Ontogeny and Phylogeny of the MHC

描述（由申请人提供）：在过去的几年中，已经有几个完整的脊椎动物基因组测序，特别是人类，小鼠和硬骨鱼（例如河豚）的基因组测序。在脊椎动物树中，软骨鱼（包括鲨鱼、鳐和鳐等软骨鱼科）和两栖动物处于重要的系统发育节点，但这些动物尚未在遗传水平上得到很好的研究。软骨鱼位于有颌脊椎动物的最底部，是最古老的脊椎动物，具有基于免疫球蛋白、T细胞受体和主要组织相容性复合体（MHC）存在的适应性免疫系统。两栖动物是最早的陆地脊椎动物，一直是研究适应性免疫系统的首选非哺乳动物模型之一（尤其是非洲爪蟾，是发育生物学家熟知的模型）。我们对护士鲨和爪蟾MHC的分析表明，与硬骨鱼不同，它们和人类一样，ⅰ类、ⅱ类和ⅲ类基因都存在于它们的MHC中；因此，这些脊椎动物类的代表性动物似乎比研究得更好的硬骨鱼（如斑马鱼）更准确地代表了假设的祖先脊椎动物MHC。然而，与人类不同的是，在MHC I类途径中，至少在非洲爪蟾中，可能在鲨鱼中，涉及肽的产生（免疫蛋白酶体）、运输（TAP1/2）和显示（经典的I类蛋白）的基因谱系很深。这些基因在一个真正的“I类区域”紧密相连，这可能反映了原始MHC的情况。在非洲爪蟾中，也有一系列的多倍体个体，范围从2n-12n，这无疑是由全基因组复制事件（异源多倍体化）引起的；适应性免疫系统的基因在多倍体中二倍体化，可能是为了维持最佳数量的MHC分子表达。为了研究MHC遗传学的进化和基因组织对免疫系统的明显功能后果，我们的具体目标是：1)编制所有脊椎动物类别的代表MHC的比较图，重点是护士鲨（软骨鱼或板鳃）和爪蟾（两栖动物）；2)通过研究免疫蛋白酶体亚基、I类肽结合、TAP 1/2生化和肽转运的特异性，以及在转基因青蛙中的特异性，检验非洲爪蟾古双等位基因I类区域谱系的意义；3)多倍体非洲爪蟾基因沉默的研究：随着非洲爪蟾（特别是真正的二倍体热带爪蟾）基因组测序项目的到来，我们将开始分析四倍体的沉默模式，并最终分析高阶八倍体和十二倍体个体的沉默模式。

DESCRIPTION (provided by applicant): In the past several years, there have been several entire vertebrate genomes sequenced, specifically those of human, mouse, and bony fish (e.g. the pufferfish). In the vertebrate tree, the cartilaginous fish (elasmobranchs including the sharks, skates, and rays) and amphibians are at important phylogenetic junctures, but these animals have not been well studied at the genetic level. Cartilaginous fish are at the base of the jawed vertebrate tree and are the oldest vertebrates to have an adaptive immune system based on the presence of immunoglobulins, T cell receptors, and the major histocompatibility complex (MHC). Amphibians, the first land vertebrates, have been one of the favored non-mammalian models for the study of the adaptive immune system (especially the frog Xenopus, a well known model for developmental biologists). Our analyses of nurse shark and Xenopus MHCs have shown that unlike the bony fish, but like humans, class I, class II, and class III genes are all present in their MHC; thus, representative animals from these vertebrate classes seemingly more accurately represent the hypothetical ancestral vertebrate MHC than the better studied bony fish (e.g. zebrafish). However, unlike humans, there are deep lineages of genes involved in the production (immunoproteasome), transport (TAP1/2), and display (classical class I proteins) of peptides in the MHC class I pathway, at least in Xenopus and probably also in shark. These genes are tightly linked in a true 'class I region,' which likely reflects the situation in the primordial MHC. In Xenopus as well, there is a series of polyploid individuals ranging from 2n-12n, which no doubt arose by genome-wide duplication events (allopolyploidization); the genes of the adaptive immune system become diploidized in the polyploids, presumably to maintain an optimal number of expressed MHC molecules. In order to study the evolution of MHC genetics and the apparent functional consequences of gene organization on the immune system our specific aims are: 1) To compile comparative maps of the MHC in representatives of all vertebrate classes, with an emphasis on nurse shark (cartilaginous fish or elasmobranch) and Xenopus (amphibian); 2) Examine the significance of Xenopus ancient biallelic class I region lineages, specifically by studying the specificity of immunoproteasome subunits, class I peptide-binding, TAP 1/2biochemistry and peptide transport, and in transgenic frogs; and 3) Study gene silencing in polyploid Xenopus: with the advent of genomic sequencing projects in Xenopus (especially the true diploid X. tropicalis), we will begin to analyze the modes of silencing in the tetraploids and eventually the higher order octo- and dodecaploid individuals.