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Yang X, Luo T, Liu Z, Liu J, Yang Z. WD repeat domain 43 as a new predictive indicator and its connection with tumor immune cell infiltration in pan-cancer. Medicine (Baltimore) 2024; 103:e39153. [PMID: 39093744 PMCID: PMC11296459 DOI: 10.1097/md.0000000000039153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 07/10/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND WD repeat domain 43 (WDR43) is a protein component that encodes WD-repeats and is involved in ribosome biogenesis. However, little is known about the role of WDR43 in cancer prognosis and immune modulation. METHODS In this study, we analyzed the expression and prognostic significance of WDR43 in pan-cancer using the Cancer Genome Atlas, the Genotype-Tissue Expression, and the Human Protein Atlas. We also examined the differential expression of WDR43 in liver hepatocellular carcinoma (LIHC) and adjacent tissues of 48 patients using immunohistochemistry. Additionally, we investigated the correlation between WDR43 and clinical characteristics, gene alterations, tumor mutation burden, microsatellite instability, mismatch repair, tumor microenvironment, immune infiltrating cells, and immune-related genes using bioinformatics methods. Gene set enrichment analysis was conducted, and potential biological mechanisms were identified. RESULTS Immunohistochemistry staining showed that WDR43 was overexpressed in LIHC among 48 patients. Upregulation of WDR43 was associated with unfavorable prognosis, including overall survival in various types of cancer such as LIHC, uterine corpus endometrial cancer, head and neck squamous cell carcinoma, and pancreatic adenocarcinoma. Differential expression of WDR43 was significantly correlated with microsatellite instability, mismatch repair, and immune cell infiltration. Gene ontology annotation analysis revealed that these genes were significantly enriched in immune-related functions, including immune response, immune regulation, and signaling pathways. CONCLUSION We conducted a thorough investigation of the clinical features, phases of tumor development, immune infiltration, gene mutation, and functional enrichment analysis of WDR43 in various types of cancer. This research offers valuable insight into the significance and function of WDR43 in clinical therapy.
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Affiliation(s)
- Xin Yang
- Department of Digestive Endoscopy, General Hospital of Northern Theater Command, Shenyang, China
| | - Ting Luo
- Department of Digestive Endoscopy, General Hospital of Northern Theater Command, Shenyang, China
| | - Zhixin Liu
- Department of Digestive Endoscopy, General Hospital of Northern Theater Command, Shenyang, China
| | - Jiao Liu
- Department of Digestive Endoscopy, General Hospital of Northern Theater Command, Shenyang, China
| | - Zhuo Yang
- Department of Digestive Endoscopy, General Hospital of Northern Theater Command, Shenyang, China
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2
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Li Z, Zhang D, Liang X, Liang J. Receptor for Activated C Kinase 1 counteracts ABSCISIC ACID INSENSITIVE5-mediated inhibition of seed germination and post-germinative growth in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3932-3945. [PMID: 38602261 DOI: 10.1093/jxb/erae153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 04/10/2024] [Indexed: 04/12/2024]
Abstract
ABSCISIC ACID INSENSITIVE5 (ABI5), a key regulator of the abscisic acid (ABA) signalling pathway, plays a fundamental role in seed germination and post-germinative development. However, the molecular mechanism underlying the repression function of ABI5 remains to be elucidated. In this study, we demonstrate that the conserved eukaryotic WD40 repeat protein Receptor for Activated C Kinase 1 (RACK1) is a novel negative regulator of ABI5 in Arabidopsis. The RACK1 loss-of-function mutant is hypersensitive to ABA, while this phenotype is rescued by a mutation in ABI5. Moreover, overexpression of RACK1 suppresses ABI5 transcriptional activation activity for ABI5-targeted genes. RACK1 may also physically interact with ABI5 and facilitate its degradation. Furthermore, we found that RACK1 and the two substrate receptors CUL4-based E3 ligases (DWA1 and DWA2) function together to mediate the turnover of ABI5, thereby efficiently reducing ABA signalling in seed germination and post-germinative growth. In addition, molecular analyses demonstrated that ABI5 may bind to the promoter of RACK1 to repress its expression. Collectively, our findings suggest that RACK1 and ABI5 might form a feedback loop to regulate the homeostasis of ABA signalling in acute seed germination and early plant development.
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Affiliation(s)
- Zhiyong Li
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
| | - Dayan Zhang
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiaoju Liang
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- College of Life Sciences, Fujian Agriculture and Forest University, Fuzhou 350002, China
| | - Jiansheng Liang
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
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3
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Suga A, Minegishi Y, Yamamoto M, Ueda K, Iwata T. Compound heterozygous mutations in a mouse model of Leber congenital amaurosis reveal the role of CCT2 in photoreceptor maintenance. Commun Biol 2024; 7:676. [PMID: 38830954 PMCID: PMC11148128 DOI: 10.1038/s42003-024-06384-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 05/24/2024] [Indexed: 06/05/2024] Open
Abstract
TRiC/CCT is a chaperonin complex required for the folding of cytoplasmic proteins. Although mutations in each subunit of TRiC/CCT are associated with various human neurodegenerative diseases, their impact in mammalian models has not yet been examined. A compound heterozygous mutation in CCT2 (p.[Thr400Pro]; p.[Arg516His]) is causal for Leber congenital amaurosis. Here, we generate mice carrying each mutation and show that Arg516His (R516H) homozygosity causes photoreceptor degeneration accompanied by a significant depletion of TRiC/CCT substrate proteins in the retina. In contrast, Thr400Pro (T400P) homozygosity results in embryonic lethality, and the compound heterozygous mutant (T400P/R516H) mouse showed aberrant cone cell lamination and died 2 weeks after birth. Finally, CCDC181 is identified as a interacting protein for CCTβ protein, and its localization to photoreceptor connecting cilia is compromised in the mutant mouse. Our results demonstrate the distinct impact of each mutation in vivo and suggest a requirement for CCTβ in ciliary maintenance.
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Affiliation(s)
- Akiko Suga
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo, Japan
| | - Yuriko Minegishi
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Megumi Yamamoto
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo, Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takeshi Iwata
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo, Japan.
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4
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Ke S, Jiang Y, Zhou M, Li Y. Genome-Wide Identification, Evolution, and Expression Analysis of the WD40 Subfamily in Oryza Genus. Int J Mol Sci 2023; 24:15776. [PMID: 37958759 PMCID: PMC10648978 DOI: 10.3390/ijms242115776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
The WD40 superfamily is widely found in eukaryotes and has essential subunits that serve as scaffolds for protein complexes. WD40 proteins play important regulatory roles in plant development and physiological processes, such as transcription regulation and signal transduction; it is also involved in anthocyanin biosynthesis. In rice, only OsTTG1 was found to be associated with anthocyanin biosynthesis, and evolutionary analysis of the WD40 gene family in multiple species is less studied. Here, a genome-wide analysis of the subfamily belonging to WD40-TTG1 was performed in nine AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, Oryza glumaepatula, Oryza nivara, and Oryza longistaminata. In this study, 383 WD40 genes in the Oryza genus were identified, and they were classified into four groups by phylogenetic analysis, with most members in group C and group D. They were found to be unevenly distributed across 12 chromosomes. A total of 39 collinear gene pairs were identified in the Oryza genus, and all were segmental duplications. WD40s had similar expansion patterns in the Oryza genus. Ka/Ks analyses indicated that they had undergone mainly purifying selection during evolution. Furthermore, WD40s in the Oryza genus have similar evolutionary patterns, so Oryza sativa ssp. indica was used as a model species for further analysis. The cis-acting elements analysis showed that many genes were related to jasmonic acid and light response. Among them, OsiWD40-26/37/42 contained elements of flavonoid synthesis, and OsiWD40-15 had MYB binding sites, indicating that they might be related to anthocyanin synthesis. The expression profile analysis at different stages revealed that most OsiWD40s were expressed in leaves, roots, and panicles. The expression of OsiWD40s was further analyzed by qRT-PCR in 9311 (indica) under various hormone treatments and abiotic stresses. OsiWD40-24 was found to be responsive to both phytohormones and abiotic stresses, suggesting that it might play an important role in plant stress resistance. And many OsiWD40s might be more involved in cold stress tolerance. These findings contribute to a better understanding of the evolution of the WD40 subfamily. The analyzed candidate genes can be used for the exploration of practical applications in rice, such as cultivar culture for colored rice, stress tolerance varieties, and morphological marker development.
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Affiliation(s)
| | | | | | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.K.); (Y.J.); (M.Z.)
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5
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Wang C, Tang Y, Li Y, Hu C, Li J, Lyu A. Genome-wide identification and bioinformatics analysis of the WD40 transcription factor family and candidate gene screening for anthocyanin biosynthesis in Rhododendron simsii. BMC Genomics 2023; 24:488. [PMID: 37633914 PMCID: PMC10463391 DOI: 10.1186/s12864-023-09604-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/19/2023] [Indexed: 08/28/2023] Open
Abstract
WD40 transcription factors (TFs) constitute a large gene family in eukaryotes, playing diverse roles in cellular processes. However, their functions in the major ornamental plant, Rhododendron simsii, remain poorly understood. In this study, we identified 258 WD40 proteins in the R. simsii genome, which exhibited an uneven distribution across chromosomes. Based on domain compositions and phylogenetic analysis, we classified these 258 RsWD40 proteins into 42 subfamilies and 47 clusters. Comparative genomic analysis suggested that the expansion of the WD40 gene family predates the divergence of green algae and higher plants, indicating an ancient origin. Furthermore, by analyzing the duplication patterns of RsWD40 genes, we found that transposed duplication played a major role in their expansion. Notably, the majority of RsWD40 gene duplication pairs underwent purifying selection during evolution. Synteny analysis identified significant orthologous gene pairs between R. simsii and Arabidopsis thaliana, Oryza sativa, Vitis vinifera, and Malus domestica. We also investigated potential candidate genes involved in anthocyanin biosynthesis during different flower development stages in R. simsii using RNA-seq data. Specifically, we identified 10 candidate genes during the bud stage and 7 candidate genes during the full bloom stage. GO enrichment analysis of these candidate genes revealed the potential involvement of the ubiquitination process in anthocyanin biosynthesis. Overall, our findings provide a valuable foundation for further investigation and functional analysis of WD40 genes, as well as research on the molecular mechanisms underlying anthocyanin biosynthesis in Rhododendron species.
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Affiliation(s)
- Cheng Wang
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Yafang Tang
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Yan Li
- Department of Biology and Chemical Engineering, Weihai Vocational College, Weihai, 264200, China
| | - Chao Hu
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Jingyi Li
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Ang Lyu
- Institute of Quality Standard and Testing Technology for Agro-Products, Hubei Academy of Agricultural Science, Wuhan, 430064, China.
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6
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Zhan Q, Shen J, Nie K, Zheng Y. MIW1 participates in ABA signaling through the regulation of MYB30 in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 332:111717. [PMID: 37105379 DOI: 10.1016/j.plantsci.2023.111717] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/22/2023] [Indexed: 05/09/2023]
Abstract
Seed germination and seedling establishment are critical biological processes, and their underlying molecular mechanisms have practical implications. The ABA signaling during seed germination and early seedling development is negatively regulated by transcription factor MYB30, but its interaction partners and downstream targets are not fully understood. In this study, we identified MIW1 (MYB30-interacting WD40 protein 1), a WD40 protein that could interact with MYB30 and promote its degradation. In the miw1 mutant, the MYB30 protein became more stable. MIW1 enhanced the ABA-mediated inhibition of postgerminative development. The miw1 mutants became hyposensitive to exogenous ABA, and this effect was suppressed by mutations in MYB30. Furthermore, we found that MYB30 negatively regulated the expression of the ABA receptor genes PYR1/PYL/RCARs. The changes in PYLs expression during early seedling development or under ABA treatment became more pronounced in the myb30 mutant. ChIP-qPCR analyses showed MYB30 could directly bind to the promoters of PYL11 and PYL12. Our study reveals that the WD40 protein MIW1 promotes the expression of PYLs by destabilizing MYB30, thus positively regulating the ABA signaling during postgermination in Arabidopsis.
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Affiliation(s)
- Qidi Zhan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; Sanya Institute of Henan University, Sanya, China
| | - Jialu Shen
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; Sanya Institute of Henan University, Sanya, China
| | - Kaili Nie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; Sanya Institute of Henan University, Sanya, China
| | - Yuan Zheng
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; Sanya Institute of Henan University, Sanya, China.
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7
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The c-MYC-WDR43 signalling axis promotes chemoresistance and tumour growth in colorectal cancer by inhibiting p53 activity. Drug Resist Updat 2023; 66:100909. [PMID: 36525936 DOI: 10.1016/j.drup.2022.100909] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/27/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
Oxaliplatin chemoresistance is a major challenge in the clinical treatment of colorectal cancer (CRC), which is one of the most common malignancies worldwide. In this study, we identified the tryptophan-aspartate repeat domain 43 (WDR43) as a potentially critical oncogenic factor in CRC pathogenesis through bioinformatics analysis. It was found that WDR43 is highly expressed in CRC tissues, and WDR43 overexpression is associated with poor prognosis of CRC patients. WDR43 knockdown significantly inhibits cell growth by arresting cell cycle and enhancing the effect of oxaliplatin chemotherapy both in vitro and in vivo. Mechanistically, upon oxaliplatin stimulation, c-MYC promotes the transcriptional regulation and expression of WDR43. WDR43 enhances the ubiquitination of p53 by MDM2 through binding to RPL11, thereby reducing the stability of the p53 protein, which induces proliferation and chemoresistance of CRC cells. Thus, the overexpression of WDR43 promotes CRC progression, and could be a potential therapeutic target of chemoresistance in CRC.
