Data from: A comprehensive analysis of teleost MHC class I sequences

Background: MHC class I (MHCI) molecules are the key presenters of peptides generated through the intracellular pathway to CD8-positive T-cells. In fish MHCI genes were first identified in the early 1990's but we still know little about their functional relevance. The expansion and presumed sub-functionalization of cod MHCI and access to many published fish genome sequences provide us with the incentive to undertake a comprehensive study of deduced teleost fish MHCI molecules. Results: We expand the known MHCI lineages in teleosts to five with identification of a new lineage defined as P. The two lineages U and Z which both include presumed peptide binding classical/typical molecules besides more derived molecules are present in all teleosts analyzed. The U lineage displays two modes of evolution most pronouncedly observed in classical-type alpha 1 domains; cod and stickleback have expanded on one of at least eight ancient alpha 1 domain lineages as opposed to many other teleosts that preserved a number of these ancient lineages. The Z lineage comes in a typical format present in all analyzed ray-finned fish species as well as lungfish. The typical Z format displays an unprecedented conservation of all residues predicted to make up the peptide binding groove. However also co-existing atypical Z sub-lineage molecules which lost the presumed peptide binding motif are found in some fish like carps and cavefish. The remaining three lineages L S and P are not predicted to bind peptides and are lost in some species. Conclusions Much like tetrapods teleosts have polymorphic classical peptide binding MHCI molecules a number of classical-similar non-classical MHCI molecules and some members of more diverged MHCI lineages. Different from tetrapods however is that in some teleosts the classical MHCI polymorphism incorporates multiple ancient MHCI domain lineages. Also different from tetrapods is that teleosts have typical Z molecules in which the residues that presumably form the peptide binding groove have been almost completely conserved for over 400 million years. The reasons for the uniquely teleost evolution modes of peptide binding MHCI molecules remain an enigma.背景：主要组织相容性复合体I类（MHC class I，MHCI）分子是经胞内途径产生的肽段向CD8阳性T细胞（CD8-positive T-cells）呈递的关键分子。鱼类的MHCI基因最早于20世纪90年代初被鉴定，但目前学界对其功能相关性仍知之甚少。鳕鱼MHCI基因的扩张及推测的亚功能化现象，加之大量已发表的鱼类基因组序列资源，为我们全面研究推定的真骨鱼类（teleost）MHCI分子提供了研究契机。 结果：本研究将已报道的真骨鱼类MHCI谱系数量拓展至5个，新鉴定出一个命名为P的谱系。U和Z两个谱系在所有被分析的真骨鱼类中均有分布，二者均包含推测具备肽结合能力的经典型/典型型分子，以及更为衍生的分子。U谱系展现出两种进化模式，这一特征在经典型α1结构域（alpha 1 domain）中最为显著：与保留了多条此类古老α1结构域谱系的多数其他真骨鱼类不同，鳕鱼和棘鱼（stickleback）仅在至少8条古老α1结构域谱系中的一条上发生了基因扩张。Z谱系存在典型形式，该形式在所有被分析的辐鳍鱼类（ray-finned fish）以及肺鱼（lungfish）中均有分布。典型Z形式展现出前所未有的保守性：所有被预测参与构成肽结合槽（peptide binding groove）的氨基酸残基均高度保守。然而在部分鱼类（如鲤鱼（carps）和穴鱼（cavefish））中，同时存在失去了推测的肽结合基序（peptide binding motif）的非典型Z亚谱系分子。剩余的L、S、P三个谱系被预测不具备肽结合能力，且在部分物种中发生了基因丢失。 结论：与四足动物（tetrapods）类似，真骨鱼类兼具三类MHCI分子：具备多态性的经典肽结合型MHCI分子、多个类经典的非经典MHCI分子，以及部分分化程度更高的MHCI谱系成员。但与四足动物不同的是，部分真骨鱼类的经典MHCI多态性整合了多条古老的MHCI结构域谱系。另一项与四足动物的差异在于，真骨鱼类拥有典型Z分子，其推测构成肽结合槽的氨基酸残基在超过4亿年的演化历程中几乎完全保守。真骨鱼类肽结合型MHCI分子所独有的进化模式的成因，至今仍是一个未解之谜。