Localization and RNA Binding of Mitochondrial Aminoacyl tRNA Synthetases

Abstract

Mitochondria contain a complete translation machinery that is used to translate its internally transcribed mRNAs. This machinery uses a distinct set of tRNAs that are charged with cognate amino acids inside the organelle. Interestingly, charging is executed by aminoacyl tRNA synthetases (aaRS) that are encoded by the nuclear genome, translated in the cytosol, and need to be imported into the mitochondria. Here, we review import mechanisms of these enzymes with emphasis on those that are localized to both mitochondria and cytosol. Furthermore, we describe RNA recognition features of these enzymes and their interaction with tRNA and non-tRNA molecules. The dual localization of mitochondria-destined aaRSs and their association with various RNA types impose diverse impacts on cellular physiology. Yet, the breadth and significance of these functions are not fully resolved. We highlight here possibilities for future explorations.

Keywords: RNA recognition; aminoacyl tRNA synthetase; mitochondria; mitochondria import; mitochondria targeting signal; tRNA; translation.

Figure 1

Protein import into mitochondria. (A) Mitochondria-destined proteins are translated by cytosolic ribosomes and maintained in an unfolded state by various chaperones. Many of these (including all mitochondrial aminoacyl tRNA synthetases (mt-aaRSs)) bare an N-terminal Mitochondria Targeting Signal (MTS, blue spheres) that enables recognition by protein a receptor on the mitochondria outer membrane (Tom20 for mt-aaRSs). Recognition is followed by insertion through the Tom40 pore and distribution into mitochondria sub-compartments. All mt-aaRSs are transferred through the Translocase of the Inner Membrane (TIM) into the matrix. The MTS of many matrix destined proteins, such as mt-aaRSs, is removed and cleaved by the Mitochondrial Processing Protease (MPP), resulting in a mature, MTS-deficient enzyme. (B) Mitochondria proteins can also be imported by a mechanism that involves localized translation near the mitochondria outer membrane [31]. The nascent MTS can interact with Tom20 while the protein is being translated. Furthermore, ribosome-associated chaperones (i.e., Nascent chain Associated Complex (NAC)) can interact with an outer membrane protein (OM14) and support protein import. Finally, the RNA-binding protein Puf3 protein assists in mRNA localization to mitochondria, presumably through interaction with the outer membrane. Notably, while all mt-aaRS mRNAs appear to localize near mitochondria, this localization is only partially affected by Puf3 or Tom20 deletion (Table 1), suggesting a novel mechanism for localization.

Figure 2

Saccharomyces cerevisiae mt-aaRS predicted-MTS and its conservation. The hundred N terminal amino acids of each S. cerevisiae mitochondrial aaRS were aligned to their human, Mus musculus, Danio rerio, Schizosaccharomyces pombe (when available) orthologs [51]. Consensus sequence is indicated above aligned sequences. Also indicated are the positions of the S. cerevisiae amphipathic helix (continues boxes), Tom20 recognition sequence (dashed red boxes) and Mitochondrial Processing Protease (MPP) cleavage site (arrowheads), predicted by MitoFates [45]. Note that MTS sequence conservation is very low and conserved regions are usually functional domains downstream to the MPP. A higher resolution image is provided as a supplementary material (Supplementary Figure S1).

Figure 3

Schematic depiction of mechanisms for aaRS dual targeting. (A) A single gene can generate two transcripts by selection of alternative transcription initiation sites. One of the transcripts contains a coding region for an MTS, and leads to synthesis of mitochondria-destined protein, while the other transcript is devoid of this region hence the protein is retained in the cytosol. (B) A single pre-mRNA can generate two mature mRNAs by alternative splicing. An exon is retained in one of the transcripts and leads to synthesis of an MTS-bearing protein, which is destined to mitochondria. (C) A single mature mRNA can be translated into two proteins, through switching of the translation machinery between two start codons. (D) A single translated protein can have a weak or hidden MTS, which leads to partial retention in the cytosol.