Mitochondrial Ribosome Profiling Reveals Rapid and Dynamic Translation Regulation During Yeast Mitochondrial Biogenesis

Abstract

Regulation of mitochondrial gene expression is essential to prevent accumulation of harmful intermediates at respiratory chain reaction centers that cause aging phenotypes and disease. Translation in mitochondria is carried out by dedicated ribosomes (mitoribosomes) that are distinct from cytoplasmic ribosomes. The mitochondrial translational response to environmental and developmental changes is currently unexplored because tools have not been developed for quantitative, time‐resolved studies in vivo. Genomic approaches have typically overlooked the mitochondrial genome either through experimental design or through biased bioinformatics approaches. We have developed mitoribosome profiling, an approach to determine quantitative, genome‐wide measures of mitochondrial translation at codon resolution. Applying mitoribosome profiling to study gene expression during mitochondrial biogenesis in S. cerevisiae, we find that translation occurs in the mitochondria even under conditions in which the translation products do not accumulate, indicating that the relative contributions of protein synthesis and turnover change depending on environment. As mitochondria differentiate when cells shift from glycolytic to oxidative metabolism, mitoribosomes are redistributed across mRNAs to regulate expression in a precise temporal pattern. Respiratory complexes are unique in the cell as their proteins are encoded by two separate genomes. To understand at a global level how mitochondrial and nuclear protein synthesis and turnover are coordinated we are now quantifying cytoplasmic translation using ribosome profiling, as well as the cellular proteome using tandem mass tags, during mitochondrial biogenesis.