二氢尿嘧啶合酶的分子进化。

BACKGROUND: Dihydrouridine (D) is a modified base found in conserved positions in the D-loop of tRNA in Bacteria, Eukaryota, and some Archaea. Despite the abundant occurrence of D, little is known about its biochemical roles in mediating tRNA function. It is assumed that D may destabilize the structure of tRNA and thus enhance its conformational flexibility. D is generated post-transcriptionally by the reduction of the 5,6-double bond of a uridine residue in RNA transcripts. The reaction is carried out by dihydrouridine synthases (DUS). DUS constitute a conserved family of enzymes encoded by the orthologous gene family COG0042. In protein sequence databases, members of COG0042 are typically annotated as "predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family". RESULTS: To elucidate sequence-structure-function relationships in the DUS family, a comprehensive bioinformatic analysis was carried out. We performed extensive database searches to identify all members of the currently known DUS family, followed by clustering analysis to subdivide it into subfamilies of closely related sequences. We analyzed phylogenetic distributions of all members of the DUS family and inferred the evolutionary tree, which suggested a scenario for the evolutionary origin of dihydrouridine-forming enzymes. For a human representative of the DUS family, the hDus2 protein suggested as a potential drug target in cancer, we generated a homology model. While this article was under review, a crystal structure of a DUS representative has been published, giving us an opportunity to validate the model. CONCLUSIONS: We compared sequences and phylogenetic distributions of all members of the DUS family and inferred the phylogenetic tree, which provides a framework to study the functional differences among these proteins and suggests a scenario for the evolutionary origin of dihydrouridine formation. Our evolutionary and structural classification of the DUS family provides a background to study functional differences among these proteins that will guide experimental analyses.

背景：二氢尿嘧啶 (D) 是一种在细菌、真核生物和一些古菌的 tRNA D 环中保守位置发现的修饰碱基。尽管 D 的大量存在，但对其在介导 tRNA 功能方面的生化作用知之甚少。人们假设 D 可能会使 tRNA 的结构不稳定，从而增强其构象灵活性。D 是由 RNA 转录物中尿嘧啶残基的 5,6-双键还原产生的。该反应由二氢尿嘧啶合酶 (DUS) 进行。DUS 构成了由同源基因家族 COG0042 编码的保守酶家族。在蛋白质序列数据库中，COG0042 的成员通常被注释为“预测 TIM 桶酶，可能是脱氢酶，nifR3 家族”。

结果：为了阐明 DUS 家族的序列-结构-功能关系，我们进行了全面的生物信息学分析。我们进行了广泛的数据库搜索，以识别所有已知 DUS 家族成员，然后进行聚类分析，将其划分为密切相关序列的亚家族。我们分析了 DUS 家族所有成员的系统发育分布，并推断了进化树，这表明了二氢尿嘧啶形成酶的进化起源情景。对于 DUS 家族的人类代表 hDus2 蛋白，我们生成了一个同源模型，它被认为是癌症的潜在药物靶点。在本文审查期间，已经发表了 DUS 代表的晶体结构，这使我们有机会验证该模型。

结论：我们比较了 DUS 家族所有成员的序列和系统发育分布，并推断了进化树，这为研究这些蛋白质之间的功能差异提供了框架，并提出了二氢尿嘧啶形成的进化起源情景。我们对 DUS 家族的进化和结构分类为研究这些蛋白质之间的功能差异提供了背景，这将指导实验分析。