAZyme activity descriptor), a multicriterion system that describes CAZymes' mechanisms, glycosidic bond orientations, subsites and inter-residue connectivities. This new system, implemented for glycoside hydrolases, glycoside phosphorylases, transglycosidases, polysaccharide lyases and lytic polysaccharide monooxygenases allows complex searches in the CAZy database to uncover the evolution of substrate specificity and mechanisms of CAZymes across families.

Plasticity and steric strain in a parallel beta-helix: rational mutations in the P22 tailspike protein

By means of genetic screens, a great number of mutations that affect the folding and stability of the tailspike protein from Salmonella phage P22 have been identified. Temperature-sensitive folding (tsf) mutations decrease folding yields at high temperature, but hardly affect thermal stability of the native trimeric structure when assembled at low temperature. Global suppressor (su) mutations mitigate this phenotype. Virtually all of these mutations are located in the central domain of tailspike, a large parallel beta-helix. We modified tailspike by rational single amino acid replacements at three sites in order to investigate the influence of mutations of two types: (1) mutations expected to cause a tsf phenotype by increasing the side-chain volume of a core residue, and (2) mutations in a similar structural context as two of the four known su mutations, which have been suggested to stabilize folding intermediates and the native structure by the release of backbone strain, an effect well known for residues that are primarily evolved for function and not for stability or folding of the protein. Analysis of folding yields, refolding kinetics and thermal denaturation kinetics in vitro show that the tsf phenotype can indeed be produced rationally by increasing the volume of side chains in the beta-helix core. The high-resolution crystal structure of mutant T326F proves that structural rearrangements only take place in the remarkably plastic lumen of the beta-helix, leaving the arrangement of the hydrogen-bonded backbone and thus the surface of the protein unaffected. This supports the notion that changes in the stability of an intermediate, in which the beta-helix domain is largely formed, are the essential mechanism by which tsf mutations affect tailspike folding. A rational design of su mutants, on the other hand, appears to be more difficult. The exchange of two residues in the active site expected to lead to a drastic release of steric strain neither enhanced the folding properties nor the stability of tailspike. Apparently, side-chain interactions in these cases overcompensate for backbone strain, illustrating the extreme optimization of the tailspike protein for conformational stability. The result exemplifies the view arising from the statistical analysis of the distribution of backbone dihedral angles in known three-dimensional protein structures that the adoption of straight phi/psi angles other than the most favorable ones is often caused by side-chain interactions. Proteins 2000;39:89-101.

Glycosidase inhibitors as antiviral and/or antitumor agents

Glycoprotein processing inhibitors prevent the normal processing of N-linked glycoproteins by inhibiting specific glycosidases involved in these reactions. Thus, a number of compounds are now known that inhibit alpha-glucosidase I and alpha-glucosidase II and therefore prevent the removal of glucoses from the high-mannose chains. Some of these compounds are more potent inhibitors of one or the other of these glucosidases. There are also a number of inhibitors that affect one of the processing alpha-mannosidases (i.e. mannosidase I or mannosidase II). These compounds; especially the glucosidase inhibitors, have been valuable tools to help us understand the role of carbohydrate in viral envelope glycoprotein function. Such processing inhibitors have also been used with various tumorigenic cell lines to determine the function of N-linked glycoproteins in cancer.

Purification and characterization of an enzyme releasing lacto-N-biose from oligosaccharides with type 1 chain

An enzyme specific for oligosaccharides with type 1 chain was purified 7,000-fold from the culture broth of Streptomyces sp. 142. The enzyme, lacto-N-biosidase, was induced and secreted into culture medium when the strain was cultured in the presence of porcine stomach mucin. The enzyme was purified by anion-exchange chromatography on Q Sepharose, cation-exchange chromatography on S Sepharose, fast protein liquid chromatography on a Mono S column, and gel filtration chromatography on TSK gel HW55S. To remove contaminating alpha-1,3/4-fucosidase and beta-N-acetylglucosaminidase, final purification was done by fast protein liquid chromatography on a Mono S column and affinity chromatography on N-acetylglucosamine agarose. The purified enzyme gave only one major protein band with an apparent M(r) of 60,000 on sodium dodesyl sulfate-polyacrylamide gel electrophoresis. The enzyme had maximum activity at pH 5.5 and was stable at the pH range of 4.0-10.0. Substrate specificity studies with oligosaccharides labeled with 2-aminopyridine showed that the enzyme specifically hydrolyzed lacto-N-tetraose and the N-acetyllactosamine type of triantennary sugar chain with the type 1 chain, but did not hydrolyze type 2 chain oligosaccharides or the type 1 chain oligosaccharides with fucose or sialic acid including lacto-N-fucopentaose I and II and alpha-2,3-sialyl lacto-N-tetraose. The enzyme released lacto-N-biose from asialofetuin, and almost all oligosaccharides in asialofetuin were found to have only type 2 chains. Sequential digestion of extended type 1 chain oligosaccharides with alpha-1,3/4-fucosidase and lacto-N-biosidase was possible.

Inactivation and conformational changes of yeast invertase during unfolding in urea and guanidinium chloride solutions

Yeast invertase exists in two different forms. The cytoplasmic enzyme is non-glycosylated, whereas the external invertase contains approximately 50% carbohydrate of the high mannose type. In this paper, the inactivation and the conformational changes of the yeast external invertase are analyzed for unfolding in urea and guanidinium chloride. The results show that much lower concentrations of denaturants are required to bring about inactivation than are required to produce significant conformational changes of the yeast external invertase. The results suggest that the active sites of the external invertase containing carbohydrate residues may display more conformational flexibility than the enzyme molecules as a whole.

