Статті в журналах: "WD40-repeat proteins"

1

Wang, Yang, Xue-Jia Hu, Xu-Dong Zou, Xian-Hui Wu, Zhi-Qiang Ye, and Yun-Dong Wu. "WDSPdb: a database for WD40-repeat proteins." Nucleic Acids Research 43, no. D1 (October 27, 2014): D339—D344. http://dx.doi.org/10.1093/nar/gku1023.

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2

Dell, Edward J., Jennifer Connor, Songhai Chen, Elizabeth G. Stebbins, Nikolai P. Skiba, Daria Mochly-Rosen та Heidi E. Hamm. "The βγ Subunit of Heterotrimeric G Proteins Interacts with RACK1 and Two Other WD Repeat Proteins". Journal of Biological Chemistry 277, № 51 (30 вересня 2002): 49888–95. http://dx.doi.org/10.1074/jbc.m202755200.

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A yeast two-hybrid approach was used to discern possible new effectors for the βγ subunit of heterotrimeric G proteins. Three of the clones isolated are structurally similar to Gβ, each exhibiting the WD40 repeat motif. Two of these proteins, thereceptor foractivatedCkinase 1 (RACK1) and the dynein intermediate chain, co-immunoprecipitate with Gβγ using an anti-Gβ antibody. The third protein, AAH20044, has no known function; however, sequence analysis indicates that it is a WD40 repeat protein. Further investigation with RACK1 shows that it not only interacts with Gβ1γ1but also unexpectedly with the transducin heterotrimer Gαtβ1γ1. Gαtalone does not interact, but it must contribute to the interaction because the apparent EC50value of RACK1 for Gαtβ1γ1is 3-fold greater than that for Gβ1γ1(0.1versus0.3 μm). RACK1 is a scaffold that interacts with several proteins, among which are activated βIIPKC and dynamin-1 (1). βIIPKC and dynamin-1 compete with Gβ1γ1and Gαtβ1γ1for interaction with RACK1. These findings have several implications: 1) that WD40 repeat proteins may interact with each other; 2) that Gβγ interacts differently with RACK1 than with its other known effectors; and/or 3) that the G protein-RACK1 complex may constitute a signaling scaffold important for intracellular responses.

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3

Song, Richard, Zhong-Duo Wang, and Matthieu Schapira. "Disease Association and Druggability of WD40 Repeat Proteins." Journal of Proteome Research 16, no. 10 (September 28, 2017): 3766–73. http://dx.doi.org/10.1021/acs.jproteome.7b00451.

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4

Schapira, Matthieu, Mike Tyers, Maricel Torrent, and Cheryl H. Arrowsmith. "WD40 repeat domain proteins: a novel target class?" Nature Reviews Drug Discovery 16, no. 11 (October 13, 2017): 773–86. http://dx.doi.org/10.1038/nrd.2017.179.

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5

Jain, Buddhi Prakash, and Shweta Pandey. "WD40 Repeat Proteins: Signalling Scaffold with Diverse Functions." Protein Journal 37, no. 5 (August 1, 2018): 391–406. http://dx.doi.org/10.1007/s10930-018-9785-7.

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6

Suganuma, T., S. G. Pattenden, and J. L. Workman. "Diverse functions of WD40 repeat proteins in histone recognition." Genes & Development 22, no. 10 (May 15, 2008): 1265–68. http://dx.doi.org/10.1101/gad.1676208.

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7

Tian, Yue, Jingjing Du, Huaitong Wu, Xueying Guan, Weihang Chen, Yan Hu, Lei Fang, et al. "The transcription factor MML4_D12 regulates fiber development through interplay with the WD40-repeat protein WDR in cotton." Journal of Experimental Botany 71, no. 12 (March 2, 2020): 3499–511. http://dx.doi.org/10.1093/jxb/eraa104.

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Abstract In planta, a vital regulatory complex, MYB–basic helix–loop–helix (bHLH)–WD40 (MBW), is involved in trichome development and synthesis of anthocyanin and proanthocyanin in Arabidopsis. Usually, WD40 proteins provide a scaffold for protein–protein interaction between MYB and bHLH proteins. Members of subgroup 9 of the R2R3 MYB transcription factors, which includes MYBMIXTA-Like (MML) genes important for plant cell differentiation, are unable to interact with bHLH. In this study, we report that a cotton (Gossypium hirsutum) seed trichome or lint fiber-related GhMML factor, GhMML4_D12, interacts with a diverged WD40 protein (GhWDR) in a process similar to but different from that of the MBW ternary complex involved in Arabidopsis trichome development. Amino acids 250–267 of GhMML4_D12 and the first and third WD40 repeat domains of GhWDR determine their interaction. GhWDR could rescue Arabidopsis ttg1 to its wild type, confirming its orthologous function in trichome development. Our findings shed more light towards understanding the key role of the MML and WD40 families in plants and in the improvement of cotton fiber production.

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8

Cho, Pyo Yun, Tae Im Kim, Shunyu Li, Sung-Jong Hong, Min-Ho Choi, Sung-Tae Hong, and Yong Je Chung. "Metacercarial proteins interacting with WD40-repeat protein of Clonorchis sinensis." Korean Journal of Parasitology 45, no. 3 (2007): 229. http://dx.doi.org/10.3347/kjp.2007.45.3.229.

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9

Kim, Tae Im, Pyo Yun Cho, Shunyu Li, Sung-Tae Hong, Min-Ho Choi, and Sung-Jong Hong. "Partner proteins that interact with Clonorchis sinensis WD40-repeat protein." Parasitology Research 101, no. 5 (July 6, 2007): 1233–38. http://dx.doi.org/10.1007/s00436-007-0625-5.

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10

Eugster, Anne, Gabriella Frigerio, Martin Dale та Rainer Duden. "The α- and β′-COP WD40 Domains Mediate Cargo-selective Interactions with Distinct Di-lysine Motifs". Molecular Biology of the Cell 15, № 3 (березень 2004): 1011–23. http://dx.doi.org/10.1091/mbc.e03-10-0724.

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Coatomer is required for the retrieval of proteins from an early Golgi compartment back to the endoplasmic reticulum. The WD40 domain of α-COP is required for the recruitment of KKTN-tagged proteins into coatomer-coated vesicles. However, lack of the domain has only minor effects on growth in yeast. Here, we show that the WD40 domain of β′-COP is required for the recycling of the KTKLL-tagged Golgi protein Emp47p. The protein is degraded more rapidly in cells with a point mutation in the WD40 domain of β′-COP (sec27-95) or in cells lacking the domain altogether, whereas a point mutation in the Clathrin Heavy Chain Repeat (sec27-1) does not affect the turnover of Emp47p. Lack of the WD40 domain of β′-COP has only minor effects on growth of yeast cells; however, absence of both WD40 domains of α- and β′-COP is lethal. Two hybrid studies together with our analysis of the maturation of KKTN-tagged invertase and the turnover of Emp47p in α- and β′-COP mutants suggest that the two WD40 domains of α- and β′-COP bind distinct but overlapping sets of di-lysine signals and hence both contribute to recycling of proteins with di-lysine signals.

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11

Salih, Haron, Wenfang Gong, Mtawa Mkulama, and Xiongming Du. "Genome-wide characterization, identification, and expression analysis of the WD40 protein family in cotton." Genome 61, no. 7 (July 2018): 539–47. http://dx.doi.org/10.1139/gen-2017-0237.

