Distinguishing xyloglucanase activity in endo-β(1 → 4)glucanases

Methods in Enzymology

Volumn 510, Issue , 2012, Pages 97-120

  Eklöf, Jens M ^a,b   Ruda, Marcus C ^c   Brumer, Harry ^a,b  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b ALBANOVA UNIVERSITY CENTER   (Sweden)

^c SweTree Technologies   (Sweden)

Author keywords

Chromogenic assay; endo Hydrolase; High performance anion exchange chromatography with pulsed amperometric detection; Reducing sugar; Size exclusion chromatography; Substrate; Xyloglucan; Xyloglucan endo transglycosylase; Xyloglucanase

Indexed keywords

BETA GALACTOSIDASE; BICINCHONINIC ACID; CELLULASE; DIMETHYL SULFOXIDE; GALACTOSAMINE; GLUCAN; GLUCAN GLUCOSIDASE; GLYCOSIDE; GLYCOSYLTRANSFERASE; HETEROCYCLIC CARBOXYLIC ACID; HYDROLASE; OLIGOSACCHARIDE; POLYSACCHARIDE; SUGAR; UNCLASSIFIED DRUG; XYLOGLUCAN; XYLOGLUCAN HYDROLASE; XYLOGLUCAN TRANSGLYCOSYLASE; XYLOGLUCANASE;

AMPEROMETRY; ANALYTIC METHOD; ANION EXCHANGE CHROMATOGRAPHY; ARTICLE; CALIBRATION; CATALYSIS; ELECTROSPRAY MASS SPECTROMETRY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME ASSAY; ENZYME ISOLATION; ENZYME KINETICS; ENZYME METABOLISM; ENZYME PURIFICATION; ENZYME SPECIFICITY; ENZYME SUBSTRATE; ENZYME SYNTHESIS; FLOW RATE; FRACTIONATION; FREEZE DRYING; GEL PERMEATION CHROMATOGRAPHY; GLYCOSIDATION; GLYCOSYLATION; HIGH PERFORMANCE ANION EXCHANGE CHROMATOGRAPHY WITH PULSED AMPEROMETRIC DETECTION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HYDROLYSIS; HYPOCREA JECORINA; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MICHAELIS MENTEN KINETICS; MOLECULAR WEIGHT; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PLANT CELL; PRIORITY JOURNAL; PROTEIN CLEAVAGE; SOLUBILIZATION; THIN LAYER CHROMATOGRAPHY; X RAY CRYSTALLOGRAPHY;

EID: 84861123861     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-415931-0.00006-9     Document Type: Chapter

References (64)

