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Zhang S, Yu Q, Li Z, Zhao Y, Sun Y. Protein neddylation and its role in health and diseases. Signal Transduct Target Ther 2024; 9:85. [PMID: 38575611 PMCID: PMC10995212 DOI: 10.1038/s41392-024-01800-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/22/2024] [Accepted: 03/04/2024] [Indexed: 04/06/2024] Open
Abstract
NEDD8 (Neural precursor cell expressed developmentally downregulated protein 8) is an ubiquitin-like protein that is covalently attached to a lysine residue of a protein substrate through a process known as neddylation, catalyzed by the enzyme cascade, namely NEDD8 activating enzyme (E1), NEDD8 conjugating enzyme (E2), and NEDD8 ligase (E3). The substrates of neddylation are categorized into cullins and non-cullin proteins. Neddylation of cullins activates CRLs (cullin RING ligases), the largest family of E3 ligases, whereas neddylation of non-cullin substrates alters their stability and activity, as well as subcellular localization. Significantly, the neddylation pathway and/or many neddylation substrates are abnormally activated or over-expressed in various human diseases, such as metabolic disorders, liver dysfunction, neurodegenerative disorders, and cancers, among others. Thus, targeting neddylation becomes an attractive strategy for the treatment of these diseases. In this review, we first provide a general introduction on the neddylation cascade, its biochemical process and regulation, and the crystal structures of neddylation enzymes in complex with cullin substrates; then discuss how neddylation governs various key biological processes via the modification of cullins and non-cullin substrates. We further review the literature data on dysregulated neddylation in several human diseases, particularly cancer, followed by an outline of current efforts in the discovery of small molecule inhibitors of neddylation as a promising therapeutic approach. Finally, few perspectives were proposed for extensive future investigations.
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Affiliation(s)
- Shizhen Zhang
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China
| | - Qing Yu
- Department of Thyroid Surgery, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, 310022, China
| | - Zhijian Li
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China
| | - Yongchao Zhao
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang University Cancer Center, Hangzhou, 310029, China.
| | - Yi Sun
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang University Cancer Center, Hangzhou, 310029, China.
- Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang, Hangzhou, 310024, China.
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, 310053, China.
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2
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Liu H, Shih YH, Wang WL, Chang WL, Wang YC. UBE1C is upregulated and promotes neddylation of p53 in lung cancer. FASEB J 2023; 37:e23181. [PMID: 37668436 DOI: 10.1096/fj.202300629r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 07/24/2023] [Accepted: 08/23/2023] [Indexed: 09/06/2023]
Abstract
NEDDylation is a type of protein post-translational modification that has high similarity to ubiquitination. UBE1C encodes NEDDylation E1 enzyme, locates at chromatin region 3p14.1 and shows high gene dosage amplification frequency in both Asian and Caucasian lung cancer patients. However, its NEDDylation substrates and roles in tumorigenesis remain elucidated. In this study, we aim to investigate the oncogenic role of UBE1C and its involvement in how NEDDylation regulates p53 in lung cancer. We found that UBE1C mRNA overexpression and DNA amplification in most of the lung cell lines and cancer patients. Patients with UBE1C overexpression showed poor prognosis. Moreover, we demonstrated that overexpression of UBE1C and NEDD8, a NEDDylation moiety, resulted in the p53 NEDDylation with inhibition of p53 acetylation at K373 residue. Importantly, UBE1C-mediated NEDDylation downregulated the transcriptional activity of p53 by inhibiting p53 ability to target promoter regions of its downstream transcription targets, consequently inhibiting the promoter activities and the expression of mRNA and protein of the p53 downstream genes including p21 and PTEN. In addition, UBE1C and NEDD8 overexpression promoted migration, invasion, and proliferation of lung cancer cells. Our findings suggest that UBE1C acts as an oncogene with prognostic potential and highlight a potential role of UBE1C-mediated NEDDylation in downregulation of p53 transcriptional activity in lung cancer.
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Affiliation(s)
- Hsun Liu
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yung-Hsin Shih
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Lun Wang
- Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Wei-Lun Chang
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Ching Wang
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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3
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Liu Y, Liu J, Peng N, Hai S, Zhang S, Zhao H, Liu W. Role of non-canonical post-translational modifications in gastrointestinal tumors. Cancer Cell Int 2023; 23:225. [PMID: 37777749 PMCID: PMC10544213 DOI: 10.1186/s12935-023-03062-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/08/2023] [Indexed: 10/02/2023] Open
Abstract
Post-translational modifications (PTMs) of proteins contribute to the occurrence and development of tumors. Previous studies have suggested that canonical PTMs such as ubiquitination, glycosylation, and phosphorylation are closely implicated in different aspects of gastrointestinal tumors. Recently, emerging evidence showed that non-canonical PTMs play an essential role in the carcinogenesis, metastasis and treatment of gastrointestinal tumors. Therefore, we summarized recent advances in sumoylation, neddylation, isoprenylation, succinylation and other non-canonical PTMs in gastrointestinal tumors, which comprehensively describe the mechanisms and functions of non-classical PTMs in gastrointestinal tumors. It is anticipated that targeting specific PTMs could benefit the treatment as well as improve the prognosis of gastrointestinal tumors.
