Unlocking the structural features for the xylobiohydrolase activity of an unusual GH11 member identified in a compost-derived consortium.

GH11 xylobiohydrolase atypical substrate recognition lignocellulosic biomass metatranscriptome plant cell wall degrading enzymes x-ray crystallography

Journal

Biotechnology and bioengineering
ISSN: 1097-0290
Titre abrégé: Biotechnol Bioeng
Pays: United States
ID NLM: 7502021

Informations de publication

Date de publication:
10 2021
Historique:
revised: 28 06 2021
received: 25 02 2021
accepted: 04 07 2021
pubmed: 8 7 2021
medline: 3 3 2022
entrez: 7 7 2021
Statut: ppublish

Résumé

The heteropolysaccharide xylan is a valuable source of sustainable chemicals and materials from renewable biomass sources. A complete hydrolysis of this major hemicellulose component requires a diverse set of enzymes including endo-β-1,4-xylanases, β-xylosidases, acetylxylan esterases, α-l-arabinofuranosidases, and α-glucuronidases. Notably, the most studied xylanases from glycoside hydrolase family 11 (GH11) have exclusively been endo-β-1,4- and β-1,3-xylanases. However, a recent analysis of a metatranscriptome library from a microbial lignocellulose community revealed GH11 enzymes capable of releasing solely xylobiose from xylan. Although initial biochemical studies clearly indicated their xylobiohydrolase mode of action, the structural features that drive this new activity still remained unclear. It was also not clear whether the enzymes acted on the reducing or nonreducing end of the substrate. Here, we solved the crystal structure of MetXyn11 in the apo and xylobiose-bound forms. The structure of MetXyn11 revealed the molecular features that explain the observed pattern on xylooligosaccharides released by this nonreducing end xylobiohydrolase.

Identifiants

pubmed: 34232504
doi: 10.1002/bit.27880
doi:

Substances chimiques

Disaccharides 0
Xylans 0
lignocellulose 11132-73-3
Lignin 9005-53-2
Glycoside Hydrolases EC 3.2.1.-
xylobiose ID02R0EG7P

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

4052-4064

Informations de copyright

© 2021 Wiley Periodicals LLC.