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WD40 repeat proteins are largely distributed across the plant kingdom and play an important role in diverse biological activities. In this work, we performed genome-wide identification, characterization, and expression level analysis of WD40 genes in cotton. A total of 579, 318, and 313 WD40 genes were found in Gossypium hirsutum, G. arboreum, and G. raimondii, respectively. Based on phylogenetic tree analyses, WD40 genes were divided into 11 groups with high similarities in exon/intron features and protein domains within the group. Expression analysis of WD40 genes showed differential expression at different stages of cotton fiber development (0 and 8 DPA) and cotton stem. A number of miRNAs were identified to target WD40 genes that are significantly involved in cotton fiber development during the initiation and elongation stages. These include miR156, miR160, miR162, miR164, miR166, miR167, miR169, miR171, miR172, miR393, miR396, miR398, miR2950, and miR7505. The findings provide a stronger indication of WD40 gene function and their involvement in the regulation of cotton fiber development during the initiation and elongation stages.

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12

Mills, Ryan D., Terrence D. Mulhern, Heung-Chin Cheng, and Janetta G. Culvenor. "Analysis of LRRK2 accessory repeat domains: prediction of repeat length, number and sites of Parkinson's disease mutations." Biochemical Society Transactions 40, no. 5 (September 19, 2012): 1086–89. http://dx.doi.org/10.1042/bst20120088.

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Various investigators have identified the major domain organization of LRRK2 (leucine-rich repeat kinase 2), which includes a GTPase ROC (Ras of complex proteins) domain followed by a COR (C-terminal of ROC) domain and a protein kinase domain. In addition, there are four domains composed of structural repeat motifs likely to be involved in regulation and localization of this complex protein. In the present paper, we report our bioinformatic analyses of the human LRRK2 amino acid sequence to predict the repeat size, number and likely boundaries for the armadillo repeat, ankyrin repeat, the leucine-rich repeat and WD40 repeat regions of LRRK2. Homology modelling using known protein structures with similar domains was used to predict structures, exposed residues and location of mutations for these repeat regions. We predict that the armadillo repeats, ankyrin repeats and leucine-rich repeats together form an extended N-terminal flexible ‘solenoid’-like structure composed of tandem repeat modules likely to be important in anchoring to the membrane and cytoskeletal structures as well as binding to other protein ligands. Near the C-terminus of LRRK2, the WD40 repeat region is predicted to form a closed propeller structure that is important for protein complex formation.

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13

Kim, Yeonjoo, and Soo-Hyun Kim. "WD40-Repeat Proteins in Ciliopathies and Congenital Disorders of Endocrine System." Endocrinology and Metabolism 35, no. 3 (September 30, 2020): 494–506. http://dx.doi.org/10.3803/enm.2020.302.

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14

CHEN, S. "Interaction of G?? with RACK1 and other WD40 repeat proteins*1." Journal of Molecular and Cellular Cardiology 37, no. 2 (August 2004): 399–406. http://dx.doi.org/10.1016/j.yjmcc.2004.04.019.

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15

Ma, Jing, Ke An, Jing-Bo Zhou, Nuo-Si Wu, Yang Wang, Zhi-Qiang Ye, and Yun-Dong Wu. "WDSPdb: an updated resource for WD40 proteins." Bioinformatics 35, no. 22 (June 4, 2019): 4824–26. http://dx.doi.org/10.1093/bioinformatics/btz460.

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AbstractSummaryThe WD40-repeat proteins are a large family of scaffold molecules that assemble complexes in various cellular processes. Obtaining their structures is the key to understanding their interaction details. We present WDSPdb 2.0, a significantly updated resource providing accurately predicted secondary and tertiary structures and featured sites annotations. Based on an optimized pipeline, WDSPdb 2.0 contains about 600 thousand entries, an increase of 10-fold, and integrates more than 37 000 variants from sources of ClinVar, Cosmic, 1000 Genomes, ExAC, IntOGen, cBioPortal and IntAct. In addition, the web site is largely improved for visualization, exploring and data downloading.Availability and implementationhttp://www.wdspdb.com/wdsp/ or http://wu.scbb.pkusz.edu.cn/wdsp/.Supplementary informationSupplementary data are available at Bioinformatics online.

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16

Sepulveda-Garcia, Edgar, Elena C. Fulton, Emily V. Parlan, Lily E. O’Connor, Anneke A. Fleming, Amy J. Replogle, Mario Rocha-Sosa, Joshua M. Gendron, and Bryan Thines. "Unique N-Terminal Interactions Connect F-BOX STRESS INDUCED (FBS) Proteins to a WD40 Repeat-like Protein Pathway in Arabidopsis." Plants 10, no. 10 (October 19, 2021): 2228. http://dx.doi.org/10.3390/plants10102228.

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SCF-type E3 ubiquitin ligases provide specificity to numerous selective protein degradation events in plants, including those that enable survival under environmental stress. SCF complexes use F-box (FBX) proteins as interchangeable substrate adaptors to recruit protein targets for ubiquitylation. FBX proteins almost universally have structure with two domains: A conserved N-terminal F-box domain interacts with a SKP protein and connects the FBX protein to the core SCF complex, while a C-terminal domain interacts with the protein target and facilitates recruitment. The F-BOX STRESS INDUCED (FBS) subfamily of plant FBX proteins has an atypical structure, however, with a centrally located F-box domain and additional conserved regions at both the N- and C-termini. FBS proteins have been linked to environmental stress networks, but no ubiquitylation target(s) or biological function has been established for this subfamily. We have identified two WD40 repeat-like proteins in Arabidopsis that are highly conserved in plants and interact with FBS proteins, which we have named FBS INTERACTING PROTEINs (FBIPs). FBIPs interact exclusively with the N-terminus of FBS proteins, and this interaction occurs in the nucleus. FBS1 destabilizes FBIP1, consistent with FBIPs being ubiquitylation targets SCFFBS1 complexes. This work indicates that FBS proteins may function in stress-responsive nuclear events, and it identifies two WD40 repeat-like proteins as new tools with which to probe how an atypical SCF complex, SCFFBS, functions via FBX protein N-terminal interaction events.

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17

Zhao, Li, Zhu, Chang, Li, and Zhang. "Identification and Characterization of MYB-bHLH-WD40 Regulatory Complex Members Controlling Anthocyanidin Biosynthesis in Blueberry Fruits Development." Genes 10, no. 7 (June 28, 2019): 496. http://dx.doi.org/10.3390/genes10070496.

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Anthocyanins is the main representative of flavonoids in blueberry fruits. The anthocyanins biosynthetic pathway has been extensively studied in numerous model plants and fruit crops at biochemical, genetic, and molecular levels. However, the mechanisms by which the MYB transcription factor/basic helix-loop-helix (bHLH) domain protein/WD-repeat (MYB-bHLH-WD40) complexes regulate anthocyanin biosynthesis in blueberry is still limited. In the present study, we identified 11 MYB, 7 bHLH, and 6 WD40 genes in blueberry fruits, using amino acid sequences of homologous MYB-bHLH-WD40 complexes in Arabidopsis, apple, grape, and strawberry. To understand these mechanisms, the expression patterns of MYB-bHLH-WD40 genes were examined and validated using differentially expressed gene (DEG) analysis and quantitative real-time reverse transcription PCR (qRT-PCR), respectively. The expression patterns of MYB-bHLH-WD40 genes positively correlated with anthocyanin accumulation and color development in blueberry fruits. Consistent with the effects of other transcriptional regulators, the VcMYBL1::GFP, VcbHLH1::GFP, and VcWDL2::GFP fusion proteins were only observed in the nucleus. The protein-protein interactions (PPIs) and bimolecular fluorescence complementation (BiFC) assay suggested a possible link between VcbHLHL1 and VcMYBL1. Finally, a model was proposed and discussed for how the expression of the MYB-bHLH-WD40 complexes can promote anthocyanin biosynthesis in blueberry fruits. To our knowledge, this study was the first to evaluate MYB-bHLH-WD40 complexes in blueberry fruits, and it provides a foundation to dissect the function of the mechanism.

