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Ibars E, Codina-Fabra J, Bellí G, Casas C, Tarrés M, Solé-Soler R, Lorite NP, Ximénez-Embún P, Muñoz J, Colomina N, Torres-Rosell J. Ubiquitin proteomics identifies RNA polymerase I as a target of the Smc5/6 complex. Cell Rep 2023; 42:112463. [PMID: 37141096 DOI: 10.1016/j.celrep.2023.112463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 12/29/2022] [Accepted: 04/18/2023] [Indexed: 05/05/2023] Open
Abstract
Ubiquitination controls numerous cellular processes, and its deregulation is associated with many pathologies. The Nse1 subunit in the Smc5/6 complex contains a RING domain with ubiquitin E3 ligase activity and essential functions in genome integrity. However, Nse1-dependent ubiquitin targets remain elusive. Here, we use label-free quantitative proteomics to analyze the nuclear ubiquitinome of nse1-C274A RING mutant cells. Our results show that Nse1 impacts the ubiquitination of several proteins involved in ribosome biogenesis and metabolism that, importantly, extend beyond canonical functions of Smc5/6. In addition, our analysis suggests a connection between Nse1 and RNA polymerase I (RNA Pol I) ubiquitination. Specifically, Nse1 and the Smc5/6 complex promote ubiquitination of K408 and K410 in the clamp domain of Rpa190, a modification that induces its degradation in response to blocks in transcriptional elongation. We propose that this mechanism contributes to Smc5/6-dependent segregation of the rDNA array, the locus transcribed by RNA Pol I.
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Affiliation(s)
- Eva Ibars
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Joan Codina-Fabra
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Gemma Bellí
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Celia Casas
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Marc Tarrés
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Roger Solé-Soler
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Neus P Lorite
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Pilar Ximénez-Embún
- Proteomics Unit, Spanish National Cancer Research Center (CNIO), Madrid, Spain; ProteoRed-ISCIII, Madrid, Spain
| | - Javier Muñoz
- Proteomics Unit, Spanish National Cancer Research Center (CNIO), Madrid, Spain; ProteoRed-ISCIII, Madrid, Spain
| | - Neus Colomina
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Jordi Torres-Rosell
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain.
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Disruption of male fertility-critical Dcaf17 dysregulates mouse testis transcriptome. Sci Rep 2022; 12:21456. [PMID: 36509865 PMCID: PMC9744869 DOI: 10.1038/s41598-022-25826-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
During mammalian spermatogenesis, the ubiquitin proteasome system maintains protein homoeostasis (proteastasis) and spermatogenic cellular functions. DCAF17 is a substrate receptor in the ubiquitin CRL4 E3 Ligase complex, absence of which causes oligoasthenoteratozoospermia in mice resulting in male infertility. To determine the molecular phenomenon underlying the infertility phenotype caused by disrupting Dcaf17, we performed RNA-sequencing-based gene expression profiling of 3-weeks and 8-weeks old Dcaf17 wild type and Dcaf17 disrupted mutant mice testes. At three weeks, 44% and 56% differentially expressed genes (DEGs) were up- and down-regulated, respectively, with 32% and 68% DEGs were up- and down-regulated, respectively at 8 weeks. DEGs include protein coding genes and lncRNAs distributed across all autosomes and the X chromosome. Gene ontology analysis revealed major biological processes including proteolysis, regulation of transcription and chromatin remodelling are affected due to Dcaf17 disruption. We found that Dcaf17 disruption up-regulated several somatic genes, while germline-associated genes were down-regulated. Up to 10% of upregulated, and 12% of downregulated, genes were implicated in male reproductive phenotypes. Moreover, a large proportion of the up-regulated genes were highly expressed in spermatogonia and spermatocytes, while the majority of downregulated genes were predominantly expressed in round spermatids. Collectively, these data show that the Dcaf17 disruption affects directly or indirectly testicular proteastasis and transcriptional signature in mouse.
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Bouron A, Fauvarque MO. Genome-wide analysis of genes encoding core components of the ubiquitin system during cerebral cortex development. Mol Brain 2022; 15:72. [PMID: 35974412 PMCID: PMC9380329 DOI: 10.1186/s13041-022-00958-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/02/2022] [Indexed: 11/21/2022] Open
Abstract
Ubiquitination involves three types of enzymes (E1, E2, and E3) that sequentially attach ubiquitin (Ub) to target proteins. This posttranslational modification controls key cellular processes, such as the degradation, endocytosis, subcellular localization and activity of proteins. Ubiquitination, which can be reversed by deubiquitinating enzymes (DUBs), plays important roles during brain development. Furthermore, deregulation of the Ub system is linked to the pathogenesis of various diseases, including neurodegenerative disorders. We used a publicly available RNA-seq database to perform an extensive genome-wide gene expression analysis of the core components of the ubiquitination machinery, covering Ub genes as well as E1, E2, E3 and DUB genes. The ubiquitination network was governed by only Uba1 and Ube2m, the predominant E1 and E2 genes, respectively; their expression was positively regulated during cortical formation. The principal genes encoding HECT (homologous to the E6-AP carboxyl terminus), RBR (RING-in-between-RING), and RING (really interesting new gene) E3 Ub ligases were also highly regulated. Pja1, Dtx3 (RING ligases) and Stub1 (U-box RING) were the most highly expressed E3 Ub ligase genes and displayed distinct developmental expression patterns. Moreover, more than 80 DUB genes were expressed during corticogenesis, with two prominent genes, Uch-l1 and Usp22, showing highly upregulated expression. Several components of the Ub system overexpressed in cancers were also highly expressed in the cerebral cortex under conditions not related to tumour formation or progression. Altogether, this work provides an in-depth overview of transcriptomic changes during embryonic formation of the cerebral cortex. The data also offer new insight into the characterization of the Ub system and may contribute to a better understanding of its involvement in the pathogenesis of neurodevelopmental disorders.
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Affiliation(s)
- Alexandre Bouron
- Université Grenoble Alpes, Inserm, CEA, UMR 1292, 38000, Grenoble, France. .,Genetics and Chemogenomics Lab, Building C3, CEA, 17 rue des Martyrs, 38054, Grenoble Cedex 9, France.
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Nozawa K, Fujihara Y, Devlin DJ, Deras RE, Kent K, Larina IV, Umezu K, Yu Z, Sutton CM, Ye Q, Dean LK, Emori C, Ikawa M, Garcia TX, Matzuk MM. The testis-specific E3 ubiquitin ligase RNF133 is required for fecundity in mice. BMC Biol 2022; 20:161. [PMID: 35831855 PMCID: PMC9277888 DOI: 10.1186/s12915-022-01368-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 07/05/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Ubiquitination is a post-translational modification required for a number of physiological functions regulating protein homeostasis, such as protein degradation. The endoplasmic reticulum (ER) quality control system recognizes and degrades proteins no longer needed in the ER through the ubiquitin-proteasome pathway. E2 and E3 enzymes containing a transmembrane domain have been shown to function in ER quality control. The ER transmembrane protein UBE2J1 is a E2 ubiquitin-conjugating enzyme reported to be essential for spermiogenesis at the elongating spermatid stage. Spermatids from Ube2j1 KO male mice are believed to have defects in the dislocation step of ER quality control. However, associated E3 ubiquitin-protein ligases that function during spermatogenesis remain unknown. RESULTS We identified four evolutionarily conserved testis-specific E3 ubiquitin-protein ligases [RING finger protein 133 (Rnf133); RING finger protein 148 (Rnf148); RING finger protein 151 (Rnf151); and Zinc finger SWIM-type containing 2 (Zswim2)]. Using the CRISPR/Cas9 system, we generated and analyzed the fertility of mutant mice with null alleles for each of these E3-encoding genes, as well as double and triple knockout (KO) mice. Male fertility, male reproductive organ, and sperm-associated parameters were analyzed in detail. Fecundity remained largely unaffected in Rnf148, Rnf151, and Zswim2 KO males; however, Rnf133 KO males displayed severe subfertility. Additionally, Rnf133 KO sperm exhibited abnormal morphology and reduced motility. Ultrastructural analysis demonstrated that cytoplasmic droplets were retained in Rnf133 KO spermatozoa. Although Rnf133 and Rnf148 encode paralogous genes that are chromosomally linked and encode putative ER transmembrane E3 ubiquitin-protein ligases based on their protein structures, there was limited functional redundancy of these proteins. In addition, we identified UBE2J1 as an E2 ubiquitin-conjugating protein that interacts with RNF133. CONCLUSIONS Our studies reveal that RNF133 is a testis-expressed E3 ubiquitin-protein ligase that plays a critical role for sperm function during spermiogenesis. Based on the presence of a transmembrane domain in RNF133 and its interaction with the ER containing E2 protein UBE2J1, we hypothesize that these ubiquitin-regulatory proteins function together in ER quality control during spermatogenesis.