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8
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Afza F, Singh N, Shriya S, Bisoyi P, Kashyap AK, Jain BP. Genome wide identification and analysis of WD40 domain containing proteins in Danio rerio. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2021.101426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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9
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CRL4Cdt2 Ubiquitin Ligase, A Genome Caretaker Controlled by Cdt2 Binding to PCNA and DNA. Genes (Basel) 2022; 13:genes13020266. [PMID: 35205311 PMCID: PMC8871960 DOI: 10.3390/genes13020266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 12/22/2022] Open
Abstract
The ubiquitin ligase CRL4Cdt2 plays a vital role in preserving genomic integrity by regulating essential proteins during S phase and after DNA damage. Deregulation of CRL4Cdt2 during the cell cycle can cause DNA re-replication, which correlates with malignant transformation and tumor growth. CRL4Cdt2 regulates a broad spectrum of cell cycle substrates for ubiquitination and proteolysis, including Cdc10-dependent transcript 1 or Chromatin licensing and DNA replication factor 1 (Cdt1), histone H4K20 mono-methyltransferase (Set8) and cyclin-dependent kinase inhibitor 1 (p21), which regulate DNA replication. However, the mechanism it operates via its substrate receptor, Cdc10-dependent transcript 2 (Cdt2), is not fully understood. This review describes the essential features of the N-terminal and C-terminal parts of Cdt2 that regulate CRL4 ubiquitination activity, including the substrate recognition domain, intrinsically disordered region (IDR), phosphorylation sites, the PCNA-interacting protein-box (PIP) box motif and the DNA binding domain. Drugs targeting these specific domains of Cdt2 could have potential for the treatment of cancer.
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10
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Müller S, Ackloo S, Al Chawaf A, Al-Lazikani B, Antolin A, Baell JB, Beck H, Beedie S, Betz UAK, Bezerra GA, Brennan PE, Brown D, Brown PJ, Bullock AN, Carter AJ, Chaikuad A, Chaineau M, Ciulli A, Collins I, Dreher J, Drewry D, Edfeldt K, Edwards AM, Egner U, Frye SV, Fuchs SM, Hall MD, Hartung IV, Hillisch A, Hitchcock SH, Homan E, Kannan N, Kiefer JR, Knapp S, Kostic M, Kubicek S, Leach AR, Lindemann S, Marsden BD, Matsui H, Meier JL, Merk D, Michel M, Morgan MR, Mueller-Fahrnow A, Owen DR, Perry BG, Rosenberg SH, Saikatendu KS, Schapira M, Scholten C, Sharma S, Simeonov A, Sundström M, Superti-Furga G, Todd MH, Tredup C, Vedadi M, von Delft F, Willson TM, Winter GE, Workman P, Arrowsmith CH. Target 2035 - update on the quest for a probe for every protein. RSC Med Chem 2022; 13:13-21. [PMID: 35211674 PMCID: PMC8792830 DOI: 10.1039/d1md00228g] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/21/2021] [Indexed: 01/11/2023] Open
Abstract
Twenty years after the publication of the first draft of the human genome, our knowledge of the human proteome is still fragmented. The challenge of translating the wealth of new knowledge from genomics into new medicines is that proteins, and not genes, are the primary executers of biological function. Therefore, much of how biology works in health and disease must be understood through the lens of protein function. Accordingly, a subset of human proteins has been at the heart of research interests of scientists over the centuries, and we have accumulated varying degrees of knowledge about approximately 65% of the human proteome. Nevertheless, a large proportion of proteins in the human proteome (∼35%) remains uncharacterized, and less than 5% of the human proteome has been successfully targeted for drug discovery. This highlights the profound disconnect between our abilities to obtain genetic information and subsequent development of effective medicines. Target 2035 is an international federation of biomedical scientists from the public and private sectors, which aims to address this gap by developing and applying new technologies to create by year 2035 chemogenomic libraries, chemical probes, and/or biological probes for the entire human proteome.
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Affiliation(s)
- Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Frankfurt 60438 Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt Frankfurt 60438 Germany
| | - Suzanne Ackloo
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
| | | | - Bissan Al-Lazikani
- Department of Data Science, The Institute of Cancer Research London SM2 5NG UK
- CRUK ICR/Imperial Convergence Science Centre London SM2 5NG UK
| | - Albert Antolin
- Department of Data Science, The Institute of Cancer Research London SM2 5NG UK
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research London SM2 5NG UK
| | - Jonathan B Baell
- Monash Institute of Pharmaceutical Sciences, Monash University Parkville Victoria 3052 Australia
- School of Pharmaceutical Sciences, Nanjing Tech University No. 30 South Puzhu Road Nanjing 211816 People's Republic of China
| | - Hartmut Beck
- Research and Development, Bayer AG, Pharmaceuticals 42103 Wuppertal Germany
| | - Shaunna Beedie
- Centre for Medicines Discovery, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
| | | | - Gustavo Arruda Bezerra
- Centre for Medicines Discovery, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
| | - Paul E Brennan
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, University of Oxford Oxford OX3 7FZ UK
| | - David Brown
- Institut Recherches de Servier 125 Chemin de Ronde 78290 Croissy France
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
| | - Alex N Bullock
- Centre for Medicines Discovery, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
| | - Adrian J Carter
- Discovery Research, Boehringer Ingelheim 55216 Ingelheim am Rhein Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Frankfurt 60438 Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt Frankfurt 60438 Germany
| | - Mathilde Chaineau
- Early Drug Discovery Unit (EDDU), Montreal Neurological Institute-Hospital, McGill University Montreal QC Canada
| | - Alessio Ciulli
- School of Life Sciences, Division of Biological Chemistry and Drug Discovery, University of Dundee James Black Centre Dundee UK
| | - Ian Collins
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research London SM2 5NG UK
| | - Jan Dreher
- Research and Development, Bayer AG, Pharmaceuticals 42103 Wuppertal Germany
| | - David Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy Chapel Hill NC USA
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Kristina Edfeldt
- Structural Genomics Consortium, Department of Medicine, Karolinska University Hospital and Karolinska Institutet Stockholm Sweden
| | - Aled M Edwards
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
| | - Ursula Egner
- Nuvisan Innovation Campus Berlin GmbH Müllerstraße 178 13353 Berlin Germany
| | - Stephen V Frye
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | | | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health Rockville Maryland 20850 USA
| | - Ingo V Hartung
- Medicinal Chemistry, Global R&D, Merck Healthcare KGaA Frankfurter Straße 250 64293 Darmstadt Germany
| | - Alexander Hillisch
- Research and Development, Bayer AG, Pharmaceuticals 42103 Wuppertal Germany
| | | | - Evert Homan
- Science for Life Laboratory, Department of Oncology-Pathology Karolinska Institutet Stockholm Sweden
| | - Natarajan Kannan
- Institute of Bioinformatics and Department of Biochemistry and Molecular Biology, University of Georgia Athens GA USA
| | - James R Kiefer
- Genentech, Inc. 1 DNA Way South San Francisco California 94080 USA
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Frankfurt 60438 Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt Frankfurt 60438 Germany
| | - Milka Kostic
- Department of Cancer Biology and Chemical Biology Program, Dana-Farber Cancer Institute 450 Brookline Ave Boston MA 02215 USA
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna Austria
| | - Andrew R Leach
- European Molecular Biology Laboratory, European Bioinformatics Institute Wellcome Genome Campus, Hinxton Cambridgeshire CB10 1SD UK
| | - Sven Lindemann
- Strategic Innovation, Global R&D, Merck Healthcare KGaA Frankfurter Straße 250 64293 Darmstadt Germany
| | - Brian D Marsden
- Centre for Medicines Discovery, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford UK
| | - Hisanori Matsui
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited Fujisawa Kanagawa Japan
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick MD USA
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Frankfurt 60438 Germany
- LMU Munich, Department of Pharmacy, Chair of Pharmaceutical and Medicinal Chemistry 81377 Munich Germany
| | - Maurice Michel
- Science for Life Laboratory, Department of Oncology-Pathology Karolinska Institutet Stockholm Sweden
| | - Maxwell R Morgan
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
| | | | - Dafydd R Owen
- Discovery Network Group, Pfizer Medicine Design Cambridge MA 02139 USA
| | - Benjamin G Perry
- Drugs for Neglected Diseases initiative 15 Chemin Camille Vidart Geneva 1202 Switzerland
| | | | - Kumar Singh Saikatendu
- Global Research Externalization, Takeda California, Inc. 9625 Towne Center Drive San Diego CA 92121 USA
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
- Department of Pharmacology & Toxicology, University of Toronto Toronto Ontario M5S 1A8 Canada
| | - Cora Scholten
- Research and Development, Bayer AG, Pharmaceuticals 13353 Berlin Germany
| | - Sujata Sharma
- Structural & Protein Sciences, Discovery Sciences, Janssen Research & Development 1400 McKean Rd Spring House PA 19477 USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health Rockville Maryland 20850 USA
| | - Michael Sundström
- Division of Rheumatology, Department of Medicine Solna, Karolinska University Hospital and Karolinska Institutet Stockholm Sweden
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna Austria
- Center for Physiology and Pharmacology, Medical University of Vienna Vienna Austria
| | - Matthew H Todd
- School of Pharmacy, University College London London WC1N 1AX UK
| | - Claudia Tredup
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Frankfurt 60438 Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt Frankfurt 60438 Germany
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
- Department of Pharmacology & Toxicology, University of Toronto Toronto Ontario M5S 1A8 Canada
| | - Frank von Delft
- Centre for Medicines Discovery, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
- Diamond Light Source Ltd Harwell Science and Innovation Campus Didcot OX11 0QX UK
- Department of Biochemistry, University of Johannesburg Auckland Park 2006 South Africa
- Research Complex at Harwell Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Timothy M Willson
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna Austria
| | - Paul Workman
- CRUK ICR/Imperial Convergence Science Centre London SM2 5NG UK
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research London SM2 5NG UK
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
- Princess Margaret Cancer Centre Toronto Ontario M5G 1L7 Canada
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11
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Human Cytomegalovirus Hijacks WD Repeat Domain 11 for Virion Assembly Compartment Formation and Virion Morphogenesis. J Virol 2022; 96:e0182721. [PMID: 35020472 DOI: 10.1128/jvi.01827-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human cytomegalovirus (HCMV) has a large (∼235-kb) genome with over 200 predicted open reading frames and exploits numerous cellular factors to facilitate its replication. A key feature of HCMV-infected cells is the emergence of a distinctive membranous cytoplasmic compartment termed the virion assembly compartment (vAC). Here we report that host protein WD repeat domain 11 (WDR11) plays a key role in vAC formation and virion morphogenesis. We found that WDR11 was up-regulated at both mRNA and protein levels during HCMV infection. At the late stage of HCMV replication, WDR11 relocated to the vAC and co-localized with markers of the trans-Golgi network (TGN) and vAC. Depletion of WDR11 hindered HCMV-induced membrane reorganization of the Golgi and TGN, altered vAC formation, and impaired HCMV secondary envelopment and virion morphogenesis. Further, motifs critical for the localization of WDR11 in TGN were identified by alanine-scanning mutagenesis. Mutation of these motifs led to WDR11 mislocation outside of the TGN and loss of vAC formation. Taken together, these data indicate that host protein WDR11 is required for efficient viral replication at the stage of virion assembly, possibly by facilitating the remodeling of the endomembrane system for vAC formation and virion morphogenesis. Importance During the late phase of human cytomegalovirus (HCMV) infection, the endomembrane system is dramatically reorganized, resulting in the formation of a unique structure termed the virion assembly compartment (vAC), which is critical for the assembly of infectious virions. The mechanism of HCMV-induced vAC formation is still not fully understood. In this report, we identified a host factor, WDR11, that plays an important role in vAC formation. Our findings argue that WDR11 contributes to the relocation of the Golgi and trans-Golgi network to the vAC, a membrane reorganization process that appears to be required for efficient virion maturation. The present work provides new insights into the vAC formation and HCMV virion morphogenesis and a potential novel target for anti-viral treatment.
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12
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Chakrabarty B, Parekh N. DbStRiPs: Database of structural repeats in proteins. Protein Sci 2022; 31:23-36. [PMID: 33641184 PMCID: PMC8740836 DOI: 10.1002/pro.4052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 01/03/2023]
Abstract
Recent interest in repeat proteins has arisen due to stable structural folds, high evolutionary conservation and repertoire of functions provided by these proteins. However, repeat proteins are poorly characterized because of high sequence variation between repeating units and structure-based identification and classification of repeats is desirable. Using a robust network-based pipeline, manual curation and Kajava's structure-based classification schema, we have developed a database of tandem structural repeats, Database of Structural Repeats in Proteins (DbStRiPs). A unique feature of this database is that available knowledge on sequence repeat families is incorporated by mapping Pfam classification scheme onto structural classification. Integration of sequence and structure-based classifications help in identifying different functional groups within the same structural subclass, leading to refinement in the annotation of repeat proteins. Analysis of complete Protein Data Bank revealed 16,472 repeat annotations in 15,141 protein chains, one previously uncharacterized novel protein repeat family (PRF), named left-handed beta helix, and 33 protein repeat clusters (PRCs). Based on their unique structural motif, ~79% of these repeat proteins are classified in one of the 14 PRFs or 33 PRCs, and the remaining are grouped as unclassified repeat proteins. Each repeat protein is provided with a detailed annotation in DbStRiPs that includes start and end boundaries of repeating units, copy number, secondary and tertiary structure view, repeat class/subclass, disease association, MSA of repeating units and cross-references to various protein pattern databases, human protein atlas and interaction resources. DbStRiPs provides easy search and download options to high-quality annotations of structural repeat proteins (URL: http://bioinf.iiit.ac.in/dbstrips/).
