Identification and characterization of the ARIADNE gene family in Arabidopsis. A group of putative E3 ligases

Abstract

ARIADNE (ARI) proteins were recently identified in fruitfly (Drosophila melanogaster), mouse, and man because of their specific interaction with the ubiquitin-conjugating (E2) enzymes UbcD10, UbcM4, UbcH7, and UbcH8. They are characterized by specific motifs and protein structures that they share with PARKIN, and there is increasing evidence that ARI/PARKIN proteins function as E2-dependent ubiquitin-protein ligases. On the basis of homology and motif searches, 16 AtARI genes were identified in Arabidopsis. Analysis of the position of exons/introns and their chromosomal localization indicates that the AtARI gene family expanded via larger and smaller genome duplications. We present evidence that retroposition of processed mRNA may have also contributed to enlarging this gene family. Phylogenetic analyses divides the AtARI proteins into three subgroups. Two groups are absent in yeast, invertebrates, and vertebrates and may therefore represent new plant-specific subfamilies. Examination of the predicted protein sequences revealed that the ARI proteins share an additional leucine-rich region at the N terminus that is highly conserved in all phyla analyzed. Furthermore, conserved consensus signals for casein kinase II-dependent phosphorylation and for nuclear localization were identified. The in silico-based analyses were complemented with experimental data to quantify expression levels. Using real-time polymerase chain reaction, we show that the ARI genes are differentially transcribed. AtARI1 is highly expressed in all organs, whereas no transcripts could be detected for AtARI11, AtARI13, and AtARI14. AtARI12 and AtARI16 are expressed in an organ-specific manner in the roots and siliques, respectively.