1. G.E. Anthon, and D.M. Barrett Determination of reducing sugars with 3-methyl-2-benzothiazolinonehydrazone Anal. Biochem. 305 2002 287 289
2. A. Ariza, J.M. Eklöf, O. Spadiut, W.A. Offen, S.M. Roberts, W. Besenmatter, E.P. Friis, M. Skojt, K.S. Wilson, H. Brumer, and G. Davies Structure and activity of Paenibacillus polymyxa xyloglucanase from glycoside hydrolase family 44 J. Biol. Chem. 286 2011 33890 33900
3. M.J. Baumann, J.M. Eklöf, G. Michel, Å.M. Kallas, T.T. Teeri, M. Czjzek, and H. Brumer III Structural evidence for the evolution of xyloglucanase activity from xyloglucan endo-transglycosylases: Biological implications for cell wall metabolism Plant Cell 19 2007 1947 1963
4. Z. Benkö, M. Siika-aho, L. Viikari, and K. Reczey Evaluation of the role of xyloglucanase in the enzymatic hydrolysis of lignocellulosic substrates Enzyme Microb. Technol. 43 2008 109 114
5. M.S. Buckeridge, H.P. dos Santos, and M.A.S. Tine Mobilisation of storage cell wall polysaccharides in seeds Plant Physiol. Biochem. 38 2000 141 156
6. E. Chanliaud, J. De Silva, B. Strongitharm, G. Jeronimidis, and M.J. Gidley Mechanical effects of plant cell wall enzymes on cellulose/xyloglucan composites Plant J. 38 2004 27 37
7. S.P.S. Chundawat, G.T. Beckham, M.E. Himmel, and B.E. Dale Deconstruction of lignocellulosic biomass to fuels and chemicals J.M. Prausnitz, Annual Review of Chemical and Biomolecular Engineering Vol. 2 2011 121 145
8. M. Claeyssens, and G. Aerts Characterization of cellulolytic activities in commercial Trichoderma reesei preparations - An approach using small, chromogenic substrates Bioresour. Technol. 39 1992 143 146
9. M. Claeyssens, and B. Henrissat Specificity mapping of cellulolytic enzymes - Classification into families of structurally related proteins confirmed by biochemical analysis Protein Sci. 1 1992 1293 1297
10. M. Claeyssens, H. Vantilbeurgh, J.P. Kamerling, J. Berg, M. Vrsanska, and P. Biely Studies of the cellulolytic system of the filamentous fungus Trichoderma reesei QM-9414 - Substrate-specificity and transfer activity of endoglucanase-I Biochem. J. 270 1990 251 256
11. D.J. Cosgrove Growth of the plant cell wall Nat. Rev. Mol. Cell Biol. 6 2005 850 861
12. G.J. Davies, K.S. Wilson, and B. Henrissat Nomenclature for sugar-binding subsites in glycosyl hydrolases Biochem. J. 321 1997 557 559
13. T. Desmet, T. Cantaert, P. Gualfetti, W. Nerinckx, L. Gross, C. Mitchinson, and K. Piens An investigation of the substrate specificity of the xyloglucanase Cel74A from Hypocrea jecorina FEBS J. 274 2007 356 363
14. J.M. Eklöf, and H. Brumer The XTH gene family: An update on enzyme structure, function, and phylogeny in xyloglucan remodeling Plant Physiol. 153 2010 456 466
15. R. Faure, M. Saura-Valls, H. Brumer, A. Planas, S. Cottaz, and H. Driguez Synthesis of a library of xylogluco-oligosaccharides for active-site mapping of xyloglucan endo-transglycosylase J. Org. Chem. 71 2006 5151 5161
16. S.C. Fry In vivo formation of xyloglucan nonasaccharide - A possible biologically-active cell-wall fragment Planta 169 1986 443 453
17. S.C. Fry, R.C. Smith, K.F. Renwick, D.J. Martin, S.K. Hodge, and K.J. Matthews Xyloglucan endotransglycosylase, a new wall-loosening enzyme-activity from plants Biochem. J. 282 1992 821 828
18. S.C. Fry, W.S. York, P. Albersheim, A. Darvill, T. Hayashi, J.P. Joseleau, Y. Kato, E.P. Lorences, G.A. Maclachlan, M. Mcneil, A.J. Mort, and J.S.G. Reid An unambiguous nomenclature for xyloglucan-derived oligosaccharides Physiol. Plant. 89 1993 1 3
19. H.J. Gilbert, H. Stalbrand, and H. Brumer How the walls come crumbling down: Recent structural biochemistry of plant polysaccharide degradation Curr. Opin. Plant Biol. 11 2008 338 348
20. T.M. Gloster, F.M. Ibatullin, K. Macauley, J.M. Eklöf, S. Roberts, J.P. Turkenburg, M.E. Bjornvad, P.L. Jorgensen, S. Danielsen, K.S. Johansen, T.V. Borchert, and K.S. Wilson Characterization and three-dimensional structures of two distinct bacterial xyloglucanases from families GH5 and GH12 J. Biol. Chem. 282 2007 19177 19189
21. L. Greffe, L. Bessueille, V. Bulone, and H. Brumer Synthesis, preliminary characterization, and application of novel surfactants from highly branched xyloglucan oligosaccharides Glycobiology 15 2005 437 445
22. S.G. Grishutin, A.V. Gusakov, A.V. Markov, B.B. Ustinov, M.V. Semenova, and A.P. Sinitsyn Specific xyloglucanases as a new class of polysaccharide- degrading enzymes Biochim. Biophys. Acta Gen. Subj. 1674 2004 268 281
