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 a Thermostable Laminarinase from Penicillium rolfsii c3-2 (1) IBRL.
Lee, K. C., Arai, T., Ibrahim, D., Kosugi, A., Prawitwong, P., Lan, D., Murata, Y. & Mori, Y. (2014). BioResources, 9(1), 1072-1084
A laminarinase (endo-β-1,3-glucanase) was purified to homogeneity from Penicillium rolfsii c3-2(1) IBRL, which was originally produced in liquid culture containing 1% xylan from birchwood, via anion-exchange chromatography, gel filtration on Sephacryl S-100, and hydrophobic interaction chromatography. A single protein band with a molecular weight of 75 kDa was detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, which had an optimum catalytic activity at pH 4.0 to 5.0 and 70°C. This purified enzyme was most stable in the pH range 4 to 7, while it was thermostable up to 55°C and retained up to 90% of its activity after 4 h pre-incubation. A substrate laminarin kinetic study yielded estimated Km and Vmax values of 0.0817 mg/mL and 372.2 µmol/min/mg, respectively. Laminari-oligosaccharide degradation, which was analyzed by thin layer chromatography, yielded the major hydrolysis products laminaribiose and glucose.
Family 6 carbohydrate binding modules recognize the non-reducing end of β-1,3-linked glucans by presenting a unique ligand binding surface.
van Bueren, A. L., Morland, C., Gilbert, H. J. & Boraston, A. B. (2005). Journal of Biological Chemistry, 280(1), 530-537.
Enzymes that hydrolyze insoluble complex polysaccharide structures contain non-catalytic carbohydrate binding modules (CBMS) that play a pivotal role in the action of these enzymes against recalcitrant substrates. Family 6 CBMs (CBM6s) are distinct from other CBM families in that these protein modules contain multiple distinct ligand binding sites, a feature that makes CBM6s particularly appropriate receptors for the β-1,3-glucan laminarin, which displays an extended U-shaped conformation. To investigate the mechanism by which family 6 CBMs recognize laminarin, we report the biochemical and structural properties of a CBM6 (designated BhCBM6) that is located in an enzyme, which is shown, in this work, to display β-1,3-glucanase activity. BhCBM6 binds β-1,3-glucooligosaccharides with affinities of ~1 × 105 M-1. The x-ray crystal structure of this CBM in complex with laminarihexaose reveals similarity with the structures of other CBM6s but a unique binding mode. The binding cleft in this protein is sealed at one end, which prevents binding of linear polysaccharides such as cellulose, and the orientation of the sugar at this site prevents glycone extension of the ligand and thus conferring specificity for the non-reducing ends of glycans. The high affinity for extended β-1,3-glucooligosaccharides is conferred by interactions with the surface of the protein located between the two binding sites common to CBM6s and thus reveals a third ligand binding site in family 6 CBMs. This study therefore demonstrates how the multiple binding clefts and highly unusual protein surface of family 6 CBMs confers the extensive range of specificities displayed by this protein family. This is in sharp contrast to other families of CBMs where variation in specificity between different members reflects differences in the topology of a single binding site.
Structural characterization of neutral oligosaccharides by laser-enhanced in-source decay of MALDI-FTICR MS.
Yang, H., Yu, Y., Song, F. & Liu, S. (2011). Journal of The American Society for Mass Spectrometry, 22(5), 845-855.
MALDI in-source decay (ISD) technique described to date has proven to be a convenient and rapid method for sequencing purified peptides and proteins. However, the general ISD still can not produce adequate fragments for the detailed structural elucidation of oligosaccharides. In this study, an efficient and practical method termed the laser-enhanced ISD (LEISD) technique of MALDI-FTICR MS allows highly reliable and abundant fragmentation of the neutral oligosaccharides, which was attributed to the ultrahigh irradiation laser of mJ level. The yield of ISD fragmentation was evaluated under different laser powers for 7 neutral oligosaccharides using DHB as matrix. Better quality ISD spectra including fragment ions in low-mass region were obtained at higher laser power. Results from the LEISD of oligosaccharides demonstrated that a significantly better signal-to-noise ratio (S/N) and more structural information could be obtained in comparison to the conventional CID. It was also suggested that the valuable A ions derived from cross-ring cleavage of the linear oligosaccharides allowed the distinction among α(1 → 4)-, α(1 → 6)-, β(1 → 4)-, and β(1 → 3)-linked isobaric structures according to fragment types and intensities. In addition, ideal fragmentation ions observed by LEISD method facilitated the determination of the sequences and branched points of complex oligosaccharides from human milk.
