The origin, expansion, and expression divergence of ethylene biosynthesis and signaling pathways in response to abiotic stresses in plants

Abstract Ethylene (ET) signaling molecules regulate seed germination, root development, flowering, fruit ripening, organ senescence, and stress responses in plants. Several vital proteins in ET biosynthesis and key ET signaling regulators have been well documented. However, the origin, evolution, and early diversification of important elements in plant ET signaling remains unknown. Here, we report the identification of the biosynthesis S-adenosyl-L-methionine synthetase (SAMS), 1-aminocyclopropane-1-carboxylate synthase (ACS), and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), receptor ETHYLENE RESPONSE (ETR), and signaling ETHYLENE-INSENSITIVE 3 (EIN3)/EIN3-LIKE (EIL) and EIN3-BINDING F-BOX PROTEIN (EBF) proteins of ET in algal and land plants. Evolutionary analysis revealed that ET pathway characterized not only by the invention of new core components (e.g., ACO genes, which absent in ferns, mosses, and algae), but also by the extensive duplication, diversification, and functional specialization of existing gene families (e.g., ACS and EIN3/EIL genes, which expanded through tandem and whole-genome duplications in seed plants). Besides, the expression of ET biosynthesis (SAMS, ACS, and ACO) and ET regulatory (ETR, EIN, and EBF) genes showed distinct patterns in diverse tissues. For instance, the ACO genes showed high expression in specific organs like flowers with deeply conserved across angiosperms, implying the fundamental role in floral biology. Besides, analysis of transcriptome revealed the potential role of ET in response to abiotic stress in evolutionary important plants including Arabidopsis thaliana, Oryza sativa, Ceratopteris richardii, and Physcomitrium patens, which exhibited a conserved core logic (e.g, the constitutive expression of SAMS genes) with extensive lineage-specific variation (e.g., the stress-induced expression of ACO genes). Functional validation through qPCR in tomato and fern confirmed differential expression of ACS and SAMS genes after ethephon treatment. Collectively, our analyses suggest that the SAMS, ACS, EIN, and EBF genes have evolved from Streptophyta and undergone different gene duplication events in terrestrialization, which could be important for adapting the diverse stress. The results could help to further elucidate the molecular mechanism of ET biosynthesis and regulatory genes to stress, which may furnish a valuable genetic reservoir for bolstering crop resilience to abiotic stresses and for steering precision varietal improvement.