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Affiliation(s)
- Yihong Liu
- Department of Gastroenterology, the First Affiliated Hospital of China Medical University, 155# North Nanjing Street, Heping District, Shenyang City, 110001, Liaoning Province, China
| | - Jingwei Liu
- Department of Anus and Intestine Surgery, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Na Peng
- Department of Gastroenterology, the First Affiliated Hospital of China Medical University, 155# North Nanjing Street, Heping District, Shenyang City, 110001, Liaoning Province, China
| | - Shuangshuang Hai
- Department of Gastroenterology, the First Affiliated Hospital of China Medical University, 155# North Nanjing Street, Heping District, Shenyang City, 110001, Liaoning Province, China
| | - Shen Zhang
- Department of Gastroenterology, the Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Haibo Zhao
- Department of Gastroenterology, the First Affiliated Hospital of China Medical University, 155# North Nanjing Street, Heping District, Shenyang City, 110001, Liaoning Province, China
| | - Weixin Liu
- Department of Gastroenterology, the First Affiliated Hospital of China Medical University, 155# North Nanjing Street, Heping District, Shenyang City, 110001, Liaoning Province, China.
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4
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Ochoa S, Hernández-Lemus E. Functional impact of multi-omic interactions in breast cancer subtypes. Front Genet 2023; 13:1078609. [PMID: 36685900 PMCID: PMC9850112 DOI: 10.3389/fgene.2022.1078609] [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: 10/24/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Abstract
Multi-omic approaches are expected to deliver a broader molecular view of cancer. However, the promised mechanistic explanations have not quite settled yet. Here, we propose a theoretical and computational analysis framework to semi-automatically produce network models of the regulatory constraints influencing a biological function. This way, we identified functions significantly enriched on the analyzed omics and described associated features, for each of the four breast cancer molecular subtypes. For instance, we identified functions sustaining over-representation of invasion-related processes in the basal subtype and DNA modification processes in the normal tissue. We found limited overlap on the omics-associated functions between subtypes; however, a startling feature intersection within subtype functions also emerged. The examples presented highlight new, potentially regulatory features, with sound biological reasons to expect a connection with the functions. Multi-omic regulatory networks thus constitute reliable models of the way omics are connected, demonstrating a capability for systematic generation of mechanistic hypothesis.
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Affiliation(s)
- Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico,Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico,*Correspondence: Enrique Hernández-Lemus,
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Tajima S, Suetake I, Takeshita K, Nakagawa A, Kimura H, Song J. Domain Structure of the Dnmt1, Dnmt3a, and Dnmt3b DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:45-68. [PMID: 36350506 PMCID: PMC11025882 DOI: 10.1007/978-3-031-11454-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In mammals, three major DNA methyltransferases, Dnmt1, Dnmt3a, and Dnmt3b, have been identified. Dnmt3a and Dnmt3b are responsible for establishing DNA methylation patterns produced through their de novo-type DNA methylation activity in implantation stage embryos and during germ cell differentiation. Dnmt3-like (Dnmt3l), which is a member of the Dnmt3 family but does not possess DNA methylation activity, was reported to be indispensable for global methylation in germ cells. Once the DNA methylation patterns are established, maintenance-type DNA methyltransferase Dnmt1 faithfully propagates them to the next generation via replication. All Dnmts possess multiple domains. For instance, Dnmt3a and Dnmt3b each contain a Pro-Trp-Trp-Pro (PWWP) domain that recognizes the histone H3K36me2/3 mark, an Atrx-Dnmt3-Dnmt3l (ADD) domain that recognizes unmodified histone H3 tail, and a catalytic domain that methylates CpG sites. Dnmt1 contains an N-terminal independently folded domain (NTD) that interacts with a variety of regulatory factors, a replication foci-targeting sequence (RFTS) domain that recognizes the histone H3K9me3 mark and H3 ubiquitylation, a CXXC domain that recognizes unmodified CpG DNA, two tandem Bromo-Adjacent-homology (BAH1 and BAH2) domains that read the H4K20me3 mark with BAH1, and a catalytic domain that preferentially methylates hemimethylated CpG sites. In this chapter, the structures and functions of these domains are described.
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Affiliation(s)
- Shoji Tajima
- Institute for Protein Research, Osaka University, Osaka, Japan.
| | - Isao Suetake
- Department of Nutritional Sciences, Faculty of Nutritional Sciences, Nakamura Gakuen University, Fukuoka, Japan
| | | | - Atsushi Nakagawa
- Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Hironobu Kimura
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Jikui Song
- Department of Biochemistry, University of California Riverside, Riverside, CA, USA.
