Disturbed RNA editing in MORF3-deficient Arabidopsis mitochondria leads to impaired assembly of complex I

Transcripts in plant mitochondria and chloroplasts undergo editing prior to translation, with approximately 500 specific sites edited in mitochondria and about 30 in plastids of the model plant Arabidopsis (Arabidopsis thaliana). Although the full role of this mechanism is not yet understood, it is presumed to compensate for unfavorable mutations accumulated over evolutionary periods. It is also conceivable that RNA editing serves a regulatory function, as proteins can be translated from partially unedited transcripts. In this study, we characterize proteins derived from such mitochondrial transcripts. To enrich these proteins, we use an Arabidopsis multiple organellar RNA editing factor 3 (MORF3) mutant, which exhibits reduced RNA editing at numerous specific sites. Despite developmental delays, the mutant plants remain fertile. Physiological and biochemical analyses reveal that complex I of the respiratory chain is particularly affected in the mutants. Consistent with these findings, a shotgun proteomic analysis identified proteins originating from partially unedited NADH dehydrogenase subunit 2 (nad2) and nad7 transcripts. Complexome profiling revealed that these proteins integrate into the holo-complex and, to a lesser extent, into the supercomplex formed by complex I and dimeric complex III. Concurrently, known assembly intermediates of complex I are enriched in the mutant. We demonstrate that the disruption of complex I assembly is caused by the absence of editing at specific sites in transcripts encoding the subunits Nad3 and Nad4L. Our results provide deep insights into the molecular consequences of perturbations within the respiratory complex I.