Young G B, Jack D L, Smith D W, Saier M H
Department of Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA.
Biochim Biophys Acta. 1999 Jan 8;1415(2):306-22. doi: 10.1016/s0005-2736(98)00196-5.
Amino acids and their derivatives are transported into and out of cells by a variety of permease types which comprise several distinct protein families. We here present a systematic analysis of a group of homologous transport proteins which together comprise the eukaryotic-specific amino acid/auxin permease (AAAP) family (TC #2. 18). In characterizing this family, we have (1) identified all sequenced members of the family, (2) aligned their sequences, (3) identified regions of striking conservation, (4) derived a family-specific signature sequence, and (5) proposed a topological model that appears to be applicable to all members of the family. We have also constructed AAAP family phylogenetic trees and dendrograms using six different programs that allow us to trace the evolutionary history of the family, estimate the relatedness of proteins from dissimilar organismal phyla, and evaluate the reliability of the different programs available for phylogenetic studies. The TREE and neighbor-joining programs gave fully consistent results while CLUSTAL W gave similar but non-identical results. Other programs gave less consistent results. The phylogenetic analyses reveal (1) that many plant AAAP family proteins arose recently by multiple gene duplication events that occurred within a single organism, (2) that some plant members of the family with strikingly different specificities diverged early in evolutionary history, and (3) that AAAP family proteins from fungi and animals diverged from the plant proteins long ago, possibly when animals, plants and fungi diverged from each other. The Neurospora protein nevertheless exhibits overlapping specificity with those found in plants. Preliminary evidence is presented suggesting that proteins of the AAAP family are distantly related to proteins of the large ubiquitous amino acid/polyamine/choline family (TC #2.3) as well as to those of two small bacterial amino acid transporter families, the ArAAP family (TC #2.42) and the STP family (TC #2.43).
氨基酸及其衍生物通过多种通透酶进出细胞，这些通透酶包含几个不同的蛋白质家族。我们在此对一组同源转运蛋白进行系统分析，这些蛋白共同构成了真核生物特有的氨基酸/生长素通透酶（AAAP）家族（转运分类编号#2.18）。在对该家族进行特征描述时，我们（1）鉴定了该家族所有已测序的成员，（2）比对了它们的序列，（3）确定了显著保守的区域，（4）推导了家族特异性的特征序列，以及（5）提出了一个似乎适用于该家族所有成员的拓扑模型。我们还使用六个不同的程序构建了AAAP家族的系统发育树和聚类图，这使我们能够追溯该家族的进化历史，估计不同生物门类中蛋白质的亲缘关系，并评估可用于系统发育研究的不同程序的可靠性。TREE程序和邻接法程序给出了完全一致的结果，而CLUSTAL W程序给出了相似但不完全相同的结果。其他程序给出的结果一致性较差。系统发育分析揭示：（1）许多植物AAAP家族蛋白是最近通过单个生物体内发生的多次基因复制事件产生的；（2）该家族中一些具有显著不同特异性的植物成员在进化历史早期就已分化；（3）真菌和动物的AAAP家族蛋白早在很久以前就与植物蛋白分化了，可能是在动物、植物和真菌彼此分化之时。然而，粗糙脉孢菌的蛋白与植物中的蛋白表现出重叠的特异性。初步证据表明，AAAP家族的蛋白与广泛存在的大氨基酸/多胺/胆碱家族（转运分类编号#2.3）的蛋白以及两个小的细菌氨基酸转运蛋白家族，即ArAAP家族（转运分类编号#2.42）和STP家族（转运分类编号#2.43）的蛋白有较远的亲缘关系。
