A metabolic flux efficiency model reveals mitochondrial triage: H2S reallocates carbon skeletons to match cysteine under cyanide stress in rice

Hydrogen sulfide (H 2 S) achieves comparable growth recovery to cysteine (Cys) in rice under cyanide (CN - ) stress, despite Cys being the direct substrate for CN - detoxification and driving a substantially higher assimilation rate via β-cyanoalanine synthase (β-CAS). This paradox implies a fundamental trade-off between immediate detoxification and long-term resilience. Here, we profiled tissue-resolved metabolomics of the TCA cycle intermediates oxaloacetate (OAA) and α-ketoglutarate (α-KG), and their cognate aspartate (Asp)- and glutamate (Glu)-family amino acids, the branches most intimately linked to CN - assimilation, together with transcriptional analysis of their biosynthetic genes. We then developed a Metabolic Flux Efficiency ( MFE ) model, a proof-of-concept framework that integrates these data to estimate relative flux efficiency within the TCA–amino acid (AA) cycle. H 2 S is proposed to execute a mitochondrial triage strategy, depleting root nitrogen reserves (Asn and Gln reduced by 92% and 67%) to liberate carbon skeletons, while boosting root α-KG (+93%) to sustain anaplerotic TCA cycle flux. The calibrated MFE model (Asp family: α = 0.39, β = 1.52; Glu family: α = 0.37, β = 1.64) suggests that metabolic conversion dominates over transcription in governing flux under CN - stress, and predicts that H 2 S redirects flow away from primary nitrogen assimilation (Glu→Gln) toward energy-generating cycles (Orn→Cit). This pattern is consistent with recovery being governed not by nitrogen abundance but by dynamic reallocation of carbon skeletons from storage to biosynthetic and anaplerotic routes. By redefining the mitochondrion as a metabolic regulatory hub that prioritizes reconstruction over mere survival, our work provides a quantitative framework for interpreting metabolic trade-offs and a conceptual basis for engineering stress-resilient crops.