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Proteomic studies on Arabidopsis thaliana
Proteomic studies on monocot plants
Proteomic studies on other plants
Xylem sap proteomes
Reviews on plant cell wall proteomics
Databases
WallProtDB

Proteomic studies on Arabidopsis thaliana

Differential extraction and protein sequencing reveals major differences in patterns of primary cell wall proteins from plants.
D Robertson, GP Mitchell, JS Gilroy, C Gerrish, GP Bolwell and AR Slabas
J. Biol. Chem., 272: 15841-15848, 1997. Full text

Proteomic analysis of the Arabidopsis thaliana cell wall.
S Chivasa, BK Ndimba, WJ Simon, D Robertson, X-L Yu, JP Knox, P Bolwell and AR Slabas
Electrophoresis, 23: 1754-1765, 2002. Full text

Proteomics of loosely bound cell wall proteins of Arabidopsis thaliana cell suspension cultures: A critical analysis.
G Borderies, E Jamet, C Lafitte, M Rossignol, A Jauneau, G Boudart, B Monsarrat, M-T Esquerré-Tugayé, A Boudet and R Pont-Lezica
Electrophoresis, 24:3421-3432, 2003. Full text

Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A proteomic and genomic analysis.
GH Borner, KS Lilley, TJ Stevens and P Dupree
Plant Physiol., 132: 568-577, 2003. Full text

The assessment of enriched apoplastic extracts using proteomic approaches.
RP Haslam, AL Downie, M Raventon, K Gallardo, D Job, KE Pallett, P John, MAJ Parry and JOD Coleman
Ann. Appl. Biol., 143: 81-91, 2003. Full text

Proteomic analysis of glycosylphosphatidylinositol-anchored membrane proteins.
F Elortza F, TS Nühse, LJ Foster, A Stensballe, SC Peck and ON Jensen
Mol. Cell. Proteomics, 2: 1261-1270, 2003. Full text

Post-translational modifications of arabinogalactan-peptides of Arabidopsis thaliana. Endoplasmic reticulum and glycosylphosphatidylinositol-anchor signal cleavage sites and hydroxylation of proline.
CJ Schultz, KL Ferguson, J Lahnstein and A Bacic
J. Biol. Chem., 279: 45503-45511, 2004. Full text

Cell wall proteins in apoplastic fluids of Arabidopsis thaliana rosettes: Identification by mass spectrometry and bioinformatics.
G Boudart, E Jamet, M Rossignol, C Lafitte, G Borderies, A Jauneau, M-T Esquerré-Tugayé and R Pont-Lezica
Proteomics, 5: 212-221, 2005. Full text

Proteomic analysis of secreted proteins from Arabidopsis thaliana seedlings: improved recovery following removal of phenolic compounds.
S Charmont, E Jamet, R Pont-Lezica and H Canut
Phytochemistry, 66: 453-461, 2005. Full text

A proteomic approach to apoplastic proteins involved in cell wall regeneration in protoplasts of Arabidopsis suspension-cultured cells.
H-K Kwon, R Yokoyama and K Nishitani
Plant Cell Physiol., 46: 843-857, 2005. Full text

Secretome analysis reveals an Arabidopsis lipase involved in defense against Alternaria brassicicola.
IS Oh, AR Park, MS Bae, SJ Kwon, YS Kim, JE Lee, NY Kang, S Lee, H Cheong and OK Park
Plant Cell, 17: 2832-2847, 2005. Full text

Extracellular proteomes of Arabidopsis thaliana and Brassica napus roots: analysis and comparison by MUdPIT and LC-MS/MS.
U Basu, JL Francis, RW Whittal, JL Stephens, Y Wang, OR Zaiane, R Goebel, DG Muench, AG Good and GJ Taylor
Plant Soil, 286: 357-376, 2006. Full text

Arabidopsis cell wall proteome defined using multidimensional protein identification technology.
EM Bayer, AR Bottrill, J Walshaw, M Vigouroux, MJ Naldrrett, CL Thomas and AJ Maule
Proteomics, 6: 301-311, 2006. Full text

Evaluation of cell wall preparations for proteomics: a new procedure for purifying cell walls from Arabidopsis hypocotyls.
L Feiz, M Irshad, RF Pont-Lezica, H Canut and E Jamet
Plant Methods, 2: 10, 2006. Full text

Modification-specific proteomics of plasma membrane proteins: Identification and characterization of glycosylphosphatidylinositol-anchored proteins released upon phospholipase D treatment.
F Elortza, S Mohammad, J Bunkenborg, L Foster, TS Nühse, U Brodbeck, SC Peck and ON Jensen
J. Proteome Res., 5: 935-943, 2006. Full text

