Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins
Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins
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DOI：
10.1093/molbev/msg038
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发表时间：
2003-02-01
影响因子：
10.7
通讯作者：
Nishikawa, K
中科院分区：
文献类型：
--
作者：
Fukami-Kobayashi, K;Tateno, Y;Nishikawa, K
细菌LacI/GalR家族的抑制子，如乳糖操纵子抑制子(LacI)、嘌呤核苷酸合成抑制子(PURR)和海藻糖操纵子抑制子(TreR)不仅包括N端螺旋-转角螺旋DNA结合域，还包括结构上与质周糖结合蛋白同源的C-末端配体结合域。这些结构特征表明，阻遏蛋白家族是通过获得祖先周质结合蛋白(PBP)N端的DNA结合结构域而进化的。对LacI/GalR家族抑制子及其PBP同源物的系统发育分析表明，DNA结合域的获得首先发生在该家族中，然后进化出配体特异性。系统发育树还表明，在真细菌的主要谱系分化之前，这种获得只发生过一次，LacI/GalR和PBP家族此后沿着进化谱系独立地经历了广泛的基因复制/丢失。多重比对进一步表明，具有相同配体特异性的抑制物和多溴联苯并在其结合部位有相同或相似的残基。这一结果与系统发育关系一起表明，尽管阻遏子和PBPs的基因编码在相同的操纵子中，但通过同型替换，它们各自获得了相同的配体特异性。
The bacterial LacI/GalR family repressors such as lactose operon repressor (LacI), purine nucleotide synthesis repressor (PurR), and trehalose operon repressor (TreR) consist of not only the N-terminal helix-turn-helix DNA-binding domain but also the C-terminal ligand-binding domain that is structurally homologous to periplasmic sugar-binding proteins. These structural features imply that the repressor family evolved by acquiring the DNA-binding domain in the N-terminal of an ancestral periplasmic binding protein (PBP). Phylogenetic analysis of the LacI/GalR family repressors and their PBP homologues revealed that the acquisition of the DNA-binding domain occurred first in the family, and ligand specificity then evolved. The phylogenetic tree also indicates that the acquisition occurred only once before the divergence of the major lineages of eubacteria, and that the LacI/GalR and the PBP families have since undergone extensive gene duplication/loss independently along the evolutionary lineages. Multiple alignments of the repressors and PBPs furthermore revealed that repressors and PBPs with the same ligand specificity have the same or similar residues in their binding sites. This result, together with the phylogenetic relationship, demonstrates that the repressors and the PBPs individually acquired the same ligand specificity by homoplasious replacement, even though their genes are encoded in the same operon.