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Interactome Analysis and Docking Site Prediction of Cockayne Syndrome A (CSA) Proteins in Arabidopsis thaliana

[ Vol. 14 , Issue. 3 ]

Author(s):

Mohamed Ragab Abdel Gawwad, Dilruba Ucuncu, Muhamed Adilović and Aida Marić   Pages 242 - 251 ( 10 )

Abstract:


Objectives: The main goal of this study was to decipher the role of CSA homologues in the DNA damage repair machinery of Arabidopsis thaliana.

Method: Bioinformatics tools were used in this work to analyse DNA Damage-Binding proteins; MSA, Phylogenetic tree construction, 3-D structure prediction, domain analysis, subcellular localization prediction, interactome analysis and docking sites.

Result: The pairwise alignment from Clustal Omega showed 92% similarity between AtCSA1A and AtCSA1B proteins, whereas 34 mismatches have been detected. The study constructed a phylogenetic tree using AtCSA1A and AtCSA1B orthologs from different plant species. It depicts the conservation of the protein throughout the plant kingdom. Furthermore, Prosite online tool available on ExPASy site was used to make the sequence logo [32]. These results showed conserved region of CSA and gave additional information on the quantity of certain residues in gene positions. The 3D structure analysis of AtCSA1A and AtCSA1B was visualized using PyMol and validated with Ramachandran plots. AtCSA1A consisted of 2 alpha helices and 24 beta sheets, while AtCSA1B was bulkier with 4 alpha helices and 26 beta sheets. Domain analysis revealed that both AtCSA1A and AtCSA1B contain five WD-40 repeat (WDR) domains. WDR, also known as beta transduction repeat is made up of 40 amino acids’ sequences and usually terminates with Trp-Asp [WD] residues. Interactome analysis revealed that both AtCSA1A and AtCSA1B interact with DDB1A, CUL4, ERCC1, CHR8, UVH3, UVH6, XPB1 and XPB2 proteins. The docking site analysis of AtCSA1A interaction with ERCC1 and DDB1A; and ERCC1, CHR8, DDB1A interaction with AtCSA1B was identified. Significantly, residues ‘LATASADSRVKLWDVR’, were found, also known as WDxR motif that are involved in the interaction of AtCSA1A and ERCC1 proteins. Additionally ‘LATASADSRVKL’ motif was found in the docking sites between AtCSA1A-DDB1A, AtCSA1B-CUL4 and AtCSA1B-DDB1A.

Conclusion: Two homologues of Cockayne Syndrome A were present in the Arabidopsis thaliana. AtCSA1A and AtCSA1B played important role in the DNA repair mechanism. This study hypothesized on the potential additional roles of CSA proteins in the DNA repair. 3D structure analysis, identification of docking sites and interactome analysis of AtCSA1A and AtCSA1B proteins reported in this study, revealed the complexity of DNA repair mechanism in plants. However, additional experimental investigations are needed to confirm these interactions and their physiological relevance.

Keywords:

3D structure, CSA protein, DNA repair mechanism, homolog, interactome, UV radiation.

Affiliation:

Genetics and Bioengineering program, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Sarajevo, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Sarajevo, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Sarajevo, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Sarajevo

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