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18

Runne, Caitlin, та Songhai Chen. "WD40-repeat proteins control the flow of Gβγ signaling for directional cell migration". Cell Adhesion & Migration 7, № 2 (березень 2013): 214–18. http://dx.doi.org/10.4161/cam.22940.

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19

Jeffries, Tim R., Stephen K. Dove, Robert H. Michell, and Peter J. Parker. "PtdIns-specific MPR Pathway Association of a Novel WD40 Repeat Protein, WIPI49." Molecular Biology of the Cell 15, no. 6 (June 2004): 2652–63. http://dx.doi.org/10.1091/mbc.e03-10-0732.

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WIPI49 is a member of a previously undescribed family of WD40-repeat proteins that we demonstrate binds 3-phosphorylated phosphoinositides. Immunofluorescent imaging indicates that WIPI49 is localized to both trans-Golgi and endosomal membranes, organelles between which it traffics in a microtubule-dependent manner. Live cell imaging establishes that WIPI49 traffics through the same set of endosomal membranes as that followed by the mannose-6-phosphate receptor (MPR), and consistent with this, WIPI49 is enriched in clathrin-coated vesicles. Ectopic expression of wild-type WIPI49 disrupts the proper functioning of this MPR pathway, whereas expression of a double point mutant (R221,222AWIPI49) unable to bind phosphoinositides does not disrupt this pathway. Finally, suppression of WIPI49 expression through RNAi, demonstrates that its presence is required for normal endosomal organization and distribution of the CI-MPR. We conclude that WIPI49 is a novel regulatory component of the endosomal and MPR pathway and that this role is dependent upon the PI-binding properties of its WD40 domain.

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Fukumoto, Yasunori, Naoshi Dohmae, and Fumio Hanaoka. "Schizosaccharomyces pombe Ddb1 Recruits Substrate-Specific Adaptor Proteins through a Novel Protein Motif, the DDB-Box." Molecular and Cellular Biology 28, no. 22 (September 15, 2008): 6746–56. http://dx.doi.org/10.1128/mcb.00757-08.

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ABSTRACT DDB1 was isolated as a UV-damaged DNA-binding protein, but recent studies established that it plays a role as a component of cullin 4A ubiquitin ligases. Cullin-RING complexes are the largest known ubiquitin ligase family, with hundreds of substrate-specific adaptor subunits and which are defined by characteristic motifs. A common motif for DDB1/cullin 4 ubiquitin ligases, a WDXR motif, was recently reported. Here, we show that Schizosaccharomyces pombe Ddb1 associates with several WD40 repeat proteins that share a novel protein motif designated the DDB-box, a motif essential for interaction with Ddb1 and independent of WD40 repeats, unlike the WDXR motif. We also show that ddb1 + and the putative CSA homolog ckn1 + are involved in transcription-coupled nucleotide excision repair and that the DDB-box is essential for the ckn1 + function in vivo. These data indicate that the DDB-box is another common motif which defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases.

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21

Pöggeler, Stefanie, and Ulrich Kück. "A WD40 Repeat Protein Regulates Fungal Cell Differentiation and Can Be Replaced Functionally by the Mammalian Homologue Striatin." Eukaryotic Cell 3, no. 1 (February 2004): 232–40. http://dx.doi.org/10.1128/ec.3.1.232-240.2004.

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ABSTRACT Fruiting body development in fungi is a complex cellular differentiation process that is controlled by more than 100 developmental genes. Mutants of the filamentous fungus Sordaria macrospora showing defects in fruiting body formation are pertinent sources for the identification of components of this multicellular differentiation process. Here we show that the sterile mutant pro11 carries a defect in the pro11 gene encoding a multimodular WD40 repeat protein. Complementation analysis indicates that the wild-type gene or C-terminally truncated versions of the wild-type protein are able to restore the fertile phenotype in mutant pro11. PRO11 shows significant homology to several vertebrate WD40 proteins, such as striatin and zinedin, which seem to be involved in Ca2+-dependent signaling in cells of the central nervous system and are supposed to function as scaffolding proteins linking signaling and eukaryotic endocytosis. Cloning of a mouse cDNA encoding striatin allowed functional substitution of the wild-type protein with restoration of fertility in mutant pro11. Our data strongly suggest that an evolutionarily conserved cellular process controlling eukaryotic cell differentiation may regulate fruiting body formation.

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22

Higa, Leigh Ann, Min Wu, Tao Ye, Ryuji Kobayashi, Hong Sun, and Hui Zhang. "CUL4–DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation." Nature Cell Biology 8, no. 11 (October 15, 2006): 1277–83. http://dx.doi.org/10.1038/ncb1490.

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23

Gurung, Raju, Darlami Om, Rabin Pun, Soonsil Hyun, and Dongyun Shin. "Recent Progress in Modulation of WD40-Repeat Domain 5 Protein (WDR5): Inhibitors and Degraders." Cancers 15, no. 15 (August 1, 2023): 3910. http://dx.doi.org/10.3390/cancers15153910.

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WD40-repeat (WDR) domain proteins play a crucial role in mediating protein–protein interactions that sustain oncogenesis in human cancers. One prominent example is the interaction between the transcription factor MYC and its chromatin co-factor, WD40-repeat domain protein 5 (WDR5), which is essential for oncogenic processes. The MYC family of proteins is frequently overexpressed in various cancers and has been validated as a promising target for anticancer therapies. The recruitment of MYC to chromatin is facilitated by WDR5, highlighting the significance of their interaction. Consequently, inhibiting the MYC–WDR5 interaction has been shown to induce the regression of malignant tumors, offering an alternative approach to targeting MYC in the development of anticancer drugs. WDR5 has two protein interaction sites, the “WDR5-binding motif” (WBM) site for MYC interaction and the histone methyltransferases SET1 recognition motif “WDR5-interacting” (WIN) site forming MLL complex. Significant efforts have been dedicated to the discovery of inhibitors that target the WDR5 protein. More recently, the successful application of targeted protein degradation technology has enabled the removal of WDR5. This breakthrough has opened up new avenues for inhibiting the interaction between WDR5 and the binding partners. In this review, we address the recent progress made in targeting WDR5 to inhibit MDR5–MYC and MDR5–MLL1 interactions, including its targeted protein degradation and their potential impact on anticancer drug discovery.

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Arıkan, Burcu, Aslı Semercі, Ozgur Cakır, and Kara Turgut. "Arabidopsis thaliana GTS1 transcripts are activated by yeast extract." Botanica Serbica 45, no. 2 (2021): 195–201. http://dx.doi.org/10.2298/botserb2102195a.

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WD40 repeat-containing proteins participate in DNA-protein and protein-protein interactions and positively regulate plant stress responses. GTS1, known as a WD40 repeat-containing protein, works as a scaffold protein and is important in ribosome biogenesis and also biomass accumulation. In this study, we evaluated the GIGANTUS1 (GTS1) gene expression in response to biotic and abiotic stress factors in Arabidopsis thaliana plants. In addition, we grew and characterized A. thaliana gts1 mutant (T-DNA SALK_010647) in order to observe the effects of its absence on plants. According to our results, 100-200 mM abscisic acid (ABA) and 100-200 mM sodium chloride (NaCl) treatment did not cause any changes in GTS1 gene expression, while only 6 h of 1 g/l and 2 g/l yeast extract (YE) treatment negatively affected GTS1 expression in 10-day-old plant explants. After 10 and 30 days of YE treatment, GTS1 gene expression was upregulated, and as a consequence plant growth efficiency was reduced. We thus concluded that through the downregulation of GTS1 transcripts, we could obtain better growth and/or higher biomass, which seems to be a good option for agricultural recruitments.