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6
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Qin W, Scicluna BP, van der Poll T. The Role of Host Cell DNA Methylation in the Immune Response to Bacterial Infection. Front Immunol 2021; 12:696280. [PMID: 34394088 PMCID: PMC8358789 DOI: 10.3389/fimmu.2021.696280] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Host cells undergo complex transcriptional reprogramming upon infection. Epigenetic changes play a key role in the immune response to bacteria, among which DNA modifications that include methylation have received much attention in recent years. The extent of DNA methylation is well known to regulate gene expression. Whilst historically DNA methylation was considered to be a stable epigenetic modification, accumulating evidence indicates that DNA methylation patterns can be altered rapidly upon exposure of cells to changing environments and pathogens. Furthermore, the action of proteins regulating DNA methylation, particularly DNA methyltransferases and ten-eleven translocation methylcytosine dioxygenases, may be modulated, at least in part, by bacteria. This review discusses the principles of DNA methylation, and recent insights about the regulation of host DNA methylation during bacterial infection.
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Affiliation(s)
- Wanhai Qin
- Center of Experimental & Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Brendon P Scicluna
- Center of Experimental & Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Tom van der Poll
- Center of Experimental & Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Division of Infectious Diseases, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
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7
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Hegde M, Joshi MB. Comprehensive analysis of regulation of DNA methyltransferase isoforms in human breast tumors. J Cancer Res Clin Oncol 2021; 147:937-971. [PMID: 33604794 PMCID: PMC7954751 DOI: 10.1007/s00432-021-03519-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/10/2021] [Indexed: 12/14/2022]
Abstract
Significant reprogramming of epigenome is widely described during pathogenesis of breast cancer. Transformation of normal cell to hyperplastic cell and to neoplastic phenotype is associated with aberrant DNA (de)methylation, which, through promoter and enhancer methylation changes, activates oncogenes and silence tumor suppressor genes in variety of tumors including breast. DNA methylation, one of the major epigenetic mechanisms is catalyzed by evolutionarily conserved isoforms namely, DNMT1, DNMT3A and DNMT3B in humans. Over the years, studies have demonstrated intricate and complex regulation of DNMT isoforms at transcriptional, translational and post-translational levels. The recent findings of allosteric regulation of DNMT isoforms and regulation by other interacting chromatin modifying proteins emphasizes functional integrity and their contribution for the development of breast cancer and progression. DNMT isoforms are regulated by several intrinsic and extrinsic parameters. In the present review, we have extensively performed bioinformatics analysis of expression of DNMT isoforms along with their transcriptional and post-transcriptional regulators such as transcription factors, interacting proteins, hormones, cytokines and dietary elements along with their significance during pathogenesis of breast tumors. Our review manuscript provides a comprehensive understanding of key factors regulating DNMT isoforms in breast tumor pathology and documents unsolved issues.
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Affiliation(s)
- Mangala Hegde
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Planetarium Complex, Manipal, 576104, India
| | - Manjunath B Joshi
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Planetarium Complex, Manipal, 576104, India.
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8
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Vaughan RM, Kupai A, Rothbart SB. Chromatin Regulation through Ubiquitin and Ubiquitin-like Histone Modifications. Trends Biochem Sci 2020; 46:258-269. [PMID: 33308996 DOI: 10.1016/j.tibs.2020.11.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/27/2020] [Accepted: 11/09/2020] [Indexed: 02/07/2023]
Abstract
Chromatin functions are influenced by the addition, removal, and recognition of histone post-translational modifications (PTMs). Ubiquitin and ubiquitin-like (UBL) PTMs on histone proteins can function as signaling molecules by mediating protein-protein interactions. Fueled by the identification of novel ubiquitin and UBL sites and the characterization of the writers, erasers, and readers, the breadth of chromatin functions associated with ubiquitin signaling is emerging. Here, we highlight recently appreciated roles for histone ubiquitination in DNA methylation control, PTM crosstalk, nucleosome structure, and phase separation. We also discuss the expanding diversity and functions associated with histone UBL modifications. We conclude with a look toward the future and pose key questions that will drive continued discovery at the interface of epigenetics and ubiquitin signaling.
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Affiliation(s)
- Robert M Vaughan
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ariana Kupai
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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9
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High levels of LINE-1 transposable elements expressed in Kaposi's sarcoma-associated herpesvirus-related primary effusion lymphoma. Oncogene 2020; 40:536-550. [PMID: 33188297 DOI: 10.1038/s41388-020-01549-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/13/2020] [Accepted: 10/28/2020] [Indexed: 11/08/2022]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV, HHV-8) is a gamma herpesvirus associated with several human malignancies. Transposable elements (TEs) are ubiquitous in eukaryotic genomes, occupying about 45% of the human genome. TEs have been linked with a variety of disorders and malignancies, though the precise nature of their contribution to many of them has yet to be elucidated. Global transcriptome analysis for differentially expressed TEs in KSHV-associated primary effusion lymphoma (PEL) cells (BCBL1 and BC3) revealed large number of differentially expressed TEs. These differentially expressed TEs include LTR transposons, long interspersed nuclear elements (LINEs), and short interspersed nuclear elements (SINEs). Further analysis of LINE-1 (L1) elements revealed expression upregulation, hypo-methylation, and transition into open chromatin in PEL. In agreement with high L1 expression, PEL cells express ORF1 protein and possess high reverse transcriptase (RT)-activity. Interestingly, inhibition of this RT-activity suppressed PEL cell growth. Collectively, we identified high expression of TEs, and specifically of L1 as a critical component in the proliferation of PEL cells. This observation is relevant for the treatment of KSHV-associated malignancies since they often develop in AIDS patients that are treated with RT inhibitors with potent inhibition for both HIV and L1 RT activity.
