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Sénéchal F, Robinson S, Van Schaik E, Trévisan M, Saxena P, Reinhardt D, Fankhauser C. Pectin methylesterification state and cell wall mechanical properties contribute to neighbor proximity-induced hypocotyl growth in Arabidopsis. Plant Direct 2024; 8:e584. [PMID: 38646567 PMCID: PMC11033045 DOI: 10.1002/pld3.584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/25/2024] [Accepted: 03/24/2024] [Indexed: 04/23/2024]
Abstract
Plants growing with neighbors compete for light and consequently increase the growth of their vegetative organs to enhance access to sunlight. This response, called shade avoidance syndrome (SAS), involves photoreceptors such as phytochromes as well as phytochrome interacting factors (PIFs), which regulate the expression of growth-mediating genes. Numerous cell wall-related genes belong to the putative targets of PIFs, and the importance of cell wall modifications for enabling growth was extensively shown in developmental models such as dark-grown hypocotyl. However, the contribution of the cell wall in the growth of de-etiolated seedlings regulated by shade cues remains poorly established. Through analyses of mechanical and biochemical properties of the cell wall coupled with transcriptomic analysis of cell wall-related genes from previously published data, we provide evidence suggesting that cell wall modifications are important for neighbor proximity-induced elongation. Further analysis using loss-of-function mutants impaired in the synthesis and remodeling of the main cell wall polymers corroborated this. We focused on the cgr2cgr3 double mutant that is defective in methylesterification of homogalacturonan (HG)-type pectins. By following hypocotyl growth kinetically and spatially and analyzing the mechanical and biochemical properties of cell walls, we found that methylesterification of HG-type pectins was required to enable global cell wall modifications underlying neighbor proximity-induced hypocotyl growth. Collectively, our work suggests that plant competition for light induces changes in the expression of numerous cell wall genes to enable modifications in biochemical and mechanical properties of cell walls that contribute to neighbor proximity-induced growth.
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Affiliation(s)
- Fabien Sénéchal
- Centre for Integrative Genomics, Faculty of Biology and Medicine, Génopode BuildingUniversity of LausanneLausanneSwitzerland
- Present address:
UMR INRAE 1158 BioEcoAgro, Plant Biology and InnovationUniversity of Picardie Jules VerneAmiensFrance
| | - Sarah Robinson
- Institute of Plant SciencesUniversity of BernBernSwitzerland
- Present address:
The Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
| | - Evert Van Schaik
- Department of BiologyUniversity of FribourgFribourgSwitzerland
- Present address:
University of Applied Sciences LeidenLeidenNetherlands
| | - Martine Trévisan
- Centre for Integrative Genomics, Faculty of Biology and Medicine, Génopode BuildingUniversity of LausanneLausanneSwitzerland
| | - Prashant Saxena
- Centre for Integrative Genomics, Faculty of Biology and Medicine, Génopode BuildingUniversity of LausanneLausanneSwitzerland
- Present address:
James Watt School of EngineeringUniversity of GlasgowGlasgowUK
| | | | - Christian Fankhauser
- Centre for Integrative Genomics, Faculty of Biology and Medicine, Génopode BuildingUniversity of LausanneLausanneSwitzerland
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2
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Hocq L, Habrylo O, Sénéchal F, Voxeur A, Pau-Roblot C, Safran J, Fournet F, Bassard S, Battu V, Demailly H, Tovar JC, Pilard S, Marcelo P, Savary BJ, Mercadante D, Njo MF, Beeckman T, Boudaoud A, Gutierrez L, Pelloux J, Lefebvre V. Mutation of AtPME2, a pH-Dependent Pectin Methylesterase, Affects Cell Wall Structure and Hypocotyl Elongation. Plant Cell Physiol 2024; 65:301-318. [PMID: 38190549 DOI: 10.1093/pcp/pcad154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 10/13/2023] [Accepted: 12/04/2023] [Indexed: 01/10/2024]
Abstract
Pectin methylesterases (PMEs) modify homogalacturonan's chemistry and play a key role in regulating primary cell wall mechanical properties. Here, we report on Arabidopsis AtPME2, which we found to be highly expressed during lateral root emergence and dark-grown hypocotyl elongation. We showed that dark-grown hypocotyl elongation was reduced in knock-out mutant lines as compared to the control. The latter was related to the decreased total PME activity as well as increased stiffness of the cell wall in the apical part of the hypocotyl. To relate phenotypic analyses to the biochemical specificity of the enzyme, we produced the mature active enzyme using heterologous expression in Pichia pastoris and characterized it through the use of a generic plant PME antiserum. AtPME2 is more active at neutral compared to acidic pH, on pectins with a degree of 55-70% methylesterification. We further showed that the mode of action of AtPME2 can vary according to pH, from high processivity (at pH8) to low processivity (at pH5), and relate these observations to the differences in electrostatic potential of the protein. Our study brings insights into how the pH-dependent regulation by PME activity could affect the pectin structure and associated cell wall mechanical properties.
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Affiliation(s)
- Ludivine Hocq
- UMRT INRAE 1158 BioEcoAgro-BIOPI Plant Biology and Innovation, University of Picardie, 33 Rue St Leu, Amiens 80039, France
| | - Olivier Habrylo
- UMRT INRAE 1158 BioEcoAgro-BIOPI Plant Biology and Innovation, University of Picardie, 33 Rue St Leu, Amiens 80039, France
| | - Fabien Sénéchal
- UMRT INRAE 1158 BioEcoAgro-BIOPI Plant Biology and Innovation, University of Picardie, 33 Rue St Leu, Amiens 80039, France
| | - Aline Voxeur
- UMRT INRAE 1158 BioEcoAgro-BIOPI Plant Biology and Innovation, University of Picardie, 33 Rue St Leu, Amiens 80039, France
| | - Corinne Pau-Roblot
- UMRT INRAE 1158 BioEcoAgro-BIOPI Plant Biology and Innovation, University of Picardie, 33 Rue St Leu, Amiens 80039, France
| | - Josip Safran
- UMRT INRAE 1158 BioEcoAgro-BIOPI Plant Biology and Innovation, University of Picardie, 33 Rue St Leu, Amiens 80039, France
| | - Françoise Fournet
- UMRT INRAE 1158 BioEcoAgro-BIOPI Plant Biology and Innovation, University of Picardie, 33 Rue St Leu, Amiens 80039, France
| | - Solène Bassard
- UMRT INRAE 1158 BioEcoAgro-BIOPI Plant Biology and Innovation, University of Picardie, 33 Rue St Leu, Amiens 80039, France
| | - Virginie Battu
- Plant Reproduction and Development Laboratory, ENS de Lyon UMR 5667, BP 7000, Lyon cedex 07 69342, France
| | - Hervé Demailly
- Molecular Biology Platform (CRRBM), University of Picardie, 33 Rue St Leu, Amiens 80039, France
| | - José C Tovar
- Arkansas Biosciences Institute, Arkansas State University, PO Box 600, Jonesboro, AR 72467, USA
| | - Serge Pilard
- Analytical Platform (PFA), University of Picardie, 33 Rue St Leu, Amiens 80039, France
| | - Paulo Marcelo
- Cellular imaging and protein analysis platform (ICAP), University of Picardie, Avenue Laënnec,CHU Sud, CURS, Amiens cedex 1 80054, France
| | - Brett J Savary
- Arkansas Biosciences Institute, Arkansas State University, PO Box 600, Jonesboro, AR 72467, USA
| | - Davide Mercadante
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Maria Fransiska Njo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Arezki Boudaoud
- Hydrodynamics Laboratory, Ecole Polytechnique, Route de Saclay, Palaiseau 91128, France
| | - Laurent Gutierrez
- Molecular Biology Platform (CRRBM), University of Picardie, 33 Rue St Leu, Amiens 80039, France
| | - Jérôme Pelloux
