Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish

Abstract

Most mitochondrial proteins are encoded by nuclear genes, synthetized in the cytosol and targeted into the organelle. To characterize the spatial organization of mitochondrial gene products in zebrafish (Danio rerio), we sequenced RNA from different cellular fractions. Our results confirmed the presence of nuclear-encoded mRNAs in the mitochondrial fraction, which in unperturbed conditions, are mainly transcripts encoding large proteins with specific properties, like transmembrane domains. To further explore the principles of mitochondrial protein compartmentalization in zebrafish, we quantified the transcriptomic changes for each subcellular fraction triggered by thechchd4a−/−mutation, causing the disorders in the mitochondrial protein import. Our results indicate that the proteostatic stress further restricts the population of transcripts on the mitochondrial surface, allowing only the largest and the most evolutionary conserved proteins to be synthetized there. We also show that many nuclear-encoded mitochondrial transcripts translated by the cytosolic ribosomes stay resistant to the global translation shutdown. Thus, vertebrates, in contrast to yeast, are not likely to use localized translation to facilitate synthesis of mitochondrial proteins under proteostatic stress conditions.

Localization of RNAs to the Mitochondria – Mechanisms and Functions

“…Notably, RNA-sequence dependent transcripts exhibit shorter polyA tails and 3' UTRs compared to RNAs relying on translation-dependent localization (i.e., ribosome-dependent RNAs). A recent study supported some of these findings by identifying mitochondria-bound RNAs derived from the larval stage of vertebrate zebrafish 7 . The comparison of 18 zebrafish orthologues derived from the mitochondria-bound fraction through OMM proximity labeling of human cells revealed 17 out of 18 RNAs common in both 6 .…”

“…In this review, we examine RNA localization to the mitochondrial surface, where mitochondrial proteins are known to be translated [5][6][7][8] . In addition, we highlight examples where mitochondria serve as a hub for vital RNA regulatory processes such as the innate immune response, piRNA biogenesis, and cytoskeletal-mediated RNA transport.…”

HKDC1, a target of TFEB, is essential to maintain both mitochondrial and lysosomal homeostasis, preventing cellular senescence

“…On one hand, an efficient translation of mRNAs and trafficking of proteins across organelles allow cells to function exactly. Increasing evidence demonstrates that mitochondrial proteins are co-translated by mRNAs in its close proximity ( 49 – 51 ). Therefore, PINK1 translation could be achieved surrounding the mitochondria, which might be affected by HKDC1 deficiency.…”