The number of tRNAs encoded in plant mitogenomes varies considerably, with some lineages exhibiting rapid reductions. Loss of these bacterial-like mitochondrial tRNAs necessitates the import of nuclear-encoded counterparts that share little sequence similarity, raising questions about the identity and trafficking of enzymes necessary for the maturation and function of these newly imported tRNAs. In particular, the aminoacyl tRNA synthetases (aaRSs) that charge tRNAs are usually divided into distinct classes that specialize on either organellar or cytosolic tRNAs. Here, we investigated the evolution of aaRS subcellular localization in five species from a plant lineage (Sileneae) that has experienced extensive and rapid mitochondrial tRNA loss. By analyzing full-length mRNA transcripts (PacBio Iso-Seq), we found predicted retargeting of many ancestrally cytosolic aaRSs to the mitochondrion as well as scenarios where enzyme localization does not appear to change despite functional tRNA replacement. In most cases of transit peptide acquisition, the cytosolic enzyme gained a coding extension prior to the loss of the cognate mitochondrial tRNAs - suggesting a transitional state where organellar and cytosolic aaRSs colocalize to mitochondria. The ongoing functional replacement of Sileneae mitochondrial tRNAs and subsequent evolution of tRNA-interacting enzymes present an opportunity to study the coevolutionary dynamics of plant cytonuclear genetics.

The number of tRNAs encoded in plant mitochondrial genomes varies considerably. Ongoing loss of bacterial-like mitochondrial tRNA genes in many lineages necessitates the import of nuclear-encoded counterparts that share little sequence similarity. Because tRNAs are involved in highly specific molecular interactions, this replacement process raises questions about the identity and trafficking of enzymes necessary for the maturation and function of newly imported tRNAs. In particular, the aminoacyl-tRNA synthetases (aaRSs) that charge tRNAs are usually divided into distinct classes that specialize on either organellar (mitochondrial and plastid) or nuclear-encoded (cytosolic) tRNAs. Here, we investigate the evolution of aaRS subcellular localization in a plant lineage (Sileneae) that has experienced extensive and rapid mitochondrial tRNA loss. By analyzing full-length mRNA transcripts (PacBio Iso-Seq), we found predicted retargeting of many ancestrally cytosolic aaRSs to the mitochondrion and confirmed these results with colocalization microscopy assays. However, we also found cases where aaRS localization does not appear to change despite functional tRNA replacement, suggesting evolution of novel interactions and charging relationships. Therefore, the history of repeated tRNA replacement in Sileneae mitochondria reveals that differing constraints on tRNA/aaRS interactions may determine which of these alternative coevolutionary paths is used to maintain organellar translation in plant cells.

This article comments on: Chustecki JM, Etherington RD, Gibbs DJ, Johnston IG. 2022. Altered collective mitochondrial dynamics in the Arabidopsis msh1 mutant compromising organelle DNA maintenance. Journal of Experimental Botany 73, 5428–5439. Plant mitochondrial DNA (mtDNA) can become damaged in many ways. A major repair mechanism is homologous recombination, which requires an undamaged DNA template. Presumably, this template comes from a different mitochondrion in the same cell. Plant mitochondria undergo fission and fusion to form transient networks which could allow the exchange of genetic information. To test this hypothesis, Chustecki et al. (2022) used msh1 mutants with defective DNA repair, and showed that mitochondrial interactions increased, revealing a link between the physical and genetic behavior of mitochondria.