PPR protein PDM1/SEL1 is involved in RNA editing and splicing of plastid genes in Arabidopsis thaliana

Abstract

After transcription, most chloroplast precursor RNAs undergo further post-transcriptional processing including cleavage, editing, and splicing. Previous investigation has shown that the cleavage of the rpoA transcript and most editing sites, including accD-1, are defective in the knockout mutant of PDM1/SEL1, a PLS-type PPR protein, and that PDM1 is associated with the rpoA transcript. In this work, we found that the splicing of group II introns in trnK and ndhA is also affected in pdm1. Co-immunoprecipitation mass spectrometry experiments were performed to identify proteins that are associated with PDM1. We obtained 126 non-redundant proteins, of which MORF9 was reported to be involved in RNA editing in chloroplast. Yeast two-hybrid assays showed that PDM1 interacts directly with MORF9, MORF2, and MORF8. RNA immunoprecipitation showed that PDM1 associates with the transcripts of trnK and ndhA, as well as accD-1, suggesting that PDM1 is involved in RNA editing and splicing. Therefore, PDM1 is an important protein for post-transcriptional regulation in chloroplast.

An evolutionarily conserved P‐subfamily pentatricopeptide repeat protein is required to splice the plastid ndhA transcript in the moss Physcomitrella patens and Arabidopsis thaliana

“…For instance, a mutation of the Arabidopsis PLS-class PPR gene PIGMENT-DEFICIENT MUTANT 1 (PDM1), which is also known as SEEDLING LETHAL 1 (SEL1) (Pyo et al, 2013), resulted in splicing deficient of ndhA, trnK and rps12-2 introns (Zhang et al, 2015). Splicing efficiency of the ndhA transcript in the pdm1-1 mutant was reduced to 10% relative to that in WT plants (Zhang et al, 2015). SEL1 protein has previously been shown to be an RNA editing factor for accD sites (Pyo et al, 2013).…”

“…On the other hand, the PLS-subfamily proteins mostly function as RNA editing site-recognition factors for both mitochondrial and plastid transcripts Takenaka et al, 2013;Ichinose and Sugita, 2017). Besides, some PLS members are reportedly required for RNA splicing of specific transcripts (Chateigner-Boutin et al, 2011;Ichinose et al, 2012;Zhang et al, 2015). Thus, both subfamilies bind to RNAs in a gene-specific manner and contribute to various RNA processing steps (Barkan and Small, 2014).…”

Fsr1, a striatin homologue, forms an endomembrane‐associated complex that regulates virulence in the maize pathogen Fusarium verticillioides

“…FvSel1 has six Sel1 repeats, similar to the Hrd3 protein in S. cerevisiae; however, the lengths of the repeated sequences and the number of repetitions can vary in different prokaryotes and eukaryotes (Mittl and Schneider-Brachert, 2007). Homologues of the Sel1 protein have been identified in several higher eukaryotes including humans, Drosophila melanogaster and A. thaliana (Mittl and Schneider-Brachert, 2007;Zhang et al, 2015). In S. cerevisiae, there are at least three SLR proteins identified (Hrd1, Hrd3 and Chs4) with functional annotations.…”

“…SLR proteins have been reported to be involved in the ER-associated protein degradation (ERAD) in S. cerevisiae and A. thaliana under stressinducing conditions (Gardner et al, 2000;Kamauchi et al, 2005). Significantly, recent studies have shown that A. thaliana Sel1 is involved in RNA editing and splicing of plastid genes (Pyo et al, 2013;Zhang et al, 2015).…”

C1 Metabolism and Photorespiration of <i>Ficus deltoidea</i> based on Peptide Mass Fingerprinting Approach

“…Pentatricopeptide repeat (PPR) protein family is one of the major plant RNA-binding proteins for post-transcriptional control. The post-transcriptional processing steps involve RNA processing, editing, and splicing before translation [26]. Proteins containing PPR motifs will participate in translation initiation by binding to specific sequence elements in the 50UTR of mRNAs.…”