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Wu, Guangyu, Svetlana Lyapina, Indranil Das, Jinhe Li, Mark Gurney, Adele Pauley, Inca Chui, Raymond J. Deshaies, and Jan Kitajewski. "SEL-10 Is an Inhibitor of Notch Signaling That Targets Notch for Ubiquitin-Mediated Protein Degradation." Molecular and Cellular Biology 21, no. 21 (November 1, 2001): 7403–15. http://dx.doi.org/10.1128/mcb.21.21.7403-7415.2001.

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ABSTRACT Notch receptors and their ligands play important roles in both normal animal development and pathogenesis. We show here that the F-box/WD40 repeat protein SEL-10 negatively regulates Notch receptor activity by targeting the intracellular domain of Notch receptors for ubiquitin-mediated protein degradation. Blocking of endogenous SEL-10 activity was done by expression of a dominant-negative form containing only the WD40 repeats. In the case of Notch1, this block leads to an increase in Notch signaling stimulated by either an activated form of the Notch1 receptor or Jagged1-induced signaling through Notch1. Expression of dominant-negative SEL-10 leads to stabilization of the intracellular domain of Notch1. The Notch4 intracellular domain bound to SEL-10, but its activity was not increased as a result of dominant-negative SEL-10 expression. SEL-10 bound Notch4 via the WD40 repeats and bound preferentially to a phosphorylated form of Notch4 in cells. We mapped the region of Notch4 essential for SEL-10 binding to the C-terminal region downstream of the ankyrin repeats. When this C-terminal fragment of Notch4 was expressed in cells, it was highly labile but could be stabilized by the expression of dominant-negative SEL-10. Ubiquitination of Notch1 and Notch4 intracellular domains in vitro was dependent on SEL-10. Although SEL-10 interacts with the intracellular domains of both Notch1 and Notch4, these proteins respond differently to interference with SEL-10 function. Thus, SEL-10 functions to promote the ubiquitination of Notch proteins; however, the fates of these proteins may differ.

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Pashkova, Natasha, Lokesh Gakhar, Stanley C. Winistorfer, Liping Yu, S. Ramaswamy, and Robert C. Piper. "WD40 Repeat Propellers Define a Ubiquitin-Binding Domain that Regulates Turnover of F Box Proteins." Molecular Cell 40, no. 3 (November 2010): 433–43. http://dx.doi.org/10.1016/j.molcel.2010.10.018.

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27

Marçal, Nathalie, Harshila Patel, Zhifeng Dong, Stephanie Belanger-Jasmin, Brad Hoffman, Cheryl D. Helgason, Jinjun Dang, and Stefano Stifani. "Antagonistic Effects of Grg6 and Groucho/TLE on the Transcription Repression Activity of Brain Factor 1/FoxG1 and Cortical Neuron Differentiation." Molecular and Cellular Biology 25, no. 24 (December 15, 2005): 10916–29. http://dx.doi.org/10.1128/mcb.25.24.10916-10929.2005.

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ABSTRACT Groucho (Gro)/TLE transcriptional corepressors are involved in a variety of developmental mechanisms, including neuronal differentiation. They contain a conserved C-terminal WD40 repeat domain that mediates interactions with several DNA-binding proteins. In particular, Gro/TLE1 interacts with forkhead transcription factor brain factor 1 (BF-1; also termed FoxG1). BF-1 is an essential regulator of neuronal differentiation during cerebral cortex development and represses transcription together with Gro/TLE1. Gro/TLE-related gene product 6 (Grg6) shares with Gro/TLEs a conserved WD40 repeat domain but is more distantly related at its N-terminal half. We demonstrate that Grg6 is expressed in cortical neural progenitor cells and interacts with BF-1. In contrast to Gro/TLE1, however, Grg6 does not promote, but rather suppresses, BF-1-mediated transcriptional repression. Consistent with these observations, Grg6 interferes with the binding of Gro/TLE1 to BF-1 and does not repress transcription when targeted to DNA. Moreover, coexpression of Grg6 and BF-1 in cortical progenitor cells leads to a decrease in the number of proliferating cells and increased neuronal differentiation. Conversely, Grg6 knockdown by RNA interference causes decreased neurogenesis. These results identify a new role for Grg6 in cortical neuron development and establish a functional link between Grg6 and BF-1.

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Imran, Ali, Brandon S. Moyer, Ashley J. Canning, Dan Kalina, Thomas M. Duncan, Kelsey J. Moody, Aaron J. Wolfe, Michael S. Cosgrove, and Liviu Movileanu. "Kinetics of the multitasking high-affinity Win binding site of WDR5 in restricted and unrestricted conditions." Biochemical Journal 478, no. 11 (June 11, 2021): 2145–61. http://dx.doi.org/10.1042/bcj20210253.

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Recent advances in quantitative proteomics show that WD40 proteins play a pivotal role in numerous cellular networks. Yet, they have been fairly unexplored and their physical associations with other proteins are ambiguous. A quantitative understanding of these interactions has wide-ranging significance. WD40 repeat protein 5 (WDR5) interacts with all members of human SET1/MLL methyltransferases, which regulate methylation of the histone 3 lysine 4 (H3K4). Here, using real-time binding measurements in a high-throughput setting, we identified the kinetic fingerprint of transient associations between WDR5 and 14-residue WDR5 interaction (Win) motif peptides of each SET1 protein (SET1Win). Our results reveal that the high-affinity WDR5-SET1Win interactions feature slow association kinetics. This finding is likely due to the requirement of SET1Win to insert into the narrow WDR5 cavity, also named the Win binding site. Furthermore, our explorations indicate fairly slow dissociation kinetics. This conclusion is in accordance with the primary role of WDR5 in maintaining the functional integrity of a large multisubunit complex, which regulates the histone methylation. Because the Win binding site is considered a key therapeutic target, the immediate outcomes of this study could form the basis for accelerated developments in medical biotechnology.

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Kannan, Meghna, Efil Bayam, Christel Wagner, Bruno Rinaldi, Perrine F. Kretz, Peggy Tilly, Marna Roos, et al. "WD40-repeat 47, a microtubule-associated protein, is essential for brain development and autophagy." Proceedings of the National Academy of Sciences 114, no. 44 (October 12, 2017): E9308—E9317. http://dx.doi.org/10.1073/pnas.1713625114.

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The family of WD40-repeat (WDR) proteins is one of the largest in eukaryotes, but little is known about their function in brain development. Among 26 WDR genes assessed, we found 7 displaying a major impact in neuronal morphology when inactivated in mice. Remarkably, all seven genes showed corpus callosum defects, including thicker (Atg16l1, Coro1c, Dmxl2, and Herc1), thinner (Kif21b and Wdr89), or absent corpus callosum (Wdr47), revealing a common role for WDR genes in brain connectivity. We focused on the poorly studied WDR47 protein sharing structural homology with LIS1, which causes lissencephaly. In a dosage-dependent manner, mice lacking Wdr47 showed lethality, extensive fiber defects, microcephaly, thinner cortices, and sensory motor gating abnormalities. We showed that WDR47 shares functional characteristics with LIS1 and participates in key microtubule-mediated processes, including neural stem cell proliferation, radial migration, and growth cone dynamics. In absence of WDR47, the exhaustion of late cortical progenitors and the consequent decrease of neurogenesis together with the impaired survival of late-born neurons are likely yielding to the worsening of the microcephaly phenotype postnatally. Interestingly, the WDR47-specific C-terminal to LisH (CTLH) domain was associated with functions in autophagy described in mammals. Silencing WDR47 in hypothalamic GT1-7 neuronal cells and yeast models independently recapitulated these findings, showing conserved mechanisms. Finally, our data identified superior cervical ganglion-10 (SCG10) as an interacting partner of WDR47. Taken together, these results provide a starting point for studying the implications of WDR proteins in neuronal regulation of microtubules and autophagy.

