RETRACTED ARTICLE:The Arabidopsis NOT4A E3 ligase promotes PGR3 expression and regulates chloroplast translation

Mark Bailey,Aiste Ivanauskaite,Oluwatunmise Akintewe,Ross D Etherington,Julia Grimmer,Paula Mulo,Anne-Marie Labandera,Adrienne C Payne,Daniel J Gibbs,Rory Osborne,Marjaana Rantala,Sacha Baginsky

doi:10.1038/s41467-020-20506-4

Abstract

Chloroplast function requires the coordinated action of nuclear- and chloroplast-derived proteins, including several hundred nuclear-encoded pentatricopeptide repeat (PPR) proteins that regulate plastid mRNA metabolism. Despite their large number and importance, regulatory mechanisms controlling PPR expression are poorly understood. Here we show that the Arabidopsis NOT4A ubiquitin-ligase positively regulates the expression of PROTON GRADIENT REGULATION 3 (PGR3), a PPR protein required for translating several thylakoid-localised photosynthetic components and ribosome subunits within chloroplasts. Loss of NOT4A function leads to a strong depletion of cytochrome b6f and NAD(P)H dehydrogenase (NDH) complexes, as well as plastid 30 S ribosomes, which reduces mRNA translation and photosynthetic capacity, causing pale-yellow and slow-growth phenotypes. Quantitative transcriptome and proteome analysis of the not4a mutant reveal it lacks PGR3 expression, and that its molecular defects resemble those of a pgr3 mutant. Furthermore, we show that normal plastid function is restored to not4a through transgenic PGR3 expression. Our work identifies NOT4A as crucial for ensuring robust photosynthetic function during development and stress-response, through promoting PGR3 production and chloroplast translation.

Highlights

Chloroplast function requires the coordinated action of nuclear- and chloroplast-derived proteins, including several hundred nuclear-encoded pentatricopeptide repeat (PPR) proteins that regulate plastid mRNA metabolism
We show that NOT4A is required for expression of the PPR protein PROTON GRADIENT REGULATION 3 (PGR3), a nuclear-encoded factor that is imported into plastids to promote cytochrome b6f and NAD(P)H dehydrogenase (NDH) complex production, and ribosome biogenesis30–33. not4a mutants, which have severely depleted PGR3 levels, resemble null pgr[3] mutants, having reduced abundance of plastid RNAs that are normally targeted by PGR3 and a depletion of 30 S ribosomes
We found that NOT4A expression was upregulated when seedlings were grown in the presence of lincomycin, suggesting NOT4A expression is controlled by plastid-to-nucleus retrograde signalling during chloroplast translational stress (Fig. 4e)

Summary

Introduction

Chloroplast function requires the coordinated action of nuclear- and chloroplast-derived proteins, including several hundred nuclear-encoded pentatricopeptide repeat (PPR) proteins that regulate plastid mRNA metabolism. Despite their large number and importance, regulatory mechanisms controlling PPR expression are poorly understood. We show that the Arabidopsis NOT4A ubiquitin-ligase positively regulates the expression of PROTON GRADIENT REGULATION 3 (PGR3), a PPR protein required for translating several thylakoidlocalised photosynthetic components and ribosome subunits within chloroplasts. We show that NOT4A is required for expression of the PPR protein PGR3, a nuclear-encoded factor that is imported into plastids to promote cytochrome b6f and NDH complex production, and ribosome biogenesis. Our work identifies NOT4A as an important mediator of PPR controlled plastid translation, uncovering a new layer of homeostatic and stress-responsive regulation controlling chloroplast form and function

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Results

Conclusion