- UMRT INRAE 1158 BioEcoAgro-BIOPI Plant Biology and Innovation, University of Picardie, 33 Rue St Leu, Amiens 80039, France
| | - Valérie Lefebvre
- UMRT INRAE 1158 BioEcoAgro-BIOPI Plant Biology and Innovation, University of Picardie, 33 Rue St Leu, Amiens 80039, France
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3
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Safran J, Tabi W, Ung V, Lemaire A, Habrylo O, Bouckaert J, Rouffle M, Voxeur A, Pongrac P, Bassard S, Molinié R, Fontaine JX, Pilard S, Pau-Roblot C, Bonnin E, Larsen DS, Morel-Rouhier M, Girardet JM, Lefebvre V, Sénéchal F, Mercadante D, Pelloux J. Plant polygalacturonase structures specify enzyme dynamics and processivities to fine-tune cell wall pectins. Plant Cell 2023:7172647. [PMID: 37202370 PMCID: PMC10396364 DOI: 10.1093/plcell/koad134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 04/11/2023] [Accepted: 04/17/2023] [Indexed: 05/20/2023]
Abstract
Polygalacturonases (PGs) fine-tune pectins to modulate cell wall chemistry and mechanics, impacting plant development. The large number of PGs encoded in plant genomes leads to questions on the diversity and specificity of distinct isozymes. Herein, we report the crystal structures of two Arabidopsis thaliana polygalacturonases, POLYGALACTURONASE LATERAL ROOT (PGLR) and ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE2 (ADPG2), which are co-expressed during root development. We first determined the amino acid variations and steric clashes that explain the absence of inhibition of the plant PGs by endogenous PG-Inhibiting Proteins (PGIPs). Although their beta helix folds are highly similar, PGLR and ADPG2 subsites in the substrate-binding groove are occupied by divergent amino acids. By combining molecular dynamic simulations, analysis of enzyme kinetics and hydrolysis products, we showed that these structural differences translated into distinct enzyme-substrate dynamics and enzyme processivities: ADPG2 showed greater substrate fluctuations with hydrolysis products, oligogalacturonides (OGs), with a degree of polymerization (DP) of ≤4, while the DP of OGs generated by PGLR was between 5 and 9. Using the Arabidopsis root as a developmental model, exogenous application of purified enzymes showed that the highly processive ADPG2 had major effects on both root cell elongation and cell adhesion. This work highlights the importance of PG processivity on pectin degradation regulating plant development.
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Affiliation(s)
- Josip Safran
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Wafae Tabi
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Vanessa Ung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Adrien Lemaire
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Olivier Habrylo
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Julie Bouckaert
- UMR 8576 Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), 50 Avenue de Halley, 59658 Villeneuve d'Ascq, France
| | - Maxime Rouffle
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Aline Voxeur
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Paula Pongrac
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Solène Bassard
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Roland Molinié
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Jean-Xavier Fontaine
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Serge Pilard
- Plateforme Analytique, Université de Picardie, 33, Rue St Leu, 80039 Amiens, France
| | - Corinne Pau-Roblot
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Estelle Bonnin
- INRAE, UR 1268 Biopolymers, Interactions Assemblies, CS 71627, 44316 Nantes Cedex 3, France
| | - Danaé Sonja Larsen
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | | | | | - Valérie Lefebvre
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Fabien Sénéchal
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Davide Mercadante
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Jérôme Pelloux
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
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Safran J, Ung V, Bouckaert J, Habrylo O, Molinié R, Fontaine JX, Lemaire A, Voxeur A, Pilard S, Pau-Roblot C, Mercadante D, Pelloux J, Sénéchal F. The specificity of pectate lyase VdPelB from Verticilium dahliae is highlighted by structural, dynamical and biochemical characterizations. Int J Biol Macromol 2023; 231:123137. [PMID: 36639075 DOI: 10.1016/j.ijbiomac.2023.123137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/29/2022] [Accepted: 01/01/2023] [Indexed: 01/12/2023]
Abstract
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.
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Affiliation(s)
- Josip Safran
- UMR INRAE 1158 BioEcoAgro - Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, 33 Rue St Leu, 80039 Amiens, France
| | - Vanessa Ung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Julie Bouckaert
- Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), UMR8576 CNRS, Université de Lille, Campus CNRS Haute Borne, Avenue de Halley, 59658, Villeneuve d'Ascq, France
| | - Olivier Habrylo
- UMR INRAE 1158 BioEcoAgro - Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, 33 Rue St Leu, 80039 Amiens, France
| | - Roland Molinié
- UMR INRAE 1158 BioEcoAgro - Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, 33 Rue St Leu, 80039 Amiens, France
| | - Jean-Xavier Fontaine
- UMR INRAE 1158 BioEcoAgro - Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, 33 Rue St Leu, 80039 Amiens, France
| | - Adrien Lemaire
- UMR INRAE 1158 BioEcoAgro - Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, 33 Rue St Leu, 80039 Amiens, France
| | - Aline Voxeur
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Serge Pilard
- Plateforme Analytique, Université de Picardie Jules Verne, 33 Rue St Leu, 80039 Amiens, France
| | - Corinne Pau-Roblot
- UMR INRAE 1158 BioEcoAgro - Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, 33 Rue St Leu, 80039 Amiens, France
| | - Davide Mercadante
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Jérôme Pelloux
- UMR INRAE 1158 BioEcoAgro - Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, 33 Rue St Leu, 80039 Amiens, France.
| | - Fabien Sénéchal
- UMR INRAE 1158 BioEcoAgro - Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, 33 Rue St Leu, 80039 Amiens, France.
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Tian P, Lemaire A, Sénéchal F, Habrylo O, Antonietti V, Sonnet P, Lefebvre V, Marin FI, Best RB, Pelloux J, Mercadante D. Design of a Protein with Improved Thermal Stability by an Evolution‐Based Generative Model. Angew Chem Int Ed Engl 2022; 61:e202202711. [PMID: 36259321 PMCID: PMC10098751 DOI: 10.1002/anie.202202711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Indexed: 11/05/2022]
Abstract
Efficient design of functional proteins with higher thermal stability remains challenging especially for highly diverse sequence variants. Considering the evolutionary pressure on protein folds, sequence design optimizing evolutionary fitness could help designing folds with higher stability. Using a generative evolution fitness model trained to capture variation patterns in natural sequences, we designed artificial sequences of a proteinaceous inhibitor of pectin methylesterase enzymes. These inhibitors have considerable industrial interest to avoid phase separation in fruit juice manufacturing or reduce methanol in distillates, averting chromatographic passages triggering unwanted aroma loss. Six out of seven designs with up to 30 % divergence to other inhibitor sequences are functional and two have improved thermal stability. This method can improve protein stability expanding functional protein sequence space, with traits valuable for industrial applications and scientific research.
