Natural Variation in Sensitivity to a Loss of Chloroplast Translation in Arabidopsis    

Abstract

Mutations that eliminate chloroplast translation in Arabidopsis (Arabidopsis thaliana) result in embryo lethality. The stage of embryo arrest, however, can be influenced by genetic background. To identify genes responsible for improved growth in the absence of chloroplast translation, we examined seedling responses of different Arabidopsis accessions on spectinomycin, an inhibitor of chloroplast translation, and crossed the most tolerant accessions with embryo-defective mutants disrupted in chloroplast ribosomal proteins generated in a sensitive background. The results indicate that tolerance is mediated by ACC2, a duplicated nuclear gene that targets homomeric acetyl-coenzyme A carboxylase to plastids, where the multidomain protein can participate in fatty acid biosynthesis. In the presence of functional ACC2, tolerance is enhanced by a second locus that maps to chromosome 5 and heightened by additional genetic modifiers present in the most tolerant accessions. Notably, some of the most sensitive accessions contain nonsense mutations in ACC2, including the "Nossen" line used to generate several of the mutants studied here. Functional ACC2 protein is therefore not required for survival in natural environments, where heteromeric acetyl-coenzyme A carboxylase encoded in part by the chloroplast genome can function instead. This work highlights an interesting example of a tandem gene duplication in Arabidopsis, helps to explain the range of embryo phenotypes found in Arabidopsis mutants disrupted in essential chloroplast functions, addresses the nature of essential proteins encoded by the chloroplast genome, and underscores the value of using natural variation to study the relationship between chloroplast translation, plant metabolism, protein import, and plant development.Embryo development in Arabidopsis (Arabidopsis thaliana) requires the coordinated expression of a large number of essential genes (Muralla et al., 2011). Recessive mutations that disrupt these nuclear genes result in an embryodefective (emb) mutant phenotype (Meinke, 2013). Many EMB genes of Arabidopsis encode chloroplast-localized proteins involved in basic metabolism, protein import, and chloroplast gene expression (Hsu et al., 2010;Bryant et al., 2011;Savage et al., 2013). Functional plastids are therefore required for embryo development in Arabidopsis. Mutations that disrupt photosynthesis alone interfere with embryo and seedling pigmentation, not embryo development. Multiple examples of EMB genes that encode chloroplast-localized aminoacyl-tRNA synthetases, RNA-binding proteins, translation factors, and ribosomal proteins have been described in the literature (Berg et al., 2005;Bryant et al., 2011;Muralla et al., 2011;Romani et al., 2012;Tiller and Bock, 2014). Translation of some chloroplast-encoded mRNAs is therefore essential for seed development. This raises a basic question: which chloroplast genes are required? In this report, we used natural variation and genetic analysis to evaluate the model (Bryant et al., 2011) that a single chloro...

Positive Selection in Rapidly Evolving Plastid–Nuclear Enzyme Complexes

“…Duplication of the homomeric ACCase and retargeting to the plastids has occurred repeatedly and independently during angiosperm evolution ( Figure S3). The observed duplication in our data set preceded the divergence between Agrostemma and Silene, but it was independent from similar duplications in grasses (Konishi and Sasaki 1994) and the Brassicaceae (Schulte et al 1997;Babiychuk et al 2011;Parker et al 2014).…”

“…Together, these enzymes convert acetyl-CoA to malonyl-CoA within the plastid, which is the first step in the fatty acid biosynthesis pathway (White et al 2005). In some lineages, the homomeric ACCase has undergone a duplication, and one copy is targeted to the plastid while the other remains in the cytosol (Konishi and Sasaki 1994;Schulte et al 1997;Babiychuk et al 2011;Parker et al 2014).…”

Analysis of Arabidopsis Accessions Hypersensitive to a Loss of Chloroplast Translation

“…Most grasses lack the heteromeric enzyme altogether and instead utilize a plastid-localized homomeric enzyme produced from a duplicated nuclear gene (Konishi and Sasaki, 1994;Chalupska et al, 2008). Previously, we showed that natural variation in the response of Arabidopsis embryos and seedlings to a loss of chloroplast translation is mediated by ACC2, and that tolerant accessions likely contain functional ACC2 along with an unlinked enhancer of ACC2 function and modifiers that extend the growth response (Parker et al, 2014). Overall, the focus of that initial study was on identifying factors that improved survival in the absence of chloroplast translation.…”

“…Weak alleles exhibit altered cuticular wax composition, cold sensitivity, and glossy inflorescence stems (Lü et al, 2011;Amid et al, 2012). Loss of the heteromeric, chloroplast-localized enzyme, by contrast, results in early embryo lethality (Li et al, 2011), with the stage of arrest dependent on genetic background (Parker et al, 2014). In some members of the Brassicaceae, including Arabidopsis, a tandem ACC1 gene duplication enables the production of a chloroplasttargeted homomeric enzyme (ACC2) that can partially suppress the early lethality associated with a loss of chloroplast translation and the absence of heteromeric ACCase (Yanai et al, 1995;Babiychuk et al, 2011;Bryant et al, 2011).…”

YCF1: A Green TIC: Response to the de Vries et al. Commentary

“…As illustrated in Figure 1, in addition to the major photosynthetic-type TIC (i.e., the green TIC containing Ycf1 that predominantly functions in green tissues), there appears to be an alternative nonphotosynthetic-type minor TIC import system for a certain subset of proteins. This system includes the Tic20 paralog Tic20-IV in Arabidopsis but lacks Tic56, Tic100, and Tic214 (Hirabayashi et al, 2011;Kikuchi et al, 2013;Parker et al, 2014;Nakai, 2015). Experimental data shown in recent work by Kö hler et al (2015) provide support for this model of more than one TIC complex.…”