caa a22 4500 606208828 CHVBK 20210128101024.0 cr unu---uuuuu 210128e20150601xx s 000 0 eng 10.1007/s00425-015-2258-8 doi (NATIONALLICENCE)springer-10.1007/s00425-015-2258-8 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 [Elektronische Daten] [Yunye Zhu, Shengxiong Huang, Min Miao, Xiaofeng Tang, Junyang Yue, Wenjie Wang, Yongsheng Liu] Main conclusions : 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-immunoprecipitationassays. 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. Springer-Verlag Berlin Heidelberg, 2015 WD40-repeat domain nationallicence Damaged DNA binding protein-1 nationallicence Phylogenetic analysis nationallicence Protein interaction nationallicence Solanum lycopersicum nationallicence CDS : Coding sequence nationallicence CRL : Cullin-ring ubiquitin ligase nationallicence DDB1/2 : Damaged DNA binding protein 1/2 nationallicence DWD : Damaged DNA binding protein 1 (DDB1)-binding WD40-repeat domain family protein nationallicence HGNC : Gene nomenclature committee of human genome organization nationallicence HMM : Hidden markov model nationallicence PGDD : Plant genome duplication database nationallicence RBX1/2 : Ring box 1/2 nationallicence ROC1/2 : Regulator of cullins 1/2 nationallicence RPKM : Reads per kilobase of exon model per million mapped reads nationallicence SGN : Sol genomics network nationallicence SKP1 : S-phase kinase-associated protein 1 nationallicence SlWDR : WD40-repeat domain family members in tomato nationallicence WD40 : WD40-repeat domain nationallicence Zhu Yunye School of Biotechnology and Food Engineering, Hefei University of Technology, 230009, Hefei, China aut Huang Shengxiong School of Biotechnology and Food Engineering, Hefei University of Technology, 230009, Hefei, China aut Miao Min School of Biotechnology and Food Engineering, Hefei University of Technology, 230009, Hefei, China aut Tang Xiaofeng School of Biotechnology and Food Engineering, Hefei University of Technology, 230009, Hefei, China aut Yue Junyang School of Biotechnology and Food Engineering, Hefei University of Technology, 230009, Hefei, China aut Wang Wenjie School of Biotechnology and Food Engineering, Hefei University of Technology, 230009, Hefei, China aut Liu Yongsheng School of Biotechnology and Food Engineering, Hefei University of Technology, 230009, Hefei, China aut Planta Springer Berlin Heidelberg 241/6(2015-06-01), 1337-1350 0032-0935 241:6<1337 2015 241 425 https://doi.org/10.1007/s00425-015-2258-8 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00425-015-2258-8 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Zhu Yunye School of Biotechnology and Food Engineering, Hefei University of Technology, 230009, Hefei, China aut NATIONALLICENCE 700 1- Huang Shengxiong School of Biotechnology and Food Engineering, Hefei University of Technology, 230009, Hefei, China aut NATIONALLICENCE 700 1- Miao Min School of Biotechnology and Food Engineering, Hefei University of Technology, 230009, Hefei, China aut NATIONALLICENCE 700 1- Tang Xiaofeng School of Biotechnology and Food Engineering, Hefei University of Technology, 230009, Hefei, China aut NATIONALLICENCE 700 1- Yue Junyang School of Biotechnology and Food Engineering, Hefei University of Technology, 230009, Hefei, China aut NATIONALLICENCE 700 1- Wang Wenjie School of Biotechnology and Food Engineering, Hefei University of Technology, 230009, Hefei, China aut NATIONALLICENCE 700 1- Liu Yongsheng School of Biotechnology and Food Engineering, Hefei University of Technology, 230009, Hefei, China aut NATIONALLICENCE 773 0- Planta Springer Berlin Heidelberg 241/6(2015-06-01), 1337-1350 0032-0935 241:6<1337 2015 241 425