title: Whole-transcriptome RNA-seq, gene set enrichment pathway analysis, and exon coverage analysis of two plastid RNA editing mutants.
abstract: In land plants, plastid and mitochondrial RNAs are subject to post-transcriptional C-to-U RNA editing. T-DNA insertions in the ORGANELLE RNA RECOGNITION MOTIF PROTEIN6 gene resulted in reduced photosystem II (PSII) activity and smaller plant and leaf sizes. Exon coverage analysis of the ORRM6 gene showed that orrm6-1 and orrm6-2 are loss-of-function mutants. Compared to other ORRM proteins, ORRM6 affects a relative small number of RNA editing sites. Sanger sequencing of reverse transcription-PCR products of plastid transcripts revealed 2 plastid RNA editing sites that are substantially affected in the orrm6 mutants: psbF-C77 and accD-C794. The psbF gene encodes the β subunit of cytochrome b559, an essential component of PSII. The accD gene encodes the β subunit of acetyl-CoA carboxylase, a protein required in plastid fatty acid biosynthesis. Whole-transcriptome RNA-seq demonstrated that editing at psbF-C77 is nearly absent and the editing extent at accD-C794 was significantly reduced. Gene set enrichment pathway analysis showed that expression of multiple gene sets involved in photosynthesis, especially photosynthetic electron transport, is significantly upregulated in both orrm6 mutants. The upregulation could be a mechanism to compensate for the reduced PSII electron transport rate in the orrm6 mutants. These results further demonstrated that Organelle RNA Recognition Motif protein ORRM6 is required in editing of specific RNAs in the Arabidopsis (Arabidopsis thaliana) plastid.
authors.affiliation: a Department of Biological Sciences , Western Michigan University , Kalamazoo , MI , USA.
authors.forename: Justin B
authors.identifier: 0000-0001-6532-4522
authors.initials: JB
authors.lastname: Hackett
authors.affiliation: a Department of Biological Sciences , Western Michigan University , Kalamazoo , MI , USA.
authors.forename: Yan
authors.identifier: 0000-0002-3374-7376
authors.initials: Y
authors.lastname: Lu
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D004269:DNA, Bacterial / Q000235:genetics; D005091:Exons / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D045332:Photosystem II Protein Complex / Q000378:metabolism; D018087:Plastids / Q000235:genetics*; D017393:RNA Editing / Q000235:genetics*; D000067776:RNA Recognition Motif Proteins / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; D004269:DNA, Bacterial; C000623372:ORRM6 protein, Arabidopsis; D045332:Photosystem II Protein Complex; D000067776:RNA Recognition Motif Proteins; D018749:RNA, Plant; C036483:T-DNA
keywords: Arabidopsis thaliana; Sanger sequencing; exon coverage analysis; generally applicable gene-set enrichment for pathway analysis; organelle RNA recognition motif; plastid RNA editing; wholetranscriptome RNA-seq