Bioinformatics and functional analysis define four distinct groups of AlkB DNA-dioxygenases in bacteria.
Bioinformatics and functional analysis define four distinct groups of AlkB DNA-dioxygenases in bacteria.
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DOI：
10.1093/nar/gkp774
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发表时间：
2009-11
影响因子：
14.9
通讯作者：
Falnes PØ
中科院分区：
文献类型：
--
作者：
van den Born E;Bekkelund A;Moen MN;Omelchenko MV;Klungland A;Falnes PØ
来自大肠杆菌（EcAlkB）的铁（II）和2-氧戊二酸（2OG）依赖的双加氧酶（EcAlkB）通过直接逆转修复DNA中的烷基化损伤。EcAlkB底物包括甲基化碱基，如1-甲基腺嘌呤（m1A）和3-甲基胞嘧啶（m3C），以及某些体积较大的损伤，如外环加合物1 n6 -乙烯腺嘌呤（εA）。EcAlkB是迄今为止唯一鉴定的细菌AlkB蛋白，我们在这里提出了广泛的生物信息学和细菌AlkB蛋白的功能分析。根据序列系统发育，我们发现这些蛋白可以细分为四组：分别表示为1A、1B、2A和2B；每一种都以在假定的核苷酸识别域中存在特定的保守氨基酸残基为特征。来自四个不同群体的AlkB蛋白在细菌界的分散分布表明AlkB基因在相当程度上的水平转移。DNA修复活性与所有测试的重组AlkB蛋白相关。值得注意的是，来自黄单胞菌的2B组蛋白和来自根瘤菌的2A组蛋白都能修复乙烯加合物，但对甲基化碱基的活性可以忽略不计。我们的数据表明，大多数（如果不是全部的话）细菌AlkB蛋白是DNA修复酶，其中一些蛋白并不主要针对甲基化碱基。
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 (m1A) and 3-methylcytosine (m3C), as well as certain bulkier lesions, for example the exocyclic adduct 1,N6-ethenoadenine (εA). 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.
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DOI：
10.1093/bioinformatics/8.3.275
发表时间：
1992-06-01
期刊：
COMPUTER APPLICATIONS IN THE BIOSCIENCES
影响因子：
--
作者：
JONES, DT;TAYLOR, WR;THORNTON, JM
通讯作者：
THORNTON, JM
影响因子：
4.4
作者：
Blatny, JM;Brautaset, T;Valla, S
通讯作者：
Valla, S
DOI：
10.1126/science.1151710
发表时间：
2007-11-30
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Gerken T;Girard CA;Tung YC;Webby CJ;Saudek V;Hewitson KS;Yeo GS;McDonough MA;Cunliffe S;McNeill LA;Galvanovskis J;Rorsman P;Robins P;Prieur X;Coll AP;Ma M;Jovanovic Z;Farooqi IS;Sedgwick B;Barroso I;Lindahl T;Ponting CP;Ashcroft FM;O'Rahilly S;Schofield CJ
通讯作者：
Schofield CJ
DOI：
10.1073/pnas.0403489101
发表时间：
2004-09-28
影响因子：
11.1
作者：
Delaney, JC;Essigmann, JM
通讯作者：
Essigmann, JM
影响因子：
4.1
作者：
Kim, Min Young;Zhou, Xinfeng;Wogan, Gerald N.
通讯作者：
Wogan, Gerald N.