Abstract
Plastoglobules (PGs) in chloroplasts are thylakoid-associated monolayer lipoprotein particles containing prenyl and neutral lipids and several dozen proteins mostly with unknown functions. An integrated view of the role of the PG is lacking. Here, we better define the PG proteome and provide a conceptual framework for further studies. The PG proteome from Arabidopsis (Arabidopsis thaliana) leaf chloroplasts was determined by mass spectrometry of isolated PGs and quantitative comparison with the proteomes of unfractionated leaves, thylakoids, and stroma. Scanning electron microscopy showed the purity and size distribution of the isolated PGs. Compared with previous PG proteome analyses, we excluded several proteins and identified six new PG proteins, including an M48 metallopeptidase and two Absence of bc1 complex (ABC1) atypical kinases, confirmed by immunoblotting. This refined PG proteome consisted of 30 proteins, including six ABC1 kinases and seven fibrillins together comprising more than 70% of the PG protein mass. Other fibrillins were located predominantly in the stroma or thylakoid and not in PGs; we discovered that this partitioning can be predicted by their isoelectric point and hydrophobicity. A genome-wide coexpression network for the PG genes was then constructed from mRNA expression data. This revealed a modular network with four distinct modules that each contained at least one ABC1K and/or fibrillin gene. Each module showed clear enrichment in specific functions, including chlorophyll degradation/senescence, isoprenoid biosynthesis, plastid proteolysis, and redox regulators and phosphoregulators of electron flow. We propose a new testable model for the PGs, in which sets of genes are associated with specific PG functions.
Highlights
Plastoglobules (PGs) in chloroplasts are thylakoid-associated monolayer lipoprotein particles containing prenyl and neutral lipids and several dozen proteins mostly with unknown functions
(1) What determines and controls their size, shape, and content? (2) How are proteins recruited to the PG proteome, and how does the PG proteome change in response to changes in developmental state or (a)biotic conditions? (3) What are the functions of the PG proteins, and how are they related to each other? This study aims to provide a better framework to help answer these questions by defining a functional network
We identified a number of new PG proteins, including an M48 metallopeptidase (M48), two additional Absence of bc1 complex kinase (ABC1K) proteins, and a senescenceassociated gene (SAG) protein
Summary
Plastoglobules (PGs) in chloroplasts are thylakoid-associated monolayer lipoprotein particles containing prenyl and neutral lipids and several dozen proteins mostly with unknown functions. PGs can be released from the thylakoid membrane by sonication, and purification based on their low density has facilitated the analysis of their metabolites (Lohmann et al, 2006; Vidi et al, 2006; Gaude et al, 2007; Zbierzak et al, 2010) and protein composition (Vidi et al, 2006; Ytterberg et al, 2006). PGs appear to play a role in chloroplast development, senescence, and stress defense Their shrinking and swelling in response to (a)biotic stresses and during developmental transitions, as well as in plastid biogenesis mutants, are well documented (Gaude et al, 2007; Simkin et al, 2007; Singh et al, 2010; Zhang et al, 2010). The surprising localization of M48, as well as two ABC1K proteins, to PGs was confirmed by immunoblotting
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