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Plant cell wall proteomics

Contact : mail to Elisabeth JAMET

For a long time considered as rigid envelopes around plant cells, cell walls now appear as dynamic compartments involved in many physiological processes such as developpement, signaling or defense against biotic and abiotic stresses. Plant cell walls are mainly composed of polysaccharides (about 90% in mass) but they also contain proteins. Their biochemical composition and the organization of their components change during development and in response to environmental factors. Both polysaccharides and proteins can be modified to allow the adaptation of cells. The present knowledge of the roles of cell wall proteins is still limited. The coming challenge is to decipher their function and to understand their interactions in muro.

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The cell wall proteome of A. thaliana

Since the beginning of the 2000’s, the team has gained renown in plant cell wall proteomics and has got a leader position in this field. It has greatly contributed to enlarge the knowledge of the cell wall proteome of the model plant Arabidopsis thaliana by analyzing different plant materials using various strategies : cell suspension cultures (Borderies et al. 2003), rosette leaves (Boudart et al. 2005, Hervé et al. 2016), etiolated hypocotyls (Feiz et al. 2006, Irshad et al. 2008), roots (Nguyen-Kim et al. 2016) and secretome of etiolated seedlings in liquid culture medium (Charmont et al. 2005). The glycoproteome of etiolated hypocotyls has been studied in detail, showing the importance of N-glycosylated cell wall proteins (Zhang, Giboulot et al. 2011). All these data, combined to others has brought to 763 the number of identified cell wall proteins of A. thaliana, that is more than one third of the expected total number of cell wall proteins (Albenne et al. 2013, Nguyen-Kim et al. 2016, Hervé et al. 2016).

Systematic cell wall proteomics has been extended to other plant species such as Brachypodium distachyon and Saccharum officinarum. The cell wall proteome of B. distachyon is the best described among monocots with 596 proteins identified (Douché et al. 2013, Francin-Allami et al. 2015, Francin-Allami et al. 2016). Cell wall proteomics data obtained by the team and other research groups have been collected in the WallProtDB database. This database presently comprises 3111 proteins from 12 plant species (Albenne et al. 2014, San Clemente and Jamet 2015). All the proteins have been re-annotated according to protein domain databases, thus facilitating the comparison between proteomes. For a clearer overview of cell wall proteomes, they have been grouped into nine functional classes (Jamet et al. 2008). WallProtDB has been referenced as a OMIC tool.

The team has created additional bioinformatic tools to facilitate proteomic analyses :
- ProtAnnDB allows to collect predictions of sub-cellular localization and of functional domains obtained with online available software (San Clemente et al. 2009). It permits quick and efficient annotation of proteins identified by mass spectrometry.
- ProTerNyc allows to predict the position of the N-terminus of mature secreted proteins as well as the presence of N-glycans from mass spectrometry data (Albenne et al. 2009).

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Identification of N-glycopeptides of the At3g32980 peroxidase by MALDI-TOF MS

Our work also allowed to study post-translational modifications of structural proteins by the use of different approaches for protein separation and the use of mass spectrometry (Canut et al. 2016). We could localize modified amino acids not yet described, N- and O-glycosylations and protein maturation sites (Albenne et al. 2009, Zhang, Giboulot et al. 2011, Hijazi et al. 2012).

These proteomic studies have enabled the identification of cell wall proteins which functional analysis is underway through genetic approaches. We are presently particularly interested in Pro/Hyp-rich proteins, lectins, proteins involved in lipid metabolism and proteins of unknown function.

ANR TBDTOMIC (2009-2012)
Collaborations :
Emmanuelle LAUBER, Matthieu ARLAT : LIPM INRA-CNRS, Auzeville
David COBESSI : IBS, Grenoble

ANR CELLWALL (2009-2012)
Collaborations :
Herman HOFTE : INRA Versailles
Staffan PERSSON : MPI, Potsdam, Germany
Ignacio ZARRA : Santiago de Compostella University, Spain

COFECUB project Improving biomass for cellulose-derived biofuels (2011-2012)
Carlos Alberto LABATE : Universidad de Sao Paulo, Brasil

WALLOMICS (2014-2017) (Financial support form IdEx, Midi-Pyrénées region, Paul Sabatier-Toulouse 3 University, coordinator : C DUNAND, LRSV)

Pr Alicia GAMBOA DE BUEN : Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico
Dr Catherine RAYON, Pr Jérôme PELLOUX : Picardie-Jules Verne University, France
Dr Mathilde FRANCIN-ALLAMI, Dr Colette LARRE : Biopolymères, Interactions, Assemblages, INRA Angers-Nantes, France
Pr Victor VITORELLO : Laboratorio de Biologia Celular e Molecular, CENA, Universidade de São Paulo, Brasil

Proteomics Platform Paris Sud-Ouest (INRA - PAPPSO) : Dr Michel ZIVY, Benoît VALOT, Thierry BALLIAU
Proteomics Platform BIBS (INRA Angers-Nantes) : Dr Hélène ROGNIAUX
Proteomics platform Toulouse Midi-Pyrénées  : Carole PICHEREAUX, Frédéric PONT

Green proteome