Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism

TY - JOUR

T1 - Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism

AU - Ito, Jun

AU - Batth, Tanveer S

AU - Petzold, Christopher J

AU - Redding-Johanson, Alyssa M

AU - Mukhopadhyay, Aindrila

AU - Verboom, Robert

AU - Meyer, Etienne H

AU - Millar, A Harvey

AU - Heazlewood, Joshua L

PY - 2011/4/1

Y1 - 2011/4/1

N2 - 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.

AB - 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.

KW - Amino Acid Sequence

KW - Arabidopsis/chemistry

KW - Arabidopsis Proteins/analysis

KW - Cation Exchange Resins

KW - Chromatography, Liquid/methods

KW - Computational Biology

KW - Cytosol/chemistry

KW - Mass Spectrometry/methods

KW - Metabolic Networks and Pathways/physiology

KW - Molecular Sequence Data

KW - Proteome/analysis

U2 - 10.1021/pr1009433

DO - 10.1021/pr1009433

M3 - Journal article

C2 - 21166475

SN - 1535-3893

VL - 10

SP - 1571

EP - 1582

JO - Journal of Proteome Research

JF - Journal of Proteome Research

IS - 4

ER -