The relationship between codon usage bias and salt resistant genes in Arabidopsis thaliana and Oryza sativa

This research is based on synonymous codon usage and its relation with the salt resistant genes. The codon usage directly affects the level or even direction of changes in protein expression in responses to environmental stimuli. Soil salinity is a major abiotic stress for plant agriculture. Sodium ions in saline soils are toxic to plants because of their adverse effects on K+ nutrition, cytosolic enzyme activities, photosynthesis, and metabolism. In the recent study codon usage biase (CUB) has been studied in Arabidopsis thaliana salt resistant and housekeeping genes and their homologs in rice (Oryza sativa) to understand the salt stress and housekeeping genes relation with CUB. Total five salt stress tolerant genes; Salt Overly sensitive (SOS1), basic lucien-Zipper Protein (bZIP), Calcinurin B like binding 10 (CBL10), Mitogen Activated Protein Kinase-3 (MPK3) and Histidine Kinase-1 (HK1) were identified in Arabidopsis thaliana. For the comparative study and removing the organism bias the orthologues of the five salt stress tolerant genes were also identified in rice. Briefly, five salinity resistant and three housekeeping genes in Arabidopsis thaliana and their orthologues in rice, were subjected to CUB analysis. The four salt resistant genes (SOS1, CBL10, bZIP and HK1) showed more than 50% (71%, 57%, 67% and 57% respectively) similar codon usage bias for Arabidopsis thaliana and rice. On the other hand fifth salt resistant gene (MPK3) showed less than 50% (29%) similar codon usage bias for Arabidopsis thaliana and rice. The three housekeeping genes (Actin, Tubulin and Ubiquitin) showed 76% similar codon usage bias for Arabidopsis thaliana and rice.this will help us to engineer the salt resistant crops by adjusting the codon usage. [PUBLICATION ABSTRACT]