title: Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism.
abstract: The plant cell cytosol is a dynamic and complex intracellular matrix that, by definition, contains no compartmentalization. Nonetheless, it maintains a wide variety of biochemical networks and often links metabolic pathways across multiple organelles. There have been numerous detailed proteomic studies of organelles in the model plant Arabidopsis thaliana, although no such analysis has been undertaken on the cytosol. The cytosolic protein fraction from cell suspensions of Arabidopsis thaliana was isolated and analyzed using offline strong cation exchange liquid chromatography and LC-MS/MS. This generated a robust set of 1071 cytosolic proteins. Functional annotation of this set revealed major activities in protein synthesis and degradation, RNA metabolism and basic sugar metabolism. This included an array of important cytosol-related functions, specifically the ribosome, the set of tRNA catabolic enzymes, the ubiquitin-proteasome pathway, glycolysis and associated sugar metabolism pathways, phenylpropanoid biosynthesis, vitamin metabolism, nucleotide metabolism, an array of signaling and stress-responsive molecules, and NDP-sugar biosynthesis. This set of cytosolic proteins provides for the first time an extensive analysis of enzymes responsible for the myriad of reactions in the Arabidopsis cytosol and defines an experimental set of plant protein sequences that are not targeted to subcellular locations following translation and folding in the cytosol.
authors.affiliation: Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road MS978-4101, Berkeley, California 94720, United States.
authors.forename: Jun
authors.initials: J
authors.lastname: Ito
authors.forename: Tanveer S
authors.initials: TS
authors.lastname: Batth
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Petzold
authors.forename: Alyssa M
authors.initials: AM
authors.lastname: Redding-Johanson
authors.forename: Aindrila
authors.initials: A
authors.lastname: Mukhopadhyay
authors.forename: Robert
authors.initials: R
authors.lastname: Verboom
authors.forename: Etienne H
authors.initials: EH
authors.lastname: Meyer
authors.forename: A Harvey
authors.initials: AH
authors.lastname: Millar
authors.forename: Joshua L
authors.initials: JL
authors.lastname: Heazlewood
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000737:chemistry* / Q000166:cytology / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000032:analysis* / Q000235:genetics; D002411:Cation Exchange Resins; D002853:Chromatography, Liquid / Q000379:methods; D019295:Computational Biology; D003600:Cytosol / Q000737:chemistry*; D013058:Mass Spectrometry / Q000379:methods; D053858:Metabolic Networks and Pathways / Q000502:physiology; D008969:Molecular Sequence Data; D020543:Proteome / Q000032:analysis*
chemical_list: D029681:Arabidopsis Proteins; D002411:Cation Exchange Resins; D020543:Proteome