Exploring the biological functions of AlkB proteins and how they relate to AAG

Abstract

Our DNA is constantly under the assault of DNA damaging agents that are ubiquitous in nature and unavoidable. Fortunately, our cells have evolved DNA repair mechanisms to maintain genomic integrity against this constant attack. An important type of DNA damage is alkylation damage, which has been the focus of this thesis, the major goal of which is to explore the biological role of a set of alkylation repair proteins, the E. coli AlkB and two human AlkB homologs (ABH2 and ABH3), and how they relate to the 3methyladenine DNA glycosylase (AAG). AAG is a base excision repair (BER) protein that has been well-studied and is known to be involved in the repair of a wide variety of substrates. On the other hand, the direct reversal protein AlkB, and its human homologs, have not been so extensively characterized, but it is known that they can repair not only DNA, but also RNA. Although there are eight human AlkB homologs, attention was focused on ABH2 and ABH3 since they are the more well-characterized homologs and recently implicated in DNA repair.In order to investigate the role of the AlkB proteins, particularly in mammalian cells, I expressed ABH2 and ABH3 in established human cell lines and investigated whether their expression would enhance cell survival after alkylation treatment. However, no detectable phenotype was observed in the cell lines upon treatment with the alkylating agent methyl methanesulfonate (MMS). This is possibly due to endogenous ABH levels being sufficient for repair. We therefore turned to characterization of the Abh2 and Abh3 null mice, as compared to wildtype and to another alkylation repair deficient animal, Aag null mice. In addition to the primary substrates 1methyladenine and 3-methylcytosine, AlkB, ABH2, and ABH3 can also repair an important class of damage, the etheno base DNA lesions, which can also be repaired by AAG.

(cont.) Here we have shown in a mouse model that Abh2 and Abh3 overlap with Aag in protecting mice from sensitivity in response to chemically induced chronic inflammation, in which etheno base lesions are readily generated. In addition, we also employed a biochemical approach using a comprehensive library of lesion-containing DNA oligonucleotides to study the redundancy in repair activity between AAG and AlkB. In doing so, we have found new substrates for AAG and in particular, 1-methylguanine, is a new substrate shared between AAG and AlkB. Thus, although these two proteins employ different mechanisms for repair, our studies established further evidence of the interplay between these proteins and the different repair pathways they represent, underscoring the importance of alkylation damage repair for proper cell homeostasis.