CAF Proteins Help SOT1 Regulate the Stability of Chloroplast ndhA Transcripts.

Xiuming Li,Yi Zhang,Wen Zhou,Xiaojing Kang,Xiaopeng Yin,Xiujin Li,Aihong Zhang,Congming Lu,Wenzhen Luo,Chenchen Jiang,Xuemei Wang,Qingqing Zhang

doi:10.3390/ijms222312639

Abstract

Protein-mediated RNA stabilization plays profound roles in chloroplast gene expression. Genetic studies have indicated that chloroplast ndhA transcripts, encoding a key subunit of the NADH dehydrogenase-like complex that mediates photosystem I cyclic electron transport and facilitates chlororespiration, are stabilized by PPR53 and its orthologs, but the underlying mechanisms are unclear. Here, we report that CHLOROPLAST RNA SPLICING 2 (CRS2)-ASSOCIATED FACTOR (CAF) proteins activate SUPPRESSOR OF THYLAKOID FORMATION 1 (SOT1), an ortholog of PPR53 in Arabidopsis thaliana, enhancing their affinity for the 5′ ends of ndhA transcripts to stabilize these molecules while inhibiting the RNA endonuclease activity of the SOT1 C-terminal SMR domain. In addition, we established that SOT1 improves the splicing efficiency of ndhA by facilitating the association of CAF2 with the ndhA intron, which may be due to the SOT1-mediated stability of the ndhA transcripts. Our findings shed light on the importance of PPR protein interaction partners in moderating RNA metabolism.

Highlights

Plant cells harbor extranuclear genomes in organelles such as mitochondria and chloroplasts
We compared the expression level of the chloroplast genes between the wild type (WT) and sot1-3 plants using their RPKM values, revealing that most were increased in the mutant by varying degrees, but the expression levels of 23S ribosomal RNAs (rRNAs), 16S rRNA, 4.5S rRNA, and ndhA were substantially reduced in sot1-3 (Supplementary Figure S2)
This was confirmed using quantitative PCR to explore the stable transcript levels of 12-day-old WT and sot1-3 plants, revealing a similar pattern to the RNA sequencing (RNA-seq) findings (Figure 1). These results confirm the previous findings that SUPPRESSOR OF THYLAKOID FORMATION 1 (SOT1) is involved in the regulation of ndhA expression and the maturation of 23S and 4.5S rRNA in the chloroplasts [23,24]

Summary

Introduction

Plant cells harbor extranuclear genomes in organelles such as mitochondria and chloroplasts. The chloroplast genome carries an average of 120 genes, which encode pivotal components of the photosynthetic apparatus and its transcriptional and translational machineries; the regulation of gene expression in chloroplasts is important for chloroplast biogenesis [1,2]. The proper expression of chloroplast genes requires the import of hundreds of proteins encoded by nuclear genes, thereby creating a coordinated regulation of nuclear and plastid genes [4]. One such example is the nuclear-encoded pentatricopeptide repeat (PPR) family of proteins, characterized by tandem repeats of a degenerate 35–amino acid helical motif [5,6]. The expansion of the PPR family may represent an evolutionary adaption for diverse organellar RNA metabolisms, such as protein-mediated RNA stabilization, RNA cleavage, RNA editing, and RNA splicing [6]

Methods

Results

Conclusion