PNPASE and RNA trafficking into mitochondria

Abstract

The mitochondrial genome encodes a very small fraction of the macromolecular components that are required to generate functional mitochondria. Therefore, most components are encoded within the nuclear genome and are imported into mitochondria from the cytosol. Understanding how mitochondria are assembled, function, and dysfunction in diseases requires detailed knowledge of mitochondrial import mechanisms and pathways. The import of nucleus-encoded RNAs is required for mitochondrial biogenesis and function, but unlike pre-protein import, the pathways and cellular machineries of RNA import are poorly defined, especially in mammals. Recent studies have shown that mammalian polynucleotide phosphorylase (PNPASE) localizes in the mitochondrial intermembrane space (IMS) to regulate the import of RNA. The identification of PNPASE as the first component of the RNA import pathway, along with a growing list of nucleus-encoded RNAs that are imported and newly developed assay systems for RNA import studies, suggest a unique opportunity is emerging to identify the factors and mechanisms that regulate RNA import into mammalian mitochondria. Here we summarize what is known in this fascinating area of mitochondrial biogenesis, identify areas that require further investigation, and speculate on the impact unraveling RNA import mechanisms and pathways will have for the field going forward. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.

Fig. 1

PNPASE structural domains are conserved between species. PNPASEs contain two RNase PH domains that are homologous to the bacterial tRNA processing enzyme, RNase PH, and these domains catalyze RNA degradation. The alpha helical domain (H) is unique to PNPASE, and the KH and S1 domain at the C terminus bind RNA. In contrast to bacteria and other mammals, plants express two forms of PNPASE, one with a chloroplast transit peptide (cTP) and the other with a mitochondrial targeting sequence (MTS). (Adapted and reprinted with permission from Chen, et al., Trends in cell biology 17 (2007) 600-608)

Fig. 2

Mammalian PNPASE is imported into the mitochondrial IMS via a Yme1-dependent mechanism. After passing through the TOM complex at the OM, the PNPASE amino-terminus extends through the TIM23 complex at the IM into the matrix, where the 37 amino-acid MTS is removed by the matrix-processing peptidase (MPP), Mas1/Mas2. The mature amino-terminus is then released into the IMS with the help of IM-localized Yme1 iAAA protease, which also helps to reel the remaining portion of PNPASE into the IMS from the cytosol. Mature, processed PNPASE then assembles into a homo-oligomeric complex, consisting of a trimer or a dimer of trimers attached to the IM facing the IMS.

Fig. 3

Routes of mitochondrial tRNA import. Two mitochondrial tRNA import mechanisms have been reported. Shown on the far left is tRNA import that utilizes the protein import pathway, including the TOM complex at the OM and the TIM23 complex at the IM. The imported tRNA is delivered to the mitochondrial OM bound to pre-mitochondrial lysyl tRNA synthetase (pre-mitoLysRS) and enolase after aminoacylation by its cognate cytosolic synthetase. Enolase dissociates at the surface of mitochondria and the remainder of the protein-tRNA complex is imported together into the matrix. Thus far, this mechanism has only been described for the import of tRNA_CUU^Lys into yeast mitochondria. A second mechanism has been reported in organisms ranging from kinetoplastids to human that does not depend on the protein import pathway. Different factors have been identified in this pathway that are organism-specific, including the VDAC channel in the OM for plants and the translation elongation factor, eEF1a, for T. brucei.

Fig. 4

PNPASE regulates the import of nucleus-encoded small RNAs including RNase P RNA, MRP RNA, and 5S rRNA into the mitochondrial matrix. PNPASE promotes the import of RNAs from the cytosol into the matrix by binding to specific stem-loop motifs in the imported RNAs. Imported non-coding RNAs function in mitochondrial replication, transcription, and translation. The mitochondrial translation products are components of the oxidative phosphorylation (OXPHOS) complexes I-IV.