Genome-wide profiling of CBL interacting protein kinases (CIPKs) in banana unveils their role in abiotic stress signaling and stress tolerance enhancement

Abstract

Calcineurin B-like (CBL)-interacting protein kinases (CIPKs) play a crucial role in the complex molecular systems of plants, acting as coordinators in different plant development processes, manage hormone signaling, and respond to environmental stress. Despite their well-established importance in various physiological process, the CIPK gene family in banana has remained an unexplored, creating a knowledge gap that this research aims to address. Through comprehensive analysis, we identified and characterized 34 CIPK genes in the banana genome. Structural diversity analysis revealed distinct clades characterized by homologs with varying intron-rich and intron-poor members. Particularly, evolutionary conservation was observed in intron-less members. Exploring conserved motifs and physicochemical properties provided insights into the detailed structure of specific homologs. Subcellular localization predictions indicated that most CIPK proteins primarily reside in the cytoplasm and nucleus, indicating their involvement in essential cellular activities. The predicted chromosomal distribution pattern suggests that the CIPK gene family largely expanded through segmental duplications in the banana genome. The phylogenetic analysis has uncovered two monophyletic clades for intron-less and intron-containing homologs, providing insights into two separate evolutionary history and expansion of the CIPK gene family. The clustering pattern in the phylogeny suggest that sequence of CIPKs members in the different genomes are largely conserved during course of evolution after evolution of higher plants. However, a few members having diverse sequences that these homologs are evolving with higher rate of evolution. Diverse physiological roles of banana CIPKs members are further supported by the presence of numerous cis-acting elements associated with growth, development, hormone responsiveness, and stress, with certain MaCIPK promoters exhibiting multiple hormone-sensitive elements. The protein-protein interaction network sheds light on the functional associations between MaCIPKs and MaCBLs, highlighting specific clusters of interactions. 3D protein structure predictions provide additional insights, revealing variations among the MaCIPK proteins. Real-time expression analysis across various tissues and developmental stages emphasizes the significant roles played by CIPKs in plant development. Under stress conditions, 16 in leaves and 22 in root MaCIPK gene transcript levels were up –regulated in response to drought and cold stress. These insights into the dynamic expression and functional roles of CIPK genes provide valuable information for understanding the mechanisms underlying banana's resilience to stress, with direct implications for the development of stress-resistant banana varieties. Overall this research offers promising prospects for enhancing global food security by ensuring the sustainability of banana production in the face of changing environmental conditions.