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1. Rewiring of aminoacyl-tRNA synthetase localization and interactions in plants with extensive mitochondrial tRNA gene loss

   https://doi.org/10.1093/molbev/msad163  

   Warren, Jessica M ; Broz, Amanda K ; Martinez-Hottovy, Ana ; Elowsky, Christian ; Christensen, Alan C ; Sloan, Daniel B ( July 2023 , Molecular Biology and Evolution)

   Warren, Jessica (Ed.)

   Abstract 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. 

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2. Importance of a tRNA anticodon loop modification and a conserved, noncanonical anticodon stem pairing in tRNA CGG Pro for decoding

   https://doi.org/10.1074/jbc.RA119.007410  

   Nguyen, Ha An ; Hoffer, Eric D. ; Dunham, Christine M. ( April 2019 , Journal of Biological Chemistry)
3. Rapid Shifts in Mitochondrial tRNA Import in a Plant Lineage with Extensive Mitochondrial tRNA Gene Loss

   https://doi.org/10.1093/molbev/msab255  

   Warren, Jessica M ; Salinas-Giegé, Thalia ; Triant, Deborah A ; Taylor, Douglas R ; Drouard, Laurence ; Sloan, Daniel B ( August 2021 , Molecular Biology and Evolution)

   Purugganan, Michael (Ed.)

   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. 

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4. Reversible inactivation of yeast mitochondrial phenylalanyl-tRNA synthetase under oxidative stress

   https://doi.org/10.1016/j.bbagen.2018.04.023  

   Chakraborty, Shruti ; Ganguli, Sayak ; Chowdhury, Aritra ; Ibba, Michael ; Banerjee, Rajat ( May 2018 , Biochimica et Biophysica Acta (BBA) - General Subjects)
5. Structural basis for tRNA-dependent cysteine biosynthesis

   https://doi.org/10.1038/s41467-017-01543-y  

   Chen, Meirong ; Kato, Koji ; Kubo, Yume ; Tanaka, Yoshikazu ; Liu, Yuchen ; Long, Feng ; Whitman, William B. ; Lill, Pascal ; Gatsogiannis, Christos ; Raunser, Stefan ; et al ( December 2017 , Nature Communications)