title: Arabidopsis thaliana root cell wall proteomics: Increasing the proteome coverage using a combinatorial peptide ligand library and description of unexpected Hyp in peroxidase amino acid sequences.
abstract: Plant cell walls (CWs) contain a large proportion of polysaccharides (90-95% of CW mass) and proteins (5-10%) that play major roles in CW plasticity during development and in response to environmental cues. Here, we present CW proteomics data of Arabidopsis thaliana roots. Plants were cultivated in hydroponic conditions. CW protein (CWP) extracts were prepared and analyzed in two different ways in order to enlarge the coverage of the root CW proteome: proteins were analyzed either directly or following an affinity chromatography on a combinatorial peptide ligand library (CPLL) to reduce the concentration dynamic range. Proteins were identified by LC-MS/MS and bioinformatics. Altogether, 424 proteins having predicted signal peptides have been identified (CWPs). CPLL permitted to identify low-abundant CWPs never described before, thus enlarging the coverage of the root CW proteome. The number of oxidoreductases is particularly high and includes a large collection of class III peroxidases (CIII Prxs; 38 out of the 73 A. thaliana CIII Prxs). For the first time, hydroxyproline residues were localized at conserved positions in CIII Prx amino acid sequences.
authors.affiliation: Laboratoire de Recherche en Sciences Végétales, UMR 5546, UPS, Université de Toulouse, BP 42617, Castanet-Tolosan, France.|UMR 5546, CNRS, BP 42617, Castanet-Tolosan, France.
authors.forename: Huan
authors.initials: H
authors.lastname: Nguyen-Kim
authors.affiliation: Laboratoire de Recherche en Sciences Végétales, UMR 5546, UPS, Université de Toulouse, BP 42617, Castanet-Tolosan, France.|UMR 5546, CNRS, BP 42617, Castanet-Tolosan, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: San Clemente
authors.affiliation: CNRS, PAPPSO, UMR 0320/UMR 8120 Génétique Végétale Quantitative et Evolution, Le Moulon, Gif sur Yvette, France.|INRA, PAPPSO, UMR 0320/UMR 8120 Génétique Végétale Quantitative et Evolution, Le Moulon, Gif sur Yvette, France.
authors.forename: Thierry
authors.initials: T
authors.lastname: Balliau
authors.affiliation: CNRS, PAPPSO, UMR 0320/UMR 8120 Génétique Végétale Quantitative et Evolution, Le Moulon, Gif sur Yvette, France.|INRA, PAPPSO, UMR 0320/UMR 8120 Génétique Végétale Quantitative et Evolution, Le Moulon, Gif sur Yvette, France.
authors.forename: Michel
authors.initials: M
authors.lastname: Zivy
authors.affiliation: Laboratoire de Recherche en Sciences Végétales, UMR 5546, UPS, Université de Toulouse, BP 42617, Castanet-Tolosan, France.|UMR 5546, CNRS, BP 42617, Castanet-Tolosan, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Dunand
authors.affiliation: Laboratoire de Recherche en Sciences Végétales, UMR 5546, UPS, Université de Toulouse, BP 42617, Castanet-Tolosan, France.|UMR 5546, CNRS, BP 42617, Castanet-Tolosan, France.
authors.forename: Cécile
authors.initials: C
authors.lastname: Albenne
authors.affiliation: Laboratoire de Recherche en Sciences Végétales, UMR 5546, UPS, Université de Toulouse, BP 42617, Castanet-Tolosan, France.|UMR 5546, CNRS, BP 42617, Castanet-Tolosan, France.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Jamet
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D002473:Cell Wall / Q000737:chemistry / Q000378:metabolism*; D002853:Chromatography, Liquid; D015870:Gene Expression; D063990:Gene Ontology; D018527:Hydroponics; D006909:Hydroxyproline / Q000378:metabolism; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D019151:Peptide Library; D010544:Peroxidases / Q000235:genetics / Q000378:metabolism*; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism*; D021382:Protein Sorting Signals; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry
chemical_list: D029681:Arabidopsis Proteins; D019151:Peptide Library; D021382:Protein Sorting Signals; D020543:Proteome; D010544:Peroxidases; D006909:Hydroxyproline
keywords: Arabidopsis thaliana; Cell wall; Combinatorial peptide ligand library; Plant proteomics; Root