Elucidating a "theoretical" proteome of the Arabidopsis thaliana thylakoid

Olof Emanuelsson
Stockholm Center for Physics, Astronomy and Biotechnology,
Stockholm University,
Stockholm Bioinformatics Center,
S-106 91 Stockholm
Sweden
telephone: +46-8-5537 8574
fax: +46-8-5537 8214
email: olof@sbc.su.se
prestype: Platform
presenter: Olof Emanuelsson

Olof Emanuelsson (1), Jean-Benoit Peltier (2), Gunnar von Heijne (1), Klaas J. van Wijk (2);
(1) Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden.
(2) Department of Plant Biology, Cornell University, Ithaca, NY, USA.

The Arabidopsis thaliana genome offers nice opportunities to develop and test whole-genome based approaches to theoretical proteomics. Using subcellular localization predictions (TargetP followed by SignalP-HMM) and subsequent transmembrane predictions (TMHMM 2.0), we have predicted the total proteome size of the lumen of the chloroplast sub-compartment thylakoid to be somewhere between 200 and 500 different proteins, whereof a substantial part lacks any functional annotation and approximately 50% contain a TAT-pathway signal. We have also evaluated the combined predictor approach in several ways, specifically addressing the SignalP performance on the signal peptide-like thylakoidal transfering domain adjacent to the chloroplast transit peptide, and it has been clear that a thylakoid-dedicated signal peptide predictor would be useful.