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Affiliation(s)
| | - Adrien Lemaire
- Picardie -Jules Verne University: Universite de Picardie Jules Verne BioEcoAgro – BIOPI Biologie des Plantes et Innovation FRANCE
| | - Fabien Sénéchal
- Picardie -Jules Verne University: Universite de Picardie Jules Verne BioEcoAgro – BIOPI Biologie des Plantes et Innovation FRANCE
| | - Olivier Habrylo
- Université de Picardie Jules Verne: Universite de Picardie Jules Verne BioEcoAgro – BIOPI Biologie des Plantes et Innovation FRANCE
| | - Viviane Antonietti
- Université de Picardie Jules Verne: Universite de Picardie Jules Verne UFR de Pharmacie FRANCE
| | - Pascal Sonnet
- Universite de Picardie Jules Verne UFR de Pharmacie FRANCE
| | - Valérie Lefebvre
- Université de Picardie Jules Verne: Universite de Picardie Jules Verne BioEcoAgro – BIOPI Biologie des Plantes et Innovation FRANCE
| | | | - Robert B. Best
- NIH: National Institutes of Health Chemical Physics UNITED STATES
| | - Jérôme Pelloux
- Picardie -Jules Verne University: Universite de Picardie Jules Verne BioEcoAgro – BIOPI Biologie des Plantes et Innovation FRANCE
| | - Davide Mercadante
- The University of Auckland School of Chemical Sciences 23, Symonds Street 1010 Auckland NEW ZEALAND
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Tian P, Lemaire A, Sénéchal F, Habrylo O, Antonietti V, Sonnet P, Lefebvre V, Marin FI, Best RB, Pelloux J, Mercadante D. Design of a Protein with Improved Thermal Stability by an Evolution‐Based Generative Model. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Adrien Lemaire
- Picardie -Jules Verne University: Universite de Picardie Jules Verne BioEcoAgro – BIOPI Biologie des Plantes et Innovation FRANCE
| | - Fabien Sénéchal
- Picardie -Jules Verne University: Universite de Picardie Jules Verne BioEcoAgro – BIOPI Biologie des Plantes et Innovation FRANCE
| | - Olivier Habrylo
- Université de Picardie Jules Verne: Universite de Picardie Jules Verne BioEcoAgro – BIOPI Biologie des Plantes et Innovation FRANCE
| | - Viviane Antonietti
- Université de Picardie Jules Verne: Universite de Picardie Jules Verne UFR de Pharmacie FRANCE
| | - Pascal Sonnet
- Universite de Picardie Jules Verne UFR de Pharmacie FRANCE
| | - Valérie Lefebvre
- Université de Picardie Jules Verne: Universite de Picardie Jules Verne BioEcoAgro – BIOPI Biologie des Plantes et Innovation FRANCE
| | | | - Robert B. Best
- NIH: National Institutes of Health Chemical Physics UNITED STATES
| | - Jérôme Pelloux
- Picardie -Jules Verne University: Universite de Picardie Jules Verne BioEcoAgro – BIOPI Biologie des Plantes et Innovation FRANCE
| | - Davide Mercadante
- The University of Auckland School of Chemical Sciences 23, Symonds Street 1010 Auckland NEW ZEALAND
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Safran J, Habrylo O, Cherkaoui M, Lecomte S, Voxeur A, Pilard S, Bassard S, Pau-Roblot C, Mercadante D, Pelloux J, Sénéchal F. New insights into the specificity and processivity of two novel pectinases from Verticillium dahliae. Int J Biol Macromol 2021; 176:165-176. [PMID: 33561463 DOI: 10.1016/j.ijbiomac.2021.02.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/22/2021] [Accepted: 02/04/2021] [Indexed: 02/02/2023]
Abstract
Pectin, the major non-cellulosic component of primary cell wall can be degraded by polygalacturonases (PGs) and pectin methylesterases (PMEs) during pathogen attack on plants. We characterized two novel enzymes, VdPG2 and VdPME1, from the fungal plant pathogen Verticillium dahliae. VdPME1 was most active on citrus methylesterified pectin (55-70%) at pH 6 and a temperature of 40 °C, while VdPG2 was most active on polygalacturonic acid at pH 5 and a temperature of 50 °C. Using LC-MS/MS oligoprofiling, and various pectins, the mode of action of VdPME1 and VdPG2 were determined. VdPME1 was shown to be processive, in accordance with the electrostatic potential of the enzyme. VdPG2 was identified as endo-PG releasing both methylesterified and non-methylesterified oligogalacturonides (OGs). Additionally, when flax roots were used as substrate, acetylated OGs were detected. The comparisons of OGs released from Verticillium-susceptible and partially resistant flax cultivars identified new possible elicitor of plant defence responses.
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Affiliation(s)
- Josip Safran
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR CNRS 3417, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Olivier Habrylo
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR CNRS 3417, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France; Current address: Groupe Soufflet, 10400 Nogent-sur-Seine, France
| | - Mehdi Cherkaoui
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR CNRS 3417, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France; Current address: UR 1258 BIA Biopolymères Interactions Assemblages, INRAE, 44316 Nantes Cedex 3, France
| | - Sylvain Lecomte
- Linéa Semences, 20 Avenue Saget, 60210 Grandvilliers, France
| | - Aline Voxeur
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Serge Pilard
- Plateforme Analytique, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Solène Bassard
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR CNRS 3417, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Corinne Pau-Roblot
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR CNRS 3417, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Davide Mercadante
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Jérôme Pelloux
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR CNRS 3417, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Fabien Sénéchal
- UMRT INRAE 1158 BioEcoAgro - BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR CNRS 3417, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France.
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Sénéchal F, Habrylo O, Hocq L, Domon JM, Marcelo P, Lefebvre V, Pelloux J, Mercadante D. Structural and dynamical characterization of the pH-dependence of the pectin methylesterase-pectin methylesterase inhibitor complex. J Biol Chem 2017; 292:21538-21547. [PMID: 29109147 DOI: 10.1074/jbc.ra117.000197] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/02/2017] [Indexed: 11/06/2022] Open
Abstract
Pectin methylesterases (PMEs) catalyze the demethylesterification of pectin, one of the main polysaccharides in the plant cell wall, and are of critical importance in plant development. PME activity generates highly negatively charged pectin and mutates the physiochemical properties of the plant cell wall such that remodeling of the plant cell can occur. PMEs are therefore tightly regulated by proteinaceous inhibitors (PMEIs), some of which become active upon changes in cellular pH. Nevertheless, a detailed picture of how this pH-dependent inhibition of PME occurs at the molecular level is missing. Herein, using an interdisciplinary approach that included homology modeling, MD simulations, and biophysical and biochemical characterizations, we investigated the molecular basis of PME3 inhibition by PMEI7 in Arabidopsis thaliana Our complementary approach uncovered how changes in the protonation of amino acids at the complex interface shift the network of interacting residues between intermolecular and intramolecular. These shifts ultimately regulate the stability of the PME3-PMEI7 complex and the inhibition of the PME as a function of the pH. These findings suggest a general model of how pH-dependent proteinaceous inhibitors function. Moreover, they enhance our understanding of how PMEs may be regulated by pH and provide new insights into how this regulation may control the physical properties and structure of the plant cell wall.
