Ribonucleotides Sneaking Into Mitochondrial DNA Spark Aging Inflammation
Misincorporated ribonucleotides in mitochondrial DNA trigger cGAS–STING inflammation and drive the senescence secretory phenotype.
Summary
Researchers discovered that nucleotide imbalance causes ribonucleotides to be erroneously inserted into mitochondrial DNA (mtDNA), destabilizing it and causing fragments to leak into the cytosol. This activates the cGAS–STING innate immune pathway, driving chronic inflammation. The phenomenon was observed in aged mouse kidneys, in mice lacking the mitochondrial exonuclease MGME1, in cells lacking the protease YME1L, and in senescent cells. Critically, supplementing cells with deoxyribonucleosides reduced ribonucleotide misincorporation and suppressed the inflammatory senescence-associated secretory phenotype (SASP), pointing toward a potential therapeutic strategy for age-related inflammatory diseases.
Detailed Summary
Chronic low-grade inflammation is a hallmark of aging, yet the molecular triggers linking mitochondrial stress to innate immunity have remained incompletely understood. This landmark Nature paper identifies aberrant incorporation of ribonucleotides (rNMPs) into mitochondrial DNA as a previously unrecognized mechanism that drives mtDNA release and inflammatory signaling, with direct implications for aging, senescence, and age-related disease.
The study began by characterizing mice lacking MGME1, a mitochondrial single-strand exonuclease required for proper mtDNA maintenance. These mice develop age-progressive kidney inflammation and premature death from renal failure around one year of age. Using NanoString mRNA profiling, the authors showed that interferon-stimulated gene (ISG) expression increased with age specifically in kidneys of Mgme1−/− mice, and that cytosolic mtDNA fragments—particularly from regions near the origin of heavy-strand replication—were elevated in the same tissue. Crossing Mgme1−/− mice with STING loss-of-function mutants abolished the ISG response and ameliorated renal pathology, confirming that cGAS–STING signaling mediates the inflammation in vivo.
To uncover the mechanistic link between MGME1 loss and mtDNA release, the team performed ribonucleotide sequencing (Rib-seq/RHII-HydEn-seq) on mitochondrial DNA. They found a dramatic increase in embedded ribonucleotides in mtDNA from Mgme1−/− mouse kidneys and from cells lacking YME1L, a mitochondrial i-AAA protease whose loss is known to disrupt pyrimidine metabolism. Metabolomic analyses confirmed a drop in deoxyribonucleotide triphosphate (dNTP) pools and an increase in rNTP:dNTP ratios in both models, explaining why the DNA polymerase gamma (POLG) misincorporates ribonucleotides. Importantly, ribonucleotide-laden mtDNA was more susceptible to strand breaks, providing the substrate for cytosolic release.
The authors then extended these findings to physiological aging and cellular senescence. Ribonucleotide content in mtDNA increased across multiple tissues (kidney, heart, brain) of naturally aged wild-type mice. In oncogene-induced and replicative senescent cells, cell-cycle arrest reduced dNTP availability via downregulation of ribonucleotide reductase (RRM2), elevating rNTP:dNTP ratios and mtDNA ribonucleotide content. This triggered mtDNA cytosolic release, cGAS–STING activation, and a robust SASP. Strikingly, supplementing senescent cells with exogenous deoxyribonucleosides restored dNTP pools, reduced ribonucleotide misincorporation, decreased cytosolic mtDNA, and suppressed SASP cytokine secretion—without reversing the senescent state itself.
These results establish a unified mechanistic framework: nucleotide imbalance → ribonucleotide misincorporation into mtDNA → mtDNA instability and fragmentation → cytosolic release → cGAS–STING activation → inflammation and SASP. Limitations include the predominant use of mouse models and cell culture systems; whether deoxyribonucleoside supplementation is safe and effective in aged humans remains to be tested. Nonetheless, the study reveals a druggable node in aging-associated inflammation and suggests that monitoring mtDNA ribonucleotide content could serve as a biomarker of mitochondrial stress and inflammatory risk.
Key Findings
- Ribonucleotide misincorporation into mtDNA increases in aged mouse tissues and MGME1-deficient kidneys, causing mtDNA fragmentation.
- Cytosolic mtDNA fragments activate cGAS–STING signaling; STING knockout eliminates kidney inflammation in Mgme1−/− mice.
- Senescent cells show reduced dNTP pools and elevated mtDNA ribonucleotide content, driving SASP via cGAS–STING.
- Exogenous deoxyribonucleoside supplementation restores dNTP balance, reduces mtDNA ribonucleotides, and suppresses SASP.
- YME1L loss disrupts pyrimidine metabolism, raising rNTP:dNTP ratios and phenocopying MGME1 deficiency in mtDNA inflammation.
Methodology
The study combined NanoString ISG profiling, digital PCR of cytosolic mtDNA fractions, ribonucleotide sequencing (Rib-seq/RHII-HydEn-seq), and targeted metabolomics across Mgme1−/− and YME1L-knockout mouse and cell models, aged wild-type mice, and senescent cell systems. In vivo genetic epistasis used Mgme1−/−/Sting1 double-knockout mice to confirm pathway dependency.
Study Limitations
Most mechanistic data derive from mouse models and immortalized cell lines; direct evidence in human aging tissue is limited. The safety and efficacy of long-term deoxyribonucleoside supplementation in vivo has not been established. It remains unclear whether ribonucleotide-enriched mtDNA is intrinsically more immunostimulatory or whether strand breaks alone drive release.
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