Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, Lyon, France.
BMC Genomics. 2010 Dec 20;11:721. doi: 10.1186/1471-2164-11-721.
Members of the makorin (mkrn) gene family encode RING/C3H zinc finger proteins with U3 ubiquitin ligase activity. Although these proteins have been described in a variety of eukaryotes such as plants, fungi, invertebrates and vertebrates including human, almost nothing is known about their structural and functional evolution.
Via partial sequencing of a testis cDNA library from the poeciliid fish Xiphophorus maculatus, we have identified a new member of the makorin gene family, that we called mkrn4. In addition to the already described mkrn1 and mkrn2, mkrn4 is the third example of a makorin gene present in both tetrapods and ray-finned fish. However, this gene was not detected in mouse and rat, suggesting its loss in the lineage leading to rodent murids. Mkrn2 and mkrn4 are located in large ancient duplicated regions in tetrapod and fish genomes, suggesting the possible involvement of ancestral vertebrate-specific genome duplication in the formation of these genes. Intriguingly, many mkrn1 and mkrn2 intronless retrocopies have been detected in mammals but not in other vertebrates, most of them corresponding to pseudogenes. The nature and number of zinc fingers were found to be conserved in Mkrn1 and Mkrn2 but much more variable in Mkrn4, with lineage-specific differences. RT-qPCR analysis demonstrated a highly gonad-biased expression pattern for makorin genes in medaka and zebrafish (ray-finned fishes) and amphibians, but a strong relaxation of this specificity in birds and mammals. All three mkrn genes were maternally expressed before zygotic genome activation in both medaka and zebrafish early embryos.
Our analysis demonstrates that the makorin gene family has evolved through large-scale duplication and subsequent lineage-specific retroposition-mediated duplications in vertebrates. From the three major vertebrate mkrn genes, mkrn4 shows the highest evolutionary dynamics, with lineage-specific loss of zinc fingers and even complete gene elimination from certain groups of vertebrates. Comparative expression analysis strongly suggests that the ancestral E3 ubiquitin ligase function of the single copy mkrn gene before duplication in vertebrates was gonad-specific, with maternal expression in early embryos.
makorin（mkrn）基因家族的成员编码具有 U3 泛素连接酶活性的 RING/C3H 锌指蛋白。尽管这些蛋白质已在包括人类在内的各种真核生物（如植物、真菌、无脊椎动物和脊椎动物）中进行了描述，但它们的结构和功能进化几乎一无所知。
通过对来自 poeciliid 鱼 Xiphophorus maculatus 的睾丸 cDNA 文库的部分测序，我们鉴定了 makorin 基因家族的一个新成员，我们称之为 mkrn4。除了已经描述的 mkrn1 和 mkrn2 之外，mkrn4 是存在于四足动物和栉齿鱼中的第三个 makorin 基因的例子。然而，该基因在小鼠和大鼠中未被检测到，表明其在导致啮齿动物鼠科的谱系中丢失。mkrn2 和 mkrn4 位于四足动物和鱼类基因组中的大型古老重复区域中，这表明祖先脊椎动物特异性基因组重复可能参与了这些基因的形成。有趣的是，在哺乳动物中检测到许多 mkrn1 和 mkrn2 无内含子的反转录拷贝，但在其他脊椎动物中未检测到，其中大多数是假基因。在 Mkrn1 和 Mkrn2 中发现锌指的性质和数量是保守的，但在 Mkrn4 中则更多变，具有谱系特异性差异。RT-qPCR 分析表明，makorin 基因在鱼类（栉齿鱼）和两栖动物中的性腺表达模式非常偏倚，而在鸟类和哺乳动物中这种特异性则大大放松。在 medaka 和 zebrafish 早期胚胎中，所有三个 mkrn 基因在合子基因组激活之前都呈母体表达。
我们的分析表明，makorin 基因家族通过脊椎动物中的大规模复制和随后的谱系特异性反转录介导的复制而进化。在三个主要的脊椎动物 mkrn 基因中，mkrn4 显示出最高的进化动态，具有谱系特异性的锌指丢失，甚至在某些脊椎动物群中完全消除了基因。比较表达分析强烈表明，在脊椎动物中复制之前的单拷贝 mkrn 基因的祖先 E3 泛素连接酶功能是性腺特异性的，在早期胚胎中具有母体表达。
