E. M. Bayer, A. R. Bottrill, J. Walshaw, M. Vigouroux, M. J. Naldrett et al., Arabidopsis cell wall proteome defined using multidimensional protein identification technology, PROTEOMICS, vol.3, issue.1, pp.301-312, 2006.
DOI : 10.1002/pmic.200500046

E. Beck and P. Ziegler, Biosynthesis and Degradation of Starch in Higher Plants, Annual Review of Plant Physiology and Plant Molecular Biology, vol.40, issue.1, pp.95-117, 1989.
DOI : 10.1146/annurev.pp.40.060189.000523

G. Boudart, E. Jamet, M. Rossignol, C. Lafitte, G. Borderies et al., rosettes: Identification by mass spectrometry and bioinformatics, PROTEOMICS, vol.120, issue.1, pp.212-221, 2005.
DOI : 10.1002/pmic.200400882
URL : https://hal.archives-ouvertes.fr/hal-00117222

J. D. Brady, I. H. Sadler, and S. C. Fry, Di-isodityrosine, a novel tetrametric derivative of tyrosine in plant cell wall proteins: a new potential cross-link, Biochemical Journal, vol.315, issue.1, pp.323-330, 1996.
DOI : 10.1042/bj3150323

F. Brunner, A. Stintzi, B. Fritig, and M. Legrand, Substrate specificities of tobacco chitinases, The Plant Journal, vol.12, issue.936, pp.225-234, 1998.
DOI : 10.1006/abio.1993.1010

B. Cantarel, P. Coutinho, C. Rancurel, T. Bernard, V. Lombard et al., The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics, Nucleic Acids Research, vol.37, issue.Database, pp.233-238, 2009.
DOI : 10.1093/nar/gkn663

N. C. Carpita and D. M. Gibeaut, Structural models of primary cell walls in flowering plants: consistency of molecular structure with the physical properties of the walls during growth, The Plant Journal, vol.99, issue.1, pp.1-30, 1993.
DOI : 10.1016/S0008-6215(00)90807-3

G. I. Cassab and J. E. Varner, Cell Wall Proteins, Annual Review of Plant Physiology and Plant Molecular Biology, vol.39, issue.1, pp.321-353, 1988.
DOI : 10.1146/annurev.pp.39.060188.001541

M. Chen, L. Huang, H. Li, Y. Chen, and S. Yu, Signal Peptide-Dependent Targeting of a Rice ??-Amylase and Cargo Proteins to Plastids and Extracellular Compartments of Plant Cells, PLANT PHYSIOLOGY, vol.135, issue.3, pp.1367-1377, 2004.
DOI : 10.1104/pp.104.042184

X. Chen, S. Kim, W. Cho, Y. Rim, S. Kim et al., Proteomics of weakly bound cell wall proteins in rice calli, Journal of Plant Physiology, vol.166, issue.7, 2008.
DOI : 10.1016/j.jplph.2008.09.010

S. Chivasa, B. K. Ndimba, W. J. Simon, D. Robertson, X. Yu et al., Proteomic analysis of the Arabidopsis thaliana cell wall, ELECTROPHORESIS, vol.23, issue.11, pp.1754-1765, 2002.
DOI : 10.1002/1522-2683(200206)23:11<1754::AID-ELPS1754>3.0.CO;2-E

W. Cho, X. Chen, H. Chu, Y. Rim, S. Kim et al., The proteomic analysis of the secretome of rice calli, Physiologia Plantarum, vol.135, pp.331-341, 2009.
DOI : 10.1111/j.1399-3054.2009.01198.x

D. J. Cosgrove, Growth of the plant cell wall, Nature Reviews Molecular Cell Biology, vol.96, issue.11, pp.850-61, 2005.
DOI : 10.1007/s004250000303

D. Matteo, A. Federici, L. Mattei, B. Salvi, G. Johnson et al., The crystal structure of polygalacturonase-inhibiting protein (PGIP), a leucine-rich repeat protein involved in plant defense, Proceedings of the National Academy of Sciences, vol.100, issue.17, pp.10124-10128, 2003.
DOI : 10.1073/pnas.1733690100

A. Edreva, Pathogenesis-related proteins: research progress in the last 15 years, Gen Appl Plant Phys, vol.31, pp.105-124, 2005.

