Tissue-type specific accumulation of the plastoglobular proteome, transcriptional networks and plastoglobular functions

Abstract

Plastoglobules (PGs) are dynamic protein-lipid micro-compartments in plastids enriched for isoprenoid-derived metabolites. Chloroplast PGs support formation, remodeling and controlled dismantling of thylakoids during developmental transitions and environmental responses. However, the specific molecular functions of most PG proteins are still poorly understood. This study harnesses recent co-mRNA expression from ATTED-II using combined microarray and RNAseq information on an updated inventory of 34 PG proteins, as well as proteomics data across 30 Arabidopsis tissue types from ATHENA. Hierarchical clustering based on relative abundance for the PG proteins across non-photosynthetic and photosynthetic tissue types showed their coordinated protein accumulation across Arabidopsis parts, tissue types, development and senescence. We generated multiple mRNA-based networks by applying different coefficient thresholds; functional enrichment was determined for each network and PG gene. Combined analysis of these stringency networks identified a central hub and four peripheral modules. Enrichment of specific nuclear transcription factors (e.g. Golden2-like) and support for cross-talk between PGs and the plastid gene expression was observed, and specific ABC1 kinases seem part of a light signaling network. Examples of other specific findings are that FBN7b is involved with upstream steps of tetrapyrrole biosynthesis and that ABC1K9 is involved in starch metabolism. HighlightThe plastoglobular proteome shows coherent tissue-specific accumulation, whereas combined analysis of transcriptional co-expression networks, at different stringencies and following in-depth functional annotation, associate selected plastoglobular proteins to specific metabolic functions.