Highly Conserved UFD1 Proteins Among Eukaryotes Exhibit Considerable C-Terminus Diversity in Different Taxa

The UFD1 protein is an important ubiquitin recognition component in the ubiquitin-mediated degradation pathway. To investigate the conservation of UFD1 genes among eukaryotes and their differentiation, two UFD1 paralogs from wheat were identified and mapped to homoeologous chromosome groups 6 and 2, respectively. TaUFD1a-6B and TaUFD1b-2D were cloned, and both genes consist of eight introns and of the same intron phases. These genes were compared with those in Arabidopsis, rice, polar, yeast, and mammals for their sequence, chromosome organization, and primary protein structure. The sequence structure, especially those corresponding to the fourth, fifth, and sixth exons of UFD1 genes, is highly conserved across these taxa. However, unlike yeast and mammals having a single UFD1 gene, higher angiosperm species have two ancient UFD1 paralogs. Besides the evolutionarily conserved ubiquitin-binding domain at the N-terminus, plant UFD1 proteins have three conserved C-terminal motifs. Motif I, near the UFD1 domain, displays a high level of similarity to the mammalian p97-binding site, and motif III is likely responsible for endoplasmic reticulum membrane retention. TaUFD1a-6B and TaUFD1b-2D are ubiquitously expressed in different plant tissues. A green fluorescent protein-transient expression assay in epidermal cells of onion demonstrated that TaUFD1 proteins primarily accumulate in the nucleus.