J. Ehlting, N. Mattheus, D. Aeschliman, B. Hamberger, I. Cullis et al., Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation, The Plant Journal, vol.9, issue.5, pp.618-640, 2005.
DOI : 10.1111/j.1365-313X.2005.02403.x

N. Farrokhi, R. Burton, L. Brownfield, M. Hrmova, S. Wilson et al., Plant cell wall biosynthesis: genetic, biochemical and functional genomics approaches to the identification of key genes, Plant Biotechnology Journal, vol.265, issue.3, pp.145-167, 2006.
DOI : 10.1104/pp.103.020420

L. Feiz, M. Irshad, R. F. Pont-lezica, H. Canut, and E. Jamet, Evaluation of cell wall preparations for proteomics: a new procedure for purifying cell walls from Arabidopsis hypocotyls, Plant Methods, vol.2, issue.1, pp.10-22, 2006.
DOI : 10.1186/1746-4811-2-10
URL : https://hal.archives-ouvertes.fr/hal-00105540

G. Fincher, Molecular and Cellular Biology Associated with Endosperm Mobilization in Germinating Cereal Grains, Annual Review of Plant Physiology and Plant Molecular Biology, vol.40, issue.1, pp.305-346, 1989.
DOI : 10.1146/annurev.pp.40.060189.001513

G. Fincher, Exploring the evolution of (1,3;1,4)-??-d-glucans in plant cell walls: comparative genomics can help!, Current Opinion in Plant Biology, vol.12, issue.2, pp.140-147, 2009.
DOI : 10.1016/j.pbi.2009.01.002

G. Fincher, Revolutionary Times in Our Understanding of Cell Wall Biosynthesis and Remodeling in the Grasses, PLANT PHYSIOLOGY, vol.149, issue.1, pp.27-37, 2009.
DOI : 10.1104/pp.108.130096

S. C. Fry, Primary cell wall metabolism: tracking the careers of wall polymers in living plant cells, New Phytologist, vol.99, issue.3, pp.641-675, 2004.
DOI : 10.1111/j.1469-8137.2004.00980.x

D. Garvin, Y. Gu, R. Hasterok, S. Hazen, G. Jenkins et al., Development of genetic and genomic resources for Brachypodium distachyon, a new model for grass crop research, Crop Sci, vol.48, pp.69-84, 2008.

K. Gebruers, K. Brijs, C. Courtin, K. Fierens, H. Goesaert et al., Properties of TAXI-type endoxylanase inhibitors, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, vol.1696, issue.2, pp.213-221, 2004.
DOI : 10.1016/j.bbapap.2003.08.013

S. Gygi, Y. Rochon, B. Franza, and R. Aebersold, Correlation between Protein and mRNA Abundance in Yeast, Molecular and Cellular Biology, vol.19, issue.3, pp.1720-1730, 1999.
DOI : 10.1128/MCB.19.3.1720

M. Irshad, H. Canut, G. Borderies, R. Pont-lezica, and E. Jamet, A new picture of cell wall protein dynamics in elongating cells of Arabidopsis thaliana: Confirmed actors and newcomers, BMC Plant Biology, vol.8, issue.1, p.94, 2008.
DOI : 10.1186/1471-2229-8-94
URL : https://hal.archives-ouvertes.fr/hal-00325843

J. Jacobs and J. L. Roe, SKS6, a multicopper oxidase-like gene, participates in cotyledon vascular patterning during Arabidopsis thaliana development, Planta, vol.43, issue.Suppl, pp.652-666, 2005.
DOI : 10.1007/s00425-005-0012-3

E. Jamet, C. Albenne, G. Boudart, M. Irshad, H. Canut et al., Recent advances in plant cell wall proteomics, PROTEOMICS, vol.65, issue.4, pp.893-908, 2008.
DOI : 10.1002/pmic.200700938
URL : https://hal.archives-ouvertes.fr/hal-00261486

