GUN1 influences the accumulation of NEP‐dependent transcripts and chloroplast protein import in Arabidopsis cotyledons upon perturbation of chloroplast protein homeostasis

Abstract

Summary Correct chloroplast development and function require co‐ordinated expression of chloroplast and nuclear genes. This is achieved through chloroplast signals that modulate nuclear gene expression in accordance with the chloroplast's needs. Genetic evidence indicates that GUN1, a chloroplast‐localized pentatricopeptide repeat (PPR) protein with a C‐terminal Small MutS‐Related (SMR) domain, is involved in integrating multiple developmental and stress‐related signals in both young seedlings and adult leaves. Recently, GUN1 was found to interact physically with factors involved in chloroplast protein homeostasis, and with enzymes of tetrapyrrole biosynthesis in adult leaves that function in various retrograde signalling pathways. Here we show that following perturbation of chloroplast protein homeostasis: (i) by growth in lincomycin‐containing medium; or (ii) in mutants defective in either the FtsH protease complex (ftsh), plastid ribosome activity (prps21‐1 and prpl11‐1) or plastid protein import and folding (cphsc70‐1), GUN1 influences NEP‐dependent transcript accumulation during cotyledon greening and also intervenes in chloroplast protein import.

GUN1 and Plastid RNA Metabolism: Learning from Genetics

“…Conversely, the expression levels of nucleus-encoded RNA polymerase (NEP)-dependent transcripts of genes, encoding the core subunits of the PEP enzymes ( rpoA , rpoB , rpoC1 ), ribosomal subunits ( rps2 and rps15 ), y cf1 (translocon at inner envelope membrane of chloroplasts 214), and clpP1 (a subunit of the 350-kDa chloroplast Clp complex), increase significantly ( Figure 1 ). A similar plastid gene expression pattern is observed in seedlings impaired in plastid transcript maturation ( pdm1 ; [ 25 ]) and in seedlings grown in the presence of Lin (Col-0 + Lin) or altered in plastid protein synthesis by depletion of plastid ribosomal proteins [ 14 ]. Strikingly, gun1 cotyledons have shown a limited increase in the accumulation of NEP-dependent transcripts when grown in the presence of Lin ( gun1 + Lin, [ 14 ]; see also Figure 1 ) and when the gun1 mutation is introgressed into genetic backgrounds lacking plastid ribosomal subunits [ 14 ].…”

“…A similar plastid gene expression pattern is observed in seedlings impaired in plastid transcript maturation ( pdm1 ; [ 25 ]) and in seedlings grown in the presence of Lin (Col-0 + Lin) or altered in plastid protein synthesis by depletion of plastid ribosomal proteins [ 14 ]. Strikingly, gun1 cotyledons have shown a limited increase in the accumulation of NEP-dependent transcripts when grown in the presence of Lin ( gun1 + Lin, [ 14 ]; see also Figure 1 ) and when the gun1 mutation is introgressed into genetic backgrounds lacking plastid ribosomal subunits [ 14 ]. Furthermore, the same set of NEP-dependent transcripts is highly downregulated after treatment of gun1 seedlings with NF ( gun1 + NF), but their levels do not exhibit major changes in Col-0 + NF and gun5 + NF seedlings, implying a specific role for GUN1 in NEP-dependent transcript accumulation ( Figure 1 ).…”

“…GUN1 does not appear to bind directly to RNAs [ 17 ], unlike typical PPR proteins [ 17 ]. But it is targeted to an organelle, the chloroplast, and has recently been reported by two independent laboratories to influence plastid transcript accumulation [ 13 , 14 , 15 ]. In particular, following perturbation of PEP activity, a peculiar pattern of plastid transcription, designated as the “ Δ-rpo phenotype”, is typically observed in different plant species [ 14 , 18 , 19 , 20 ].…”

“…But it is targeted to an organelle, the chloroplast, and has recently been reported by two independent laboratories to influence plastid transcript accumulation [ 13 , 14 , 15 ]. In particular, following perturbation of PEP activity, a peculiar pattern of plastid transcription, designated as the “ Δ-rpo phenotype”, is typically observed in different plant species [ 14 , 18 , 19 , 20 ]. For example, Arabidopsis seedlings lacking proteins required for PEP-mediated transcription and regulation, such as sigma factors ( sig6 ; [ 21 ]), PEP-associated proteins ( pap2 and pap8 ; [ 22 ]), and the plastid redox insensitive 2 ( prin2 ) protein [ 23 , 24 ], show a decrease in the expression of genes, coding for subunits of the photosynthetic apparatus ( petB , psaB , psbA , psbB , psbC , psbD , rbcL ), which are normally transcribed by PEP (see Figure 1 ).…”

“…Here, we propose a new model for GUN1 function in plastids and GUN1-mediated retrograde communication, which integrates the interactions observed between GUN1 and the machinery that controls plastid protein homeostasis with the recently discovered role of GUN1 in plastid RNA metabolism [ 12 , 13 , 14 , 15 , 16 ]. The many additive phenotypic effects and the very few suppressor phenotypes observed in higher-order (compound) mutants containing gun1 together with mutations affecting various aspects of plastid protein homeostasis, sugar sensing, and plastid osmosis can all be interpreted as pleiotropic phenotypic effects of a primary alteration in plastid transcription and plastid transcript editing attributable to the lack of the GUN1 protein under conditions that would otherwise trigger plastid-to-nucleus retrograde communication.…”