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Affiliation(s)
- Broto Chakrabarty
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information TechnologyHyderabadIndia
| | - Nita Parekh
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information TechnologyHyderabadIndia
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13
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Lanzafame M, Branca G, Landi C, Qiang M, Vaz B, Nardo T, Ferri D, Mura M, Iben S, Stefanini M, Peverali FA, Bini L, Orioli D. Cockayne syndrome group A and ferrochelatase finely tune ribosomal gene transcription and its response to UV irradiation. Nucleic Acids Res 2021; 49:10911-10930. [PMID: 34581821 PMCID: PMC8565352 DOI: 10.1093/nar/gkab819] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 08/10/2021] [Accepted: 09/12/2021] [Indexed: 11/14/2022] Open
Abstract
CSA and CSB proteins are key players in transcription-coupled nucleotide excision repair (TC-NER) pathway that removes UV-induced DNA lesions from the transcribed strands of expressed genes. Additionally, CS proteins play relevant but still elusive roles in other cellular pathways whose alteration may explain neurodegeneration and progeroid features in Cockayne syndrome (CS). Here we identify a CS-containing chromatin-associated protein complex that modulates rRNA transcription. Besides RNA polymerase I (RNAP1) and specific ribosomal proteins (RPs), the complex includes ferrochelatase (FECH), a well-known mitochondrial enzyme whose deficiency causes erythropoietic protoporphyria (EPP). Impairment of either CSA or FECH functionality leads to reduced RNAP1 occupancy on rDNA promoter that is associated to reduced 47S pre-rRNA transcription. In addition, reduced FECH expression leads to an abnormal accumulation of 18S rRNA that in primary dermal fibroblasts from CS and EPP patients results in opposed rRNA amounts. After cell irradiation with UV light, CSA triggers the dissociation of the CSA–FECH–CSB–RNAP1–RPs complex from the chromatin while it stabilizes its binding to FECH. Besides disclosing a function for FECH within nucleoli, this study sheds light on the still unknown mechanisms through which CSA modulates rRNA transcription.
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Affiliation(s)
- Manuela Lanzafame
- Institute of Molecular Genetics -L.L. Cavalli Sforza, CNR, 27100 Pavia, Italy
| | - Giulia Branca
- Institute of Molecular Genetics -L.L. Cavalli Sforza, CNR, 27100 Pavia, Italy
| | - Claudia Landi
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Mingyue Qiang
- Department of Dermatology and Allergic Diseases, Ulm University, Albert-Einstein Allee 23, 89081 Ulm, Germany
| | - Bruno Vaz
- Institute of Molecular Genetics -L.L. Cavalli Sforza, CNR, 27100 Pavia, Italy
| | - Tiziana Nardo
- Institute of Molecular Genetics -L.L. Cavalli Sforza, CNR, 27100 Pavia, Italy
| | - Debora Ferri
- Institute of Molecular Genetics -L.L. Cavalli Sforza, CNR, 27100 Pavia, Italy
| | - Manuela Mura
- Institute of Molecular Genetics -L.L. Cavalli Sforza, CNR, 27100 Pavia, Italy
| | - Sebastian Iben
- Department of Dermatology and Allergic Diseases, Ulm University, Albert-Einstein Allee 23, 89081 Ulm, Germany
| | - Miria Stefanini
- Institute of Molecular Genetics -L.L. Cavalli Sforza, CNR, 27100 Pavia, Italy
| | - Fiorenzo A Peverali
- Institute of Molecular Genetics -L.L. Cavalli Sforza, CNR, 27100 Pavia, Italy
| | - Luca Bini
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Donata Orioli
- Institute of Molecular Genetics -L.L. Cavalli Sforza, CNR, 27100 Pavia, Italy
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14
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Nivedita, Rawoof A, Ramchiary N, Abdin MZ. A high-throughput RNA-Seq approach to elucidate the transcriptional response of Piriformospora indica to high salt stress. Sci Rep 2021; 11:4129. [PMID: 33602957 PMCID: PMC7893156 DOI: 10.1038/s41598-021-82136-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 12/15/2020] [Indexed: 12/05/2022] Open
Abstract
Piriformospora indica, a root endophytic fungus, augments plant nutrition and productivity as well as protects plants against pathogens and abiotic stresses. High salinity is a major problem faced by plants as well as by microbes. Until now, the precise mechanism of salt stress tolerance in P. indica has remained elusive. In this study, the transcriptomes of control and salt-treated (0.5 M NaCl) P. indica were sequenced via the RNA-seq approach. A total of 30,567 transcripts and 15,410 unigenes for P. indica were obtained from 7.3 Gb clean reads. Overall 661 differentially expressed genes (DEGs) between control and treated samples were retrieved. Gene ontology (GO) and EuKaryotic Orthologous Groups (KOG) enrichments revealed that DEGs were specifically involved in metabolic and molecular processes, such as "response to salt stress", "oxidoreductase activity", "ADP binding", "translation, ribosomal structure and biogenesis", "cytoskeleton", and others. The unigenes involved in "cell wall integrity", "sterol biosynthesis", and "oxidative stress" such as Rho-type GTPase, hydroxymethylglutaryl-CoA synthase, and thioredoxin peroxidase were up-regulated in P. indica subjected to salt stress. The salt-responsive DEGs have shown that they might have a potential role in salt stress regulation. Our study on the salt-responsive DEGs established a foundation for the elucidation of molecular mechanisms related to P. indica stress adaptation and a future reference for comparative functional genomics studies of biotechnologically important fungal species.
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Affiliation(s)
- Nivedita
- Department of Biotechnology, Jamia Hamdard, New Delhi, India
| | - Abdul Rawoof
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Malik Z Abdin
- Department of Biotechnology, Jamia Hamdard, New Delhi, India.
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15
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Topolska M, Roelants FM, Si EP, Thorner J. TORC2-Dependent Ypk1-Mediated Phosphorylation of Lam2/Ltc4 Disrupts Its Association with the β-Propeller Protein Laf1 at Endoplasmic Reticulum-Plasma Membrane Contact Sites in the Yeast Saccharomyces cerevisiae. Biomolecules 2020; 10:biom10121598. [PMID: 33255682 PMCID: PMC7760575 DOI: 10.3390/biom10121598] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 12/11/2022] Open
Abstract
Membrane-tethered sterol-binding Lam/Ltc proteins localize at junctions between the endoplasmic reticulum (ER) membrane and other organelles. Two of the six family members-Lam2/Ltc4 (initially Ysp2) and paralog Lam4/Ltc3-localize to ER-plasma membrane (PM) contact sites (CSs) and mediate retrograde ergosterol transport from the PM to the ER. Our prior work demonstrated that Lam2 and Lam4 are substrates of TORC2-regulated protein kinase Ypk1, that Ypk1-mediated phosphorylation inhibits their function in retrograde sterol transport, and that PM sterol retention bolsters cell survival under stressful conditions. At ER-PM CSs, Lam2 and Lam4 associate with Laf1/Ymr102c and Dgr2/Ykl121w (paralogous WD40 repeat-containing proteins) that reportedly bind sterol. Using fluorescent tags, we found that Lam2 and Lam4 remain at ER-PM CSs when Laf1 and Dgr2 are absent, whereas neither Laf1 nor Dgr2 remain at ER-PM CSs when Lam2 and Lam4 are absent. Loss of Laf1 (but not Dgr2) impedes retrograde ergosterol transport, and a laf1∆ mutation does not exacerbate the transport defect of lam2∆ lam4∆ cells, indicating a shared function. Lam2 and Lam4 bind Laf1 and Dgr2 in vitro in a pull-down assay, and the PH domain in Lam2 hinders its interaction with Laf1. Lam2 phosphorylated by Ypk1, and Lam2 with phosphomimetic (Glu) replacements at its Ypk1 sites, exhibited a marked reduction in Laf1 binding. Thus, phosphorylation prevents Lam2 interaction with Laf1 at ER-PM CSs, providing a mechanism by which Ypk1 action inhibits retrograde sterol transport.
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Affiliation(s)
- Magdalena Topolska
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA; (M.T.); (F.M.R.); (E.P.S.)
- Villum Center for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5000 Odense, Denmark
| | - Françoise M. Roelants
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA; (M.T.); (F.M.R.); (E.P.S.)
| | - Edward P. Si
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA; (M.T.); (F.M.R.); (E.P.S.)
- Eastern Virginia Medical School, P.O. Box 1980, Norfolk, VA 23501-1980, USA
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA; (M.T.); (F.M.R.); (E.P.S.)
- Correspondence: ; Tel.: +1-510-642-2558; Fax: +1-510-642-6420
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16
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Guo M, Wang J, Zhang Y, Zhang L. Increased WD40 motifs in Planctomycete bacteria and their evolutionary relevance. Mol Phylogenet Evol 2020; 155:107018. [PMID: 33242584 DOI: 10.1016/j.ympev.2020.107018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 10/05/2020] [Accepted: 11/17/2020] [Indexed: 10/22/2022]
Abstract
Species of the family Planctomycetes have a complex intracellular structure, which is distinct from that of the majority of non-Planctomycetes bacteria. At present, genomic evidence of the evolution of intracellular complexity is lacking, cognitions of Planctomycetes's intracellular structure mainly rely on electron microscope observation. As the presence of WD40 motifs in eukaryotic proteins probably links to intracellular complexity, bioinformatic studies were conducted to detect and enumerate WD40 motifs, WD40 domains, and WD40 motif-bearing proteins in the genomes of 11 Planctomycetes species, 2775 non-Planctomycetes bacteria, and 63 representative eukaryotes. Compared to non-Planctomycetes bacteria (average 5 WD40 motifs and 1 WD40 motif-bearing protein per genome), a large increase in the number of WD40 motifs in Planctomycetes species (average 116 WD40 motifs and 26 WD40 motif-bearing proteins per genome) was observed. However, the average number of WD40 motifs in Planctomycetes species was significantly lower than that of eukaryotes (average 584 WD40 motifs and 193 WD40 motif-bearing proteins per genome). The number of WD40 motif-bearing proteins was found to correlate with genome size and gene number. Most WD40 motif-bearing proteins of Planctomycetes species belonged to the categories of 'ribosome assembly protein 4' and 'eukaryotic-like serine/threonine protein kinase.' Collinearity analysis of amino acid compositions of Planctomycetes and eukaryotic WD40 motifs revealed that the sequences of the four anti-parallel β-sheets of WD40 motifs were conserved. However, a number of Planctomycetes WD40 motifs had increased size of the interval region of β-sheets D and A. Taken together, results of this study suggest a positive correlation between the number of WD40 motif-bearing proteins and the evolution of Planctomycetes species toward a complex intracellular structure similar to that of eukaryotes.
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Affiliation(s)
- Min Guo
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Junhua Wang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yuzhi Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China.
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17
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Wang Z, Ren Z, Cheng C, Wang T, Ji H, Zhao Y, Deng Z, Zhi L, Lu J, Wu X, Xu S, Cao M, Zhao H, Liu L, Zhu J, Li X. Counteraction of ABA-Mediated Inhibition of Seed Germination and Seedling Establishment by ABA Signaling Terminator in Arabidopsis. MOLECULAR PLANT 2020; 13:1284-1297. [PMID: 32619606 DOI: 10.1016/j.molp.2020.06.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 06/02/2020] [Accepted: 06/26/2020] [Indexed: 05/07/2023]
Abstract
Seed germination and seedling establishment are important for the reproductive success of plants, but seeds and seedlings typically encounter constantly changing environmental conditions. By inhibiting seed germination and post-germinative growth through the PYR1/PYL/RCAR ABA receptors and PP2C co-receptors, the phytohormone abscisic acid (ABA) prevents premature germination and seedling growth under unfavorable conditions. However, little is known about how the ABA-mediated inhibition of seed germination and seedling establishment is thwarted. Here, we report that ABA Signaling Terminator (ABT), a WD40 protein, efficiently switches off ABA signaling and is critical for seed germination and seedling establishment. ABT is induced by ABA in a PYR1/PYL/RCAR-PP2C-dependent manner. Overexpression of ABT promotes seed germination and seedling greening in the presence of ABA, whereas knockout of ABT has the opposite effect. We found that ABT interacts with the PYR1/PYL/RCAR and PP2C proteins, interferes with the interaction between PYR1/PYL4 and ABI1/ABI2, and hampers the inhibition of ABI1/ABI2 by ABA-bound PYR1/PYL4, thereby terminating ABA signaling. Taken together, our results reveal a core mechanism of ABA signaling termination that is critical for seed germination and seedling establishment in Arabidopsis.
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Affiliation(s)
- Zhijuan Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Ziyin Ren
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Chunhong Cheng
- Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Tao Wang
- Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, P.R. China
| | - Hongtao Ji
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Yang Zhao
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai Institutes for Biological Sciences, Shanghai 200032, P.R. China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Zhiping Deng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 3210021, P.R. China
| | - Liya Zhi
- Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, P.R. China
| | - Jingjing Lu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Xinying Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Shimin Xu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Mengmeng Cao
- Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, P.R. China
| | - Hongtao Zhao
- Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, P.R. China
| | - Liu Liu
- Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Jiankang Zhu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai Institutes for Biological Sciences, Shanghai 200032, P.R. China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China.