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Affiliation(s)
- Fabien Sénéchal
- From the EA3900-BIOPI Biologie des Plantes et Innovation SFR Condorcet FR CNRS 3417, Université de Picardie, 80039 Amiens, France
| | - Olivier Habrylo
- From the EA3900-BIOPI Biologie des Plantes et Innovation SFR Condorcet FR CNRS 3417, Université de Picardie, 80039 Amiens, France
| | - Ludivine Hocq
- From the EA3900-BIOPI Biologie des Plantes et Innovation SFR Condorcet FR CNRS 3417, Université de Picardie, 80039 Amiens, France
| | - Jean-Marc Domon
- From the EA3900-BIOPI Biologie des Plantes et Innovation SFR Condorcet FR CNRS 3417, Université de Picardie, 80039 Amiens, France
| | - Paulo Marcelo
- the Plateforme ICAP, Centre Universitaire de Recherche en Santé, Université de Picardie Jules Verne, 80054 Amiens, France
| | - Valérie Lefebvre
- From the EA3900-BIOPI Biologie des Plantes et Innovation SFR Condorcet FR CNRS 3417, Université de Picardie, 80039 Amiens, France
| | - Jérôme Pelloux
- From the EA3900-BIOPI Biologie des Plantes et Innovation SFR Condorcet FR CNRS 3417, Université de Picardie, 80039 Amiens, France,
| | - Davide Mercadante
- the Heidelberg Institute for Theoretical Studies, Heidelberg-HITS, 16920 Heidelberg, Germany, and .,the IWR-Interdisciplinary Center for Scientific Computing, Heidelberg University, 69120 Heidelberg, Germany
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9
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Hocq L, Sénéchal F, Lefebvre V, Lehner A, Domon JM, Mollet JC, Dehors J, Pageau K, Marcelo P, Guérineau F, Kolšek K, Mercadante D, Pelloux J. Combined Experimental and Computational Approaches Reveal Distinct pH Dependence of Pectin Methylesterase Inhibitors. Plant Physiol 2017; 173:1075-1093. [PMID: 28034952 PMCID: PMC5291010 DOI: 10.1104/pp.16.01790] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 12/22/2016] [Indexed: 05/13/2023]
Abstract
The fine-tuning of the degree of methylesterification of cell wall pectin is a key to regulating cell elongation and ultimately the shape of the plant body. Pectin methylesterification is spatiotemporally controlled by pectin methylesterases (PMEs; 66 members in Arabidopsis [Arabidopsis thaliana]). The comparably large number of proteinaceous pectin methylesterase inhibitors (PMEIs; 76 members in Arabidopsis) questions the specificity of the PME-PMEI interaction and the functional role of such abundance. To understand the difference, or redundancy, between PMEIs, we used molecular dynamics (MD) simulations to predict the behavior of two PMEIs that are coexpressed and have distinct effects on plant development: AtPMEI4 and AtPMEI9. Simulations revealed the structural determinants of the pH dependence for the interaction of these inhibitors with AtPME3, a major PME expressed in roots. Key residues that are likely to play a role in the pH dependence were identified. The predictions obtained from MD simulations were confirmed in vitro, showing that AtPMEI9 is a stronger, less pH-independent inhibitor compared with AtPMEI4. Using pollen tubes as a developmental model, we showed that these biochemical differences have a biological significance. Application of purified proteins at pH ranges in which PMEI inhibition differed between AtPMEI4 and AtPMEI9 had distinct consequences on pollen tube elongation. Therefore, MD simulations have proven to be a powerful tool to predict functional diversity between PMEIs, allowing the discovery of a strategy that may be used by PMEIs to inhibit PMEs in different microenvironmental conditions and paving the way to identify the specific role of PMEI diversity in muro.
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Affiliation(s)
- Ludivine Hocq
- EA3900-BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR, Centre National de la Recherche Scientifique 3417, Université de Picardie, F-80039 Amiens, France (L.H., F.S., V.L., J.-M.D., K.P., F.G., J.P.)
- Normandie Université, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale, EA 4358, VASI, 76821 Mont-Saint-Aignan, France (A.L., J.-C.M., J.D.)
- Plateforme d'Ingénierie Cellulaire en Analyses des Protéines, Université de Picardie Jules Verne, 80039 Amiens, France (P.M.); and
- HITS GmbH, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany (K.K., D.M.)
| | - Fabien Sénéchal
- EA3900-BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR, Centre National de la Recherche Scientifique 3417, Université de Picardie, F-80039 Amiens, France (L.H., F.S., V.L., J.-M.D., K.P., F.G., J.P.)
- Normandie Université, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale, EA 4358, VASI, 76821 Mont-Saint-Aignan, France (A.L., J.-C.M., J.D.)
- Plateforme d'Ingénierie Cellulaire en Analyses des Protéines, Université de Picardie Jules Verne, 80039 Amiens, France (P.M.); and
- HITS GmbH, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany (K.K., D.M.)
| | - Valérie Lefebvre
- EA3900-BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR, Centre National de la Recherche Scientifique 3417, Université de Picardie, F-80039 Amiens, France (L.H., F.S., V.L., J.-M.D., K.P., F.G., J.P.)
- Normandie Université, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale, EA 4358, VASI, 76821 Mont-Saint-Aignan, France (A.L., J.-C.M., J.D.)
- Plateforme d'Ingénierie Cellulaire en Analyses des Protéines, Université de Picardie Jules Verne, 80039 Amiens, France (P.M.); and
- HITS GmbH, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany (K.K., D.M.)
| | - Arnaud Lehner
- EA3900-BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR, Centre National de la Recherche Scientifique 3417, Université de Picardie, F-80039 Amiens, France (L.H., F.S., V.L., J.-M.D., K.P., F.G., J.P.)
- Normandie Université, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale, EA 4358, VASI, 76821 Mont-Saint-Aignan, France (A.L., J.-C.M., J.D.)
- Plateforme d'Ingénierie Cellulaire en Analyses des Protéines, Université de Picardie Jules Verne, 80039 Amiens, France (P.M.); and
- HITS GmbH, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany (K.K., D.M.)
| | - Jean-Marc Domon
- EA3900-BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR, Centre National de la Recherche Scientifique 3417, Université de Picardie, F-80039 Amiens, France (L.H., F.S., V.L., J.-M.D., K.P., F.G., J.P.)
- Normandie Université, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale, EA 4358, VASI, 76821 Mont-Saint-Aignan, France (A.L., J.-C.M., J.D.)
