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Huang R, Nie W, Mi L, Yao C, Zhu H. EIF3B stabilizes PCNA by counteracting SYVN1-mediated ubiquitination to serve as a promotor in cholangiocarcinoma. Aging (Albany NY) 2024; 16:7311-7330. [PMID: 38687509 PMCID: PMC11087095 DOI: 10.18632/aging.205759] [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: 04/25/2023] [Accepted: 03/05/2024] [Indexed: 05/02/2024]
Abstract
Cholangiocarcinoma, a prevalent hepatic malignancy, exhibits a progressively rising incidence. While Eukaryotic translation initiation factor 3 subunit B (EIF3B) has been implicated in the occurrence and development of various cancers, its specific roles in cholangiocarcinoma remain unexplored. Immunohistochemical (IHC) analysis was employed to detect EIF3B/PCNA expression in cholangiocarcinoma. Cells were manipulated using short hairpin RNA (shRNA)-mediated lentiviruses or overexpression plasmids. Statistical significance was assessed using the Student's t-test and one-way ANOVA, with P < 0.05 considered statistically significant. EIF3B exhibited robust expression in cholangiocarcinoma, demonstrating a significant correlation with the pathological grade of cholangiocarcinoma patients. Furthermore, modulation of EIF3B expression, either depletion or elevation, demonstrated the ability to inhibit or enhance cholangiocarcinoma cell survival and migration in vitro. Mechanistically, we identified Proliferating Cell Nuclear Antigen (PCNA) as a downstream gene of EIF3B, driving cholangiocarcinoma. EIF3B stabilized PCNA by inhibiting PCNA ubiquitination, a process mediated by E3 ligase SYVN1. Similar to EIF3B, PCNA levels were also abundant in cholangiocarcinoma, and knocking down PCNA impeded cholangiocarcinoma development. Intriguingly, silencing PCNA attenuated the promotion induced by EIF3B overexpression. Furthermore, the elevated P21 protein level in shEIF3B RBE cells was partially attenuated after UC2288 (P21 signaling pathway inhibitor) treatment. Our findings underscored the potential of EIF3B as a therapeutic target for cholangiocarcinoma. Unraveling its functions holds promise for the development of more specific and effective targeted therapy strategies.
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Affiliation(s)
- Ranglang Huang
- Department of Hepatobiliary and Pancreatic Surgery, The Third Xiangya Hospital of the Central South University, Changsha 400013, Hunan, P.R. China
| | - Wanpin Nie
- Department of Hepatobiliary and Pancreatic Surgery, The Third Xiangya Hospital of the Central South University, Changsha 400013, Hunan, P.R. China
| | - Liangliang Mi
- Department of Hepatobiliary and Pancreatic Surgery, The Third Xiangya Hospital of the Central South University, Changsha 400013, Hunan, P.R. China
| | - Chenjiao Yao
- Department of General Medicine, Third Xiangya Hospital, Central South University, Changsha 400013, Hunan, P.R. China
| | - Haixia Zhu
- Department of General Medicine, Third Xiangya Hospital, Central South University, Changsha 400013, Hunan, P.R. China
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2
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Qu H, Wang Y, Yan Q, Fan C, Zhang X, Wang D, Guo C, Chen P, Shi L, Liao Q, Zhou M, Wang F, Zeng Z, Xiang B, Xiong W. CircCDYL2 bolsters radiotherapy resistance in nasopharyngeal carcinoma by promoting RAD51 translation initiation for enhanced homologous recombination repair. J Exp Clin Cancer Res 2024; 43:122. [PMID: 38654320 PMCID: PMC11036759 DOI: 10.1186/s13046-024-03049-0] [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] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Radiation therapy stands to be one of the primary approaches in the clinical treatment of malignant tumors. Nasopharyngeal Carcinoma, a malignancy predominantly treated with radiation therapy, provides an invaluable model for investigating the mechanisms underlying radiation therapy resistance in cancer. While some reports have suggested the involvement of circRNAs in modulating resistance to radiation therapy, the underpinning mechanisms remain unclear. METHODS RT-qPCR and in situ hybridization were used to detect the expression level of circCDYL2 in nasopharyngeal carcinoma tissue samples. The effect of circCDYL2 on radiotherapy resistance in nasopharyngeal carcinoma was demonstrated by in vitro and in vivo functional experiments. The HR-GFP reporter assay determined that circCDYL2 affected homologous recombination repair. RNA pull down, RIP, western blotting, IF, and polysome profiling assays were used to verify that circCDYL2 promoted the translation of RAD51 by binding to EIF3D protein. RESULTS We have identified circCDYL2 as highly expressed in nasopharyngeal carcinoma tissues, and it was closely associated with poor prognosis. In vitro and in vivo experiments demonstrate that circCDYL2 plays a pivotal role in promoting radiotherapy resistance in nasopharyngeal carcinoma. Our investigation unveils a specific mechanism by which circCDYL2, acting as a scaffold molecule, recruits eukaryotic translation initiation factor 3 subunit D protein (EIF3D) to the 5'-UTR of RAD51 mRNA, a crucial component of the DNA damage repair pathway to facilitate the initiation of RAD51 translation and enhance homologous recombination repair capability, and ultimately leads to radiotherapy resistance in nasopharyngeal carcinoma. CONCLUSIONS These findings establish a novel role of the circCDYL2/EIF3D/RAD51 axis in nasopharyngeal carcinoma radiotherapy resistance. Our work not only sheds light on the underlying molecular mechanism but also highlights the potential of circCDYL2 as a therapeutic sensitization target and a promising prognostic molecular marker for nasopharyngeal carcinoma.
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Affiliation(s)
- Hongke Qu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Yumin Wang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China.
| | - Qijia Yan
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China
| | - Chunmei Fan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Xiangyan Zhang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Dan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Can Guo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Pan Chen
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Lei Shi
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Ming Zhou
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Fuyan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China.
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, China.
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3
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Kong L, Jin X. Dysregulation of deubiquitination in breast cancer. Gene 2024; 902:148175. [PMID: 38242375 DOI: 10.1016/j.gene.2024.148175] [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: 10/25/2023] [Revised: 12/04/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
Breast cancer (BC) is a highly frequent malignant tumor that poses a serious threat to women's health and has different molecular subtypes, histological subtypes, and biological features, which act by activating oncogenic factors and suppressing cancer inhibitors. The ubiquitin-proteasome system (UPS) is the main process contributing to protein degradation, and deubiquitinases (DUBs) are reverse enzymes that counteract this process. There is growing evidence that dysregulation of DUBs is involved in the occurrence of BC. Herein, we review recent research findings in BC-associated DUBs, describe their nature, classification, and functions, and discuss the potential mechanisms of DUB-related dysregulation in BC. Furthermore, we present the successful treatment of malignant cancer with DUB inhibitors, as well as analyzing the status of targeting aberrant DUBs in BC.
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Affiliation(s)
- Lili Kong
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo 315211, Zhejiang, China
| | - Xiaofeng Jin
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo 315211, Zhejiang, China.
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4
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Raposo de Magalhães C, Sandoval K, Kagan F, McCormack G, Schrama D, Carrilho R, Farinha AP, Cerqueira M, Rodrigues PM. Transcriptomic changes behind Sparus aurata hepatic response to different aquaculture challenges: An RNA-seq study and multiomics integration. PLoS One 2024; 19:e0300472. [PMID: 38517901 PMCID: PMC10959376 DOI: 10.1371/journal.pone.0300472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/13/2024] [Indexed: 03/24/2024] Open
Abstract
Gilthead seabream (Sparus aurata) is an important species in Mediterranean aquaculture. Rapid intensification of its production and sub-optimal husbandry practices can cause stress, impairing overall fish performance and raising issues related to sustainability, animal welfare, and food safety. The advent of next-generation sequencing technologies has greatly revolutionized the study of fish stress biology, allowing a deeper understanding of the molecular stress responses. Here, we characterized for the first time, using RNA-seq, the different hepatic transcriptome responses of gilthead seabream to common aquaculture challenges, namely overcrowding, net handling, and hypoxia, further integrating them with the liver proteome and metabolome responses. After reference-guided transcriptome assembly, annotation, and differential gene expression analysis, 7, 343, and 654 genes were differentially expressed (adjusted p-value < 0.01, log2|fold-change| >1) in the fish from the overcrowding, net handling, and hypoxia challenged groups, respectively. Gene set enrichment analysis (FDR < 0.05) suggested a scenario of challenge-specific responses, that is, net handling induced ribosomal assembly stress, whereas hypoxia induced DNA replication stress in gilthead seabream hepatocytes, consistent with proteomics and metabolomics' results. However, both responses converged upon the downregulation of insulin growth factor signalling and induction of endoplasmic reticulum stress. These results demonstrate the high phenotypic plasticity of this species and its differential responses to distinct challenging environments at the transcriptomic level. Furthermore, it provides significant resources for characterizing and identifying potentially novel genes that are important for gilthead seabream resilience and aquaculture production efficiency with regard to fish welfare.
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Affiliation(s)
- Cláudia Raposo de Magalhães
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Kenneth Sandoval
- Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute & School of Natural Sciences, University of Galway, Galway, Ireland
| | | | - Grace McCormack
- Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute & School of Natural Sciences, University of Galway, Galway, Ireland
| | - Denise Schrama
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Raquel Carrilho
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Ana Paula Farinha
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Escola Superior Agrária de Santarém, Santarém, Portugal
| | - Marco Cerqueira
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Pedro M. Rodrigues
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
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5
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Fedry J, Silva J, Vanevic M, Fronik S, Mechulam Y, Schmitt E, des Georges A, Faller WJ, Förster F. Visualization of translation reorganization upon persistent ribosome collision stress in mammalian cells. Mol Cell 2024; 84:1078-1089.e4. [PMID: 38340715 PMCID: PMC7615912 DOI: 10.1016/j.molcel.2024.01.015] [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: 04/21/2023] [Revised: 11/06/2023] [Accepted: 01/18/2024] [Indexed: 02/12/2024]
Abstract
Aberrantly slow ribosomes incur collisions, a sentinel of stress that triggers quality control, signaling, and translation attenuation. Although each collision response has been studied in isolation, the net consequences of their collective actions in reshaping translation in cells is poorly understood. Here, we apply cryoelectron tomography to visualize the translation machinery in mammalian cells during persistent collision stress. We find that polysomes are compressed, with up to 30% of ribosomes in helical polysomes or collided disomes, some of which are bound to the stress effector GCN1. The native collision interface extends beyond the in vitro-characterized 40S and includes the L1 stalk and eEF2, possibly contributing to translocation inhibition. The accumulation of unresolved tRNA-bound 80S and 60S and aberrant 40S configurations identifies potentially limiting steps in collision responses. Our work provides a global view of the translation machinery in response to persistent collisions and a framework for quantitative analysis of translation dynamics in situ.
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Affiliation(s)
- Juliette Fedry
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, the Netherlands; MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
| | - Joana Silva
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mihajlo Vanevic
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Stanley Fronik
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Amédée des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, USA; Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA; Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, City University of New York, New York, NY, USA
| | - William James Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, the Netherlands
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6
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Jin H, Huang X, Pan Q, Ma N, Xie X, Wei Y, Yu F, Wen W, Zhang B, Zhang P, Chen X, Wang J, Liu RY, Lin J, Meng X, Lee MH. The EIF3H-HAX1 axis increases RAF-MEK-ERK signaling activity to promote colorectal cancer progression. Nat Commun 2024; 15:2551. [PMID: 38514606 PMCID: PMC10957977 DOI: 10.1038/s41467-024-46521-3] [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: 05/03/2023] [Accepted: 02/29/2024] [Indexed: 03/23/2024] Open
Abstract
Eukaryotic initiation translation factor 3 subunit h (EIF3H) plays critical roles in regulating translational initiation and predicts poor cancer prognosis, but the mechanism underlying EIF3H tumorigenesis remains to be further elucidated. Here, we report that EIF3H is overexpressed in colorectal cancer (CRC) and correlates with poor prognosis. Conditional Eif3h deletion suppresses colorectal tumorigenesis in AOM/DSS model. Mechanistically, EIF3H functions as a deubiquitinase for HAX1 and stabilizes HAX1 via antagonizing βTrCP-mediated ubiquitination, which enhances the interaction between RAF1, MEK1 and ERK1, thereby potentiating phosphorylation of ERK1/2. In addition, activation of Wnt/β-catenin signaling induces EIF3H expression. EIF3H/HAX1 axis promotes CRC tumorigenesis and metastasis in mouse orthotopic cancer model. Significantly, combined targeting Wnt and RAF1-ERK1/2 signaling synergistically inhibits tumor growth in EIF3H-high patient-derived xenografts. These results uncover the important roles of EIF3H in mediating CRC progression through regulating HAX1 and RAF1-ERK1/2 signaling. EIF3H represents a promising therapeutic target and prognostic marker in CRC.
