An improved prediction of chloroplast proteins reveals diversities and commonalities in the chloroplast proteomes of Arabidopsis and rice

Abstract

Proteins that form part of the chloroplast proteome can be identified by computational prediction of the N-terminal presequences (chloroplast transit peptides, cTPs) of their cytoplasmic precursor proteins. The accuracy of four different cTP predictors has been evaluated on a test set of 4500 proteins whose subcellular localization is known, and was found to be substantially lower than previously reported. A combination of cTP prediction programs was superior to any one of the predictors alone. This combination was employed to estimate the size and composition of the chloroplast proteomes of Arabidopsis and rice, and about 2,100 (Arabidopsis thaliana) and 4800 (Oryza sativa) different chloroplast proteins with a cTP are predicted to be encoded by their nuclear genomes. A subset of around 900 chloroplast proteins, predominantly derived from the cyanobacterial endosymbiont and with functions mostly related to metabolism, energy and transcription, is shared by the two species. This points to the existence of both conserved nucleus-encoded chloroplast proteins that are predominantly of prokaryotic origin, and a large fraction of taxon-specific chloroplast-targeted proteins, in flowering plants. D

Analysis of 101 nuclear transcriptomes reveals 23 distinct regulons and their relationship to metabolism, chromosomal gene distribution and co-ordination of nuclear and plastid gene expression

“…Many associations of regulons to specific functions or subcellular locations might have gone, however, undetected in our study due to incomplete A. thaliana gene annotation. The experimental and computational prediction of subcellular protein targeting is also still error-prone (Richly et al, 2003b;Richly and Leister, 2004).…”

“…Assignment of subcellular location to the encoded proteins was based on experimental evidence (Kruft et al, 2001;Friso et al, 2004;Heazlewood et al, 2004;Kleffmann et al, 2004) or on stringent computational prediction of subcellular targeting (Richly et al, 2003b;Richly and Leister, 2004). A list of all 1590 genes contained in the 23 regulons, as well as their assignment to functional classes and the subcellular location of the encoded proteins, is provided as Supplementary Material 2.…”

“…Assignment was based on experimental evidence (Kruft et al, 2001;Friso et al, 2004;Heazlewood et al, 2004;Kleffmann et al, 2004) or on stringent computational prediction of subcellular targeting (Richly et al, 2003b;Richly and Leister, 2004). Because the location of only a minority of chloroplast and mitochondrial proteins has been reliably experimentally determined, and because the computational prediction applied was of high specificity but relatively low sensitivity (Richly et al, 2003b;Richly and Leister, 2004), our classification underestimates the number of proteins located in chloroplasts or mitochondria (it follows that in Fig.…”

Genomics-based dissection of the cross-talk of chloroplasts with the nucleus and mitochondria in Arabidopsis

“…Nitric oxide and ascorbate have been proposed to act as mitochondrion-to-plastid signals (reviewed in: Raghavendra and Padmasree, 2003). Numbers of chloroplast (¨3000) and mitochondrial (¨2000) proteins encoded in the nucleus are according to Richly and Leister (2004c). A selection of chloroplast properties, discussed in the frame of experiments addressing signalling within chloroplasts and with the potential to be also involved in retrograde signalling, is listed in the green circle: DpH, pH-gradient between thylakoid lumen and stroma; ATP/ADP, ratio of ATP and ADP; NADPH/NADP, ratio of NADPH and NADP; PQH/PQ, redox state of the plastoquinone pool; GSH, glutathione; Trx, thioredoxins.…”

“…This implies that the successful establishment of the chloroplast organelle was paralleled by a substantial change in the composition of the proteomes of all cellular compartments (Leister and Schneider, 2004). At present, the Arabidopsis chloroplast is predicted to contain between 2500 and 3000 proteins, of which about half is of cyanobacterial origin (Richly and Leister, 2004c).…”