Oxidative dealkylation DNA repair mediated by the mononuclear non-heme iron AlkB proteins

Abstract

DNA can be damaged by various intracellular and environmental alkylating agents to produce alkylation base lesions. These base damages, if not repaired promptly, may cause genetic changes that lead to diseases such as cancer. Recently, it was discovered that some of the alkylation DNA base damage can be directly removed by a family of proteins called the AlkB proteins that utilize a mononuclear non-heme iron(II) and α-ketoglutarate as cofactor and cosubstrate. These proteins activate dioxygen and perform an unprecedented oxidative deal-kylation of the alkyl adducts on DNA heteroatoms. This review summarizes the discovery of this activity and the recent research advances in studying this unique DNA repair pathway. The focus is placed on the chemical mechanism and function of these proteins. KeywordsDNA repair; AlkB; ABH; Direct repair; Mononuclear non-heme iron; Dioxygenase; Oxidative dealkylation; Demethylation Direct repair of alkylation DNA damageCellular DNA is subject to nonenzymatic alkylation (methylation) by environmental or chemical mutagens, resulting in adducts that are toxic and mutagenic [1][2][3][4][5][6]. Organisms have evolved a variety of mechanisms to repair these mutagenic damages. Escherichia coli (E. coli) responds to this threat by activating an adaptive responsive pathway, mediated by the E. coli Ada protein [7]. Upon receiving a methyl group from the damaged DNA, Ada turns into a transcriptional activator and activates its own expression and that of the alkB gene and two other genes, alkA and aidB ( Fig. 1(a)) [4,7,8]. The upregulated Ada is a bifunctional protein, which uses a N-terminal Cys38 residue to remove a methyl group fromS p -methylphosphotriester and a C-terminal Cys321 residue to remove a methyl adduct from O 6 -methylguanaine ( Fig. 1(b)) [9][10][11]. Both repair functions are irreversible and represent rare examples of direct repair of DNA damage. AlkA is a glycosylase that cleaves methylated bases from DNA and performs the first step of the well-known base excision repair of base lesions [12][13][14]. The precise function of AidB is still unknown. The function of the last member of this adaptive response, AlkB, also remained unknown until recently despite extensive research efforts. E. coli AlkBSince the first genetic study in 1983 isolating the E. coli mutant with specific sensitivity to the alkylating agent methylmethane sulfonate, MMS [15], the activity of AlkB was undisclosed The Fe II /αKG-dependent dioxygenase superfamily is widespread from bacteria to humans [19] and is the largest known non-heme iron protein family [20][21][22][23]. It represents a wide diversity of enzymes that catalyze the hydroxylation of unactivated C-H groups of a variety of substrates by coupling reductive activation of dioxygen with a decarbox-ylation of αKG, the co-substrate, to succinate. In the event of oxidation one of the oxygen atoms from O 2 is incorporated into the succinate and the other as a hydroxyl in the product [24]. This group of enzymes is known for their importance in ...

Protein Arginine Methyltransferase 7 Regulates Cellular Response to DNA Damage by Methylating Promoter Histones H2A and H4 of the Polymerase δ Catalytic Subunit Gene, POLD1

“…More recently, ALKB has been found to be highly conserved in various species, and currently there are eight homologs in human cells, including ALKBH5 (hABH5) (32)(33)(34). Although all hABH proteins share sequence similarities with bacterial ALKB, only hABH2 and hABH3 have DNA repair functions and catalyze oxidative demethylation in the presence of Fe(II) and ␣-ketoglutarate.…”

High-Valent Iron(IV)–Oxo Complexes of Heme and Non-Heme Ligands in Oxygenation Reactions

“…64,65 Non-heme iron enzymes participate in oxidative Ndealkylationreactionsinnature,andhigh-valentiron(IV)-oxo species have been invoked as an active oxidant that effects the oxygenation of organic substrates. 66 We , N-methylaniline was produced as a major product with the concurrent formation of CH 2 O. 26 Detailed mechanistic studies were carried out in an effort to understand whether the oxidative N-dealkylation occurs via an electron transfer-proton transfer (ET-PT) mechanism or a hydrogen atom transfer (HAT) (Scheme 8).…”

Oxygen Atom Transfer

“…34 Nonheme iron(IV) oxo complexes have also been shown to effect oxidative N-dealkylation, a reaction recognized in nature for nonheme iron enzymes. 43 Mechanistic studies on the reaction of synthetic models with N,N-dimethylaniline demonstrated that rather than HAT the reaction proceeds via electron transfer followed by proton transfer. 40 Finally, nonheme iron(IV) oxo species undergo complete intermetallic OAT to Fe II .…”