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Affiliation(s)
- Huilin Jin
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Hepatobiliary, Pancreatic and Splenic surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoling Huang
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qihao Pan
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Obstetrics and Gynecology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ning Ma
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoshan Xie
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yue Wei
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Fenghai Yu
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Weijie Wen
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Boyu Zhang
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Peng Zhang
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xijie Chen
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jie Wang
- Department of Radiation Oncology, Dalian Municipal Central Hospital, Dalian, China
| | - Ran-Yi Liu
- State Key Laboratory of Oncology in South China & Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Junzhong Lin
- State Key Laboratory of Oncology in South China & Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiangqi Meng
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Mong-Hong Lee
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
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7
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Syriste L, Patel DT, Stogios PJ, Skarina T, Patel D, Savchenko A. An acetyltransferase effector conserved across Legionella species targets the eukaryotic eIF3 complex to modulate protein translation. mBio 2024; 15:e0322123. [PMID: 38335095 PMCID: PMC10936415 DOI: 10.1128/mbio.03221-23] [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: 12/05/2023] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
The survival of Legionella spp. as intracellular pathogens relies on the combined action of protein effectors delivered inside their eukaryotic hosts by the Dot/Icm (defective in organelle trafficking/intracellular multiplication) type IVb secretion system. The specific repertoire of effector arsenals varies dramatically across over 60 known species of this genera with Legionella pneumophila responsible for most cases of Legionnaires' disease in humans encoding over 360 Dot/Icm effectors. However, a small subset of "core" effectors appears to be conserved across all Legionella species raising an intriguing question of their role in these bacteria's pathogenic strategy, which for most of these effectors remains unknown. L. pneumophila Lpg0103 effector, also known as VipF, represents one of the core effector families that features a tandem of Gcn5-related N-acetyltransferase (GNAT) domains. Here, we present the crystal structure of the Lha0223, the VipF representative from Legionella hackeliae in complex with acetyl-coenzyme A determined to 1.75 Å resolution. Our structural analysis suggested that this effector family shares a common fold with the two GNAT domains forming a deep groove occupied by residues conserved across VipF homologs. Further analysis suggested that only the C-terminal GNAT domain of VipF effectors retains the active site composition compatible with catalysis, whereas the N-terminal GNAT domain binds the ligand in a non-catalytical mode. We confirmed this by in vitro enzymatic assays which revealed VipF activity not only against generic small molecule substrates, such as chloramphenicol, but also against poly-L-lysine and histone-derived peptides. We identified the human eukaryotic translation initiation factor 3 (eIF3) complex co-precipitating with Lpg0103 and demonstrated the direct interaction between the several representatives of the VipF family, including Lpg0103 and Lha0223 with the K subunit of eIF3. According to our data, these interactions involve primarily the C-terminal tail of eIF3-K containing two lysine residues that are acetylated by VipF. VipF catalytic activity results in the suppression of eukaryotic protein translation in vitro, revealing the potential function of VipF "core" effectors in Legionella's pathogenic strategy.IMPORTANCEBy translocating effectors inside the eukaryotic host cell, bacteria can modulate host cellular processes in their favor. Legionella species, which includes the pneumonia-causing Legionella pneumophila, encode a widely diverse set of effectors with only a small subset that is conserved across this genus. Here, we demonstrate that one of these conserved effector families, represented by L. pneumophila VipF (Lpg0103), is a tandem Gcn5-related N-acetyltransferase interacting with the K subunit of human eukaryotic initiation factor 3 complex. VipF catalyzes the acetylation of lysine residues on the C-terminal tail of the K subunit, resulting in the suppression of eukaryotic translation initiation factor 3-mediated protein translation in vitro. These new data provide the first insight into the molecular function of this pathogenic factor family common across Legionellae.
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Affiliation(s)
- Lukas Syriste
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Deepak T. Patel
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Peter J. Stogios
- Department of Chemical Engineering and Applied Chemistry, Toronto University, Toronto, Ontario, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, Toronto University, Toronto, Ontario, Canada
| | - Dhruvin Patel
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Chemical Engineering and Applied Chemistry, Toronto University, Toronto, Ontario, Canada
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8
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Brito Querido J, Sokabe M, Díaz-López I, Gordiyenko Y, Fraser CS, Ramakrishnan V. The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A. Nat Struct Mol Biol 2024; 31:455-464. [PMID: 38287194 PMCID: PMC10948362 DOI: 10.1038/s41594-023-01196-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 11/30/2023] [Indexed: 01/31/2024]
Abstract
Eukaryotic translation initiation involves recruitment of the 43S pre-initiation complex to the 5' end of mRNA by the cap-binding complex eIF4F, forming the 48S translation initiation complex (48S), which then scans along the mRNA until the start codon is recognized. We have previously shown that eIF4F binds near the mRNA exit channel of the 43S, leaving open the question of how mRNA secondary structure is removed as it enters the mRNA channel on the other side of the 40S subunit. Here we report the structure of a human 48S that shows that, in addition to the eIF4A that is part of eIF4F, there is a second eIF4A helicase bound at the mRNA entry site, which could unwind RNA secondary structures as they enter the 48S. The structure also reveals conserved interactions between eIF4F and the 43S, probaby explaining how eIF4F can promote mRNA recruitment in all eukaryotes.
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Affiliation(s)
- Jailson Brito Querido
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Masaaki Sokabe
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA, USA
| | | | | | - Christopher S Fraser
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA, USA.
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9
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Brito Querido J, Díaz-López I, Ramakrishnan V. The molecular basis of translation initiation and its regulation in eukaryotes. Nat Rev Mol Cell Biol 2024; 25:168-186. [PMID: 38052923 DOI: 10.1038/s41580-023-00624-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2023] [Indexed: 12/07/2023]
Abstract
The regulation of gene expression is fundamental for life. Whereas the role of transcriptional regulation of gene expression has been studied for several decades, it has been clear over the past two decades that post-transcriptional regulation of gene expression, of which translation regulation is a major part, can be equally important. Translation can be divided into four main stages: initiation, elongation, termination and ribosome recycling. Translation is controlled mainly during its initiation, a process which culminates in a ribosome positioned with an initiator tRNA over the start codon and, thus, ready to begin elongation of the protein chain. mRNA translation has emerged as a powerful tool for the development of innovative therapies, yet the detailed mechanisms underlying the complex process of initiation remain unclear. Recent studies in yeast and mammals have started to shed light on some previously unclear aspects of this process. In this Review, we discuss the current state of knowledge on eukaryotic translation initiation and its regulation in health and disease. Specifically, we focus on recent advances in understanding the processes involved in assembling the 43S pre-initiation complex and its recruitment by the cap-binding complex eukaryotic translation initiation factor 4F (eIF4F) at the 5' end of mRNA. In addition, we discuss recent insights into ribosome scanning along the 5' untranslated region of mRNA and selection of the start codon, which culminates in joining of the 60S large subunit and formation of the 80S initiation complex.
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Affiliation(s)
- Jailson Brito Querido
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Irene Díaz-López
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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10
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Zhang Q, Xian W, Li Z, Lu Q, Chen X, Ge J, Tang Z, Liu B, Chen Z, Gao X, Hottiger MO, Zhang P, Qiu J, Shao F, Liu X. Shigella induces stress granule formation by ADP-riboxanation of the eIF3 complex. Cell Rep 2024; 43:113789. [PMID: 38368608 DOI: 10.1016/j.celrep.2024.113789] [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: 04/20/2023] [Revised: 01/09/2024] [Accepted: 01/29/2024] [Indexed: 02/20/2024] Open
Abstract
Under stress conditions, translationally stalled mRNA and associated proteins undergo liquid-liquid phase separation and condense into cytoplasmic foci called stress granules (SGs). Many viruses hijack SGs for their pathogenesis; however, whether pathogenic bacteria also exploit this pathway remains unknown. Here, we report that members of the OspC family of Shigella flexneri induce SG formation in infected cells. Mechanistically, the OspC effectors target multiple subunits of the host translation initiation factor 3 complex by ADP-riboxanation. The modification of eIF3 leads to translational arrest and thus the formation of SGs. Furthermore, OspC-mediated SGs are beneficial for S. flexneri replication within infected host cells, and bacterial strains unable to induce SGs are attenuated for virulence in a murine model of infection. Our findings reveal a mechanism by which bacterial pathogens induce SG assembly by inactivating host translational machinery and promote bacterial proliferation in host cells.
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Affiliation(s)
- Qinxin Zhang
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Wei Xian
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zilin Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - Qian Lu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xindi Chen
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jinli Ge
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Zhiheng Tang
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Bohao Liu
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zhe Chen
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, School of Life Science, Shandong University, Qingdao 266000, China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, School of Life Science, Shandong University, Qingdao 266000, China
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Peipei Zhang
- Key Laboratory for Neuroscience, Ministry of Education/National Health and Family Planning Commission, Department of Biochemistry, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| | - Jiazhang Qiu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
| | - Feng Shao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xiaoyun Liu
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
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11
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Williams TD, Rousseau A. Translation regulation in response to stress. FEBS J 2024. [PMID: 38308808 DOI: 10.1111/febs.17076] [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: 11/09/2023] [Revised: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 02/05/2024]
Abstract
Cell stresses occur in a wide variety of settings: in disease, during industrial processes, and as part of normal day-to-day rhythms. Adaptation to these stresses requires cells to alter their proteome. Cells modify the proteins they synthesize to aid proteome adaptation. Changes in both mRNA transcription and translation contribute to altered protein synthesis. Here, we discuss the changes in translational mechanisms that occur following the onset of stress, and the impact these have on stress adaptation.
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Affiliation(s)
- Thomas D Williams
- MRC-PPU, School of Life Sciences, University of Dundee, UK
- Sir William Dunn School of Pathology, University of Oxford, UK
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12
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Chang J, Shin MK, Park J, Hwang HJ, Locker N, Ahn J, Kim D, Baek D, Park Y, Lee Y, Boo SH, Kim HI, Kim YK. An interaction between eIF4A3 and eIF3g drives the internal initiation of translation. Nucleic Acids Res 2023; 51:10950-10969. [PMID: 37811880 PMCID: PMC10639049 DOI: 10.1093/nar/gkad763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 08/30/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Abstract
An RNA structure or modified RNA sequences can provide a platform for ribosome loading and internal translation initiation. The functional significance of internal translation has recently been highlighted by the discovery that a subset of circular RNAs (circRNAs) is internally translated. However, the molecular mechanisms underlying the internal initiation of translation in circRNAs remain unclear. Here, we identify eIF3g (a subunit of eIF3 complex) as a binding partner of eIF4A3, a core component of the exon-junction complex (EJC) that is deposited onto spliced mRNAs and plays multiple roles in the regulation of gene expression. The direct interaction between eIF4A3-eIF3g serves as a molecular linker between the eIF4A3 and eIF3 complex, thereby facilitating internal ribosomal entry. Protein synthesis from in vitro-synthesized circRNA demonstrates eIF4A3-driven internal translation, which relies on the eIF4A3-eIF3g interaction. Furthermore, our transcriptome-wide analysis shows that efficient polysomal association of endogenous circRNAs requires eIF4A3. Notably, a subset of endogenous circRNAs can express a full-length intact protein, such as β-catenin, in an eIF4A3-dependent manner. Collectively, our results expand the understanding of the protein-coding potential of the human transcriptome, including circRNAs.
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Affiliation(s)
- Jeeyoon Chang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Min-Kyung Shin
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Joori Park
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyun Jung Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Nicolas Locker
- Department of Microbial and Cellular Sciences, University of Surrey, Guildford GU2 7HX, UK
| | - Junhak Ahn
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Doyeon Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Daehyun Baek
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeonkyoung Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yujin Lee
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Sung Ho Boo
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyeong-In Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yoon Ki Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
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13
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Volegova MP, Hermosillo C, Cate JHD. The Helix-Loop-Helix motif of human EIF3A regulates translation of proliferative cellular mRNAs. PLoS One 2023; 18:e0292080. [PMID: 37768948 PMCID: PMC10538695 DOI: 10.1371/journal.pone.0292080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/12/2023] [Indexed: 09/30/2023] Open
Abstract
Improper regulation of translation initiation, a vital checkpoint of protein synthesis in the cell, has been linked to a number of cancers. Overexpression of protein subunits of eukaryotic translation initiation factor 3 (eIF3) is associated with increased translation of mRNAs involved in cell proliferation. In addition to playing a major role in general translation initiation by serving as a scaffold for the assembly of translation initiation complexes, eIF3 regulates translation of specific cellular mRNAs and viral RNAs. Mutations in the N-terminal Helix-Loop-Helix (HLH) RNA-binding motif of the EIF3A subunit interfere with Hepatitis C Virus Internal Ribosome Entry Site (IRES) mediated translation initiation in vitro. Here we show that the EIF3A HLH motif controls translation of a small set of cellular transcripts enriched in oncogenic mRNAs, including MYC. We demonstrate that the HLH motif of EIF3A acts specifically on the 5' UTR of MYC mRNA and modulates the function of EIF4A1 on select transcripts during translation initiation. In Ramos lymphoma cell lines, which are dependent on MYC overexpression, mutations in the HLH motif greatly reduce MYC expression, impede proliferation and sensitize cells to anti-cancer compounds. These results reveal the potential of the EIF3A HLH motif in eIF3 as a promising chemotherapeutic target.
