Cross talk between energy cost and expression of Methyl Jasmonate-regulated genes: from DNA to protein
2019
Sadeghnezhad, Ehsan | Sharifi, Mohsen | Zare-maivan, Hassan | Khorsand, Babak | Zahiri, Javad
Plant cell balances energy consumption for its different biological processes under oxidative circumstances. The aim of the present study is to deepen our knowledge of the regulation of Methyl Jasmonate (MeJA) responsive genes, especially the discussion on energy index from DNA to protein. The cis- and trans-responsive elements, the translation efficiency and accuracy, the codon adaptation, the amount of entropy in the codon usage of a sequence and finally, co-expression patterns of up-regulated genes by MeJA in shoot and root of Arabidopsis plant under 8 different abiotic stresses (UV, cold, drought, heat, wounding, osmotic, oxidative, and salinity) were analyzed. We designed an R package, namely SADEG (https://cran.r-project.org/web/packages/SADEG/) to estimate the relative stability of the DNA sequence. Cost of amino acids biosynthesis was weakly correlated with the energy consumption for each triplet-triplet binding related to each amino acid during the translation process. Our results also demonstrated that natural selection, gene length, gene expression levels, and influence of GC3s on the codon bias could affect the codon usage patterns of MeJA-responsive genes in Arabidopsis.
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