- Plateforme d'Ingénierie Cellulaire en Analyses des Protéines, Université de Picardie Jules Verne, 80039 Amiens, France (P.M.); and
- HITS GmbH, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany (K.K., D.M.)
| | - Jean-Claude Mollet
- EA3900-BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR, Centre National de la Recherche Scientifique 3417, Université de Picardie, F-80039 Amiens, France (L.H., F.S., V.L., J.-M.D., K.P., F.G., J.P.)
- Normandie Université, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale, EA 4358, VASI, 76821 Mont-Saint-Aignan, France (A.L., J.-C.M., J.D.)
- Plateforme d'Ingénierie Cellulaire en Analyses des Protéines, Université de Picardie Jules Verne, 80039 Amiens, France (P.M.); and
- HITS GmbH, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany (K.K., D.M.)
| | - Jérémy Dehors
- EA3900-BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR, Centre National de la Recherche Scientifique 3417, Université de Picardie, F-80039 Amiens, France (L.H., F.S., V.L., J.-M.D., K.P., F.G., J.P.)
- Normandie Université, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale, EA 4358, VASI, 76821 Mont-Saint-Aignan, France (A.L., J.-C.M., J.D.)
- Plateforme d'Ingénierie Cellulaire en Analyses des Protéines, Université de Picardie Jules Verne, 80039 Amiens, France (P.M.); and
- HITS GmbH, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany (K.K., D.M.)
| | - Karine Pageau
- EA3900-BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR, Centre National de la Recherche Scientifique 3417, Université de Picardie, F-80039 Amiens, France (L.H., F.S., V.L., J.-M.D., K.P., F.G., J.P.)
- Normandie Université, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale, EA 4358, VASI, 76821 Mont-Saint-Aignan, France (A.L., J.-C.M., J.D.)
- Plateforme d'Ingénierie Cellulaire en Analyses des Protéines, Université de Picardie Jules Verne, 80039 Amiens, France (P.M.); and
- HITS GmbH, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany (K.K., D.M.)
| | - Paulo Marcelo
- EA3900-BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR, Centre National de la Recherche Scientifique 3417, Université de Picardie, F-80039 Amiens, France (L.H., F.S., V.L., J.-M.D., K.P., F.G., J.P.)
- Normandie Université, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale, EA 4358, VASI, 76821 Mont-Saint-Aignan, France (A.L., J.-C.M., J.D.)
- Plateforme d'Ingénierie Cellulaire en Analyses des Protéines, Université de Picardie Jules Verne, 80039 Amiens, France (P.M.); and
- HITS GmbH, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany (K.K., D.M.)
| | - François Guérineau
- EA3900-BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR, Centre National de la Recherche Scientifique 3417, Université de Picardie, F-80039 Amiens, France (L.H., F.S., V.L., J.-M.D., K.P., F.G., J.P.)
- Normandie Université, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale, EA 4358, VASI, 76821 Mont-Saint-Aignan, France (A.L., J.-C.M., J.D.)
- Plateforme d'Ingénierie Cellulaire en Analyses des Protéines, Université de Picardie Jules Verne, 80039 Amiens, France (P.M.); and
- HITS GmbH, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany (K.K., D.M.)
| | - Katra Kolšek
- EA3900-BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR, Centre National de la Recherche Scientifique 3417, Université de Picardie, F-80039 Amiens, France (L.H., F.S., V.L., J.-M.D., K.P., F.G., J.P.);
- Normandie Université, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale, EA 4358, VASI, 76821 Mont-Saint-Aignan, France (A.L., J.-C.M., J.D.);
- Plateforme d'Ingénierie Cellulaire en Analyses des Protéines, Université de Picardie Jules Verne, 80039 Amiens, France (P.M.); and
- HITS GmbH, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany (K.K., D.M.)
| | - Davide Mercadante
- EA3900-BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR, Centre National de la Recherche Scientifique 3417, Université de Picardie, F-80039 Amiens, France (L.H., F.S., V.L., J.-M.D., K.P., F.G., J.P.);
- Normandie Université, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale, EA 4358, VASI, 76821 Mont-Saint-Aignan, France (A.L., J.-C.M., J.D.);
- Plateforme d'Ingénierie Cellulaire en Analyses des Protéines, Université de Picardie Jules Verne, 80039 Amiens, France (P.M.); and
- HITS GmbH, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany (K.K., D.M.)
| | - Jérôme Pelloux
- EA3900-BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR, Centre National de la Recherche Scientifique 3417, Université de Picardie, F-80039 Amiens, France (L.H., F.S., V.L., J.-M.D., K.P., F.G., J.P.);
- Normandie Université, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale, EA 4358, VASI, 76821 Mont-Saint-Aignan, France (A.L., J.-C.M., J.D.);
- Plateforme d'Ingénierie Cellulaire en Analyses des Protéines, Université de Picardie Jules Verne, 80039 Amiens, France (P.M.); and
- HITS GmbH, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany (K.K., D.M.)
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Kohnen MV, Schmid-Siegert E, Trevisan M, Petrolati LA, Sénéchal F, Müller-Moulé P, Maloof J, Xenarios I, Fankhauser C. Neighbor Detection Induces Organ-Specific Transcriptomes, Revealing Patterns Underlying Hypocotyl-Specific Growth. Plant Cell 2016; 28:2889-2904. [PMID: 27923878 PMCID: PMC5240736 DOI: 10.1105/tpc.16.00463] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 11/20/2016] [Accepted: 12/05/2016] [Indexed: 05/18/2023]
Abstract
In response to neighbor proximity, plants increase the growth of specific organs (e.g., hypocotyls) to enhance access to sunlight. Shade enhances the activity of Phytochrome Interacting Factors (PIFs) by releasing these bHLH transcription factors from phytochrome B-mediated inhibition. PIFs promote elongation by inducing auxin production in cotyledons. In order to elucidate spatiotemporal aspects of the neighbor proximity response, we separately analyzed gene expression patterns in the major light-sensing organ (cotyledons) and in rapidly elongating hypocotyls of Arabidopsis thaliana PIFs initiate transcriptional reprogramming in both organs within 15 min, comprising regulated expression of several early auxin response genes. This suggests that hypocotyl growth is elicited by both local and distal auxin signals. We show that cotyledon-derived auxin is both necessary and sufficient to initiate hypocotyl growth, but we also provide evidence for the functional importance of the local PIF-induced response. With time, the transcriptional response diverges increasingly between organs. We identify genes whose differential expression may underlie organ-specific elongation. Finally, we uncover a growth promotion gene expression signature shared between different developmentally regulated growth processes and responses to the environment in different organs.