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18
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Mistry BV, Alanazi M, Fitwi H, Al-Harazi O, Rajab M, Altorbag A, Almohanna F, Colak D, Assiri AM. Expression profiling of WD40 family genes including DDB1- and CUL4- associated factor (DCAF) genes in mice and human suggests important regulatory roles in testicular development and spermatogenesis. BMC Genomics 2020; 21:602. [PMID: 32867693 PMCID: PMC7457511 DOI: 10.1186/s12864-020-07016-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 08/20/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The WD40-repeat containing proteins, including DDB1-CUL4-associated factors (DCAFs), are abundant and conserved proteins that play important roles in different cellular processes including spermatogenesis. DCAFs are subset of WD40 family proteins that contain WDxR motif and have been proposed to function as substrate receptor for Cullin4-RING-based E3 ubiquitin ligase complexes to recruit diverse proteins for ubiquitination, a vital process in spermatogenesis. Large number of WD40 genes has been identified in different species including mouse and human. However, a systematic expression profiling of WD40 genes in different tissues of mouse and human has not been investigated. We hypothesize that large number of WD40 genes may express highly or specifically in the testis, where their expression is uniquely regulated during testis development and spermatogenesis. Therefore, the objective of this study is to mine and characterize expression patterns of WD40 genes in different tissues of mouse and human with particular emphasis on DCAF genes expressions during mouse testicular development. RESULTS Publically available RNA sequencing (RNA seq) data mining identified 347 and 349 WD40 genes in mouse and human, respectively. Hierarchical clustering and heat map analyses of RNA seq datasets revealed differential expression patterns of WD40 genes with around 60-73% of the genes were highly or specifically expressed in testis. Similarly, around 74-83% of DCAF genes were predominantly or specifically expressed in testis. Moreover, WD40 genes showed distinct expression patterns during embryonic and postnatal testis development in mice. Finally, different germ cell populations of testis showed specific patterns of WD40 genes expression. Predicted gene ontology analyses revealed more than 80% of these proteins are implicated in cellular, metabolic, biological regulation and cell localization processes. CONCLUSIONS We have identified large number of WD40 family genes that are highly or specifically expressed in the testes of mouse and human. Moreover, WD40 genes have distinct expression patterns during embryonic and postnatal development of the testis in mice. Further, different germ cell populations within the testis showed specific patterns of WD40 genes expression. These results provide foundation for further research towards understanding the functional genomics and molecular mechanisms of mammalian testis development and spermatogenesis.
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Affiliation(s)
- Bhavesh V Mistry
- Department of Comparative Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Maha Alanazi
- Department of Comparative Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Hanae Fitwi
- Department of Comparative Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Olfat Al-Harazi
- Biostatistics, Epidemiology and Scientific Computing Department, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Mohamed Rajab
- Department of Comparative Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Abdullah Altorbag
- Department of Comparative Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Falah Almohanna
- Department of Comparative Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Dilek Colak
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Abdullah M Assiri
- Department of Comparative Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia. .,Biostatistics, Epidemiology and Scientific Computing Department, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia. .,Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
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19
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Weber M, Beyene B, Nagler N, Herfert J, Schempp S, Klecker M, Clemens S. A mutation in the essential and widely conserved DAMAGED DNA BINDING1-Cullin4 ASSOCIATED FACTOR gene OZS3 causes hypersensitivity to zinc excess, cold and UV stress in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:995-1009. [PMID: 32314481 DOI: 10.1111/tpj.14779] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 02/18/2020] [Accepted: 04/01/2020] [Indexed: 05/28/2023]
Abstract
The overly zinc sensitive Arabidopsis thaliana mutant ozs3 shows reduced growth of the primary root, which is exacerbated by an excess specifically of Zn ions. In addition, ozs3 plants display various subtle developmental phenotypes, such as longer petioles and early flowering. Also, ozs3 seedlings are completely but reversibly growth-arrested when shifted to 4°C. The causal mutation was mapped to a gene encoding a putative substrate-recognition receptor of cullin4 E3 ligases. OZS3 orthologous genes can be found in almost all eukaryotic genomes. Most species from Schizosaccharomyces pombe to Homo sapiens, and including A. thaliana, possess one ortholog. No functional data are available for these genes in any of the multicellular model systems. CRISPR-Cas9-mediated knockout demonstrated that a complete loss of OZS3 function is embryo-lethal, indicating essentiality of OZS3 and its orthologs. The OZS3 protein interacts with the adaptor protein DAMAGED DNA BINDING1 (DDB1) in the nucleus. Thus, it is indeed a member of the large yet poorly characterized family of DDB1-cullin4 associated factors in plants. Mutant phenotypes of ozs3 plants are apparently caused by the weakened DDB1-OZS3 interaction as a result of the exchange of a conserved amino acid near the conserved WDxR motif.
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Affiliation(s)
- Michael Weber
- Department of Plant Physiology, University of Bayreuth, Bayreuth, 95440, Germany
| | - Blen Beyene
- Department of Plant Physiology, University of Bayreuth, Bayreuth, 95440, Germany
| | - Nicole Nagler
- Department of Plant Physiology, University of Bayreuth, Bayreuth, 95440, Germany
| | - Jörn Herfert
- Department of Plant Physiology, University of Bayreuth, Bayreuth, 95440, Germany
| | - Stefanie Schempp
- Department of Plant Physiology, University of Bayreuth, Bayreuth, 95440, Germany
| | - Maria Klecker
- Department of Plant Physiology, University of Bayreuth, Bayreuth, 95440, Germany
| | - Stephan Clemens
- Department of Plant Physiology, University of Bayreuth, Bayreuth, 95440, Germany
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20
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Qian W, Li Z, Song W, Zhao T, Wang W, Peng J, Wei L, Xia Q, Cheng D. A novel transcriptional cascade is involved in Fzr-mediated endoreplication. Nucleic Acids Res 2020; 48:4214-4229. [PMID: 32182338 PMCID: PMC7192621 DOI: 10.1093/nar/gkaa158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/29/2020] [Indexed: 01/08/2023] Open
Abstract
Endoreplication, known as endocycle, is a variant of the cell cycle that differs from mitosis and occurs in specific tissues of different organisms. Endoreplicating cells generally undergo multiple rounds of genome replication without chromosome segregation. Previous studies demonstrated that Drosophila fizzy-related protein (Fzr) and its mammalian homolog Cdh1 function as key regulators of endoreplication entrance by activating the anaphase-promoting complex/cyclosome to initiate the ubiquitination and subsequent degradation of cell cycle factors such as Cyclin B (CycB). However, the molecular mechanism underlying Fzr-mediated endoreplication is not completely understood. In this study, we demonstrated that the transcription factor Myc acts downstream of Fzr during endoreplication in Drosophila salivary gland. Mechanistically, Fzr interacts with chromatin-associated histone H2B to enhance H2B ubiquitination in the Myc promoter and promotes Myc transcription. In addition to negatively regulating CycB transcription, the Fzr-ubiquitinated H2B (H2Bub)-Myc signaling cascade also positively regulates the transcription of the MCM6 gene that is involved in DNA replication by directly binding to specific motifs within their promoters. We further found that the Fzr-H2Bub-Myc signaling cascade regulating endoreplication progression is conserved between insects and mammalian cells. Altogether, our work uncovers a novel transcriptional cascade that is involved in Fzr-mediated endoreplication.
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Affiliation(s)
- Wenliang Qian
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Zheng Li
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Wei Song
- Medical Research Institute, Wuhan University, Wuhan 430071, China.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Tujing Zhao
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Weina Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Jian Peng
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Ling Wei
- School of Life Science, Southwest University, Chongqing 400715, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Daojun Cheng
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
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21
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Timmers HTM. SAGA and TFIID: Friends of TBP drifting apart. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194604. [PMID: 32673655 DOI: 10.1016/j.bbagrm.2020.194604] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 01/24/2023]
Abstract
Transcription initiation constitutes a major checkpoint in gene regulation across all living organisms. Control of chromatin function is tightly linked to this checkpoint, which is best illustrated by the SAGA coactivator. This evolutionary conserved complex of 18-20 subunits was first discovered as a Gcn5p-containing histone acetyltransferase, but it also integrates a histone H2B deubiquitinase. The SAGA subunits are organized in a modular fashion around its central core. Strikingly, this central module of SAGA shares a number of proteins with the central core of the basal transcription factor TFIID. In this review I will compare the SAGA and TFIID complexes with respect to their shared subunits, structural organization, enzymatic activities and chromatin binding. I will place a special emphasis on the ancestry of SAGA and TFIID subunits, which suggests that these complexes evolved to control the activity of TBP (TATA-binding protein) in directing the assembly of transcription initiation complexes.
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Affiliation(s)
- H Th Marc Timmers
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK) partner site Freiburg, 79106 Freiburg, Germany; Department of Urology, Medical Center-University of Freiburg, Breisacher Straße 66, 79106 Freiburg, Germany.
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22
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Venturutti L, Teater M, Zhai A, Chadburn A, Babiker L, Kim D, Béguelin W, Lee TC, Kim Y, Chin CR, Yewdell WT, Raught B, Phillip JM, Jiang Y, Staudt LM, Green MR, Chaudhuri J, Elemento O, Farinha P, Weng AP, Nissen MD, Steidl C, Morin RD, Scott DW, Privé GG, Melnick AM. TBL1XR1 Mutations Drive Extranodal Lymphoma by Inducing a Pro-tumorigenic Memory Fate. Cell 2020; 182:297-316.e27. [PMID: 32619424 DOI: 10.1016/j.cell.2020.05.049] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/24/2020] [Accepted: 05/27/2020] [Indexed: 12/30/2022]
Abstract
The most aggressive B cell lymphomas frequently manifest extranodal distribution and carry somatic mutations in the poorly characterized gene TBL1XR1. Here, we show that TBL1XR1 mutations skew the humoral immune response toward generating abnormal immature memory B cells (MB), while impairing plasma cell differentiation. At the molecular level, TBL1XR1 mutants co-opt SMRT/HDAC3 repressor complexes toward binding the MB cell transcription factor (TF) BACH2 at the expense of the germinal center (GC) TF BCL6, leading to pre-memory transcriptional reprogramming and cell-fate bias. Upon antigen recall, TBL1XR1 mutant MB cells fail to differentiate into plasma cells and instead preferentially reenter new GC reactions, providing evidence for a cyclic reentry lymphomagenesis mechanism. Ultimately, TBL1XR1 alterations lead to a striking extranodal immunoblastic lymphoma phenotype that mimics the human disease. Both human and murine lymphomas feature expanded MB-like cell populations, consistent with a MB-cell origin and delineating an unforeseen pathway for malignant transformation of the immune system.
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Affiliation(s)
- Leandro Venturutti
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Matt Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Andrew Zhai
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Leena Babiker
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Daleum Kim
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Wendy Béguelin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Tak C Lee
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Youngjun Kim
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Christopher R Chin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Tri-Institutional Program in Computational Biology and Medicine, New York, NY 10065, USA
| | - William T Yewdell
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Brian Raught
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Jude M Phillip
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Yanwen Jiang
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Louis M Staudt
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael R Green
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jayanta Chaudhuri
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA; Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Pedro Farinha
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Andrew P Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada; Department of Pathology and Lab Medicine, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Michael D Nissen
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Ryan D Morin
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Gilbert G Privé
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, and Princess Margaret Cancer Centre, Toronto, ON M5S 1A8, Canada
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
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23
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Ma J, An K, Zhou JB, Wu NS, Wang Y, Ye ZQ, Wu YD. WDSPdb: an updated resource for WD40 proteins. Bioinformatics 2020; 35:4824-4826. [PMID: 31161214 PMCID: PMC6853709 DOI: 10.1093/bioinformatics/btz460] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 04/28/2019] [Accepted: 05/29/2019] [Indexed: 11/18/2022] Open
Abstract
Summary The 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 implementation http://www.wdspdb.com/wdsp/ or http://wu.scbb.pkusz.edu.cn/wdsp/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jing Ma
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Ke An
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jing-Bo Zhou
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Nuo-Si Wu
- College of Information Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yang Wang
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Zhi-Qiang Ye
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yun-Dong Wu
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China.,College of Chemistry, Peking University, Beijing 100871, China
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24
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Hiltpold M, Niu G, Kadri NK, Crysnanto D, Fang ZH, Spengeler M, Schmitz-Hsu F, Fuerst C, Schwarzenbacher H, Seefried FR, Seehusen F, Witschi U, Schnieke A, Fries R, Bollwein H, Flisikowski K, Pausch H. Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility. PLoS Genet 2020; 16:e1008804. [PMID: 32407316 PMCID: PMC7252675 DOI: 10.1371/journal.pgen.1008804] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 05/27/2020] [Accepted: 04/28/2020] [Indexed: 12/30/2022] Open
Abstract
Cattle are ideally suited to investigate the genetics of male reproduction, because semen quality and fertility are recorded for all ejaculates of artificial insemination bulls. We analysed 26,090 ejaculates of 794 Brown Swiss bulls to assess ejaculate volume, sperm concentration, sperm motility, sperm head and tail anomalies and insemination success. The heritability of the six semen traits was between 0 and 0.26. Genome-wide association testing on 607,511 SNPs revealed a QTL on bovine chromosome 6 that was associated with sperm motility (P = 2.5 x 10−27), head (P = 2.0 x 10−44) and tail anomalies (P = 7.2 x 10−49) and insemination success (P = 9.9 x 10−13). The QTL harbors a recessive allele that compromises semen quality and male fertility. We replicated the effect of the QTL on fertility (P = 7.1 x 10−32) in an independent cohort of 2481 Brown Swiss bulls. The analysis of whole-genome sequencing data revealed that a synonymous variant (BTA6:58373887C>T, rs474302732) in WDR19 encoding WD repeat-containing protein 19 was in linkage disequilibrium with the fertility-associated haplotype. WD repeat-containing protein 19 is a constituent of the intraflagellar transport complex that is essential for the physiological function of motile cilia and flagella. Bioinformatic and transcription analyses revealed that the BTA6:58373887 T-allele activates a cryptic exonic splice site that eliminates three evolutionarily conserved amino acids from WDR19. Western blot analysis demonstrated that the BTA6:58373887 T-allele decreases protein expression. We make the remarkable observation that, in spite of negative effects on semen quality and bull fertility, the BTA6:58373887 T-allele has a frequency of 24% in the Brown Swiss population. Our findings are the first to uncover a variant that is associated with quantitative variation in semen quality and male fertility in cattle. In cattle farming, artificial insemination is the most common method of breeding. To ensure high fertilization rates, ejaculate quality and insemination success are closely monitored in artificial insemination bulls. We analyse semen quality, insemination success and microarray-called genotypes at more than 600,000 genome-wide SNP markers of 794 bulls to identify a recessive allele that compromises semen quality. We take advantage of whole-genome sequencing to pinpoint a variant in the coding sequence of WDR19 encoding WD repeat-containing protein 19 that activates a novel exonic splice site. Our results indicate that cryptic splicing in WDR19 is associated with reduced male reproductive performance. This is the first report of a variant that contributes to quantitative variation in bovine semen quality.
