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

Damaged DNA Binding 1 (DDB1)-binding WD40 (DWD) proteins are highly conserved and involved in a plethora of developmental and physiological processes such as flowering time control, photomorphogenesis, and abiotic stress responses. The phylogeny of this family of proteins in plants and algae of viridiplante is a critical area to understand the emergence of this family in such important and diverse functions. We aimed to investigate the putative homologs of DWD in the viridiplante and establish a deeper DWD evolutionary grasp. The advancement in publicly available genomic data allowed us to perform an extensive genome-wide DWD retrieval. Using annotated Arabidopsis thaliana DWDs as the reference , we generated and characterized a comprehensive DWD database for the studied photoautotrophs. Further, a generic DWD classification system (Type A to K), based on (i) position of DWD motifs, (ii) number of DWD motifs, and (iii) presence/absence of other domains, was adopted. About 72-80% DWDs have one DWD motif, whereas 17-24% DWDs have two and 0.5-4.7% DWDs have three DWD motifs. Neighbor-joining phyloge-netic construction of A. thaliana DWDs facilitated us to tune these substrate receptors into 15 groups. Though the DWD count increases from microalgae to higher land plants, the ratio of DWD to WD40 remained constant throughout the viridiplante. The DWD expansion appeared to be the consequence of consistent DWD genetic flow accompanied by several gene duplication events. The network, phylogenetic, and statistical analysis delineated DWD evolutionary relevance in the viridiplante.

Genome-wide analysis of DWD proteins in soybean (Glycine max): Significance of Gm08DWD and GmMYB176 interaction in isoflavonoid biosynthesis

“…Evidently, some chromosomes exhibited dense distribution of DWD genes, whereas others contained sparse distribution of them (Fig 3). Similar DWD gene distribution on chromosomes was reported in foxtail millet [12] and tomato [15]. The uneven distribution of the DWD genes suggested diverse contributions of soybean chromosomes to the formation and expansion of DWD gene family.…”

“…Each candidate protein identified from Phytozome soybean database was confirmed for their WD40 domain annotation and architecture by using Simple Modular Architecture Research Tool (SMART) database available at http://smart.embl.de [31]. Following the methods used by Lee et al [14] and Zhu et al [15], we first confirmed for the presence of WD40 repeat in each WDR protein using SMART, and then DWD motif was manually identified by using the conserved amino acid sequence ([IFVL]-[IFVL]-[AGST]-[AGST]-[AGST]-x-[DE]-x(2)-[IFVL]-x-[IFVL]-[WY]-[DE]-[IFVL]-[RK]) search against each WD40 repeat sequence. Additional conserved motifs or domains other than DWD were identified using the SMART database.…”

“…For example, Arabidopsis genome contains at least 269 putative WDR proteins [11] whereas foxtail millet [12] and rice [13] genomes encode 225 and 200 WDRs, respectively. Among these WDR proteins, 85 and 78 are putative DWD proteins in Arabidopsis and rice, respectively [14] whereas out of 269 putative WDR proteins, 100 are DWDs in tomato [15]. A total of 27 Arabidopsis DWD proteins interact with DDB1 protein [9, 16–18].…”

Genome-wide Analysis of WD40 Protein Family in Human

“…Evolutionary analysis showed that both tandem duplication and segmental duplication contributed to the expansion of WD40 gene family, and revealed that plant-specific domain architectures and functions emerged with the family expansion in the plant lineage. In a study of tomato genome, the authors specifically analysed the DDB1-binding WD40 proteins, a subfamily presumably serving as substrates recognition components of CUL4 E3 ligases, and experimentally confirmed 14 proteins interacting with DDB123.…”

WD Repeat‐containing Protein 73, A Novel Gene Correlated with Gonad Development in Large Yellow Croaker, Larimichthys crocea

“…WD repeat‐containing (WDR, also called WD40) protein consists of 40 amino acids with a glycine‐histidine (GH) di‐peptide near the N‐terminus, a conserved aspartic acid (D) located before the WD repeats, and the signature WD di‐peptide at the C‐terminus (Neer et al ; Smith et al ). The WD40 proteins are involved in diverse biological functions including signal transduction, protein ubiquitination, cell cycle regulation, abiotic tolerance, histone methylation, transcriptional regulation, and so forth (Xu and Min ; Mishra et al ; Dahlberg and Juo ; Kong et al ; Zhu et al ). The genomic sequences from large yellow croaker, Larimichthys crocea , in our laboratory encode more than 200 putative WD40 proteins.…”