title: Novel modes of RNA editing in mitochondria.
abstract: Gene structure and expression in diplonemid mitochondria are unparalleled. Genes are fragmented in pieces (modules) that are separately transcribed, followed by the joining of module transcripts to contiguous RNAs. Some instances of unique uridine insertion RNA editing at module boundaries were noted, but the extent and potential occurrence of other editing types remained unknown. Comparative analysis of deep transcriptome and genome data from Diplonema papillatum mitochondria reveals ∼220 post-transcriptional insertions of uridines, but no insertions of other nucleotides nor deletions. In addition, we detect in total 114 substitutions of cytosine by uridine and adenosine by inosine, amassed into unusually compact clusters. Inosines in transcripts were confirmed experimentally. This is the first report of adenosine-to-inosine editing of mRNAs and ribosomal RNAs in mitochondria. In mRNAs, editing causes mostly amino-acid additions and non-synonymous substitutions; in ribosomal RNAs, it permits formation of canonical secondary structures. Two extensively edited transcripts were compared across four diplonemids. The pattern of uridine-insertion editing is strictly conserved, whereas substitution editing has diverged dramatically, but still rendering diplonemid proteins more similar to other eukaryotic orthologs. We posit that RNA editing not only compensates but also sustains, or even accelerates, ultra-rapid evolution of genome structure and sequence in diplonemid mitochondria.
authors.affiliation: Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics; Université de Montréal, Montreal, H3C 3J7, Canada.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Moreira
authors.affiliation: Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics; Université de Montréal, Montreal, H3C 3J7, Canada.
authors.forename: Matus
authors.initials: M
authors.lastname: Valach
authors.affiliation: Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics; Université de Montréal, Montreal, H3C 3J7, Canada.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Aoulad-Aissa
authors.affiliation: Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, D-04109, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Otto
authors.affiliation: Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics; Université de Montréal, Montreal, H3C 3J7, Canada Gertraud.Burger@umontreal.ca.
authors.forename: Gertraud
authors.initials: G
authors.lastname: Burger
mesh_terms: D000241:Adenosine / Q000378:metabolism; D003641:Deamination; D056898:Euglenozoa / Q000235:genetics* / Q000378:metabolism; D050259:Genes, Mitochondrial; D020459:Genes, rRNA; D007288:Inosine / Q000378:metabolism; D008928:Mitochondria / Q000235:genetics*; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D017393:RNA Editing; D000077278:RNA, Mitochondrial; D020040:Trans-Splicing; D059467:Transcriptome
chemical_list: D000077278:RNA, Mitochondrial; D007288:Inosine; D012313:RNA; D000241:Adenosine