Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains.
Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains.
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DOI：
10.1093/nar/gki709
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发表时间：
2005
影响因子：
14.9
通讯作者：
Aravind L
中科院分区：
文献类型：
--
作者：
Balaji S;Babu MM;Iyer LM;Aravind L
比较基因组学的apicomplexans，如疟疾寄生虫疟原虫，牛寄生虫泰勒虫和新兴的人类寄生虫隐孢子虫，提出了一个意想不到的缺乏特定的转录因子（TF）的DNA结合结构域，是密切相关的主要家庭的TF从其他真核生物。这种明显缺乏特定的转录因子是矛盾的，因为顶复门在一个或多个宿主中显示出复杂的发育周期，并且在这个周期中具有可重复的差异基因表达模式。使用敏感的序列分析搜索，我们表明，apicomplexans拥有一个新的家族的蛋白质的一个版本的AP 2（Apetala 2）-整合酶DNA结合域，这是目前在许多植物TF的谱系特异性扩展。大约20-27个apicomplexan AP 2（ApiAP 2）家族成员在不同的apicomplexan基因组中编码，每个蛋白质含有一到四个拷贝的AP 2 DNA结合结构域。利用恶性疟原虫的基因表达数据，我们表明，公会的ApiAP 2基因表达在红细胞内发育的不同阶段。通过类比植物AP 2蛋白的表达模式的基础上，我们预测，ApiAP 2蛋白很可能作为以前未知的特定TF在apicomplexans和调节其发育周期的进展。除了ApiAP 2家族，我们还在细菌和转座子中鉴定了另外两个新的AP 2 DNA结合结构域家族。使用结构相似性搜索，我们还确定了不同版本的AP 2-整合酶DNA结合结构域折叠的DNA结合区域的PI-SceI归巢核酸内切酶和C-末端结构域的普列克底物蛋白同源性（PH）结构域样模块的真核生物。整合这些发现，我们提出了一个重建的AP 2整合酶DNA结合域折叠的进化方案，这表明它经历了多个独立的组合与不同类型的移动的核酸内切酶或重组酶。似乎真核生物的版本已经从与移动的元件相关的结构域的版本中出现，随后是独立的谱系特异性扩增，这伴随着它们对转录调节功能的募集。
The comparative genomics of apicomplexans, such as the malarial parasite Plasmodium, the cattle parasite Theileria and the emerging human parasite Cryptosporidium, have suggested an unexpected paucity of specific transcription factors (TFs) with DNA binding domains that are closely related to those found in the major families of TFs from other eukaryotes. This apparent lack of specific TFs is paradoxical, given that the apicomplexans show a complex developmental cycle in one or more hosts and a reproducible pattern of differential gene expression in course of this cycle. Using sensitive sequence profile searches, we show that the apicomplexans possess a lineage-specific expansion of a novel family of proteins with a version of the AP2 (Apetala2)-integrase DNA binding domain, which is present in numerous plant TFs. About 20–27 members of this apicomplexan AP2 (ApiAP2) family are encoded in different apicomplexan genomes, with each protein containing one to four copies of the AP2 DNA binding domain. Using gene expression data from Plasmodium falciparum, we show that guilds of ApiAP2 genes are expressed in different stages of intraerythrocytic development. By analogy to the plant AP2 proteins and based on the expression patterns, we predict that the ApiAP2 proteins are likely to function as previously unknown specific TFs in the apicomplexans and regulate the progression of their developmental cycle. In addition to the ApiAP2 family, we also identified two other novel families of AP2 DNA binding domains in bacteria and transposons. Using structure similarity searches, we also identified divergent versions of the AP2-integrase DNA binding domain fold in the DNA binding region of the PI-SceI homing endonuclease and the C-terminal domain of the pleckstrin homology (PH) domain-like modules of eukaryotes. Integrating these findings, we present a reconstruction of the evolutionary scenario of the AP2-integrase DNA binding domain fold, which suggests that it underwent multiple independent combinations with different types of mobile endonucleases or recombinases. It appears that the eukaryotic versions have emerged from versions of the domain associated with mobile elements, followed by independent lineage-specific expansions, which accompanied their recruitment to transcription regulation functions.
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影响因子：
9.8
作者：
Bozdech, Zbynek;Llinas, Manuel;Pulliam, Brian Lee;Wong, Edith D;Zhu, Jingchun;DeRisi, Joseph L
通讯作者：
DeRisi, Joseph L
DOI：
10.1073/pnas.94.11.5961
发表时间：
1997-05-27
影响因子：
11.1
作者：
Buttner, M;Singh, KB
通讯作者：
Singh, KB
影响因子：
7
作者：
Coulson, RMR;Hall, N;Ouzounis, CA
通讯作者：
Ouzounis, CA
影响因子：
5.8
作者：
Cuff, JA;Clamp, ME;Barton, GJ
通讯作者：
Barton, GJ
影响因子：
13.8
作者：
Aravind, L
通讯作者：
Aravind, L