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Affiliation(s)
- Marina P. Volegova
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States of America
| | - Cynthia Hermosillo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States of America
| | - Jamie H. D. Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States of America
- Department of Chemistry, University of California, Berkeley, CA, United States of America
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
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14
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Pan Q, Yu F, Jin H, Zhang P, Huang X, Peng J, Xie X, Li X, Ma N, Wei Y, Wen W, Zhang J, Zhang B, Yu H, Xiao Y, Liu R, Liu Q, Meng X, Lee M. eIF3f Mediates SGOC Pathway Reprogramming by Enhancing Deubiquitinating Activity in Colorectal Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300759. [PMID: 37544925 PMCID: PMC10520677 DOI: 10.1002/advs.202300759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/25/2023] [Indexed: 08/08/2023]
Abstract
Numerous studies have demonstrated that individual proteins can moonlight. Eukaryotic Initiation translation factor 3, f subunit (eIF3f) is involved in critical biological functions; however, its role independent of protein translation in regulating colorectal cancer (CRC) is not characterized. Here, it is demonstrated that eIF3f is upregulated in CRC tumor tissues and that both Wnt and EGF signaling pathways are participating in eIF3f's oncogenic impact on targeting phosphoglycerate dehydrogenase (PHGDH) during CRC development. Mechanistically, EGF blocks FBXW7β-mediated PHGDH ubiquitination through GSK3β deactivation, and eIF3f antagonizes FBXW7β-mediated PHGDH ubiquitination through its deubiquitinating activity. Additionally, Wnt signals transcriptionally activate the expression of eIF3f, which also exerts its deubiquitinating activity toward MYC, thereby increasing MYC-mediated PHGDH transcription. Thereby, both impacts allow eIF3f to elevate the expression of PHGDH, enhancing Serine-Glycine-One-Carbon (SGOC) signaling pathway to facilitate CRC development. In summary, the study uncovers the intrinsic role and underlying molecular mechanism of eIF3f in SGOC signaling, providing novel insight into the strategies to target eIF3f-PHGDH axis in CRC.
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Affiliation(s)
- Qihao Pan
- Department of General SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Department of Obstetrics and GynecologyThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Fenghai Yu
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Huilin Jin
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Peng Zhang
- Department of General SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Xiaoling Huang
- Department of General SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Jingxuan Peng
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Xiaoshan Xie
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Xiangli Li
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Ning Ma
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Yue Wei
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Weijie Wen
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Jieping Zhang
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Boyu Zhang
- Department of General SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Hongyan Yu
- Department of Clinical Biological Resource BankGuangzhou Institute of PediatricsGuangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhou510623China
| | - Yuanxun Xiao
- Burn Plastic SurgeryYue bei People's HospitalWujiang512099China
| | - Ran‐yi Liu
- State Key Laboratory of Oncology in South China & Collaborative Innovation Center of Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Qingxin Liu
- Department of General SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Xiangqi Meng
- Department of General SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Mong‐Hong Lee
- Department of General SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Department of OncologyThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
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15
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Abaeva IS, Arhab Y, Miścicka A, Hellen CUT, Pestova TV. In vitro reconstitution of SARS-CoV-2 Nsp1-induced mRNA cleavage reveals the key roles of the N-terminal domain of Nsp1 and the RRM domain of eIF3g. Genes Dev 2023; 37:844-860. [PMID: 37821106 PMCID: PMC10620056 DOI: 10.1101/gad.350829.123] [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: 05/25/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023]
Abstract
SARS CoV-2 nonstructural protein 1 (Nsp1) is the major pathogenesis factor that inhibits host translation using a dual strategy of impairing initiation and inducing endonucleolytic cleavage of cellular mRNAs. To investigate the mechanism of cleavage, we reconstituted it in vitro on β-globin, EMCV IRES, and CrPV IRES mRNAs that use unrelated initiation mechanisms. In all instances, cleavage required Nsp1 and only canonical translational components (40S subunits and initiation factors), arguing against involvement of a putative cellular RNA endonuclease. Requirements for initiation factors differed for these mRNAs, reflecting their requirements for ribosomal attachment. Cleavage of CrPV IRES mRNA was supported by a minimal set of components consisting of 40S subunits and eIF3g's RRM domain. The cleavage site was located in the coding region 18 nt downstream from the mRNA entrance, indicating that cleavage occurs on the solvent side of the 40S subunit. Mutational analysis identified a positively charged surface on Nsp1's N-terminal domain (NTD) and a surface above the mRNA-binding channel on eIF3g's RRM domain that contain residues essential for cleavage. These residues were required for cleavage on all three mRNAs, highlighting general roles of the Nsp1 NTD and eIF3g's RRM domain in cleavage per se, irrespective of the mode of ribosomal attachment.
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Affiliation(s)
- Irina S Abaeva
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Yani Arhab
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Anna Miścicka
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Tatyana V Pestova
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
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16
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Bakti F, Stupperich H, Schmitt K, Valerius O, Köhler AM, Meister C, Strohdiek A, Harting R, Sasse C, Heimel K, Neumann P, Ficner R, Braus GH. Fungal COP9 signalosome assembly requires connection of two trimeric intermediates for integration of intrinsic deneddylase. Proc Natl Acad Sci U S A 2023; 120:e2305049120. [PMID: 37603767 PMCID: PMC10477865 DOI: 10.1073/pnas.2305049120] [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: 03/29/2023] [Accepted: 08/01/2023] [Indexed: 08/23/2023] Open
Abstract
The conserved eight-subunit COP9 signalosome (CSN) is required for multicellular fungal development. The CSN deneddylase cooperates with the Cand1 exchange factor to control replacements of E3 ubiquitin cullin RING ligase receptors, providing specificity to eukaryotic protein degradation. Aspergillus nidulans CSN assembles through a heptameric pre-CSN, which is activated by integration of the catalytic CsnE deneddylase. Combined genetic and biochemical approaches provided the assembly choreography within a eukaryotic cell for native fungal CSN. Interactomes of functional GFP-Csn subunit fusions in pre-CSN deficient fungal strains were compared by affinity purifications and mass spectrometry. Two distinct heterotrimeric CSN subcomplexes were identified as pre-CSN assembly intermediates. CsnA-C-H and CsnD-F-G form independently of CsnB, which connects the heterotrimers to a heptamer and enables subsequent integration of CsnE to form the enzymatically active CSN complex. Surveillance mechanisms control accurate Csn subunit amounts and correct cellular localization for sequential assembly since deprivation of Csn subunits changes the abundance and location of remaining Csn subunits.
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Affiliation(s)
- Fruzsina Bakti
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Helena Stupperich
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Kerstin Schmitt
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Anna M. Köhler
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Cindy Meister
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Anja Strohdiek
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Rebekka Harting
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Christoph Sasse
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Kai Heimel
- Department of Microbial Cell Biology, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
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17
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Tang J, Long G, Li X, Zhou L, Zhou Y, Wu Z. The deubiquitinase EIF3H promotes hepatocellular carcinoma progression by stabilizing OGT and inhibiting ferroptosis. Cell Commun Signal 2023; 21:198. [PMID: 37559097 PMCID: PMC10413709 DOI: 10.1186/s12964-023-01220-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/09/2023] [Indexed: 08/11/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent and lethal human malignancies, and with quite limited treatment alternatives. The proteasome is responsible for most of the protein degradation in eukaryotic cells and required for the maintenance of intracellular homeostasis. However, its potential role in HCC is largely unknown. In the current study, we identified eukaryotic translation initiation factor 3 subunit H (EIF3H), belonging to the JAB1/MPN/MOV34 (JAMM) superfamily, as a bona fide deubiquitylase of O-GlcNAc transferase (OGT) in HCC. We explored that EIF3H was positively associated with OGT in HCC and was related to the unfavorable prognosis. EIF3H could interact with, deubiquitylate, and stabilize OGT in a deubiquitylase-dependent manner. Specifically, EIF3H was associated with the GT domain of ERα via its JAB/MP domain, thus inhibiting the K48-linked ubiquitin chain on OGT. Besides, we demonstrated that the knockdown of EIF3H significantly reduced OGT protein expression, cell proliferation and invasion, and caused G1/S arrest of HCC. We also found that the deletion of EIF3H prompted ferroptosis in HCC cells. Finally, the effects of EIF3H depletion could be reversed by further OGT overexpression, implying that the OGT status is indispensable for EIF3H function in HCC carcinogenesis. In summary, our study described the oncogenic function of EIF3H and revealed an interesting post-translational mechanism between EIF3H, OGT, and ferroptosis in HCC. Targeting the EIF3H may be a promising approach in HCC. Video Abstract.
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Affiliation(s)
- Jianing Tang
- Department of Liver Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Guo Long
- Department of Liver Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xuanxuan Li
- Department of Liver Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ledu Zhou
- Department of Liver Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yangying Zhou
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Zheyu Wu
- Department of Liver Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Department of Orthopedics, The Second Affiliated Hospital of Naval Medical University, Shanghai, 200000, China.
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18
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Metzner K, O’Meara MJ, Halligan B, Wotring JW, Sexton JZ, O’Meara TR. Imaging-Based Screening Identifies Modulators of the eIF3 Translation Initiation Factor Complex in Candida albicans. Antimicrob Agents Chemother 2023; 67:e0050323. [PMID: 37382550 PMCID: PMC10353439 DOI: 10.1128/aac.00503-23] [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: 04/18/2023] [Accepted: 06/07/2023] [Indexed: 06/30/2023] Open
Abstract
Fungal pathogens like Candida albicans can cause devastating human disease. Treatment of candidemia is complicated by the high rate of resistance to common antifungal therapies. Additionally, there is host toxicity associated with many antifungal compounds due to the conservation between essential mammalian and fungal proteins. An attractive new approach for antimicrobial development is to target virulence factors: non-essential processes that are required for the organism to cause disease in human hosts. This approach expands the potential target space while reducing the selective pressure toward resistance, as these targets are not essential for viability. In C. albicans, a key virulence factor is the ability to transition to hyphal morphology. We developed a high-throughput image analysis pipeline to distinguish between yeast and filamentous growth in C. albicans at the single cell level. Based on this phenotypic assay, we screened the FDA drug repurposing library of 2,017 compounds for their ability to inhibit filamentation and identified 33 compounds that block the hyphal transition in C. albicans with IC50 values ranging from 0.2 to 150 μM. Multiple compounds showed a phenyl sulfone chemotype, prompting further analysis. Of these phenyl sulfones, NSC 697923 displayed the most efficacy, and by selecting for resistant mutants, we identified eIF3 as the target of NSC 697923 in C. albicans.
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Affiliation(s)
- Katura Metzner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Matthew J. O’Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Benjamin Halligan
- University of Michigan Center for Drug Repurposing, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jesse W. Wotring
- University of Michigan Center for Drug Repurposing, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, College of Pharmacy, Ann Arbor, Michigan, USA
| | - Jonathan Z. Sexton
- University of Michigan Center for Drug Repurposing, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, College of Pharmacy, Ann Arbor, Michigan, USA
| | - Teresa R. O’Meara
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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19
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Meng Q, Schatten H, Zhou Q, Chen J. Crosstalk between m6A and coding/non-coding RNA in cancer and detection methods of m6A modification residues. Aging (Albany NY) 2023; 15:6577-6619. [PMID: 37437245 PMCID: PMC10373953 DOI: 10.18632/aging.204836] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/15/2023] [Indexed: 07/14/2023]
Abstract
N6-methyladenosine (m6A) is one of the most common and well-known internal RNA modifications that occur on mRNAs or ncRNAs. It affects various aspects of RNA metabolism, including splicing, stability, translocation, and translation. An abundance of evidence demonstrates that m6A plays a crucial role in various pathological and biological processes, especially in tumorigenesis and tumor progression. In this article, we introduce the potential functions of m6A regulators, including "writers" that install m6A marks, "erasers" that demethylate m6A, and "readers" that determine the fate of m6A-modified targets. We have conducted a review on the molecular functions of m6A, focusing on both coding and noncoding RNAs. Additionally, we have compiled an overview of the effects noncoding RNAs have on m6A regulators and explored the dual roles of m6A in the development and advancement of cancer. Our review also includes a detailed summary of the most advanced databases for m6A, state-of-the-art experimental and sequencing detection methods, and machine learning-based computational predictors for identifying m6A sites.
