AP2/ERF transcription factors enriched in the drought-response transcriptome of the Thar desert treeProsopis cinerariashow higher copy number and greater DNA-binding affinity than orthologs in drought-sensitive species

Abstract

We sequenced the drought-response transcriptome of the keystone tree speciesProsopis cinerariafrom the Indian Thar desert to understand the key factors in its drought tolerance mechanism. We identified a network of genes activated inP. cinerariainvolved in osmotic stress response, phytohormone, calcium, and phosphorelay signal transduction. Of these, up-regulation of 54 APETALA2/Ethylene-Responsive Factor (AP2/ERF) transcription factor genes, validated by real-time PCR, suggests their key role in the drought tolerance ofP. cineraria.We conducted a genome-wide study of the AP2/ERF superfamily inP. cineraria, classifying its 232 proteins into 15 clades and analyzing their protein structures, gene structure, and promoter organization. TheP. cinerariagenome contains more copies ofAP2/ERFgenes than drought-sensitive plants. Further, we identified sequence polymorphisms inAP2/ERFgenes between Arabian and Indian cultivars ofP. cineraria. We modeled the DNA-protein complex structures of AP2/ERFs from drought-tolerant and sensitive species using AlphaFold to compare their DNA binding ability. Though the DNA binding domain (DBD) is relatively conserved across species, the unstructured region of these proteins possesses different charge distributions, which might contribute differently to their DNA search and binding. Using all-atom molecular dynamics simulations, we teased out a higher number of specific DBD-DNA hydrogen bonds inP. cineraria,leading to a stronger DNA-binding affinity compared to drought-sensitiveArabidopsis thaliana. These results directly support copy number expansion of AP2/ERF transcription factors and the evolution of their structures for more efficient DNA search and binding as drought adaptation mechanisms inP. cineraria.