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Affiliation(s)
- Kaori Nozawa
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yoshitaka Fujihara
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Suita, Osaka, 564-8565, Japan
| | - Darius J Devlin
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ricardo E Deras
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Katarzyna Kent
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Irina V Larina
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kohei Umezu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhifeng Yu
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Courtney M Sutton
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Qiuji Ye
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Laura K Dean
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chihiro Emori
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Thomas X Garcia
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Martin M Matzuk
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA.
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Abstract
AbstractThe druggable genome is limited by structural features that can be targeted by small molecules in disease-relevant proteins. While orthosteric and allosteric protein modulators have been well studied, they are limited to antagonistic/agonistic functions. This approach to protein modulation leaves many disease-relevant proteins as undruggable targets. Recently, protein-protein interaction modulation has emerged as a promising therapeutic field for previously undruggable protein targets. Molecular glues and heterobifunctional degraders such as PROTACs can facilitate protein interactions and bring the proteasome into proximity to induce targeted protein degradation. In this review, we discuss the function and rational design of molecular glues, heterobifunctional degraders, and hydrophobic tag degraders. We also review historic and novel molecular glues and targets and discuss the challenges and opportunities in this new therapeutic field.
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Li T, Zheng C, Han WJ, Chen ZZ. Regulation of STUB1 expression and its biological significance in mouse Sertoli cells. Syst Biol Reprod Med 2022; 68:298-313. [PMID: 35343345 DOI: 10.1080/19396368.2022.2027554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
STIP1 Homology and U-Box Containing Protein 1 (STUB1), a ubiquitin E3 ligase initially involved in immune responses, has recently emerged as a pleiotropic regulator of different biological systems, including skeletal and male reproduction systems. On the latter, a homozygous mutation in the STUB1 gene has been identified in patients with hypogonadism. However, the pattern of expression and biological actions of STUB1 in testis remains so far unexplored. Herein, we report analyses on the testicular expression of STUB1 in human testes with impaired spermatogenesis and paracrine regulation of STUB1 expression in mouse testis development and the direct effects of ablation STUB1 on Sertoli cell (SC) functions. STUB1 was expressed abundantly in pachytene spermatocytes and SCs, and weakly in spermatogonia and differentiating spermatids in normal human testis. In contrast, Sertoli-specific expression of STUB1 was significantly decreased in the human testes with impaired spermatogenesis. Throughout postnatal development of mouse testis, however, STUB1 was expressed exclusively in the nuclei of the functionally mature SCs. The adjacent germ cell (GC)-derived IL-1α overtly regulated STUB1 expression through promoting the ETS domain transcription factor Elk-1 (ELK1)-mediated transactivation. Importantly, ablation of endogenous STUB1 caused lipid accumulation and senescence in GC co-incubated SCs. Together with previous reports on the stimulatory effects of IL-1α on cell senescence, our findings suggest that STUB1 may serve as an important negative feedback signaling to modulate the magnitude of GCs-derived IL-1α, which is normally maintained at low levels within testis.
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Affiliation(s)
- Tao Li
- Reproductive Center, Baoji Maternal and Child Health Hospital, Baoji, P. R. China
| | - Chao Zheng
- Department of Urology, Baoji Traditional Chinese Medicine Hospital, Baoji, P. R. China
| | - Wei-Jun Han
- Department of Urology, Baoji Traditional Chinese Medicine Hospital, Baoji, P. R. China
| | - Zhen-Zhen Chen
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, P. R. China.,Department of Human Anatomy, Histology and Embryology, Air Force Military Medical University, Xi'an, P. R. China
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Lv C, Xiong M, Guo S, Gui Y, Liu X, Wang X, Wu Y, Feng S, Zhang J, Zhang Y, Liu Y, Qin W, Yuan S. WDFY1, a WD40 repeat protein, is not essential for spermatogenesis and male fertility in mice. Biochem Biophys Res Commun 2022; 596:71-75. [PMID: 35121371 DOI: 10.1016/j.bbrc.2022.01.084] [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: 01/13/2022] [Accepted: 01/23/2022] [Indexed: 11/23/2022]
Abstract
The mouse WD repeat and FYVE domain containing 1 (Wdfy1) gene is located in chromosome 1qC4 and spans over 73.7 kilobases. It encodes a protein of 410-amino acid protein that shares 97.8% amino acid sequence identity with the human WDFY1 protein. However, the expression pattern of WDFY1 in reproductive organs and its function in male fertility remain unknown. In this study, we generated transgenic mice expressing FLAG-Wdfy1-mCherry cDNA driven by the Wdfy1 promoter to clarify the expression of WDFY1. The results showed that WDFY1 is highly expressed in mouse testes and located in the cytoplasm of late pachytene spermatocytes to elongated spermatids. Interestingly, the global Wdfy1 knockout (KO) male mice displayed normal growth, development, and fertility. Further histological analysis of Wdfy1 knockout mouse testes revealed that all spermatogenic cells are present in Wdfy1 KO seminiferous tubules. Together, our data demonstrate that WDFY1 is dispensable for mouse spermatogenesis and male fertility.
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Affiliation(s)
- Chunyu Lv
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
| | - Mengneng Xiong
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Shuangshuang Guo
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yiqian Gui
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaohua Liu
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, 510600, China
| | - Xiaoli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yanqing Wu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Shenglei Feng
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jin Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yan Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yu Liu
- State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Weibing Qin
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, 510600, China.
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong, 518057, China.
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Shen C, Xu J, Zhou Q, Lin M, Lv J, Zhang X, Wu Y, Chen X, Yu J, Huang X, Zheng B. E3 ubiquitin ligase ASB17 is required for spermiation in mice. Transl Androl Urol 2022; 10:4320-4332. [PMID: 35070814 PMCID: PMC8749070 DOI: 10.21037/tau-21-789] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/06/2021] [Indexed: 12/11/2022] Open
Abstract
Background A major goal of spermiation is to degrade the apical ectoplasmic specialization (ES) junction between Sertoli cells and elongating spermatids in preparation for the eventual disengagement of spermatids into the lumen. E3 ubiquitin ligases mediate the process of ubiquitination and the subsequent proteasomal degradation, but their specific role during spermiation remains largely unexplored. Methods Ankyrin repeat and SOCS box protein 17 (Asb17)-knockout mice were generated via a CRISPR/Cas9 approach. Epididymal sperm parameters were assessed by a computer-assisted sperm analysis (CASA) system, and morphological analysis of testicular tissues were performed based on histological and immunostaining staining, and transmission electron microscopy (TEM). The interactions between ASB17 and Espin (ESPN) were predicted by HawkDock server and validated through protein pull-down and immunoprecipitation assays. Results We report that ASB17, an E3 ligase, is required for the completion of spermiation and that mice lacking Asb17 are oligozoospermic owing to spermiation failure. ASB17-deficient mice are fertile; however, spermatids exhibit a disorganized ES junction, resulting in retention within the seminiferous epithelium. Mechanistically, ASB17 deficiency leads to excess accumulation of ESPN, an actin-binding essential structural component of the ES. We determined that ASB17 regulates the removal of the ES through ubiquitin mediated protein degradation of ESPN. Conclusions In summary, our study describes a role for ASB17 in the regulation of cell-cell junctions between germ cells and somatic cells in the testis. These findings establish a novel mechanism for the regulatory role of E3 ligases during spermatogenesis.
