Mitochondrial L-2-hydroxyglutarate is a physiologic signaling metabolite [CUT&Run]

L-2-hydroxyglutarate (L-2-HG) is a low-abundance metabolite in mammals due to the mitochondrial enzyme L-2-HG dehydrogenase (L2HGDH), which oxidizes L-2-HG to 2-oxoglutarate (2-OG) to prevent its accumulation1. In humans lacking L2HGDH activity, L-2-HG builds up, leading to L-2-HG aciduria, a rare childhood neurometabolic disorder2. Thus, L-2-HG is often classified as a toxic metabolite2–5. Furthermore, L-2-HG is produced in response to hypoxia, acidic pH, and electron transport chain (ETC) impairment6–10. However, whether L-2-HG has a physiological function is unclear. Here, we investigated whether L-2-HG qualifies as a physiological signaling metabolite by testing three criteria: regulated levels, defined molecular targets, and a measurable physiological function. We report that elevated mitochondrial NADH/NAD⁺ ratio drives malate dehydrogenase 2 (MDH2) to reduce 2-oxoglutarate (2-OG) into L-2-HG, while L-2-hydroxyglutarate dehydrogenase (L2HGDH) reversibly oxidizes L-2-HG to 2-OG within the mitochondrial matrix, independently of the ETC. Proteome integral solubility alteration (PISA) assays revealed KDM4 family of H3K9 demethylases as L-2-HG-responsive targets. Consistent with the targets, elevated L-2-HG repressed nascent transcription of specific gene sets and promoted accumulation of the repressive histone mark H3K9me3 at those loci. In vivo, early embryonic L2HGDH overexpression lowered L-2-HG broadly, reduced postnatal growth, and caused postnatal mortality. Despite systemic lowering, kidneys displayed a unique vulnerability, developing fibrosis and functional decline. Mechanistically, L-2-HG depletion in the postnatal kidney resulted in a specific loss of H3K9me3 at L1MdTf retrotransposons, leading to their de-repression and coinciding with activation of the integrated stress response and inflammation pathways. Our findings establish mitochondrial L-2-HG as a physiological signaling metabolite that couples mitochondrial redox to chromatin regulation and is essential for postnatal kidney development and survival. These findings suggest that metabolites previously regarded as toxic may also serve critical physiological functions.