A sub-proteome of Arabidopsis thaliana trapped on Concanavalin A is enriched in cell wall glycoside hydrolases.
Z Minic, E Jamet, L Negroni, PA der Garabedian, M Zivy and L Jouanin
J. Exp. Bot., 58: 2503-2512, 2007. Full text

Proteomic analysis of alterations in the secretome of Arabidopsis thaliana suspension cells subjected to nutritional phosphate deficiency.
HT Tran and WC Plaxton
Proteomics, 8: 4317-4326, 2008. Full text

A new picture of cell wall protein dynamics in elongating cells of Arabidopsis thaliana : confirmed actors and newcomers.
M Irshad, H Canut, G Borderies, R Pont-Lezica and E Jamet
BMC Plant Biol., 8: 94, 2008. Full text

Absolute protein quantification by LC/MS for global analysis of salicylic acid-induced plant protein secretion responses.
F-Y Cheng, K Blackburn, Y-M Lin, MB Goshe and JD Wiliamson
J. Proteome Res., 8: 82-93, 2009. Full text

Plant cell wall proteomics: mass spectrometry data, a trove for research on protein structure/function relationships.
C Albenne, H Canut, G Boudart, Y Zhang, H San Clemente, R Pont-Lezica and E Jamet
Mol. Plant, 2: 977-989, 2009. Full text

Identification by 2-D DIGE of apoplastic proteins regulated by oligogalacturonides in Arabidopsis thaliana.
M Casasoli, S Spadoni, KS Lilley, F Cervone, G De Lorenzo and B Mattei
Proteomics, 8: 1042-1054, 2008. Full text

Combining various strategies to increase the coverage of the plant cell wall glycoproteome.
Y Zhang, A Giboulot, M Zivy, B Valot, E Jamet and C Albenne
Phytochemistry, 72: 1109-1123, 2011. Full text

Identification of the abundant hydroxyproline-rich glycoproteins in the root walls of wild-type Arabidopsis, an ext3 mutant line, and its phenotypic revertant
Y Chen, D Ye, MA, Held, MC Cannon, T Ray, P Saha, AN Frye, AJ Mort and MJ Kieliszewski
Plants, 4: 85-111, 2015. Full text

Proteome readjustments in the apoplastic space of Arabidopsis thaliana ggt1 mutant leaves exposed to UV-B radiation
AR Trentin, M Pivato, SMM Mehdi, LE Barnabas, S Giaretta, M Fabrega-Prats, D Prasad, G Arrigoni and A Masi
Front. Plant Sci, 6: 128, 2015. Full text

Ascorbate deficiency influences the leaf cell wall glycoproteome in Arabidopsis thaliana
N Sultana, HV Florance, A Johns and N Smirnoff
Plant Cell Environ., 38: 375-384, 2015. Full text

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.
H Nguyen-Kim, H San Clemente, T Balliau, M Zivy, C Dunand, C Albenne and E Jamet
Proteomics, 16: 491-503, 2016. Full text

An enlarged cell wall proteome of Arabidopsis thaliana rosettes
V Hervé, H Duruflé, H San Clemente, C Albenne, T Balliau, M Zivy, C Dunand and E Jamet
Proteomics, 16: 3183-3187, 2016.

N-Glycopeptide profiling in Arabidopsis inflorescence
S-L Xu, KM Medzihradszky, Z-Y Wang, AL Burlingame and RJ Chalkley
Mol Cell Proteomics, 15: 2048-2054, 2016.

Cell wall proteome analysis of Arabidopsis thaliana mature stems
H Duruflé, H San Clemente, T Balliau, M Zivy, C Dunand and E Jamet
Proteomics, DOI: 10.1002/pmic.201600449, 2017. Full text

Cell wall adaptation of two contrasted ecotypes of Arabidopsis thaliana, Col and Sha, to sub-optimal growth conditions: an integrative study
H Duruflé, V Hervé, P Ranocha, T Balliau, M Zivy, J Chourré, H San Clemente, V Burlat, C Albenne, S Déjean, E Jamet and C Dunand
Plant Sci., 263: 183-193, 2017.

Identification and characterization of Arabidopsis seed coat mucilage proteins.
AYL Tsai, T Kunieda, J Rogalski, LJ Foster, BE Ellis and GH Haughn
Plant Physiol., 173: 1059-1074, 2017.


