Bioinformatics and functional analysis define four distinct groups of AlkB DNA-dioxygenases in bacteria.
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.
van den Born
Erwin
E
Department of Molecular Biosciences, University of Oslo, PO Box 1041 Blindern, 0316 Oslo, Norway.
Bekkelund
Anders
A
Moen
Marivi N
MN
Omelchenko
Marina V
MV
Klungland
Arne
A
Falnes
Pål Ø
PØ
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000145:classification* / Q000235:genetics; D019295:Computational Biology; D004247:DNA / Q000378:metabolism; D004249:DNA Damage; D019175:DNA Methylation; D004260:DNA Repair; D045643:DNA Repair Enzymes / Q000737:chemistry / Q000145:classification* / Q000235:genetics; D004277:DNA, Single-Stranded / Q000378:metabolism; D049308:Dioxygenases / Q000737:chemistry / Q000145:classification* / Q000235:genetics; D029968:Escherichia coli Proteins / Q000737:chemistry; D005816:Genetic Complementation Test; D006899:Mixed Function Oxygenases / Q000737:chemistry; D008969:Molecular Sequence Data; D010802:Phylogeny; D012313:RNA / Q000378:metabolism; D020539:Sequence Analysis, Protein
D001426:Bacterial Proteins; D004277:DNA, Single-Stranded; D029968:Escherichia coli Proteins; D012313:RNA; D004247:DNA; D006899:Mixed Function Oxygenases; D049308:Dioxygenases; C466427:AlkB protein, E coli; D045643:DNA Repair Enzymes