Autophagy mutants show delayed chloroplast development during de-etiolation in carbon limiting conditions

Autophagy is a conserved catabolic process that plays an essential role under nutrient starvation condition and influences different developmental processes. We observed that seedlings of autophagy mutants (atg2, atg5, atg7, and atg9) germinated in the dark showed delayed chloroplast development following illumination. The delayed chloroplast development was characterized by a decrease in photosynthetic and chlorophyll biosynthetic proteins, lower chlorophyll content, reduced chloroplast size, and increased levels of proteins involved in lipid biosynthesis. Confirming the biological impact of these differences, photosynthetic performance was impaired in autophagy mutants 12h post illumination. We observed that while gene expression for photosynthetic machinery during de-etiolation was largely unaffected in atg mutants, several genes involved in photosystem assembly were transcriptionally downregulated. We also investigated if the delayed chloroplast development could be explained by lower lipid import to the chloroplast or lower triglyceride (TAG) turnover. We observed that the limitations in the chloroplast lipid import imposed by trigalactosyldiacylglycerol1 are unlikely to explain the delay in chloroplast development. However, we found that lower TAG mobility in the triacylglycerol lipase mutant sugardependent1 significantly affected de-etiolation. Moreover, we showed that lower levels of carbon resources exacerbated the slow-greening phenotype whereas higher levels of carbon resources had an opposite effect. This work suggests a lack of autophagy machinery limits chloroplast development during de-etiolation, and this is exacerbated by limited lipid turnover (lipophagy) that physically or energetically restrains chloroplast development. Overall design: We used Arabidopsis (Arabidopsis thaliana) seeds of Col-0 as WT, four autophagic mutants atg2-1 (SALK_076727, Yoshimoto et al. 2009), atg5-1 (SAIL_129B07, Chen et al. 2015), atg7-2 (GABI_655B06, Lai et al. 2011) and atg9-2 (SALK_130796, Zhuang et al. 2017) which we referred as atg2, atg5, atg7 and atg9 respectively, a lipid thylakoid permease mutant tgd1 (Xu et al., 2003), a TAG lipase mutant (sugar-dependent 1-4) sdp1-4 (Eastmond, 2006; Fan et al., 2017) and the respective lipid and autophagy double mutants tgd1atg2-1, tgd1 atg5-1, sdp1atg2-1, and sdp1 atg5-1 (Fan et al., 2019). Seeds were surface-sterilized and carefully dispensed on a stainless-steel wire mesh platform (mesh size 1 mm; 3 cm x 3 cm x 3 cm) layered previously with 1% sterilized agarose in a round plastic vessel containing 300 mL of liquid medium (1/4- strength Murashige and Skoog -MS- medium without vitamins, 1/4- strength Gamborg B5 vitamins solution, 2 mM MES, 1% [w/v] sucrose, pH 5.8). Seeds were grown for five days in the dark, then transferred to light (100-125 µE) at 22oC. Samples were collected in biological triplicate at 0, 12, and 24 post-illumination.