title: Classification, expression pattern, and E3 ligase activity assay of rice U-box-containing proteins.
abstract: Ubiquitin ligases play a central role in determining the specificity of the ubiquitination system by selecting a myriad of appropriate candidate proteins for modification. The U-box is a recently identified, ubiquitin ligase activity-related protein domain that shows greater presence in plants than in other organisms. In this study, we identified 77 putative U-box proteins from the rice genome using a battery of whole genome analysis algorithms. Most of the U-box protein genes are expressed, as supported by the identification of their corresponding expressed sequence tags (ESTs), full-length cDNAs, or massively parallel signature sequencing (MPSS) tags. Using the same algorithms, we identified 61 U-box proteins from the Arabidopsis genome. The rice and Arabidopsis U-box proteins were classified into nine major classes based on their domain compositions. Comparison between rice and Arabidopsis U-box proteins indicates that the majority of rice and Arabidopsis U-box proteins have the same domain organizations. The inferred phylogeny established the homology between rice and Arabidopsis U-box/ARM proteins. Cell death assay using the rice protoplast system suggests that one rice U-box gene, OsPUB51, might act as a negative regulator of cell death signaling. In addition, the selected U-box proteins were found to be functional E3 ubiquitin ligases. The identification and analysis of rice U-box proteins hereby at the genomic level will help functionally characterize this class of E3 ubiquitin ligase in the future.
authors.affiliation: Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Li-Rong
authors.initials: LR
authors.lastname: Zeng
authors.forename: Chan Ho
authors.initials: CH
authors.lastname: Park
authors.forename: R C
authors.initials: RC
authors.lastname: Venu
authors.forename: Julian
authors.initials: J
authors.lastname: Gough
authors.forename: Guo-Liang
authors.initials: GL
authors.lastname: Wang
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics; D001681:Biological Assay; D016923:Cell Death / Q000235:genetics; D019295:Computational Biology; D017124:Conserved Sequence; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D007113:Immunity, Innate / Q000235:genetics; D008969:Molecular Sequence Data; D012275:Oryza / Q000201:enzymology* / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D017434:Protein Structure, Tertiary; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015398:Signal Transduction / Q000235:genetics; D044767:Ubiquitin-Protein Ligases / Q000737:chemistry / Q000145:classification* / Q000235:genetics* / Q000378:metabolism
chemical_list: D010940:Plant Proteins; D044767:Ubiquitin-Protein Ligases