Minisymposium 26: Proteomics

Abs # 47003: PLprot: a proteome database for different plastid types

Presenter:	Gruissem, Wilhelm , wilhelm.gruissem@ipw.biol.ethz.ch
Authors	Kleffmann, Torsten  (A)   von Zychlinski, Anne  (A)   Siddique, Asim  (A)   Russenberger, Doris  (A)   Hirsch-Hoffmann, Matthias  (A)   Gruissem, Wilhelm  (A) (B)  Baginsky, Sacha  (A) (B)
Affiliations:	(A): Institute of Plant Sciences, Swiss Federal Institute Of Technology, ETH Zürich, Universitaetstrasse 2, 8092 Zürich, Switzerland (B): Functional Genomics Center Zurich
Web Site:	http://www.pb.ethz.ch

Most plastid-localized proteins are encoded in the nuclear genome and imported into the plastid after translation in the cytoplasm. But our present knowledge of the proteomes and the metabolic capacities of different plastid types is only very limited. We have developed a large-scale and high-throughput analysis of the proteomes from Arabidopsis chloroplasts, rice etioplasts, and the undifferentiated proplastids from a tobacco BY-2 cell culture. Together we identified more than 1,200 plastid proteins at the submission of this abstract. Many of the 690 Arabidopsis chloroplast proteins could be assigned to known protein complexes and metabolic pathways, but more than 30% of the proteins have unknown functions and many are not predicted to localize to the chloroplast. Parallel RNA profiling revealed a pathway-dependent correlation between transcript and relative protein abundance, suggesting gene regulation at different levels. We also identified 207 proteins from BY2 plastids and 231 proteins from rice etioplasts. The comparison of the three plastid proteomes revealed significant differences in the protein profiles that suggest diverse metabolic activities. While the chloroplast proteome is dominated by proteins that function in photosynthesis, most enzymes from BY2 plastid are active in amino acid biosynthetic pathways. Interestingly, the majority of the etioplast proteins functions in plastid gene expression. We have assembled all information about the proteome of these three plastid types in a plastid protein database named “PLprot”. This database is available at http://www.pb.ethz.ch/proteomics/ and contains a search functions and display options. We suggest that “PLprot” becomes an online source for information about the proteomes of different plastid types.