Hydrophobic nature of mammalian ceramide glycanases: purified from rabbit and rat mammary tissues

The ceramide glycanase (CGase) activities, which cleave the intact oligosaccharide chain and the ceramide moiety of a glycosphingolipid, have been characterized from two mammalian sources. The enzymatic activities are almost comparable in rabbit and rat mammary tissues. The majority of the activities has been concentrated in the soluble fraction which could be partially purified using hydrophobic columns. The rabbit mammary ceramide glycanase activity has been purified up to 1438-fold using ion exchange and hydrophobic columns in tandem. The purified protein exhibited a molecular mass of 54 kDa which could be immunostained on the Western blot with clam anti-CGase polyclonal antibody. In addition, a 98 kDa protein also exhibited positive immunostain in a successive purified fraction with that antibody and is under investigation. The requirement for the optimal enzymatic activities are similar for both rabbit and rat CGase activities. The CGase activity requires the presence of detergent for optimal activity but is not dependent on the presence of any divalent cations. However, Hg2+, Zn2+, and Cu2+ are inhibitory to the enzymatic activities. It has been observed that rat as well as rabbit CGases are inhibited by both D- and L-PDMP (1-phenyl-2-decanoylamino-3-morpholino-1-propanol.HCl) and its higher analogue PPMP (1-phenyl-2-palmitoylamino-3-morpholino-1-propanol.HCl). Alkyl amines containing C12 and higher chains are also found to inhibit both rat and rabbit CGase activities. Substantial levels of CGase activities have also been observed in various human tumor cells as well as in developing avian brains. These observations are significant in view of the recent findings that ceramide, which is one of the enzymatic reaction products of CGase activity, is mediating different cellular events like signal transduction and apoptosis. The role of this enzyme in development, metastasis and cellular regulation are anticipated.

Purification and characterization of a levanbiose-producing levanase from Pseudomonas sp. No. 43

A levanbiose-accumulating levanase from Pseudomonas sp. No. 43 was purified to a homogeneous state by (NH4)2SO4 fractionation and by chromatography on DEAE-Toyopearl 650 M and phenyl-Toyopearl 650 M columns. The molecular mass and isoelectric point of the enzyme were estimated to be 36 kDa and 5.7 respectively; the optimal pH and temperature for the enzyme reaction were pH 7.0 and 40 degrees C respectively. The purified enzyme was stable in the pH range 6.0-8.0 at 20 degrees C and stable up to 50 degrees C at pH 7.0. The enzyme's activity was inhibited by MnCl2, CoCl2, AlCl3, EDTA and potassium permanganate. The levanase was specific towards the 2, 6-beta-D-fructosidic linkages of levan and did not hydrolyse other polysaccharides among those examined. The enzyme is an exohydrolase of levan and produced levanbiose as a sole product; the limits of hydrolysis of levans from Zymomonas mobilis and Serratia sp. were 65% and 80% respectively.

[Purification and physico-chemical properties of glycosidase of Aspergillus niger 185sh]

A scheme has been developed for isolation and purification of the enzyme with alpha-N-acetylgalactosaminidase and alpha-galactosidase activities which included fractionation by ammonium sulphate and chromatography on TSK-gels Toyopearl HW-60 and Fractogel DEAE-650-s and Sepharose 6B. The enzyme was purified 600 times with the yield of 28%. The enzyme preparation did not contain fucosidase, invertase and proteolytic activities. Molecular mass of the enzyme from the data of gel-filtration on Sepharose 6B was 430 kDa, according to the data of electrophoresis in DS-PAAG--70 kDa. It is shown that acidic and hydrophobic aminoacids prevail in the enzyme molecule, the carbohydrate component containing galactose, mannose, glucosamine and two nonidentified hexosamines is also present there. The enzyme preparation is stable during 48 hours at 20 degrees C; its pH-optimum is at pH 3.5-4.1. Michaelis constants concerning n-nitrophenyl-alpha-N-acetylgalactopyranoside and n-nitrophenyl-alpha-D-galactopyranoside were 1.18 and 1.25 mM, respectively.

[Characterization of a chitosanase from Fusarium solani and its expression in an industrial strain of Saccharomyces cerevisiae]

OBJECTIVE

To investigate the biochemical characteristics of the chitosanase from Fusarium solani, and its application in chitooligosaccharides production, and express the chitosanase gene (csn) in a Saccharomyces cerevisiae industrial strain.

METHODS

The chitosanase cDNA (EU263917) was amplified by reverse transcription-mediated PCR (RT-PCR). A His-chitosanase fusion protein was expressed in E. coli DE3. This protein was purified and characterized. Thin-layer chromatography (TLC) and high performance liquid chromatography (HPLC) were used to analyze the hydrolysates of this enzyme when it acted on 85% deacetylated chitosan. In addition, the csn cDNA was also fused to the inulinase (INU1A) signal sequence from Kluyveromyces marxianus. The fusion sequence was transferred into S. cerevisiae industrial strain N-27.

RESULTS

The purified chitosanase had a specific activity of 2.5 U/mg. The enzyme showed the maximum activity at 50 degrees C, which was different from the first reported chitosanase that from F. solanif. sp. Phaseoli. TLC and HPLC results indicated that most of the hydrolysis products were chitooligosaccharides with a polymerization below 10, and no monomers were detected. Furthermore, chitosanase activity was detected in the culture medium of the recombinant S. cerevisiae cultures, and the volume activity reached 50.2 mU/mL. This result indicated that the recombinant protein was secretively expressed in S. cerevisiae.

CONCLUSION

The chitosanase from F. solani 0114 is an endochitosanase. Because of its special characteristics, this enzyme is very useful in chitooligosaccharides production, and the construction of recombinant S. cerevisiae made a step towards the large-scale production of this enzyme.