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Affiliation(s)
| | - Guanglin Niu
- Livestock Biotechnology, TU München, Freising, Germany
| | | | | | - Zih-Hua Fang
- Animal Genomics, ETH Zürich, Lindau, Switzerland
| | | | | | | | | | | | - Frauke Seehusen
- Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | | | | | - Ruedi Fries
- Animal Breeding, TU München, Freising, Germany
| | - Heinrich Bollwein
- Clinic of Reproductive Medicine, University of Zurich, Zürich, Switzerland
| | | | - Hubert Pausch
- Animal Genomics, ETH Zürich, Lindau, Switzerland
- * E-mail:
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25
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Structure-based view of the druggable genome. Drug Discov Today 2020; 25:561-567. [PMID: 32084498 DOI: 10.1016/j.drudis.2020.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 12/15/2022]
Abstract
International efforts are underway to develop chemical probes for specific protein families, and a 'Target 2035' call to expand these efforts towards a comprehensive chemical coverage of the druggable human genome was recently announced. But what is the druggable genome? Here, we systematically review structures of proteins bound to drug-like ligands available from the Protein Data Bank (PDB) and use ligand desolvation upon binding as a druggability metric to draw a landscape of the human druggable genome. The vast majority of druggable protein families, including some highly populated and disease-associated families, are almost orphan of small-molecule ligands. We propose a list of 46 druggable domains representing 3440 human proteins that could be the focus of large chemical probe discovery efforts.
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26
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Thole V, Bassard JE, Ramírez-González R, Trick M, Ghasemi Afshar B, Breitel D, Hill L, Foito A, Shepherd L, Freitag S, Nunes dos Santos C, Menezes R, Bañados P, Naesby M, Wang L, Sorokin A, Tikhonova O, Shelenga T, Stewart D, Vain P, Martin C. RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics. BMC Genomics 2019; 20:995. [PMID: 31856735 PMCID: PMC6924045 DOI: 10.1186/s12864-019-6183-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 10/15/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Flavonoids are produced in all flowering plants in a wide range of tissues including in berry fruits. These compounds are of considerable interest for their biological activities, health benefits and potential pharmacological applications. However, transcriptomic and genomic resources for wild and cultivated berry fruit species are often limited, despite their value in underpinning the in-depth study of metabolic pathways, fruit ripening as well as in the identification of genotypes rich in bioactive compounds. RESULTS To access the genetic diversity of wild and cultivated berry fruit species that accumulate high levels of phenolic compounds in their fleshy berry(-like) fruits, we selected 13 species from Europe, South America and Asia representing eight genera, seven families and seven orders within three clades of the kingdom Plantae. RNA from either ripe fruits (ten species) or three ripening stages (two species) as well as leaf RNA (one species) were used to construct, assemble and analyse de novo transcriptomes. The transcriptome sequences are deposited in the BacHBerryGEN database (http://jicbio.nbi.ac.uk/berries) and were used, as a proof of concept, via its BLAST portal (http://jicbio.nbi.ac.uk/berries/blast.html) to identify candidate genes involved in the biosynthesis of phenylpropanoid compounds. Genes encoding regulatory proteins of the anthocyanin biosynthetic pathway (MYB and basic helix-loop-helix (bHLH) transcription factors and WD40 repeat proteins) were isolated using the transcriptomic resources of wild blackberry (Rubus genevieri) and cultivated red raspberry (Rubus idaeus cv. Prestige) and were shown to activate anthocyanin synthesis in Nicotiana benthamiana. Expression patterns of candidate flavonoid gene transcripts were also studied across three fruit developmental stages via the BacHBerryEXP gene expression browser (http://www.bachberryexp.com) in R. genevieri and R. idaeus cv. Prestige. CONCLUSIONS We report a transcriptome resource that includes data for a wide range of berry(-like) fruit species that has been developed for gene identification and functional analysis to assist in berry fruit improvement. These resources will enable investigations of metabolic processes in berries beyond the phenylpropanoid biosynthetic pathway analysed in this study. The RNA-seq data will be useful for studies of berry fruit development and to select wild plant species useful for plant breeding purposes.
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Affiliation(s)
- Vera Thole
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jean-Etienne Bassard
- Department of Plant and Environmental Science, University of Copenhagen, 1871 Frederiksberg, Denmark
- Present address: Institute of Plant Molecular Biology, CNRS, University of Strasbourg, 12 Rue General Zimmer, 67084 Strasbourg, France
| | | | - Martin Trick
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Bijan Ghasemi Afshar
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Dario Breitel
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Present address: Tropic Biosciences UK LTD, Norwich Research Park, Norwich, NR4 7UG UK
| | - Lionel Hill
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | | | | | - Sabine Freitag
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | - Cláudia Nunes dos Santos
- Instituto de Biologia Experimental e Tecnológica, Av. República, Qta. do Marquês, 2780-157 Oeiras, Portugal
- CEDOC, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Rua Câmara Pestana 6, 1150-082 Lisbon, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Regina Menezes
- Instituto de Biologia Experimental e Tecnológica, Av. República, Qta. do Marquês, 2780-157 Oeiras, Portugal
- CEDOC, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Rua Câmara Pestana 6, 1150-082 Lisbon, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Pilar Bañados
- Facultad De Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna Ote, 4860 Macul, Chile
| | | | - Liangsheng Wang
- Institute of Botany, The Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093 China
| | - Artem Sorokin
- Fruit Crops Genetic Resources Department, N. I. Vavilov Research Institute of Plant Industry, B. Morskaya Street 42-44, St. Petersburg, 190000 Russia
| | - Olga Tikhonova
- Fruit Crops Genetic Resources Department, N. I. Vavilov Research Institute of Plant Industry, B. Morskaya Street 42-44, St. Petersburg, 190000 Russia
| | - Tatiana Shelenga
- Fruit Crops Genetic Resources Department, N. I. Vavilov Research Institute of Plant Industry, B. Morskaya Street 42-44, St. Petersburg, 190000 Russia
| | - Derek Stewart
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
- Institute of Mechanical, Process and Energy Engineering, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh, UK
| | - Philippe Vain
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Cathie Martin
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
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27
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Yu Y, Jia W, Lyu Y, Su D, Bai M, Shen J, Qiao J, Han T, Liu W, Chen J, Chen W, Ye D, Guo X, Zhu S, Xi J, Zhu R, Wan X, Gao S, Zhu J, Kang J. Pwp1 regulates telomere length by stabilizing shelterin complex and maintaining histone H4K20 trimethylation. Cell Discov 2019; 5:47. [PMID: 31754456 PMCID: PMC6868014 DOI: 10.1038/s41421-019-0116-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 07/24/2019] [Indexed: 01/02/2023] Open
Abstract
Telomere maintenance is critical for chromosome stability. Here we report that periodic tryptophan protein 1 (PWP1) is involved in regulating telomere length homeostasis. Pwp1 appears to be essential for mouse development and embryonic stem cell (ESC) survival, as homozygous Pwp1-knockout mice and ESCs have never been obtained. Heterozygous Pwp1-knockout mice had shorter telomeres and decreased reproductive capacity. Pwp1 depletion induced rapid telomere shortening accompanied by reduced shelterin complex and increased DNA damage in telomeric regions. Mechanistically, PWP1 bound and stabilized the shelterin complex via its WD40 domains and regulated the overall level of H4K20me3. The rescue of telomere length in Pwp1-deficient cells by PWP1 overexpression depended on SUV4-20H2 co-expression and increased H4K20me3. Therefore, our study revealed a novel protein involved in telomere homeostasis in both mouse and human cells. This knowledge will improve our understanding of how chromatin structure and histone modifications are involved in maintaining telomere integrity.
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Affiliation(s)
- Yangyang Yu
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Wenwen Jia
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China.,2Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200123 China
| | - Yao Lyu
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Dingwen Su
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Mingliang Bai
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Junwei Shen
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Jing Qiao
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Tong Han
- 3Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 201204 P. R. China
| | - Wenqiang Liu
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Jiayu Chen
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Wen Chen
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Dan Ye
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Xudong Guo
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Songcheng Zhu
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Jiajie Xi
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Ruixin Zhu
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Xiaoping Wan
- 3Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 201204 P. R. China
| | - Shaorong Gao
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Jiyue Zhu
- 4Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, Spokane, WA 99210 USA
| | - Jiuhong Kang
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China.,2Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200123 China
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28
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Lepore R, Kryshtafovych A, Alahuhta M, Veraszto HA, Bomble YJ, Bufton JC, Bullock AN, Caba C, Cao H, Davies OR, Desfosses A, Dunne M, Fidelis K, Goulding CW, Gurusaran M, Gutsche I, Harding CJ, Hartmann MD, Hayes CS, Joachimiak A, Leiman PG, Loppnau P, Lovering AL, Lunin VV, Michalska K, Mir-Sanchis I, Mitra AK, Moult J, Phillips GN, Pinkas DM, Rice PA, Tong Y, Topf M, Walton JD, Schwede T. Target highlights in CASP13: Experimental target structures through the eyes of their authors. Proteins 2019; 87:1037-1057. [PMID: 31442339 PMCID: PMC6851490 DOI: 10.1002/prot.25805] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/09/2019] [Accepted: 08/19/2019] [Indexed: 01/10/2023]
Abstract
The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment.
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Affiliation(s)
- Rosalba Lepore
- BSC-CNS Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado
| | - Harshul A Veraszto
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Yannick J Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado
| | - Joshua C Bufton
- Nuffield Department of Medicine; Structural Genomics Consortium, University of Oxford, Oxford, UK.,School of Biochemistry, University of Bristol, Bristol, UK
| | - Alex N Bullock
- Nuffield Department of Medicine; Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Cody Caba
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Hongnan Cao
- Department of BioSciences, Rice University, Houston, Texas.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
| | - Owen R Davies
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Ambroise Desfosses
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Matthew Dunne
- Institute of Food, Nutrition and Health, Zurich, Switzerland
| | | | - Celia W Goulding
- Department of Molecular Biology and Biochemistry; Pharmaceutical Sciences, University of California Irvine, Irvine, California
| | - Manickam Gurusaran
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | | | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, Biomolecular Science and Engineering Program, University of California, Santa Barbara, California
| | - Andrzej Joachimiak
- Structural Biology Center, Biosciences Division, Midwest Center for Structural Genomics, Argonne.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Vladimir V Lunin
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado
| | - Karolina Michalska
- Structural Biology Center, Biosciences Division, Midwest Center for Structural Genomics, Argonne
| | - Ignacio Mir-Sanchis
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - A K Mitra
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - John Moult
- Institute for Bioscience and Biotechnology Research, Department of Cell Biology and Molecular genetics, University of Maryland, Rockville, Maryland, USA
| | - George N Phillips
- Department of BioSciences, Rice University, Houston, Texas.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
| | - Daniel M Pinkas
- Nuffield Department of Medicine; Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck, University College London, London, UK
| | - Jonathan D Walton
- Great Lakes Bioenergy Research Center and Department of Plant Biology, Michigan State University, East Lansing, Michigan
| | - Torsten Schwede
- Biozentrum University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum University of Basel, Basel, Switzerland
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29
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Bergstrand S, O'Brien EM, Farnebo M. The Cajal Body Protein WRAP53β Prepares the Scene for Repair of DNA Double-Strand Breaks by Regulating Local Ubiquitination. Front Mol Biosci 2019; 6:51. [PMID: 31334247 PMCID: PMC6624377 DOI: 10.3389/fmolb.2019.00051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/20/2019] [Indexed: 12/27/2022] Open
Abstract
Proper repair of DNA double-strand breaks is critical for maintaining genome integrity and avoiding disease. Modification of damaged chromatin has profound consequences for the initial signaling and regulation of repair. One such modification involves ubiquitination by E3 ligases RNF8 and RNF168 within minutes after DNA double-strand break formation, altering chromatin structure and recruiting factors such as 53BP1 and BRCA1 for repair via non-homologous end-joining (NHEJ) and homologous recombination (HR), respectively. The WD40 protein WRAP53β plays an essential role in localizing RNF8 to DNA breaks by scaffolding its interaction with the upstream factor MDC1. Loss of WRAP53β impairs ubiquitination at DNA lesions and reduces downstream repair by both NHEJ and HR. Intriguingly, WRAP53β depletion attenuates repair of DNA double-strand breaks more than depletion of RNF8, indicating functions other than RNF8-mediated ubiquitination. WRAP53β plays key roles with respect to the nuclear organelles Cajal bodies, including organizing the genome to promote associated transcription and collecting factors involved in maturation of the spliceosome and telomere elongation within these organelles. It is possible that similar functions may aid also in DNA repair. Here we describe the involvement of WRAP53β in Cajal bodies and DNA double-strand break repair in detail and explore whether and how these processes may be linked. We also discuss the possibility that the overexpression of WRAP53β detected in several cancer types may reflect its normal participation in the DNA damage response rather than oncogenic properties.
