Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics.
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.
Baerenfaller
Katja
K
Institute of Plant Sciences, ETH (Swiss Federal Institute of Technology) Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland. kbaerenfaller@ethz.ch
Grossmann
Jonas
J
Grobei
Monica A
MA
Hull
Roger
R
Hirsch-Hoffmann
Matthias
M
Yalovsky
Shaul
S
Zimmermann
Philip
P
Grossniklaus
Ueli
U
Gruissem
Wilhelm
W
Baginsky
Sacha
S
D000465:Algorithms; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000737:chemistry* / Q000166:cytology / Q000235:genetics* / Q000502:physiology; D029681:Arabidopsis Proteins / Q000032:analysis* / Q000737:chemistry / Q000235:genetics; D001483:Base Sequence; D015415:Biomarkers / Q000032:analysis; D002478:Cells, Cultured; D019295:Computational Biology; D030541:Databases, Genetic; D035264:Flowers / Q000737:chemistry / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis / Q000737:chemistry; D018517:Plant Roots / Q000737:chemistry / Q000235:genetics; D020543:Proteome / Q000032:analysis*; D040901:Proteomics; D012639:Seeds / Q000737:chemistry / Q000235:genetics; D014158:Transcription, Genetic
D029681:Arabidopsis Proteins; D015415:Biomarkers; D010455:Peptides; D020543:Proteome