Références

Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Echols, N., Headd, J. J., Hung, L. W., Jain, S., Kapral, G. J., Grosse Kunstleve, R. W., McCoy, A. J., Moriarty, N. W., Oeffner, R. D., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C., & Zwart, P. H. (2011). The Phenix software for automated determination of macromolecular structures. Methods, 55, 94-106.
Biely, P., Kratky, Z., & Vrsanska, M. (1981). Substrate-binding site of endo-1,4-beta-xylanase of the yeast Cryptococcus albidus. European Journal of Biochemistry, 119, 559-564. https://doi.org/10.1111/j.1432-1033.1981.tb05644.x
Biely, P., Singh, S., & Puchart, V. (2016). Towards enzymatic breakdown of complex plant xylan structures: State of the art. Biotechnology Advances, 34, 1260-1274.
Biely, P., Vršanská, M., Tenkanen, M., & Kluepfel, D. (1997). Endo-β−1,4-xylanase families: Differences in catalytic properties. Journal of Biotechnology, 57, 151-166.
Boonyapakron, K., Jaruwat, A., Liwnaree, B., Nimchua, T., Champreda, V., & Chitnumsub, P. (2017). Structure-based protein engineering for thermostable and alkaliphilic enhancement of endo-β−1,4-xylanase for applications in pulp bleaching. Journal of Biotechnology, 259, 95-102.
Busse-Wicher, M., Li, A., Silveira, R. L., Pereira, C. S., Tryfona, T., Gomes, T. C. F., Skaf, M. S., & Dupree, P. (2016). Evolution of xylan substitution patterns in gymnosperms and angiosperms: Implications for xylan interaction with cellulose. Plant Physiology, 171, 2418-2431.
Davies, G. J., Wilson, K. S., & Henrissat, B. (1997). Nomenclature for sugar-binding subsites in glycosyl hydrolases [1]. Biochem. J. Portland Press Ltd, 321, 557-559.
Davis, I. W., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2004). MOLPROBITY: Structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Research, 32, W615-W619. http://www.ncbi.nlm.nih.gov/pubmed/15215462
Deutschmann, R., & Dekker, R. F. H. (2012). From plant biomass to bio-based chemicals: Latest developments in xylan research. Biotechnology Advances, 30, 1627-1640.
Emsley, P., & Cowtan, K. (2004). Coot: Model-building tools for molecular graphics. Acta Crystallographica Section D: Biological Crystallography, 60, 2126-2132.
Evangelista, D. E., de Oliveira Arnoldi Pellegrini, V., Santo, M. E., McQueen-Mason, S., Bruce, N. C., & Polikarpov, I. (2019). Biochemical characterization and low-resolution SAXS shape of a novel GH11 exo-1,4-β-xylanase identified in a microbial consortium. Applied Microbiology and Biotechnology, 103, 8035-8049.
Evans, P. R., & Murshudov, G. N. (2013). How good are my data and what is the resolution? Acta Crystallographica Section D: Biological Crystallography, 69, 1204-1214. http://www.ncbi.nlm.nih.gov/pubmed/23793146
Fujimoto, Z., Kishine, N., Teramoto, K., Tsutsui, S., & Kaneko, S. (2021). Structure-based substrate specificity analysis of GH11 xylanase from Streptomyces olivaceoviridis E-86. Applied Microbiology and Biotechnology, 105(5), 1943-1952. https://pubmed.ncbi.nlm.nih.gov/33564921/
Fushinobu, S., Hidaka, M., Honda, Y., Wakagi, T., Shoun, H., & Kitaoka, M. (2005). Structural basis for the specificity of the reducing end xylose-releasing exo-oligoxylanase from Bacillus halodurans C-125. Journal of Biological Chemistry, 280, 17180-17186.
Fährrolfes, R., Bietz, S., Flachsenberg, F., Meyder, A., Nittinger, E., Otto, T., Volkamer, A., & Rarey, M. (2017). ProteinsPlus: A web portal for structure analysis of macromolecules. Nucleic Acids Research, 45, W337-W343. https://doi.org/10.1093/nar/gkx333
Goubet, F., Barton, C. J., Mortimer, J. C., Yu, X., Zhang, Z., Miles, G. P., Richens, J., Liepman, A. H., Seffen, K., & Dupree, P. (2009). Cell wall glucomannan in Arabidopsis is synthesised by CSLA glycosyltransferases, and influences the progression of embryogenesis. The Plant Journal, 60, 527-538.
Goubet, F., Jackson, P., Deery, M. J., & Dupree, P. (2002). Polysaccharide analysis using carbohydrate gel electrophoresis. A method to study plant cell wall polysaccharides and polysaccharide hydrolases. Analytical Biochemistry, 300, 53-68.