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Xie L, Ji X, Tu Y, Wang K, Zhu L, Zeng X, Wang X, Zhang J, Zhu M. MLN4924 inhibits hedgehog signaling pathway and activates autophagy to alleviate mouse laser-induced choroidal neovascularization lesion. Biomed Pharmacother 2020; 130:110654. [PMID: 34321162 DOI: 10.1016/j.biopha.2020.110654] [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: 06/19/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 10/23/2022] Open
Abstract
Neovascular age-related macular degeneration (nAMD), featured as choroidal neovascularization (CNV), can cause blindness in the elderly population. MLN4924, a highly selective small-molecule inhibitor of NEDD8 (neuronal precursor cell-expressed developmentally down-regulated protein 8)-activating enzyme (NAE), inhibits the proliferation, angiogenesis and inflammation of multiple cancers via up-regulating hedgehog pathway-regulated autophagy. MLN4924 intraperitoneal injection mitigated the leakage, area and volume of mouse laser-induced CNV lesion. Additionally, compared to CNV 7 d group, MLN4924 treated mouse retina-retinal pigment epithelium (RPE)-choroid complex showed decreased expression of hedgehog pathway-associated molecules patched 1 (PTCH1), smoothened (SMO), GLI family zinc finger 1 (GLI1) and GLI family zinc finger 2 (GLI2) with increased expression of autophagy-associated molecules sequestosome 1 (p62) and LC microtubule-associated protein 1 light chain 3 (LC3). Meanwhile, human choroidal endothelial cells (HCECs) exposed to hypoxia condition also showed decreased expression of hedgehog pathway-associated molecules and increased expression of autophagy-associated molecules. Compared to hypoxia + MLN4924 group, SMO agonist SAG up-regulated hedgehog pathway and down-regulated autophagy, whereas autophagy inhibitor PIK-III inhibited autophagy with no effect on hedgehog pathway, indicating that MLN4924 facilitated autophagy of HCECs via hindering hedgehog pathway under hypoxia condition. Finally, MLN4924 inhibited proliferation, migration and tube formation of HCECs via boosting hedgehog pathway-regulated autophagy. In summary, MLN4924 relieved the formation of mouse laser-induced CNV lesion might via up-regulating hedgehog pathway-regulated autophagy. The results provide a potential interfering strategy for nAMD targeting the autophagy of choroidal endothelial cells.
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Affiliation(s)
- Laiqing Xie
- Department of Ophthalmology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xiaoyan Ji
- Department of Ophthalmology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yuanyuan Tu
- Department of Ophthalmology, Lixiang Eye Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Kun Wang
- Department of Ophthalmology, Lixiang Eye Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Linling Zhu
- Department of Ophthalmology, Lixiang Eye Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xinwei Zeng
- Department of Ophthalmology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xue Wang
- Department of Ophthalmology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Ji Zhang
- Department of Ophthalmology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China.
| | - Manhui Zhu
- Department of Ophthalmology, Lixiang Eye Hospital of Soochow University, Suzhou, Jiangsu, China.
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Saravanaraman P, Selvam M, Ashok C, Srijyothi L, Baluchamy S. De novo methyltransferases: Potential players in diseases and new directions for targeted therapy. Biochimie 2020; 176:85-102. [PMID: 32659446 DOI: 10.1016/j.biochi.2020.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 06/06/2020] [Accepted: 07/07/2020] [Indexed: 12/16/2022]
Abstract
Epigenetic modifications govern gene expression by guiding the human genome on 'what to express and what not to'. DNA methyltransferases (DNMTs) establish methylation patterns on DNA, particularly in CpG islands, and such patterns play a major role in gene silencing. DNMTs are a family of proteins/enzymes (DNMT1, 2, 3A, 3B, and 3L), among which, DNMT1 (maintenance methyltransferase) and DNMT3 (de novo methyltransferases) that direct mammalian development and genome imprinting are highly investigated. In recent decades, many studies revealed a strong association of DNA methylation patterns with gene expression in various clinical conditions. Differential expression of DNMT3 family proteins and their splice variants result in changes in methylation patterns and such alterations have been associated with the initiation and progression of various diseases, especially cancer. This review will discuss the aberrant modifications generated by DNMT3 proteins under various clinical conditions, suggesting a potential signature for de novo methyltransferases in targeted disease therapy. Further, this review discusses the possibility of using 'CpG island methylation signatures' as promising biomarkers and emphasizes 'targeted hypomethylation' by disrupting the interaction of specific DNMT-protein complexes as the future of cancer therapeutics.
