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

Abstract

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.

Selection and Validation of Appropriate Reference Genes for Quantitative Real-Time PCR Normalization in Staminate and Perfect Flowers of Andromonoecious Taihangia rupestris

“…For andromonoecious T. rupestris , the stability of ADF3 in staminate and perfect flowers probably attributed to its function for basic cellular processes, such as cell proliferation and regulation of actin dynamics in cells (Ruzicka et al, 2007 ). In plants, UFD1 is an essential ubiquitin recognition component in the ubiquitin-mediated degradation pathway (Wei et al, 2009 ). Given that possible basic function in cell processes, UFD1 should be suitable as reference gene for qRT-PCR normalization in T. rupestris , although it was not reported as reference gene in plant species.…”

Identification of systemic responses in soybean nodulation by xylem sap feeding and complete transcriptome sequencing reveal a novel component of the autoregulation pathway

“…No other significant domains were identified in the remainder of the protein; however, two well‐conserved regions of 16 and 13 amino acids were identified in the C‐terminal region of sequence alignments with the most similar Arabidopsis and soybean genes (Figure S1). To our knowledge, these regions do not have a defined function, although it has been proposed that they may play a role in binding of protein or ER targets of UFD1 (Wei et al. , 2009).…”

Genome-wide identification and characterization of grapevine UFD1 genes during berry development and salt stress response

“…However, only few of UFD1-like proteins were isolated and function analyzed from plants species until recently, although they have been predicted from genome sequence of many plants. Wei et al (2009) reported two UFD1 paralog proteins from wheat, which showed highly evolutionarily conserved ubiquitin-binding domain. In addition, another UFD1 gene was cloned from tomato (Lai et al 2012).…”