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Affiliation(s)
- Qingren Meng
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People’s Hospital, The Second Hospital Affiliated with the Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Heide Schatten
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Qian Zhou
- International Cancer Center, Shenzhen University Medical School, Shenzhen, Guangdong Province, China
| | - Jun Chen
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People’s Hospital, The Second Hospital Affiliated with the Southern University of Science and Technology, Shenzhen, Guangdong Province, China
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20
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Dobrescu I, Hammam E, Dziekan JM, Claës A, Halby L, Preiser P, Bozdech Z, Arimondo PB, Scherf A, Nardella F. Plasmodium falciparum Eukaryotic Translation Initiation Factor 3 is Stabilized by Quinazoline-Quinoline Bisubstrate Inhibitors. ACS Infect Dis 2023; 9:1257-1266. [PMID: 37216290 PMCID: PMC10262199 DOI: 10.1021/acsinfecdis.3c00127] [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: 03/16/2023] [Indexed: 05/24/2023]
Abstract
Malaria drug resistance is hampering the fight against the deadliest parasitic disease affecting over 200 million people worldwide. We recently developed quinoline-quinazoline-based inhibitors (as compound 70) as promising new antimalarials. Here, we aimed to investigate their mode of action by using thermal proteome profiling (TPP). The eukaryotic translation initiation factor 3 (EIF3i) subunit I was identified as the main target protein stabilized by compound 70 in Plasmodium falciparum. This protein has never been characterized in malaria parasites. P. falciparum parasite lines were generated expressing either a HA tag or an inducible knockdown of the PfEIF3i gene to further characterize the target protein. PfEIF3i was stabilized in the presence of compound 70 in a cellular thermal shift Western blot assay, pointing that PfEIF3i indeed interacts with quinoline-quinazoline-based inhibitors. In addition, PfEIF3i-inducible knockdown blocks intra-erythrocytic development in the trophozoite stage, indicating that it has a vital function. We show that PfEIF3i is mostly expressed in late intra-erythrocytic stages and localizes in the cytoplasm. Previous mass spectrometry reports show that PfEIF3i is expressed in all parasite life cycle stages. Further studies will explore the potential of PfEIF3i as a target for the design of new antimalarial drugs active all along the life cycle of the parasite.
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Affiliation(s)
- Irina Dobrescu
- Unité
Biology of Host-Parasite Interactions, Department of Parasites and
Insect Vectors, Institut Pasteur, Université
de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue Du Dr Roux, Paris 75015, France
| | - Elie Hammam
- Unité
Biology of Host-Parasite Interactions, Department of Parasites and
Insect Vectors, Institut Pasteur, Université
de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue Du Dr Roux, Paris 75015, France
| | - Jerzy M. Dziekan
- School
of Biological Sciences, Nanyang Technological
University, Singapore 639798, Singapore
| | - Aurélie Claës
- Unité
Biology of Host-Parasite Interactions, Department of Parasites and
Insect Vectors, Institut Pasteur, Université
de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue Du Dr Roux, Paris 75015, France
| | - Ludovic Halby
- Epigenetic
Chemical Biology, Department of Structural Biology and Chemistry,
Institut Pasteur, Université de Paris-Cité,
UMR n3523 Chem4Life, CNRS, 28 Rue Du Dr Roux, Paris 75015, France
| | - Peter Preiser
- School
of Biological Sciences, Nanyang Technological
University, Singapore 639798, Singapore
| | - Zbynek Bozdech
- School
of Biological Sciences, Nanyang Technological
University, Singapore 639798, Singapore
| | - Paola B. Arimondo
- Epigenetic
Chemical Biology, Department of Structural Biology and Chemistry,
Institut Pasteur, Université de Paris-Cité,
UMR n3523 Chem4Life, CNRS, 28 Rue Du Dr Roux, Paris 75015, France
| | - Artur Scherf
- Unité
Biology of Host-Parasite Interactions, Department of Parasites and
Insect Vectors, Institut Pasteur, Université
de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue Du Dr Roux, Paris 75015, France
| | - Flore Nardella
- Unité
Biology of Host-Parasite Interactions, Department of Parasites and
Insect Vectors, Institut Pasteur, Université
de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue Du Dr Roux, Paris 75015, France
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21
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Bose P, Baron N, Pullaiahgari D, Ben-Zvi A, Shapira M. LeishIF3d is a non-canonical cap-binding protein in Leishmania. Front Mol Biosci 2023; 10:1191934. [PMID: 37325473 PMCID: PMC10266417 DOI: 10.3389/fmolb.2023.1191934] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Translation of most cellular mRNAs in eukaryotes proceeds through a cap-dependent pathway, whereby the cap-binding complex, eIF4F, anchors the pre-initiation complex at the 5' end of mRNAs driving translation initiation. The genome of Leishmania encodes a large repertoire of cap-binding complexes that fulfill a variety of functions possibly involved in survival along the life cycle. However, most of these complexes function in the promastigote life form that resides in the sand fly vector and decrease their activity in amastigotes, the mammalian life form. Here we examined the possibility that LeishIF3d drives translation in Leishmania using alternative pathways. We describe a non-canonical cap-binding activity of LeishIF3d and examine its potential role in driving translation. LeishIF3d is required for translation, as reducing its expression by a hemizygous deletion reduces the translation activity of the LeishIF3d(+/-) mutant cells. Proteomic analysis of the mutant cells highlights the reduced expression of flagellar and cytoskeletal proteins, as reflected in the morphological changes observed in the mutant cells. Targeted mutations in two predicted alpha helices diminish the cap-binding activity of LeishIF3d. Overall, LeishIF3d could serve as a driving force for alternative translation pathways, although it does not seem to offer an alternative pathway for translation in amastigotes.
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Affiliation(s)
- Priyanka Bose
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Nofar Baron
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | | | - Anat Ben-Zvi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Michal Shapira
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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22
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Yao Z, Ramachandran S, Huang S, Jami-Alahmadi Y, Wohlschlegel JA, Li MMH. Chikungunya virus glycoproteins transform macrophages into productive viral dissemination vessels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.542714. [PMID: 37398144 PMCID: PMC10312455 DOI: 10.1101/2023.05.29.542714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Despite their role as innate sentinels, macrophages are cellular reservoirs for chikungunya virus (CHIKV), a highly pathogenic arthropod-borne alphavirus that has caused unprecedented epidemics worldwide. Here, we took interdisciplinary approaches to elucidate the CHIKV determinants that subvert macrophages into virion dissemination vessels. Through comparative infection using chimeric alphaviruses and evolutionary selection analyses, we discovered for the first time that CHIKV glycoproteins E2 and E1 coordinate efficient virion production in macrophages with the domains involved under positive selection. We performed proteomics on CHIKV-infected macrophages to identify cellular proteins interacting with the precursor and/or mature forms of viral glycoproteins. We uncovered two E1-binding proteins, signal peptidase complex subunit 3 (SPCS3) and eukaryotic translation initiation factor 3 (eIF3k), with novel inhibitory activities against CHIKV production. These results highlight how CHIKV E2 and E1 have been evolutionarily selected for viral dissemination likely through counteracting host restriction factors, making them attractive targets for therapeutic intervention.
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Affiliation(s)
- Zhenlan Yao
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sangeetha Ramachandran
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Serina Huang
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Melody M H Li
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
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23
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Abaeva IS, Arhab Y, Miścicka A, Hellen CUT, Pestova TV. In vitro reconstitution of SARS CoV-2 Nsp1-induced mRNA cleavage reveals the key roles of the N-terminal domain of Nsp1 and the RRM domain of eIF3g. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542379. [PMID: 37292671 PMCID: PMC10245999 DOI: 10.1101/2023.05.25.542379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
SARS CoV-2 nonstructural protein 1 (Nsp1) is the major pathogenesis factor that inhibits host translation using a dual strategy of impairing initiation and inducing endonucleolytic cleavage of cellular mRNAs. To investigate the mechanism of cleavage, we reconstituted it in vitro on β-globin, EMCV IRES and CrPV IRES mRNAs that use unrelated initiation mechanisms. In all instances, cleavage required Nsp1 and only canonical translational components (40S subunits and initiation factors), arguing against involvement of a putative cellular RNA endonuclease. Requirements for initiation factors differed for these mRNAs, reflecting their requirements for ribosomal attachment. Cleavage of CrPV IRES mRNA was supported by a minimal set of components consisting of 40S subunits and eIF3g's RRM domain. The cleavage site was located in the coding region 18 nucleotides downstream from the mRNA entrance indicating that cleavage occurs on the solvent side of the 40S subunit. Mutational analysis identified a positively charged surface on Nsp1's N-terminal domain (NTD) and a surface above the mRNA-binding channel on eIF3g's RRM domain that contain residues essential for cleavage. These residues were required for cleavage on all three mRNAs, highlighting general roles of Nsp1-NTD and eIF3g's RRM domain in cleavage per se, irrespective of the mode of ribosomal attachment.
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Affiliation(s)
- Irina S. Abaeva
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Yani Arhab
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Anna Miścicka
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | | | - Tatyana V. Pestova
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
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24
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Duan H, Zhang S, Zarai Y, Öllinger R, Wu Y, Sun L, Hu C, He Y, Tian G, Rad R, Kong X, Cheng Y, Tuller T, Wolf DA. eIF3 mRNA selectivity profiling reveals eIF3k as a cancer-relevant regulator of ribosome content. EMBO J 2023:e112362. [PMID: 37155573 DOI: 10.15252/embj.2022112362] [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: 08/16/2022] [Revised: 03/04/2023] [Accepted: 04/20/2023] [Indexed: 05/10/2023] Open
Abstract
eIF3, whose subunits are frequently overexpressed in cancer, regulates mRNA translation from initiation to termination, but mRNA-selective functions of individual subunits remain poorly defined. Using multiomic profiling upon acute depletion of eIF3 subunits, we observed that while eIF3a, b, e, and f markedly differed in their impact on eIF3 holo-complex formation and translation, they were each required for cancer cell proliferation and tumor growth. Remarkably, eIF3k showed the opposite pattern with depletion promoting global translation, cell proliferation, tumor growth, and stress resistance through repressing the synthesis of ribosomal proteins, especially RPS15A. Whereas ectopic expression of RPS15A mimicked the anabolic effects of eIF3k depletion, disruption of eIF3 binding to the 5'-UTR of RSP15A mRNA negated them. eIF3k and eIF3l are selectively downregulated in response to endoplasmic reticulum and oxidative stress. Supported by mathematical modeling, our data uncover eIF3k-l as a mRNA-specific module which, through controlling RPS15A translation, serves as a rheostat of ribosome content, possibly to secure spare translational capacity that can be mobilized during stress.
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Affiliation(s)
- Haoran Duan
- State Key Laboratory of Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Siqiong Zhang
- State Key Laboratory of Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Yoram Zarai
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics and Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Yanmeng Wu
- State Key Laboratory of Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Li Sun
- State Key Laboratory of Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Cheng Hu
- State Key Laboratory of Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Yaohui He
- State Key Laboratory of Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Guiyou Tian
- State Key Laboratory of Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics and Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Xiangquan Kong
- Department of Radiation Oncology, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
| | - Yabin Cheng
- State Key Laboratory of Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
- The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel
| | - Dieter A Wolf
- State Key Laboratory of Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
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25
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Zhang D, Zhu L, Wang F, Li P, Wang Y, Gao Y. Molecular mechanisms of eukaryotic translation fidelity and their associations with diseases. Int J Biol Macromol 2023; 242:124680. [PMID: 37141965 DOI: 10.1016/j.ijbiomac.2023.124680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Abstract
Converting genetic information into functional proteins is a complex, multi-step process, with each step being tightly regulated to ensure the accuracy of translation, which is critical to cellular health. In recent years, advances in modern biotechnology, especially the development of cryo-electron microscopy and single-molecule techniques, have enabled a clearer understanding of the mechanisms of protein translation fidelity. Although there are many studies on the regulation of protein translation in prokaryotes, and the basic elements of translation are highly conserved in prokaryotes and eukaryotes, there are still great differences in the specific regulatory mechanisms. This review describes how eukaryotic ribosomes and translation factors regulate protein translation and ensure translation accuracy. However, a certain frequency of translation errors does occur in translation, so we describe diseases that arise when the rate of translation errors reaches or exceeds a threshold of cellular tolerance.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
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26
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Metzner K, O’Meara MJ, Halligan B, Wotring JW, Sexton JZ, O’Meara TR. Imaging-based screening identifies modulators of the eIF3 translation initiation factor complex in Candida albicans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537517. [PMID: 37131825 PMCID: PMC10153179 DOI: 10.1101/2023.04.19.537517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Fungal pathogens like Candida albicans can cause devastating human disease. Treatment of candidemia is complicated by the high rate of resistance to common antifungal therapies. Additionally, there is host toxicity associated with many antifungal compounds due to the conservation between essential mammalian and fungal proteins. An attractive new approach for antimicrobial development is to target virulence factors: non-essential processes that are required for the organism to cause disease in human hosts. This approach expands the potential target space while reducing the selective pressure towards resistance, as these targets are not essential for viability. In C. albicans, a key virulence factor is the ability to transition to hyphal morphology. We developed a high-throughput image analysis pipeline to distinguish between yeast and filamentous growth in C. albicans at the single cell level. Based on this phenotypic assay, we screened the FDA drug repurposing library of 2,017 compounds for their ability to inhibit filamentation and identified 33 compounds that block the hyphal transition in C. albicans with IC 50 values ranging from 0.2 to 150 µM. Multiple compounds showed a phenyl vinyl sulfone chemotype, prompting further analysis. Of these phenyl vinyl sulfones, NSC 697923 displayed the most efficacy, and by selecting for resistant mutants, we identified eIF3 as the target of NSC 697923 in C. albicans .
