In silico Comparative Analysis of Transcriptional Factor Binding Sites in Rice and Arabidopsis Calmodulin Binding Protein 60s Genes

Abstract

Plants are usually subjected to one or more biotic stresses either alone or together which reduces agricultural output significantly, leading to huge losses. To cope with the various stimuli generated by diverse environmental stresses, plants have evolved with a complex mechanism of signal perception and transduction. Several phytohormones and secondary messengers are the main players in mediating cellular responses to various stimuli. Of the various secondary messengers in eukaryotes, the role of calcium ion (Ca2+) has been most extensively studied. The Ca2+ is a well-known universal second messenger in plants regulating the responses of growth and development as well as different environmental stimuli in the plant. Changing cytosolic-free calcium concentration ([Ca2+]cyt) is one of the earliest responses to biotic stresses. These changes in cellular Ca2+ level are being mediated by different Ca2+ binding proteins like calmodulin (CaM). CaM interacts with calmodulin binding protein (CBP) and activates downstream defence response. Among the several CBPs, CBP60 family of proteins is found to be involved in several environmental stresses in Arabidopsis. However, no rice CBP60 (OsCBP60) has been identified in relation to pathogen infection. In this study, we have identified 15 OsCBP60 genes using bioinformatics studies. The transcription of a gene is mainly regulated by the presence of transcriptional binding sites (BSs) that are specifically bound by regulatory proteins called transcription factors (TFs). In silico analysis using promoter scanning software is being widely used for identification of TFBSs. We carried out an in silico search for identification of TFBSs in CBP60s using Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN2.itps.ncku.edu.tw). Several TFBSs including WRKY, MYB, bZIP, bHLH, EIN3, CG-1, GATA, NAC/NAM were identified in our analysis. These TFs are responsible for modulation of several biotic stress-responsive genes.