Submitted on March 18, 2008
Accepted on April 15, 2008
Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics
Katja Baerenfaller 1*, Jonas Grossmann 2, Monica A. Grobei 3, Roger Hull 4, Matthias Hirsch-Hoffmann 5, Shaul Yalovsky 6, Philip Zimmermann 5, Ueli Grossniklaus 3, Wilhelm Gruissem 2*, Sacha Baginsky 1*
1 Institute of Plant Sciences, ETH (Swiss Federal Institute of Technology) Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland.; Center for Model Organism Proteomes, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
2 Institute of Plant Sciences, ETH (Swiss Federal Institute of Technology) Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland.; Center for Model Organism Proteomes, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.; Functional Genomics Center Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
3 Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.; Center for Model Organism Proteomes, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
4 Faculty of Life Sciences, University of Manchester, Brunswick Street, Manchester, United Kingdom
5 Institute of Plant Sciences, ETH (Swiss Federal Institute of Technology) Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland.
6 Department of Plant Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
* To whom correspondence should be addressed.
Katja Baerenfaller , E-mail: kbaerenfaller{at}ethz.ch
Wilhelm Gruissem , E-mail: wgruissem{at}ethz.ch
Sacha Baginsky , E-mail: sbaginsky{at}ethz.ch
We have assembled a proteome map for Arabidopsis thaliana from high-density, organ-specific proteome catalogs that we generated for different organs, developmental stages, and undifferentiated cultured cells. We matched 86,456 unique peptides to 13,029 proteins and provide expression evidence for 57 gene models that are not represented in the TAIR7 protein database. Analysis of the proteome identified organ-specific biomarkers and allowed us to compile an organ-specific set of proteotypic peptides for 4105 proteins to facilitate targeted quantitative proteomics surveys. Quantitative information for the identified proteins was used to establish correlations between transcript and protein accumulation in different plant organs. The Arabidopsis proteome map provides information about genome activity and proteome assembly and is available as a resource for plant systems biology.
