Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52.
Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52.
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DOI：
10.1186/1471-2164-3-8
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发表时间：
2002-03-21
期刊：
影响因子：
4.4
通讯作者：
Aravind L
中科院分区：
文献类型：
--
作者：
Iyer LM;Koonin EV;Aravind L
RECT、红色β、ERF和RAD52等单链退火蛋白在RECA依赖和非RECA依赖的DNA重组途径中发挥作用。最近，它们被证明形成了类似的螺旋四元超结构。然而，尽管这些不同的SSAP之间在功能上有相似之处，但它们实际的进化亲和力却鲜为人知。利用灵敏的计算序列分析，我们发现RECT和REDβ蛋白与其他几种细菌蛋白一起形成了一个不同的超家族。ERF和Rad52家族与这些蛋白没有直接的进化关系，并定义了它们自己的新的超家族。我们确定了每个超家族中以前未知的几个成员，并首次报告了Rad52的细菌和病毒同源物。此外，我们预测RAD52中存在可能参与DNA结合的异常HHH模块。利用从基因邻域分析中获得的上下文信息，我们提供了每个SSAP超家族的细菌成员与一组相似的DNA修复/重组蛋白相互作用的证据。这些包括不同的核酸酶或Holliday连接解析酶，ABC ATPase SBCC和单链结合蛋白。我们还提供了一些编码SSAP的预测操纵子的独立组装和功能相似基因的原位移位的证据。在进化上有三个不同的超家族，即RECT/REDβ、ERF和RAD52，它们具有不同的序列保守模式和预测的折叠。所有这些SSAP似乎主要是由噬菌体起源的，并由许多系统发育上遥远的细胞基因组获得。它们通常出现在编码一组保守的DNA重组蛋白中的一个或多个的预测操纵子中，这些蛋白似乎是SSAP的主要功能伙伴。
The DNA single-strand annealing proteins (SSAPs), such as RecT, Redβ, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. Recently, they have been shown to form similar helical quaternary superstructures. However, despite the functional similarities between these diverse SSAPs, their actual evolutionary affinities are poorly understood. Using sensitive computational sequence analysis, we show that the RecT and Redβ proteins, along with several other bacterial proteins, form a distinct superfamily. The ERF and Rad52 families show no direct evolutionary relationship to these proteins and define novel superfamilies of their own. We identify several previously unknown members of each of these superfamilies and also report, for the first time, bacterial and viral homologs of Rad52. Additionally, we predict the presence of aberrant HhH modules in RAD52 that are likely to be involved in DNA-binding. Using the contextual information obtained from the analysis of gene neighborhoods, we provide evidence of the interaction of the bacterial members of each of these SSAP superfamilies with a similar set of DNA repair/recombination protein. These include different nucleases or Holliday junction resolvases, the ABC ATPase SbcC and the single-strand-binding protein. We also present evidence of independent assembly of some of the predicted operons encoding SSAPs and in situ displacement of functionally similar genes. There are three evolutionarily distinct superfamilies of SSAPs, namely the RecT/Redβ, ERF, and RAD52, that have different sequence conservation patterns and predicted folds. All these SSAPs appear to be primarily of bacteriophage origin and have been acquired by numerous phylogenetically distant cellular genomes. They generally occur in predicted operons encoding one or more of a set of conserved DNA recombination proteins that appear to be the principal functional partners of the SSAPs.
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