LncRNAs modulate nitrogen metabolism gene expression in rice leaves under elevated CO₂ and/or Cd stress.

With rising atmospheric CO₂ and intensifying cadmium (Cd) pollution negatively affect rice growth and development. Rice seedlings "Liaoxing No. 1" (Oryza sativa L.) were treated under four treatments (AC: CO2 400 ± 20 μmol·mol-1 and CdCl2 0 μmol·L-1; EC: CO2 800 ± 20 μmol·mol-1 and CdCl2 0 μmol·L-1; Cd: CO2 400 ± 20 μmol·mol-1 and CdCl2150 μmol·L-1; EC + Cd: CO2 800 ± 20 μmol·mol-1and CdCl2 150 μmol·L-1) for 7 days. Integrated transcriptome sequencing and quantitative real-time PCR (qPCR) were used to analyze the expression patterns and regulatory networks of long non-coding RNAs (lncRNAs) in rice leaves under elevated CO₂ and/or Cd stress. A total of 841 lncRNAs were identified, and KEGG enrichment analysis showed that differentially expressed lncRNAs (DE-lncRNAs) were primarily associated with nitrogen metabolism. Cd stress significantly inhibited nitrogen assimilation via a lncRNA-mediated network: MSTRG.25360.1 downregulated nitrate reductase (NR) genes, reducing NR activity; MSTRG.19531.1 positively regulated glutamate synthase (GOGAT) activity; and MSTRG.16002.2 was involved in inhibiting carbonic anhydrase (CA) activity. Elevated CO₂ (EC) also suppressed the activities of key enzymes, including NR, nitrite reductase (NIR), GOGAT, and CA, while shifting ammonia assimilation toward the glutamine synthetase (GS) pathway, a process involving MSTRG.1264.1. Under combined stress (EC + Cd), EC partially alleviated Cd toxicity by activating NIR and glutamate dehydrogenase (GDH), leading to a higher nitrogen metabolism efficiency than under Cd stress alone. However, the activities of NR and GOGAT failed to recover, and CA activity was further suppressed synergistically via MSTRG.25184.5. In conclusion, elevated CO₂ only partially mitigates Cd-induced inhibition of nitrogen assimilation in an enzyme-specific manner, which is mediated by distinct lncRNA regulatory networks targeting key nitrogen metabolism enzymes.