Cross talk between energy cost and expression of Methyl Jasmonate-regulated genes: from DNA to protein
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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.
KeywordsAbiotic stress Energy cost Methyl Jasmonate-responsive genes SADEG package Stacking energy
Average free energy
Bio-analytic resource database
Codon adaptation index
Codon usage bias
Down-regulated genes by MeJA
Expect- codon adaptation index
Effective number of codons
Genes co-expression percentage
Up-regulated genes by MeJA
The authors greatly appreciate Tarbiat Modares University for supporting this research.
Author contribution statement
ES, M.S, and H.Z.M designed the research and collected the experimental data. B.K, E.S, and J.Z created SADEG package and performed the computational analysis. E.S wrote the original manuscript and all co-authors edited the manuscript and package manual.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
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