title: Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulatory components, provides assessment of targeting prediction programs, and indicates plant-specific mitochondrial proteins.
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.
authors.affiliation: Plant Molecular Biology Group, School of Biomedical and Chemical Sciences, University of Western Australia, Crawley 6009, Western Australia, Australia.
authors.forename: Joshua L
authors.initials: JL
authors.lastname: Heazlewood
authors.forename: Julian S
authors.initials: JS
authors.lastname: Tonti-Filippini
authors.forename: Alexander M
authors.initials: AM
authors.lastname: Gout
authors.forename: David A
authors.initials: DA
authors.lastname: Day
authors.forename: James
authors.initials: J
authors.lastname: Whelan
authors.forename: A Harvey
authors.initials: AH
authors.lastname: Millar
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000032:analysis / Q000378:metabolism; D002352:Carrier Proteins / Q000378:metabolism; D002736:Chloroplasts / Q000378:metabolism; D019295:Computational Biology; D018744:DNA, Plant / Q000235:genetics / Q000378:metabolism; D016208:Databases, Factual; D045222:Electron Transport Chain Complex Proteins / Q000378:metabolism; D006801:Humans; D013058:Mass Spectrometry; D024101:Mitochondrial Proteins / Q000032:analysis / Q000378:metabolism*; D020675:Peroxisomes / Q000378:metabolism; D020543:Proteome / Q000032:analysis / Q000378:metabolism*; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D029681:Arabidopsis Proteins; D002352:Carrier Proteins; D018744:DNA, Plant; D045222:Electron Transport Chain Complex Proteins; D024101:Mitochondrial Proteins; D020543:Proteome; D018749:RNA, Plant