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

Abstract

Supplemental Table S1. Co-expressed genes and their functional annotation (from PPDB for 34 PG proteins in co-expression networks at different threshold levels from ATTEDII (ath-u.1 for ATATH8) (downloaded August 2020).(A) Top 100 most tightly co-expressed genes for all PG baits with their Logit Score Mutual Rank and annotations and membership to the top20 and threshold networks.(B) Non-redundant list of the Top 100 most tightly co-expressed genes for all PG baits and their annotations and membership to the top20 and threshold networks. Supplemental Figure S1. Side-by-side comparison on top20 mRNA co-expression forced networks for the PG proteome from this study and our previous study (Lundquist et al 2012). (A) Top20 network based for 34 PG proteins on combined micro-array and RNA-seq based gene expression data using the 20 genes with the highest correlation values (Logit Score Mutual Rank).Details for all co-expressors and correlations are listed in Supplemental Table S1. (B) Top20 network for 25 PG proteins based on only microarray data from Metaomgraph from Lundquist et al 2012. Supplemental Figure S2. mRNA co-expression forced network (L≥5) for the extended PG proteome (34 baits) based on combined micro-array and RNA-seq based gene expression data and minimal threshold correlation value (ath-u.1 for ATATH8) from ATTEDII. Details for all coexpressors and their baits are listed in Supplemental Table S1.

Proteomics, phylogenetics, and coexpression analyses indicate novel interactions in the plastid CLP chaperone-protease system

“…Finally, fibrillins 1A and 1B were highly enriched in the CLPC1-TRAP. These fibrillins mostly function as components of plastoglobules and they respond to a wide range of abiotic stress conditions, but their molecular function is not known ( 39 ). The enriched proteins described above are candidate substrates for degradation by CLPPR protease and less likely to function as CLP substrate adaptors or regulators.…”

More than just lipid balls: quantitative analysis of plastoglobule attributes and their stress-related responses

“…Thus, changes in particular components have been observed in response to a specific stress as is the case of high light stress, that induces little but specific alterations in proteins and prenyl lipids (Espinoza-Corral et al 2021 ). In addition, changes in specific FBNs can be observed upon different stressors (Singh and McNellis 2011 ), and relate to specific metabolic pathways, depending as well on plant tissue type (Michel et al 2021 ).…”

“…However, the characterisation of its proteome in 2006 revealed an unexpectedly active metabolic role (Vidi et al 2006 ; Ytterberg et al 2006 ). Since then, the physiological roles of PGs have been the subject of several reviews (Bréhélin and Kessler 2008 ; Eugeni Piller et al 2012 ; Nacir and Bréhélin 2013 ; Rottet et al 2015 ; van Wijk and Kessler 2017 ; Wójtowicz and Gieczewska 2020 ; Michel et al 2021 ).…”

“…Among them, some major functional groups can be identified (Lundquist et al 2012 ; Nacir and Bréhélin 2013 ): structural proteins, kinases, transporters and enzymes involved in the breakdown of carotenoids, chlorophyll and lipids, and in the biosynthesis of jasmonate, carotenoids and prenylquinones. Overall, PG metabolome and proteome can be integrated in four major physiological modules (Lundquist et al 2012 ; Michel et al 2021 ): chlorophyll degradation, thylakoid remodelling, biosynthesis of prenylquinones and carotenoid metabolism. Within their proteome some of the identified proteins are: tocopherol cyclase (VTE1), involved in the biosynthesis of tocopherol and plastochromanol-8 (Porfirova et al 2002 ; Vidi et al 2006 ); NAD(P)H dehydrogenase C1 (NDC1) that reduces the plastoquinone pool in PGs (Eugeni Piller et al 2011 ); carotenoid cleavage dioxygenase (CCD4) implicated in carotenoid catabolism (Huang et al 2009 ); and phytol ester synthase 1 (PES1) and 2 (PES2), which participate in the formation of phytyl ester derived from chlorophyll and of fatty acids derived from galactolipids (Lippold et al 2012 ).…”

“Omics” insights into plastid behavior toward improved carotenoid accumulation

“…Most of the work related to the plastid proteome has been conducted on chloroplasts, including sub-organelle protein localization for the thylakoid and lumen as well as the stroma, envelope, and plastoglobules ( Wojtowicz and Gieczewska, 2020 ; Zhu et al., 2022 ). Sub-plastidial proteomic studies locate most carotenogenic enzymes in chloroplast envelopes ( Figure 2 ) ( Vishnevetsky et al., 1999 ; Michel et al., 2021 ), with ZEP being found both in envelopes and thylakoids, whereas VDE appears only in the latter ( Sun et al., 2018 ). According to proteomic analysis of chloroplasts, lycopene cyclization, responsible for the formation of β-carotene, lutein, and zeaxanthin, occurs in the envelope membranes ( Facchinelli and Weber, 2011 ).…”