Identification and functional characterization of the PP2C gene family reveal their negative regulatory roles in stress adaptation in Solanaceae

Abstract

Abstract Background The plant protein phosphatases 2C (PP2Cs) are key regulators of plant growth and development, hormone signaling, and responses to environmental stresses. In Solanaceae crops, which are frequently challenged by environmental stresses leading to yield losses, a comprehensive cross-species understanding of PP2C family evolution and function remains limited. This study aimed to systematically identify PP2C gene family members in tobacco and eggplant and to perform comparative genomic and functional analyses across representative Solanaceae species, thereby clarifying their evolutionary relationships and stress-responsive roles. Results In this study, we identified 204 NtPP2C genes in tobacco ( Nicotiana tabacum L.) and 89 SmPP2C genes in eggplant ( Solanum melongena L.). The PP2C genes in both species were unevenly distributed across chromosomes, and segmental duplication appeared to be the major driving force underlying family expansion, with most homologous gene pairs subjected to purifying selection. Phylogenetic analysis classified these PP2C proteins into 12 subgroups (A–L). Members within different subgroups exhibited both conserved and divergent features in conserved motifs, exon-intron organization, and the composition of upstream promoter elements. Analyses of cis -acting elements, protein-protein interaction networks, and gene expression profiles indicated that NtPP2C and SmPP2C genes are broadly involved in light responses, developmental regulation, ABA signaling, drought, cold and heat stress responses, and pathogen infection-related processes. Subcellular localization analysis showed that NtPP2C91 and SmPP2C24, both belonging to the functionally important subgroup A, were localized to the nucleus. Further functional validation showed that CRISPR/Cas9-mediated knockout of NtPP2C91 in tobacco and virus-induced gene silencing (VIGS) of SmPP2C24 in eggplant significantly enhanced plant tolerance to low temperature and resistance to Ralstonia solanacearum ( Ras ) infection, while modulating the transcriptional dynamics of ABA signaling components and PP2C homologs. Conclusions These findings provide valuable genetic resources and a theoretical basis for dissecting ABA-mediated stress-resistance regulatory networks in solanaceous crops and offer potential targets for molecular breeding aimed at improving stress tolerance.