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Affiliation(s)
- Cong Shen
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, China
| | - Jinfu Xu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Qiao Zhou
- Department of Reproduction, The affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University; Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Meng Lin
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Jinxing Lv
- Suzhou Dushu Lake Hospital (Dushu Lake Hospital Affiliated to Soochow University), Suzhou, China
| | - Xi Zhang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Yangyang Wu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Xia Chen
- Department of Obstetrics and Gynecology, Affiliated Hospital 2 of Nantong University and First People's Hospital of Nantong City, Nantong, China
| | - Jun Yu
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, China
| | - Xiaoyan Huang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Bo Zheng
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, China
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9
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Kolesar P, Stejskal K, Potesil D, Murray JM, Palecek JJ. Role of Nse1 Subunit of SMC5/6 Complex as a Ubiquitin Ligase. Cells 2022; 11:165. [PMID: 35011726 PMCID: PMC8750328 DOI: 10.3390/cells11010165] [Citation(s) in RCA: 4] [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: 11/08/2021] [Revised: 12/15/2021] [Accepted: 01/01/2022] [Indexed: 11/16/2022] Open
Abstract
Structural Maintenance of Chromosomes (SMC) complexes are important for many aspects of the chromosomal organization. Unlike cohesin and condensin, the SMC5/6 complex contains a variant RING domain carried by its Nse1 subunit. RING domains are characteristic for ubiquitin ligases, and human NSE1 has been shown to possess ubiquitin-ligase activity in vitro. However, other studies were unable to show such activity. Here, we confirm Nse1 ubiquitin-ligase activity using purified Schizosaccharomyces pombe proteins. We demonstrate that the Nse1 ligase activity is stimulated by Nse3 and Nse4. We show that Nse1 specifically utilizes Ubc13/Mms2 E2 enzyme and interacts directly with ubiquitin. We identify the Nse1 mutation (R188E) that specifically disrupts its E3 activity and demonstrate that the Nse1-dependent ubiquitination is particularly important under replication stress. Moreover, we determine Nse4 (lysine K181) as the first known SMC5/6-associated Nse1 substrate. Interestingly, abolition of Nse4 modification at K181 leads to suppression of DNA-damage sensitivity of other SMC5/6 mutants. Altogether, this study brings new evidence for Nse1 ubiquitin ligase activity, significantly advancing our understanding of this enigmatic SMC5/6 function.
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Affiliation(s)
- Peter Kolesar
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Karel Stejskal
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (K.S.); (D.P.)
| | - David Potesil
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (K.S.); (D.P.)
| | - Johanne M. Murray
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RH, UK;
| | - Jan J. Palecek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (K.S.); (D.P.)
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10
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Liao HZ, Liao WJ, Zou DX, Zhang RQ, Ma JL. Identification and expression analysis of PUB genes in tea plant exposed to anthracnose pathogen and drought stresses. PLANT SIGNALING & BEHAVIOR 2021; 16:1976547. [PMID: 34633911 PMCID: PMC9208792 DOI: 10.1080/15592324.2021.1976547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
The plant U-box (PUB) gene family, one of the major ubiquitin ligase families in plants, plays important roles in multiple cellular processes including environmental stress responses and resistance. The function of U-box genes has been well characterized in Arabidopsis and other plants. However, little is known about the tea plant (Camellia sinensis) PUB genes. Here, 89 U-box proteins were identified from the chromosome-scale referenced genome of tea plant. According to the domain organization and phylogenetic analysis, the tea plant PUB family were classified into ten classes, named Class I to X, respectively. Using previously released stress-related RNA-seq data in tea plant, we identified 34 stress-inducible CsPUB genes. Specifically, eight CsPUB genes were expressed differentially under both anthracnose pathogen and drought stresses. Moreover, six of the eight CsPUBs were upregulated in response to these two stresses. Expression profiling performed by qRT-PCR was consistent with the RNA-seq analysis, and stress-related cis-acting elements were identified in the promoter regions of the six upregulated CsPUB genes. These results strongly implied the putative functions of U-box ligase genes in response to biotic and abiotic stresses in tea plant.
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Affiliation(s)
- Hong-Ze Liao
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation and Utilization, Guangxi Forestry Research Institute, NanningChina
- Key Laboratory of Ministry of Education for Non-Wood Forest Cultivation and Protection, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Protection and Utilization of Marine Resources, Guangxi University for Nationalities, Nanning, China
| | - Wang-Jiao Liao
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation and Utilization, Guangxi Forestry Research Institute, NanningChina
| | - Dong-Xia Zou
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation and Utilization, Guangxi Forestry Research Institute, NanningChina
| | - Ri-Qing Zhang
- Key Laboratory of Ministry of Education for Non-Wood Forest Cultivation and Protection, Central South University of Forestry and Technology, Changsha, China
| | - Jin-Lin Ma
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation and Utilization, Guangxi Forestry Research Institute, NanningChina
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11
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Wang S, Qiao H, Wang P, Wang Y, Qin D. ZDHHC19 Is Dispensable for Spermatogenesis, but Is Essential for Sperm Functions in Mice. Int J Mol Sci 2021; 22:ijms22168894. [PMID: 34445597 PMCID: PMC8396176 DOI: 10.3390/ijms22168894] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 02/05/2023] Open
Abstract
Spermatogenesis is a complicated process involving mitotically proliferating spermatogonial cells, meiotically dividing spermatocytes, and spermatid going through maturation into spermatozoa. The post-translational modifications of proteins play important roles in this biological process. S-palmitoylation is one type of protein modifications catalyzed by zinc finger Asp-His-His-Cys (ZDHHC)-family palmitoyl S-acyltransferases. There are 23 mammalian ZDHHCs that have been identified in mouse. Among them, Zdhhc19 is highly expressed in adult testis. However, the in vivo function of Zdhhc19 in mouse spermatogenesis and fertility remains unknown. In this study, we knocked out the Zdhhc19 gene by generating a 2609 bp deletion from exon 3 to exon 6 in mice. No differences were found in testis morphology and testis/body weight ratios upon Zdhhc19 deletion. Spermatogenesis was not disrupted in Zdhhc19 knockout mice, in which properly developed TRA98+ germ cells, SYCP3+ spermatocytes, and TNP1+ spermatids/spermatozoa were detected in seminiferous tubules. Nevertheless, Zdhhc19 knockout mice were male infertile. Zdhhc19 deficient spermatozoa exhibited multiple defects including abnormal morphology of sperm tails and heads, decreased motility, and disturbed acrosome reaction. All of these led to the inability of Zdhhc19 mutant sperm to fertilize oocytes in IVF assays. Taken together, our results support the fact that Zdhhc19 is a testis enriched gene dispensable for spermatogenesis, but is essential for sperm functions in mice.
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Affiliation(s)
- Shuai Wang
- Department of Physiology, Shantou University Medical College, Shantou 515041, China; (S.W.); (H.Q.)
| | - Hongjie Qiao
- Department of Physiology, Shantou University Medical College, Shantou 515041, China; (S.W.); (H.Q.)
| | - Pengxiang Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China;
| | - Yuan Wang
- Department of Animal Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI 48824, USA
- Correspondence: (Y.W.); (D.Q.)
| | - Danian Qin
- Department of Physiology, Shantou University Medical College, Shantou 515041, China; (S.W.); (H.Q.)
