116: Silent but Stalling: A Synonymous mtDNA Variant Shapes CD8+ T Cells

Lareau CA et al., PNAS - Single-cell multiomic profiling identifies a mosaic synonymous mtDNA variant (m.7076A>G) in MT-CO1 that is selectively depleted in CD8+ effector memory T cells. Mechanistic assays show the variant forces wobble decoding, stalls mitochondrial ribosomes, and impairs differentiation of high-demand effector T cells. Key terms: mitochondria, synonymous mutation, mtDNA, CD8+ T cells, translation. Study Highlights:The study identifies a mosaic synonymous mtDNA mutation m.7076A>G in MT-CO1 present at ~47% heteroplasmy in a healthy donor and shows selective depletion of the mutant allele specifically in CD8+ effector memory/short-lived effector T cells. MT-CO1 transcript abundance is unchanged by genotype, but mitochondrial ribosome profiling reveals enrichment of the mutant allele in ribosome-protected fragments, consistent with translational stalling. The effect is explained by the limited mitochondrial tRNA pool: the mutant GGG codon requires wobble/super-wobble decoding by the single mt-tRNAGly, reducing codon:anticodon affinity and slowing translation. Short-lived effector CD8+ T cells have elevated translational and metabolic demands that amplify dependence on efficient MT-CO1 translation, driving lineage-specific purifying selection. Conclusion:A synonymous mtDNA change can have cell type–specific functional consequences by altering codon syntax and translation efficiency; single-cell multiomics reveals purifying selection of such variants in metabolically demanding immune states. These results expand annotation of mitochondrial variation and motivate targeted studies of codon optimality in mtDNA. Music:Enjoy the music based on this article at the end of the episode. Article title:Cell type–specific purifying selection of synonymous mitochondrial DNA variation First author:Lareau CA Journal:PNAS DOI:10.1073/pnas.2505704122 Reference:Lareau CA, Zielinski S, Stickels RR, et al. Cell type–specific purifying selection of synonymous mitochondrial DNA variation. PNAS. 2025;122(30):e2505704122. doi:10.1073/pnas.2505704122 License:Creative Commons Attribution License 4.0 (CC BY) Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.com/episodes/cell-typespecific-purifying-selection-of-synonymous-mtdna-variation QC:This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-08-24. QC Scope:- article metadata and core scientific claims from the narration- excludes analogies, intro/outro, and music- transcript coverage: Audited the scientific content describing (1) identification of the mosaic mtDNA variant m.7076A>G in MT-CO1, (2) CD8+ TEM–specific depletion of the mutant allele, (3) stable MT-CO1 mRNA across genotypes, (4) ribosome profiling showing translational stalling of the mutant codon, (5) wobble decoding due to mt-tRNA limit- transcript topics: Identification of mosaic mtDNA variant m.7076A>G in MT-CO1; CD8+ TEM depletion of m.7076G allele; MT-CO1 transcript levels remain stable; Mitochondrial ribosome profiling and translation pausing; Glycine tRNA limitation and super-wobble decoding; SLEC metabolic dependence on OXPHOS and puromycin/SCENITH data QC Summary:- factual score: 10/10- metadata score: 10/10- supported core claims: 7- claims flagged for review: 0- metadata checks passed: 4- metadata issues found: 0 Metadata Audited:- article_doi- article_title- article_journal- license Factual Items Audited:- m...