Spatial analysis of mitochondrial gene expression reveals dynamic translation hubs and remodeling in stress

Protein- and RNA-rich bodies contribute to the spatial organization of gene expression in the cell and are also sites of quality control critical to cell fitness. In most eukaryotes, mitochondria harbor their own genome, and all steps of mitochondrial gene expression co-occur within a single compartment – the matrix. Here, we report that processed mitochondrial RNAs are consolidated into micron-scale translation hubs distal to mitochondrial DNA transcription and RNA processing sites in human cells. We find that, during stress, mitochondrial messenger and ribosomal RNA is sequestered in mesoscale bodies containing mitoribosome components, concurrent with suppression of active translation. Stress bodies are triggered by proteotoxic stress downstream of double-stranded RNA accumulation in cells lacking unwinding activity of the highly conserved helicase SUPV3L1/SUV3. We propose that the spatial organization of nascent polypeptide synthesis into discrete domains serves to throttle the flow of genetic information to support recovery of mitochondrial quality control.

Methods
This dataset contains raw data and analyses used to produce figures in the referenced manuscript by Begeman, et al. A detailed description of the methods can be found in the manuscript. Additionally, a stepwise protocol for labeling cells with key reagent L-Homopropargylglycine is available in the protocols.io repository via the following doi: https://dx.doi.org/10.17504/protocols.io.3byl4wedrvo5/v1.

Raw microscopy data are provided as 16-bit .CZI files that are native to Carl Zeiss Microscopy ZEN software version 3.7 or higher, or as TIFF files. CZI files can also be opened with ImageJ/Fiji with the Bioformats plugin.

Data analysis on which manuscript figures are based is provided as: csv files, text files, Prism analysis files, or Microsoft Excel spreadsheets.