- Correspondence: (Y.W.); (D.Q.)
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12
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Zhang X, Xia Z, Lv X, Li D, Liu M, Zhang R, Ji T, Liu P, Ren R. DDB1- and CUL4-associated factor 8 plays a critical role in spermatogenesis. Front Med 2021; 15:302-312. [PMID: 33855678 DOI: 10.1007/s11684-021-0851-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/20/2021] [Indexed: 11/26/2022]
Abstract
Cullin-RING E3 ubiquitin ligase (CRL)-4 is a member of the large CRL family in eukaryotes. It plays important roles in a wide range of cellular processes, organismal development, and physiological and pathological conditions. DDB1- and CUL4-associated factor 8 (DCAF8) is a WD40 repeat-containing protein, which serves as a substrate receptor for CRL4. The physiological role of DCAF8 is unknown. In this study, we constructed Dcaf8 knockout mice. Homozygous mice were viable with no noticeable abnormalities. However, the fertility of Dcaf8-deficient male mice was markedly impaired, consistent with the high expression of DCAF8 in adult mouse testis. Sperm movement characteristics, including progressive motility, path velocity, progressive velocity, and track speed, were significantly lower in Dcaf8 knockout mice than in wild-type (WT) mice. However, the total motility was similar between WT and Dcaf8 knockout sperm. More than 40% of spermatids in Dcaf8 knockout mice showed pronounced morphological abnormalities with typical bent head malformation. The acrosome and nucleus of Dcaf8 knockout sperm looked similar to those of WT sperm. In vitro tests showed that the fertilization rate of Dcaf8 knockout mice was significantly reduced. The results demonstrated that DCAF8 plays a critical role in spermatogenesis, and DCAF8 is a key component of CRL4 function in the reproductive system.
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Affiliation(s)
- Xiuli Zhang
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhizhou Xia
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xingyu Lv
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Donghe Li
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Mingzhu Liu
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ruihong Zhang
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Tong Ji
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Ping Liu
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Ruibao Ren
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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13
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E3 Ubiquitin Ligase ASB17 Promotes Apoptosis by Ubiquitylating and Degrading BCLW and MCL1. BIOLOGY 2021; 10:biology10030234. [PMID: 33803505 PMCID: PMC8003104 DOI: 10.3390/biology10030234] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 12/26/2022]
Abstract
Simple Summary B-cell lymphoma-2 family proteins have been widely accepted as the critical regulators in cell apoptosis, often found to be abnormally expressed in many cancers. Among them, B-cell leukemia/lymphoma w and myeloid cell leukemia-1 are two pro-survival proteins. Here, we reported that the ankyrin repeat and SOCS box protein 17 can degrade the two proteins in a ubiquitylation -dependent way. Furthermore, we generated the first ASB17 knockout C57BL/6J mice line. The results revealed that ASB17 deficiency inhibited apoptosis but did not affect testes development. Moreover, the ASB17-deficient mice were more resistant to the stimuli of etoposide, Altogether, these findings indicate that ASB17 is a novel positive mediator of cell apoptosis. Abstract Apoptosis is a very important process of cell death controlled by multiple genes during which cells undergo certain events before dying. Apoptosis helps to clean the unnecessary cells and has critical physiological significance. Altered apoptosis results in a disorder of cell death and is associated with many diseases such as neurodegenerative diseases and cancers. Here, we reported that the ankyrin repeat and SOCS box protein 17 (ASB17) was mainly expressed in the testis and promoted apoptosis both in vivo and in vitro. Analyzing ASB17-deficient mice generated by using the CRISPR/Cas9 system, we demonstrated that ASB17 deficiency resulted in the reduction of apoptosis in spermatogenic cells, but it did not affect the development of spermatozoa or normal fertility. Next, in an in vivo model, ASB17 deficiency prevented the apoptosis of spermatogonia induced by etoposide in male mice. We noted that ASB17 promoted apoptosis in a caspase-dependent manner in vitro. Moreover, ASB17 interacted with the members of the BCL2 family, including BCL2, BCLX, BCLW, and MCL1. Interestingly, ASB17 specifically degraded the two anti-apoptotic factors, BCLW and MCL1, in a ubiquitylation-dependent fashion. Collectively, our findings suggested that ASB17 acted as a distinct positive regulator of cell apoptosis.
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14
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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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15
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Manning J, Windley SP, Sandow JJ, Shah SS, Western P, Wilhelm D, Kumar S. Identification of novel interacting partners of the NEDD4 ubiquitin ligase in mouse testis. J Proteomics 2020; 223:103830. [PMID: 32450490 DOI: 10.1016/j.jprot.2020.103830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 04/14/2020] [Accepted: 05/14/2020] [Indexed: 12/24/2022]
Abstract
Posttranslational modification by ubiquitination targets proteins for degradation, recycling, stabilization or altered trafficking, and as such can alter cellular signaling pathways. The substrate specificity of this multistep process is controlled by ubiquitin ligases, including those of the HECT domain-containing NEDD4 family. In the testis, ubiquitination of many proteins contributes to organ development and maturation of spermatozoa and NEDD4 is known to be important in the control of spermatogonial stem cell homeostasis. However, a comprehensive understanding of NEDD4 substrates in testis development is lacking. Here we demonstrate high expression of Nedd4 in somatic cells of the mouse testis and in the murine Leydig cell-like cell line TM3. Immunoprecipitation of NEDD4 tagged with GFP at either the amino or carboxyl terminus was subjected to proteomic analysis for interacting proteins. We identified a substantial list of potential interaction partners, including known NEDD4 substrates, proteins involved in ubiquitination and proteins important for testis development and spermatogenesis. We confirmed the interaction of NEDD4 with a subset of these putative interacting proteins, validating the integrity of the dataset. These potential interactors may be further explored to reveal important roles of NEDD4-mediated ubiquitination in the testis. SIGNIFICANCE: Ubiquitination is important for testis development and function, and NEDD4 is known to ubiquitinate various proteins to affect cellular signaling and development, including those implicated in spermatogenesis. However, substrates of NEDD4 that are important during testis development remain to be identified. Here we report NEDD4 expression in the developing testis and TM3 testicular cell line. This study identifies a substantial list of NEDD4 interacting proteins in the TM3 testicular cell line, with validation of some of these interactions. Hence, this provides novel NEDD4 targets that may contribute to testis development and function that may be further explored.
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Affiliation(s)
- JantinaA Manning
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia.
| | - Simon P Windley
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jarrod J Sandow
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Sonia S Shah
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia
| | - Patrick Western
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC 3800, Australia
| | - Dagmar Wilhelm
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, VIC 3010, Australia
| | - Sharad Kumar
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia.
