1. The specificity of pectate lyase VdPelB from Verticilium dahliae is highlighted by structural, dynamical and biochemical characterizations
- Author
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Safran, J. (Josip), Ung, V. (Vanessa), Bouckaert, J. (Julie), Habrylo, O. (Olivier), Molinié, R. (Roland), Fontaine, J-X. (Jean-Xavier), Lemaire, A. (Adrien), Voxeur, A. (Aline), Pilard, S. (Serge), Pau-Roblot, C. (Corinne), Mercadante, D. (Davide), Pelloux, J. (Jérôme), Sénéchal, F. (Fabien), Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Biologie des Plantes et Innovation - UR UPJV 3900 (BIOPI), Université de Picardie Jules Verne (UPJV)-Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Université d'Artois (UA)-Université de Liège-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), School of Chemical Sciences [Auckland], University of Auckland [Auckland], Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Picardie Jules Verne (UPJV), Plateforme Analytique (PFA), Université de Lille, CNRS, Transfrontalière BioEcoAgro - UMR 1158 [BioEcoAgro], Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576, Institut Charles Viollette (ICV) - ULR 7394, Université Paris Saclay (COmUE), and Université de Picardie Jules Verne [UPJV]
- Subjects
Verticillium dahliae ,Structural Biology ,Pectins ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Pectate lyase ,Homogalacturonan ,Oligogalacturonides ,General Medicine ,Molecular Biology ,Biochemistry - Abstract
International audience; Pectins, complex polysaccharides and major components of the plant primary cell wall, can be degraded by pectate lyases (PLs). PLs cleave glycosidic bonds of homogalacturonans (HG), the main pectic domain, by β-elimination, releasing unsaturated oligogalacturonides (OGs). To understand the catalytic mechanism and structure/function of these enzymes, we characterized VdPelB from Verticillium dahliae. We first solved the crystal structure of VdPelB at 1.2 Å resolution showing that it is a right-handed parallel β-helix structure. Molecular dynamics (MD) simulations further highlighted the dynamics of the enzyme in complex with substrates that vary in their degree of methylesterification, identifying amino acids involved in substrate binding and cleavage of non-methylesterified pectins. We then biochemically characterized wild type and mutated forms of VdPelB. Pectate lyase VdPelB was most active on non-methylesterified pectins, at pH 8.0 in presence of Ca2+ ions. The VdPelB-G125R mutant was most active at pH 9.0 and showed higher relative activity compared to native enzyme. The OGs released by VdPelB differed to that of previously characterized PLs, showing its peculiar specificity in relation to its structure. OGs released from Verticillium-partially tolerant and sensitive flax cultivars differed which could facilitate the identification VdPelB-mediated elicitors of defence responses.
- Published
- 2023