E. Jamet, H. Canut, G. Boudart, and R. F. Pont-lezica, Cell wall proteins: a new insight through proteomics, Trends in Plant Science, vol.11, issue.1, pp.33-39, 2006.
DOI : 10.1016/j.tplants.2005.11.006
URL : https://hal.archives-ouvertes.fr/hal-00105840

E. Jamet, D. Roujol, H. San-clemente, M. Irshad, L. Soubigou-taconnat et al., Cell wall biogenesis of Arabidopsis thaliana elongating cells: transcriptomics complements proteomics, BMC Genomics, vol.10, issue.1, 2009.
DOI : 10.1186/1471-2164-10-505
URL : https://hal.archives-ouvertes.fr/hal-00431884

A. M. Jones, V. Thomas, B. Truman, K. Lilley, J. Mansfield et al., Specific changes in the Arabidopsis proteome in response to bacterial challenge: differentiating basal and R-gene mediated resistance, Phytochemistry, vol.65, issue.12, pp.1805-1821, 2004.
DOI : 10.1016/j.phytochem.2004.04.005

N. Juge, Plant protein inhibitors of cell wall degrading enzymes, Trends in Plant Science, vol.11, issue.7, pp.359-367, 2006.
DOI : 10.1016/j.tplants.2006.05.006

Y. Jung, S. Jeong, S. Kim, R. Singh, J. Lee et al., Systematic Secretome Analyses of Rice Leaf and Seed Callus Suspension-Cultured Cells: Workflow Development and Establishment of High-Density Two-Dimensional Gel Reference Maps, Journal of Proteome Research, vol.7, issue.12, pp.5187-5210, 2008.
DOI : 10.1021/pr8005149

R. Kaida, T. Hayashi, and T. Kaneko, Purple acid phosphatase in the walls of tobacco cells, Phytochemistry, vol.69, issue.14, pp.2546-2551, 2008.
DOI : 10.1016/j.phytochem.2008.07.008

M. J. Kieliszewski and D. T. Lamport, Extensin: repetitive motifs, functional sites, post-translational codes, and phylogeny, The Plant Journal, vol.5, issue.2, pp.157-72, 1994.
DOI : 10.1046/j.1365-313X.1994.05020157.x

J. Ko, K. Han, S. Park, and J. Yang, Plant Body Weight-Induced Secondary Growth in Arabidopsis and Its Transcription Phenotype Revealed by Whole-Transcriptome Profiling, PLANT PHYSIOLOGY, vol.135, issue.2, pp.1069-1083, 2004.
DOI : 10.1104/pp.104.038844

A. Kolkman, P. Daran-lapujade, A. Fullaondo, M. Olsthoorn, J. Pronk et al., Proteome analysis of yeast response to various nutrient limitations, Molecular Systems Biology, vol.101, issue.2, pp.26-41, 2006.
DOI : 10.1038/msb4100069

A. Kolkman, P. Daran-lapujade, A. Fullaondo, M. M. Olsthoorn, J. T. Pronk et al., Proteome analysis of yeast response to various nutrient limitations, Molecular Systems Biology, vol.101, pp.26-42, 2006.
DOI : 10.1038/msb4100069

S. Kurdyukov, A. Faust, C. Nawrath, S. Bär, D. Voisin et al., The Epidermis-Specific Extracellular BODYGUARD Controls Cuticle Development and Morphogenesis in Arabidopsis, THE PLANT CELL ONLINE, vol.18, issue.2, pp.321-339, 2006.
DOI : 10.1105/tpc.105.036079

F. Micheli, Pectin methylesterases: cell wall enzymes with important roles in plant physiology, Trends in Plant Science, vol.6, issue.9, pp.414-419, 2001.
DOI : 10.1016/S1360-1385(01)02045-3

Z. Minic, Physiological roles of plant glycoside hydrolases, Planta, vol.140, issue.4, pp.723-740, 2008.
DOI : 10.1007/s00425-007-0668-y

