Chloroplast ATP synthase biogenesis requires peripheral stalk subunits AtpF and ATPG and stabilization of atpE mRNA by OPR protein MDE1

SUMMARY Chloroplast ATP synthase contains subunits of plastid and nuclear genetic origin. To investigate the coordinated biogenesis of this complex, we isolated novel ATP synthase mutants in the green alga Chlamydomonas reinhardtii by screening for high light sensitivity. We report here the characterization of mutants affecting the two peripheral stalk subunits b and b′, encoded respectively by the atpF and ATPG genes, and of three independent mutants which identify the nuclear factor MDE1, required to stabilize the chloroplast‐encoded atpE mRNA. Whole‐genome sequencing revealed a transposon insertion in the 3′UTR of ATPG while mass spectrometry shows a small accumulation of functional ATP synthase in this knock‐down ATPG mutant. In contrast, knock‐out ATPG mutants, obtained by CRISPR‐Cas9 gene editing, fully prevent ATP synthase function and accumulation, as also observed in an atpF frame‐shift mutant. Crossing ATP synthase mutants with the ftsh1‐1 mutant of the major thylakoid protease identifies AtpH as an FTSH substrate, and shows that FTSH significantly contributes to the concerted accumulation of ATP synthase subunits. In mde1 mutants, the absence of atpE transcript fully prevents ATP synthase biogenesis and photosynthesis. Using chimeric atpE genes to rescue atpE transcript accumulation, we demonstrate that MDE1, a novel octotricopeptide repeat (OPR) protein, genetically targets the atpE 5′UTR. In the perspective of the primary endosymbiosis (~1.5 Gy), the recruitment of MDE1 to its atpE target exemplifies a nucleus/chloroplast interplay that evolved rather recently, in the ancestor of the CS clade of Chlorophyceae, ~300 My ago. Significance statement Using screening and CRISPR‐Cas9 genome editing in Chlamydomonas reinhardtii, we generate the as‐yet missing ATP synthase mutant of subunit ATPG and show the absolute requirement of the AtpF‐ATPG heterodimer to form the peripheral stalk. We also identify the nucleus‐encoded MDE1 gene, establishing this octotricopeptide protein as an essential trans‐acting factor ensuring the stability of atpE transcript, widely conserved among the Reinhardtinia clade of Chlorophyceae algae.