Non-redundant functions of three CRM proteins in mitochondrial group II intron splicing and maize seed development

Group II introns are abundant in plant mitochondrial genomes and require numerous nuclear-encoded RNA-binding proteins for their splicing. Chloroplast RNA splicing and ribosome maturation (CRM) proteins constitute an evolutionarily conserved RNA-binding protein family, yet their intron splicing specificity and underlying molecular mechanisms remain poorly understood. Here, we show that three mitochondria-localized CRM proteins play non-redundant roles in mitochondrial group II intron splicing and maize seed development. Genome-wide analysis identifies 16 maize CRM genes, which are classified into four subfamilies and harbor variable numbers of CRM domains. ZmCFM5 and ZmmCSF2 are targeted to mitochondria, whereas ZmCFM3 exhibits dual localization to mitochondria and chloroplasts. Loss-of-function mutants of these three CRM genes display impaired intron splicing and arrested seed development. ZmCFM5 mediates the splicing of nad1 intron4 and nad4 intron1, while ZmmCSF2 and ZmCFM3 act on nad5 intron4 and nad1 intron2, respectively. The cfm5 mutant exhibits abnormal mitochondrial morphology and reduced complex I activity. ZmCFM5 specifically binds to a conserved motif within domain V of target introns and physically interacts with the splicing factor ZmSPR2. Our findings support a model wherein CRM proteins cooperate with other RNA-binding proteins to assemble dynamic ribonucleoprotein complexes, which confer splicing specificity and efficiency to group II introns.