High resolution imaging of nascent mitochondrial protein synthesis in cultured human cells

Abstract

Human mitochondria contain their own genome, mtDNA, that is expressed in the mitochondrial matrix. This genome encodes thirteen vital polypeptides that are components of the multi-subunit complexes that couple oxidative phosphorylation (OXPHOS). The inner mitochondrial membrane that houses these complexes comprises the inner boundary membrane that runs parallel to the outer membrane, infoldings that form the cristae membranes, and the cristae junctions that separate the two. It is in these cristae membranes that the OXPHOS complexes have been shown to reside in various species. The majority of the OXPHOS subunits are nuclear-encoded and must therefore be imported from the cytosol through the outer membrane at contact sites with the inner boundary membrane. As the mitochondrially-encoded components are also integral members of these complexes, where does nascent protein synthesis occur? Transcription, mRNA processing, maturation and at least part of the mitoribosome assembly process occur at the nucleoid and the spatially juxtaposed mitochondrial RNA granules, is protein synthesis also performed at the RNA granules close to these entities, or does it occur distal to these sites ? We have adapted a click chemistry based method, coupled with STED nanoscopy to address these questions. We report that in human cells in culture, within the limits of our methodology, the majority of mitochondrial protein synthesis occurs at the cristae membranes and is spatially separated from the sites of RNA processing and maturation. the architecture of the membranes (11) and iii) large (10 -40nm) complexes termed cristae junctions (CJ), composed of the Mitochondrial contact site and Cristae Organising System (MICOS; (12-14)), which forms the cristae and separates them from the IBM.There has also been much focus on the mitochondrial genome, how and where it is expressed. This has led to the identity and characterisation of the nucleoid (15-18) and more recently the mitochondrial RNA granule, a complex formed by phase transition where transcripts are processed and matured (19)(20)(21). Translation occurs on membraneassociated mitochondrial ribosomes, which are also at least partially assembled in the RNA granule (22,23). Exactly where, however, protein synthesis is performed in human mitochondria, whether at the CM, CJ or IBM, within, close to, or distal to the RNA granules, is unknown. To follow this process in yeast mitochondria, Jakobs and colleagues harnessed an elegant series of experimental approaches (24). The yeast S. cerevisiae express a battery of translational activators that show specificity to mt-mRNAs, which encode individual components of OXPHOS complexes III, IV and V (25). Using immuno-labelling super resolution and electron microscopy, data were produced that were consistent with mtDNA-encoded complex V subunits being synthesised predominantly on the cristae membranes, whilst complex III and IV components were synthesised both at the IBM and CM. This approach is not feasible in human cells as with the exception of TAC...

Human Elp3/Kat9 is a mitochondrial tRNA modifying enzyme

“…Thus, we reasoned that overexpressing mt-ELP3 might increase mitochondrial translation. To examine mitochondrial translation activity, we used a non-radioactive pulse- labelling click chemistry experiment (Zorkau et al, 2020). Specifically, we treated control cells and cells overexpressing mt-ELP3 with the alkyne-methionine derivative, L- homopropargylglycine (HPG), with or without cycloheximide (specific inhibitor of cytosolic translation) and/or chloramphenicol (a specific inhibitor of mitochondrial translation).…”

“…Specifically, we treated control cells and cells overexpressing mt-ELP3 with the alkyne-methionine derivative, L- homopropargylglycine (HPG), with or without cycloheximide (specific inhibitor of cytosolic translation) and/or chloramphenicol (a specific inhibitor of mitochondrial translation). The methionine analogue HPG was incorporated into nascent protein in the place of methionine and subsequently visualized using chemoselective fluorescence-tagging by means of click chemistry (Dieterich et al, 2010)(Zorkau et al, 2020).…”

“…De novo mitochondrial protein synthesis was performed as described (Zorkau et al, 2020). HEK239T cells were seeded in lab-tek chamber slides (ThermoFisher Scientific) and transfected with pcDNA-T0 or Flag-tagged pcDNA-mt-ELP3.…”

Controlling the topology of mammalian mitochondrial DNA

“…Unlike nuclear gene expression, protein synthesis in mitochondria is not compartmentalized, with transcription and translation both taking place within the mitochondrial matrix. Mitochondrial transcripts are processed within structures termed RNA granules [34], found adjacent to the mtDNA, and their protein products are embedded directly into the IMM by the mitoribosome during translation [35][36][37]. The ability of mtDNA to diffuse freely around the mitochondrial network is limited [38].…”