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Background  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.    Results  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.    Conclusion  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.

bmc genomics

The vertebrate makorin ubiquitin ligase gene family has been shaped by large-scale duplication and retroposition from an ancestral gonad-specific, maternal-effect gene