Prediction and Investigation of Novel Proteins in DNA Double Stranded Break Repair

DNA double stranded breaks (DSBs) are the most genotoxic forms of DNA lesions, causing fragmentation of the DNA strands. Mis-repaired and unrepaired DSBs lead to chromosomal rearrangement and genomic instability promoting tumorigenesis. DSBs are primarily repaired by two independent and highly conserved pathways: homologous recombination (HR) and non-homologous end joining (NHEJ). HR requires a homologous sequence to repair DNA breaks, whereas NHEJ repair is achieved through direct ligation of the broken ends of DNA. The process of NHEJ involves three main protein complexes: Yku70/Yku80 initiates and stabilizes the DNA ends, Mre11/Rad50/Xrs2 brings broken ends to close proximity and Dnl4/Lif1/Nej1 ligates the DNA ends. Protein-protein interaction (PPI) has been utilized in functional genomics studies to identify novel proteins involved in different pathways based on their PPI profiles. In this study we aim to screen for novel proteins involved in NHEJ using PPI predictions. We use a computational tool to predict novel PPIs between DNA repair proteins and human proteome. Using this method, we predicted 271 novel PPIs, expanding the reported human DNA repair interactome by 75%. Yeast homologs of the novel human gene candidates were subjected to a plasmid-based repair assay, in which deletion of eight of 12 yeast genes showed reduction in the repair efficiency. We further investigated the roles of Tpk1, Arp6 and Psk1/Psk2 in NHEJ repair. Deletion of TPK1, ARP6, PSK1 and PSK2 reduced efficiency of repair in chromosomal and plasmid based assays and showed sensitivity to different DNA damaging agents. We suggest that Tpk1, catalytic subunit of protein kinase A, is involved in recruitment of Nej1 to the site of damage and its role in NHEJ is dependent on Nej1. We propose that the involvement of actin related protein 6, Arp6, in NHEJ is linked to Rsc2 and Mre11. Additionally, we suggest a role for PAS kinase complex, Psk1/Psk2, that is connected to DNA damage checkpoint proteins.

Name thesis:degree_name

Doctor of Philosophy (Ph.D.)

Level thesis:degree_level

Doctoral

Discipline thesis:degree_discipline

Biology

Grantor dc:publisher

Carleton University

Year dc:date.issued

2016

Author dc:creator

• Hooshyar, Mohsen

Statement dc:rights

• Copyright © 2016 the author(s). Theses may be used for non-commercial research, educational, or related academic purposes only. Such uses include personal study, research, scholarship, and teaching. Theses may only be shared by linking to Carleton University Institutional Repository and no part may be used without proper attribution to the author. No part may be used for commercial purposes directly or indirectly via a for-profit platform; no adaptation or derivative works are permitted without consent from the copyright owner.

Language dc:language.iso

en

DOI

10.22215/etd/2016-11472

OAI identifier oai:identifier

oai:carleton.scholaris.ca:20.500.14718/38887