Department of Molecular Biosciences, University of Oslo, PO Box 1041 Blindern, 0316 Oslo, Norway.
Nucleic Acids Res. 2009 Nov;37(21):7124-36. doi: 10.1093/nar/gkp774.
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.
大肠杆菌（EcAlkB）中的铁(II)和 2-氧戊二酸（2OG）依赖性双加氧酶 AlkB 通过直接逆转来修复 DNA 中的烷基化损伤。EcAlkB 的底物包括甲基化碱基，如 1-甲基腺嘌呤（m(1)A）和 3-甲基胞嘧啶（m(3)C），以及某些更大的损伤，例如外切加合物 1,N(6)-乙烯腺嘌呤（epsilonA）。EcAlkB 是迄今为止唯一被表征的细菌 AlkB 蛋白，我们在此对细菌 AlkB 蛋白进行了广泛的生物信息学和功能分析。基于序列系统发育，我们表明这些蛋白质可以分为四组：分别表示为 1A、1B、2A 和 2B；每组在假定的核苷酸识别结构域中都具有特定的保守氨基酸残基。细菌界中四个不同组的 AlkB 蛋白的分散分布表明 AlkB 基因存在大量水平转移。所有测试的重组 AlkB 蛋白都具有 DNA 修复活性。值得注意的是，来自野油菜黄单胞菌的 2B 组蛋白和来自根瘤菌的 2A 组蛋白都能修复乙撑加合物，但对甲基化碱基的活性可忽略不计。我们的数据表明，大多数（如果不是全部）细菌 AlkB 蛋白都是 DNA 修复酶，并且其中一些蛋白并非主要针对甲基化碱基。
