Experimental Analysis of the Arabidopsis Mitochondrial Proteome Highlights Signaling and Regulatory Components, Provides Assessment of Targeting Prediction Programs, and Indicates Plant-Specific Mitochondrial Proteins  [W]

Abstract

A novel insight into Arabidopsis mitochondrial function was revealed from a large experimental proteome derived by liquid chromatography-tandem mass spectrometry. Within the experimental set of 416 identified proteins, a significant number of low-abundance proteins involved in DNA synthesis, transcriptional regulation, protein complex assembly, and cellular signaling were discovered. Nearly 20% of the experimentally identified proteins are of unknown function, suggesting a wealth of undiscovered mitochondrial functions in plants. Only approximately half of the experimental set is predicted to be mitochondrial by targeting prediction programs, allowing an assessment of the benefits and limitations of these programs in determining plant mitochondrial proteomes. Maps of putative orthology networks between yeast, human, and Arabidopsis mitochondrial proteomes and the Rickettsia prowazekii proteome provide detailed insights into the divergence of the plant mitochondrial proteome from those of other eukaryotes. These show a clear set of putative cross-species orthologs in the core metabolic functions of mitochondria, whereas considerable diversity exists in many signaling and regulatory functions.

Proteomic Analysis of Chloroplast-to-Chromoplast Transition in Tomato Reveals Metabolic Shifts Coupled with Disrupted Thylakoid Biogenesis Machinery and Elevated Energy-Production Components

“…The percentage of proteins predicted by all three programs is only 7.3% (142). Previous reports have indicated similar proportions of mitochondrial proteins predicted in common by four prediction programs (Heazlewood et al, 2004). Predotar and TargetP were the closest in terms of predictions with 485 proteins in common.…”

A reference map of the Arabidopsis thaliana mature pollen proteome

“…This number is essentially in accordance with the respective transcriptome data (see below). A large set of unclassified proteins was also found in recent plant, human, and yeast mitochondrial proteome analyses [28][29][30] and interpreted as an indication for a putative wealth of as yet undiscovered mitochondrial functions. By analogy, presence of a major set of proteins with unknown functions in pollen may hint at as yet unidentified cellular processes, of which some might be specific for the male gametophyte.…”

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

“…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.…”