Mitochondrial L-2-hydroxyglutarate is a physiologic signaling metabolite [scRNA-seq]

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 accumulation. In humans lacking L2HGDH activity, L-2-HG builds up, leading to L-2-hydroxyglutaric aciduria, a rare childhood neurometabolic disorder. Thus, L-2-HG is often classified as a toxic metabolite. Furthermore, L-2-HG is produced in response to hypoxia, acidic pH, and electron transport chain (ETC) impairment. However, whether L-2-HG has a physiological function is unclear. Here, we investigated whether L-2-HG qualifies as a physiologic signaling metabolite by testing three criteria: regulated levels, defined molecular targets, and a measurable physiological function. We report that an elevated mitochondrial NADH/NAD⁺ ratio drives malate dehydrogenase 2 (MDH2) to reduce 2-OG into L-2-HG, while L2HGDH oxidizes L-2-HG back to 2-OG within the mitochondrial matrix without requiring a functional ETC. Proteome integral solubility alteration (PISA) assays revealed the KDM4 family of H3K9 demethylases as L-2-HG-responsive targets. Consistent with this, 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, ubiquitous early embryonic L2HGDH overexpression lowered L-2-HG, reduced postnatal growth, and caused postnatal mortality. Despite systemic lowering of L-2-HG levels, kidneys exhibited a unique vulnerability, displaying functional impairments and histologic alterations. Mechanistically, L-2-HG depletion in the postnatal kidney resulted in the loss of H3K9me3 specifically at L1MdTf retrotransposons, leading to their derepression and coinciding with activation of the integrated stress response (ISR) and inflammation pathways. Our findings establish mitochondrial L-2-HG as a physiologic signaling metabolite that couples mitochondrial redox state to chromatin regulation, which is essential for postnatal kidney function and survival. These findings suggest that metabolites previously regarded as toxic may also serve critical physiological functions.