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Affiliation(s)
- Sofie Bergstrand
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Eleanor M O'Brien
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Marianne Farnebo
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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30
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Fiorucci AS, Bourbousse C, Concia L, Rougée M, Deton-Cabanillas AF, Zabulon G, Layat E, Latrasse D, Kim SK, Chaumont N, Lombard B, Stroebel D, Lemoine S, Mohammad A, Blugeon C, Loew D, Bailly C, Bowler C, Benhamed M, Barneche F. Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in H3K4me3 independently from histone H2B monoubiquitination. Genome Biol 2019; 20:100. [PMID: 31113491 PMCID: PMC6528313 DOI: 10.1186/s13059-019-1705-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/02/2019] [Indexed: 12/19/2022] Open
Abstract
Background The functional determinants of H3K4me3, their potential dependency on histone H2B monoubiquitination, and their contribution to defining transcriptional regimes are poorly defined in plant systems. Unlike in Saccharomyces cerevisiae, where a single SET1 protein catalyzes H3K4me3 as part of COMPlex of proteins ASsociated with Set1 (COMPASS), in Arabidopsis thaliana, this activity involves multiple histone methyltransferases. Among these, the plant-specific SET DOMAIN GROUP 2 (SDG2) has a prominent role. Results We report that SDG2 co-regulates hundreds of genes with SWD2-like b (S2Lb), a plant ortholog of the Swd2 axillary subunit of yeast COMPASS. We show that S2Lb co-purifies with the AtCOMPASS core subunit WDR5, and both S2Lb and SDG2 directly influence H3K4me3 enrichment over highly transcribed genes. S2Lb knockout triggers pleiotropic developmental phenotypes at the vegetative and reproductive stages, including reduced fertility and seed dormancy. However, s2lb seedlings display little transcriptomic defects as compared to the large repertoire of genes targeted by S2Lb, SDG2, or H3K4me3, suggesting that H3K4me3 enrichment is important for optimal gene induction during cellular transitions rather than for determining on/off transcriptional status. Moreover, unlike in budding yeast, most of the S2Lb and H3K4me3 genomic distribution does not rely on a trans-histone crosstalk with histone H2B monoubiquitination. Conclusions Collectively, this study unveils that the evolutionarily conserved COMPASS-like complex has been co-opted by the plant-specific SDG2 histone methyltransferase and mediates H3K4me3 deposition through an H2B monoubiquitination-independent pathway in Arabidopsis. Electronic supplementary material The online version of this article (10.1186/s13059-019-1705-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anne-Sophie Fiorucci
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France.,Present address: Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Clara Bourbousse
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Lorenzo Concia
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
| | - Martin Rougée
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Anne-Flore Deton-Cabanillas
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Gérald Zabulon
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Elodie Layat
- Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, 75005, Paris, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
| | - Soon Kap Kim
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
| | - Nicole Chaumont
- Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, 75005, Paris, France
| | - Bérangère Lombard
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - David Stroebel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Sophie Lemoine
- Genomic Facility, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, Paris, 75005, France
| | - Ammara Mohammad
- Genomic Facility, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, Paris, 75005, France
| | - Corinne Blugeon
- Genomic Facility, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, Paris, 75005, France
| | - Damarys Loew
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Christophe Bailly
- Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, 75005, Paris, France
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France.
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31
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Willison KR. The substrate specificity of eukaryotic cytosolic chaperonin CCT. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0192. [PMID: 29735743 DOI: 10.1098/rstb.2017.0192] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2018] [Indexed: 12/22/2022] Open
Abstract
The cytosolic chaperonin CCT (chaperonin containing TCP-1) is an ATP-dependent double-ring protein machine mediating the folding of members of the eukaryotic cytoskeletal protein families. The actins and tubulins are obligate substrates of CCT because they are completely dependent on CCT activity to reach their native states. Genetic and proteomic analysis of the CCT interactome in the yeast Saccharomyces cerevisiae revealed a CCT network of approximately 300 genes and proteins involved in many fundamental biological processes. We classified network members into sets such as substrates, CCT cofactors and CCT-mediated assembly processes. Many members of the 7-bladed propeller family of proteins are commonly found tightly bound to CCT isolated from human and plant cells and yeasts. The anaphase promoting complex (APC/C) cofactor propellers, Cdh1p and Cdc20p, are also obligate substrates since they both require CCT for folding and functional activation. In vitro translation analysis in prokaryotic and eukaryotic cell extracts of a set of yeast propellers demonstrates their highly differential interactions with CCT and GroEL (another chaperonin). Individual propeller proteins have idiosyncratic interaction modes with CCT because they emerged independently with neo-functions many times throughout eukaryotic evolution. We present a toy model in which cytoskeletal protein biogenesis and folding flux through CCT couples cell growth and size control to time dependent cell cycle mechanisms.This article is part of a discussion meeting issue 'Allostery and molecular machines'.
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Affiliation(s)
- Keith R Willison
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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32
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Genome Wide Analysis of WD40 Proteins in Saccharomyces cerevisiae and Their Orthologs in Candida albicans. Protein J 2019; 38:58-75. [PMID: 30511317 DOI: 10.1007/s10930-018-9804-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The WD40 domain containing proteins are present in the lower organisms (Monera) to higher complex metazoans with involvement in diverse cellular processes. The WD40 repeats fold into β propeller structure due to which the proteins harbouring WD40 domains function as scaffold by offering platform for interactions, bring together diverse cellular proteins to form a single complex for mediating downstream effects. Multiple functions of WD40 domain containing proteins in lower eukaryote as in Fungi have been reported with involvement in vegetative and reproductive growth, virulence etc. In this article insilico analysis of the WDR proteins in the budding yeast Saccharomyces cerevisiae was performed. By WDSP software 83 proteins in S. cerevisiae were identified with at least one WD40 motif. WD40 proteins with 6 or more WD40 motifs were considered for further studies. The WD40 proteins in yeast which are involved in various biological processes show distribution on all chromosomes (16 chromosomes in yeast) except chromosome 1. Besides the WD40 domain some of these proteins also contain other protein domains which might be responsible for the diversity in the functions of WD40 proteins in the budding yeast. These proteins in budding yeast were analysed by DAVID and Blast2Go software for functional and domains categorization. Candida albicans, an opportunistic fungal pathogen also have orthologs of these WD40 proteins with possible similar functions. This is the first time genome wide analysis of WD40 proteins in lower eukaryote i.e. budding yeast. This data may be useful in further study of the functional diversity of yeast proteomes.
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33
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Liu X, Galli M, Camehl I, Gallavotti A. RAMOSA1 ENHANCER LOCUS2-Mediated Transcriptional Repression Regulates Vegetative and Reproductive Architecture. PLANT PHYSIOLOGY 2019; 179:348-363. [PMID: 30348817 PMCID: PMC6324236 DOI: 10.1104/pp.18.00913] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/11/2018] [Indexed: 05/17/2023]
Abstract
Transcriptional repression in multicellular organisms orchestrates dynamic and precise gene expression changes that enable complex developmental patterns. Here, we present phenotypic and molecular characterization of the maize (Zea mays) transcriptional corepressor RAMOSA1 ENHANCER LOCUS2 (REL2), a unique member of the highly conserved TOPLESS (TPL) family. Analysis of single recessive mutations in rel2 revealed an array of vegetative and reproductive phenotypes, many related to defects in meristem initiation and maintenance. To better understand how REL2-mediated transcriptional complexes relate to rel2 phenotypes, we performed protein interaction assays and transcriptional profiling of mutant inflorescences, leading to the identification of different maize transcription factors and regulatory pathways that employ REL2 repression to control traits directly impacting maize yields. In addition, we used our REL2 interaction data to catalog conserved repression motifs present on REL2 interactors and showed that two of these, RLFGV- and DLN-type motifs, interact with the C-terminal WD40 domain of REL2 rather than the N terminus, which is known to bind LxLxL EAR motifs. These findings establish that the WD40 domain of TPL family proteins is an independent protein interaction surface that may work together with the N-terminal domain to allow the formation of large macromolecular complexes of functionally related transcription factors.
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Affiliation(s)
- Xue Liu
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020
| | - Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020
| | - Iris Camehl
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey USA 08901
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34
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Urbanska P, Joachimiak E, Bazan R, Fu G, Poprzeczko M, Fabczak H, Nicastro D, Wloga D. Ciliary proteins Fap43 and Fap44 interact with each other and are essential for proper cilia and flagella beating. Cell Mol Life Sci 2018; 75:4479-4493. [PMID: 29687140 PMCID: PMC6208767 DOI: 10.1007/s00018-018-2819-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 11/08/2022]
Abstract
Cilia beating is powered by the inner and outer dynein arms (IDAs and ODAs). These multi-subunit macrocomplexes are arranged in two rows on each outer doublet along the entire cilium length, except its distal end. To generate cilia beating, the activity of ODAs and IDAs must be strictly regulated locally by interactions with the dynein arm-associated structures within each ciliary unit and coordinated globally in time and space between doublets and along the axoneme. Here, we provide evidence of a novel ciliary complex composed of two conserved WD-repeat proteins, Fap43p and Fap44p. This complex is adjacent to another WD-repeat protein, Fap57p, and most likely the two-headed inner dynein arm, IDA I1. Loss of either protein results in altered waveform, beat stroke and reduced swimming speed. The ciliary localization of Fap43p and Fap44p is interdependent in the ciliate Tetrahymena thermophila.
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Affiliation(s)
- Paulina Urbanska
- Laboratory of Cytoskeleton and Cilia Biology, Department of Cell Biology, Nencki Institute of Experimental Biology PAS, Pasteur 3, 02-093, Warsaw, Poland
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Department of Cell Biology, Nencki Institute of Experimental Biology PAS, Pasteur 3, 02-093, Warsaw, Poland
| | - Rafał Bazan
- Laboratory of Cytoskeleton and Cilia Biology, Department of Cell Biology, Nencki Institute of Experimental Biology PAS, Pasteur 3, 02-093, Warsaw, Poland
| | - Gang Fu
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, USA
| | - Martyna Poprzeczko
- Laboratory of Cytoskeleton and Cilia Biology, Department of Cell Biology, Nencki Institute of Experimental Biology PAS, Pasteur 3, 02-093, Warsaw, Poland
| | - Hanna Fabczak
- Laboratory of Cytoskeleton and Cilia Biology, Department of Cell Biology, Nencki Institute of Experimental Biology PAS, Pasteur 3, 02-093, Warsaw, Poland
| | - Daniela Nicastro
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, USA
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Department of Cell Biology, Nencki Institute of Experimental Biology PAS, Pasteur 3, 02-093, Warsaw, Poland.
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35
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Krasovec M, Vancaester E, Rombauts S, Bucchini F, Yau S, Hemon C, Lebredonchel H, Grimsley N, Moreau H, Sanchez-Brosseau S, Vandepoele K, Piganeau G. Genome Analyses of the Microalga Picochlorum Provide Insights into the Evolution of Thermotolerance in the Green Lineage. Genome Biol Evol 2018; 10:2347-2365. [PMID: 30113623 PMCID: PMC6141220 DOI: 10.1093/gbe/evy167] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2018] [Indexed: 01/11/2023] Open
Abstract
While the molecular events involved in cell responses to heat stress have been extensively studied, our understanding of the genetic basis of basal thermotolerance, and particularly its evolution within the green lineage, remains limited. Here, we present the 13.3-Mb haploid genome and transcriptomes of a halotolerant and thermotolerant unicellular green alga, Picochlorum costavermella (Trebouxiophyceae) to investigate the evolution of the genomic basis of thermotolerance. Differential gene expression at high and standard temperatures revealed that more of the gene families containing up-regulated genes at high temperature were recently evolved, and less originated at the ancestor of green plants. Inversely, there was an excess of ancient gene families containing transcriptionally repressed genes. Interestingly, there is a striking overlap between the thermotolerance and halotolerance transcriptional rewiring, as more than one-third of the gene families up-regulated at 35 °C were also up-regulated under variable salt concentrations in Picochlorum SE3. Moreover, phylogenetic analysis of the 9,304 protein coding genes revealed 26 genes of horizontally transferred origin in P. costavermella, of which five were differentially expressed at higher temperature. Altogether, these results provide new insights about how the genomic basis of adaptation to halo- and thermotolerance evolved in the green lineage.
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Affiliation(s)
- Marc Krasovec
- Sorbonne Université, CNRS, Biologie Integrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France.,Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Emmelien Vancaester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - François Bucchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Sheree Yau
- Sorbonne Université, CNRS, Biologie Integrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Claire Hemon
- Sorbonne Université, CNRS, Biologie Integrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Hugo Lebredonchel
- Sorbonne Université, CNRS, Biologie Integrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Nigel Grimsley
- Sorbonne Université, CNRS, Biologie Integrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Hervé Moreau
- Sorbonne Université, CNRS, Biologie Integrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Sophie Sanchez-Brosseau
- Sorbonne Université, CNRS, Biologie Integrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Belgium
| | - Gwenael Piganeau
- Sorbonne Université, CNRS, Biologie Integrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
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36
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Shen C, Du Y, Qiao F, Kong T, Yuan L, Zhang D, Wu X, Li D, Wu YD. Biophysical and structural characterization of the thermostable WD40 domain of a prokaryotic protein, Thermomonospora curvata PkwA. Sci Rep 2018; 8:12965. [PMID: 30154510 PMCID: PMC6113231 DOI: 10.1038/s41598-018-31140-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/10/2018] [Indexed: 01/25/2023] Open
Abstract
WD40 proteins belong to a big protein family with members identified in every eukaryotic proteome. However, WD40 proteins were only reported in a few prokaryotic proteomes. Using WDSP (http://wu.scbb.pkusz.edu.cn/wdsp/), a prediction tool, we identified thousands of prokaryotic WD40 proteins, among which few proteins have been biochemically characterized. As shown in our previous bioinformatics study, a large proportion of prokaryotic WD40 proteins have higher intramolecular sequence identity among repeats and more hydrogen networks, which may indicate better stability than eukaryotic WD40s. Here we report our biophysical and structural study on the WD40 domain of PkwA from Thermomonospora curvata (referred as tPkwA-C). We demonstrated that the stability of thermophilic tPkwA-C correlated to ionic strength and tPkwA-C exhibited fully reversible unfolding under different denaturing conditions. Therefore, the folding kinetics was also studied through stopped-flow circular dichroism spectra. The crystal structure of tPkwA-C was further resolved and shed light on the key factors that stabilize its beta-propeller structure. Like other WD40 proteins, DHSW tetrad has a significant impact on the stability of tPkwA-C. Considering its unique features, we proposed that tPkwA-C should be a great structural template for protein engineering to study key residues involved in protein-protein interaction of a WD40 protein.