23. D.J. Harvey Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for the period 2005-2006 Mass Spectrom. Rev. 30 2011 1 100
24. B. Henrissat A new cellulase family Mol. Microbiol. 23 1997 848 849
25. H. Hilz, L.E. de Jong, M.A. Kabel, R. Verhoef, H.A. Schols, and A.G.J. Voragen Bilberry xyloglucan - Novel building blocks containing beta-xylose within a complex structure Carbohydr. Res. 342 2007 170 181
26. M.E. Himmel, S.Y. Ding, D.K. Johnson, W.S. Adney, M.R. Nimlos, J.W. Brady, and T.D. Foust Biomass recalcitrance: Engineering plants and enzymes for biofuels production Science 315 2007 804 807
27. M. Hoffman, Z.H. Jia, M.J. Pena, M. Cash, A. Harper, A.R. Blackburn, A. Darvill, and W.S. York Structural analysis of xyloglucans in the primary cell walls of plants in the subclass Asteridae Carbohydr. Res. 340 2005 1826 1840
28. Y.S.Y. Hsieh, and P.J. Harris Xyloglucans of monocotyledons have diverse structures Mol. Plant 2 2009 943 965
29. F.M. Ibatullin, M.J. Baumann, L. Greffe, and H. Brumer Kinetic analyses of retaining endo-(xylo)glucanases from plant and microbial sources using new chromogenic xylogluco-oligosaccharide aryl glycosides Biochemistry 47 2008 7762 7769
30. F.M. Ibatullin, A. Banasiak, M.J. Baumann, L. Greffe, J. Takahashi, E.J. Mellerowicz, and H. Brumer A real-time fluorogenic assay for the visualization of glycoside hydrolase activity in planta Plant Physiol. 151 2009 1741 1750
31. D.C. Irwin, M. Cheng, B.S. Xiang, J.K.C. Rose, and D.B. Wilson Cloning, expression and characterization of a family-74 xyloglucanase from Thermobifida fusca Eur. J. Biochem. 270 2003 3083 3091
32. P. Johansson, H. Brumer, M.J. Baumann, Å.M. Kallas, H. Henriksson, S.E. Denman, T.T. Teeri, and T.A. Jones Crystal structures of a poplar xyloglucan endotransglycosylase reveal details of transglycosylation acceptor binding Plant Cell 16 2004 874 886
33. N. Kaewthai In vitro and in vivo approaches in the characterization of XTH gene products Ph.D. Thesis. Royal Institute of Technology, Stockholm, p. 48 (plus appendices). Available at http://urn.kb.se/resolve?urn=urn:nbn:se:kth: diva-28222 2011
34. J. Larsbrink, A. Izumi, F.M. Ibatullin, A. Nakhai, H.J. Gilbert, G.J. Davies, and H. Brumer Structural and enzymatic characterization of a glycoside hydrolase family 31 alpha-xylosidase from Cellvibrio japonicus involved in xyloglucan saccharification Biochem. J. 436 2011 567 580
35. M. Lever New reaction for colorimetric determination of carbohydrates Anal. Biochem. 47 1972 273 279
36. A.M. MacLeod, D. Tull, K. Rupitz, R.A.J. Warren, and S.G. Withers Mechanistic consequences of mutation of active site carboxylates in a retaining beta-1,4-glycanase from Cellulomonas fimi Biochemistry 35 1996 13165 13172
37. P. Mark, M.J. Baumann, J.M. Eklöf, F. Gullfot, G. Michel, Å.M. Kallas, T.T. Teeri, H. Brumer, and M. Czjzek Analysis of nasturtium TmNXG1 complexes by crystallography and molecular dynamics provides detailed insight into substrate recognition by family GH16 xyloglucan endo-transglycosylases and endo-hydrolases Proteins. 75 2009 820 836
38. M. Marry, D.M. Cavalier, J.K. Schnurr, J. Netland, Z.Y. Yang, V. Pezeshk, W.S. York, M. Pauly, and A.R. White Structural characterization of chemically and enzymatically derived standard oligosaccharides isolated from partially purified tamarind xyloglucan Carbohydr. Polym. 51 2003 347 356
39. C. Martinez-Fleites, C.I. Guerreiro, M.J. Baumann, E.J. Taylor, J.A. Prates, L.M. Ferreira, C.M. Fontes, H. Brumer, and G.J. Davies Crystal structures of Clostridium thermocellum xyloglucanase, XGH74A, reveal the structural basis for xyloglucan recognition and degradation J. Biol. Chem. 281 2006 24922 24933
40. E.R. Master, Y. Zheng, R. Storms, A. Tsang, and J. Powlowski A xyloglucan-specific family 12 glycosyl hydrolase from Aspergillus niger: Recombinant expression, purification and characterization Biochem. J. 411 2008 161 170
41. G.J. McDougall, and S.C. Fry Purification and analysis of growth-regulating xyloglucan derived oligosaccharides by high-pressure liquid-chromatography Carbohydr. Res. 219 1991 123 132
42. R.F. McFeeters A manual method for reducing sugar determinations with 2,2'-bicinchoninate reagent Anal. Biochem. 103 1980 302 306
