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

Abstract

BackgroundMembers 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.ResultsVia 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.ConclusionOur 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.

LEP-2/Makorin regulates LIN-28 stability to promote the juvenile-to-adult transition in Caenorhabditis elegans

“…How LEP-2 regulates LIN-28 is not yet clear, but one simple model is that LEP-2 functions as an E3 ubiquitin ligase to tag LIN-28 for proteasomal degradation. Like other Mkrns, LEP-2 has a RING domain that is typical of many E3 ligases (Bohne et al, 2010;Gray et al, 2000). Indeed, Mkrn1 in mammals functions as an E3 ligase, targeting several proteins and even itself, although has not yet been identified as one of its targets (Kim et al, 2005;Salvatico et al, 2010;Lee et al, 2009Lee et al, , 2012Ko et al, 2012;Shimada et al, 2009;Ko et al, 2010;Kim et al, 2014;Cassar et al, 2015).…”

A new pathway in the control of the initiation of puberty: the MKRN3 gene

“…Several other retrocopies of MKRN1 have been identified in mammalian genomes, most of them probably corresponding to pseudogenes. Nine MKRN family loci distributed throughout the human genome have been identified so far, with only three functional genes - MKRN1 , MKRN2 and MKRN3 - identified in vertebrates (Bohne, et al 2010; Gray et al 2000). …”

New Causes of Central Precocious Puberty: The Role of Genetic Factors

“…C3H zinc finger motifs have been implicated in RNA binding, while the RING zinc finger motif is found in most E3 ubiquitin ligases and is responsible for the ubiquitin ligase activity [38]. The widespread species conservation of the MAKORIN protein family points to vital cellular roles, with abundant expression in the developing brain, including the arcuate nucleus, where there is a group of genes whose expression is relevant to puberty [39].…”