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Affiliation(s)
- Markus V Kohnen
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Emanuel Schmid-Siegert
- SIB Swiss Institute of Bioinformatics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Martine Trevisan
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Laure Allenbach Petrolati
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Fabien Sénéchal
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Patricia Müller-Moulé
- Section of Plant Biology, Division of Biological Sciences, University of California, Davis, California 95616
| | - Julin Maloof
- Section of Plant Biology, Division of Biological Sciences, University of California, Davis, California 95616
| | - Ioannis Xenarios
- SIB Swiss Institute of Bioinformatics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Christian Fankhauser
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
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Boitiaux J, Pham S, Gosset-Woimant M, Sénéchal F, Philippe B. Sarcoïdose avec manifestations initiales sévères : quelle évolution ? Rev Mal Respir 2016. [DOI: 10.1016/j.rmr.2015.10.234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Sénéchal F, L'Enfant M, Domon JM, Rosiau E, Crépeau MJ, Surcouf O, Esquivel-Rodriguez J, Marcelo P, Mareck A, Guérineau F, Kim HR, Mravec J, Bonnin E, Jamet E, Kihara D, Lerouge P, Ralet MC, Pelloux J, Rayon C. Tuning of Pectin Methylesterification: PECTIN METHYLESTERASE INHIBITOR 7 MODULATES THE PROCESSIVE ACTIVITY OF CO-EXPRESSED PECTIN METHYLESTERASE 3 IN A pH-DEPENDENT MANNER. J Biol Chem 2015; 290:23320-35. [PMID: 26183897 DOI: 10.1074/jbc.m115.639534] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Indexed: 11/06/2022] Open
Abstract
Pectin methylesterases (PMEs) catalyze the demethylesterification of homogalacturonan domains of pectin in plant cell walls and are regulated by endogenous pectin methylesterase inhibitors (PMEIs). In Arabidopsis dark-grown hypocotyls, one PME (AtPME3) and one PMEI (AtPMEI7) were identified as potential interacting proteins. Using RT-quantitative PCR analysis and gene promoter::GUS fusions, we first showed that AtPME3 and AtPMEI7 genes had overlapping patterns of expression in etiolated hypocotyls. The two proteins were identified in hypocotyl cell wall extracts by proteomics. To investigate the potential interaction between AtPME3 and AtPMEI7, both proteins were expressed in a heterologous system and purified by affinity chromatography. The activity of recombinant AtPME3 was characterized on homogalacturonans (HGs) with distinct degrees/patterns of methylesterification. AtPME3 showed the highest activity at pH 7.5 on HG substrates with a degree of methylesterification between 60 and 80% and a random distribution of methyl esters. On the best HG substrate, AtPME3 generates long non-methylesterified stretches and leaves short highly methylesterified zones, indicating that it acts as a processive enzyme. The recombinant AtPMEI7 and AtPME3 interaction reduces the level of demethylesterification of the HG substrate but does not inhibit the processivity of the enzyme. These data suggest that the AtPME3·AtPMEI7 complex is not covalently linked and could, depending on the pH, be alternately formed and dissociated. Docking analysis indicated that the inhibition of AtPME3 could occur via the interaction of AtPMEI7 with a PME ligand-binding cleft structure. All of these data indicate that AtPME3 and AtPMEI7 could be partners involved in the fine tuning of HG methylesterification during plant development.
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Affiliation(s)
- Fabien Sénéchal
- From the EA3900-BIOPI, Biologie des Plantes et Innovation and
| | | | - Jean-Marc Domon
- From the EA3900-BIOPI, Biologie des Plantes et Innovation and
| | - Emeline Rosiau
- From the EA3900-BIOPI, Biologie des Plantes et Innovation and
| | - Marie-Jeanne Crépeau
- INRA, UMR 1268, Biopolymères-Interactions-Assemblages, BP 71627, 44316 Nantes, France
| | - Ogier Surcouf
- the Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, UPRES EA 4358, Institut de Recherche et d'Innovation Biomédicale, Grand Réseau de Recherche-Végétal, Agronomie, Sol, Innovation, UFR des Sciences et Techniques, Normandie Université-Université de Rouen, 76821 Mont-Saint-Aignan Cedex 1, France
| | | | - Paulo Marcelo
- Plateforme d'Ingénierie Cellulaire and Analyses des Protéines (ICAP), Université de Picardie Jules Verne, 80039 Amiens, France
| | - Alain Mareck
- the Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, UPRES EA 4358, Institut de Recherche et d'Innovation Biomédicale, Grand Réseau de Recherche-Végétal, Agronomie, Sol, Innovation, UFR des Sciences et Techniques, Normandie Université-Université de Rouen, 76821 Mont-Saint-Aignan Cedex 1, France
| | | | - Hyung-Rae Kim
- Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Jozef Mravec
- the Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark, and
| | - Estelle Bonnin
- INRA, UMR 1268, Biopolymères-Interactions-Assemblages, BP 71627, 44316 Nantes, France
| | - Elisabeth Jamet
- the LRSV, UMR 5546 Université Toulouse 3/CNRS, 31326 Castanet-Tolosan, France
| | - Daisuke Kihara
- the Departments of Computer Sciences and Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Patrice Lerouge
- the Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, UPRES EA 4358, Institut de Recherche et d'Innovation Biomédicale, Grand Réseau de Recherche-Végétal, Agronomie, Sol, Innovation, UFR des Sciences et Techniques, Normandie Université-Université de Rouen, 76821 Mont-Saint-Aignan Cedex 1, France
| | - Marie-Christine Ralet
- INRA, UMR 1268, Biopolymères-Interactions-Assemblages, BP 71627, 44316 Nantes, France
| | - Jérôme Pelloux
- From the EA3900-BIOPI, Biologie des Plantes et Innovation and
| | - Catherine Rayon
- From the EA3900-BIOPI, Biologie des Plantes et Innovation and
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Samain C, Lévy P, Boitiaux J, Gosset-Woimant M, Pham S, Sénéchal F, Philippe B. Influence de la prise préalable d’anti-inflammatoires non stéroïdiens sur la présentation et l’évolution de pneumonies aiguës communautaires hospitalisées. Rev Mal Respir 2015. [DOI: 10.1016/j.rmr.2014.11.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Sénéchal F, Mareck A, Marcelo P, Lerouge P, Pelloux J. Arabidopsis PME17 Activity can be Controlled by Pectin Methylesterase Inhibitor4. Plant Signal Behav 2015; 10:e983351. [PMID: 25826258 PMCID: PMC4622950 DOI: 10.4161/15592324.2014.983351] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/15/2014] [Accepted: 09/15/2014] [Indexed: 05/18/2023]
Abstract
The degree of methylesterification (DM) of homogalacturonans (HGs), the main constituent of pectins in Arabidopsis thaliana, can be modified by pectin methylesterases (PMEs). Regulation of PME activity occurs through interaction with PME inhibitors (PMEIs) and subtilases (SBTs). Considering the size of the gene families encoding PMEs, PMEIs and SBTs, it is highly likely that specific pairs mediate localized changes in pectin structure with consequences on cell wall rheology and plant development. We previously reported that PME17, a group 2 PME expressed in root, could be processed by SBT3.5, a co-expressed subtilisin-like serine protease, to mediate changes in pectin properties and root growth. Here, we further report that a PMEI, PMEI4, is co-expressed with PME17 and is likely to regulate its activity. This sheds new light on the possible interplay of specific PMEs, PMEIs and SBTs in the fine-tuning of pectin structure.
