Department of Molecular Pathogenesis, Medical Research Institute, and Laboratory of Genome Diversity, Graduate School of Biomedical Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.
Immunogenetics. 2011 Jul;63(7):417-28. doi: 10.1007/s00251-011-0519-7. Epub 2011 Mar 10.
Genes of the immunoglobulin superfamily (IgSF) have a wide variety of cellular activities. In this study, we investigated molecular evolution of IgSF genes in primates by comparing orthologous sequences of 249 IgSF genes among human, chimpanzee, orangutan, rhesus macaque, and common marmoset. To evaluate the non-synonymous/synonymous substitution ratio (ω), we applied Bn-Bs program and PAML program. IgSF genes were classified into 11 functional categories based on the Gene Ontology (GO) database. Among them, IgSF genes in three functional categories, immune system process (GO:0002376), defense response (GO:0006952), and multi-organism process (GO:0051704), which are tightly linked to the regulation of immune system had much higher values of ω than genes in the other GO categories. In addition, we estimated the average values of ω for each primate lineage. Although each primate lineage had comparable average values of ω, the human lineage showed the lowest ω value for the immune-related genes. Furthermore, 11 IgSF genes, SIGLEC5, SLAMF6, CD33, CD3E, CEACAM8, CD3G, FCER1A, CD48, CD4, TIM4, and FCGR2A, were implied to have been under positive selective pressure during the course of primate evolution. Further sequence analyses of CD3E and CD3G from 23 primate species suggested that the Ig domains of CD3E and CD3G underwent the positive Darwinian selection.
免疫球蛋白超家族（IgSF）的基因具有广泛的细胞活性。在这项研究中，我们通过比较人类、黑猩猩、猩猩、恒河猴和普通狨猴 249 个 IgSF 基因的直系同源序列，研究了灵长类动物 IgSF 基因的分子进化。为了评估非同义/同义替换比（ω），我们应用了 Bn-Bs 程序和 PAML 程序。根据基因本体论（GO）数据库，IgSF 基因被分为 11 个功能类别。其中，三个功能类别，即免疫系统过程（GO:0002376）、防御反应（GO:0006952）和多器官过程（GO:0051704），与免疫系统的调节密切相关，其 ω 值远高于其他 GO 类别的基因。此外，我们估计了每个灵长类动物谱系的 ω 平均值。尽管每个灵长类动物谱系的 ω 平均值相当，但人类谱系的免疫相关基因的 ω 值最低。此外，11 个 IgSF 基因，SIGLEC5、SLAMF6、CD33、CD3E、CEACAM8、CD3G、FCER1A、CD48、CD4、TIM4 和 FCGR2A，被认为在灵长类动物进化过程中受到了正选择压力。对来自 23 种灵长类动物的 CD3E 和 CD3G 的进一步序列分析表明，CD3E 和 CD3G 的 Ig 结构域经历了正达尔文选择。
