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Molecular Characterization, 3D Model Analysis, and Expression Pattern of the CmUBC Gene Encoding the Melon Ubiquitin-Conjugating Enzyme Under Drought and Salt Stress Conditions

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Abstract

Ubiquitin-conjugating (UBC) enzyme is a key enzyme in ubiquitination. Here, we describe the cloning, characterization, and expression pattern of a novel gene, CmUBC, from a melon. Comparison of the deduced amino acid sequences allowed the identification of highly conserved motifs. Synteny analysis between Cucumis sativus L. and Arabidopsis demonstrated that homologs of several Cucumis UBC genes were found in corresponding syntenic blocks of Arabidopsis. The homology structure model of the CmUBC protein was constructed. UBCs from melon, yeast, and Arabidopsis were highly conserved in their three-dimensional folding. CmUBC was ubiquitously expressed in all melon tissues. Increased transcript levels of CmUBC were observed during drought and salinity stresses, which suggested that the expression of the CmUBC gene in melon plants is responsive to physiological water stress. These results suggested that the CmUBC gene might play an important role in the modulation of the ubiquitination pathway.

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Acknowledgments

This study was supported by the Research Fund of Kastamonu University Grant No. KÜBAP-01/2012-34.

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Authors and Affiliations

  1. Department of Genetics and Bioengineering, Kastamonu University, 37100, Kastamonu, Turkey

    Mehmet Cengiz Baloglu

  2. Centre for Organismal Studies, University of Heidelberg, 69120, Heidelberg, Germany

    Meliha Gorkem Patir

Authors
  1. Mehmet Cengiz Baloglu
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  2. Meliha Gorkem Patir
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Corresponding author

Correspondence to Mehmet Cengiz Baloglu.

Additional information

GenBank Accession No. The CmUBC gene was deposited in GenBank under the accession number EU853458.

Electronic Supplementary Material

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Supplementary Fig. 1

Comparison of Ub1 and Ub5 of melon CmUBC and yeast UBC4. (a) The 3D model of CmUBC (red) was first constructed with the experimental X-ray crystal structure of UBC4 (green) and then superposed on it. The superposed residues that form ubiquitin thioester intermediate interaction residues Ub1 (b) and Ub5 (c) in the superposed structures are shown as sticks. The residues of CmUBC are shown in red and those of the superposed structures in green. The RMSD value between the template UBC4 and the model CmUBC was 0.89 Å (JPEG 156 kb)

Supplementary Fig. 2

Comparison of Ub1, Ub4, Ub5, and E3 of melon CmUBC and Arabidopsis UBC1. (a) The 3D model of CmUBC (red) was first constructed with the experimental X-ray crystal structure of UBC1 (green) and then superposed on it. The superposed residues that form ubiquitin thioester intermediate interaction residues Ub1 (b), Ub4 (c), Ub5 (d), and E3 interaction residues (e) in the superposed structures are shown as sticks. The residues of CmUBC are shown in red and those of the superposed structures in green. The RMSD value between the template UBC1 and the model CmUBC was 1.71 Å (JPEG 208 kb)

Supplementary Fig. 3

Construction of standard curve for CmUBC gene quantification. Amplification curve of different concentrations of a pCR8/GW/TOPO-CmUBC plasmid DNA and its standard curve. Plasmid dilutions, left to right: (p7) 107, (p6) 106, (p5) 105, (p4) 104, (p3) 103, (p2) 102, and (p1) 101 copies/µL (TIFF 1375 kb)

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Baloglu, M.C., Patir, M.G. Molecular Characterization, 3D Model Analysis, and Expression Pattern of the CmUBC Gene Encoding the Melon Ubiquitin-Conjugating Enzyme Under Drought and Salt Stress Conditions. Biochem Genet 52, 90–105 (2014). https://doi.org/10.1007/s10528-013-9630-9

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  • DOI: https://doi.org/10.1007/s10528-013-9630-9

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