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Affiliation(s)
- Chen Shen
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Ye Du
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.,Medical Research Center, The People's Hospital of Longhua, Shenzhen, 518109, China
| | - Fangfang Qiao
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Tian Kong
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Lirong Yuan
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Delin Zhang
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Xianhui Wu
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Dongyang Li
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China. .,SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Yun-Dong Wu
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China. .,College of Chemistry, Peking University, Beijing, 100871, China.
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Amick J, Tharkeshwar AK, Amaya C, Ferguson SM. WDR41 supports lysosomal response to changes in amino acid availability. Mol Biol Cell 2018; 29:2213-2227. [PMID: 29995611 PMCID: PMC6249801 DOI: 10.1091/mbc.e17-12-0703] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
C9orf72 mutations are a major cause of amyotrophic lateral sclerosis and frontotemporal dementia. The C9orf72 protein undergoes regulated recruitment to lysosomes and has been broadly implicated in control of lysosome homeostasis. However, although evidence strongly supports an important function for C9orf72 at lysosomes, little is known about the lysosome recruitment mechanism. In this study, we identify an essential role for WDR41, a prominent C9orf72 interacting protein, in C9orf72 lysosome recruitment. Analysis of human WDR41 knockout cells revealed that WDR41 is required for localization of the protein complex containing C9orf72 and SMCR8 to lysosomes. Such lysosome localization increases in response to amino acid starvation but is not dependent on either mTORC1 inhibition or autophagy induction. Furthermore, WDR41 itself exhibits a parallel pattern of regulated association with lysosomes. This WDR41-dependent recruitment of C9orf72 to lysosomes is critical for the ability of lysosomes to support mTORC1 signaling as constitutive targeting of C9orf72 to lysosomes relieves the requirement for WDR41 in mTORC1 activation. Collectively, this study reveals an essential role for WDR41 in supporting the regulated binding of C9orf72 to lysosomes and solidifies the requirement for a larger C9orf72 containing protein complex in coordinating lysosomal responses to changes in amino acid availability.
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Affiliation(s)
- Joseph Amick
- Department of Cell Biology and Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Arun Kumar Tharkeshwar
- Department of Cell Biology and Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Catherine Amaya
- Department of Cell Biology and Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Shawn M Ferguson
- Department of Cell Biology and Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
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38
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Zou XD, An K, Wu YD, Ye ZQ. PPI network analyses of human WD40 protein family systematically reveal their tendency to assemble complexes and facilitate the complex predictions. BMC SYSTEMS BIOLOGY 2018; 12:41. [PMID: 29745845 PMCID: PMC5998875 DOI: 10.1186/s12918-018-0567-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Background WD40 repeat proteins constitute one of the largest families in eukaryotes, and widely participate in various fundamental cellular processes by interacting with other molecules. Based on individual WD40 proteins, previous work has demonstrated that their structural characteristics should confer great potential of interaction and complex formation, and has speculated that they may serve as hubs in the protein-protein interaction (PPI) network. However, what roles the whole family plays in organizing the PPI network, and whether this information can be utilized in complex prediction remain unclear. To address these issues, quantitative and systematic analyses of WD40 proteins from the perspective of PPI networks are highly required. Results In this work, we built two human PPI networks by using data sets with different confidence levels, and studied the network properties of the whole human WD40 protein family systematically. Our analyses have quantitatively confirmed that the human WD40 protein family, as a whole, tends to be hubs with an odds ratio of about 1.8 or greater, and the network decomposition has revealed that they are prone to enrich near the global center of the whole network with a fold change of two in the median k-values. By integrating expression profiles, we have further shown that WD40 hub proteins are inclined to be intramodular, which is indicative of complex assembling. Based on this information, we have further predicted 1674 potential WD40-associated complexes by choosing a clique-based method, which is more sensitive than others, and an indirect evaluation by co-expression scores has demonstrated its reliability. Conclusions At the systems level but not sporadic examples’ level, this work has provided rich knowledge for better understanding WD40 proteins’ roles in organizing the PPI network. These findings and predicted complexes can offer valuable clues for prioritizing candidates for further studies. Electronic supplementary material The online version of this article (10.1186/s12918-018-0567-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xu-Dong Zou
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, People's Republic of China
| | - Ke An
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, People's Republic of China
| | - Yun-Dong Wu
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, People's Republic of China. .,College of Chemistry, Peking University, Beijing, 100871, People's Republic of China.
| | - Zhi-Qiang Ye
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, People's Republic of China.
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39
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Genome-Wide Identification and Characterization of WD40 Protein Genes in the Silkworm, Bombyx mori. Int J Mol Sci 2018; 19:ijms19020527. [PMID: 29425159 PMCID: PMC5855749 DOI: 10.3390/ijms19020527] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/27/2018] [Accepted: 02/06/2018] [Indexed: 12/18/2022] Open
Abstract
WD40 proteins are scaffolding molecules in protein-protein interactions and play crucial roles in fundamental biological processes. Genome-wide characterization of WD40 proteins in animals has been conducted solely in humans. We retrieved 172 WD40 protein genes in silkworm (BmWD40s) and identified these genes in 7 other insects, 9 vertebrates and 5 nematodes. Comparative analysis revealed that the WD40 protein gene family underwent lineage-specific expansions during animal evolution, but did not undergo significant expansion during insect evolution. The BmWD40s were categorized into five clusters and 12 classes according to the phylogenetic classification and their domain architectures, respectively. Sequence analyses indicated that tandem and segmental duplication played minor roles in producing the current number of BmWD40s, and domain recombination events of multi-domain BmWD40s might have occurred mainly after gene duplication events. Gene Ontology (GO) analysis revealed that a higher proportion of BmWD40s was involved in processes, such as binding, transcription-regulation and cellular component biogenesis, compared to all silkworm genes annotated in GO. Microarray-based analysis demonstrated that many BmWD40s had tissue-specific expression and exhibited high and/or sex-related expression during metamorphosis. These findings contribute to a better understanding of the evolution of the animal WD40 protein family and assist the study of the functions of BmWD40s.
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40
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Hofmeister W, Pettersson M, Kurtoglu D, Armenio M, Eisfeldt J, Papadogiannakis N, Gustavsson P, Lindstrand A. Targeted copy number screening highlights an intragenic deletion of WDR63 as the likely cause of human occipital encephalocele and abnormal CNS development in zebrafish. Hum Mutat 2018; 39:495-505. [PMID: 29285825 DOI: 10.1002/humu.23388] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/21/2017] [Accepted: 12/15/2017] [Indexed: 02/04/2023]
Abstract
Congenital malformations affecting the neural tube can present as isolated malformations or occur in association with other developmental abnormalities and syndromes. Using high-resolution copy number screening in 66 fetuses with neural tube defects, we identified six fetuses with likely pathogenic mutations, three aneuploidies (one trisomy 13 and two trisomy 18) and three deletions previously reported in NTDs (one 22q11.2 deletion and two 1p36 deletions) corresponding to 9% of the cohort. In addition, we identified five rare deletions and two duplications of uncertain significance including a rare intragenic heterozygous in-frame WDR63 deletion in a fetus with occipital encephalocele. Whole genome sequencing verified the deletion and excluded known pathogenic variants. The deletion spans exons 14-17 resulting in the expression of a protein missing the third and fourth WD-repeat domains. These findings were supported by CRISPR/Cas9-mediated somatic deletions in zebrafish. Injection of two different sgRNA-pairs targeting relevant intronic regions resulted in a deletion mimicking the human deletion and a concomitant increase of abnormal embryos with body and brain malformations (41%, n = 161 and 62%, n = 224, respectively), including a sac-like brain protrusion (7% and 9%, P < 0.01). Similar results were seen with overexpression of RNA encoding the deleted variant in zebrafish (total abnormal; 46%, n = 255, P < 0.001) compared with the overexpression of an equivalent amount of wild-type RNA (total abnormal; 3%, n = 177). We predict the in-frame WDR63 deletion to result in a dominant negative or gain-of-function form of WDR63. These are the first findings supporting a role for WDR63 in encephalocele formation.
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Affiliation(s)
- Wolfgang Hofmeister
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Deniz Kurtoglu
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Miriam Armenio
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Nikos Papadogiannakis
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Huddinge, Sweden
| | - Peter Gustavsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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41
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Tevatia R, Oyler GA. Evolution of DDB1-binding WD40 (DWD) in the viridiplantae. PLoS One 2018; 13:e0190282. [PMID: 29293590 PMCID: PMC5749748 DOI: 10.1371/journal.pone.0190282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/11/2017] [Indexed: 12/16/2022] Open
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 phylogenetic 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.
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Affiliation(s)
- Rahul Tevatia
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (RT); (GAO)
| | - George A. Oyler
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Synaptic Research LLC, Baltimore, Maryland, United States of America
- * E-mail: (RT); (GAO)
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42
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Karimi E, Ramos M, Gonçalves JMS, Xavier JR, Reis MP, Costa R. Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium. Front Microbiol 2017; 8:2499. [PMID: 29312205 PMCID: PMC5735121 DOI: 10.3389/fmicb.2017.02499] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/30/2017] [Indexed: 12/14/2022] Open
Abstract
Current knowledge of sponge microbiome functioning derives mostly from comparative analyses with bacterioplankton communities. We employed a metagenomics-centered approach to unveil the distinct features of the Spongia officinalis endosymbiotic consortium in the context of its two primary environmental vicinities. Microbial metagenomic DNA samples (n = 10) from sponges, seawater, and sediments were subjected to Hiseq Illumina sequencing (c. 15 million 100 bp reads per sample). Totals of 10,272 InterPro (IPR) predicted protein entries and 784 rRNA gene operational taxonomic units (OTUs, 97% cut-off) were uncovered from all metagenomes. Despite the large divergence in microbial community assembly between the surveyed biotopes, the S. officinalis symbiotic community shared slightly greater similarity (p < 0.05), in terms of both taxonomy and function, to sediment than to seawater communities. The vast majority of the dominant S. officinalis symbionts (i.e., OTUs), representing several, so-far uncultivable lineages in diverse bacterial phyla, displayed higher residual abundances in sediments than in seawater. CRISPR-Cas proteins and restriction endonucleases presented much higher frequencies (accompanied by lower viral abundances) in sponges than in the environment. However, several genomic features sharply enriched in the sponge specimens, including eukaryotic-like repeat motifs (ankyrins, tetratricopeptides, WD-40, and leucine-rich repeats), and genes encoding for plasmids, sulfatases, polyketide synthases, type IV secretion proteins, and terpene/terpenoid synthases presented, to varying degrees, higher frequencies in sediments than in seawater. In contrast, much higher abundances of motility and chemotaxis genes were found in sediments and seawater than in sponges. Higher cell and surface densities, sponge cell shedding and particle uptake, and putative chemical signaling processes favoring symbiont persistence in particulate matrices all may act as mechanisms underlying the observed degrees of taxonomic connectivity and functional convergence between sponges and sediments. The reduced frequency of motility and chemotaxis genes in the sponge microbiome reinforces the notion of a prevalent mutualistic mode of living inside the host. This study highlights the S. officinalis “endosymbiome” as a distinct consortium of uncultured prokaryotes displaying a likely “sit-and-wait” strategy to nutrient foraging coupled to sophisticated anti-viral defenses, unique natural product biosynthesis, nutrient utilization and detoxification capacities, and both microbe–microbe and host–microbe gene transfer amenability.
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Affiliation(s)
- Elham Karimi
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Miguel Ramos
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Jorge M S Gonçalves
- Fisheries, Biodiversity and Conservation Research Group, Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Joana R Xavier
- Department of Biology and K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Margarida P Reis
- Faculty of Science and Technology, University of Algarve, Faro, Portugal
| | - Rodrigo Costa
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, University of Algarve, Faro, Portugal.,Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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43
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Schapira M, Tyers M, Torrent M, Arrowsmith CH. WD40 repeat domain proteins: a novel target class? Nat Rev Drug Discov 2017; 16:773-786. [PMID: 29026209 PMCID: PMC5975957 DOI: 10.1038/nrd.2017.179] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antagonism of protein-protein interactions (PPIs) with small molecules is becoming more feasible as a therapeutic approach. Successful PPI inhibitors tend to target proteins containing deep peptide-binding grooves or pockets rather than the more common large, flat protein interaction surfaces. Here, we review one of the most abundant PPI domains in the human proteome, the WD40 repeat (WDR) domain, which has a central peptide-binding pocket and is a member of the β-propeller domain-containing protein family. Recently, two WDR domain-containing proteins, WDR5 and EED, as well as other β-propeller domains have been successfully targeted by potent, specific, cell-active, drug-like chemical probes. Could WDR domains be a novel target class for drug discovery? Although the research is at an early stage and therefore not clinically validated, cautious optimism is justified, as WDR domain-containing proteins are involved in multiple disease-associated pathways. The druggability and structural diversity of WDR domain binding pockets suggest that understanding how to target this prevalent domain class will open up areas of disease biology that have so far resisted drug discovery efforts.