Proteomic studies on monocot plants

Systematic secretome analyses of rice leaf and seed callus suspension-cultured cells: Workflow development and establishment of high-density two-dimensional gel reference maps.
Y-H Jung, S-H Jeong, SH Kim, R Singh, J-E Lee, Y-S Cho, GK Agrawal, R Rakwal and N-S Jwa
J. Proteome Res., 7: 5187-5210, 2008. Full text

Proteomics of weakly bound cell wall proteins in rice calli.
XY Chen, ST Kim, WK Cho, Y Rim, S Kim, SW Kim, KY Kang, ZY Park and JY Kim
J. Plant Physiol., 166: 675-685, 2009. Full text

The proteomic analysis of the secretome of rice calli.
WK Cho, XY Chen, H Chu, Y Rim, S Kim, ST Kim, S-W Kim, Z-Y Park and J-Y Kim
Physiol. Plant., 135: 331-341, 2009. Full text

Comparative proteomics analysis of the root apoplasts of rice seedlings in response to hydrogen peroxide.
L Zhou, SA Bokhari, CJ Dong and JY Liu
PLoS ONE, 6: e16723, 2011. Full text

Brachypodium distachyon as a model plant towards improved biofuel crops:
Search for secreted proteins involved in biogenesis and disassembly of cell wall polymers.

T Douché, H San Clemente,V Burlat, D Roujol, M Zivy, B Valot, R Pont-Lezica and E Jamet
Proteomics, 13: 2438-2454, 2013. Full text

Cell wall proteomics of sugarcane cell suspension cultures
MJ Calderan-Rodrigues, E Jamet, MB Calderan Rodrigues Bonassi, S Guidetti-Gonzalez, A Carmanhanis Begossi, L Vaz Setem, LM Franceschini, J Guimaraes Fonseca and CA Labate
Proteomics, 14: 738-749, 2014. Full text

Cell wall proteomic of Brachypodium distachyon grains: A focus on cell wall remodeling proteins
M Francin-Allami, K Merah, C Albenne, H Rogniaux,M Pavlovic, V Lollier, R Sibout, F Guillon, E Jamet and C Larré
Proteomics, 15: 2296-2306, 2015. Full text

N-linked glycoproteome profiling of seedling leaf in Brachypodium distachyon L.
M Zhang, G Chen, D Lv, X Li and Y Yan
J Proteome Res, 14: 1727-1738, 2015. Full text

Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases
MJ Calderan-Rodrigues, E Jamet, T Douche, MB Rodrigues-Bonassi, T Regiani Cataldi, J Fonseca Guimarães, H San Clemente, R Pont-Lezica and CA Labate
BMC Plant Biol., 16: 14, 2016. Full text

Understanding the remodelling of cell walls during Brachypodium distachyon grain development through a sub-cellular quantitative proteomic approach
M Francin-Allami, V Lollier, M Pavlovic, H San Clemente, H Rogniaux, E Jamet, F Guillon and C Larré
Proteomes, 4: 21, 2016. Full text


Proteomic studies on other plants

Apoplast proteome reveals that extracellular matrix contributes to multistress response in poplar.
O Pechanova, C-Y Hsu, JP Adams, T Pechan, L Vandervelde, J Drnevich, S Jawdy, A adeli, JC Suttle, AM Lawrence TJ Tschaplinski, A Seguin and C Yuceer
BMC Genomics, 11: 674 2010. Full text

Mining the surface proteome of tomato (Solanum lycopersicum) fruit for proteins associated with cuticle biogenesis.
TH Yeats, KJ Howe, AJ Matas, GJ Buda, TW Thannhauser and JKC Rose
J Exp Bot, 61: 3759-3771 2010. Full text

Towards characterization of the glycoproteome of tomato (Solanum lycopersicum) fruit using Concanavalin A lectin affinity chromatography and LC-MALDI-MS/MS analysis.
C Catala, KJ Howe, S Hicko, JKC Rose and TW Thannhauser
Proteomics, 11: 1530-1544 2011. Full text

Protein profiling in potato (Solanum tuberosum L.) leaf tissues by differential centrifugation.
S Lim, K Chisholm, RH Coffin, RD Peters, KI Al-Mughrabi, G Wang-Pruski and DM Pinto
J Proteome Res, 11: 2594-2601 2012. Full text

Proteomic analysis of cell walls of two developmental stages of alfalfa stems
JC Verdonk, RD Hatfield and ML Sullivan
Front Plant Sci, 3 : 279 2012. Full text