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Affiliation(s)
- Ponne Saravanaraman
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Murugan Selvam
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Cheemala Ashok
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Loudu Srijyothi
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Sudhakar Baluchamy
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India.
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12
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Abortive herpes simplex virus infection of nonneuronal cells results in quiescent viral genomes that can reactivate. Proc Natl Acad Sci U S A 2019; 117:635-640. [PMID: 31871148 DOI: 10.1073/pnas.1910537117] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abortive viral infections are usually studied in populations of susceptible but nonpermissive cells. Single-cell studies of viral infections have demonstrated that even in susceptible and permissive cell populations, abortive infections can be detected in subpopulations of the infected cells. We have previously identified abortive infections in HeLa cells infected with herpes simplex virus 1 (HSV-1) at high multiplicity of infection (MOI). Here, we tested 4 additional human-derived nonneuronal cell lines (cancerous or immortalized) and found significant subpopulations that remain abortive. To characterize these abortive cells, we recovered cell populations that survived infection with HSV-1 at high MOI. The surviving cells retained proliferative potential and the ability to be reinfected. These recovered cell populations maintained the viral genomes in a quiescent state for at least 5 wk postinfection. Our results indicate that these viral genomes are maintained inside the nucleus, bound to cellular histones and occasionally reactivated to produce new progeny viruses. We conclude that abortive HSV-1 infection is a common feature during infection of nonneuronal cells and results in a latency-like state in the infected cells. Our findings question the longstanding paradigm that alphaherpesviruses can establish spontaneous latency only in neuronal cells and emphasize the stochastic nature of lytic versus latency decision of HSV-1 in nonneuronal cells.
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13
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Yin L, Xue Y, Shang Q, Zhu H, Liu M, Liu Y, Hu Q. Pharmaceutical Inhibition of Neddylation as Promising Treatments for Various Cancers. Curr Top Med Chem 2019; 19:1059-1069. [PMID: 30854973 DOI: 10.2174/1568026619666190311110646] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Neddylation is an important post-translational modification of proteins, in which a NEDD8 (neural-precursor-cell-expressed developmentally down-regulated 8) is covalently introduced onto the substrate proteins to regulate their functions and homeostasis. As neddylation is frequently up-regulated in various cancers, its interference was proposed as a promising therapy of related diseases. OBJECTIVE The recent advances in developing neddylation interfering agents were summarized to provide an overview of current achievements and perspectives for future development. METHODS Reports on neddylation interfering agents were acquired from Pubmed as well as the EPO and clinicaltrials.gov websites, which were subsequently analyzed and summarized according to targets, chemical structures and biological activities. RESULTS Neddylation as a sophisticated procedure comprises proteolytic processing of NEDD8 precursor, deploying conjugating enzymes E1 (NAE), E2 (UBE2M and UBE2F) and various E3, as well as translocating NEDD8 along these conjugating enzymes sequentially and finally to substrate proteins. Among these nodes, NAE, UBE2M and the interaction between UBE2M-DCN1 have been targeted by small molecules, metal complexes, peptides and RNAi. A NAE inhibitor pevonedistat (MLN4924) is currently under evaluation in clinical trials for the treatment of various cancers. CONCLUSION With multiple inhibitory approaches of neddylation being introduced, the development of neddylation interference as a novel cancer therapy is significantly boosted recently, although its efficacy and the best way to achieve that are still to be demonstrated in clinical trials.
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Affiliation(s)
- Lina Yin
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuanyuan Xue
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qiannan Shang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Haichao Zhu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Meihua Liu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yingxiang Liu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qingzhong Hu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
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14
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Hervouet E, Peixoto P, Delage-Mourroux R, Boyer-Guittaut M, Cartron PF. Specific or not specific recruitment of DNMTs for DNA methylation, an epigenetic dilemma. Clin Epigenetics 2018; 10:17. [PMID: 29449903 PMCID: PMC5807744 DOI: 10.1186/s13148-018-0450-y] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/30/2018] [Indexed: 11/28/2022] Open
Abstract
Our current view of DNA methylation processes is strongly moving: First, even if it was generally admitted that DNMT3A and DNMT3B are associated with de novo methylation and DNMT1 is associated with inheritance DNA methylation, these distinctions are now not so clear. Secondly, since one decade, many partners of DNMTs have been involved in both the regulation of DNA methylation activity and DNMT recruitment on DNA. The high diversity of interactions and the combination of these interactions let us to subclass the different DNMT-including complexes. For example, the DNMT3L/DNMT3A complex is mainly related to de novo DNA methylation in embryonic states, whereas the DNMT1/PCNA/UHRF1 complex is required for maintaining global DNA methylation following DNA replication. On the opposite to these unspecific DNA methylation machineries (no preferential DNA sequence), some recently identified DNMT-including complexes are recruited on specific DNA sequences. The coexistence of both types of DNA methylation (un/specific) suggests a close cooperation and an orchestration between these systems to maintain genome and epigenome integrities. Deregulation of these systems can lead to pathologic disorders.