Grantham, N. J., Wurman-Rodrich, J., Terrett, O. M., Lyczakowski, J. J., Stott, K., Iuga, D., Simmons, T. J., Durand-Tardif, M., Brown, S. P., Dupree, R., Busse-Wicher, M., & Dupree, P. (2017). An even pattern of xylan substitution is critical for interaction with cellulose in plant cell walls. Nature Plants, 3, 859-865.
Guimaraes, B. G., Sanfelici, L., Neuenschwander, R. T., Rodrigues, F., Grizolli, W. C., Raulik, M. A., Piton, J. R., Meyer, B. C., Nascimento, A. S., & Polikarpov, I. (2009). The MX2 macromolecular crystallography beamline: A wiggler X-ray source at the LNLS. Journal of Synchrotron Radiation, 16, 69-75. https://doi.org/10.1107/S0909049508034870
Jiménez-Ortega, E., Valenzuela, S., Ramírez-Escudero, M., Pastor, F. J., & Sanz-Aparicio, J. (2020). Structural analysis of the reducing-end xylose-releasing exo-oligoxylanase Rex8A from Paenibacillus barcinonensis BP-23 deciphers its molecular specificity. FEBS Journal 287, 15332-15374.
Juturu, V., & Wu, J. C. (2012). Microbial xylanases: Engineering, production and industrial applications. Biotechnology Advances, 30, 1219-1227.
Juturu, V., & Wu, J. C (2014). Microbial exo-xylanases: A mini review. Applied Biochemistry and Biotechnology 174, 81-92.
Kabsch, W. (2010). Xds. Acta Crystallographica Section D: Biological Crystallography, 66, 125-132. http://www.ncbi.nlm.nih.gov/pubmed/20124692
Katsimpouras, C., Dedes, G., Thomaidis, N. S., & Topakas, E. (2019). A novel fungal GH30 xylanase with xylobiohydrolase auxiliary activity. Biotechnology for Biofuels, 12, 120.
Laskowski, R. A., Jabłońska, J., Pravda, L., Vařeková, R. S., & Thornton, J. M. (2018). PDBsum: Structural summaries of PDB entries. Protein Science, 27, 129-134.
Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P. M., & Henrissat, B. (2014). The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Research, 42, 42-45.
McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., & Read, R. J. (2007). Phaser crystallographic software. Journal of Applied Crystallography, 40, 658-674. http://www.ncbi.nlm.nih.gov/pubmed/19461840
Mello, B. L., Alessi, A. M., Riaño-Pachón, D. M., DeAzevedo, E. R., Guimarães, F. E. G., Espirito Santo, M. C., McQueen-Mason, S., Bruce, N. C., & Polikarpov, I. (2017). Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity. Biotechnology for Biofuels, 10, 10.
Nakamichi, Y., Fouquet, T., Ito, S., Watanabe, M., Matsushika, A., & Inoue, H. (2019). Structural and functional characterization of a bifunctional GH30-7 xylanase B from the filamentous fungus Talaromyces cellulolyticus. Journal of Biological Chemistry, 294, 4065-4078. http://www.cbs.dtu.dk/services/NetNGlyc/
Nordberg Karlsson, E., Schmitz, E., Linares-Pastén, J. A., & Adlercreutz, P. (2018). Endo-xylanases as tools for production of substituted xylooligosaccharides with prebiotic properties. Applied Microbiology and Biotechnology, 102, 9081-9088.
Paës, G., Berrin, J. G., & Beaugrand, J. (2012). GH11 xylanases: Structure/function/properties relationships and applications. Biotechnology Advances 30, 564-592.
Van Petegem, F., Collins, T., Meuwis, M. A., Gerday, C., Feller, G., Van, & Beeumen, J. (2003). The structure of a cold-adapted family 8 xylanase at 1.3 Å resolution. Structural adaptations to cold and investigation of the active site. Journal of Biological Chemistry, 278, 7531-7539.
Pollet, A., Delcour, J. A., & Courtin, C. M. (2010). Structural determinants of the substrate specificities of xylanases from different glycoside hydrolase families. Critical Reviews in Biotechnology, 30, 176-191.
Pérez, S., Tubiana, T., Imberty, A., & Baaden, M. (2015). Sequence based method. Glycobiology, 25, 483-491.
Ridlova, G., Mortimer, J. C., Maslen, S. L., Dupree, P., & Stephens, E. (2008). Oligosaccharide relative quantitation using isotope tagging and normal-phase liquid chromatography/mass spectrometry. Rapid Communications in Mass Spectrometry, 22, 2723-2730.
Robert, X., & Gouet, P. (2014). Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Research, 42, W320-W324. https://doi.org/10.1093/nar/gku316
