R-loop control and mitochondrial genome stability require the 5′-3′ exonuclease/flap endonuclease OEX1

Maintenance of the plant organelle genomes involves factors mostly inherited from their symbiotic ancestors. In bacteria, DNA polymerase I (Pol I) performs multiple replication and repair functions through its 5'-3'-exonuclease/flap-endonuclease domain. Plant organelles possess 2 DNA polymerases that are evolutionarily derived from Pol I but lack this key domain. ORGANELLAR EXONUCLEASES 1 and 2 (OEX1 and OEX2) compensate for this missing function and are targeted to mitochondria and chloroplasts, respectively, in Arabidopsis (Arabidopsis thaliana). Loss of OEX1 causes developmental and fertility defects that increase with increasing differential segregation of mitochondrial DNA (mtDNA) subgenomes generated by recombination. OEX1 activity is modulated by alternative splicing, which generates 2 isoforms that variably affect mtDNA stability and repair. OEX1 has 5'-3'-exonuclease and flap endonuclease activities, with a high affinity for RNA-DNA hybrids. It rapidly degrades RNA in Okazaki-like structures and R-loops. Consistent with a role in suppressing R-loops, oex1 mutant plants accumulate RNA-DNA hybrids in highly transcribed mtDNA regions. Taken together, our results identify OEX1 as an important factor that compensates for the missing activity of plant organellar polymerases, playing multiple important roles in the processing of replication and recombination intermediates, such as replication primers and R-loops, whose accumulation can lead to genome instability.