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Affiliation(s)
- Katura Metzner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Matthew J O’Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Benjamin Halligan
- University of Michigan Center for Drug Repurposing, USA
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jesse W. Wotring
- Department of Medicinal Chemistry, College of Pharmacy, Ann Arbor, MI, USA
- University of Michigan Center for Drug Repurposing, USA
| | - Jonathan Z Sexton
- Department of Medicinal Chemistry, College of Pharmacy, Ann Arbor, MI, USA
- University of Michigan Center for Drug Repurposing, USA
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Teresa R O’Meara
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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27
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Fedry J, Silva J, Vanevic M, Fronik S, Mechulam Y, Schmitt E, des Georges A, Faller W, Förster F. Visualization of translation reorganization upon persistent collision stress in mammalian cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533914. [PMID: 36993420 PMCID: PMC10055323 DOI: 10.1101/2023.03.23.533914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Aberrantly slow mRNA translation leads to ribosome stalling and subsequent collision with the trailing neighbor. Ribosome collisions have recently been shown to act as stress sensors in the cell, with the ability to trigger stress responses balancing survival and apoptotic cell-fate decisions depending on the stress level. However, we lack a molecular understanding of the reorganization of translation processes over time in mammalian cells exposed to an unresolved collision stress. Here we visualize the effect of a persistent collision stress on translation using in situ cryo electron tomography. We observe that low dose anisomycin collision stress leads to the stabilization of Z-site bound tRNA on elongating 80S ribosomes, as well as to the accumulation of an off-pathway 80S complex possibly resulting from collision splitting events. We visualize collided disomes in situ, occurring on compressed polysomes and revealing a stabilized geometry involving the Z-tRNA and L1 stalk on the stalled ribosome, and eEF2 bound to its collided rotated-2 neighbor. In addition, non-functional post-splitting 60S complexes accumulate in the stressed cells, indicating a limiting Ribosome associated Quality Control clearing rate. Finally, we observe the apparition of tRNA-bound aberrant 40S complexes shifting with the stress timepoint, suggesting a succession of different initiation inhibition mechanisms over time. Altogether, our work visualizes the changes of translation complexes under persistent collision stress in mammalian cells, indicating how perturbations in initiation, elongation and quality control processes contribute to an overall reduced protein synthesis.
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Affiliation(s)
- Juliette Fedry
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Joana Silva
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mihajlo Vanevic
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Stanley Fronik
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Amédée des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, USA
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, City University of New York, New York, NY, USA
| | - William Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands
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28
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Montiel-Dávalos A, Ayala Y, Hernández G. The dark side of mRNA translation and the translation machinery in glioblastoma. Front Cell Dev Biol 2023; 11:1086964. [PMID: 36994107 PMCID: PMC10042294 DOI: 10.3389/fcell.2023.1086964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/03/2023] [Indexed: 03/14/2023] Open
Abstract
Among the different types of cancer affecting the central nervous system (CNS), glioblastoma (GB) is classified by the World Health Organization (WHO) as the most common and aggressive CNS cancer in adults. GB incidence is more frequent among persons aged 45–55 years old. GB treatments are based on tumor resection, radiation, and chemotherapies. The current development of novel molecular biomarkers (MB) has led to a more accurate prediction of GB progression. Moreover, clinical, epidemiological, and experimental studies have established genetic variants consistently associated with the risk of suffering GB. However, despite the advances in these fields, the survival expectancy of GB patients is still shorter than 2 years. Thus, fundamental processes inducing tumor onset and progression remain to be elucidated. In recent years, mRNA translation has been in the spotlight, as its dysregulation is emerging as a key cause of GB. In particular, the initiation phase of translation is most involved in this process. Among the crucial events, the machinery performing this phase undergoes a reconfiguration under the hypoxic conditions in the tumor microenvironment. In addition, ribosomal proteins (RPs) have been reported to play translation-independent roles in GB development. This review focuses on the research elucidating the tight relationship between translation initiation, the translation machinery, and GB. We also summarize the state-of-the-art drugs targeting the translation machinery to improve patients’ survival. Overall, the recent advances in this field are shedding new light on the dark side of translation in GB.
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Bustamante HA, Albornoz N, Morselli E, Soza A, Burgos PV. Novel insights into the non-canonical roles of PSMD14/POH1/Rpn11 in proteostasis and in the modulation of cancer progression. Cell Signal 2023; 101:110490. [PMID: 36241058 DOI: 10.1016/j.cellsig.2022.110490] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/28/2022] [Accepted: 10/04/2022] [Indexed: 11/07/2022]
Abstract
PSMD14/POH1/Rpn11 plays a crucial role in cellular homeostasis. PSMD14 is a structural subunit of the lid subcomplex of the proteasome 19S regulatory particle with constitutive deubiquitinase activity. Canonically, PSMD14 removes the full ubiquitin chains with K48-linkages by hydrolyzing the isopeptide bond between the substrate and the C-terminus of the first ubiquitin, a crucial step for the entry of substrates into the catalytic barrel of the 20S proteasome and their subsequent degradation, all in context of the 26S proteasome. However, more recent discoveries indicate PSMD14 DUB activity is not only coupled to the translocation of substrates into the core of 20S proteasome. During the assembly of the lid, activity of PSMD14 has been detected in the context of the heterodimer with PSMD7. Additionally, assembly of the lid subcomplex occurs as an independent event of the base subcomplex and 20S proteasome. This feature opens the possibility that the regulatory particle, free lid subcomplex or the heterodimer PSMD14-PSMD7 might play other physiological roles including a positive function on protein stability through deubiquitination. Here we discuss scenarios that could enhance this PSMD14 non-canonical pathway, the potential impact in preventing degradation of substrates by autophagy highlighting the main findings that support this hypothesis. Finally, we discuss why this information should be investigated in biomedicine specifically with focus on cancer progression to design new therapeutic strategies against the lid subcomplex and the heterodimer PSMD14-PSMD7, highlighting PSMD14 as a druggable target for cancer therapy.
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Affiliation(s)
- Hianara A Bustamante
- Instituto de Microbiología Clínica, Facultad de Medicina, Universidad Austral de Chile, Valdivia 5110566, Chile.
| | - Nicolás Albornoz
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago 7510157, Chile; Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago 7780272, Chile.
| | - Eugenia Morselli
- Departamento de Ciencias Básicas, Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago 7510157, Chile; Centro de Investigación en Autofagia, Santiago, Chile.
| | - Andrea Soza
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago 7510157, Chile; Centro de Envejecimiento y Regeneración (CARE-UC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica, Santiago 8331150, Chile; Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago 7780272, Chile.
| | - Patricia V Burgos
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago 7510157, Chile; Centro de Investigación en Autofagia, Santiago, Chile; Centro de Envejecimiento y Regeneración (CARE-UC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica, Santiago 8331150, Chile; Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago 7780272, Chile.
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Fang P, Han Y, Qu Y, Wang X, Zhang Y, Zhang W, Zhang N, Li G, Ma W. EIF3B stabilizes PTGS2 expression by counteracting MDM2-mediated ubiquitination to promote the development and progression of malignant melanoma. Cancer Sci 2022; 113:4181-4192. [PMID: 36050601 DOI: 10.1111/cas.15543] [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: 08/02/2021] [Revised: 08/05/2022] [Accepted: 08/10/2022] [Indexed: 12/15/2022] Open
Abstract
Malignant melanoma (MM) is a neoplasm that develops from human melanocytes. It was reported that eukaryotic translation initiation factor 3 subunit B (EIF3B) is associated with multiple types of cancers, but its role in MM has not been reported. In the present study, we found that EIF3B was abundantly expressed in MM and was strongly related to lymphatic metastasis and pathological stage of MM patients. In addition, EIF3B depletion could block the progression of MM in vitro and in vivo. In contrast, EIF3B overexpression increased cell proliferation and migration in melanoma cells. More importantly, we identified that EIF3B's driver role in MM was mediated by PTGS2. In detail, we found that EIF3B stabilized PTGS2 expression by inhibiting PTGS2 ubiquitination, which is mediated by the E3 ligase MDM2. Moreover, like EIF3B, silencing PTGS2 could suppress MM development, and more interestingly, it could reverse the situation caused by overexpression of EIF3B in vitro and in vivo. Furthermore, the proliferation and migration inhibited by silencing of EIF3B were also partially recovered by overexpression of PTGS2. Overall, our findings revealed the potential of EIF3B as a therapeutic target for MM. Identification of EIF3B's function in MM may pave the way for future development of more specific and more effective targeted therapy strategies against MM.
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Affiliation(s)
- Pengli Fang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yikai Han
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanhong Qu
- Oncology Department of Laiyang People's Hospital, Laiyang, China
| | - Xin Wang
- Department of Radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yong Zhang
- Department of Cancer Biotherapy Center, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Wei Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Na Zhang
- Department of Dermatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guangshuai Li
- Department of Plastic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wang Ma
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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31
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Lin Z, Shen D, Yang B, Woo CM. Molecular and Structural Characterization of Lenalidomide-Mediated Sequestration of eIF3i. ACS Chem Biol 2022; 17:3229-3237. [PMID: 36325969 DOI: 10.1021/acschembio.2c00706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Lenalidomide is a ligand of the E3 ligase substrate adapter cereblon (CRBN) that achieves its clinical effects in part by the promotion of substrate recruitment and degradation. In contrast to prior targets, eIF3i is recruited but not degraded upon complex formation with lenalidomide and CRBN, although the structural details and mechanistic outcomes of this interaction are unresolved. Here, we characterize the structural basis and mechanistic outcomes of lenalidomide-induced sequestration of eIF3i from the eIF3 complex. Identification of the binding interface on eIF3i by a covalent lenalidomide probe and mass spectrometry rationalizes the sequestration event. We further connect eIF3i and CRBN to lenalidomide-driven effects on angiogenic markers, Akt1 phosphorylation, and associated antiangiogenesis phenotypes. Finally, we find that eIF3i sequestration is observed in MM.1S and MOLM13 cells after the degradation of other substrates, such as IKZF1. The defined binding interface elucidated by chemical proteomics and the observation of eIF3i sequestration as a lenalidomide function open future directions in designing new chemical adapters for protein sequestration as a strategy to selectively control protein functions.
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Affiliation(s)
- Zhi Lin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Dacheng Shen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Bo Yang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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32
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Song Z, Lin J, Su R, Ji Y, Jia R, Li S, Shan G, Huang C. eIF3j inhibits translation of a subset of circular RNAs in eukaryotic cells. Nucleic Acids Res 2022; 50:11529-11549. [PMID: 36330957 PMCID: PMC9723666 DOI: 10.1093/nar/gkac980] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/04/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Increasing studies have revealed that a subset of circular RNAs (circRNAs) harbor an open reading frame and can act as protein-coding templates to generate functional proteins that are closely associated with multiple physiological and disease-relevant processes, and thus proper regulation of synthesis of these circRNA-derived proteins is a fundamental cellular process required for homeostasis maintenance. However, how circRNA translation initiation is coordinated by different trans-acting factors remains poorly understood. In particular, the impact of different eukaryotic translation initiation factors (eIFs) on circRNA translation and the physiological relevance of this distinct regulation have not yet been characterized. In this study, we screened all 43 Drosophila eIFs and revealed the conflicting functions of eIF3 subunits in the translational control of the translatable circRNA circSfl: eIF3 is indispensable for circSfl translation, while the eIF3-associated factor eIF3j is the most potent inhibitor. Mechanistically, the binding of eIF3j to circSfl promotes the disassociation of eIF3. The C-terminus of eIF3j and an RNA regulon within the circSfl untranslated region (UTR) are essential for the inhibitory effect of eIF3j. Moreover, we revealed the physiological relevance of eIF3j-mediated circSfl translation repression in response to heat shock. Finally, additional translatable circRNAs were identified to be similarly regulated in an eIF3j-dependent manner. Altogether, our study provides a significant insight into the field of cap-independent translational regulation and undiscovered functions of eIF3.