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Dou, Xiaoying, Jinrong Bai, Huan Wang, Ying Kong, Lixin Lang, Fang Bao, and Hongzhong Shang. "Cloning and Characterization of a Tryptophan–Aspartic Acid Repeat Gene Associated with the Regulation of Anthocyanin Biosynthesis in Oriental Hybrid Lily." Journal of the American Society for Horticultural Science 145, no. 2 (March 2020): 131–40. http://dx.doi.org/10.21273/jashs04791-19.

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Anthocyanins are major pigments responsible for the color of lily (Lilium sp.) flowers. Anthocyanin synthesis is part of the flavonoid metabolic pathway. Numerous transcription factors, including R2R3-MYBs, basic helix-loop-helix (bHLH), and tryptophan–aspartic acid repeat (also known as WD40 or WD repeat) proteins, known to regulate flavonoid biosynthesis have been identified in various plant species. However, there is limited information available on WD repeat proteins in lilies. In this study, we identified a WD repeat gene in the Oriental hybrid lily ‘Sorbonne’ (Lilium hybrid WD repeat, LhWDR). LhWDR contains no introns, and has a 1100–base pair open reading frame, encoding a putative protein of 370 amino acids. LhWDR was found to be localized in the cytoplasm of transgenic Arabidopsis thaliana root cells. Expression patterns of LhWDR in different organs and at different periods of lily tepal growth revealed that the expression levels of this gene are closely associated with anthocyanin accumulation. A yeast two-hybrid assay demonstrated that full-length LhWDR interacts with the 420 N-terminal amino acids of Lilium hybrid bHLH2. Interestingly, overexpression of LhWDR in A. thaliana led to an upregulation of the dihydroflavonol 4-reductase gene, which is an important structural gene downstream of the anthocyanin pathway. These results indicate that the WD repeat protein LhWDR might interact with a bHLH transcription factor to regulate anthocyanin biosynthesis.

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Close, Viola, William Close, Sabrina Julia Kugler, Michaela Reichenzeller, Deyan Yordanov Yosifov, Johannes Bloehdorn, Leiling Pan, et al. "FBXW7 mutations reduce binding of NOTCH1, leading to cleaved NOTCH1 accumulation and target gene activation in CLL." Blood 133, no. 8 (February 21, 2019): 830–39. http://dx.doi.org/10.1182/blood-2018-09-874529.

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Abstract NOTCH1 is mutated in 10% of chronic lymphocytic leukemia (CLL) patients and is associated with poor outcome. However, NOTCH1 activation is identified in approximately one-half of CLL cases even in the absence of NOTCH1 mutations. Hence, there appear to be additional factors responsible for the impairment of NOTCH1 degradation. E3-ubiquitin ligase F-box and WD40 repeat domain containing-7 (FBXW7), a negative regulator of NOTCH1, is mutated in 2% to 6% of CLL patients. The functional consequences of these mutations in CLL are unknown. We found heterozygous FBXW7 mutations in 36 of 905 (4%) untreated CLL patients. The majority were missense mutations (78%) that mostly affected the WD40 substrate binding domain; 10% of mutations occurred in the first exon of the α-isoform. To identify target proteins of FBXW7 in CLL, we truncated the WD40 domain in CLL cell line HG-3 via clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 (Cas9). Homozygous truncation of FBXW7 resulted in an increase of activated NOTCH1 intracellular domain (NICD) and c-MYC protein levels as well as elevated hypoxia-inducible factor 1-α activity. In silico modeling predicted that novel mutations G423V and W425C in the FBXW7-WD40 domain change the binding of protein substrates. This differential binding was confirmed via coimmunoprecipitation of overexpressed FBXW7 and NOTCH1. In primary CLL cells harboring FBXW7 mutations, activated NICD levels were increased and remained stable upon translation inhibition. FBXW7 mutations coincided with an increase in NOTCH1 target gene expression and explain a proportion of patients characterized by dysregulated NOTCH1 signaling.

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Mascheretti, Iride, Raffaella Battaglia, Davide Mainieri, Andrea Altana, Massimiliano Lauria, and Vincenzo Rossi. "The WD40-Repeat Proteins NFC101 and NFC102 Regulate Different Aspects of Maize Development through Chromatin Modification." Plant Cell 25, no. 2 (February 2013): 404–20. http://dx.doi.org/10.1105/tpc.112.107219.

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33

Wu, Xian-Hui, Rong-Chang Chen, Ying Gao, and Yun-Dong Wu. "The Effect of Asp-His-Ser/Thr-Trp Tetrad on the Thermostability of WD40-Repeat Proteins." Biochemistry 49, no. 47 (November 30, 2010): 10237–45. http://dx.doi.org/10.1021/bi101321y.

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Lan, Jingqiu, Jinzhe Zhang, Rongrong Yuan, Hao Yu, Fengying An, Linhua Sun, Haodong Chen, et al. "TCP transcription factors suppress cotyledon trichomes by impeding a cell differentiation-regulating complex." Plant Physiology 186, no. 1 (February 12, 2021): 434–51. http://dx.doi.org/10.1093/plphys/kiab053.

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Abstract Trichomes are specialized epidermal cells that act as barriers against biotic and abiotic stresses. Although the formation of trichomes on hairy organs is well studied, the molecular mechanisms of trichome inhibition on smooth organs are still largely unknown. Here, we demonstrate that the CINCINNATA (CIN)-like TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors inhibit the formation of trichomes on cotyledons in Arabidopsis (Arabidopsis thaliana). The tcp2/3/4/5/10/13/17 septuple mutant produces cotyledons with ectopic trichomes on the adaxial sides. The expression patterns of TCP genes are developmentally regulated during cotyledon development. TCP proteins directly interact with GLABRA3 (GL3), a key component of the MYB transcription factor/basic helix–loop–helix domain protein/WD40-repeat proteins (MYB–bHLH–WD40, MBW) complex essential for trichome formation, to interfere with the transactivation activity of the MBW complex in cotyledons. TCPs also disrupt the MBW complex–R3 MYB negative feedback loop by directly promoting the expression of R3 MYB genes, which enhance the repression of the MBW complex. Our findings reveal a molecular framework in which TCPs suppress trichome formation on adaxial sides of cotyledons by repressing the activity of the MBW complex at the protein level and the transcripts of R3 MYB genes at the transcriptional level.

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35

Liu, Xuezhao, Yang Li, Xin Wang, Ruxiao Xing, Kai Liu, Qiwen Gan, Changyong Tang, et al. "The BEACH-containing protein WDR81 coordinates p62 and LC3C to promote aggrephagy." Journal of Cell Biology 216, no. 5 (April 12, 2017): 1301–20. http://dx.doi.org/10.1083/jcb.201608039.

