Cross talk between energy cost and expression of Methyl Jasmonate-regulated genes: from DNA to protein

  • Ehsan Sadeghnezhad
  • Mohsen SharifiEmail author
  • Hassan Zare-maivan
  • Babak Khorsand
  • Javad Zahiri
Original Article


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 ( 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.


Abiotic 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


Gene ontology


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.

Supplementary material

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Supplementary material 1 (DOCX 1309 kb)
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Supplementary material 2 (XLSX 438 kb)
13562_2018_480_MOESM3_ESM.xlsx (320 kb)
Supplementary material 3 (XLSX 320 kb)


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Copyright information

© Society for Plant Biochemistry and Biotechnology 2018

Authors and Affiliations

  • Ehsan Sadeghnezhad
    • 1
  • Mohsen Sharifi
    • 1
    Email author
  • Hassan Zare-maivan
    • 1
  • Babak Khorsand
    • 2
  • Javad Zahiri
    • 3
  1. 1.Department of Plant Biology, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
  2. 2.Department of Computer Engineering, Faculty of EngineeringFerdowsi University of MashhadMashhadIran
  3. 3.Bioinformatics and Computational Omics. Lab (BioCOOL), Department of Biophysics, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran

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