The evolutionary repertoires of the eukaryotic-type ABC transporters in terms of the phylogeny of ATP-binding domains in eukaryotes and prokaryotes
The evolutionary repertoires of the eukaryotic-type ABC transporters in terms of the phylogeny of ATP-binding domains in eukaryotes and prokaryotes
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DOI：
10.1093/molbev/msh226
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发表时间：
2004-11-01
影响因子：
10.7
通讯作者：
Kanehisa, M
中科院分区：
文献类型：
--
作者：
Igarashi, Y;Aoki, KF;Kanehisa, M
ABC（ATP结合盒）转运蛋白在各种底物跨细胞膜的通讯中起重要作用。它们普遍存在于原核生物和真核生物中，真核生物类型（EK型）在基因和结构域组织方面与原核生物类型（PK型）不同。EK型和PK型主要分别由出口商和进口商组成。原核生物有EK型和PK型。原核生物中的EK型通常被称为“细菌多药ABC转运蛋白”，但与真核生物中的多药ABC转运蛋白相比，它们的特征并不明显。因此，在不同生物中详尽地搜索EK型并进行详细的序列分类和分析将阐明EK型的进化历史。这也将有助于揭示真核生物中多药ABC转运蛋白沟通的各种底物的基本特征。在这项工作中，我们已经确定了EK型ABC转运蛋白在126个原核生物使用的轮廓的ATP结合结构域（NBD）的EK型ABC转运蛋白从12个真核生物。结果，从1,046个EK型ABC转运蛋白中鉴定出11个簇。特别是，出现了两个大的新簇，对应于与ABCB和ABCB相关的细菌多药ABC转运蛋白。真核生物中的ABCC家族。在基因组背景下，这些基因中的大多数单独定位或与来自相同簇的基因相邻。此外，为了检测NBD中的功能差异，在这些细菌多药物转运蛋白中测量Kullback-Leibler差异。结果，鉴定了几个推定的功能区域，其中一些对应于预测的二级结构。我们还分析了原核生物和真核生物中的EK型ABC转运蛋白的同源性，这表明原核生物中的EK型ABC转运蛋白具有与真核生物中的常规ABC蛋白组相对应的某些库。在此基础上，我们提出了一个更新的进化假说，即真核生物和原核生物中的EK型ABC转运蛋白是由真核细胞和原核细胞分化前的几种假定祖先细胞中的ABC转运蛋白组成的。
ABC (ATP-binding cassette) transporters play an important role in the communication of various substrates across cell membranes. They are ubiquitous in prokaryotes and eukaryotes, and eukaryotic types (EK-types) are distinguished from prokaryotic types (PK-types) in terms of their genes and domain organizations. The EK-types and PK-types mainly consist of exporters and importers, respectively. Prokaryotes have both the EK-types and the PK-types. The EK-types in prokaryotes are usually called "bacterial multidrug ABC transporters," but they are not well characterized in comparison with the multidrug ABC transporters in eukaryotes. Thus, an exhaustive search of the EK-types among diverse organisms and detailed sequence classification and analysis would elucidate the evolutionary history of EK-types. It would also help shed some light on the fundamental repertoires of the wide variety of substrates through which multidrug ABC transporters in eukaryotes communicate. In this work, we have identified the EK-type ABC transporters in 126 prokaryotes using the profiles of the ATP-binding domain (NBD) of the EK-type ABC transporters from 12 eukaryotes. As a result, 11 clusters were identified from 1,046 EK-types ABC transporters. In particular, two large novel clusters emerged, corresponding to the bacterial multidrug ABC transporters related to the ABCB and. ABCC families in eukaryotes, respectively. In the genomic context, most of these genes are located alone or adjacent to genes from the same clusters. Additionally, to detect functional divergences in the NBDs, the Kullback-Leibler divergence was measured among these bacterial multidrug transporters. As a result, several putative functional regions were identified, some corresponding to the predicted secondary structures. We also analyzed a phylogeny of the EK-type ABC transporters in both prokaryotes and eukaryotes, which revealed that the EK-type ABC transporters in prokaryotes have certain repertoires corresponding to the conventional ABC protein groups in eukaryotes. On the basis of these findings, we propose an updated evolutionary hypothesis in which the EK-type ABC transporters in both eukaryotes and prokaryotes consisted of several kinds of ABC transporters in putative ancestor cells before the divergence of eukaryotic and prokaryotic cells.