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Affiliation(s)
- Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Mount Sinai Hospital, The Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
| | - Maricel Torrent
- Discovery Research, AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, 101 College St., Toronto, ON M5G 1L7, Canada
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44
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Sapam TD, Velmurugan Ilavarasi A, Palaka BK, Elumalai E, Kanika ND, Ampasala DR. Identifying novel small molecule antagonists for mLST8 protein using computational approaches. J Recept Signal Transduct Res 2017; 38:1-11. [PMID: 29041842 DOI: 10.1080/10799893.2017.1387920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Mammalian lethal with SEC13 protein 8 (mLST8), is an indispensable protein subunit of mammalian target of rapamycin (mTOR) signaling pathway that interacts with the kinase domain of mTOR protein, thereby stabilizing its active site. Experimental studies reported the over expression of mLST8 in human colon and prostate cancers by activation of both mTORC1/2 complexes and subsequent downstream substrates leading to tumor progression. Considering its role, targeting mLST8 protein would be a therapeutic approach against tumor progression in colon and prostate cancers. Hence, using in silico structure based drug design approach, the comparative binding patterns of 1,1'-binapthyl-2,2'diol (BINOL), 1-(2-carboxynaphth-1yl)-2-naphthoic acid (SCF-12) and their analogs in the cavity of mLST8 were explored. ADME and binding energy calculations led to the identification of five compounds with favorable Glide (G) scores and implicated the importance of Asn132 and Gln225 as key binding residues. Molecular dynamics (MD) simulations and free energy landscape (FEL) approaches helped in elucidating the binding mechanism and suggested the possibility of ligands 1-3 namely, ZINC01765622, ZINC62723702 and ZINC02576980 to be promising antagonists for mLST8. Thus, this study substantiates the prospect of targeting mLST8 protein using potent hits which could hinder tumor progression in colon and prostate cancers.
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Affiliation(s)
- Tuleshwori Devi Sapam
- a Centre for Bioinformatics, School of Life Sciences , Pondicherry University , Puducherry , India
| | | | - Bhagath Kumar Palaka
- a Centre for Bioinformatics, School of Life Sciences , Pondicherry University , Puducherry , India
| | - Elakkiya Elumalai
- a Centre for Bioinformatics, School of Life Sciences , Pondicherry University , Puducherry , India
| | | | - Dinakara Rao Ampasala
- a Centre for Bioinformatics, School of Life Sciences , Pondicherry University , Puducherry , India
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45
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Song R, Wang ZD, Schapira M. Disease Association and Druggability of WD40 Repeat Proteins. J Proteome Res 2017; 16:3766-3773. [DOI: 10.1021/acs.jproteome.7b00451] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Richard Song
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Zhong-Duo Wang
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Matthieu Schapira
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department
of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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46
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Feeney L, Muñoz IM, Lachaud C, Toth R, Appleton PL, Schindler D, Rouse J. RPA-Mediated Recruitment of the E3 Ligase RFWD3 Is Vital for Interstrand Crosslink Repair and Human Health. Mol Cell 2017; 66:610-621.e4. [PMID: 28575657 PMCID: PMC5459755 DOI: 10.1016/j.molcel.2017.04.021] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 01/25/2017] [Accepted: 04/04/2017] [Indexed: 02/07/2023]
Abstract
Defects in the repair of DNA interstrand crosslinks (ICLs) are associated with the genome instability syndrome Fanconi anemia (FA). Here we report that cells with mutations in RFWD3, an E3 ubiquitin ligase that interacts with and ubiquitylates replication protein A (RPA), show profound defects in ICL repair. An amino acid substitution in the WD40 repeats of RFWD3 (I639K) found in a new FA subtype abolishes interaction of RFWD3 with RPA, thereby preventing RFWD3 recruitment to sites of ICL-induced replication fork stalling. Moreover, single point mutations in the RPA32 subunit of RPA that abolish interaction with RFWD3 also inhibit ICL repair, demonstrating that RPA-mediated RFWD3 recruitment to stalled replication forks is important for ICL repair. We also report that unloading of RPA from sites of ICL induction is perturbed in RFWD3-deficient cells. These data reveal important roles for RFWD3 localization in protecting genome stability and preserving human health. RFWD3-deficient human cells show profound defects in ICL repair RFWD3 regulates RPA dynamics to promote homologous recombination The FA-associated I639K mutation prevents RPA-dependent recruitment of RFWD3 to ICLs RPA32 mutations that abolish interaction with RFWD3 also inhibit ICL repair
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Affiliation(s)
- Laura Feeney
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, Sir James Black Centre, University of Dundee, Dundee DD1 5EH, Scotland
| | - Ivan M Muñoz
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, Sir James Black Centre, University of Dundee, Dundee DD1 5EH, Scotland
| | - Christophe Lachaud
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, Sir James Black Centre, University of Dundee, Dundee DD1 5EH, Scotland
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, Sir James Black Centre, University of Dundee, Dundee DD1 5EH, Scotland
| | - Paul L Appleton
- Dundee Imaging Facility, School of Life Sciences, Sir James Black Centre, University of Dundee, Dundee DD1 5EH, Scotland
| | - Detlev Schindler
- Department of Human Genetics, University of Würzburg Biozentrum, 97074 Würzburg, Germany
| | - John Rouse
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, Sir James Black Centre, University of Dundee, Dundee DD1 5EH, Scotland.
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47
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Hu XJ, Li T, Wang Y, Xiong Y, Wu XH, Zhang DL, Ye ZQ, Wu YD. Prokaryotic and Highly-Repetitive WD40 Proteins: A Systematic Study. Sci Rep 2017; 7:10585. [PMID: 28878378 PMCID: PMC5587647 DOI: 10.1038/s41598-017-11115-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 08/18/2017] [Indexed: 12/22/2022] Open
Abstract
As an ancient protein family, the WD40 repeat proteins often play essential roles in fundamental cellular processes in eukaryotes. Although investigations of eukaryotic WD40 proteins have been frequently reported, prokaryotic ones remain largely uncharacterized. In this paper, we report a systematic analysis of prokaryotic WD40 proteins and detailed comparisons with eukaryotic ones. About 4,000 prokaryotic WD40 proteins have been identified, accounting for 6.5% of all WD40s. While their abundances are less than 0.1% in most prokaryotes, they are enriched in certain species from Cyanobacteria and Planctomycetes, and participate in various functions such as prokaryotic signal transduction and nutrient synthesis. Comparisons show that a higher proportion of prokaryotic WD40s tend to contain multiple WD40 domains and a large number of hydrogen bond networks. The observation that prokaryotic WD40 proteins tend to show high internal sequence identity suggests that a substantial proportion of them (~20%) should be formed by recent or young repeat duplication events. Further studies demonstrate that the very young WD40 proteins, i.e., Highly-Repetitive WD40s, should be of higher stability. Our results have presented a catalogue of prokaryotic WD40 proteins, and have shed light on their evolutionary origins.
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Affiliation(s)
- Xue-Jia Hu
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Tuan Li
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Yang Wang
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Yao Xiong
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Xian-Hui Wu
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - De-Lin Zhang
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Zhi-Qiang Ye
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China.
| | - Yun-Dong Wu
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China.
- College of Chemistry, Peking University, Beijing, 100871, P.R. China.
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48
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The mutational landscape of ocular marginal zone lymphoma identifies frequent alterations in TNFAIP3 followed by mutations in TBL1XR1 and CREBBP. Oncotarget 2017; 8:17038-17049. [PMID: 28152507 PMCID: PMC5370020 DOI: 10.18632/oncotarget.14928] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/30/2016] [Indexed: 12/12/2022] Open
Abstract
Ocular marginal zone lymphoma is a common type of low-grade B-cell lymphoma. To investigate the genomic changes that occur in ocular marginal zone lymphoma, we analyzed 10 cases of ocular marginal zone lymphoma using whole-genome and RNA sequencing and an additional 38 cases using targeted sequencing. Major genetic alterations affecting genes involved in nuclear factor (NF)-κB pathway activation (60%), chromatin modification and transcriptional regulation (44%), and B-cell differentiation (23%) were identified. In whole-genome sequencing, the 6q23.3 region containing TNFAIP3 was deleted in 5 samples (50%). In addition, 5 structural variation breakpoints in the first intron of IL20RA located in the 6q23.3 region was found in 3 samples (30%). In targeted sequencing, a disruptive mutation of TNFAIP3 was the most common alteration (54%), followed by mutations of TBL1XR1 (18%), cAMP response element binding proteins (CREBBP) (17%) and KMT2D (6%). All TBL1XR1 mutations were located within the WD40 domain, and TBL1XR1 mutants transfected into 293T cells increased TBL1XR1 binding with nuclear receptor corepressor (NCoR), leading to increased degradation of NCoR and the activation of NF-κB and JUN target genes. This study confirms genes involving in the activation of the NF-kB signaling pathway is the major driver in the oncogenesis of ocular MZL.
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49
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Nguyen TMT, Hull S, Roepman R, van den Born LI, Oud MM, de Vrieze E, Hetterschijt L, Letteboer SJF, van Beersum SEC, Blokland EA, Yntema HG, Cremers FPM, van der Zwaag PA, Arno G, van Wijk E, Webster AR, Haer-Wigman L. Missense mutations in the WD40 domain of AHI1 cause non-syndromic retinitis pigmentosa. J Med Genet 2017; 54:624-632. [PMID: 28442542 PMCID: PMC5574394 DOI: 10.1136/jmedgenet-2016-104200] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 02/02/2017] [Accepted: 02/27/2017] [Indexed: 12/31/2022]
Abstract
Background Recent findings suggesting that Abelson helper integration site 1 (AHI1) is involved in non-syndromic retinal disease have been debated, as the functional significance of identified missense variants was uncertain. We assessed whether AHI1 variants cause non-syndromic retinitis pigmentosa (RP). Methods Exome sequencing was performed in three probands with RP. The effects of the identified missense variants in AHI1 were predicted by three-dimensional structure homology modelling. Ciliary parameters were evaluated in patient’s fibroblasts, and recombinant mutant proteins were expressed in ciliated retinal pigmented epithelium cells. Results In the three patients with RP, three sets of compound heterozygous variants were detected in AHI1 (c.2174G>A; p.Trp725* and c.2258A>T; p.Asp753Val, c.660delC; p.Ser221Glnfs*10 and c.2090C>T; p.Pro697Leu, c.2087A>G; p.His696Arg and c.2429C>T; p.Pro810Leu). All four missense variants were present in the conserved WD40 domain of Jouberin, the ciliary protein encoded by AHI1, with variable predicted implications for the domain structure. No significant changes in the percentage of ciliated cells, nor in cilium length or intraflagellar transport were detected. However, expression of mutant recombinant Jouberin in ciliated cells showed a significantly decreased enrichment at the ciliary base. Conclusions This report confirms that mutations in AHI1 can underlie autosomal recessive RP. Moreover, it structurally and functionally validates the effect of the RP-associated AHI1 variants on protein function, thus proposing a new genotype–phenotype correlation for AHI1 mutation associated retinal ciliopathies.
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Affiliation(s)
- Thanh-Minh T Nguyen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sarah Hull
- UniversityCollege London, Instituteof Ophthalmology, London, United Kingdom.,Moorfields Eye Hospital, London, United Kingdom
| | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Machteld M Oud
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Erik de Vrieze
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Lisette Hetterschijt
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Stef J F Letteboer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sylvia E C van Beersum
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ellen A Blokland
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Paul A van der Zwaag
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gavin Arno
- UniversityCollege London, Instituteof Ophthalmology, London, United Kingdom.,Moorfields Eye Hospital, London, United Kingdom
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Andrew R Webster
- UniversityCollege London, Instituteof Ophthalmology, London, United Kingdom.,Moorfields Eye Hospital, London, United Kingdom
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
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50
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Planar Cell Polarity Effector Fritz Interacts with Dishevelled and Has Multiple Functions in Regulating PCP. G3-GENES GENOMES GENETICS 2017; 7:1323-1337. [PMID: 28258110 PMCID: PMC5386880 DOI: 10.1534/g3.116.038695] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Planar cell Polarity Effector (PPE) genes inturned, fuzzy, and fritz are downstream components in the frizzled/starry night signaling pathway, and their function is instructed by upstream Planar Cell Polarity (PCP) core genes such as frizzled and dishevelled. PPE proteins accumulate asymmetrically in wing cells and function in a protein complex mediated by direct interactions between In and Frtz and In and Fy. How the PCP proteins instruct the accumulation of PPE protein is unknown. We found a likely direct interaction between Dishevelled and Fritz and Dishevelled and Fuzzy that could play a role in this. We previously found that mild overexpression of frtz rescued a weak in allele. To determine if this was due to extra Frtz stabilizing mutant In or due to Frtz being able to bypass the need for In we generate a precise deletion of the inturned gene (inPD). We found that mild overexpression of Fritz partially rescued inPD, indicating that fritz has In independent activity in PCP. Previous studies of PPE proteins used fixed tissues, and did not provide any insights into the dynamic properties of PPE proteins. We used CRISPR/Cas9 genome editing technology to edit the fritz gene to add a green fluorescent protein tag. fritzmNeonGreen provides complete rescue activity and works well for in vivo imaging. Our data showed that Fritz is very dynamic in epidermal cells and preferentially distributed to discrete membrane subdomains (“puncta”). Surprisingly, we found it in stripes in developing bristles.
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