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.
Tagging saccharides for signal enhancement in mass spectrometric analysis.
Chang, Y. L., Liao, S. K. S., Chen, Y. C., Hung, W. T., Yu, H. M., Yang, W. B., Fang, J. M., Chen, C. H. & Lee, Y. C. (2011). Journal of mass spectrometry, 46(3), 247-255.
MALDI-MS provides a rapid and sensitive analysis of large biomolecules such as proteins and nucleic acids. However, oligo- and polysaccharides are less sensitive in MS analysis partly due to their neutral and hydrophilic nature to cause low ionization efficiency. In this study, four types of oligosaccharides including aldoses, aminoaldoses, alduronic acids and α-keto acids were modified by appropriate tags at the reducing termini to improve their ionization efficiency. Bradykinin (BK), a vasoactive nonapeptide (RPPGFSPFR), containing two arginine and two phenylalanine residues turned out to be an excellent MS signal enhancer for maltoheptaose, GlcNAc oligomers and oligogalacturonic acids. In the MALDI-TOF-MS analysis using 2,5-dihydroxybenzoic acid (2,5-DHB) as the matrix, the GalA4–BK and GalA5–BK conjugates prepared by reductive amination showed the detection limit at 0.1 fmol, i.e. ∼800-fold enhancement over the unmodified pentagalacturonic acids. The remarkable MS enhancement was attributable to the synergistic effect of the basic arginine residues for high proton affinity and the hydrophobic property phenylalanine residues for facile ionization. A tetrapeptide GFGR(OMe) and an arginine linked phenylenediamine (H2N)2Ph-R(OMe) were thus designed to act as potent tags of oligosaccharides in MS analysis. Interestingly, concurrent condensation and lactonization of α2,8-linked tetrasialic acid (SA4) was carried out with (H2N)2Ph-R(OMe) to obtain a quinoxalinone derivative, which showed > 200-fold enhancement over unmodified SA4 in the MALDI-TOF-MS analysis.
The directionality of processive enzymes acting on recalcitrant polysaccharides is reflected in the kinetic signatures of oligomer degradation.
Hamre, A. G., Schaupp, D., Eijsink, V. G. & Sørlie, M. (2015). FEBS Letters, 589(15), 1807-1812.
The enzymatic degradation of the closely related insoluble polysaccharides; cellulose (β(1–4)-linked glucose) by cellulases and chitin (β(1–4)-linked N-acetylglucosamine) by chitinases, is of large biological and economical importance. Processive enzymes with different inherent directionalities, i.e. attacking the polysaccharide chains from opposite ends, are crucial for the efficiency of this degradation process. While processive cellulases with complementary functions differ in structure and catalytic mechanism, processive chitinases belong to one single protein family with similar active site architectures. Using the unique model system of Serratia marcescens with two processive chitinases attacking opposite ends of the substrate, we here show that different directionalities of processivity are correlated to distinct differences in the kinetic signatures for hydrolysis of oligomeric tetra-N-acetyl chitotetraose.
Purification, physico-chemical characterization and thermodynamics of chitooligosaccharide binding to cucumber (Cucumis sativus) phloem lectin.
Nareddy, P. K., Bobbili, K. B. & Swamy, M. J. (2017). International Journal of Biological Macromolecules, 95, 910-919.
A chitooligosaccharide-specific lectin has been purified from the phloem exudate of cucumber (Cucumis sativus) by affinity chromatography on chitin. The molecular weight of the cucumber phloem lectin (CPL) was determined as 51912.8 Da by mass spectrometry whereas SDS-PAGE yielded a single band with a subunit mass of 26 kDa, indicating that the protein is a homodimer. Peptide mass fingerprinting studies strongly suggest that CPL is identical to the 26 kDa phloem protein 2 (PP2) from cucumber. CD spectroscopy indicated that CPL is a predominantly β-sheets protein. Hemagglutination activity of CPL was mostly unaffected between 4 and 90°C and between pH 4.0 and 10.0, indicating functional stability of the protein. Isothermal titration calorimetric studies indicate that the CPL dimer binds to two chitooligosaccharide ((GlcNAc)2-6) molecules with association constants ranging from 1.0 × 103 to 17.5 × 105 M-1. The binding reaction was strongly enthalpy driven (δHb = −ve) with negative contribution from binding entropy (δSb = −ve). The enthalpy-driven nature of binding reactions suggests that hydrogen bonding and van der Waals interactions stabilize the CPL-chitooligosaccharide association. Enthalpy-entropy compensation was observed for the CPL-chitooligosaccharide interaction, indicating that water molecules play an important role in the binding process.
An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase.
Wong, J. E. M. M., Midtgaard, S. R., Gysel, K., Thygesen, M. B., Sørensen, K. K., Jensen, K. J., Stougaard, J., Thirup, S. & Blaise, M. (2015). Acta Crystallographica Section D: Biological Crystallography, 71(3), 592-605.
LysM domains, which are frequently present as repetitive entities in both bacterial and plant proteins, are known to interact with carbohydrates containing N-acetylglucosamine (GlcNAc) moieties, such as chitin and peptidoglycan. In bacteria, the functional significance of the involvement of multiple LysM domains in substrate binding has so far lacked support from high-resolution structures of ligand-bound complexes. Here, a structural study of the Thermus thermophilus NlpC/P60 endopeptidase containing two LysM domains is presented. The crystal structure and small-angle X-ray scattering solution studies of this endopeptidase revealed the presence of a homodimer. The structure of the two LysM domains co-crystallized with N-acetyl-chitohexaose revealed a new intermolecular binding mode that may explain the differential interaction between LysM domains and short or long chitin oligomers. By combining the structural information with the three-dimensional model of peptidoglycan, a model suggesting how protein dimerization enhances the recognition of peptidoglycan is proposed.
Activation of enzymatic chitin degradation by a lytic polysaccharide monooxygenase.
Hamre, A. G., Eide, K. B., Wold, H. H. & Sørlie, M. (2015). Carbohydrate Research, 407, 166-169.
For decades, the enzymatic conversion of recalcitrant polysaccharides such as cellulose and chitin was thought to solely rely on the synergistic action of hydrolytic enzymes, but recent work has shown that lytic polysaccharide monooxygenases (LPMOs) are important contributors to this process. Here, we have examined the initial rate enhancement an LPMO (CBP21) has on the hydrolytic enzymes (ChiA, ChiB, and ChiC) of the chitinolytic machinery of Serratia marcescens through determinations of apparent kcat (kcatapp) values on a β-chitin substrate. kcatapp values were determined to be
1.7±0.1 s-1 and 1.7±0.1 s-1 for the exo-active ChiA and ChiB, respectively and 1.2±0.1 s-1 for the endo-active ChiC. The addition of CBP21 boosted the kcatapp values of ChiA and ChiB giving values of 11.1±1.5 s-1 and 13.9±1.4 s-1, while there was no effect on ChiC (0.9±0.1 s-1).