Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors.
Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors.
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DOI：
10.1186/gb-2002-3-3-research0012
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发表时间：
2002
期刊：
影响因子：
12.3
通讯作者：
Aravind L
中科院分区：
文献类型：
--
作者：
Iyer LM;Koonin EV;Aravind L
病毒DNA结合蛋白已成为研究转录调控和染色质动力学的生物化学的良好模型。病毒DNA结合调节蛋白的计算分析和识别其以前未检测到的同源物编码的细胞基因组可能会导致更好地了解它们的功能和进化的病毒和细胞系统。痘病毒D 6 R/N1 R和杆状病毒Bro蛋白家族的病毒调节蛋白的谱系范围和保守的DNA结合结构域以前没有被定义。使用计算分析，我们表明，D 6 R/N1 R蛋白的氨基末端模块定义了一个新的，保守的DNA结合域（KilA-N域），发现在大范围的蛋白质的细菌和真核DNA病毒。KilA-N结构域被认为与真菌DNA结合APSES结构域同源。我们提供的证据KilA-N和APSES域共享一个共同的折叠与核酸结合模块的LAGLIDADG核酸酶和氨基末端结构域的tRNA内切酶。Bro蛋白的氨基末端模块是另一个不同的DNA结合结构域（Bro-N结构域），其存在于结构域结构与含有KilA-N结构域的蛋白质的结构域结构相似的蛋白质中。对KilA-N和Bro-N结构域以及相关结构域的详细分析表明，DNA病毒基因组内存在广泛的结构域改组和谱系特异性基因家族扩增。我们定义了一大类新的病毒DNA结合蛋白和它们的细胞同源物，并确定它们的结构域架构。在系统模式分析的基础上，我们提出了一个可能的病毒起源的真菌特异性细胞周期调控转录因子含有APSES DNA结合域的证据。我们还证明了广泛的作用，谱系特异性基因扩增和结构域改组，在一组有限的约24个域，在产生的多样性的病毒特异性调节蛋白。
Viral DNA-binding proteins have served as good models to study the biochemistry of transcription regulation and chromatin dynamics. Computational analysis of viral DNA-binding regulatory proteins and identification of their previously undetected homologs encoded by cellular genomes might lead to a better understanding of their function and evolution in both viral and cellular systems. The phyletic range and the conserved DNA-binding domains of the viral regulatory proteins of the poxvirus D6R/N1R and baculoviral Bro protein families have not been previously defined. Using computational analysis, we show that the amino-terminal module of the D6R/N1R proteins defines a novel, conserved DNA-binding domain (the KilA-N domain) that is found in a wide range of proteins of large bacterial and eukaryotic DNA viruses. The KilA-N domain is suggested to be homologous to the fungal DNA-binding APSES domain. We provide evidence for the KilA-N and APSES domains sharing a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease. The amino-terminal module of the Bro proteins is another, distinct DNA-binding domain (the Bro-N domain) that is present in proteins whose domain architectures parallel those of the KilA-N domain-containing proteins. A detailed analysis of the KilA-N and Bro-N domains and the associated domains points to extensive domain shuffling and lineage-specific gene family expansion within DNA virus genomes. We define a large class of novel viral DNA-binding proteins and their cellular homologs and identify their domain architectures. On the basis of phyletic pattern analysis we present evidence for a probable viral origin of the fungus-specific cell-cycle regulatory transcription factors containing the APSES DNA-binding domain. We also demonstrate the extensive role of lineage-specific gene expansion and domain shuffling, within a limited set of approximately 24 domains, in the generation of the diversity of virus-specific regulatory proteins.