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Affiliation(s)
| | | | - Rui Su
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Yu Ji
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ruirui Jia
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Shi Li
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ge Shan
- School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chuan Huang
- To whom correspondence should be addressed. Tel: +86 19956025374;
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Paul EE, Marintchev A. The PCI domains are “winged” HEAT domains. PLoS One 2022; 17:e0268664. [PMID: 36094910 PMCID: PMC9467303 DOI: 10.1371/journal.pone.0268664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022] Open
Abstract
The HEAT domains are a family of helical hairpin repeat domains, composed of four or more hairpins. HEAT is derived from the names of four family members: huntingtin, eukaryotic translation elongation factor 3 (eEF3), protein phosphatase 2 regulatory A subunit (PP2A), and mechanistic target of rapamycin (mTOR). HEAT domain-containing proteins play roles in a wide range of cellular processes, such as protein synthesis, nuclear transport and metabolism, and cell signaling. The PCI domains are a related group of helical hairpin domains, with a “winged-helix” (WH) subdomain at their C-terminus, which is responsible for multi-subunit complex formation with other PCI domains. The name is derived from the complexes, where these domains are found: the 26S Proteasome “lid” regulatory subcomplex, the COP9 signalosome (CSN), and eukaryotic translation initiation factor 3 (eIF3). We noted that in structure similarity searches using HEAT domains, sometimes PCI domains appeared in the search results ahead of other HEAT domains, which indicated that the PCI domains could be members of the HEAT domain family, and not a related but separate group, as currently thought. Here, we report extensive structure similarity analysis of HEAT and PCI domains, both within and between the two groups of proteins. We present evidence that the PCI domains as a group have greater structural similarity with individual groups of HEAT domains than some of the HEAT domain groups have among each other. Therefore, our results indicate that the PCI domains have evolved from a HEAT domain that acquired a WH subdomain. The WH subdomain in turn mediated self-association into a multi-subunit complex, which eventually evolved into the common ancestor of the Proteasome lid/CSN/eIF3.
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Affiliation(s)
- Eleanor Elise Paul
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Assen Marintchev
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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Hayek H, Eriani G, Allmang C. eIF3 Interacts with Selenoprotein mRNAs. Biomolecules 2022; 12:biom12091268. [PMID: 36139107 PMCID: PMC9496622 DOI: 10.3390/biom12091268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
The synthesis of selenoproteins requires the co-translational recoding of an in-frame UGASec codon. Interactions between the Selenocysteine Insertion Sequence (SECIS) and the SECIS binding protein 2 (SBP2) in the 3'untranslated region (3'UTR) of selenoprotein mRNAs enable the recruitment of the selenocysteine insertion machinery. Several selenoprotein mRNAs undergo unusual cap hypermethylation and are not recognized by the translation initiation factor 4E (eIF4E) but nevertheless translated. The human eukaryotic translation initiation factor 3 (eIF3), composed of 13 subunits (a-m), can selectively recruit several cellular mRNAs and plays roles in specialized translation initiation. Here, we analyzed the ability of eIF3 to interact with selenoprotein mRNAs. By combining ribonucleoprotein immunoprecipitation (RNP IP) in vivo and in vitro with cross-linking experiments, we found interactions between eIF3 and a subgroup of selenoprotein mRNAs. We showed that eIF3 preferentially interacts with hypermethylated capped selenoprotein mRNAs rather than m7G-capped mRNAs. We identified direct contacts between GPx1 mRNA and eIF3 c, d, and e subunits and showed the existence of common interaction patterns for all hypermethylated capped selenoprotein mRNAs. Differential interactions of eIF3 with selenoprotein mRNAs may trigger specific translation pathways independent of eIF4E. eIF3 could represent a new player in the translation regulation and hierarchy of selenoprotein expression.
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Affiliation(s)
- Hassan Hayek
- Architecture et Réactivité de l’ARN, Université de Strasbourg, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg, France
- Department of Microbiology, Immunology, and Inflammation, Center for Inflammation and Lung Research, Temple University, Philadelphia, PA 19140, USA
| | - Gilbert Eriani
- Architecture et Réactivité de l’ARN, Université de Strasbourg, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg, France
| | - Christine Allmang
- Architecture et Réactivité de l’ARN, Université de Strasbourg, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg, France
- Correspondence:
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35
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Genome-Wide Identification and Expression Analysis of eIF Family Genes from Brassica rapa in Response to TuMV Resistance. PLANTS 2022; 11:plants11172248. [PMID: 36079630 PMCID: PMC9460045 DOI: 10.3390/plants11172248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/13/2022] [Accepted: 08/23/2022] [Indexed: 11/28/2022]
Abstract
Brassica rapa is one of the most important leafy vegetables worldwide, and has a long history of cultivation. However, it has not been possible to completely control the damage of turnip mosaic virus (TuMV), a serious virus in B. rapa, to production. In this study, the genome-wide identification and expression detection of eIF family genes from B. rapa in response to TuMV resistance were analyzed, including the identification of eIF family genes, chromosomal distribution, three-dimensional (3D) structure and sequence logo analyses, and the expression characterization as well as differential metabolite analysis of eIF family genes in resistant/susceptible lines, which may further prove the whole-genome tripling (WGT) event in B. rapa evolution and provide evidence for the functional redundancy and functional loss of multicopy eIF genes in evolution. A qRT-PCR analysis revealed that the relative expressions of eIF genes in a susceptible line (80461) were higher than those in a resistant line (80124), which may prove that, when TuMV infects host plants, the eIF genes can combine with the virus mRNA 5′ end cap structure and promote the initiation of virus mRNA translation in the susceptible B. rapa line. In addition, the metabolite substances were detected, the differences in metabolites between disease-resistant and disease-susceptible plants were mainly manifested by altered compounds such as flavonoids, jasmonic acid, salicylic acid, ketones, esters, etc., which inferred that the different metabolite regulations of eIF family genes and reveal the resistance mechanisms of eIF genes against TuMV in brassica crops. This study may lay a new theoretical foundation for revealing eIF family gene resistance to TuMV in B. rapa, as well as advancing our understanding of virus–host interactions.
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The Potential Role of m6A in the Regulation of TBI-Induced BGA Dysfunction. Antioxidants (Basel) 2022; 11:antiox11081521. [PMID: 36009239 PMCID: PMC9405408 DOI: 10.3390/antiox11081521] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 02/01/2023] Open
Abstract
The brain–gut axis (BGA) is an important bidirectional communication pathway for the development, progress and interaction of many diseases between the brain and gut, but the mechanisms remain unclear, especially the post-transcriptional regulation of BGA after traumatic brain injury (TBI). RNA methylation is one of the most important modifications in post-transcriptional regulation. N6-methyladenosine (m6A), as the most abundant post-transcriptional modification of mRNA in eukaryotes, has recently been identified and characterized in both the brain and gut. The purpose of this review is to describe the pathophysiological changes in BGA after TBI, and then investigate the post-transcriptional bidirectional regulation mechanisms of TBI-induced BGA dysfunction. Here, we mainly focus on the characteristics of m6A RNA methylation in the post-TBI BGA, highlight the possible regulatory mechanisms of m6A modification in TBI-induced BGA dysfunction, and finally discuss the outcome of considering m6A as a therapeutic target to improve the recovery of the brain and gut dysfunction caused by TBI.
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37
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Brown ZP, Abaeva IS, De S, Hellen CUT, Pestova TV, Frank J. Molecular architecture of 40S translation initiation complexes on the hepatitis C virus IRES. EMBO J 2022; 41:e110581. [PMID: 35822879 DOI: 10.15252/embj.2022110581] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/01/2022] [Accepted: 06/14/2022] [Indexed: 02/05/2023] Open
Abstract
Hepatitis C virus mRNA contains an internal ribosome entry site (IRES) that mediates end-independent translation initiation, requiring a subset of eukaryotic initiation factors (eIFs). Biochemical studies revealed that direct binding of the IRES to the 40S ribosomal subunit places the initiation codon into the P site, where it base pairs with eIF2-bound Met-tRNAiMet forming a 48S initiation complex. Subsequently, eIF5 and eIF5B mediate subunit joining, yielding an elongation-competent 80S ribosome. Initiation can also proceed without eIF2, in which case Met-tRNAiMet is recruited directly by eIF5B. However, the structures of initiation complexes assembled on the HCV IRES, the transitions between different states, and the accompanying conformational changes have remained unknown. To fill these gaps, we now obtained cryo-EM structures of IRES initiation complexes, at resolutions up to 3.5 Å, that cover all major stages from the initial ribosomal association, through eIF2-containing 48S initiation complexes, to eIF5B-containing complexes immediately prior to subunit joining. These structures provide insights into the dynamic network of 40S/IRES contacts, highlight the role of IRES domain II, and reveal conformational changes that occur during the transition from eIF2- to eIF5B-containing 48S complexes and prepare them for subunit joining.
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Affiliation(s)
- Zuben P Brown
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Irina S Abaeva
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Swastik De
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.,Department of Biological Sciences, Columbia University, New York, NY, USA
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38
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Lapointe CP, Grosely R, Sokabe M, Alvarado C, Wang J, Montabana E, Villa N, Shin BS, Dever TE, Fraser CS, Fernández IS, Puglisi JD. eIF5B and eIF1A reorient initiator tRNA to allow ribosomal subunit joining. Nature 2022; 607:185-190. [PMID: 35732735 PMCID: PMC9728550 DOI: 10.1038/s41586-022-04858-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/11/2022] [Indexed: 01/03/2023]
Abstract
Translation initiation defines the identity and quantity of a synthesized protein. The process is dysregulated in many human diseases1,2. A key commitment step is when the ribosomal subunits join at a translation start site on a messenger RNA to form a functional ribosome. Here, we combined single-molecule spectroscopy and structural methods using an in vitro reconstituted system to examine how the human ribosomal subunits join. Single-molecule fluorescence revealed when the universally conserved eukaryotic initiation factors eIF1A and eIF5B associate with and depart from initiation complexes. Guided by single-molecule dynamics, we visualized initiation complexes that contained both eIF1A and eIF5B using single-particle cryo-electron microscopy. The resulting structure revealed how eukaryote-specific contacts between the two proteins remodel the initiation complex to orient the initiator aminoacyl-tRNA in a conformation compatible with ribosomal subunit joining. Collectively, our findings provide a quantitative and architectural framework for the molecular choreography orchestrated by eIF1A and eIF5B during translation initiation in humans.
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Affiliation(s)
- Christopher P Lapointe
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Masaaki Sokabe
- Department of Molecular and Cellular Biology College of Biological Sciences, University of California, Davis, CA, USA
| | - Carlos Alvarado
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elizabeth Montabana
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nancy Villa
- Department of Molecular and Cellular Biology College of Biological Sciences, University of California, Davis, CA, USA
| | - Byung-Sik Shin
- Section on Protein Biosynthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Thomas E Dever
- Section on Protein Biosynthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Christopher S Fraser
- Department of Molecular and Cellular Biology College of Biological Sciences, University of California, Davis, CA, USA
| | - Israel S Fernández
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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39
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Friedrich D, Marintchev A, Arthanari H. The metaphorical swiss army knife: The multitude and diverse roles of HEAT domains in eukaryotic translation initiation. Nucleic Acids Res 2022; 50:5424-5442. [PMID: 35552740 PMCID: PMC9177959 DOI: 10.1093/nar/gkac342] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 11/24/2022] Open
Abstract
Biomolecular associations forged by specific interaction among structural scaffolds are fundamental to the control and regulation of cell processes. One such structural architecture, characterized by HEAT repeats, is involved in a multitude of cellular processes, including intracellular transport, signaling, and protein synthesis. Here, we review the multitude and versatility of HEAT domains in the regulation of mRNA translation initiation. Structural and cellular biology approaches, as well as several biophysical studies, have revealed that a number of HEAT domain-mediated interactions with a host of protein factors and RNAs coordinate translation initiation. We describe the basic structural architecture of HEAT domains and briefly introduce examples of the cellular processes they dictate, including nuclear transport by importin and RNA degradation. We then focus on proteins in the translation initiation system featuring HEAT domains, specifically the HEAT domains of eIF4G, DAP5, eIF5, and eIF2Bϵ. Comparative analysis of their remarkably versatile interactions, including protein–protein and protein–RNA recognition, reveal the functional importance of flexible regions within these HEAT domains. Here we outline how HEAT domains orchestrate fundamental aspects of translation initiation and highlight open mechanistic questions in the area.