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16
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Kavarthapu R, Anbazhagan R, Sharma AK, Shiloach J, Dufau ML. Linking Phospho-Gonadotropin Regulated Testicular RNA Helicase (GRTH/DDX25) to Histone Ubiquitination and Acetylation Essential for Spermatid Development During Spermiogenesis. Front Cell Dev Biol 2020; 8:310. [PMID: 32478068 PMCID: PMC7242631 DOI: 10.3389/fcell.2020.00310] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/08/2020] [Indexed: 11/13/2022] Open
Abstract
GRTH/DDX25 is a testicular RNA helicase expressed in germ cells that plays a crucial role in completion of spermatogenesis. Previously, we demonstrated a missense mutation (R242H) of GRTH gene in Japanese infertile patients (5.8%) with non-obstructive azoospermia. This mutation upon expression in COS-1 cells revealed absence of the 61 kDa phosphorylated GRTH in cytoplasm and the presence of the 56 kDa non-phosphorylated GRTH in the nucleus. GRTH knock-in (KI) mice carrying the human GRTH (R242H) mutation, lack phosphorylated GRTH, and sperm due to failure of round spermatid elongation during spermiogenesis. To determine the impact of phosphorylated GRTH on molecular events/pathways participating in spermatid development during spermiogenesis, we analyzed transcriptome profiles obtained from RNA-Seq of germ cells from KI and WT mice. RNA-Seq analysis of 2624 differentially expressed genes revealed 1404 down-regulated and 1220 up-regulated genes in KI mice. Genes relevant to spermatogenesis, spermatid development and spermatid differentiation were significantly down-regulated. KEGG enrichment analysis showed genes related to ubiquitin-mediated proteolysis and protein processing in endoplasmic reticulum pathway genes were significantly down-regulated while the up-regulated genes were found to be involved in Focal adhesion and ECM-receptor interaction pathways. Real-Time PCR analysis confirmed considerable reduction in transcripts of ubiquitination related genes Ube2j1, Ube2k, Ube2w, Rnf8, Rnf133, Rnf138, Cul3 and increased expression of Ccnd2, Col1a, Lamb1, Cav1, Igf1, Itga9 mRNA's in KI mice compared to WT. Also, marked reduction in protein expression of UBE2J1, RNF8, RNF138 (ubiquitination network), MOF (histone acetyltransferase), their modified Histone substrates (H2AUb, H2BUb) and H4Ac, H4K16Ac were observed in KI mice. GRTH-IP mRNA binding studies revealed that Rnf8 and Ube2J1 mRNAs from WT mice associated with GRTH protein and the binding is greatly impaired in the KI mice. Immunohistochemistry analysis showed significantly reduced expression of RNF8, MOF, H4Ac and H4K16Ac in round spermatids of KI mice. Absence of phosphorylated GRTH impairs UBE2J1, RNF8 and MOF-dependent histone ubiquitination and acetylation essential for histone replacement, chromatin condensation and spermatid elongation during spermiogenesis.
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Affiliation(s)
- Raghuveer Kavarthapu
- Section on Molecular Endocrinology, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Rajakumar Anbazhagan
- Section on Molecular Endocrinology, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Ashish K. Sharma
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Joseph Shiloach
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Maria L. Dufau
- Section on Molecular Endocrinology, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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17
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Wang T, Gao H, Li W, Liu C. Essential Role of Histone Replacement and Modifications in Male Fertility. Front Genet 2019; 10:962. [PMID: 31649732 PMCID: PMC6792021 DOI: 10.3389/fgene.2019.00962] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/10/2019] [Indexed: 01/19/2023] Open
Abstract
Spermiogenesis is a complex cellular differentiation process that the germ cells undergo a distinct morphological change, and the protamines replace the core histones to facilitate chromatin compaction in the sperm head. Recent studies show the essential roles of epigenetic events during the histone-to-protamine transition. Defects in either the replacement or the modification of histones might cause male infertility with azoospermia, oligospermia or teratozoospermia. Here, we summarize recent advances in our knowledge of how epigenetic regulators, such as histone variants, histone modification and their related chromatin remodelers, facilitate the histone-to-protamine transition during spermiogenesis. Understanding the molecular mechanism underlying the modification and replacement of histones during spermiogenesis will enable the identification of epigenetic biomarkers of male infertility, and shed light on potential therapies for these patients in the future.
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Affiliation(s)
- Tong Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hui Gao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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18
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Inducing the Degradation of Disease-Related Proteins Using Heterobifunctional Molecules. Molecules 2019; 24:molecules24183272. [PMID: 31500395 PMCID: PMC6766870 DOI: 10.3390/molecules24183272] [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: 07/12/2019] [Revised: 08/02/2019] [Accepted: 08/07/2019] [Indexed: 01/02/2023] Open
Abstract
Current drug development strategies that target either enzymatic or receptor proteins for which specific small molecule ligands can be designed for modulation, result in a large portion of the proteome being overlooked as undruggable. The recruitment of natural degradation cascades for targeted protein removal using heterobifunctional molecules (or degraders) provides a likely avenue to expand the druggable proteome. In this review, we discuss the use of this drug development strategy in relation to degradation cascade-recruiting mechanisms and successfully targeted disease-related proteins. Essential characteristics to be considered in degrader design are deliberated upon and future development challenges mentioned.
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19
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Wang X, Kang JY, Wei L, Yang X, Sun H, Yang S, Lu L, Yan M, Bai M, Chen Y, Long J, Li N, Li D, Huang J, Lei M, Shao Z, Yuan W, Zuo E, Lu K, Liu MF, Li J. PHF7 is a novel histone H2A E3 ligase prior to histone-to-protamine exchange during spermiogenesis. Development 2019; 146:dev.175547. [PMID: 31189663 DOI: 10.1242/dev.175547] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/28/2019] [Indexed: 12/11/2022]
Abstract
Epigenetic regulation, including histone-to-protamine exchanges, controls spermiogenesis. However, the underlying mechanisms of this regulation are largely unknown. Here, we report that PHF7, a testis-specific PHD and RING finger domain-containing protein, is essential for histone-to-protamine exchange in mice. PHF7 is specifically expressed during spermiogenesis. PHF7 deletion results in male infertility due to aberrant histone retention and impaired protamine replacement in elongated spermatids. Mechanistically, PHF7 can simultaneously bind histone H2A and H3; its PHD domain, a histone code reader, can specifically bind H3K4me3/me2, and its RING domain, a histone writer, can ubiquitylate H2A. Thus, our study reveals that PHF7 is a novel E3 ligase that can specifically ubiquitylate H2A through binding H3K4me3/me2 prior to histone-to-protamine exchange.
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Affiliation(s)
- Xiukun Wang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Science, Shanghai 200031, China
| | - Jun-Yan Kang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Science, Shanghai 200031, China
| | - Leixin Wei
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Science, Shanghai 200031, China.,Department of Orthopaedic Surgery, Changzheng Hospital, The Second Military Medical University, Shanghai 200003, China
| | - Xiaogan Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Hongduo Sun
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Suming Yang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Science, Shanghai 200031, China
| | - Lei Lu
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Science, Shanghai 200031, China
| | - Meng Yan
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Science, Shanghai 200031, China
| | - Meizhu Bai
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Science, Shanghai 200031, China
| | - Yanyan Chen
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201203, China
| | - Juanjuan Long
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201203, China
| | - Na Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Science, Shanghai 200031, China
| | - Dangsheng Li
- CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai 200031, China
| | - Jing Huang
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201203, China
| | - Ming Lei
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201203, China
| | - Zhen Shao
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wen Yuan
- Department of Orthopaedic Surgery, Changzheng Hospital, The Second Military Medical University, Shanghai 200003, China
| | - Erwei Zuo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China .,Research Center of Animal Genomics, Agricultural Genomics Institute at Shengzhen, Chinese Academy of Agricultural Sciences, Shengzhen, Guangdong 518210, China
| | - Kehuan Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Mo-Fang Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Science, Shanghai 200031, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Science, Shanghai 200031, China
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20
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Ali A, Mistry BV, Ahmed HA, Abdulla R, Amer HA, Prince A, Alazami AM, Alkuraya FS, Assiri A. Deletion of DDB1- and CUL4- associated factor-17 (Dcaf17) gene causes spermatogenesis defects and male infertility in mice. Sci Rep 2018; 8:9202. [PMID: 29907856 PMCID: PMC6003934 DOI: 10.1038/s41598-018-27379-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 05/31/2018] [Indexed: 01/26/2023] Open
Abstract
DDB1– and CUL4–associated factor 17 (Dcaf17) is a member of DCAF family genes that encode substrate receptor proteins for Cullin-RING E3 ubiquitin ligases, which play critical roles in many cellular processes. To unravel the function of DCAF17, we performed expression profiling of Dcaf17 in different tissues of wild type mouse by qRT-PCR and generated Dcaf17 knockout mice by gene targeting. Expression profiling of Dcaf17 showed highest expression in testis. Analyses of Dcaf17 transcripts during post-natal development of testis at different ages displayed gradual increase in Dcaf17 mRNA levels with the age. Although Dcaf17 disruption did not have any effect on female fertility, Dcaf17 deletion led to male infertility due to abnormal sperm development. The Dcaf17−/− mice produced low number of sperm with abnormal shape and significantly low motility. Histological examination of the Dcaf17−/− testis revealed impaired spermatogenesis with presence of vacuoles and sloughed cells in the seminiferous tubules. Disruption of Dcaf17 caused asymmetric acrosome capping, impaired nuclear compaction and abnormal round spermatid to elongated spermatid transition. For the first time, these data indicate that DCAF17 is essential for spermiogenesis.