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Key Words
- ARF, Auxin response factor
- Arabidopsis thaliana
- BES1/BIM1-3, BRI1 EMS suppressor 1/BES1 interaction MYC-like 1-3
- Col-0, Columbia-0
- DM, Degree of methylesterification
- Gal-A, Galacturonic acid
- HG, Homogalacturonan
- IEF, Isoelectric focusing
- KO, Knock-out
- OG, Oligogalacturonide
- PG, Polygalacturonase
- PL, Pectate lyase
- PM, Plasma membrane
- PME, Pectin methylesterase
- PMEI, Pectin methylesterase inhibitor
- RLK, Receptor-like kinase
- SBT, Subtilase
- TF, Transcription factor
- WAK, Wall-associated kinase
- cell wall
- co-expression
- growth
- pectin
- pectin methylesterase
- pectin methylesterase inhibitor
- root
- subtilase
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Affiliation(s)
- Fabien Sénéchal
- EA3900-BIOPI Biologie des Plantes et Innovation, Université de Picardie Jules Verne; Amiens, France
| | - Alain Mareck
- EA4358-GlycoMEV Glycobiologie et Matrice Extracellulaire Végétale; IFRMP 23; UFR des Sciences et Techniques; Université de Rouen; Mont-Saint-Aignan, France
| | - Paulo Marcelo
- ICAP Plateforme d’Ingénierie Cellulaire et Analyses des Protéines; Université de Picardie Jules Verne; Amiens, France
| | - Patrice Lerouge
- EA4358-GlycoMEV Glycobiologie et Matrice Extracellulaire Végétale; IFRMP 23; UFR des Sciences et Techniques; Université de Rouen; Mont-Saint-Aignan, France
| | - Jérôme Pelloux
- EA3900-BIOPI Biologie des Plantes et Innovation, Université de Picardie Jules Verne; Amiens, France
- Correspondence to: Jérôme Pelloux;
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15
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Sénéchal F, Graff L, Surcouf O, Marcelo P, Rayon C, Bouton S, Mareck A, Mouille G, Stintzi A, Höfte H, Lerouge P, Schaller A, Pelloux J. Arabidopsis PECTIN METHYLESTERASE17 is co-expressed with and processed by SBT3.5, a subtilisin-like serine protease. Ann Bot 2014; 114:1161-75. [PMID: 24665109 PMCID: PMC4195543 DOI: 10.1093/aob/mcu035] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 02/13/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS In Arabidopsis thaliana, the degree of methylesterification (DM) of homogalacturonans (HGs), the main pectic constituent of the cell wall, can be modified by pectin methylesterases (PMEs). In all organisms, two types of protein structure have been reported for PMEs: group 1 and group 2. In group 2 PMEs, the active part (PME domain, Pfam01095) is preceded by an N-terminal extension (PRO part), which shows similarities to PME inhibitors (PMEI domain, Pfam04043). This PRO part mediates retention of unprocessed group 2 PMEs in the Golgi apparatus, thus regulating PME activity through a post-translational mechanism. This study investigated the roles of a subtilisin-type serine protease (SBT) in the processing of a PME isoform. METHODS Using a combination of functional genomics, biochemistry and proteomic approaches, the role of a specific SBT in the processing of a group 2 PME was assessed together with its consequences for plant development. KEY RESULTS A group 2 PME, AtPME17 (At2g45220), was identified, which was highly co-expressed, both spatially and temporally, with AtSBT3.5 (At1g32940), a subtilisin-type serine protease (subtilase, SBT), during root development. PME activity was modified in roots of knockout mutants for both proteins with consequent effects on root growth. This suggested a role for SBT3.5 in the processing of PME17 in planta. Using transient expression in Nicotiana benthamiana, it was indeed shown that SBT3.5 can process PME17 at a specific single processing motif, releasing a mature isoform in the apoplasm. CONCLUSIONS By revealing the potential role of SBT3.5 in the processing of PME17, this study brings new evidence of the complexity of the regulation of PMEs in plants, and highlights the need for identifying specific PME-SBT pairs.
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Affiliation(s)
- Fabien Sénéchal
- EA3900-BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, F-80039 Amiens, France
| | - Lucile Graff
- Universität Hohenheim, Institut für Physiologie und Biotechnologie der Pflanzen (260), D-70593 Stuttgart, Germany
| | - Ogier Surcouf
- EA4358-Glyco-MEV, IFRMP 23, Université de Rouen, F-76821 Mont-Saint-Aignan, France
| | - Paulo Marcelo
- ICAP, UPJV, 1-3 Rue des Louvels, F-80037 Amiens, France
| | - Catherine Rayon
- EA3900-BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, F-80039 Amiens, France
| | - Sophie Bouton
- EA3900-BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, F-80039 Amiens, France
| | - Alain Mareck
- EA4358-Glyco-MEV, IFRMP 23, Université de Rouen, F-76821 Mont-Saint-Aignan, France
| | - Gregory Mouille
- IJPB, UMR1318 INRA-AgroParisTech, Bâtiment 2, INRA Centre de Versailles-Grignon, Route de St Cyr (RD 10), F-78026 Versailles, France
| | - Annick Stintzi
- Universität Hohenheim, Institut für Physiologie und Biotechnologie der Pflanzen (260), D-70593 Stuttgart, Germany
| | - Herman Höfte
- IJPB, UMR1318 INRA-AgroParisTech, Bâtiment 2, INRA Centre de Versailles-Grignon, Route de St Cyr (RD 10), F-78026 Versailles, France
| | - Patrice Lerouge
- EA4358-Glyco-MEV, IFRMP 23, Université de Rouen, F-76821 Mont-Saint-Aignan, France
| | - Andreas Schaller
- Universität Hohenheim, Institut für Physiologie und Biotechnologie der Pflanzen (260), D-70593 Stuttgart, Germany
| | - Jérôme Pelloux
- EA3900-BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, F-80039 Amiens, France
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16
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Sénéchal F, Wattier C, Rustérucci C, Pelloux J. Homogalacturonan-modifying enzymes: structure, expression, and roles in plants. J Exp Bot 2014; 65:5125-60. [PMID: 25056773 PMCID: PMC4400535 DOI: 10.1093/jxb/eru272] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 05/20/2014] [Accepted: 05/22/2014] [Indexed: 05/18/2023]
Abstract
Understanding the changes affecting the plant cell wall is a key element in addressing its functional role in plant growth and in the response to stress. Pectins, which are the main constituents of the primary cell wall in dicot species, play a central role in the control of cellular adhesion and thereby of the rheological properties of the wall. This is likely to be a major determinant of plant growth. How the discrete changes in pectin structure are mediated is thus a key issue in our understanding of plant development and plant responses to changes in the environment. In particular, understanding the remodelling of homogalacturonan (HG), the most abundant pectic polymer, by specific enzymes is a current challenge in addressing its fundamental role. HG, a polymer that can be methylesterified or acetylated, can be modified by HGMEs (HG-modifying enzymes) which all belong to large multigenic families in all species sequenced to date. In particular, both the degrees of substitution (methylesterification and/or acetylation) and polymerization can be controlled by specific enzymes such as pectin methylesterases (PMEs), pectin acetylesterases (PAEs), polygalacturonases (PGs), or pectate lyases-like (PLLs). Major advances in the biochemical and functional characterization of these enzymes have been made over the last 10 years. This review aims to provide a comprehensive, up to date summary of the recent data concerning the structure, regulation, and function of these fascinating enzymes in plant development and in response to biotic stresses.
