GUN1 and Plastid RNA Metabolism: Learning from Genetics

Abstract

GUN1 (genomes uncoupled 1), a chloroplast-localized pentatricopeptide repeat (PPR) protein with a C-terminal small mutS-related (SMR) domain, plays a central role in the retrograde communication of chloroplasts with the nucleus. This flow of information is required for the coordinated expression of plastid and nuclear genes, and it is essential for the correct development and functioning of chloroplasts. Multiple genetic and biochemical findings indicate that GUN1 is important for protein homeostasis in the chloroplast; however, a clear and unified view of GUN1's role in the chloroplast is still missing. Recently, GUN1 has been reported to modulate the activity of the nucleus-encoded plastid RNA polymerase (NEP) and modulate editing of plastid RNAs upon activation of retrograde communication, revealing a major role of GUN1 in plastid RNA metabolism. In this opinion article, we discuss the recently identified links between plastid RNA metabolism and retrograde signaling by providing a new and extended concept of GUN1 activity, which integrates the multitude of functional genetic interactions reported over the last decade with its primary role in plastid transcription and transcript editing.

Keywords: GUN1; RNA polymerase; retrograde signaling; transcript accumulation; transcript editing.

Figure 2

Schematic overview of the role of GUN1 protein during the early stages of chloroplast biogenesis. (a) Under optimal conditions, i.e., environmental and genetic conditions, the abundance of the GUN1 protein is rather low, and no GUN1-dependent negative retrograde signal is sent from the developing chloroplasts to the nucleus to downregulate the expression of PhANGs. As a result, proper chloroplast biogenesis occurs in cotyledons and leaves. (b) Under conditions that alter plastid activity, i.e., genetic defects that impair plastid gene expression (PGE), plastid protein homeostasis (proteostasis), sugar sensing, and plastid osmosis, the abundance of GUN1 protein increases in developing chloroplasts. As a consequence, NEP activity is favored over PEP, changes in plastid RNA editing levels take place, and a GUN1-dependent negative signal reaches the nucleus and reduces expression of PhANGs. In this scenario, seedlings show defects in chloroplast development, photosynthetic performance, and growth. (c) The importance of the GUN1 protein in chloroplast biogenesis becomes evident when the gun1 mutation is introgressed into Arabidopsis mutants with defects in PGE, proteostasis, sugar sensing, and maintenance of plastid osmosis. Under these conditions, chloroplast biogenesis is altered, and the GUN1-dependent negative retrograde signal is absent. These conditions, in most of the analyzed cases (20 out of 31, 64.5%), result in exacerbated phenotypes, characterized by a marked reduction in leaf pigmentation and reduced photosynthetic performance and growth. Only in few cases (25.8%), the lack of GUN1 protein fails to cause additive phenotypic effects, while in the remaining three cases (9.7%), lack of GUN1 suppresses the mutant phenotypes. pl, proplastid; nu, nucleus; chl, chloroplast.

Figure 1

Expression analyses of a subset of PEP- and NEP-dependent plastid genes in different genetic backgrounds and after treatments that alter PEP activity. Values are expressed as the logarithm of the fold-change (log₂-FC) relative to wild-type seedlings grown under optimal conditions. Data are retrieved from the literature in the case of sig6 [26], pap2 and pap8 [27], prin2 [23], and pdm1 (pigment-deficient mutant 1) [28] and from the GEO public repository in the case of gun1, Col-0 + Lin, gun1 + Lin (GEO accession GSE5770; [2]), Col-0 + NF, gun1 + NF, and gun5 + NF (GEO accession GSE12887;[2]). Lincomycin treatment of wild-type Arabidopsis seedlings (Col-0 + Lin) leads to a drop in PEP-dependent transcript accumulation. As an adaptive response, NEP-dependent transcript levels are increased in plastids, giving rise to what is known as the “Δ-rpo phenotype”. Similar behavior is observed in mutants, such as sig6, pap2, pap8, prin2, and pdm1, which lack either nucleus-encoded plastid proteins required for PEP activity (SIG6, PAP2, PAP8, PRIN2) or mRNA maturation factors (PDM1). However, gun1 seedlings grown in the presence of lincomycin (gun1 + Lin) show an impaired “Δ-rpo phenotype”: i.e., NEP-dependent transcripts show a very limited degree of upregulation. Similarly to lincomycin, gun1 seedlings grown on norflurazon-containing medium (gun1 + NF) undergo severe repression of PEP-dependent genes, and repression is even more pronounced if NEP-dependent transcripts are considered. On the contrary, Col-0 and gun5 (genomes uncoupled 5) seedlings in the presence of norflurazon (Col-0 + NF and gun5 + NF) show a wild-type-like plastid gene expression, indicating that the drastically reduced accumulation of PEP- and NEP-dependent transcripts upon NF treatment is a characteristic of the gun1 genetic background.