Rapid shifts in mitochondrial tRNA import in a plant lineage with extensive mitochondrial tRNA gene loss

Abstract

In most eukaryotes, transfer RNAs (tRNAs) are one of the very few classes of genes remaining in the mitochondrial genome, but some mitochondria have lost these vestiges of their prokaryotic ancestry. Sequencing of mitogenomes from the flowering plant genus Silene previously revealed a large range in tRNA gene content, suggesting rapid and ongoing gene loss/replacement. Here, we use this system to test longstanding hypotheses about how mitochondrial tRNA genes are replaced by importing nuclear-encoded tRNAs. We traced the evolutionary history of these gene loss events by sequencing mitochondrial genomes from key outgroups (Agrostemma githago and Silene [=Lychnis] chalcedonica). We then performed the first global sequencing of purified plant mitochondrial tRNA populations to characterize the expression of mitochondrial-encoded tRNAs and the identity of imported nuclear-encoded tRNAs. We also confirmed the utility of high-throughput sequencing methods for the detection of tRNA import by sequencing mitochondrial tRNA populations in a species (Solanum tuberosum) with known tRNA trafficking patterns. Mitochondrial tRNA sequencing in Silene revealed substantial shifts in the abundance of some nuclear-encoded tRNAs in conjunction with their recent history of mt-tRNA gene loss and surprising cases where tRNAs with anticodons still encoded in the mitochondrial genome also appeared to be imported. These data suggest that nuclear-encoded counterparts are likely replacing mitochondrial tRNAs even in systems with recent mitochondrial tRNA gene loss, and the redundant import of a nuclear-encoded tRNA may provide a mechanism for functional replacement between translation systems separated by billions of years of evolutionary divergence.

PlantRNA 2.0: an updated database dedicated to tRNAs of photosynthetic eukaryotes

“…Interestingly, even only considering embryophytes, there is a great fluctuation in their number: from 0 in the lycophyte S. moellendorffii to 126 in the basal angiosperm A. trichopoda . To compensate for the lack of mitochondria‐encoded tRNAs, this likely implies mitochondrial import of a full set of nuclear‐encoded tRNAs in the lycophyte, a process experimentally demonstrated in several photosynthetic organisms (Warren et al., 2021). Conversely, the high number of mitochondria‐encoded tRNAs in A. trichopoda reflects the presence of numerous horizontal transfers of foreign mitochondrial DNA from green algae, mosses and angiosperms (Rice et al., 2013).…”

Aminoacyl-tRNA synthetase evolution within the dynamic tripartite translation system of plant cells

“…Despite the recent and major changes in subcellular targeting of tRNAs and aaRSs in Sileneae (Warren, et al 2021;Warren, et al 2022), we found little evidence that this rewiring of tRNA interaction networks has created positive selection for changes in aaRS protein sequence (Tables 1 and 2). One possible explanation for this apparently limited effect is that Sileneae organellar aaRS enzymes that have evolved to charge a newly imported cytosolic tRNA substrate were already preadapted to successfully recognize these tRNAs and, thus, required few changes to enzyme sequence.…”

“…The extent of cytosolic import varies among plant species as there is recent and ongoing mt tRNA gene loss in many lineages. The angiosperm tribe Sileneae is a striking example, with some species retaining as many as 14 mt tRNA genes while other close relatives have only two or three (Warren, et al 2021).…”

PlantRNA 2.0: an updated database dedicated to tRNAs of photosynthetic eukaryotes

“…Interestingly, even only considering embryophytes, there is a great fluctuation in their number: from 0 in the lycophyte Selaginella moellendorffii to 126 in the basal angiosperm Amborella trichopoda . To compensate for the lack of mitochondria-encoded tRNAs, this likely implies mitochondrial import of a full set of nuclear-encoded tRNAs in the lycophyte, a process experimentally demonstrated in several photosynthetic organisms (26). Conversely, the high number of mitochondria-encoded tRNAs in A. trichopoda reflects the presence of numerous horizontal transfers of foreign mitochondrial DNA from green algae, mosses and angiosperms (27).…”