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bioRxiv · 10.64898/2025.12.04.692323

The mitochondrial splicing factor PPR9 encoded by the AT1G03560 gene-locus is essential for the maturation of several nad transcripts in Arabidopsis plants

Kobaivanov, E.·Kitel, M.·Matan, R.·Mizrahi, R.·Carmi, N.·Ostersetzer-Biran, O.
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Abstract

The biogenesis of plant mitochondria and their respiratory machinery relies on the transcription and proper processing of primary transcripts into functional, mature organellar RNAs. This includes the removal of introns that reside within many essential organellar genes, an essential step in mitochondria gene-expression that relies on the coordinated action of nuclear-encoded RNA-binding cofactors, such as members of the pentatricopeptide repeat (PPR) protein family. Here, we report the analysis of PPR9 (At1g03560), a mitochondrial P-type PPR protein originally identified in genetic screens for essential protein cofactors. Loss of PPR9 function results in embryonic arrest at early stages of seed development. Nevertheless, homozygous ppr9 mutants can be maintained using a modified embryo-rescue method. The rescued ppr9 mutants display delayed germination and growth retardation associated with mitochondrial dysfunctions. Molecular analyses of ppr9 plantlets reveal that PPR9 is required for the splicing of several mitochondrial transcripts encoding respiratory subunits, including nad2 intron 3 and nad7 introns 1 and 2. Accordingly, defects in the processing of nad2 and nad7 pre-RNAs in ppr9 mutant plantlets impair the biogenesis of respiratory complex I (CI), disrupt OXPHOS activity, and consequently affect plants growth and development. Together, these findings identify PPR9 as a key regulator of mt-RNA maturation in Arabidopsis, enabling CI biogenesis and cellular energy metabolism, and further highlight the roles of nuclear-encoded RNA-processing factors in coordinating mitochondria functions and (early) plant growth and development. Significance statementOur study identifies PPR9 as a key mitochondrial RNA-processing factor required for the splicing of multiple group II introns that reside within genes encoding subunits essential for respiratory complex I biogenesis in Arabidopsis. By linking nuclear control of RNA maturation to mitochondrial function and plant development, this work emphasizes a critical layer of coordination between organellar gene expression, energy metabolism, and developmental regulation in land plants.

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Kobaivanov, E., Kitel, M., Matan, R., Mizrahi, R., Carmi, N., Ostersetzer-Biran, O.. 2025-12-05. The mitochondrial splicing factor PPR9 encoded by the AT1G03560 gene-locus is essential for the maturation of several nad transcripts in Arabidopsis plants. https://doi.org/10.64898/2025.12.04.692323

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