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Affiliation(s)
- Eric Hervouet
- INSERM unit 1098, University of Bourgogne Franche-Comté, Besançon, France.,EPIGENExp (EPIgenetics and GENe EXPression Technical Platform), Besançon, France
| | - Paul Peixoto
- INSERM unit 1098, University of Bourgogne Franche-Comté, Besançon, France.,EPIGENExp (EPIgenetics and GENe EXPression Technical Platform), Besançon, France
| | | | | | - Pierre-François Cartron
- 3INSERM unit S1232, University of Nantes, Nantes, France.,4Institut de cancérologie de l'Ouest, Nantes, France.,REpiCGO (Cancéropole Grand-Ouest), Nantes, France.,EpiSAVMEN Networks, Nantes, Région Pays de la Loire France
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15
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Bayraktar G, Kreutz MR. Neuronal DNA Methyltransferases: Epigenetic Mediators between Synaptic Activity and Gene Expression? Neuroscientist 2017; 24:171-185. [PMID: 28513272 PMCID: PMC5846851 DOI: 10.1177/1073858417707457] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
DNMT3A and 3B are the main de novo DNA methyltransferases (DNMTs) in the brain that introduce new methylation marks to non-methylated DNA in postmitotic neurons. DNA methylation is a key epigenetic mark that is known to regulate important cellular processes in neuronal development and brain plasticity. Accumulating evidence disclosed rapid and dynamic changes in DNA methylation of plasticity-relevant genes that are important for learning and memory formation. To understand how DNMTs contribute to brain function and how they are regulated by neuronal activity is a prerequisite for a deeper appreciation of activity-dependent gene expression in health and disease. This review discusses the functional role of de novo methyltransferases and in particular DNMT3A1 in the adult brain with special emphasis on synaptic plasticity, memory formation, and brain disorders.
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Affiliation(s)
- Gonca Bayraktar
- 1 RG Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Michael R Kreutz
- 1 RG Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany.,2 Leibniz Group "Dendritic Organelles and Synaptic Function", ZMNH, Magdeburg, Germany
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16
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He S, Cao Y, Xie P, Dong G, Zhang L. The Nedd8 Non-covalent Binding Region in the Smurf HECT Domain is Critical to its Ubiquitn Ligase Function. Sci Rep 2017; 7:41364. [PMID: 28169289 PMCID: PMC5294409 DOI: 10.1038/srep41364] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 12/19/2016] [Indexed: 11/24/2022] Open
Abstract
Nedd8 is a ubiquitin-like protein that controls vital biological events through conjugation to target proteins. We previously identified the HECT-type ubiquitin ligase Smurf1 which controls diverse cellular processes is activated by Nedd8 through covalent neddylation. However, the effect of non-covalent binding to Nedd8 remains unknown. In this study, we demonstrate that both Smurf1 and its homologue Smurf2 carry a non-covalent Nedd8-binding site within its catalytic HECT domain. Structural analysis reveals that Smurf2 has Nedd8-binding sites within the small sub-domain of N-lobe and the C-lobe of HECT domain. Interestingly, the consensus Nedd8 binding sequence, L(X7)R(X5)F(X)ALQ is conserved in both Smurfs. Mutational studies reveal that all the five residues in the conserved sequence are required for binding to Nedd8. Functional studies suggest that mutations that disrupt Smurf interaction with Nedd8 reduce its neddylation and stabilize the protein. Furthermore, Nedd8 binding site in Smurf is shown to be necessary for its ubiquitin ligase activity towards the substrate and also the self-ubiquitylation. Finally, we show that Nedd8 binding to Smurf plays important roles in the regulation of cell migration and the BMP and TGFβ signaling pathways.
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Affiliation(s)
- Shan He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Collaborative Innovation Center for Cancer Medicine, Beijing 100850, China
| | - Yu Cao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Collaborative Innovation Center for Cancer Medicine, Beijing 100850, China.,Georgia Cancer Center, Augusta University, Augusta GA, USA
| | - Ping Xie
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Collaborative Innovation Center for Cancer Medicine, Beijing 100850, China
| | - Guanglong Dong
- Department of General Surgery, Chinese People's Liberation Army General Hospital, Beijing 100853, China
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Collaborative Innovation Center for Cancer Medicine, Beijing 100850, China
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17
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Taylor JY, Schwander K, Kardia SLR, Arnett D, Liang J, Hunt SC, Rao DC, Sun YV. A Genome-wide study of blood pressure in African Americans accounting for gene-smoking interaction. Sci Rep 2016; 6:18812. [PMID: 26752167 PMCID: PMC4707536 DOI: 10.1038/srep18812] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 11/09/2015] [Indexed: 12/28/2022] Open
Abstract
Cigarette smoking has been shown to be a health hazard. In addition to being considered a negative lifestyle behavior, studies have shown that cigarette smoking has been linked to genetic underpinnings of hypertension. Because African Americans have the highest incidence and prevalence of hypertension, we examined the joint effect of genetics and cigarette smoking on health among this understudied population. The sample included African Americans from the genome wide association studies of HyperGEN (N = 1083, discovery sample) and GENOA (N = 1427, replication sample), both part of the FBPP. Results suggested that 2 SNPs located on chromosomes 14 (NEDD8; rs11158609; raw p = 9.80 × 10−9, genomic control-adjusted p = 2.09 × 10−7) and 17 (TTYH2; rs8078051; raw p = 6.28 × 10−8, genomic control-adjusted p = 9.65 × 10−7) were associated with SBP including the genetic interaction with cigarette smoking. These two SNPs were not associated with SBP in a main genetic effect only model. This study advances knowledge in the area of main and joint effects of genetics and cigarette smoking on hypertension among African Americans and offers a model to the reader for assessing these risks. More research is required to determine how these genes play a role in expression of hypertension.
