Phylogenomic analysis of the GIY-YIG nuclease superfamily.
Phylogenomic analysis of the GIY-YIG nuclease superfamily.
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DOI：
10.1186/1471-2164-7-98
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发表时间：
2006-04-28
期刊：
影响因子：
4.4
通讯作者：
Bujnicki JM
中科院分区：
文献类型：
--
作者：
Dunin-Horkawicz S;Feder M;Bujnicki JM
GIY-YIG结构域最初在归巢核酸内切酶中被鉴定，后来在其他自私的移动的遗传元件（包括限制性酶和非LTR反转录转座子）和参与DNA修复和重组的酶中被鉴定。然而，迄今为止，没有系统的搜索新的成员的GIY-YIG超家族或比较分析这些酶的报道。我们进行了数据库搜索，以确定已知的GIY-YIG核酸酶家族的所有成员。多重序列比对以及预测的二级结构的确定的家庭表示为隐马尔可夫模型（HMM）和比较的HH搜索方法收集的COG，KOG和PFAM数据库中的未表征的蛋白质家族。该分析允许扩展GIY-YIG超家族以包括COG 3680的成员和未分类在COG中的许多蛋白质，并预测这些蛋白质可能作为核酸酶起作用，潜在地参与DNA重组和/或修复。最后，对GIY-YIG超家族的所有新老成员进行了比较分析，构建了系统发育树。首次对GIY-YIG超家族进行了进化分类，并沿着对所有（子）家族进行了结构注释。它提供了这个核酸酶超家族中序列-结构-功能关系的全面图片，这将有助于设计实验来研究已知成员（特别是未表征的成员）的作用机制，并将有助于预测新发现的成员的功能。
The GIY-YIG domain was initially identified in homing endonucleases and later in other selfish mobile genetic elements (including restriction enzymes and non-LTR retrotransposons) and in enzymes involved in DNA repair and recombination. However, to date no systematic search for novel members of the GIY-YIG superfamily or comparative analysis of these enzymes has been reported. We carried out database searches to identify all members of known GIY-YIG nuclease families. Multiple sequence alignments together with predicted secondary structures of identified families were represented as Hidden Markov Models (HMM) and compared by the HHsearch method to the uncharacterized protein families gathered in the COG, KOG, and PFAM databases. This analysis allowed for extending the GIY-YIG superfamily to include members of COG3680 and a number of proteins not classified in COGs and to predict that these proteins may function as nucleases, potentially involved in DNA recombination and/or repair. Finally, all old and new members of the GIY-YIG superfamily were compared and analyzed to infer the phylogenetic tree. An evolutionary classification of the GIY-YIG superfamily is presented for the very first time, along with the structural annotation of all (sub)families. It provides a comprehensive picture of sequence-structure-function relationships in this superfamily of nucleases, which will help to design experiments to study the mechanism of action of known members (especially the uncharacterized ones) and will facilitate the prediction of function for the newly discovered ones.
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影响因子：
10.5
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