title: Genome-wide identification, sequence characterization, and protein-protein interaction properties of DDB1 (damaged DNA binding protein-1)-binding WD40-repeat family members in Solanum lycopersicum.
abstract: One hundred DDB1 (damaged DNA binding protein-1)-binding WD40-repeat domain (DWD) family genes were identified in the S. lycopersicum genome. The DWD genes encode proteins presumably functioning as the substrate recognition subunits of the cullin4-ring ubiquitin E3 ligase complex. These findings provide candidate genes and a research platform for further gene functionality and molecular breeding study. A subclass of DDB1 (damaged DNA binding protein-1)-binding WD40-repeat domain (DWD) family proteins has been demonstrated to function as the substrate recognition subunits of the cullin4-ring ubiquitin E3 ligase complex. However, little information is available about the cognate subfamily genes in tomato (S. lycopersicum). In this study, based on the recently released tomato genome sequences, 100 tomato genes encoding DWD proteins that potentially interact with DDB1 were identified and characterized, including analyses of the detailed annotations, chromosome locations and compositions of conserved amino acid domains. In addition, a phylogenetic tree, which comprises of three main groups, of the subfamily genes was constructed. The physical interaction between tomato DDB1 and 14 representative DWD proteins was determined by yeast two-hybrid and co-immunoprecipitation assays. The subcellular localization of these 14 representative DWD proteins was determined. Six of them were localized in both nucleus and cytoplasm, seven proteins exclusively in cytoplasm, and one protein either in nucleus and cytoplasm, or exclusively in cytoplasm. Comparative genomic analysis demonstrated that the expansion of these subfamily members in tomato predominantly resulted from two whole-genome triplication events in the evolution history.
authors: School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China.
authors: Yunye
authors: Y
authors: Zhu
authors: Shengxiong
authors: S
authors: Huang
authors: Min
authors: M
authors: Miao
authors: Xiaofeng
authors: X
authors: Tang
authors: Junyang
authors: J
authors: Yue
authors: Wenjie
authors: W
authors: Wang
authors: Yongsheng
authors: Y
authors: Liu
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics; D017124:Conserved Sequence; D017343:Genes, Plant; D018745:Genome, Plant; D018551:Solanum lycopersicum / Q000235:genetics*; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D025941:Protein Interaction Mapping; D017434:Protein Structure, Tertiary; D021381:Protein Transport; D020539:Sequence Analysis, Protein; D013347:Subcellular Fractions / Q000378:metabolism; D014026:Nicotiana
chemical_list: D010940:Plant Proteins