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Affiliation(s)
| | - Karen Schwander
- Division of Biostatistics, School of Medicine, Washington University in St. Louis, St. Louis
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor
| | - Donna Arnett
- Department of Epidemiology, School of Public Health, University of Alabama, Birmingham
| | - Jingjing Liang
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland
| | - Steven C Hunt
- Cardiovascular Genetics Division, School of Medicine, University of Utah, Salt Lake City
| | - D C Rao
- Division of Biostatistics, School of Medicine, Washington University in St. Louis, St. Louis
| | - Yan V Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University.,Department of Biomedical Informatics, School of Medicine, Emory University, Atlanta
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18
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Tajima S, Suetake I, Takeshita K, Nakagawa A, Kimura H. Domain Structure of the Dnmt1, Dnmt3a, and Dnmt3b DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:63-86. [PMID: 27826835 DOI: 10.1007/978-3-319-43624-1_4] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In mammals, three DNA methyltransferases, Dnmt1, Dnmt3a, and Dnmt3b, have been identified. Dnmt3a and Dnmt3b are responsible for establishing DNA methylation patterns produced through their de novo-type DNA methylation activity in implantation stage embryos and during germ cell differentiation. Dnmt3-like (Dnmt3l), which is a member of the Dnmt3 family but does not possess DNA methylation activity, was reported to be indispensable for global methylation in germ cells. Once the DNA methylation patterns are established, maintenance-type DNA methyltransferase Dnmt1 faithfully propagates them to the next generation via replication. All Dnmts possess multiple domains, and in this chapter, the structures and functions of these domains are described.
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Affiliation(s)
- Shoji Tajima
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Isao Suetake
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- CREST/AMED, 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Kohei Takeshita
- Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- PRESTO/JST, Saitama, 332-0012, Japan
| | - Atsushi Nakagawa
- Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hironobu Kimura
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
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19
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Abstract
NEDD8 (neural precursor cell expressed developmentally downregulated protein 8) is a ubiquitin-like protein that activates the largest ubiquitin E3 ligase family, the cullin-RING ligases. Many non-cullin neddylation targets have been proposed in recent years. However, overexpression of exogenous NEDD8 can trigger NEDD8 conjugation through the ubiquitylation machinery, which makes validating potential NEDD8 targets challenging. Here, we re-evaluate studies of non-cullin targets of NEDD8 in light of the current understanding of the neddylation pathway, and suggest criteria for identifying genuine neddylation substrates under homeostatic conditions. We describe the biological processes that might be regulated by non-cullin neddylation, and the utility of neddylation inhibitors for research and as potential therapies. Understanding the biological significance of non-cullin neddylation is an exciting research prospect primed to reveal fundamental insights.
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20
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Wu Y, Lv Z, Yang Y, Dong G, Yu Y, Cui Y, Tong M, Wang L, Zhou Z, Zhu H, Zhou Q, Sha J. Blastomere biopsy influences epigenetic reprogramming during early embryo development, which impacts neural development and function in resulting mice. Cell Mol Life Sci 2014; 71:1761-74. [PMID: 24037382 PMCID: PMC11114061 DOI: 10.1007/s00018-013-1466-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 08/20/2013] [Accepted: 08/29/2013] [Indexed: 10/26/2022]
Abstract
Blastomere biopsy is used in preimplantation genetic diagnosis; however, the long-term implications on the offspring are poorly characterized. We previously reported a high risk of memory defects in adult biopsied mice. Here, we assessed nervous function of aged biopsied mice and further investigated the mechanism of neural impairment after biopsy. We found that aged biopsied mice had poorer spatial learning ability, increased neuron degeneration, and altered expression of proteins involved in neural degeneration or dysfunction in the brain compared to aged control mice. Furthermore, the MeDIP assay indicated a genome-wide low methylation in the brains of adult biopsied mice when compared to the controls, and most of the genes containing differentially methylated loci in promoter regions were associated with neural disorders. When we further compared the genomic DNA methylation profiles of 7.5-days postconception (dpc) embryos between the biopsy and control group, we found the whole genome low methylation in the biopsied group, suggesting that blastomere biopsy was an obstacle to de novo methylation during early embryo development. Further analysis on mRNA profiles of 4.5-dpc embryos indicated that reduced expression of de novo methylation genes in biopsied embryos may impact de novo methylation. In conclusion, we demonstrate an abnormal neural development and function in mice generated after blastomere biopsy. The impaired epigenetic reprogramming during early embryo development may be the latent mechanism contributing to the impairment of the nervous system in the biopsied mice, which results in a hypomethylation status in their brains.