Identification of cell wall proteins in the flax (Linum usitatissimum) stem.
A Day, S FĂ©nart, G Neutelings, S Hawkins, C Rolando and C Tokarski
Proteomics, 13: 812-825 2013. Full text

Glycoproteome of elongating cotton fiber cells.
S Kumar, K Kumar, P Pandey, V Rajamani, KV Padmalatha, G Dhandapani, M Kanakachari, S Leelavathi, PA Kumar and VS Reddy
Mol Cell Proteomics, 12: 3677-3689, 2013. Full text

A proteomic approach to Physcomitrella patens rhizoid exudates
T Martinez-Cortés, F Pomar, F Merino and E Novo-Uzal
J Plant Physiol, 171: 1671-1678, 2014. Full text

Proteomics and transcriptomics of the BABA-induced resistance response in potato using a novel functional annotation approach
T Bengtsson, D Weighill, F Levander, S Resjö, DDBurra, LI Moushib, PE Hedley, E Liljeroth, D Jacobson and E Alexandersson
BMC Genomics, 15: 315, 2014. Full text

An improved protocol to study the plant cell wall proteome
B Printz, R Dos Santos Morais, S Wienkoop, K Sergeant, S Lutts, JF Hausman and J Renaut
Front Plant Sci, 6 : 237, 2015. Full text


Xylem sap proteomes

Analysis of xylem sap proteins from Brassica napus.
J Kehr, A Buhtz and P Giavalisco
BMC Plant Biol., 5, 11, 2005. Full text

Defence reactions in the apoplastic proteome of oilseed rape (Brassica napus var. napus) attenuate Verticillium longisporum growth but not disease symptoms.
S Floerl, C Druebert, A Majcherczyk, P Karlovsky, U Kües and A Polle
BMC Plant Biol., 8, 129, 2008. Full text

Proteomic analysis of hybrid poplar xylem sap.
NJ Dafoe and P Constabel
Phytochemistry, 70: 856-863, 2009. Full text

Analysis of the xylem sap proteome of Brassica oleracea reveals a high content in secreted proteins.
L Ligat, E Lauber, C Albenne, H San Clemente, B Valot, M Zivy, R Pont-Lezica, M Arlat and E Jamet
Proteomics, 11: 1798-1813, 2011. Full text

Xylem sap proteomics.
T Dugé de Bernonville, C Albenne, M Arlat, L Hoffmann, E Lauber and E Jamet
Methods Mol Biol, 1072: 391-405, 2014. Full text

Xylem sap in cotton contains proteins that contribute to environmental stress responsae and cell wall development.
Z Zhang, W Xin, S Wang, X Zhang, H dai, R Sun, T Frazier, B Zhang and Q Wang
Funct Integr Genomics, 15: 17-26, 2015. Full text


Reviews on plant cell wall proteomics

Digging deeper into the plant cell wall proteome.
SJ Lee, RS Saravanan, CM Damasceno, H Yamane, BD Kim and JK Rose
Plant Physiol. Biochem., 42: 979-988, 2004. Full text

Tackling the plant proteome: practical approaches, hurdles, and experimental tools.
JKC Rose, S Bashir, JJ Giovannoni, MM Jahn and RS Saravanan
Plant J., 39: 715-733, 2004. Full text

The plot thickens: New perspectives of primary cell wall modification.
JK Rose, M Saladié and C Catalá
Curr. Opin. Plant Biol., 7: 296-301, 2004. Full text

Proteomic analysis of the Arabidopsis cell wall reveals unexpected proteins with new cellular locations.
AR Slabas, B Ndimba, WJ Simon and S Chivasa
Biochem. Soc. Trans., 32: 524-528, 2004. Full text

Cell wall proteins: a new insight through proteomics.
E Jamet, H Canut, G Boudart and RF Pont-Lezica
Trends Plant Sci., 11: 33-39, 2006. Full text

Cell wall proteome.
G Boudart, Z Minic, C Albenne, H Canut, E Jamet and R Pont-Lezica
In: Plant proteomics (eds. S. Samaj, J. Thelen), Springer, Berlin, pp 169-185, 2007. Full text

Cell wall.
E Jamet, H Canut, C Albenne, G Boudart and R Pont-Lezica
In: Plant Proteomics: Technologies, Strategies, and Applications (eds. G.K. Agrawal, R. Rakwal), Wiley, USA, pp-293-307, 2008. Full text

Isolation of plant cell wall proteins.
E Jamet, G Boudart, G Borderies, S Charmont, C Lafitte, M Rossignol, H Canut and R Pont-Lezica
Methods Mol. Biol., 425: 187-201, 2008. Full text

Recent advances in plant cell wall proteomics.
E Jamet, C Albenne, G Boudart, M Irshad, H Canut and R Pont-Lezica
Proteomics, 8: 893-908, 2008. Full text

The puzzle of protein location in plant proteomics.
E Jamet and R Pont-Lezica
In Proteomics: Methods, Applications and Limitations, G Rancourt ed, Nova Science
Publishers, Inc., Hauppauge, NY, USA, 2010.

