Versatile high resolution oligosaccharide microarrays for plant glycobiology and cell wall research.
Pedersen, H. L., Fangel, J. U., McCleary, B., Ruzanski, C., Rydahl, M. G., Ralet, M. C., Farkas, V., Von Schantz, L., Marcus, S. E., Andersen, M.C. F., Field, R., Ohlin, M., Knox, J. P., Clausen, M. H. & Willats, W. G. T. (2012). Journal of Biological Chemistry, 287(47), 39429-39438.
Microarrays are powerful tools for high throughput analysis, and hundreds or thousands of molecular interactions can be assessed simultaneously using very small amounts of analytes. Nucleotide microarrays are well established in plant research, but carbohydrate microarrays are much less established, and one reason for this is a lack of suitable glycans with which to populate arrays. Polysaccharide microarrays are relatively easy to produce because of the ease of immobilizing large polymers noncovalently onto a variety of microarray surfaces, but they lack analytical resolution because polysaccharides often contain multiple distinct carbohydrate substructures. Microarrays of defined oligosaccharides potentially overcome this problem but are harder to produce because oligosaccharides usually require coupling prior to immobilization. We have assembled a library of well characterized plant oligosaccharides produced either by partial hydrolysis from polysaccharides or by de novo chemical synthesis. Once coupled to protein, these neoglycoconjugates are versatile reagents that can be printed as microarrays onto a variety of slide types and membranes. We show that these microarrays are suitable for the high throughput characterization of the recognition capabilities of monoclonal antibodies, carbohydrate-binding modules, and other oligosaccharide-binding proteins of biological significance and also that they have potential for the characterization of carbohydrate-active enzymes.
Purification and characterization of two β-mannanases from Trichoderma reesei.
Stålbrand, H., Siika-aho, M., Tenkanen, M. & Viikari, L. (1993). Journal of Biotechnology, 29(3), 229-242.
Five enzymes with mannanase activity were separated from Trichoderma reesei culture filtrate using analytical isoelectric focusing and subsequently detected with the zymogram technique. The crude enzymes had isoelectric points in the range of 3.6–6.5. Two of the mannanases with pI values of 4.6 and 5.4 were purified using ion-exchange chromatography, affinity chromatography and chromatofocusing. The molecular weights determined with SDS-PAGE were 51 000 (mannanase pI 4.6) and 53 000 (mannanase pI 5.4). The two enzymes had similar properties with respect to pH optimae and pH stabilities. Both mannanases hydrolyzed ivory nut mannan mainly to mannotriose and mannobiose. The specific activities (against locust bean gum) of the purified enzymes were 1860 and 1430 nkat mg-1 for the pI 4.6 and pI 5.4 mannanases, respectively.
New microbial mannan catabolic pathway that involves a novel mannosylglucose phosphorylase.
Senoura, T., Ito, S., Taguchi, H., Higa, M., Hamada, S., Matsui, H., Ozawa, T., Jin, S., Watanabe, J., Wasaki, J. & Ito, S. (2011). Biochemical and Biophysical Research Communications, 408(4), 701-706.
The consecutive genes BF0771–BF0774 in the genome of Bacteroidesfragilis NCTC 9343 were found to constitute an operon. The functional analysis of BF0772 showed that the gene encoded a novel enzyme, mannosylglucose phosphorylase that catalyzes the reaction, 4-O-β-
D-mannopyranosyl-D-glucose + Pi → mannose-1-phosphate + glucose. Here we propose a new mannan catabolic pathway in the anaerobe, which involves 1,4-β-mannanase (BF0771), a mannobiose and/or sugar transporter (BF0773), mannobiose 2-epimerase (BF0774), and mannosylglucose phosphorylase (BF0772), finally progressing to glycolysis. This pathway is distributed in microbes such as Bacteroides, Parabacteroides, Flavobacterium, and Cellvibrio.
Discovery of β-1, 4-D-Mannosyl-N-acetyl-D-glucosamine Phosphorylase Involved in the Metabolism of N-Glycans.
Nihira, T., Suzuki, E., Kitaoka, M., Nishimoto, M., Ohtsubo, K. I. & Nakai, H. (2013). Journal of Biological Chemistry, 288(38), 27366-27374.
A gene cluster involved in N-glycan metabolism was identified in the genome of Bacteroides thetaiotaomicron VPI-5482. This gene cluster encodes a major facilitator superfamily transporter, a starch utilization system-like transporter consisting of a TonB-dependent oligosaccharide transporter and an outer membrane lipoprotein, four glycoside hydrolases (α-
mannosidase, β-N-acetylhexosaminidase, exo-α-sialidase, and endo-β-N-acetylglucosaminidase), and a phosphorylase (BT1033) with unknown function. It was demonstrated that BT1033 catalyzed the reversible phosphorolysis of β-1,4-D-mannosyl-N-acetyl-D-glucosamine in a typical sequential Bi Bi mechanism. These results indicate that BT1033 plays a crucial role as a key enzyme in the N-glycan catabolism where β-1,4-D-mannosyl-N-acetyl-D-glucosamine is liberated from N-glycans by sequential glycoside hydrolase-catalyzed reactions, transported into the cell, and intracellularly converted into α-D-mannose 1-phosphate and N-acetyl-D-glucosamine. In addition, intestinal anaerobic bacteria such as Bacteroides fragilis, Bacteroides helcogenes, Bacteroides salanitronis, Bacteroides vulgatus, Prevotella denticola, Prevotella dentalis, Prevotella melaninogenica, Parabacteroides distasonis, and Alistipes finegoldii were also suggested to possess the similar metabolic pathway for N-glycans. A notable feature of the new metabolic pathway for N-glycans is the more efficient use of ATP-stored energy, in comparison with the conventional pathway where β-mannosidase and ATP-dependent hexokinase participate, because it is possible to directly phosphorylate the D-mannose residue of β-1,4-D-mannosyl-N-acetyl-D-glucosamine to enter glycolysis. This is the first report of a metabolic pathway for N-glycans that includes a phosphorylase. We propose 4-O-β-D-mannopyranosyl-N-acetyl-D-glucosamine:phosphate α-D-mannosyltransferase as the systematic name and β-1,4-D-mannosyl-N-acetyl-D-glucosamine phosphorylase as the short name for BT1033.