Z. Minic, E. Jamet, L. Negroni, P. A. Der-garabedian, M. Zivy et al., A sub-proteome of Arabidopsis thaliana mature stems trapped on Concanavalin A is enriched in cell wall glycoside hydrolases, Journal of Experimental Botany, vol.58, issue.10, p.46, 2007.
DOI : 10.1093/jxb/erm082
URL : https://hal.archives-ouvertes.fr/hal-00154429

Z. Minic, E. Jamet, H. San-clemente, S. Pelletier, J. Renou et al., Transcriptomic analysis of Arabidopsis developing stems: a close-up on cell wall genes, BMC Plant Biology, vol.9, issue.1, p.47, 2009.
DOI : 10.1186/1471-2229-9-6
URL : https://hal.archives-ouvertes.fr/hal-00365273

Z. Minic and L. Jouanin, Plant glycoside hydrolases involved in??cell wall polysaccharide degradation, Plant Physiology and Biochemistry, vol.44, issue.7-9, pp.435-449, 2006.
DOI : 10.1016/j.plaphy.2006.08.001

A. M. Nersissian and E. L. Shipp, Blue copper-binding domains, Adv Protein Chem, vol.60, pp.271-340, 2002.
DOI : 10.1016/S0065-3233(02)60056-7

R. Newton, A. Brenton, . Smith, and E. Dudley, Plant proteome analysis by mass spectrometry: principles, problems, pitfalls and recent developments, Phytochemistry, vol.65, issue.11, pp.1449-1485, 2004.
DOI : 10.1016/j.phytochem.2004.04.015

F. Passardi, C. Penel, and C. Dunand, Performing the paradoxical: how plant peroxidases modify the cell wall, Trends in Plant Science, vol.9, issue.11, pp.534-540, 2004.
DOI : 10.1016/j.tplants.2004.09.002

S. Peck, Update on Proteomics in Arabidopsis. Where Do We Go From Here?, PLANT PHYSIOLOGY, vol.138, issue.2, pp.591-599, 2005.
DOI : 10.1104/pp.105.060285

M. Pollard, F. Beisson, Y. Li, and J. Ohlrogge, Building lipid barriers: biosynthesis of cutin and suberin, Trends in Plant Science, vol.13, issue.5, pp.236-246, 2008.
DOI : 10.1016/j.tplants.2008.03.003

K. Pruitt, T. Tatusova, and D. Maglott, NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins, Nucleic Acids Res, vol.34, p.55, 2007.

M. Ranik, N. Creux, and A. Myburg, Within-tree transcriptome profiling in wood-forming tissues of a fast-growing Eucalyptus tree, Tree Physiology, vol.26, issue.3, pp.365-375, 2006.
DOI : 10.1093/treephys/26.3.365

J. Rose, J. Braam, S. Fry, and K. Nishitani, The XTH Family of Enzymes Involved in Xyloglucan Endotransglucosylation and Endohydrolysis: Current Perspectives and a New Unifying Nomenclature, Plant and Cell Physiology, vol.43, issue.12, pp.1421-1435, 2002.
DOI : 10.1093/pcp/pcf171

S. Clemente, H. Pont-lezica, R. Jamet, and E. , Bioinformatics as a tool for assessing the quality of sub-cellular proteomic strategies and inferring functions of proteins: plant cell wall proteomics as a test case, Bioinform Biol Insights, vol.3, pp.15-28, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00362927

C. Sasaki, K. Vårum, Y. Itoh, M. Tamoi, and T. Fukamizo, Rice chitinases: sugar recognition specificities of the individual subsites, Glycobiology, vol.16, issue.12, pp.1242-1250, 2006.
DOI : 10.1093/glycob/cwl043

F. Schröder, J. Lisso, P. Lange, and C. Müssig, The extracellular EXO protein mediates cell expansion in Arabidopsis leaves, BMC Plant Biology, vol.9, issue.1, pp.9-20, 2009.
DOI : 10.1186/1471-2229-9-20

C. J. Schultz, K. L. Ferguson, J. Lahnstein, and A. Bacic, Post-translational modifications of arabinogalactan-peptides of Arabidopsis thaliana, J. Biol. Chem, vol.279, pp.455103-45511, 2004.

