Profiling of mRNA localization of nuclear-encoded mitochondrial proteins in zebrafish.

Current evidence suggests that nuclear-encoded mitochondrial proteins can be locally translated at the mitochondrial surface and co-translationally or post-translationally imported into mitochondria. mRNA localization on the mitochondrial membrane, a prerequisite for localized translation, remains uncharacterized in higher eukaryotic organisms. We employed fractionation-sequencing to profile mitochondria-associated mRNAs in zebrafish larvae. Our transcriptome-wide analysis reveals the localization of mRNAs of only 12% of the nuclear-encoded mitochondrial proteins to the mitochondrial surface, which suggests that post-translational import is the dominant mode of protein import to mitochondria. Additionally, the mRNAs which were localized to the mitochondrial membrane consisted mostly of those encoding proteins involved in mitochondrial dynamics, suggesting their site-specific translation. Finally, we show that the loss of function of the MIA pathway responsible for the post-translational import of a subclass of mitochondrial proteins, triggers mitochondrial localization of mRNAs encoding proteins that are imported to mitochondria via other pathways. Thus, our study suggests that mRNA targeting and localized translation could be relevant in higher eukaryotes to combat stress conditions affecting mitochondrial biogenesis in general. Biochemical fractionation of WT (AB) and chchd4abns292/bns292 5dpf zebrafish larvae was perfomed to obtain MARS and HSF fractions. Three replicates each of whole unfractionated RNA samples, as well as RNA isolated from MARS, HSF, and PNS were sequenced on Illumina Nextseq platform using paired end sequencing. Differential enrichment analysis was performed by comparing the fractions against whole unfractionated sample.