Abstract
Mitogen activated protein kinase (MAPK) genes provide resistance to various biotic and abiotic stresses. Codon usage profiling of the genes reveals the characteristic features of the genes like nucleotide composition, gene expressivity, optimal codons etc. The present study is a comparative analysis of codon usage patterns for different MAPK genes in three organisms, viz. Arabidopsis thaliana, Glycine max (soybean) and Oryza sativa (rice). The study has revealed a high AT content in MAPK genes of Arabidopsis and soybean whereas in rice a balanced AT-GC content at the third synonymous position of codon. The genes show a low bias in codon usage profile as reflected in the higher values (50.83 to 56.55) of effective number of codons (Nc). The prediction of gene expression profile in the MAPK genes revealed that these genes might be under the selective pressure of translational optimization as reflected in the low codon adaptation index (CAI) values ranging from 0.147 to 0.208.
Highlights
Many codons in the genetic code are functionally synonymous
The overall GC content in rice and soybean gene sequences is 43.99% and 53.10% respectively. This result suggests that there exists a balance between the AT and GC content in the soybean genes, while in rice the overall AT content slightly exceeds the overall GC content for Mitogen activated protein kinase (MAPK) genes
The results suggest that the codon usage pattern in all the MAPK genes in the three species used in the study might be influenced by their base compositional properties
Summary
Many codons in the genetic code are functionally synonymous. A single amino acid is encoded by two to six codons, a phenomenon called synonymous codon usage. All the synonymous codons of an amino acid show a variation in the occurrence in a gene frequency. The synonymous codons show variation between as well as within the genome of an organism [2, 3]. Study of the synonymous codon usage patterns of a gene in various organisms could provide an insight into the evolution profile and the level of gene expression as well [4, 5]. Mitogen activated protein kinase (MAPK) genes present in the plants actively respond to various stresses. The string of reactions in the stress signalling pathways involve these three MAPK families; MAPKKKs phosphorylate the serine/threonine of MAPKKs at their activation loop which in turn double phosphorylate the MAPKs at their T-D-Y motif in the activation loop. The cascade actions acts downstream of the receptors on extracellular surface or acts as a sensor that’s transduces the extracellular signals into intracellular responses [8]
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