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Affiliation(s)
- Asmaa Ali
- Comparative Medicine Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Bhavesh V Mistry
- Comparative Medicine Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Hala A Ahmed
- Comparative Medicine Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Razan Abdulla
- Comparative Medicine Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Hassan A Amer
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Cairo University, Giza, 12613, Egypt
| | - Abdelbary Prince
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Cairo University, Giza, 12613, Egypt
| | - Anas M Alazami
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Abdullah Assiri
- Comparative Medicine Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia. .,College of Medicine, AlFaisal University, Riyadh, Saudi Arabia. .,Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
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21
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George AJ, Hoffiz YC, Charles AJ, Zhu Y, Mabb AM. A Comprehensive Atlas of E3 Ubiquitin Ligase Mutations in Neurological Disorders. Front Genet 2018; 9:29. [PMID: 29491882 PMCID: PMC5817383 DOI: 10.3389/fgene.2018.00029] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/22/2018] [Indexed: 01/11/2023] Open
Abstract
Protein ubiquitination is a posttranslational modification that plays an integral part in mediating diverse cellular functions. The process of protein ubiquitination requires an enzymatic cascade that consists of a ubiquitin activating enzyme (E1), ubiquitin conjugating enzyme (E2) and an E3 ubiquitin ligase (E3). There are an estimated 600-700 E3 ligase genes representing ~5% of the human genome. Not surprisingly, mutations in E3 ligase genes have been observed in multiple neurological conditions. We constructed a comprehensive atlas of disrupted E3 ligase genes in common (CND) and rare neurological diseases (RND). Of the predicted and known human E3 ligase genes, we found ~13% were mutated in a neurological disorder with 83 total genes representing 70 different types of neurological diseases. Of the E3 ligase genes identified, 51 were associated with an RND. Here, we provide an updated list of neurological disorders associated with E3 ligase gene disruption. We further highlight research in these neurological disorders and discuss the advanced technologies used to support these findings.
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Affiliation(s)
- Arlene J. George
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
| | - Yarely C. Hoffiz
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
| | | | - Ying Zhu
- Creative Media Industries Institute & Department of Computer Science, Georgia State University, Atlanta, GA, United States
| | - Angela M. Mabb
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
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22
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MicroRNA-300 Regulates the Ubiquitination of PTEN through the CRL4B DCAF13 E3 Ligase in Osteosarcoma Cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 10:254-268. [PMID: 29499938 PMCID: PMC5768150 DOI: 10.1016/j.omtn.2017.12.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 12/18/2017] [Accepted: 12/18/2017] [Indexed: 12/24/2022]
Abstract
Cullins, critical members of the cullin-RING ubiquitin ligases (CRLs), are often aberrantly expressed in different cancers. However, the underlying mechanisms regarding aberrant expression of these cullins and the specific substrates of CRLs in different cancers are mostly unknown. Here, we demonstrate that overexpressed CUL4B in human osteosarcoma cells forms an E3 complex with DNA damage binding protein 1 (DDB1) and DDB1- and CUL4-associated factor 13 (DCAF13). In vitro and in vivo analyses indicated that the CRL4BDCAF13 E3 ligase specifically recognized the tumor suppressor PTEN (phosphatase and tensin homolog deleted on chromosome 10) for degradation, and disruption of this E3 ligase resulted in PTEN accumulation. Further analyses indicated that miR-300 directly targeted the 3' UTR of CUL4B, and DNA hypermethylation of a CpG island in the miR-300 promoter region contributed to the downregulation of miR-300. Interestingly, ectopic expression of miR-300 or treatment with 5-AZA-2'-deoxycytidine, a DNA methylation inhibitor, decreased the stability of CRL4BDCAF13 E3 ligase and reduced PTEN ubiquitination. By applying in vitro screening to identify small molecules that specifically inhibit CUL4B-DDB1 interaction, we found that TSC01131 could greatly inhibit osteosarcoma cell growth and could disrupt the stability of the CRL4BDCAF13 E3 ligase. Collectively, our findings shed new light on the molecular mechanism of CUL4B function and might also provide a new avenue for osteosarcoma therapy.
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23
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Rnf138 deficiency promotes apoptosis of spermatogonia in juvenile male mice. Cell Death Dis 2017; 8:e2795. [PMID: 28518149 PMCID: PMC5520686 DOI: 10.1038/cddis.2017.110] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 01/24/2017] [Accepted: 02/01/2017] [Indexed: 11/09/2022]
Abstract
Spermatogenesis, the process by which haploid sperm cells are produced from a diploid precursor cell, is essential for sexual reproduction. Here, we report that RING-finger protein 138 (Rnf138) is highly expressed in testes, especially in spermatogonia and spermatocytes. The role of Rnf138 in spermatogenesis was examined using a Rnf138-knockout mouse model. Rnf138 deficiency resulted in increased apoptosis in spermatogenic cells, loss of proliferative spermatogonia, delayed development of spermatozoa and impaired fertility. The proportion of PLZF+Ki67+ cells within the PLZF+ population decreased in the knockout mice. The phenotype was further assessed by RNA-sequencing (RNA-seq), which determined that the expression levels of many genes involved in spermatogenesis were altered in the testis of Rnf138-knockout mice. Thus, Rnf138 deficiency promotes the apoptosis of spermatogenic cells, which may have been caused by the aberrant proliferation of spermatogonia in mouse testis development.
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24
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Yin H, Zheng L, Liu W, Zhang D, Li W, Yuan L. Rootletin prevents Cep68 from VHL-mediated proteasomal degradation to maintain centrosome cohesion. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:645-654. [DOI: 10.1016/j.bbamcr.2017.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 01/05/2017] [Accepted: 01/11/2017] [Indexed: 01/22/2023]
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25
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Devkota S, Jeong H, Kim Y, Ali M, Roh JI, Hwang D, Lee HW. Functional characterization of EI24-induced autophagy in the degradation of RING-domain E3 ligases. Autophagy 2016; 12:2038-2053. [PMID: 27541728 PMCID: PMC5103340 DOI: 10.1080/15548627.2016.1217371] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Historically, the ubiquitin-proteasome system (UPS) and autophagy pathways were believed to be independent; however, recent data indicate that these pathways engage in crosstalk. To date, the players mediating this crosstalk have been elusive. Here, we show experimentally that EI24 (EI24, autophagy associated transmembrane protein), a key component of basal macroautophagy/autophagy, degrades 14 physiologically important E3 ligases with a RING (really interesting new gene) domain, whereas 5 other ligases were not degraded. Based on the degradation results, we built a statistical model that predicts the RING E3 ligases targeted by EI24 using partial least squares discriminant analysis. Of 381 RING E3 ligases examined computationally, our model predicted 161 EI24 targets. Those targets are primarily involved in transcription, proteolysis, cellular bioenergetics, and apoptosis and regulated by TP53 and MTOR signaling. Collectively, our work demonstrates that EI24 is an essential player in UPS-autophagy crosstalk via degradation of RING E3 ligases. These results indicate a paradigm shift regarding the fate of E3 ligases.