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Autophagy-dependent clearance of ubiquitinated and aggregated proteins is critical to protein quality control, but the underlying mechanisms are not well understood. Here, we report the essential role of the BEACH (beige and Chediak–Higashi) and WD40 repeat-containing protein WDR81 in eliminating ubiquitinated proteins through autophagy. WDR81 associates with ubiquitin (Ub)-positive protein foci, and its loss causes accumulation of Ub proteins and the autophagy cargo receptor p62. WDR81 interacts with p62, facilitating recognition of Ub proteins by p62. Furthermore, WDR81 interacts with LC3C through canonical LC3-interacting regions in the BEACH domain, promoting LC3C recruitment to ubiquitinated proteins. Inactivation of LC3C or defective autophagy results in accumulation of Ub protein aggregates enriched for WDR81. In mice, WDR81 inactivation causes accumulation of p62 bodies in cortical and striatal neurons in the brain. These data suggest that WDR81 coordinates p62 and LC3C to facilitate autophagic removal of Ub proteins, and provide important insights into CAMRQ2 syndrome, a WDR81-related developmental disorder.

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36

Espagne, Eric, Pascale Balhadère, Marie-Louise Penin, Christian Barreau, and Béatrice Turcq. "HET-E and HET-D Belong to a New Subfamily of WD40 Proteins Involved in Vegetative Incompatibility Specificity in the Fungus Podospora anserina." Genetics 161, no. 1 (May 1, 2002): 71–81. http://dx.doi.org/10.1093/genetics/161.1.71.

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Abstract Vegetative incompatibility, which is very common in filamentous fungi, prevents a viable heterokaryotic cell from being formed by the fusion of filaments from two different wild-type strains. Such incompatibility is always the consequence of at least one genetic difference in specific genes (het genes). In Podospora anserina, alleles of the het-e and het-d loci control heterokaryon viability through genetic interactions with alleles of the unlinked het-c locus. The het-d2Y gene was isolated and shown to have strong similarity with the previously described het-e1A gene. Like the HET-E protein, the HET-D putative protein displayed a GTP-binding domain and seemed to require a minimal number of 11 WD40 repeats to be active in incompatibility. Apart from incompatibility specificity, no other function could be identified by disrupting the het-d gene. Sequence comparison of different het-e alleles suggested that het-e specificity is determined by the sequence of the WD40 repeat domain. In particular, the amino acids present on the upper face of the predicted β-propeller structure defined by this domain may confer the incompatible interaction specificity.

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37

Wen, Danni, Lingran Bao, Xuanzhu Huang, Xueduo Qian, Eryong Chen, and Bo Shen. "OsABT Is Involved in Abscisic Acid Signaling Pathway and Salt Tolerance of Roots at the Rice Seedling Stage." International Journal of Molecular Sciences 23, no. 18 (September 13, 2022): 10656. http://dx.doi.org/10.3390/ijms231810656.

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Rice is a staple cereal crop worldwide, and increasing its yields is vital to ensuring global food security. Salinity is a major factor that affects rice yield. Therefore, it is necessary to investigate salt tolerance mechanisms in rice. Proteins containing WD40 repeats play important roles in eukaryotic development and environmental adaptation. Here, we showed that overexpression of OsABT, a gene encoding a WD40-repeat protein, enhanced salt tolerance in rice seedlings by regulating root activity, relative conductivity, malondialdehyde and H2O2 content, and O2•− production rate. Root ion concentrations indicated that OsABT overexpression lines could maintain lower Na+ and higher K+/Na+ ratios and upregulated expression of salt-related genes OsSOS1 and OsHAK5 compared with the wild-type (WT) Nipponbare plants. Furthermore, Overexpression of OsABT decreased the abscisic acid (ABA) content, while downregulating the ABA synthesis genes OsNCED3 and OsNCED4 and upregulating the ABA catabolic gene OsABA8ox2. The yeast two-hybrid and bimolecular fluorescence complementation analyses showed that OsABT interacted with the ABA receptor proteins OsPYL4, OsPYL10, and PP2C phosphatase OsABIL2. A transcriptome analysis revealed that the differentially expressed genes between OsABT overexpression lines and WT plants were enriched in plant hormone signal transduction, including ABA signaling pathway under salt stress. Thus, OsABT can improve the salt tolerance in rice seedling roots by inhibiting reactive oxygen species accumulation, thereby regulating the intracellular Na+/K+ balance, ABA content, and ABA signaling pathway.

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Gadelha, Renan Brito, Caio Bezerra Machado, Flávia Melo Cunha de Pinho Pessoa, Laudreísa da Costa Pantoja, Igor Valentim Barreto, Rodrigo Monteiro Ribeiro, Manoel Odorico de Moraes Filho, Maria Elisabete Amaral de Moraes, André Salim Khayat, and Caroline Aquino Moreira-Nunes. "The Role of WRAP53 in Cell Homeostasis and Carcinogenesis Onset." Current Issues in Molecular Biology 44, no. 11 (November 4, 2022): 5498–515. http://dx.doi.org/10.3390/cimb44110372.

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The WD repeat containing antisense to TP53 (WRAP53) gene codifies an antisense transcript for tumor protein p53 (TP53), stabilization (WRAP53α), and a functional protein (WRAP53β, WDR79, or TCAB1). The WRAP53β protein functions as a scaffolding protein that is important for telomerase localization, telomere assembly, Cajal body integrity, and DNA double-strand break repair. WRAP53β is one of many proteins known for containing WD40 domains, which are responsible for mediating a variety of cell interactions. Currently, WRAP53 overexpression is considered a biomarker for a diverse subset of cancer types, and in this study, we describe what is known about WRAP53β’s multiple interactions in cell protein trafficking, Cajal body formation, and DNA double-strand break repair and its current perspectives as a biomarker for cancer.

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39

Twiddy, Davina, David G. Brown, Colin Adrain, Rebekah Jukes, Seamus J. Martin, Gerald M. Cohen, Marion MacFarlane, and Kelvin Cain. "Pro-apoptotic Proteins Released from the Mitochondria Regulate the Protein Composition and Caspase-processing Activity of the Native Apaf-1/Caspase-9 Apoptosome Complex." Journal of Biological Chemistry 279, no. 19 (March 1, 2004): 19665–82. http://dx.doi.org/10.1074/jbc.m311388200.

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The apoptosome is a large caspase-activating (∼700–1400 kDa) complex, which is assembled from Apaf-1 and caspase-9 when cytochromecis released during mitochondrial-dependent apoptotic cell death. Apaf-1 the core scaffold protein is ∼135 kDa and contains CARD (caspaserecruitmentdomain), CED-4, and multiple (13) WD40 repeat domains, which can potentially interact with a variety of unknown regulatory proteins. To identify such proteins we activated THP.1 lysates with dATP/cytochromecand used sucrose density centrifugation and affinity-based methods to purify the apoptosome for analysis by MALDI-TOF mass spectrometry. First, we used a glutathioneS-transferase (GST) fusion protein (GST-casp91–130) containing the CARD domain of caspase-9-(1–130), which binds to the CARD domain of Apaf-1 when it is in the apoptosome and blocks recruitment/activation of caspase-9. This affinity-purified apoptosome complex contained only Apaf-1XL and GST-casp91–130, demonstrating that the WD40 and CED-4 domains of Apaf-1 do not stably bind other cytosolic proteins. Next we used a monoclonal antibody to caspase-9 to immunopurify the native active apoptosome complex from cell lysates, containing negligible levels of cytochromec,secondmitochondria-derivedactivator ofcaspase (Smac), or Omi/HtrA2. This apoptosome complex exhibited low caspase-processing activity and contained four stably associated proteins, namely Apaf-1, pro-p35/34 forms of caspase-9, pro-p20 forms of caspase-3, X-linkedinhibitor ofapoptosis (XIAP), and cytochromec, which was only bound transiently to the complex. However, in lysates containing Smac and Omi/HtrA2, the caspase-processing activity of the purified apoptosome complex increased 6–8-fold and contained only Apaf-1 and the p35/p34-processed subunits of caspase-9. During apoptosis, Smac, Omi/HtrA2, and cytochromecare released simultaneously from mitochondria, and thus it is likely that the functional apoptosome complex in apoptotic cells consists primarily of Apaf-1 and processed caspase-9.