43. A. Mishra, and A.V. Malhotra Tamarind xyloglucan: A polysaccharide with versatile application potential J. Mater. Chem. 19 2009 8528 8536
44. N. Nelson A photometric adaptation of the Somogyi method for the determination of glucose J. Biol. Chem. 153 1944 375 380
45. N. Nishikubo, T. Awano, A. Banasiak, V. Bourquin, F. Ibatullin, R. Funada, H. Brumer, T.T. Teeri, T. Hayashi, B. Sundberg, and E.J. Mellerowicz Xyloglucan endo-transglycosylase (XET) functions in gelatinous layers of tension wood fibers in poplar - A glimpse into the mechanism of the balancing act of trees Plant Cell Physiol. 48 2007 843 855
46. N. Nishikubo, J. Takahashi, A.A. Roos, M. Derba-Maceluch, K. Piens, H. Brumer, T.T. Teeri, H. Stalbrand, and E.J. Mellerowicz Xyloglucan endo-transglycosylase-mediated xyloglucan rearrangements in developing wood of hybrid aspen Plant Physiol. 155 2011 399 413
47. G. Noelting, and P. Bernfeld Sur les enzymes amylolytiques III. La beta-amylase: Dosage d'activité et contrôle de l'absence d'alpha-amylase Helv. Chim. Acta 31 1948 286 290
48. B.J.S.C. Olson, and J. Markwell Assays for determination of protein concentration Current Protocols in Pharmacology, Appendix 3A 2007 John Wiley & Sons, Inc New York pp. 1-29
49. M. Pauly, P. Albersheim, A. Darvill, and W.S. York Molecular domains of the cellulose/xyloglucan network in the cell walls of higher plants Plant J. 20 1999 629 639
50. Z.A. Popper, G. Michel, C. Herve, D.S. Domozych, W.G.T. Willats, M.G. Tuohy, B. Kloareg, and D.B. Stengel Evolution and diversity of plant cell walls: From algae to flowering plants S.S. Merchant, W.R. Briggs, D. Ort, Annual Review of Plant Biology Vol. 62 2011 567 588
51. J. Powlowski, S. Mahajan, M. Schapira, and E.R. Master Substrate recognition and hydrolysis by a fungal xyloglucan-specific family 12 hydrolase Carbohydr. Res. 344 2009 1175 1179
52. M. Saura-Valls, R. Faure, H. Brumer, T.T. Teeri, S. Cottaz, H. Driguez, and A. Planas Active-site mapping of a Populus xyloglucan endo-transglycosylase with a library of xylogluco-oligosaccharides J. Biol. Chem. 283 2008 21853 21863
53. P.K. Smith, R.I. Krohn, G.T. Hermanson, A.K. Mallia, F.H. Gartner, M.D. Provenzano, E.K. Fujimoto, N.M. Goeke, B.J. Olson, and D.C. Klenk Measurement of protein using bicinchoninic acid Anal. Biochem. 150 1985 76 85
54. Z. Sulová, M. Lednicka, and V. Farkaš A colorimetric assay for xyloglucan-endotransglycosylase from germinating seeds Anal. Biochem. 229 1995 80 85
55. J.P. Vincken, G. Beldman, and A. Voragen The effect of xyloglucans on the degradation of cell-wall-embedded cellulose by the combined action of cellobiohydrolase and endoglucanases from Trichoderma viride Plant Physiol. 104 1994 99 107
56. J.P. Vincken, G. Beldman, and A.G.J. Voragen Substrate specificity of endoglucanases: What determines xyloglucanase activity? Carbohydr. Res. 298 1997 299 310
57. J.P. Vincken, W.S. York, G. Beldman, and A.G.J. Voragen Two general branching patterns of xyloglucan, XXXG and XXGG Plant Physiol. 114 1997 9 13
58. E. Vlasenko, M. Schulein, J. Cherry, and F. Xu Substrate specificity of family 5, 6, 7, 9, 12, and 45 endoglucanases Bioresour. Technol. 101 2010 2405 2411
59. J. Vogel Unique aspects of the grass cell wall Curr. Opin. Plant Biol. 11 2008 301 307
60. D. Wong, V.J. Chan, A.A. McCormack, and S.B. Batt A novel xyloglucan-specific endo-beta-1,4-glucanase: Biochemical properties and inhibition studies Appl. Microbiol. Biotechnol. 86 2010 1463 1471
61. K. Yaoi, H. Kondo, A. Hiyoshi, N. Noro, H. Sugimoto, S. Tsuda, Y. Mitsuishi, and K. Miyazaki The structural basis for the exo-mode of action in GH74 oligoxyloglucan reducing end-specific cellobiohydrolase J. Mol. Biol. 370 2007 53 62
62. W.S. York, and R. Hawkins Preparation of oligomeric beta-glycosides from cellulose and hemicellulosic polysaccharides via the glycosyl transferase activity of a Trichoderma reesei cellulase Glycobiology 10 2000 193 201
63. W.S. York, H. Vanhalbeek, A.G. Darvill, and P. Albersheim The structure of plant cell walls. 29. Structural analysis of xyloglucan oligosaccharides by H-1-NMR spectroscopy and fast atom bombardment mass spectrometry Carbohydr. Res. 200 1990 9 31
64. W.S. York, L.K. Harvey, R. Guillen, P. Albersheim, and A.G. Darvill The structure of plant cell walls. 36. Structural analysis of tamarind seed xyloglucan oligosaccharides using beta-galactosidase digestion and spectroscopic methods Carbohydr. Res. 248 1993 285 301