An in-silico study of Polymerase Epsilon catalytic subunit proteins in Arabidopsis thaliana

Adoum Mahamat Baraka,Kanita Šabanović,Mohamed Ragab Abdel Gawwad

doi:10.37868/bes.v1i1.id114

Abstract

Arabidopsis thaliana genome encodes two POLE2 homologs known as polymerase epsilon catalytic subunit A (POLE2A) and polymerase epsilon catalytic subunit B (POLE2B). They play a very important role in DNA repair mechanisms. In this study, bioinformatics tools were used to understand DNA repair mechanisms in A. thaliana in which POLE2A and POLE2B proteins are involved. Through interactome analysis of POLE2A and POLE2B homolog proteins in A. thaliana, their additional roles in DNA repair were explored. The most important proteins that are participating in DNA repairs, like MSH2, MSH5, PCNA1, PCNA2, PRL, and CDC45 were identified as interactors of both POLE2A and POLE2B. The three-dimensional structure of POLE2 proteins was identified to decipher the complexity of NER, GG-NER, MMR, TFIIH, and TC-NER repair mechanisms through the identification of docking sites. The interaction complex of POLE2A and POLE2B with six proteins was confirmed and found to have a significant role in DNA repair processes and UV-B tolerance. The interactome analysis of POLE2A and POLE2B performed here once again confirms the complexity of the DNA repair mechanism in plants.

Highlights

Our results showed the structure of AtPOLE2A and confirmed that 93.8% of the residues are in favored region, 4.4% are in allowed region and 1.8% are in outlier region, whereas AtPOLE2B showed that 93.0% of the residues are in favored region, 5.8% are in allowed region and 1.2% are in outlier regions are predicted 3D Structure Models/Ramachandran Plot Validation
The 3D structure of POLE2 proteins was identified to decipher the complexity of Nucleotide excision repair (NER), GG-NER and TC-NER mechanisms through identification of docking sites. We found that both POLE2A and POLE2B are interacting with MSH2, MSH5, PCNA1, PCNA2, PRL and CDC45 and we confirmed the interaction complex, which has a significant role in DNA repair processes and UV-B tolerance
We have provided additional roles of POLE2A and POLE2B in A. thaliana through interactome analysis, and we have identified other important proteins that participate in DNA repair

Summary

Introduction

Arabidopsis thaliana as a plan model organism. Arabidopsis thaliana emerged a model organism for research in plant biology. A consensus was reached about the need to focus on a single organism to integrate the classical disciplines of plant science with the expanding fields of genetics and molecular biology. Ten years after publication of its genome sequence, A. thaliana remains the standard reference plant for all of fields of biology. A. thaliana has been proven to release volatile compounds when irradiated by UVC radiation (mostly methyl salicylate and methyl jasmonate), that cause genomic instability in neighboring plants, which even belongs to other species, like Nicotiana tabacum. To analyze and understand the specificities of plant DNA repair mechanisms, starting from well-researched model higher plant like A. thaliana is an inevitable step of plant science research, with far-reaching consequences [2]

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Conclusion