Evolutionary history and higher order classification of AAA plus ATPases
Evolutionary history and higher order classification of AAA plus ATPases
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DOI：
10.1016/j.jsb.2003.10.010
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发表时间：
2004-04-01
影响因子：
3
通讯作者：
Aravind, L
中科院分区：
文献类型：
--
作者：
Iyer, LM;Leipe, DD;Aravind, L
AAA+ ATP酶是含有P-环NTR结构域的酶，并且作为分子伴侣、蛋白酶的ATP酶亚基、解旋酶或核酸刺激的ATP酶起作用。所有可用的AAA+蛋白结构域的序列和结构进行了比较，目的是确定这些结构域的确定性序列和结构特征，并推断其进化中的主要事件。AAA+类的进化分类开发使用标准的系统发育方法，分析共享的序列和结构特征，和基于相似性的聚类。该分析导致在AAA+ ATP酶类内鉴定出26个主要家族。我们还描述了AAA+ ATP酶相对于RecA/F1，解旋酶超家族I/II，PilT和ABC类的P-环NTPases的位置。AAA+类似乎已经经历了早期辐射到clamp-loader，DnaA/Orc/Cdc 6，经典AAA和“前传感器1 β-发夹”（PS1 BH）进化枝。在PS1 BH进化枝内，螯合酶、MoxR、YifB、McrB、动力蛋白-midasin、NtrC和MCM形成由保守ATP酶核心的螺旋-2中的不同插入物以及核心ATP酶结构域和C-末端α-螺旋束之间的额外螺旋区段限定的单系组装体。至少有6种不同的AAA+蛋白，代表不同的主要进化枝，可追溯到现存细胞生命的最后一个普遍共同祖先（LUCA）。此外，属于PS1 BH组合的超家族III解旋酶可能在此阶段存在于病毒样“自私”复制子中。下一个主要的辐射，在两个原核生物王国的基础上，细菌和。古生菌，产生了几个不同的伴侣，ATP酶亚基的蛋白酶，DNA解旋酶，和转录因子。第三个主要的辐射，在真核生物进化的开始，促成了一些真核生物特有的适应性与核和细胞骨架功能的起源。新的关系和以前未检测到的域报告这里可能提供新的线索，研究AAA+ ATP酶的生物学。爱思唯尔公司出版
The AAA+ ATPases are enzymes containing a P-loop NTPase domain, and function as molecular chaperones, ATPase subunits of proteases, helicases or nucleic-acid-stimulated ATPases. All available sequences and structures of AAA+ protein domains were compared with the aim of identifying the definitive sequence and structure features of these domains and inferring the principal events in their evolution. An evolutionary classification of the AAA+ class was developed using standard phylogenetic methods, analysis of shared sequence and structural signatures, and similarity-based clustering. This analysis resulted in the identification of 26 major families within the AAA+ ATPase class. We also describe the position of the AAA+ ATPases with respect to the RecA/F1, helicase superfamilies I/II, PilT, and ABC classes of P-loop NTPases. The AAA+ class appears to have undergone an early radiation into the clamp-loader, DnaA/Orc/Cdc6, classic AAA, and "pre-sensor 1 beta-hairpin" (PS1BH) clades. Within the PS1BH clade, chelatases, MoxR, YifB, McrB, Dynein-midasin, NtrC, and MCMs form a monophyletic assembly defined by a distinct insert in helix-2 of the conserved ATPase core, and additional helical segment between the core ATPase domain and the C-terminal alpha-helical bundle. At least 6 distinct AAA+ proteins, which represent the different major clades, are traceable to the last universal common ancestor (LUCA) of extant cellular life. Additionally, superfamily III helicases, which belong to the PS1BH assemblage, were probably present at this stage in virus-like "selfish" replicons. The next major radiation, at the base of the two prokaryotic kingdoms, bacteria an. archaea, gave rise to several distinct chaperones, ATPase subunits of proteases, DNA helicases, and transcription factors. The third major radiation, at the outset of eukaryotic evolution, contributed to the origin of several eukaryote-specific adaptations related to nuclear and cytoskeletal functions. The new relationships and previously undetected domains reported here might provide new leads for investigating the biology of AAA+ ATPases. Published by Elsevier Inc.