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Affiliation(s)
- Fabien Sénéchal
- EA3900 BIOPI Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 33 Rue St Leu, F-80039 Amiens, France
| | - Christopher Wattier
- EA3900 BIOPI Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 33 Rue St Leu, F-80039 Amiens, France
| | - Christine Rustérucci
- EA3900 BIOPI Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 33 Rue St Leu, F-80039 Amiens, France
| | - Jérôme Pelloux
- EA3900 BIOPI Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 33 Rue St Leu, F-80039 Amiens, France
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Guénin S, Mareck A, Rayon C, Lamour R, Assoumou Ndong Y, Domon JM, Sénéchal F, Fournet F, Jamet E, Canut H, Percoco G, Mouille G, Rolland A, Rustérucci C, Guerineau F, Van Wuytswinkel O, Gillet F, Driouich A, Lerouge P, Gutierrez L, Pelloux J. Identification of pectin methylesterase 3 as a basic pectin methylesterase isoform involved in adventitious rooting in Arabidopsis thaliana. New Phytol 2011; 192:114-126. [PMID: 21692803 DOI: 10.1111/j.1469-8137.2011.03797.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
• Here, we focused on the biochemical characterization of the Arabidopsis thaliana pectin methylesterase 3 gene (AtPME3; At3g14310) and its role in plant development. • A combination of biochemical, gene expression, Fourier transform-infrared (FT-IR) microspectroscopy and reverse genetics approaches were used. • We showed that AtPME3 is ubiquitously expressed in A. thaliana, particularly in vascular tissues. In cell wall-enriched fractions, only the mature part of the protein was identified, suggesting that it is processed before targeting the cell wall. In all the organs tested, PME activity was reduced in the atpme3-1 mutant compared with the wild type. This was related to the disappearance of an activity band corresponding to a pI of 9.6 revealed by a zymogram. Analysis of the cell wall composition showed that the degree of methylesterification (DM) of galacturonic acids was affected in the atpme3-1 mutant. A change in the number of adventitious roots was found in the mutant, which correlated with the expression of the gene in adventitious root primordia. • Our results enable the characterization of AtPME3 as a major basic PME isoform in A. thaliana and highlight its role in adventitious rooting.
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Affiliation(s)
- Stéphanie Guénin
- EA3900-BioPI Biologie des Plantes et Contrôle des Insectes Ravageurs, Université de Picardie, 33 Rue St Leu, F-80039 Amiens, France
- CRRBM - Bâtiment Serres Transfert, Université de Picardie Jules Verne, 33 Rue St Leu, F-80039 Amiens, France
| | - Alain Mareck
- Laboratoire 'Glycobiologie et Matrice Extracellulaire Végétale' UPRES-EA 4358, IFRMP 23, UFR des Sciences et Techniques, F-76821 Mont-Saint-Aignan, France
| | - Catherine Rayon
- EA3900-BioPI Biologie des Plantes et Contrôle des Insectes Ravageurs, Université de Picardie, 33 Rue St Leu, F-80039 Amiens, France
| | - Romain Lamour
- Laboratoire 'Glycobiologie et Matrice Extracellulaire Végétale' UPRES-EA 4358, IFRMP 23, UFR des Sciences et Techniques, F-76821 Mont-Saint-Aignan, France
| | - Yves Assoumou Ndong
- EA3900-BioPI Biologie des Plantes et Contrôle des Insectes Ravageurs, Université de Picardie, 33 Rue St Leu, F-80039 Amiens, France
| | - Jean-Marc Domon
- EA3900-BioPI Biologie des Plantes et Contrôle des Insectes Ravageurs, Université de Picardie, 33 Rue St Leu, F-80039 Amiens, France
| | - Fabien Sénéchal
- EA3900-BioPI Biologie des Plantes et Contrôle des Insectes Ravageurs, Université de Picardie, 33 Rue St Leu, F-80039 Amiens, France
| | - Françoise Fournet
- EA3900-BioPI Biologie des Plantes et Contrôle des Insectes Ravageurs, Université de Picardie, 33 Rue St Leu, F-80039 Amiens, France
| | - Elisabeth Jamet
- UPS, CNRS, UMR 5546 Surfaces Cellulaires et Signalisation chez les Végétaux, Université de Toulouse, BP42617, F-31326 Castanet-Tolosan, France
| | - Hervé Canut
- UPS, CNRS, UMR 5546 Surfaces Cellulaires et Signalisation chez les Végétaux, Université de Toulouse, BP42617, F-31326 Castanet-Tolosan, France
| | - Giuseppe Percoco
- Laboratoire 'Glycobiologie et Matrice Extracellulaire Végétale' UPRES-EA 4358, IFRMP 23, UFR des Sciences et Techniques, F-76821 Mont-Saint-Aignan, France
| | - Grégory Mouille
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Bâtiment 2, INRA Centre de Versailles-Grignon, Route de St Cyr (RD 10), F-78026 Versailles Cedex France
| | - Aurélia Rolland
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Bâtiment 2, INRA Centre de Versailles-Grignon, Route de St Cyr (RD 10), F-78026 Versailles Cedex France
| | - Christine Rustérucci
- EA3900-BioPI Biologie des Plantes et Contrôle des Insectes Ravageurs, Université de Picardie, 33 Rue St Leu, F-80039 Amiens, France
| | - François Guerineau
- EA3900-BioPI Biologie des Plantes et Contrôle des Insectes Ravageurs, Université de Picardie, 33 Rue St Leu, F-80039 Amiens, France
| | - Olivier Van Wuytswinkel
- EA3900-BioPI Biologie des Plantes et Contrôle des Insectes Ravageurs, Université de Picardie, 33 Rue St Leu, F-80039 Amiens, France
| | - Françoise Gillet
- EA3900-BioPI Biologie des Plantes et Contrôle des Insectes Ravageurs, Université de Picardie, 33 Rue St Leu, F-80039 Amiens, France
| | - Azeddine Driouich
- Laboratoire 'Glycobiologie et Matrice Extracellulaire Végétale' UPRES-EA 4358, IFRMP 23, UFR des Sciences et Techniques, F-76821 Mont-Saint-Aignan, France
| | - Patrice Lerouge
- Laboratoire 'Glycobiologie et Matrice Extracellulaire Végétale' UPRES-EA 4358, IFRMP 23, UFR des Sciences et Techniques, F-76821 Mont-Saint-Aignan, France
| | - Laurent Gutierrez
- CRRBM - Bâtiment Serres Transfert, Université de Picardie Jules Verne, 33 Rue St Leu, F-80039 Amiens, France
| | - Jérôme Pelloux
- EA3900-BioPI Biologie des Plantes et Contrôle des Insectes Ravageurs, Université de Picardie, 33 Rue St Leu, F-80039 Amiens, France
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