DOI: 10.1126/science.1157956. Genome-Scale Proteomics Reveals <i>Arabidopsis thaliana</i> Gene Models and Proteome Dynamics

Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

10.1126/science.1157956

Crossref journal-article

American Association for the Advancement of Science (AAAS)

Science (221)

Abstract

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.

Bibliography

Baerenfaller, K., Grossmann, J., Grobei, M. A., Hull, R., Hirsch-Hoffmann, M., Yalovsky, S., Zimmermann, P., Grossniklaus, U., Gruissem, W., & Baginsky, S. (2008). Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics. Science, 320(5878), 938â941.

Authors 10

Katja Baerenfaller (first)
Jonas Grossmann (additional)
Monica A. Grobei (additional)
Roger Hull (additional)
Matthias Hirsch-Hoffmann (additional)
Shaul Yalovsky (additional)
Philip Zimmermann (additional)
Ueli Grossniklaus (additional)
Wilhelm Gruissem (additional)
Sacha Baginsky (additional)

References 29 Referenced 406

10.1038/35048692
10.1016/j.cell.2007.07.032
10.1038/nbt1300
10.1038/nbt1315
Materials and methods are available as supporting material on Science Online.
A. I. Nesvizhskii, Methods Mol. Biol.367, 87 (2007). / Methods Mol. Biol. (2007)
10.1093/bioinformatics/btm417
10.1093/nar/gkj472
P. Joneset al., Nucleic Acids Res.36, D878 (2008). / Nucleic Acids Res. (2008)
10.1038/nbt1329
10.1104/pp.104.040071
10.1093/bioinformatics/btl140
10.1021/pr049764u
E. R. Stadtman, Free Radic. Res.40, 1250 (2006). (10.1080/10715760600918142) / Free Radic. Res. (2006)
10.1126/science.1088305
10.1016/S0959-440X(98)80069-9
10.1038/nbt1270
10.1104/pp.104.046367
10.1373/49.7.1041
10.1038/nbt1275
10.1186/gb-2006-7-4-106
10.1093/nar/gkj040
10.1101/gr.5646507
10.1074/mcp.M700171-MCP200
10.1016/j.cub.2004.02.039
10.1038/nrm1683
10.1093/bioinformatics/17.suppl_1.S140
10.1186/1471-2105-6-25
We thank the Functional Genomics Center Zurich especially B. Roschitzki C. Panse and M. Schmidt for providing infrastructure and technical support; E. Brunner from the Center for Model Organism Proteomes (C-MOP) for project coordination; and J. Fütterer from the Institute of Plant Sciences for critical reading of the manuscript. We also thank our colleagues at the European Bioinformatics Institute for their help in building the PRIDE Arabidopsis peptide database. This work was supported by the SystemsX initiative of ETH Zurich (K.B. W.G. S.B.) and the University Research Priority Program in Systems Biology/Functional Genomics (U.G. and M.A.G.) in the framework of the C-MOP project and by the European Framework Programme 6 AGRON-OMICS project (LSHG–CT–2006–037704 W.G.). S.Y. was supported by a sabbatical fellowship provided by ETH Zurich.

Dates

Type	When
Created	17 years, 4 months ago (April 24, 2008, 9:36 p.m.)
Deposited	1 year, 7 months ago (Jan. 10, 2024, 3:50 a.m.)
Indexed	1 month ago (July 23, 2025, 8:50 a.m.)
Issued	17 years, 3 months ago (May 16, 2008)
Published	17 years, 3 months ago (May 16, 2008)
Published Print	17 years, 3 months ago (May 16, 2008)

Funders 0

None

BibTeX

@article{Baerenfaller_2008, title={Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics}, volume={320}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.1157956}, DOI={10.1126/science.1157956}, number={5878}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Baerenfaller, Katja and Grossmann, Jonas and Grobei, Monica A. and Hull, Roger and Hirsch-Hoffmann, Matthias and Yalovsky, Shaul and Zimmermann, Philip and Grossniklaus, Ueli and Gruissem, Wilhelm and Baginsky, Sacha}, year={2008}, month=may, pages={938–941} }

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