Balanced mitochondrial and cytosolic translatomes underlie the biogenesis of human respiratory complexes

Abstract

Background Oxidative phosphorylation (OXPHOS) complexes consist of nuclear and mitochondrial DNA-encoded subunits. Their biogenesis requires cross-compartment gene regulation to mitigate the accumulation of disproportionate subunits. To determine how human cells coordinate mitochondrial and nuclear gene expression processes, we tailored ribosome profiling for the unique features of the human mitoribosome. Results We resolve features of mitochondrial translation initiation and identify a small ORF in the 3′ UTR of MT-ND5. Analysis of ribosome footprints in five cell types reveals that average mitochondrial synthesis levels correspond precisely to cytosolic levels across OXPHOS complexes, and these average rates reflect the relative abundances of the complexes. Balanced mitochondrial and cytosolic synthesis does not rely on rapid feedback between the two translation systems, and imbalance caused by mitochondrial translation deficiency is associated with the induction of proteotoxicity pathways. Conclusions Based on our findings, we propose that human OXPHOS complexes are synthesized proportionally to each other, with mitonuclear balance relying on the regulation of OXPHOS subunit translation across cellular compartments, which may represent a proteostasis vulnerability.

Nonstop mRNAs generate a ground state of mitochondrial gene expression noise

“…In contrast, the synthesis of MT-ND1, which does not encode a stop codon within the mRNA ( Fig. 1B and table S1) and considered a low-expressed protein by ribosome profiling ( 41 ), was only modestly affected. The reduced synthesis was not due to changes in mitochondrial mRNA abundance.…”

“…8E ). Several proteins exhibited a profound impairment in synthesis that did not correlate with known synthesis rates in fibroblasts or myoblasts ( 41 ) nor composition within an oxidative phosphorylation complex ( Fig. 8E ).…”

“…We hypothesize that the defect in mitochondrial protein synthesis with MTRFR deficiency arises as a negative feedback response from the accumulative impairment in protein synthesis termination. Recent mitochondrial ribosome profiling data for human proliferating cultured cells (e.g., fibroblasts and myoblasts) indicate that there are robust differences in the synthesis rates for the 13 mitochondrial proteins ( 41 ). Thus, the frequency by which a selected mRNA is translated and the inherent propensity of that transcript to be missing a stop codon would be contributing factors to generating nonstop ribosome complexes in mitochondrial gene expression.…”

“…For example, MT-ATP6, which encodes a stop codon within the mRNA ( Fig. 1B and table S1) and is one of the most highly synthesized proteins ( 41 ), was profoundly inhibited by MTRFR deficiency. In contrast, the synthesis of MT-ND1, which does not encode a stop codon within the mRNA ( Fig.…”

Evolution is in the details: Regulatory differences in modern human and Neanderthal

“…In the mitonuclear compensatory coevolution hypothesis, nuclear-encoded genes coding for aminoacyl tRNA synthetases (like FARS2) and OXPHOS complex components (like LYRM4) are expected, and in some cases have been shown, to evolve more rapidly in response to high rates of evolutionary change in mitochondrially-encoded genes, with which their protein products subsequently directly interact [101]. Another consideration is how to regulate translation of OXPHOS complex components when the corresponding genes exist in both mitochondrial and nuclear genomes [104, 105]. The high number of observed DB TFBSs in the bidirectional promoter of the nuclear FARS2 and LYRM4 genes thus potentially allow more well-regulated coordination of cross-compartment OXPHOS component gene expression, and may even contribute to the effects of both mitonuclear compensation and speciation.…”