Dysregulated 3′-end processing of 18S pre-rRNA decreases mtPNPase efficiency in plant mitochondria

In plant mitochondria, mitochondrial polynucleotide phosphorylase (mtPNPase) is a key 3'→5' exoribonuclease. Here, we describe the accumulation of mtPNPase substrates in Arabidopsis mutants, such as rps10 (deficient in the mitoribosomal protein uS10m), mtran1-2/2-2 (lacking the mitoribosomal proteins mTRAN1 and mTRAN2), and rpoTmp (deficient in plastid- and mitochondrial-targeted RNA polymerase). This accumulation is not due to a reduced mtPNPase expression; instead, all three mutants exhibit perturbations in mitoribosome biogenesis associated with inefficient mtPNPase-dependent 3'-end processing of 18S pre-ribosomal RNA. We propose a spatial sequestration model in which mtPNPase becomes trapped by incompletely matured 18S precursors, limiting its availability for other substrates. In addition, the rps10 mutant displays a partial shift of both mtPNPase and mitoribosomes from membrane-associated to soluble fractions, suggesting a mutant-specific alteration that may further modulate mtPNPase function. Together, these findings demonstrate that proper mitochondrial small-subunit (mtSSU) biogenesis is essential for effective mtPNPase function and balanced mitochondrial RNA metabolism. Thus, mitoribosomes act not only as translation machines but also as regulators of mitochondrial RNA homeostasis, linking ribosome biogenesis to the composition and turnover of the mitochondrial transcriptome.