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Affiliation(s)
- Daniel Friedrich
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Assen Marintchev
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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40
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Yi SH, Petrychenko V, Schliep JE, Goyal A, Linden A, Chari A, Urlaub H, Stark H, Rodnina MV, Adio S, Fischer N. Conformational rearrangements upon start codon recognition in human 48S translation initiation complex. Nucleic Acids Res 2022; 50:5282-5298. [PMID: 35489072 PMCID: PMC9122606 DOI: 10.1093/nar/gkac283] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/08/2022] [Accepted: 04/20/2022] [Indexed: 01/10/2023] Open
Abstract
Selection of the translation start codon is a key step during protein synthesis in human cells. We obtained cryo-EM structures of human 48S initiation complexes and characterized the intermediates of codon recognition by kinetic methods using eIF1A as a reporter. Both approaches capture two distinct ribosome populations formed on an mRNA with a cognate AUG codon in the presence of eIF1, eIF1A, eIF2–GTP–Met-tRNAiMet and eIF3. The ‘open’ 40S subunit conformation differs from the human 48S scanning complex and represents an intermediate preceding the codon recognition step. The ‘closed’ form is similar to reported structures of complexes from yeast and mammals formed upon codon recognition, except for the orientation of eIF1A, which is unique in our structure. Kinetic experiments show how various initiation factors mediate the population distribution of open and closed conformations until 60S subunit docking. Our results provide insights into the timing and structure of human translation initiation intermediates and suggest the differences in the mechanisms of start codon selection between mammals and yeast.
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Affiliation(s)
- Sung-Hui Yi
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Valentyn Petrychenko
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Jan Erik Schliep
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Akanksha Goyal
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Andreas Linden
- Bioanalytical Mass Spectroscopy Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen 37075, Germany
| | - Ashwin Chari
- Research Group Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectroscopy Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen 37075, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Sarah Adio
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Georg-August University of Göttingen, Göttingen 37077, Germany
| | - Niels Fischer
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
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41
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Powell P, Bhardwaj U, Goss D. Eukaryotic initiation factor 4F promotes a reorientation of eukaryotic initiation factor 3 binding on the 5' and the 3' UTRs of barley yellow dwarf virus mRNA. Nucleic Acids Res 2022; 50:4988-4999. [PMID: 35446425 PMCID: PMC9122605 DOI: 10.1093/nar/gkac284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 11/14/2022] Open
Abstract
Viral mRNAs that lack a 5′ m7GTP cap and a 3′ poly-A tail rely on structural elements in their untranslated regions (UTRs) to form unique RNA-protein complexes that regulate viral translation. Recent studies of the barley yellow dwarf virus (BYDV) have revealed eukaryotic initiation factor 3 (eIF3) plays a significant role in facilitating communication between its 5′ and 3′ UTRs by binding both UTRs simultaneously. This report uses in vitro translation assays, fluorescence anisotropy binding assays, and selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) footprinting to identify secondary structures that are selectively interacting with eIF3. SHAPE data also show that eIF3 alters its interaction with BYDV structures when another factor crucial for BYDV translation, eIF4F, is introduced by the 3′ BYDV translational enhancer (BTE). The observed BTE and eIF4F-induced shift of eIF3 position on the 5’ UTR and the translational effects of altering eIF3-binding structures (SLC and SLII) support a new model for BYDV translation initiation that requires the reorientation of eIF3 on BYDV UTRs. This eIF3 function in BYDV translation initiation is both reminiscent of and distinct from eIF3–RNA interactions found in other non-canonically translating mRNAs (e.g. HCV). This characterization of a new role in translation initiation expands the known functionality of eIF3 and may be broadly applicable to other non-canonically translating mRNAs.
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Affiliation(s)
- Paul Powell
- Department of Chemistry, Hunter College, CUNY, New York, NY 10065, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Usha Bhardwaj
- Department of Chemistry, Hunter College, CUNY, New York, NY 10065, USA
| | - Dixie Goss
- Department of Chemistry, Hunter College, CUNY, New York, NY 10065, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA.,Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
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42
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Li H, Li M, Guo H, Lin G, Huang Q, Qiu M. Integrative Analyses of Circulating mRNA and lncRNA Expression Profile in Plasma of Lung Cancer Patients. Front Oncol 2022; 12:843054. [PMID: 35433477 PMCID: PMC9008738 DOI: 10.3389/fonc.2022.843054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Circulating-free RNAs (cfRNAs) have been regarded as potential biomarkers for “liquid biopsy” in cancers. However, the circulating messenger RNA (mRNA) and long noncoding RNA (lncRNA) profiles of lung cancer have not been fully characterized. In this study, we profiled circulating mRNA and lncRNA profiles of 16 lung cancer patients and 4 patients with benign pulmonary nodules. Compared with benign pulmonary nodules, 806 mRNAs and 1,762 lncRNAs were differentially expressed in plasma of lung adenocarcinoma patients. For lung squamous cell carcinomas, 256 mRNAs and 946 lncRNAs were differentially expressed. A total of 231 mRNAs and 298 lncRNAs were differentially expressed in small cell lung cancer. Eleven mRNAs, 51 lncRNAs, and 207 canonical pathways were differentially expressed in lung cancer in total. Forty-five blood samples were collected to verify our findings via performing qPCR. There are plenty of meaningful mRNAs and lncRNAs that were found. MYC, a transcription regulator associated with the stemness of cancer cells, is overexpressed in lung adenocarcinoma. Transforming growth factor beta (TGFB1), which plays pleiotropic roles in cancer progression, was found to be upregulated in lung squamous carcinoma. MALAT1, a well-known oncogenic lncRNA, was also found to be upregulated in lung squamous carcinoma. Thus, this study provided a systematic resource of mRNA and lncRNA expression profiles in lung cancer plasma.
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Affiliation(s)
- Haoran Li
- Department of Thoracic Surgery, Peking University People’s Hospital, Beijing, China
| | - Mingru Li
- Department of Thoracic Surgery, Aerospace 731 Hospital, Beijing, China
| | - Haifa Guo
- The First Department of Thoracic Surgery, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Guihu Lin
- Department of Thoracic Surgery, Aerospace 731 Hospital, Beijing, China
| | - Qi Huang
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Qi Huang, ; Mantang Qiu,
| | - Mantang Qiu
- Department of Thoracic Surgery, Peking University People’s Hospital, Beijing, China
- *Correspondence: Qi Huang, ; Mantang Qiu,
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43
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Zheng R, Zhang K, Tan S, Gao F, Zhang Y, Xu W, Wang H, Gu D, Zhu L, Li S, Chu H, Zhang Z, Liu L, Du M, Wang M. Exosomal circLPAR1 functions in colorectal cancer diagnosis and tumorigenesis through suppressing BRD4 via METTL3–eIF3h interaction. Mol Cancer 2022; 21:49. [PMID: 35164758 PMCID: PMC8842935 DOI: 10.1186/s12943-021-01471-y] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/26/2021] [Indexed: 02/07/2023] Open
Abstract
Background Exosomes have emerged as vital biomarkers of multiple cancers and contain abundant circular RNAs (circRNAs). However, the potential for exosomal circRNAs to be used in diagnostics and their molecular mechanism of action in colorectal cancer (CRC) remain unclear. Methods CRC-specific exosomal circRNAs were identified by RNA sequencing, exoRBase database and a tissue microarray. The diagnostic performance of plasma exosomal circRNAs was evaluated among cancer-free controls, precancer individuals, CRC patients, and patients with other types of cancer. The corresponding biological functions were mainly assessed using circRNA pull-down, proteomic analysis, and RNA immunoprecipitation assay underlying cellular and mouse models. Results CircLPAR1 was encapsulated in exosomes with high stability and detectability, and its expression in plasma exosomes was remarkably decreased during CRC development but recovered after surgery. Exosomal circLPAR1 showed cancer specificity in CRC diagnosis and increased the diagnostic performance to an area under the receiver operating characteristic curve of 0.875, as determined by analysing its performance in combination with common clinical biomarkers CEA and CA19–9. Additionally, circLPAR1 was downregulated in CRC tissues and was associated with overall survival. Mechanistically, exosomal circLPAR1 was internalized by CRC cells, and it suppressed tumor growth, likely because exosomal circLPAR1 directly bound with eIF3h specifically suppressed the METTL3-eIF3h interaction, decreasing the translation of oncogene BRD4. Conclusions This comprehensive study highlights plasma exosomal circLPAR1 as a promising predictor in CRC diagnosis and describes its biological regulation of colorectal tumorigenesis. This study provides a new perspective on early diagnosis in the clinic and pathogenesis in disease development. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-021-01471-y.
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44
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Dynamic eIF3a O-GlcNAcylation controls translation reinitiation during nutrient stress. Nat Chem Biol 2022; 18:134-141. [PMID: 34887587 PMCID: PMC8810738 DOI: 10.1038/s41589-021-00913-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 09/29/2021] [Indexed: 01/05/2023]
Abstract
In eukaryotic cells, many messenger RNAs (mRNAs) possess upstream open reading frames (uORFs) in addition to the main coding region. After uORF translation, the ribosome could either recycle at the stop codon or resume scanning for downstream start codons in a process known as reinitiation. Accumulating evidence suggests that some initiation factors, including eukaryotic initiation factor 3 (eIF3), linger on the early elongating ribosome, forming an eIF3-80S complex. Very little is known about how eIF3 is carried along with the 80S during elongation and whether the eIF3-80S association is subject to regulation. Here, we report that eIF3a undergoes dynamic O-linked N-acetylglucosamine (O-GlcNAc) modification in response to nutrient starvation. Stress-induced de-O-GlcNAcylation promotes eIF3 retention on the elongating ribosome and facilitates activating transcription factor 4 (ATF4) reinitiation. Eliminating the modification site from eIF3a via CRISPR genome editing induces ATF4 reinitiation even under the nutrient-rich condition. Our findings illustrate a mechanism in balancing ribosome recycling and reinitiation, thereby linking the nutrient stress response and translational reprogramming.
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45
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Paul EE, Lin KY, Gamble N, Tsai AWL, Swan SHK, Yang Y, Doran M, Marintchev A. Dynamic interaction network involving the conserved intrinsically disordered regions in human eIF5. Biophys Chem 2022; 281:106740. [PMID: 34923394 PMCID: PMC8741751 DOI: 10.1016/j.bpc.2021.106740] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 02/03/2023]
Abstract
Translation initiation in eukaryotes requires multiple eukaryotic translation initiation factors (eIFs) and involves continuous remodeling of the ribosomal preinitiation complex (PIC). The GTPase eIF2 brings the initiator Met-tRNAi to the PIC. Upon start codon selection and GTP hydrolysis, promoted by eIF5, eIF2-GDP is released in complex with eIF5. Here, we report that two intrinsically disordered regions (IDRs) in eIF5, the DWEAR motif and the C-terminal tail (CTT) dynamically contact the folded C-terminal domain (CTD) and compete with each other. The eIF5-CTD•CTT interaction favors eIF2β binding to eIF5-CTD, whereas the eIF5-CTD•DWEAR interaction favors eIF1A binding, which suggests how intramolecular contact rearrangement could play a role in PIC remodeling. We show that eIF5 phosphorylation by CK2, which is known to stimulate translation and cell proliferation, significantly increases the eIF5 affinity for eIF2. Our results also indicate that the eIF2β subunit has at least two, and likely three eIF5-binding sites.
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Affiliation(s)
- Eleanor Elise Paul
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany St. W336, Boston, MA 02118, USA
| | - Kay Ying Lin
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany St. W336, Boston, MA 02118, USA
| | - Nathan Gamble
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany St. W336, Boston, MA 02118, USA
| | - Amy Wei-Lun Tsai
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany St. W336, Boston, MA 02118, USA
| | - Simon H. K. Swan
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany St. W336, Boston, MA 02118, USA
| | - Yu Yang
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany St. W336, Boston, MA 02118, USA
| | - Matthew Doran
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany St. W336, Boston, MA 02118, USA
| | - Assen Marintchev
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany St. W336, Boston, MA 02118, USA
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46
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Su R, Dong L, Li Y, Gao M, He PC, Liu W, Wei J, Zhao Z, Gao L, Han L, Deng X, Li C, Prince E, Tan B, Qing Y, Qin X, Shen C, Xue M, Zhou K, Chen Z, Xue J, Li W, Qin H, Wu X, Sun M, Nam Y, Chen CW, Huang W, Horne D, Rosen ST, He C, Chen J. METTL16 exerts an m 6A-independent function to facilitate translation and tumorigenesis. Nat Cell Biol 2022; 24:205-216. [PMID: 35145225 PMCID: PMC9070413 DOI: 10.1038/s41556-021-00835-2] [Citation(s) in RCA: 131] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 12/21/2021] [Indexed: 12/23/2022]
Abstract
METTL16 has recently been identified as an RNA methyltransferase responsible for the deposition of N6-methyladenosine (m6A) in a few transcripts. Whether METTL16 methylates a large set of transcripts, similar to METTL3 and METTL14, remains unclear. Here we show that METTL16 exerts both methyltransferase activity-dependent and -independent functions in gene regulation. In the cell nucleus, METTL16 functions as an m6A writer to deposit m6A into hundreds of its specific messenger RNA targets. In the cytosol, METTL16 promotes translation in an m6A-independent manner. More specifically, METTL16 directly interacts with the eukaryotic initiation factors 3a and -b as well as ribosomal RNA through its Mtase domain, thereby facilitating the assembly of the translation-initiation complex and promoting the translation of over 4,000 mRNA transcripts. Moreover, we demonstrate that METTL16 is critical for the tumorigenesis of hepatocellular carcinoma. Collectively, our studies reveal previously unappreciated dual functions of METTL16 as an m6A writer and a translation-initiation facilitator, which together contribute to its essential function in tumorigenesis.