Rogowski, A., Baslé, A., Farinas, C. S., Solovyova, A., Mortimer, J. C., Dupree, P., Gilbert, H. J., & Bolam, D. N. (2014). Evidence that GH115 α-glucuronidase activity, which is required to degrade plant biomass, is dependent on conformational flexibility. Journal of Biological Chemistry, 289, 53-64.
Saha, B. C. (2003). Hemicellulose bioconversion. Journal of Industrial Microbiology and Biotechnology, 30, 279-291.
Scheller, H. V., & Ulvskov, P. (2010). Hemicelluloses. Annual Review of Plant Biology, 61, 263-289.
Silva, C. O. G., Vaz, R. P., & Filho, E. X. F. (2018). Bringing plant cell wall-degrading enzymes into the lignocellulosic biorefinery concept. Biofuels, Bioproducts and Biorefining, 12, 277-289.
Sims, R. E. H., Mabee, W., Saddler, J. N., & Taylor, M. (2010). An overview of second generation biofuel technologies. Bioresource Technology, 101, 1570-1580.
Stierand, K., Maaß, P. C., & Rarey, M. (2006). Molecular complexes at a glance: Automated generation of two-dimensional complex diagrams. Bioinformatics, 22, 1710-1716. https://doi.org/10.1093/bioinformatics/btl150
Šuchová, K., Puchart, V., & Biely, P. (2021). A novel bacterial GH30 xylobiohydrolase from Hungateiclostridium clariflavum. Applied Microbiology and Biotechnology, 105, 185-195. https://doi.org/10.1007/s00253-020-11023-x
Šuchová, K., Puchart, V., Spodsberg, N., Mørkeberg Krogh, K. B. R., & Biely, P. (2020). A novel GH30 xylobiohydrolase from Acremonium alcalophilum releasing xylobiose from the non-reducing end. Enzyme and Microbial Technology, 134, 109484.
Terwilliger, T. C., Grosse-Kunstleve, R. W., Afonine, P. V., Moriarty, N. W., Zwart, P. H., Hung, L. W., Read, R. J., & Adams, P. D. (2007). Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallographica Section D: Biological Crystallography, 64, 61-69.
Di Tommaso, P., Moretti, S., Xenarios, I., Orobitg, M., Montanyola, A., Chang, J. M., Taly, J. F., & Notredame, C. (2011). T-Coffee: A web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Research, 39, 39-7.
Urbániková, Ä., Vršanská, M., Mørkeberg Krogh, K. B. R., Hoff, T., & Biely, P. (2011). Structural basis for substrate recognition by Erwinia chrysanthemi GH30 glucuronoxylanase. FEBS Journal, 278, 2105-2116.
Vardakou, M., Dumon, C., Murray, J. W., Christakopoulos, P., Weiner, D. P., Juge, N., Lewis, R. J., Gilbert, H. J., & Flint, J. E. (2008). Understanding the structural basis for substrate and inhibitor recognition in eukaryotic GH11 xylanases. Journal of Molecular Biology, 375, 1293-1305.
Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G., McCoy, A., McNicholas, S. J., Murshudov, G. N., Pannu, N. S., Potterton, E. A., Powell, H. R., Read, R. J., Vagin, A., & Wilson, K. S. (2011). Overview of the CCP4 suite and current developments. Acta Crystallographica Section D: Biological Crystallography, 67, 235-242. http://www.ncbi.nlm.nih.gov/pubmed/21460441
Xin, Z., & Browse, J. (1998). eskimo1 mutants of Arabidopsis are constitutively freezing-tolerant. Proceedings of the National Academy of Sciences of the United States of America, 95, 7799-7804.

Auteurs

Marco A S Kadowaki (MAS)

Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil.
PhotoBioCatalysis-Biomass transformation Lab (BTL), École Interfacultaire de Bioingénieurs (EIB), Université Libre de Bruxelles, Brussels, Belgium.

Lorenzo Briganti (L)

Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil.

Danilo E Evangelista (DE)

Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil.
Instituto de Criminalística de Andradina, Superintendência da Polícia Técnico Científica de São Paulo, Andradina, São Paulo, Brazil.

Alberto Echevarría-Poza (A)

Department of Biochemistry, University of Cambridge, Cambridge, UK.

Theodora Tryfona (T)

Department of Biochemistry, University of Cambridge, Cambridge, UK.

Vanessa O A Pellegrini (VOA)

Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil.

Darlan G Nakayama (DG)

Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil.

Paul Dupree (P)

Department of Biochemistry, University of Cambridge, Cambridge, UK.

Igor Polikarpov (I)

Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil.

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