G. Seifert and K. Roberts, The Biology of Arabinogalactan Proteins, Annual Review of Plant Biology, vol.58, issue.1, pp.137-161, 2007.
DOI : 10.1146/annurev.arplant.58.032806.103801

K. Shah, C. Penel, J. Gagnon, and C. Dunand, Purification and identification of a Ca2+-pectate binding peroxidase from Arabidopsis leaves, Phytochemistry, vol.65, issue.3, pp.307-312, 2004.
DOI : 10.1016/j.phytochem.2003.11.019
URL : https://hal.archives-ouvertes.fr/hal-00141329

S. H. Shiu and A. B. Bleecker, Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases, Proceedings of the National Academy of Sciences, vol.98, issue.19, pp.10763-10771, 2001.
DOI : 10.1073/pnas.181141598

E. Shpak, J. Leykam, and M. Kieliszewski, Synthetic genes for glycoprotein design and the elucidation of hydroxyproline-O-glycosylation codes, Proceedings of the National Academy of Sciences, vol.96, issue.26, pp.14736-14741, 1999.
DOI : 10.1073/pnas.96.26.14736

A. Smith, S. Zeeman, and S. Smith, STARCH DEGRADATION, Annual Review of Plant Biology, vol.56, issue.1, pp.73-98, 2005.
DOI : 10.1146/annurev.arplant.56.032604.144257

M. Sohani, P. Schenk, C. Schultz, and O. Schmidt, reveals involvement in plant defence responses, Plant Biology, vol.98, issue.1, pp.105-117, 2009.
DOI : 10.1111/j.1438-8677.2008.00139.x

S. Spadoni, O. Zabotina, D. Matteo, A. Mikkelsen, J. Cervone et al., Polygalacturonase-Inhibiting Protein Interacts with Pectin through a Binding Site Formed by Four Clustered Residues of Arginine and Lysine, PLANT PHYSIOLOGY, vol.141, issue.2, pp.557-564, 2006.
DOI : 10.1104/pp.106.076950

J. Thelen and S. R. Peck, Quantitative proteomics in plants: choices in abundance Plant proteases: from phenotypes to molecular mechanisms, Plant Cell Annu Rev Plant Biol, vol.19, issue.59, pp.3339-3346, 2007.

V. Wasinger, S. Cordwell, A. Cerpa-poljak, J. Yan, A. Gooley et al., Progress with gene-product mapping of the Mollicutes:Mycoplasma genitalium, Electrophoresis, vol.13, issue.1, pp.1090-1094, 1995.
DOI : 10.1002/elps.11501601185

W. Willats, L. Mccartney, W. Mackie, and J. Knox, Pectin: cell biology and prospects for functional analysis, Plant Mol Biol, vol.47, pp.9-27, 2001.
DOI : 10.1007/978-94-010-0668-2_2

R. Yokoyama and K. Nishitani, Genomic Basis for Cell-Wall Diversity in Plants. A Comparative Approach to Gene Families in Rice and Arabidopsis, Plant and Cell Physiology, vol.45, issue.9, pp.1111-1121, 2004.
DOI : 10.1093/pcp/pch151

R. Yokoyama and K. Nishitani, Identification and characterization of Arabidopsis thaliana genes involved in xylem secondary cell walls, Journal of Plant Research, vol.14, issue.3, pp.189-194, 2006.
DOI : 10.1007/s10265-006-0261-7

Z. Zhao, L. Tan, A. Showalter, D. Lamport, and M. Kieliszewski, Tomato LeAGP-1 arabinogalactan-protein purified from transgenic tobacco corroborates the Hyp contiguity hypothesis, The Plant Journal, vol.190, issue.4, pp.431-444, 2002.
DOI : 10.1046/j.1365-313X.2002.01365.x

M. Zhu, S. Dai, S. Mcclung, X. Yan, and S. Chen, Functional Differentiation of Brassica napus Guard Cells and Mesophyll Cells Revealed by Comparative Proteomics, Molecular & Cellular Proteomics, vol.8, issue.4, pp.752-766, 2009.
DOI : 10.1074/mcp.M800343-MCP200