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Affiliation(s)
- Sushil Devkota
- a Department of Biochemistry, College of Life Science and Biotechnology and Yonsei Laboratory Animal Research Center , Yonsei University , Seoul , Republic of Korea
| | - Hyobin Jeong
- b Department of New Biology and Center for Plant Aging Research , Institute for Basic Science, DGIST , Daegu , Republic of Korea
| | - Yunmi Kim
- a Department of Biochemistry, College of Life Science and Biotechnology and Yonsei Laboratory Animal Research Center , Yonsei University , Seoul , Republic of Korea
| | - Muhammad Ali
- a Department of Biochemistry, College of Life Science and Biotechnology and Yonsei Laboratory Animal Research Center , Yonsei University , Seoul , Republic of Korea
| | - Jae-Il Roh
- a Department of Biochemistry, College of Life Science and Biotechnology and Yonsei Laboratory Animal Research Center , Yonsei University , Seoul , Republic of Korea
| | - Daehee Hwang
- b Department of New Biology and Center for Plant Aging Research , Institute for Basic Science, DGIST , Daegu , Republic of Korea
| | - Han-Woong Lee
- a Department of Biochemistry, College of Life Science and Biotechnology and Yonsei Laboratory Animal Research Center , Yonsei University , Seoul , Republic of Korea
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26
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Wu Y, Hu X, Li Z, Wang M, Li S, Wang X, Lin X, Liao S, Zhang Z, Feng X, Wang S, Cui X, Wang Y, Gao F, Hess RA, Han C. Transcription Factor RFX2 Is a Key Regulator of Mouse Spermiogenesis. Sci Rep 2016; 6:20435. [PMID: 26853561 PMCID: PMC4745085 DOI: 10.1038/srep20435] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/04/2016] [Indexed: 12/15/2022] Open
Abstract
The regulatory factor X (RFX) family of transcription factors is crucial for ciliogenesis throughout evolution. In mice, Rfx1-4 are highly expressed in the testis where flagellated sperm are produced, but the functions of these factors in spermatogenesis remain unknown. Here, we report the production and characterization of the Rfx2 knockout mice. The male knockout mice were sterile due to the arrest of spermatogenesis at an early round spermatid step. The Rfx2-null round spermatids detached from the seminiferous tubules, forming large multinucleated giant cells that underwent apoptosis. In the mutants, formation of the flagellum was inhibited at its earliest stage. RNA-seq analysis identified a large number of cilia-related genes and testis-specific genes that were regulated by RFX2. Many of these genes were direct targets of RFX2, as revealed by chromatin immunoprecipitation-PCR assays. These findings indicate that RFX2 is a key regulator of the post-meiotic development of mouse spermatogenic cells.
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Affiliation(s)
- Yujian Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiangjing Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhen Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Graduate University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sisi Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Graduate University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiuxia Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiwen Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shangying Liao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhuqiang Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xue Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Si Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Graduate University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiuhong Cui
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanling Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fei Gao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rex A Hess
- Comparative Biosciences, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802-6199, USA
| | - Chunsheng Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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27
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Kozakova L, Vondrova L, Stejskal K, Charalabous P, Kolesar P, Lehmann AR, Uldrijan S, Sanderson CM, Zdrahal Z, Palecek JJ. The melanoma-associated antigen 1 (MAGEA1) protein stimulates the E3 ubiquitin-ligase activity of TRIM31 within a TRIM31-MAGEA1-NSE4 complex. Cell Cycle 2015; 14:920-30. [PMID: 25590999 PMCID: PMC4614679 DOI: 10.1080/15384101.2014.1000112] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The MAGE (Melanoma-associated antigen) protein family members are structurally related to each other by a MAGE-homology domain comprised of 2 winged helix motifs WH/A and WH/B. This family specifically evolved in placental mammals although single homologs designated NSE3 (non-SMC element) exist in most eukaryotes. NSE3, together with its partner proteins NSE1 and NSE4 form a tight subcomplex of the structural maintenance of chromosomes SMC5–6 complex. Previously, we showed that interactions of the WH/B motif of the MAGE proteins with their NSE4/EID partners are evolutionarily conserved (including the MAGEA1-NSE4 interaction). In contrast, the interaction of the WH/A motif of NSE3 with NSE1 diverged in the MAGE paralogs. We hypothesized that the MAGE paralogs acquired new RING-finger-containing partners through their evolution and form MAGE complexes reminiscent of NSE1-NSE3-NSE4 trimers. In this work, we employed the yeast 2-hybrid system to screen a human RING-finger protein library against several MAGE baits. We identified a number of potential MAGE-RING interactions and confirmed several of them (MDM4, PCGF6, RNF166, TRAF6, TRIM8, TRIM31, TRIM41) in co-immunoprecipitation experiments. Among these MAGE-RING pairs, we chose to examine MAGEA1-TRIM31 in detail and showed that both WH/A and WH/B motifs of MAGEA1 bind to the coiled-coil domain of TRIM31 and that MAGEA1 interaction stimulates TRIM31 ubiquitin-ligase activity. In addition, TRIM31 directly binds to NSE4, suggesting the existence of a TRIM31-MAGEA1-NSE4 complex reminiscent of the NSE1-NSE3-NSE4 trimer. These results suggest that MAGEA1 functions as a co-factor of TRIM31 ubiquitin-ligase and that the TRIM31-MAGEA1-NSE4 complex may have evolved from an ancestral NSE1-NSE3-NSE4 complex.
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Affiliation(s)
- Lucie Kozakova
- a From the Mendel Center for Plant Genomics and Proteomics; Central European Institute of Technology; Masaryk University ; Brno , Czech Republic
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28
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Hong SE, Nho KJ, Song HK, Kim DH. Deep sequencing-generated modules demonstrate coherent expression patterns for various cardiac diseases. Gene 2015; 574:53-60. [PMID: 26232333 DOI: 10.1016/j.gene.2015.07.080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 06/19/2015] [Accepted: 07/24/2015] [Indexed: 11/30/2022]
Abstract
As sequencing technology rapidly develops, gene annotations have also become increasingly sophisticated with incorporation of information regarding the temporal-spatial context of alternative splicing patterns, developmental stages, and tissue specificity. The present study aimed to identify the heart-enriched genes based on next-generation sequencing data and to investigate the gene modules demonstrating coherent expression patterns for various cardiac disease-related perturbations. Seven gene modules, including 382 heart-enriched genes, were identified. At least two modules containing differentially expressed genes were experimentally confirmed to be highly sensitive to various cardiac diseases. Transcription factors regulating the gene modules were then analyzed based on knowledgebase information; the expression of eight transcription factors changed significantly during pressure-overload cardiac hypertrophy, suggesting possible regulation of the modules by the identified transcription factors. Collectively, our results contribute to the classification of heart-enriched genes and their modules and would aid in identification of the transcription factors involved in cardiac pathogenesis in the future.
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Affiliation(s)
- Seong-Eui Hong
- College of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea.
| | - Kyoung Jin Nho
- College of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea.
| | - Hong Ki Song
- College of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea.
| | - Do Han Kim
- College of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea.