Softwood hemicellulose-degrading enzymes from Aspergillus niger: Purification and properties of a β-mannanase.
Ademark, P., Varga, A., Medve, J., Harjunpää, V., Drakenberg, T., Tjerneld, F. & Stålbrand, H. (1998). Journal of Biotechnology, 63(3), 199-210.
The enzymes needed for galactomannan hydrolysis, i.e. β-mannanase, α-galactosidase and β-mannosidase, were produced by the filamentous fungus Aspergillus niger. The β-mannanase was purified to electrophoretic homogeneity in three steps using ammonium sulfate precipitation, anion-exchange chromatography and gel filtration. The purified enzyme had an isoelectric point of 3.7 and a molecular mass of 40 kDa. Ivory nut mannan was degraded mainly to mannobiose and mannotriose when incubated with the β-mannanase. Analysis by 1H NMR spectroscopy during hydrolysis of mannopentaose showed that the enzyme acts by the retaining mechanism. The N-terminus of the purified A. niger β-mannanase was sequenced by Edman degradation, and comparison with Aspergillus aculeatus β-mannanase indicated high identity. The enzyme most probably lacks a cellulose binding domain since it was unable to adsorb on cellulose.
Substrate specificity of cellobiose dehydrogenase from Phanerochaete chrysosporium.
Henriksson, G., Sild, V., Szabó, I. J., Pettersson, G. & Johansson, G. (1998). Biochimica et Biophysica Acta (BBA)-Protein Structure and Molecular Enzymology, 1383(1), 48-54.
Substrate structural mapping suggests that the catalytic site of cellobiose dehydrogenase from Phanerochaete chrysosporium forms a narrow cave with two hexose binding subsites. Kinetic data also show that β-di or oligosaccharides are favored electron donors with respect to both KM andkcat. Surprisingly, thiocellobiose showed an even higher kcat than cellobiose, although the KM value was somewhat higher. The CDH was purified using an updated protocol.
Molecular and biochemical characterization of endo-β-mannanases from germinating coffee (Coffea Arabica) grains.
Marraccini, P., Rogers, J. W., Allard, C., André, M. L., Caillet, V., Lacoste, N., Lausamme, F. & Michaux, S. (2001). Planta, 213(2), 296-308.
The activity of endo-β-mannanase ([1→4]-β-mannan endohydrolase EC 184.108.40.206) is likely to be central to the metabolism of cell wall mannans during the germination of grains of coffee (Coffea spp.). In the present paper, we report the cloning and sequencing of two endo-β-mannanase cDNAs (manA and manB) by different strategies from Coffea arabica L. The manA cDNA was obtained by the use of oligonucleotides homologous to published sequences of other endo-β-mannanases and manB by the use of oligonucleotides deduced from a purified enzyme from coffee. ManA and B proteins share about 56% sequence homology and include highly conserved regions found in other mannan endohydrolases. Purification of the activity by chromatography followed by separation by two-dimensional electrophoresis and amino acid sequencing demonstrated the existence of at least seven isomers of the ManB form. The existence of multiple manB genes was also indicated by Southern analysis, whereas only one or two gene copies were detected for manA. Northern hybridizations with manA- and manB-specific probes showed that mRNA transcripts for both cDNAs were present at the same periods of bean germination with transcript peaks at 20 days after imbibition of water (DAI). Transcripts were not detected during grain maturation or in the other tissues such as roots, stems, flowers and leaves. The peak endo-β-mannanase activity occurred at approximately 28 DAI and was not detected in grains prior to imbibition. Activity and mRNA levels appeared to be tightly co-ordinated. Tests of substrate specificity with the purified ManB enzyme showed that activity required a minimum of five mannose units to function efficiently.
Model for random hydrolysis and end degradation of linear polysaccharides: Application to the thermal treatment of mannan in solution.
Nattorp, A., Graf, M., Spühler, C. & Renken, A. (1999). Industrial & Engineering Chemistry Research, 38(8), 2919-2926.
The kinetics for homogeneous hydrolysis of mannan is studied in a batch reactor at temperatures from 160 to 220°C. A formate buffer ensures a pH of 3.8−4.0, measured at 25°C. Samples are analyzed for oligosaccharides up to a degree of polymerization of 6 and also for the total amount of mannose after acid hydrolysis. A mathematical model with two reactions (1, random hydrolysis of the glucosidic bonds; 2, degradation of the reducing end of the molecule) describes accurately the time course of oligosaccharides. Optimized rate constants follow closely an Arrhenius relationship, with the degradation having a higher activation energy (140 kJ/mol) than the hydrolysis (113 kJ/mol). The mathematical model has the advantage that production of small molecules is independent of the initial chain-length distribution as long as the average initial chain length is some 5 times longer than the largest species measured. It can be applied to first-order depolymerization of other linear polymers with one link type in order to determine reaction rate constants or make predictions about molecular weight distribution on the base of known reaction rate constants.