Bioinformatic mapping of AlkB homology domains in viruses.
Bioinformatic mapping of AlkB homology domains in viruses.
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DOI：
10.1186/1471-2164-6-1
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发表时间：
2005-01-03
期刊：
影响因子：
4.4
通讯作者：
Drabløs F
中科院分区：
文献类型：
--
作者：
Bratlie MS;Drabløs F
AlkB样蛋白是2-酮戊二酸和Fe（II）依赖性加氧酶超家族的成员。在大肠杆菌中，这种蛋白质保护RNA和DNA免受甲基化剂的损害。1-甲基腺嘌呤和3-甲基胞嘧啶通过氧化去甲基化和甲基化碱基直接逆转回到其未甲基化形式来修复。AlkB同源物的基因在自然界中广泛存在，真核生物通常具有几个编码AlkB样蛋白的基因。在某些植物病毒中也观察到类似的结构域。病毒结构域的功能尚不清楚，但有人认为它可能参与保护病毒免受植物中发现的转录后基因沉默（PTGS）系统的影响。我们希望对病毒AlkB样结构域进行基因组定位，作为分析这些结构域功能方面的基础，因为这可能与理解AlkB同源物的可能替代作用有关，例如在真核生物中。蛋白质序列库的基于配置文件的搜索显示，AlkB样结构域中发现至少22个不同的单链RNA正链植物病毒，但主要是在一个亚组的病毒科。序列分析表明，AlkB结构域可能是功能上保守的，并且它们很可能是最近在地理上不同的位置被整合到几个病毒基因组中。这种模式似乎更符合增加的环境压力，例如从甲基化农药，而不是与PTGS系统的相互作用。在病毒基因组中发现的AlkB结构域最有可能是一种常规的DNA/RNA修复结构域，其保护病毒RNA基因组免受来自环境的甲基化化合物的侵害。
AlkB-like proteins are members of the 2-oxoglutarate- and Fe(II)-dependent oxygenase superfamily. In Escherichia coli the protein protects RNA and DNA against damage from methylating agents. 1-methyladenine and 3-methylcytosine are repaired by oxidative demethylation and direct reversal of the methylated base back to its unmethylated form. Genes for AlkB homologues are widespread in nature, and Eukaryotes often have several genes coding for AlkB-like proteins. Similar domains have also been observed in certain plant viruses. The function of the viral domain is unknown, but it has been suggested that it may be involved in protecting the virus against the post-transcriptional gene silencing (PTGS) system found in plants. We wanted to do a phylogenomic mapping of viral AlkB-like domains as a basis for analysing functional aspects of these domains, because this could have some relevance for understanding possible alternative roles of AlkB homologues e.g. in Eukaryotes. Profile-based searches of protein sequence libraries showed that AlkB-like domains are found in at least 22 different single-stranded RNA positive-strand plant viruses, but mainly in a subgroup of the Flexiviridae family. Sequence analysis indicated that the AlkB domains probably are functionally conserved, and that they most likely have been integrated relatively recently into several viral genomes at geographically distinct locations. This pattern seems to be more consistent with increased environmental pressure, e.g. from methylating pesticides, than with interaction with the PTGS system. The AlkB domain found in viral genomes is most likely a conventional DNA/RNA repair domain that protects the viral RNA genome against methylating compounds from the environment.
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DOI：
10.1073/pnas.89.22.10915
发表时间：
1992-11-15
影响因子：
11.1
作者：
HENIKOFF, S;HENIKOFF, JG
通讯作者：
HENIKOFF, JG
DOI：
10.2307/2413385
发表时间：
1986-09-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
DAY, WHE
通讯作者：
DAY, WHE
影响因子：
2.7
作者：
Adams, MJ;Antoniw, JF;Fauquet, CM
通讯作者：
Fauquet, CM
影响因子：
13.8
作者：
Begley, TJ;Samson, LD
通讯作者：
Samson, LD
影响因子：
1.7
作者：
Müller, T;Vingron, M
通讯作者：
Vingron, M