Isoliquiritigenin (4,2′,4′-trihydroxychalcone): A new matrix-assisted laser desorption/ionization matrix with outstanding properties for the analysis of neutral oligosaccharides.
Yang, H., Wang, J., Song, F., Zhou, Y. & Liu, S. (2011). Analytica Chimica Acta, 701(1), 45-51.
A novel matrix of isoliquiritigenin (ISL), a flavonoid with a chalcone structure (4,2′,4′-trihydroxychalcone), was demonstrated to be advantageous in the analysis of neutral oligosaccharides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). With ISL as a matrix, adequate signal for an analyte can be obtained in much lower matrix concentrations and laser intensity compared to commonly used MALDI matrices. Four different sample preparation methods were tested, and the dried droplet method exhibited the best performance on MALDI-TOF-MS analysis of oligosaccharides with ISL as a matrix. For the analysis of carbohydrates, compared with popular matrices such as 2,5-dihydroxybenzoic acid (DHB) and 2,4,6-trihydroxyacetophenone (THAP), ISL exhibited outstanding matrix properties as follows: (1) higher homogeneity of crystallization thus allowing automatic data acquisition, (2) better spectral quality in terms of resolution and signal to noise ratio (S N-1), (3) better salt tolerance, (4) higher sensitivity, and (5) enough fragmentation yield to use LIFT-TOF/TOF MS to get richer structural information. In addition, reliable quantitative analysis of oligosaccharides with a good linearity over two concentration orders (1–100 pmol µL-1) and good reproducibility of the signal intensity (RSD less than 15%) were achieved using this matrix. These results give a new outlook on high-speed analysis of neutral carbohydrates by MALDI-TOF MS.
An olive pollen protein with allergenic activity, Ole e 10, defines a novel family of carbohydrate-binding modules and is potentially implicated in pollen germination.
Barral, P., Suarez, C., Batanero, E., Alfonso, C., de Dios Alche, J., Rodriguez-Garcia, M. I., Villalba, M., Rivas, G. & Rodriguez, R. (2005). Biochem. J, 390, 77-84.
CBMs (carbohydrate-binding modules) are the most common non-catalytic modules associated with enzymes active in plant cell-wall hydrolysis. They have been frequently identified by amino acid sequence alignments, but only a few have been experimentally established to have a carbohydrate-binding activity. A small olive pollen protein, Ole e 10 (10 kDa), has been described as a major inducer of type I allergy in humans. In the present study, the ability of Ole e 10 to bind several polysaccharides has been analysed by affinity gel electrophoresis, which demonstrated that the protein bound 1,3-β-glucans preferentially. Analytical ultracentrifugation studies confirmed binding to laminarin, at a protein/ligand ratio of 1:1. The interaction of Ole e 10 with laminarin induced a conformational change in the protein, as detected by CD and fluorescence analyses, and an increase of 3.6°C in the thermal denaturation temperature of Ole e 10 in the presence of the glycan. These results, and the absence of alignment of the sequence of Ole e 10 with that of any classified CBM, indicate that this pollen protein defines a novel family of CBMs, which we propose to name CBM43. Immunolocalization of Ole e 10 in mature and germinating pollen by transmission electron microscopy and confocal laser scanning microscopy demonstrated the co-localization of Ole e 10 and callose (1,3-β-glucan) in the growing pollen tube, suggesting a role for this protein in the metabolism of carbohydrates and in pollen tube wall re-formation during germination.
Gas-phase fragmentation of oligosaccharides in MALDI laser-enhanced in-source decay induced by thermal hydrogen radicals.
Yang, H., Li, M., Li, Z. & Liu, S. (2012). Analyst, 137(16), 3624-3626.
Laser-enhanced in-source decay (LEISD) MALDI MS recently proposed for structural analysis of oligosaccharides was used to systematically investigate ISD fragmentation of oligosaccharides, which was found to be mediated by thermal hydrogen radicals from a matrix and underwent a charge-induced process, depending on the nature of the matrix and the structure of an oligosaccharide.