Beyond assimilation: Cysteine fuels metabolic defense while hydrogen sulfide orchestrates transcriptional efficiency in cyanide-stressed rice

Cyanide (CN⁻) contamination poses a critical threat to agricultural systems by disrupting mitochondrial function and triggering oxidative damages. Although exogenous cysteine (Cys) and hydrogen sulfide (H 2 S) are known to enhance CN⁻ resilience, their underlying regulatory mechanisms remain incompletely understood. Here, we integrate physiological profiling with multi-tissue transcriptomics to demonstrate that Cys and H 2 S employ fundamentally distinct protective strategies in rice. Cys acts as a metabolic amplifier, driving high-capacity CN⁻ assimilation via β-cyanoalanine synthase (β-CAS) and fueling broad-spectrum defense pathways, including hyperactivated phenylpropanoid flux and polyketide diversification. In contrast, H 2 S functions as a transcriptional optimizer, achieving comparable growth recovery with only 44 % of the assimilation capacity of Cys. H 2 S conferred resilience through a streamlined transcriptomic response, reducing differentially expressed genes (DEGs) by nearly 40 % in roots, while enhancing metabolic coordination in shoots. Core regulatory hubs centered on NAC-bHLH-MYB transcription factors, yet protectant-specific rewiring was evident: Cys enhanced sulfur-assisted secondary metabolism, while H 2 S promoted cuticular fortification (DWA1), diterpenoid phytoalexins ( OsMAS1 ), and tissue-optimized hormonal rebalancing. Crucially, H 2 S resolved metabolic conflicts by expanding precursor pools ( OsFPS5 ), whereas Cys diverted CN⁻-derived resources toward non-terpenoid defense synthesis. We propose a dual-axis model: Cys repurposes CN⁻ into defense metabolites, whereas H 2 S fine-tunes the growth-defense balance through transcriptional efficiency. These findings position sulfur-dependent protectants as strategic tools for engineering multifunctional stress resilience in crops facing CN⁻ contamination. • Cys and H 2 S deploy distinct CN − detoxification strategies. • H 2 S confers resilience with superior transcriptional efficiency. • Cys fuels defense metabolism via sulfur-assisted reprogramming. • H 2 S streamlines transcriptomes and optimizes hormone trade-offs. • A core NAC-bHLH-MYB hub integrates protection signaling.