Phylogenetic Studies of the Homeodomain Protein Family

该研究计划主要侧重于蛋白质同源结构域组的计算分析，这些蛋白质在后生动物发育过程中的身体计划，模式形成和细胞命运决定的规范中发挥着重要作用。各种生物信息学方法用于了解这些蛋白质的进化和功能及其在人类疾病中的最终作用。 同源异型框（或Hox）基因在一系列系统发育分类群中被组织成保守的基因组簇。在进化过程中，这些Hox基因的功能多样化有助于动物身体计划的多样化。基于这些Hox基因的起源和早期进化的先前工作，我们的重点已经转向分析早期分支后生动物门的基因组，以更好地了解基因组复杂性和形态复杂性之间的关系，以及新细胞类型进化的分子基础。鉴于栉水母是最后剩下的非两侧门缺乏一个物种的测序基因组（因此，一个完整的检查同源框库），我们使用下一代测序方法来序列和组装的150 MB的叶状栉水母，Mnemiopsis leydii。利用这些数据，我们能够确定一组76个同源框含有基因的拟记忆。我们将这一组基因家族和类进行遗传学分类，并能够确定几个重要的类和亚类的同源结构域是不存在的Mnemiopsis和poriferan Amphimedon queenslandica。 作为第一项研究，比较完整的同源框目录的物种从所有的非bilaterian门，沿着与两个主要的bilaterian谱系，其中完整的基因组序列数据是可用的，这项工作提供了一个主要的缺失的证据，是至关重要的了解化妆的同源结构域家庭在早期后生动物的历史。这些数据反过来又使我们能够开始破译同源结构域超家族的扩展在动物门的进化中扮演了什么角色。这项工作也使我们能够评估最近提出的早期分支门的系统发育关系的同源结构域数据的一致性。我们的研究结果表明，孔类和Ctenophora的第一个现存的血统，从其余的动物分歧。 我们利用手头的高质量序列数据来研究在人类代谢过程和发育中起关键作用的其他蛋白质家族的进化。首先，我们与夏威夷大学的合作者一起研究了Wnt/β-连环蛋白信号通路。分子系统发育分析表明，四个不同的Wnt配体，和大多数（但不是全部）的受体和细胞内信号通路的组件被检测到。值得注意的是，在拟记忆体基因组中不存在最主要的分泌拮抗剂，这表明这种分泌信号传导途径的复杂调节可能在动物进化后期进化。与我们在伍兹霍尔海洋研究所的合作者一起，我们专注于核受体（NR），它在生殖，发育和能量稳态的调节中起着关键作用。利用基因组学方法，我们发现所有的栉水母核受体都缺乏高度保守的DNA结合结构域，这是迄今为止核受体的特征。 这可能反映了一个祖先NR域结构或该域从包含DNA结合域的祖先NR的谱系特异性损失。NR的系统发育分析支持NR超家族以逐步方式扩展的观点。 作为我们对蛋白质同源结构域类研究的产物，我们已经开发并继续维护同源结构域资源。同源结构域资源是同源结构域家族的序列，结构，相互作用，基因组和功能信息的精选集合。目前的版本建立在以前的版本，通过添加新的，完整的套同源结构域序列从完全测序的基因组，现有的策划同源结构域信息的扩展和改善数据的可访问性，通过更好的搜索工具和更完整的数据集成。目前的版本包含1536个全长同源结构域包含序列，107个实验衍生的同源结构域结构，101个同源结构域蛋白质蛋白质相互作用，107个同源结构域DNA结合位点，53个同源结构域蛋白质与记录的等位基因变体，和186个同源结构域蛋白质涉及人类遗传疾病。Homeodomain资源可在http：/research.nhgri.nih.gov/homeodomain/上免费获得。

This research program focuses primarily on the computational analysis of the homeodomain group of proteins, which play a fundamental role in the specification of body plan, pattern formation, and cell fate determination during metazoan development. A variety of bioinformatic approaches are used to understand the evolution and function of these proteins and their ultimate role in human disease. Homeobox (or Hox) genes are organized in conserved genomic clusters across a range of phylogenetic taxa. Over evolutionary time, the functional diversification of these Hox genes has contributed to the diversification of animal body plans. Building upon prior work on the origin and early evolution of these Hox genes, our focus has turned to analyzing the genomes of early-branching metazoan phyla to better-understand the relationship between genomic complexity and morphological complexity, as well as the molecular basis for the evolution of novel cell types. Given that Ctenophora was the last remaining non-bilaterian phylum lacking a species with a sequenced genome (and, therefore, a completely examined homeobox repertoire), we used next-generation sequencing approaches to sequence and assemble the 150 MB of the lobate ctenophore, Mnemiopsis leydii. Using these data, we were able to identify a set of 76 homeobox-containing genes in Mnemiopsis. We phylogenetically categorized this set into established gene families and classes, and were able to determine that several important classes and subclasses of homeodomains are absent from both Mnemiopsis and from the poriferan Amphimedon queenslandica. As the first study to compare the complete homeobox catalog of species from all of the non-bilaterian phyla, along with that of the two major bilaterian lineages where complete genomic sequence data is available, this work provides a major missing piece of evidence that is critical to understanding the makeup of the homeodomain family in early metazoan history. These data, in turn, enable us to begin to decipher what role the expansion of the homeodomain superfamily has played in the evolution of animal phyla. This work has also enabled us to evaluate the congruency of the homeodomain data with recently proposed phylogenetic relationships of the early branching phyla. Our results suggest that Porifera and Ctenophora were the first two extant lineages to diverge from the rest of the animals. We have taken advantage of having this high-quality sequence data in-hand to investigate the evolution of additional protein families that play a critical role in human metabolic processes and development. First, with our collaborators at the University of Hawaii, we examined the Wnt/beta-catenin signaling pathway. Molecular phylogenetic analysis shows four distinct Wnt ligands, and most (but not all) components of the receptor and intracellular signaling pathways were detected. Notably absent in the Mnemiopsis geneome are most major secreted antagonists, which suggests that complex regulation of this secreted signaling pathway likely evolved later in animal evolution. With our collaborators at the Woods Hole Oceanographic Institute, we focused on nuclear receptors (NRs), which play key roles in the regulation of reproduction, development, and energetic homeostasis. Using phylogenomic approaches, we found that all ctenophore NRs lacked the highly conserved DNA-binding domain that has heretofore been characteristic of nuclear receptors. This may reflect an ancestral NR domain structure or a lineage-specific loss of this domain from an ancestral NR that contained the DNA-binding domain. Phylogenetic analyses of NRs support the idea that expansion of the NR superfamily occurred in a stepwise fashion. As an outgrowth of our studies on the homeodomain class of proteins, we have developed and continue to maintain the Homeodomain Resource. The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. The current version builds upon previous versions by the addition of new, complete sets of homeodomain sequences from fully sequenced genomes, the expansion of existing curated homeodomain information and the improvement of data accessibility through better search tools and more complete data integration. The current release contains 1536 full-length homeodomain-containing sequences, 107 experimentally derived homeodomain structures, 101 homeodomain proteinprotein interactions, 107 homeodomain DNA-binding sites, 53 homeodomain proteins with documented allelic variants, and 186 homeodomain proteins implicated in human genetic disorders. The Homeodomain Resource is freely available at http:/research.nhgri.nih.gov/homeodomain/.