Straying off the highway: trafficking of secreted plant proteins and complexity in the plant cell wall proteome.
JKC Rose and S-J Lee
Plant Physiol, 153: 433-436, 2010. Full text

Analytical technologies for identification and characterization of the plant N-glycoproteome.
E Ruiz-May, TW Thannhauser, S Zhang and JKC Rose
Front. Plant Sci. 3: 150,2012

Plant cell wall proteomics: the leadership of Arabidopsis thaliana.
C Albenne, H Canut and E Jamet
Front Plant Sci 4: 111, 2013. Full text

Plant secretome - From cellular process to biological activity.
C Krause, S Richter, C Knöll and G Jürgens
Biochim. Biophys. Acta., 1834: 2429-2441,2013

Plant cell wall proteins: a large body of data, but what about runaways?
C Albenne, H Canut, L Hoffmann and E Jamet
Proteomes 2: 224-242, 2014. Full text

Post-translational modifications of plant cell wall proteins and peptides: A survey from a proteomics point of view.
H Canut H, C Albenne C and E Jamet
Biochim. Biophys. Acta., 1864: 983-990,2016

Plant fluid proteomics: Delving into the xylem sap, phloem sap and apoplastic fluid proteomes.
J Rodríguez-Celma, L Ceballos-Laita, MA Grusak, J Abadí and AF López-Millán
Biochim. Biophys. Acta., 1864: 991-1002,2016

Unconventional protein secretion in plants: a critical assessment.
DG Robinson, Y Ding and L Jiang
Protoplasma, 253: 31-43,2016

Cell wall proteomics as a means to identify target genes to improve second generation biofuel production
MJ Calderan-Rodrigues, JG Fonseca, CA Labate and E Jamet
In Frontiers in Bioenergy and Biofuels (E Jacob-Lopes and L Queiroz Zepka ed), InTech Open access Publisher, Croatia, pp 5-24.

Extraction and characterization of extracellular proteins and their post-translational modifications from Arabidopsis thaliana suspension cell cultures and seedlings: a critical review.
M Ghahremani, A Kyla and W Plaxton
Proteomes, 4:25, 2016

Protein dynamics in the plant extracellular space.
L Guerra-Guimarães, C Pinheiro, I Chaves, DR Barros and CP Ricardo
Proteomes, 4:22, 2016

Isolation of the cell wall
H Canut, C Albenne and E Jamet
Methods Mol Biol. 1511: 171-185,2017


Databases

The Cell Wall Navigator database. A systems-based approach to organism-unrestricted mining of protein families involved in cell wall metabolism.
T Girke, J Lauricha, H Tran, K Keegstra and N Raikhel
Plant Physiol, 136: 3003-3008, 2004. Full text

PPDB, the Plant Proteomics Database at Cornell.
Q Sun, B Zybailov, W Majeran, G Friso, P Olinares and K van Wijk
Nucleic Acids Res, 37(Database issue): D969-D974, 2008. Full text

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.
H San Clemente, R Pont-Lezica and E Jamet
Bioinform. Biol. Insights, 3: 15-28, 2009. Full text

SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis.
S Tanz, I Castelden, C Hooper, M Vacher, I Small and H Millar
Nucleic Acids Res, 41(Database issue): D1185-D1191, 2013. Full text


WallProtDB

Plant cell wall functional genomics: Novelties from proteomics.
R Pont-Lezica, Z Minic, H San Clemente, D Roujol and E Jamet
In Advances in Genetics Research, vol 1, M Osborne ed, Nova Science Publishers, Inc,
Hauppauge, NY, USA, vol. 1, pp 265-281, 2010. Full text

Analysis of the xylem sap proteome of Brassica oleracea reveals a high content in secreted proteins.
L Ligat, E Lauber, C Albenne, H San Clemente, B Valot, M Zivy, R Pont-Lezica, M Arlat and E Jamet
Proteomics, 11: 1798-1813, 2011. Full text

WallProtDB, a database resource for plant cell wall proteomics.
San Clemente H and Jamet E
Plant Methods, 11: 2, 2015. Full text