Article

Bioinformatics and functional analysis define four distinct groups of AlkB DNA-dioxygenases in bacteria

Department of Molecular Biosciences, University of Oslo, PO Box 1041 Blindern, 0316 Oslo, Norway.
Nucleic Acids Research (Impact Factor: 9.11). 09/2009; 37(21):7124-36. DOI: 10.1093/nar/gkp774
Source: PubMed

ABSTRACT The iron(II)- and 2-oxoglutarate (2OG)-dependent dioxygenase AlkB from Escherichia coli (EcAlkB) repairs alkylation damage in DNA by direct reversal. EcAlkB substrates include methylated bases, such as 1-methyladenine (m(1)A) and 3-methylcytosine (m(3)C), as well as certain bulkier lesions, for example the exocyclic adduct 1,N(6)-ethenoadenine (epsilonA). EcAlkB is the only bacterial AlkB protein characterized to date, and we here present an extensive bioinformatics and functional analysis of bacterial AlkB proteins. Based on sequence phylogeny, we show that these proteins can be subdivided into four groups: denoted 1A, 1B, 2A and 2B; each characterized by the presence of specific conserved amino acid residues in the putative nucleotide-recognizing domain. A scattered distribution of AlkB proteins from the four different groups across the bacterial kingdom indicates a substantial degree of horizontal transfer of AlkB genes. DNA repair activity was associated with all tested recombinant AlkB proteins. Notably, both a group 2B protein from Xanthomonas campestris and a group 2A protein from Rhizobium etli repaired etheno adducts, but had negligible activity on methylated bases. Our data indicate that the majority, if not all, of the bacterial AlkB proteins are DNA repair enzymes, and that some of these proteins do not primarily target methylated bases.

Download full-text

Full-text

Available from: Pål Ø Falnes, Aug 28, 2015
0 Followers
 · 
124 Views
  • Source
    • "Although homologues of EcAlkB can be found in viruses, eubacteria and eukaryotes, many organisms within these groups lack AlkB homologues (20–24). However, the genomes of multicellular eukaryotes typically encode several different AlkB homologues, and mammals have eight such proteins, ALKBH1–8, as well as the somewhat more distantly related FTO (ALKBH9) protein (21,25,26). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The Escherichia coli AlkB protein (EcAlkB) is a DNA repair enzyme which reverses methylation damage such as 1-methyladenine (1-meA) and 3-methylcytosine (3-meC). The mammalian AlkB homologues ALKBH2 and ALKBH3 display EcAlkB-like repair activity in vitro, but their substrate specificities are different, and ALKBH2 is the main DNA repair enzyme for 1-meA in vivo. The genome of the model plant Arabidopsis thaliana encodes several AlkB homologues, including the yet uncharacterized protein AT2G22260, which displays sequence similarity to both ALKBH2 and ALKBH3. We have here characterized protein AT2G22260, by us denoted ALKBH2, as both our functional studies and bioinformatics analysis suggest it to be an orthologue of mammalian ALKBH2. The Arabidopsis ALKBH2 protein displayed in vitro repair activities towards methyl and etheno adducts in DNA, and was able to complement corresponding repair deficiencies of the E. coli alkB mutant. Interestingly, alkbh2 knock-out plants were sensitive to the methylating agent methylmethanesulphonate (MMS), and seedlings from these plants developed abnormally when grown in the presence of MMS. The present study establishes ALKBH2 as an important enzyme for protecting Arabidopsis against methylation damage in DNA, and suggests its homologues in other plants to have a similar function.
    Nucleic Acids Research 04/2012; 40(14):6620-31. DOI:10.1093/nar/gks327 · 9.11 Impact Factor
  • Source
    • "Earlier bioinformatics methods had been used to show the relatedness between the different human homologues of Alkb proteins (Kurowski et al., 2003) as well as for the theoretical investigations of structure and function of hABH1 (Shankaracharya et al., 2010a) and hABH4 (Shankaracharya et al., 2010b) proteins. It was also observed, in another study, that majority of the bacterial AlkB proteins are DNA repair enzymes, and some of these proteins do not primarily target methylated bases (Born et al., 2009). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Newly discovered human homologues of ALKB protein have shown the activity of DNA damaging drugs, used for cancer therapy. Little is known about the structure and function of hABH5, one of the members of this superfamily. Therefore, in the present study we intend to predict its structure and function using various bioinformatics tools. Modeling was done with modeler 9v7 to predict the 3D structure of the hABH5 protein. 3-D model of hABH5, ALKBH5.B99990005.pdb was predicted and evaluated. Validation results showed 96.8% residues in favor and an additional allowed region of the Ramachandran plot. Ligand binding residues prediction showed four ligand clusters, having 25 ligands in cluster 1. Importantly, conserved pattern of Pro158-X-Asp160-Xn-His266 in the functional domain was detected. DNA and RNA binding sites were also predicted in the model. The predicted and validated model of human homologue hABH5 resulting from this study may unveil the mechanism of DNA damage repair in humans and accelerate research on designing appropriate inhibitors, aiding in chemotherapy and cancer related diseases.
    Nature Precedings 01/2011; DOI:10.1038/npre.2011.5597.2
  • Source
    • "Earlier bioinformatics methods had been used to show the relatedness between the different human homologues of Alkb proteins (Kurowski et al., 2003) as well as for the theoretical investigations of structure and function of hABH1 (Shankaracharya et al., 2010a) and hABH4 (Shankaracharya et al., 2010b) proteins. It was also observed, in another study, that majority of the bacterial AlkB proteins are DNA repair enzymes, and some of these proteins do not primarily target methylated bases (Born et al., 2009). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Newly discovered human homologues of ALKB protein have shown the activity of DNA damaging drugs, used for cancer therapy. Little is known about the structure and function of hABH5, one of the members of this superfamily. Therefore, in the present study we intend to predict its structure and function using various bioinformatics tools. Modeling was done with modeler 9v7 to predict the 3D structure of the hABH5 protein. 3-D model of hABH5, ALKBH5.B99990005.pdb was predicted and evaluated. Validation results showed 96.8% residues in favor and an additional allowed region of the Ramachandran plot. Ligand binding residues prediction showed four ligand clusters, having 25 ligands in cluster 1. Importantly, conserved pattern of Pro158-X-Asp160-Xn-His266 in the functional domain was detected. DNA and RNA binding sites were also predicted in the model. The predicted and validated model of human homologue hABH5 resulting from this study may unveil the mechanism of DNA damage repair in humans and accelerate research on designing appropriate inhibitors, aiding in chemotherapy and cancer related diseases.
    Nature Precedings 01/2011; DOI:10.1038/npre.2011.5597.1
Show more