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MESH Headings
- Adenosine/analogs & derivatives
- Adenosine/metabolism
- Animals
- Carcinogenesis/genetics
- Carcinogenesis/metabolism
- Carcinogenesis/pathology
- Carcinoma, Hepatocellular/enzymology
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/pathology
- Cytosol/enzymology
- Eukaryotic Initiation Factor-3/genetics
- Eukaryotic Initiation Factor-3/metabolism
- Gene Expression Regulation, Neoplastic
- HEK293 Cells
- Hep G2 Cells
- Humans
- Liver Neoplasms/enzymology
- Liver Neoplasms/genetics
- Liver Neoplasms/pathology
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Mice, Inbred NOD
- Mice, SCID
- Protein Biosynthesis
- RNA Processing, Post-Transcriptional
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Signal Transduction
- Tumor Burden
- Mice
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Affiliation(s)
- Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA.
| | - Lei Dong
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Yangchan Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- Department of Radiation Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Min Gao
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- Department of Pharmaceutics, School of Pharmaceutical Science, Jiangnan University, Wuxi, China
| | - P Cody He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Wei Liu
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- Department of Immunology, Hebei Medical University, Shijiazhuang, China
| | - Jiangbo Wei
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Zhicong Zhao
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Gao
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Li Han
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- School of Pharmacy, China Medical University, Shenyang, China
| | - Xiaolan Deng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Chenying Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- Key Laboratory of Hematopoietic Malignancies, The First Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Emily Prince
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Brandon Tan
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Ying Qing
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Xi Qin
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Chao Shen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Meilin Xue
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Keren Zhou
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Zhenhua Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Jianhuang Xue
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Wei Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Hanjun Qin
- The Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Xiwei Wu
- The Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Miao Sun
- Keck School of Medicine, University of Southern California, and Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Yunsun Nam
- Laboratory of RNA Biology, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
| | - Wendong Huang
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
- Graduate School of Biological Science, City of Hope, Duarte, CA, USA
| | - David Horne
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Steven T Rosen
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, CA, USA
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA.
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA.
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, USA.
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Stanciu A, Luo J, Funes L, Galbokke Hewage S, Kulkarni SD, Aitken CE. eIF3 and Its mRNA-Entry-Channel Arm Contribute to the Recruitment of mRNAs With Long 5′-Untranslated Regions. Front Mol Biosci 2022; 8:787664. [PMID: 35087868 PMCID: PMC8787345 DOI: 10.3389/fmolb.2021.787664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/13/2021] [Indexed: 01/21/2023] Open
Abstract
Translation initiation in eukaryotes is a multi-step pathway and the most regulated phase of translation. Eukaryotic initiation factor 3 (eIF3) is the largest and most complex of the translation initiation factors, and it contributes to events throughout the initiation pathway. In particular, eIF3 appears to play critical roles in mRNA recruitment. More recently, eIF3 has been implicated in driving the selective translation of specific classes of mRNAs. However, unraveling the mechanism of these diverse contributions—and disentangling the roles of the individual subunits of the eIF3 complex—remains challenging. We employed ribosome profiling of budding yeast cells expressing two distinct mutations targeting the eIF3 complex. These mutations either disrupt the entire complex or subunits positioned near the mRNA-entry channel of the ribosome and which appear to relocate during or in response to mRNA binding and start-codon recognition. Disruption of either the entire eIF3 complex or specific targeting of these subunits affects mRNAs with long 5′-untranslated regions and whose translation is more dependent on eIF4A, eIF4B, and Ded1 but less dependent on eIF4G, eIF4E, and PABP. Disruption of the entire eIF3 complex further affects mRNAs involved in mitochondrial processes and with structured 5′-untranslated regions. Comparison of the suite of mRNAs most sensitive to both mutations with those uniquely sensitive to disruption of the entire complex sheds new light on the specific roles of individual subunits of the eIF3 complex.
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Affiliation(s)
- Andrei Stanciu
- Computer Science Department, Vassar College, Poughkeepsie, NY, United States
| | - Juncheng Luo
- Biochemistry Program, Vassar College, Poughkeepsie, NY, United States
| | - Lucy Funes
- Biology Department, Vassar College, Poughkeepsie, NY, United States
| | | | - Shardul D. Kulkarni
- Department of Biochemistry and Molecular Biology, Penn State Eberly College of Medicine, University Park, PA, United States
| | - Colin Echeverría Aitken
- Biochemistry Program, Vassar College, Poughkeepsie, NY, United States
- Biology Department, Vassar College, Poughkeepsie, NY, United States
- *Correspondence: Colin Echeverría Aitken,
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Apcher S, Tovar-Fernadez M, Ducellier S, Thermou A, Nascimento M, Sroka E, Fahraeus R. mRNA translation from an antigen presentation perspective: A tribute to the works of Nilabh Shastri. Mol Immunol 2021; 141:305-308. [PMID: 34920325 DOI: 10.1016/j.molimm.2021.12.010] [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: 07/23/2021] [Revised: 10/04/2021] [Accepted: 12/07/2021] [Indexed: 10/19/2022]
Abstract
The field of mRNA translation has witnessed an impressive expansion in the last decade. The once standard model of translation initiation has undergone, and is still undergoing, a major overhaul, partly due to more recent technical advancements detailing, for example, initiation at non-AUG codons. However, some of the pioneering works in this area have come from immunology and more precisely from the field of antigen presentation to the major histocompatibility class I (MHC-I) pathway. Despite early innovative studies from the lab of Nilabh Shastri demonstrating alternative mRNA translation initiation as a source for MHC-I peptide substrates, the mRNA translation field did not include these into their models. It was not until the introduction of the ribo-sequence technique that the extent of non-canonical translation initiation became widely acknowledged. The detection of peptides on MHC-I molecules by CD8 + T cells is extremely sensitive, making this a superior model system for studying alternative mRNA translation initiation from specific mRNAs. In view of this, we give a brief history on alternative initiation from an immunology perspective and its fundamental role in allowing the immune system to distinguish self from non-self and at the same time pay tribute to the works of Nilabh Shastri.
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Affiliation(s)
- Sebastien Apcher
- Université Paris-Saclay, Institut Gustave Roussy, Inserm UMR1015, Immunologie des tumeurs et Immunothérapie contre le cancer, 94805, Villejuif, France.
| | - Maria Tovar-Fernadez
- ICCVS, University of Gdańsk, Science, ul. Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Sarah Ducellier
- Université Paris-Saclay, Institut Gustave Roussy, Inserm UMR1015, Immunologie des tumeurs et Immunothérapie contre le cancer, 94805, Villejuif, France
| | - Aikaterini Thermou
- ICCVS, University of Gdańsk, Science, ul. Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Megane Nascimento
- Université Paris-Saclay, Institut Gustave Roussy, Inserm UMR1015, Immunologie des tumeurs et Immunothérapie contre le cancer, 94805, Villejuif, France
| | - Ewa Sroka
- ICCVS, University of Gdańsk, Science, ul. Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Robin Fahraeus
- ICCVS, University of Gdańsk, Science, ul. Wita Stwosza 63, 80-308, Gdańsk, Poland; Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, F-75010, Paris, France; RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 65653, Brno, Czech Republic; Department of Medical Biosciences, Building 6M, Umeå University, 901 85, Umeå, Sweden.
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Sweeney TR, Dhote V, Guca E, Hellen CUT, Hashem Y, Pestova T. Functional role and ribosomal position of the unique N-terminal region of DHX29, a factor required for initiation on structured mammalian mRNAs. Nucleic Acids Res 2021; 49:12955-12969. [PMID: 34883515 PMCID: PMC8682770 DOI: 10.1093/nar/gkab1192] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/12/2021] [Accepted: 11/22/2021] [Indexed: 02/05/2023] Open
Abstract
Translation initiation on structured mammalian mRNAs requires DHX29, a DExH protein that comprises a unique 534-aa-long N-terminal region (NTR) and a common catalytic DExH core. DHX29 binds to 40S subunits and possesses 40S-stimulated NTPase activity essential for its function. In the cryo-EM structure of DHX29-bound 43S preinitiation complexes, the main DHX29 density resides around the tip of helix 16 of 18S rRNA, from which it extends through a linker to the subunit interface forming an intersubunit domain next to the eIF1A binding site. Although a DExH core model can be fitted to the main density, the correlation between the remaining density and the NTR is unknown. Here, we present a model of 40S-bound DHX29, supported by directed hydroxyl radical cleavage data, showing that the intersubunit domain comprises a dsRNA-binding domain (dsRBD, aa 377-448) whereas linker corresponds to the long α-helix (aa 460-512) that follows the dsRBD. We also demonstrate that the N-terminal α-helix and the following UBA-like domain form a four-helix bundle (aa 90-166) that constitutes a previously unassigned section of the main density and resides between DHX29's C-terminal α-helix and the linker. In vitro reconstitution experiments revealed the critical and specific roles of these NTR elements for DHX29's function.
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Affiliation(s)
- Trevor R Sweeney
- Correspondence may also be addressed to Trevor R. Sweeney. Tel: +44 1483232441; Fax: +44 1483232448;
| | | | - Ewelina Guca
- INSERM U1212 Acides nucléiques : Régulations Naturelle et Artificielle (ARNA), Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Health Sciences University, 450 Clarkson Avenue, MSC 44, Brooklyn, NY 11203, USA
| | - Yaser Hashem
- Correspondence may also be addressed to Yaser Hashem. Tel: +33 5 40 00 88 22;
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Zhu YD, Ba H, Chen J, Zhang M, Li P. Celastrus orbiculatus Extract Reduces Stemness of Gastric Cancer Stem Cells by Targeting PDCD4 and EIF3H. Integr Cancer Ther 2021; 20:15347354211058168. [PMID: 34802261 PMCID: PMC8606975 DOI: 10.1177/15347354211058168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Celastrus orbiculatus ethyl acetate extract (COE) has shown a strong anti-gastric cancer effect, but the understanding of its mechanism is still lacking. The results of previous studies indicated that COE may be able to inhibit the stemness of gastric cancer stem cells (GCSCs) by regulating PDCD4 and EIF3H expression. AIMS To explore if COE could inhibit the stemness of GCSCs by regulating PDCD4 and EIF3H expression in vitro and in vivo. PROCEDURE The GCSCs model was established by stem cell-conditioned culture. Spheroid formation and flow cytometry assays were used to detect the effect of COE on the spheroid formation ability of GCSCs and the percentage of CD44+/CD24+ and ALDH+ cell subpopulations. Western blot analysis was applied to measure the expression of GCSCs biomarkers (Nanog, Oct-4, and SOX-2), PDCD4, and EIF3H in GCSCs treated with COE; and RT-PCR was performed to investigate the effect of COE on PDCD4 mRNA expression in GCSCs. An in vivo tumorigenicity experiment was also conducted to evaluate the effect of COE on tumor-initiating ability of GCSCs in vivo; and the expression of PDCD4 and EIF3H in xenograft tissues was examined by immunohistochemistry (IHC) staining. RESULTS After culture in stem cell-conditioned medium, SGC7901 cells manifested significantly enhanced spheroid formation ability, upregulated Nanog, Oct-4, and SOX-2 expression and increased percentages of CD44+/CD24+ and ALDH+ cell subpopulations, indicating successful establishment of the GCSCs model. COE treatment significantly inhibited the spheroid formation ability of GCSCs and reduced the percentage of CD44+/CD24+ and ALDH+ cell subpopulations. The western blot analysis showed a significant decrease of Nanog, Oct-4, SOX-2, and EIF3H expression and an increase of PDCD4 expression in GCSCs after COE treatment in a concentration-dependent manner. COE treatment also significantly upregulated the mRNA expression of PDCD4 in GCSCs. In addition, COE displayed a strong inhibitory effect on the tumor-initiating ability of GCSCs in vivo and upregulated PDCD4 and downregulated EIF3H expression in xenograft tissues. CONCLUSION COE may be able to inhibit GC growth by suppressing the stemness of GCSCs via regulating PDCD4 and EIF3H expression.
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Affiliation(s)
| | - He Ba
- Medical University of Anhui, Anhui, China
| | - Jie Chen
- Medical University of Anhui, Anhui, China
| | - Mei Zhang
- Medical University of Anhui, Anhui, China
| | - Ping Li
- Medical University of Anhui, Anhui, China
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