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Podolec, Roman, Emilie Demarsy, and Roman Ulm. "Perception and Signaling of Ultraviolet-B Radiation in Plants." Annual Review of Plant Biology 72, no. 1 (June 17, 2021): 793–822. http://dx.doi.org/10.1146/annurev-arplant-050718-095946.

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Ultraviolet-B (UV-B) radiation is an intrinsic fraction of sunlight that plants perceive through the UVR8 photoreceptor. UVR8 is a homodimer in its ground state that monomerizes upon UV-B photon absorption via distinct tryptophan residues. Monomeric UVR8 competitively binds to the substrate binding site of COP1, thus inhibiting its E3 ubiquitin ligase activity against target proteins, which include transcriptional regulators such as HY5. The UVR8–COP1 interaction also leads to the destabilization of PIF bHLH factor family members. Additionally, UVR8 directly interacts with and inhibits the DNA binding of a different set of transcription factors. Each of these UVR8 signaling mechanisms initiates nuclear gene expression changes leading to UV-B-induced photomorphogenesis and acclimation. The two WD40-repeat proteins RUP1 and RUP2 provide negative feedback regulation and inactivate UVR8 by facilitating redimerization. Here, we review the molecular mechanisms of the UVR8 pathway from UV-B perception and signal transduction to gene expression changes and physiological UV-B responses.

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Mahajan, Mayank, Benjamin Yee, Emil Hägglund, Lionel Guy, John A. Fuerst, and Siv G. E. Andersson. "Paralogization and New Protein Architectures in Planctomycetes Bacteria with Complex Cell Structures." Molecular Biology and Evolution 37, no. 4 (December 11, 2019): 1020–40. http://dx.doi.org/10.1093/molbev/msz287.

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Abstract Bacteria of the phylum Planctomycetes have a unique cell plan with an elaborate intracellular membrane system, thereby resembling eukaryotic cells. The origin and evolution of these remarkable features is debated. To study the evolutionary genomics of bacteria with complex cell architectures, we have resequenced the 9.2-Mb genome of the model organism Gemmata obscuriglobus and sequenced the 10-Mb genome of G. massiliana Soil9, the 7.9-Mb genome of CJuql4, and the 6.7-Mb genome of Tuwongella immobilis, all of which belong to the family Gemmataceae. A gene flux analysis of the Planctomycetes revealed a massive emergence of novel protein families at multiple nodes within the Gemmataceae. The expanded protein families have unique multidomain architectures composed of domains that are characteristic of prokaryotes, such as the sigma factor domain of extracytoplasmic sigma factors, and domains that have proliferated in eukaryotes, such as the WD40, leucine-rich repeat, tetratricopeptide repeat and Ser/Thr kinase domains. Proteins with identifiable domains in the Gemmataceae have longer lengths and linkers than proteins in most other bacteria, and the analyses suggest that these traits were ancestrally present in the Planctomycetales. A broad comparison of protein length distribution profiles revealed an overlap between the longest proteins in prokaryotes and the shortest proteins in eukaryotes. We conclude that the many similarities between proteins in the Planctomycetales and the eukaryotes are due to convergent evolution and that there is no strict boundary between prokaryotes and eukaryotes with regard to features such as gene paralogy, protein length, and protein domain composition patterns.

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Hodul, Molly, Rakesh Ganji, Caroline L. Dahlberg, Malavika Raman, and Peter Juo. "The WD40-repeat protein WDR-48 promotes the stability of the deubiquitinating enzyme USP-46 by inhibiting its ubiquitination and degradation." Journal of Biological Chemistry 295, no. 33 (June 25, 2020): 11776–88. http://dx.doi.org/10.1074/jbc.ra120.014590.

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Ubiquitination is a reversible post-translational modification that has emerged as a critical regulator of synapse development and function. However, the mechanisms that regulate the deubiquitinating enzymes (DUBs) responsible for the removal of ubiquitin from target proteins are poorly understood. We have previously shown that the DUB ubiquitin-specific protease 46 (USP-46) removes ubiquitin from the glutamate receptor GLR-1 and regulates its trafficking and degradation in Caenorhabditis elegans. We found that the WD40-repeat proteins WDR-20 and WDR-48 bind and stimulate the catalytic activity of USP-46. Here, we identified another mechanism by which WDR-48 regulates USP-46. We found that increased expression of WDR-48, but not WDR-20, promotes USP-46 abundance in mammalian cells in culture and in C. elegans neurons in vivo. Inhibition of the proteasome increased USP-46 abundance, and this effect was nonadditive with increased WDR-48 expression. We found that USP-46 is ubiquitinated and that expression of WDR-48 reduces the levels of ubiquitin–USP-46 conjugates and increases the t1/2 of USP-46. A point-mutated WDR-48 variant that disrupts binding to USP-46 was unable to promote USP-46 abundance in vivo. Finally, siRNA-mediated knockdown of wdr48 destabilizes USP46 in mammalian cells. Together, these results support a model in which WDR-48 binds and stabilizes USP-46 protein levels by preventing the ubiquitination and degradation of USP-46 in the proteasome. Given that a large number of USPs interact with WDR proteins, we propose that stabilization of DUBs by their interacting WDR proteins may be a conserved and widely used mechanism that controls DUB availability and function.

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Balk, Janneke, Daili J. Aguilar Netz, Katharina Tepper, Antonio J. Pierik, and Roland Lill. "The Essential WD40 Protein Cia1 Is Involved in a Late Step of Cytosolic and Nuclear Iron-Sulfur Protein Assembly." Molecular and Cellular Biology 25, no. 24 (December 15, 2005): 10833–41. http://dx.doi.org/10.1128/mcb.25.24.10833-10841.2005.

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ABSTRACT The assembly of cytosolic and nuclear iron-sulfur (Fe/S) proteins in yeast is dependent on the iron-sulfur cluster assembly and export machineries in mitochondria and three recently identified extramitochondrial proteins, the P-loop NTPases Cfd1 and Nbp35 and the hydrogenase-like Nar1. However, the molecular mechanism of Fe/S protein assembly in the cytosol is far from being understood, and more components are anticipated to take part in this process. Here, we have identified and functionally characterized a novel WD40 repeat protein, designated Cia1, as an essential component required for Fe/S cluster assembly in vivo on cytosolic and nuclear, but not mitochondrial, Fe/S proteins. Surprisingly, Nbp35 and Nar1, themselves Fe/S proteins, could assemble their Fe/S clusters in the absence of Cia1, demonstrating that these components act before Cia1. Consequently, Cia1 is involved in a late step of Fe/S cluster incorporation into target proteins. Coimmunoprecipitation assays demonstrated a specific interaction between Cia1 and Nar1. In contrast to the mostly cytosolic Nar1, Cia1 is preferentially localized to the nucleus, suggesting an additional function of Cia1. Taken together, our results indicate that Cia1 is a new member of the cytosolic Fe/S protein assembly (CIA) machinery participating in a step after Nbp35 and Nar1.

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Moreno, Carlos S., Susan Park, Kasey Nelson, Danita Ashby, Frantisek Hubalek, William S. Lane, and David C. Pallas. "WD40 Repeat Proteins Striatin and S/G2Nuclear Autoantigen Are Members of a Novel Family of Calmodulin-binding Proteins That Associate with Protein Phosphatase 2A." Journal of Biological Chemistry 275, no. 8 (February 25, 2000): 5257–63. http://dx.doi.org/10.1074/jbc.275.8.5257.