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29
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Yuan S, Swiggin HMC, Zheng H, Yan W. A testis-specific gene, Ubqlnl, is dispensable for mouse embryonic development and spermatogenesis. Mol Reprod Dev 2015; 82:408-9. [PMID: 26043068 DOI: 10.1002/mrd.22504] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 05/14/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Shuiqiao Yuan
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Nevada
| | - Hayden M C Swiggin
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Nevada
| | - Huili Zheng
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Nevada
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Nevada.,Department of Biology, College of Sciences, University of Nevada, Nevada
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30
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The ubiquilin gene family: evolutionary patterns and functional insights. BMC Evol Biol 2014; 14:63. [PMID: 24674348 PMCID: PMC4230246 DOI: 10.1186/1471-2148-14-63] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 03/17/2014] [Indexed: 12/12/2022] Open
Abstract
Background Ubiquilins are proteins that function as ubiquitin receptors in eukaryotes. Mutations in two ubiquilin-encoding genes have been linked to the genesis of neurodegenerative diseases. However, ubiquilin functions are still poorly understood. Results In this study, evolutionary and functional data are combined to determine the origin and diversification of the ubiquilin gene family and to characterize novel potential roles of ubiquilins in mammalian species, including humans. The analysis of more than six hundred sequences allowed characterizing ubiquilin diversity in all the main eukaryotic groups. Many organisms (e. g. fungi, many animals) have single ubiquilin genes, but duplications in animal, plant, alveolate and excavate species are described. Seven different ubiquilins have been detected in vertebrates. Two of them, here called UBQLN5 and UBQLN6, had not been hitherto described. Significantly, marsupial and eutherian mammals have the most complex ubiquilin gene families, composed of up to 6 genes. This exceptional mammalian-specific expansion is the result of the recent emergence of four new genes, three of them (UBQLN3, UBQLN5 and UBQLNL) with precise testis-specific expression patterns that indicate roles in the postmeiotic stages of spermatogenesis. A gene with related features has independently arisen in species of the Drosophila genus. Positive selection acting on some mammalian ubiquilins has been detected. Conclusions The ubiquilin gene family is highly conserved in eukaryotes. The infrequent lineage-specific amplifications observed may be linked to the emergence of novel functions in particular tissues.
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31
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The role of E3 ligases in the ubiquitin-dependent regulation of spermatogenesis. Semin Cell Dev Biol 2014; 30:27-35. [PMID: 24632385 DOI: 10.1016/j.semcdb.2014.03.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 03/02/2014] [Indexed: 12/23/2022]
Abstract
The ubiquitination of proteins is a post-translational modification that was first described as a means to target misfolded or unwanted proteins for degradation by the proteasome. It is now appreciated that the ubiquitination of proteins also serves as a mechanism to modify protein function and cellular functions such as protein trafficking, cell signaling, DNA repair, chromatin modifications, cell-cycle progression and cell death. The ubiquitination of proteins occurs through the hierarchal transfer of ubiquitin from an E1 ubiquitin-activating enzyme to an E2 ubiquitin-conjugating enzyme and finally to an E3 ubiquitin ligase that transfers the ubiquitin to its target protein. It is the final E3 ubiquitin ligase that confers the substrate specificity for ubiquitination and is the focus of this review. Spermatogenesis is a complex and highly regulated process by which spermatogonial stem cells undergo mitotic proliferation and expansion of the diploid spermatogonial population, differentiate into spermatocytes and progress through two meiotic divisions to produce haploid spermatids that proceed through a final morphogenesis to generate mature spermatozoa. The ubiquitination of proteins in the cells of the testis occurs in many of the processes required for the progression of mature spermatozoa. Since it is the E3 ubiquitin ligase that recognizes the target protein and provides the specificity and selectivity for ubiquitination, this review highlights known examples of E3 ligases in the testis and the differing roles that they play in maintaining functional spermatogenesis.
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32
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Wang SS, Wang F, Tan SJ, Wang MX, Sui N, Zhang XS. Transcript profiles of maize embryo sacs and preliminary identification of genes involved in the embryo sac-pollen tube interaction. FRONTIERS IN PLANT SCIENCE 2014; 5:702. [PMID: 25566277 PMCID: PMC4269116 DOI: 10.3389/fpls.2014.00702] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 11/25/2014] [Indexed: 05/05/2023]
Abstract
The embryo sac, the female gametophyte of flowering plants, plays important roles in the pollination and fertilization process. Maize (Zea mays L.) is a model monocot, but little is known about the interactions between its embryo sac and the pollen tube. In this study, we compared the transcript profiles of mature embryo sacs, mature embryo sacs 14-16 h after pollination, and mature nucelli. Comparing the transcript profiles of the embryo sacs before and after the entry of the pollen tube, we identified 3467 differentially expressed transcripts (3382 differentially expressed genes; DEGs). The DEGs were grouped into 22 functional categories. Among the DEGs, 221 genes were induced upon the entry of the pollen tube, and many of them encoded proteins involved in RNA binding, processing, and transcription, signaling, miscellaneous enzyme family processes, and lipid metabolism processes. Genes in the DEG dataset were grouped into 17 classes in a gene ontology enrichment analysis. The DEGs included many genes encoding proteins involved in protein amino acid phosphorylation and protein ubiquitination, implying that these processes might play important roles in the embryo sac-pollen tube interaction. Additionally, our analyses indicate that the expression of 112 genes encoding cysteine-rich proteins (CRPs) is induced during pollination and fertilization. The CRPs likely regulate pollen tube guidance and embryo sac development. These results provide important information on the genes involved in the embryo sac-pollen tube interaction in maize.
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Affiliation(s)
- Shuai Shuai Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural UniversityTai'an, China
| | - Fang Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural UniversityTai'an, China
| | - Su Jian Tan
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural UniversityTai'an, China
| | - Ming Xiu Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural UniversityTai'an, China
| | - Na Sui
- College of Life Sciences, Shandong Normal UniversityJi'nan, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural UniversityTai'an, China
- *Correspondence: Xian Sheng Zhang, State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong Province, 271018 Shandong, China e-mail:
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33
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Nakamura N. Ubiquitination regulates the morphogenesis and function of sperm organelles. Cells 2013; 2:732-50. [PMID: 24709878 PMCID: PMC3972651 DOI: 10.3390/cells2040732] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 11/12/2013] [Accepted: 11/29/2013] [Indexed: 11/29/2022] Open
Abstract
It is now understood that protein ubiquitination has diverse cellular functions in eukaryotes. The molecular mechanism and physiological significance of ubiquitin-mediated processes have been extensively studied in yeast, Drosophila and mammalian somatic cells. Moreover, an increasing number of studies have emphasized the importance of ubiquitination in spermatogenesis and fertilization. The dysfunction of various ubiquitin systems results in impaired sperm development with abnormal organelle morphology and function, which in turn is highly associated with male infertility. This review will focus on the emerging roles of ubiquitination in biogenesis, function and stability of sperm organelles in mammals.
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Affiliation(s)
- Nobuhiro Nakamura
- Department of Biological Sciences, Tokyo Institute of Technology, 4259-B13 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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Li Z, Yao F, Chen Y, Zhang R, Lv Y, Zhao N, Wang T, Xin W, Hou L, Zou X. Molecular cloning, characterization and expression analysis of ubiquitin protein ligase gene (As-ubpl) from Artemia sinica. Comp Biochem Physiol B Biochem Mol Biol 2013; 165:90-8. [PMID: 23511337 DOI: 10.1016/j.cbpb.2013.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 03/07/2013] [Accepted: 03/09/2013] [Indexed: 10/27/2022]
Abstract
Ubiquitylation is an important protein post-translational regulation pathway, which is involved in controlling protein degradation, tumor occurrence and cell cycle regulation. E3 ubiquitin protein ligase (UBPL) plays a crucial role of the conjugation of activated ubiquitin to protein substrates and leads to targeting proteins for degradation by the proteasome. We amplified one full-length cDNA of the A. sinica UBPL (As-ubpl) gene by RACE technology. The full-length cDNA of As-ubpl is composed of 2931 bp, with a 2571 bp open reading frame (ORF) that encodes a polypeptide of 856 amino acids with a C2 domain, two domains with two conserved Trp (W) residues (WW) and a homologous to E6-AP Carboxyl Terminus (HECT) domain. The amount of As-ubpl showed from real-time PCR indicates that a high expression levels of As-ubpl at 20 h, 40 h and 3 days of embryo development, with highest expression levels appearing in the larval stage (40 h). Furthermore, As-ubpl transcripts were highly up-regulated under salinity (50‰) and low temperature stress (15 °C). These results indicate that As-ubpl is involved in protein regulation of the postdiapause development and in responses to salinity and low temperature stress.
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Affiliation(s)
- Zengrong Li
- College of Life Sciences, Liaoning Normal University, Dalian 116081, PR China
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