Plant and Soil

, Volume 286, Issue 1–2, pp 357–376 | Cite as

Extracellular Proteomes of Arabidopsis Thaliana and Brassica Napus Roots: Analysis and Comparison by MudPIT and LC-MS/MS

  • Urmila Basu
  • Jennafer L. Francis
  • Randy M. Whittal
  • Julie L. Stephens
  • Yang Wang
  • Osmar R. Zaiane
  • Randy Goebel
  • Douglas G. Muench
  • Allen G. Good
  • Gregory J. Taylor


An important principle of the functional organization of plant cells is the targeting of proteins to specific subcellular locations. The physical location of proteins within the apoplasm/rhizosphere at the root–soil interface positions them to play a strategic role in plant response to biotic and abiotic stress. We previously demonstrated that roots of Triticum aestivum and Brassica napus exude a large suite of proteins to the apoplasm/rhizosphere [Basu et al. (1994) Plant Physiol 106:151–158; Basu et al. (1999) Physiol Plant 106:53–61]. This study is a first step to identify low abundance extracytosolic proteins from Arabidopsis thaliana and Brassica napus roots using recent advances in the field of proteomics. A total of 16 extracytosolic proteins were identified from B. napus using two-dimensional gel electrophoresis, tandem mass spectrometry (LC-MS/MS) and de novo sequencing. Another high-throughput proteomics approach, Multidimensional Protein Identification Technology (Mud PIT) was used to identify 52 extracytosolic proteins from A. thaliana. Signal peptide cleavage sites, the presence/absence of transmembrane domains and GPI modification were determined for these proteins. Functional classification grouped the extracellular proteins into different families including glycoside hydrolases, trypsin/protease inhibitors, plastocyanin-like domains, copper–zinc superoxide dismutases, gamma-thioinins, thaumatins, ubiquitins, protease inhibitor/seed storage/lipid transfer proteins, transcription factors, class III peroxidase, and plant basic secretory proteins (BSP). We have also developed an on-line, Extracytosolic Plant Proteins Database (EPPdb, to provide information about these extracytosolic proteins.


Arabidopsis thaliana Brassica napus Extracellular proteins Proteomics 



mass spectrometry




immobilized pH gradient


3-[(3-Cholamidopropyl) Dimethyl-Ammonio]-1-Propanesulfonate


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This work was funded by an Alberta Agricultural Research Institute (AARI) grant to GJT and RMW, Natural Sciences and Engineering Research Council of Canada (NSERC) grant to GJT, RG, OZ and AGG and FGAS project to DGM, AGG and GJT. The FGAS project is supported by Genome Prairie, in part through Genome Canada, a not-for-profit corporation which is leading a national strategy on genomics with $375 million in funding from the Government of Canada. The personnel at the Institute for Biomolecular Design (IBD), University of Alberta, Edmonton, AB, Canada and University of Victoria BC Proteomics Centre staffs are gratefully acknowledged for their expertise and assistance with mass spectrometry.


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Copyright information

© Springer Science+Business Media B.V. 2006

Authors and Affiliations

  • Urmila Basu
    • 1
    • 2
  • Jennafer L. Francis
    • 2
  • Randy M. Whittal
    • 3
  • Julie L. Stephens
    • 4
  • Yang Wang
    • 5
  • Osmar R. Zaiane
    • 5
  • Randy Goebel
    • 5
  • Douglas G. Muench
    • 6
  • Allen G. Good
    • 2
  • Gregory J. Taylor
    • 2
  1. 1.Department of Agricultural, Food and Nutritional ScienceUniversity of AlbertaEdmontonCanada
  2. 2.Department of Biological SciencesUniversity of AlbertaEdmontonCanada
  3. 3.Department of ChemistryUniversity of AlbertaEdmontonCanada
  4. 4.Research Services OfficeUniversity of AlbertaEdmontonCanada
  5. 5.Department of Computing SciencesUniversity of AlbertaEdmontonCanada
  6. 6.Department of Biological SciencesUniversity of CalgaryCalgaryCanada

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