AlkB HOMOLOG 1, HISTONE H2A DIOXYGENASE; ALKBH

Alternative titles; symbols

• AlkB, E. COLI, HOMOLOG OF, 1
• ABH1
• ABH

HGNC Approved Gene Symbol: ALKBH1

Cytogenetic location: 14q24.3 Genomic coordinates (GRCh38): 14:77,672,403-77,708,037 (from NCBI)

▼ Cloning and Expression
DNA alkylating agents can lead to mutation, neoplasia, and cell death. Based on selective toxicity, alkylating agents are employed as antiviral drugs and in the chemotherapy of cancer. The Escherichia coli AlkB protein protects cells from mutation and cell death caused by SN2-type alkylating agents, such as methyl methanesulfonate (MMS). By EST database searching with E. coli AlkB as probe, followed by screening of a human synovial sarcoma cDNA library, Wei et al. (1996) cloned ALKBH1, which they called ABH. The ABH cDNA encodes a deduced 299-amino acid protein that is 52% similar and 23% identical to AlkB. Northern blot analysis revealed ubiquitous expression of a 2.1-kb ABH transcript. SDS-PAGE analysis showed that ABH was expressed as a 34-kD protein.

By PCR of a testis cDNA library, Tsujikawa et al. (2007) cloned full-length ABH1. The deduced 389-amino acid protein has a C-terminal AlkB homology domain that is predicted to function as a 2-oxoglutarate- and Fe(II)-dependent oxygenase domain. Quantitative real-time PCR detected ABH1 expression in all 16 tissues examined, with highest expression in spleen, followed by pancreas and placenta. Fluorescence-tagged ABH1 was expressed predominantly in the nucleus of transfected HeLa cells, with weaker cytoplasmic staining.

▼ Gene Function
Wei et al. (1996) found that expression of ABH in E. coli increased cell survival in the presence of MMS. Expression of ABH in fibroblasts resulted in no change in expression after exposure to MMS, suggesting that ABH may be regulated differently from E. coli AlkB.

It had been widely accepted that 5-methylcytosine is the only form of DNA methylation in mammalian genomes. Wu et al. (2016) identified N(6)-methyladenine as another form of DNA modification in mouse embryonic stem cells. Alkbh1 encodes a demethylase for N(6)-methyladenine. An increase of N(6)-methyladenine levels in Alkbh1-deficient cells leads to transcriptional silencing. N(6)-methyladenine deposition is inversely correlated with the evolutionary age of LINE-1 transposons; its deposition is strongly enriched at young (less than 1.5 million years old) but not old (more than 6 million years old) L1 elements. The deposition of N(6)-methyladenine correlates with epigenetic silencing of such LINE-1 transposons, together with their neighboring enhancers and genes, thereby resisting the gene activation signals during embryonic stem cell differentiation. As young full-length LINE-1 transposons are strongly enriched on the X chromosome, genes located on the X chromosome are also silenced. Thus, N(6)-methyladenine developed a role in epigenetic silencing in mammalian evolution distinct from its role in gene activation in other organisms. Wu et al. (2016) concluded that their results demonstrated that N(6)-methyladenine constitutes a crucial component of the epigenetic regulation repertoire in mammalian genomes.

Besides the conventional AUG methionine codon, mitochondrial tRNA(met) (MTTM; 590065) recognizes AUU and AUA as methionine for translation initiation and protein elongation, respectively. Haag et al. (2016) found that recognition of unconventional methionine codons required modification of C34 within the wobble position of MTTM. The 5-methylcytosine (m5C) methyltransferase NSUN3 (617491) recognized the anticodon stem loop of MTTM and methylated C34 to m5C34. ABH1 subsequently oxidized m5C34 to 5-formylcytosine (f5C34). Knockdown of ABH1 abolished f5C34 formation, whereas depletion of NSUN3 reduced MTTM modification. Knockdown of either enzyme led to significant reduction in mitochondrial translation.

▼ Biochemical Features
Crystal Structure

Yu et al. (2006) determined the crystal structures of substrate and product complexes of E. coli AlkB at resolutions from 1.8 to 2.3 angstroms. Whereas the Fe-2-oxoglutarate dioxygenase core matches that in other superfamily members, a unique subdomain holds a methylated trinucleotide substrate into the active site through contacts with the polynucleotide backbone. Amide hydrogen exchange studies and crystallographic analyses suggested that this substrate-binding 'lid' is conformationally flexible, which may enable docking of diverse alkylated nucleotide substrates in optimal catalytic geometry. Different crystal structures showed open and closed states of a tunnel putatively gating oxygen diffusion into the active site. Exposing crystals of the anaerobic Michaelis complex to air yielded slow but substantial oxidation of 2-oxoglutarate that was inefficiently coupled to nucleotide oxidation. Yu et al. (2006) concluded that protein dynamics modulate redox chemistry and that a hypothesized migration of the reactive oxy-ferryl ligand on the catalytic Fe ion may be impeded when the protein is constrained in the crystal lattice.

▼ Mapping
By FISH, Wei et al. (1996) mapped the ALKBH1 gene to chromosome 14q24, just at the border with 14q31. The authors noted that this region is frequently altered in leiomyoma.