In silico identification, characterization and expression analysis of the shaggy-like kinase genes in Cicer arietinum (chickpea)

Abstract Shaggy like kinase (SK)/Glycogen Synthase-3 (GSK3) is a highly conserved serine/threonine kinase present in all the eukaryotes including yeast, protozoa, plants and animals. The Cicer arietinum (Chickpea) SKs structure and functions are poorly understood. Therefore, in silico study was performed to characterize chickpea putative SKs using various computational tools. The data revealed that chickpea has 8 putative SKs that are located at four different chromosomes. mRNA analysis showed that the average length of the 5′ leader was ~ 267 bases while 3′-UTR was ~ 334 bases. The 5′ leader sequences of these genes were also found to contain upstream Open Reading Frames (uORFs) and upstream AUGs (uUAGs). Interestingly, analysis of the promoter sequences of these genes revealed 57 different types of cis-acting regulatory elements, which were randomly scattered in their promoter regions. Furthermore, multiple sequence alignment of chickpea putative SKs indicate conserved kinase domain but variable N and C-terminal ends. Phylogenetic analysis indicated that the chickpea putative SKs group into 4 established SK classes. 3D structures of the chickpea putative SKs show high similarity in the kinase domain but variability at the N and C-terminal ends. Chickpea putative SKs showed high structural similarity in the kinase domain and variable N and C-terminal ends due to disordered N and C-terminal regions. Protein interaction network of putative chickpea SKs showed enrichment of metabolic and signaling pathways. Chickpea putative SKs were also predicted to contain post-translational modification sites. Gene expression analysis revealed that these putative genes are differentially expressed in chickpea tissues. Altogether, our study sheds light on the structural and functional role of putative chickpea SKs using computational tools and would be interesting to further extend and validate our findings through in vivo experiments.