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Wu, Xian-Hui, Hui Zhang, and Yun-Dong Wu. "Is Asp-His-Ser/Thr-Trp tetrad hydrogen-bond network important to WD40-repeat proteins: A statistical and theoretical study." Proteins: Structure, Function, and Bioinformatics 78, no. 5 (October 16, 2009): 1186–94. http://dx.doi.org/10.1002/prot.22638.

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46

Wu, Xian-Hui, Yang Wang, Zhu Zhuo, Fan Jiang та Yun-Dong Wu. "Identifying the Hotspots on the Top Faces of WD40-Repeat Proteins from Their Primary Sequences by β-Bulges and DHSW Tetrads". PLoS ONE 7, № 8 (15 серпня 2012): e43005. http://dx.doi.org/10.1371/journal.pone.0043005.

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Yu, Shiyi, Zhengyan Liang, Zhehao Fan, Binjie Cao, Ning Wang, Rui Wu, and Haibo Sun. "A Comprehensive Analysis Revealing FBXW9 as a Potential Prognostic and Immunological Biomarker in Breast Cancer." International Journal of Molecular Sciences 24, no. 6 (March 9, 2023): 5262. http://dx.doi.org/10.3390/ijms24065262.

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The WD40 repeat-containing F-box proteins (FBXWs) family belongs to three major classes of F-box proteins. Consistent with the function of other F-box proteins, FBXWs are E3 ubiquitin ligases to mediate protease-dependent protein degradation. However, the roles of several FBXWs remain elusive. In the present study, via integrative analysis of transcriptome profiles from The Cancer Genome Atlas (TCGA) datasets, we found that FBXW9 was upregulated in the majority of cancer types, including breast cancer. FBXW expression was correlated with the prognosis of patients with various types of cancers, especially for FBXW4, 5, 9, and 10. Moreover, FBXWs were associated with infiltration of immune cells, and expression of FBXW9 was associated with poor prognosis of patients receiving anti-PD1 therapy. We predicted several substrates of FBXW9, and TP53 was the hub gene in the list. Downregulation of FBXW9 increased the expression of p21, a target of TP53, in breast cancer cells. FBXW9 was also strongly correlated with cancer cell stemness, and genes correlated with FBXW9 were associated with several MYC activities according to gene enrichment analysis in breast cancer. Cell-based assays showed that silencing of FBXW9 inhibited cell proliferation and cell cycle progression in breast cancer cells. Our study highlights the potential role of FBXW9 as a biomarker and promising target for patients with breast cancer.

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Suzuki, Hiroshi, Tomoki Chiba, Masato Kobayashi, Masahiro Takeuchi, Toshiaki Suzuki, Arata Ichiyama, Tsuneo Ikenoue, Masao Omata, Kiyoshi Furuichi та Keiji Tanaka. "IκBα Ubiquitination Is Catalyzed by an SCF-like Complex Containing Skp1, Cullin-1, and Two F-Box/WD40-Repeat Proteins, βTrCP1 and βTrCP2". Biochemical and Biophysical Research Communications 256, № 1 (березень 1999): 127–32. http://dx.doi.org/10.1006/bbrc.1999.0289.

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49

Li, Qiuhong, Leifu Chang, Shintaro Aibara, Jing Yang, Ziguo Zhang, and David Barford. "WD40 domain of Apc1 is critical for the coactivator-induced allosteric transition that stimulates APC/C catalytic activity." Proceedings of the National Academy of Sciences 113, no. 38 (September 6, 2016): 10547–52. http://dx.doi.org/10.1073/pnas.1607147113.

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The anaphase-promoting complex/cyclosome (APC/C) is a large multimeric cullin–RING E3 ubiquitin ligase that orchestrates cell-cycle progression by targeting cell-cycle regulatory proteins for destruction via the ubiquitin proteasome system. The APC/C assembly comprises two scaffolding subcomplexes: the platform and the TPR lobe that together coordinate the juxtaposition of the catalytic and substrate-recognition modules. The platform comprises APC/C subunits Apc1, Apc4, Apc5, and Apc15. Although the role of Apc1 as an APC/C scaffolding subunit has been characterized, its specific functions in contributing toward APC/C catalytic activity are not fully understood. Here, we report the crystal structure of the N-terminal domain of human Apc1 (Apc1N) determined at 2.2-Å resolution and provide an atomic-resolution description of the architecture of its WD40 (WD40 repeat) domain (Apc1WD40). To understand how Apc1WD40 contributes to APC/C activity, a mutant form of the APC/C with Apc1WD40 deleted was generated and evaluated biochemically and structurally. We found that the deletion of Apc1WD40 abolished the UbcH10-dependent ubiquitination of APC/C substrates without impairing the Ube2S-dependent ubiquitin chain elongation activity. A cryo-EM structure of an APC/C–Cdh1 complex with Apc1WD40 deleted showed that the mutant APC/C is locked into an inactive conformation in which the UbcH10-binding site of the catalytic module is inaccessible. Additionally, an EM density for Apc15 is not visible. Our data show that Apc1WD40 is required to mediate the coactivator-induced conformational change of the APC/C that is responsible for stimulating APC/C catalytic activity by promoting UbcH10 binding. In contrast, Ube2S activity toward APC/C substrates is not dependent on the initiation-competent conformation of the APC/C.

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Chen, Siyu, and Shucai Wang. "GLABRA2, a Common Regulator for Epidermal Cell Fate Determination and Anthocyanin Biosynthesis in Arabidopsis." International Journal of Molecular Sciences 20, no. 20 (October 9, 2019): 4997. http://dx.doi.org/10.3390/ijms20204997.

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Epidermal cell fate determination—including trichome initiation, root hair formation, and flavonoid and mucilage biosynthesis in Arabidopsis (Arabidopsis thaliana)—are controlled by a similar transcriptional regulatory network. In the network, it has been proposed that the MYB-bHLH-WD40 (MBW) activator complexes formed by an R2R3 MYB transcription factor, a bHLH transcription factor and the WD40-repeat protein TRANSPARENT TESTA GLABRA1 (TTG1) regulate the expression of downstream genes required for cell fate determination, flavonoid or mucilage biosynthesis, respectively. In epidermal cell fate determination and mucilage biosynthesis, the MBW activator complexes activate the expression of GLABRA2 (GL2). GL2 is a homeodomain transcription factor that promotes trichome initiation in shoots, mucilage biosynthesis in seeds, and inhibits root hair formation in roots. The MBW activator complexes also activate several R3 MYB genes. The R3 MYB proteins, in turn, competing with the R2R3 MYBs for binding bHLH transcription factors, therefore inhibiting the formation of the MBW activator complexes, lead to the inhibition of trichome initiation in shoots, and promotion of root hair formation in roots. In flavonoid biosynthesis, the MBW activator complexes activate the expression of the late biosynthesis genes in the flavonoid pathway, resulting in the production of anthocyanins or proanthocyanidins. Research progress in recent years suggests that the transcriptional regulatory network that controls epidermal cell fate determination and anthocyanin biosynthesis in Arabidopsis is far more complicated than previously thought. In particular, more regulators of GL2 have been identified, and GL2 has been shown to be involved in the regulation of anthocyanin biosynthesis. This review focuses on the research progress on the regulation of GL2 expression, and the roles of GL2 in the regulation of epidermal cell fate determination and anthocyanin biosynthesis in Arabidopsis.

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