Small RNAs Regulating Gene Expression In Mitochondria

Mitochondria are found in most eukaryotic cells. They are primary energy producing system using electron transport chain to catalyze the addition of inorganic phosphate to ADP to yield ATP, which is the chemical form of energy. In addition to providing energy, mitochondria play an important part in cellular metabolism, signaling, and apoptosis. Mitochondria have their own genome (mtDNA), which encodes a specific set of protein, tRNA and rRNA, and some non-coding RNA. The mtDNA is transcribed and translated within mitochondrial inner membrane. All protein products are components of the mitochondrial electron transport chain.Small regulatory RNAs mainly include siRNA and microRNA, which are well known to induce mRNA degradation and repress protein synthesis since they were originally discovered, but recent evidence suggests that microRNA can also enhance translation under specific cellular conditions or through gene-specific mechanisms. Both siRNA and microRNA-mediated reactions have been shown to take place in the cytoplasm and in multiple membrane-compartmentalized organelles in the cell. The key RISC component Ago2appears detectable in mitochondria, but the functional significance for this observation has not been established.By analyzing Argonaute2-RNA interactions revealed by CLIP-Seq in our lab and reported by others, we found that Argonaute2binds extensively to mitochondria-encoded mRNAs. Ago2is the catalytic component of RISC, indicating that RNA interference may occur in mitochondria. Indeed, using siRNA against mitochondria-encoded ETC (electron transport chain) components, we found that siRNA can specifically down-regulate the mRNA level of corresponding mitochondrial genes, and weaken the mitochondrial function. This work demonstrated that RNA interference functions in mitochondria as in the cytoplasm.On the basis of miRNA base-pairing with the target mRNA in RISC, we developed a method for identifying miRNA targets, which we call miRACE. Using this method, we identified target genes of the cardiac and muscle specific miR-1in differentiated C2C12cells. Many target genes are nucleus-encoded as expected, while others are encoded by mitochondria. Remarkably, we found that, while negatively regulating the expression of nucleus-encoded genes, miR-1elicits a positive effect on mitochondria-encoded genes, boosting their expression at the protein level.Several micro RNAs, including miR-1, are induced during the muscle differentiation. We now show that miR-1acts to boost the respiratory chain and elevate ATP production through enhancing translation in mitochondria. We speculate that the mechanism for microRNA-mediated enhancement of translation might be due to the restriction of certain translation repressive proteins from mitochondria.We also found that there is a strong correlation between miR-1expression and mitochondrial gene expression in muscle development, both of which are increased during the muscle differentiation. Blocking miR-1during mouse muscle differentiation or deleting miR-1in Caenorhabditis elegance can weaken the function of muscle.In conclusion, we report that the small RNA machinery exists and functions to regulate the expression of mitochondria-encoded transcripts in mitochondria. In contrast to the function of microRNA in the cytoplasm, however, we found that microRNA enhances translation of mitochondria-encoded mRNAs, which may contribute to modulation of a broad array of physiological processes in development and cell differentiation.