title: The potato tuber mitochondrial proteome.
abstract: Mitochondria are called the powerhouses of the cell. To better understand the role of mitochondria in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from dormant potato tubers (Solanum tuberosum 'Folva') and their proteome investigated. Proteins were resolved by one-dimensional gel electrophoresis, and tryptic peptides were extracted from gel slices and analyzed by liquid chromatography-tandem mass spectrometry using an Orbitrap XL. Using four different search programs, a total of 1,060 nonredundant proteins were identified in a quantitative manner using normalized spectral counts including as many as 5-fold more "extreme" proteins (low mass, high isoelectric point, hydrophobic) than previous mitochondrial proteome studies. We estimate that this compendium of proteins represents a high coverage of the potato tuber mitochondrial proteome (possibly as high as 85%). The dynamic range of protein expression spanned 1,800-fold and included nearly all components of the electron transport chain, tricarboxylic acid cycle, and protein import apparatus. Additionally, we identified 71 pentatricopeptide repeat proteins, 29 membrane carriers/transporters, a number of new proteins involved in coenzyme biosynthesis and iron metabolism, the pyruvate dehydrogenase kinase, and a type 2C protein phosphatase that may catalyze the dephosphorylation of the pyruvate dehydrogenase complex. Systematic analysis of prominent posttranslational modifications revealed that more than 50% of the identified proteins harbor at least one modification. The most prominently observed class of posttranslational modifications was oxidative modifications. This study reveals approximately 500 new or previously unconfirmed plant mitochondrial proteins and outlines a facile strategy for unbiased, near-comprehensive identification of mitochondrial proteins and their modified forms.
authors.affiliation: Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211.
authors.forename: Fernanda
authors.initials: F
authors.lastname: Salvato
authors.forename: Jesper F
authors.initials: JF
authors.lastname: Havelund
authors.forename: Mingjie
authors.initials: M
authors.lastname: Chen
authors.forename: R Shyama Prasad
authors.initials: RS
authors.lastname: Rao
authors.forename: Adelina
authors.initials: A
authors.lastname: Rogowska-Wrzesinska
authors.forename: Ole N
authors.initials: ON
authors.lastname: Jensen
authors.forename: David R
authors.initials: DR
authors.lastname: Gang
authors.forename: Jay J
authors.initials: JJ
authors.lastname: Thelen
authors.forename: Ian Max
authors.initials: IM
authors.lastname: Møller
mesh_terms: D017360:Arabidopsis / Q000378:metabolism; D002853:Chromatography, Liquid; D030562:Databases, Protein; D005453:Fluorescence; D008928:Mitochondria / Q000378:metabolism*; D024101:Mitochondrial Proteins / Q000737:chemistry / Q000378:metabolism; D010455:Peptides / Q000378:metabolism; D019441:Plant Epidermis / Q000166:cytology; D010940:Plant Proteins / Q000737:chemistry / Q000378:metabolism; D035281:Plant Tubers / Q000378:metabolism*; D011499:Protein Processing, Post-Translational; D021381:Protein Transport; D020543:Proteome / Q000737:chemistry / Q000378:metabolism*; D011198:Solanum tuberosum / Q000378:metabolism*; D013347:Subcellular Fractions / Q000378:metabolism; D053719:Tandem Mass Spectrometry; D014026:Nicotiana / Q000166:cytology
chemical_list: D024101:Mitochondrial Proteins; D010455:Peptides; D010940:Plant Proteins; D020543:Proteome