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Affiliation(s)
- Yibo Wu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 210029 China
| | - Zhuo Lv
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1st Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Yang Yang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 210029 China
| | - Guoying Dong
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 210029 China
| | - Yang Yu
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1st Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Yiqiang Cui
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 210029 China
| | - Man Tong
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1st Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Liu Wang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1st Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Zuomin Zhou
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 210029 China
| | - Hui Zhu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 210029 China
| | - Qi Zhou
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1st Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Jiahao Sha
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 210029 China
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21
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Cajee UF, Hull R, Ntwasa M. Modification by ubiquitin-like proteins: significance in apoptosis and autophagy pathways. Int J Mol Sci 2012; 13:11804-11831. [PMID: 23109884 PMCID: PMC3472776 DOI: 10.3390/ijms130911804] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 09/11/2012] [Accepted: 09/13/2012] [Indexed: 01/31/2023] Open
Abstract
Ubiquitin-like proteins (Ubls) confer diverse functions on their target proteins. The modified proteins are involved in various biological processes, including DNA replication, signal transduction, cell cycle control, embryogenesis, cytoskeletal regulation, metabolism, stress response, homeostasis and mRNA processing. Modifiers such as SUMO, ATG12, ISG15, FAT10, URM1, and UFM have been shown to modify proteins thus conferring functions related to programmed cell death, autophagy and regulation of the immune system. Putative modifiers such as Domain With No Name (DWNN) have been identified in recent times but not fully characterized. In this review, we focus on cellular processes involving human Ubls and their targets. We review current progress in targeting these modifiers for drug design strategies.
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Affiliation(s)
- Umar-Faruq Cajee
- School of Molecular & Cell Biology, Gatehouse 512, University of the Witwatersrand, Johannesburg, 2050, South Africa; E-Mails: (U.-F.C.); (R.H.)
| | - Rodney Hull
- School of Molecular & Cell Biology, Gatehouse 512, University of the Witwatersrand, Johannesburg, 2050, South Africa; E-Mails: (U.-F.C.); (R.H.)
| | - Monde Ntwasa
- School of Molecular & Cell Biology, Gatehouse 512, University of the Witwatersrand, Johannesburg, 2050, South Africa; E-Mails: (U.-F.C.); (R.H.)
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22
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A protein array screen for Kaposi's sarcoma-associated herpesvirus LANA interactors links LANA to TIP60, PP2A activity, and telomere shortening. J Virol 2012; 86:5179-91. [PMID: 22379092 DOI: 10.1128/jvi.00169-12] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The Kaposi's sarcoma-associated herpesvirus (KSHV) LANA protein functions in latently infected cells as an essential participant in KSHV genome replication and as a driver of dysregulated cell growth. To identify novel LANA protein-cell protein interactions that could contribute to these activities, we performed a proteomic screen in which purified, adenovirus-expressed Flag-LANA protein was incubated with an array displaying 4,192 nonredundant human proteins. Sixty-one interacting cell proteins were consistently detected. LANA interactions with high-mobility group AT-hook 1 (HMGA1), HMGB1, telomeric repeat binding factor 1 (TRF1), xeroderma pigmentosum complementation group A (XPA), pygopus homolog 2 (PYGO2), protein phosphatase 2A (PP2A)B subunit, Tat-interactive protein 60 (TIP60), replication protein A1 (RPA1), and RPA2 proteins were confirmed in coimmunoprecipitation assays. LANA-associated TIP60 retained acetyltransferase activity and, unlike human papillomavirus E6 and HIV-1 TAT proteins, LANA did not reduce TIP60 stability. The LANA-bound PP2A B subunit was associated with the PP2A A subunit but not the catalytic C subunit, suggesting a disruption of PP2A phosphatase activity. This is reminiscent of the role of simian virus 40 (SV40) small t antigen. Chromatin immunoprecipitation (ChIP) assays showed binding of RPA1 and RPA2 to the KSHV terminal repeats. Interestingly, LANA expression ablated RPA1 and RPA2 binding to the cell telomeric repeats. In U2OS cells that rely on the alternative mechanism for telomere maintenance, LANA expression had minimal effect on telomere length. However, LANA expression in telomerase immortalized endothelial cells resulted in telomere shortening. In KSHV-infected cells, telomere shortening may be one more mechanism by which LANA contributes to the development of malignancy.
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