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Choi JH, Luo J, Hesketh GG, Guo S, Pistofidis A, Ladak RJ, An Y, Naeli P, Alain T, Schmeing TM, Gingras AC, Duchaine T, Zhang X, Sonenberg N, Jafarnejad SM. Repression of mRNA translation initiation by GIGYF1 via disrupting the eIF3-eIF4G1 interaction. SCIENCE ADVANCES 2024; 10:eadl5638. [PMID: 39018414 PMCID: PMC466957 DOI: 10.1126/sciadv.adl5638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 06/13/2024] [Indexed: 07/19/2024]
Abstract
Viruses can selectively repress the translation of mRNAs involved in the antiviral response. RNA viruses exploit the Grb10-interacting GYF (glycine-tyrosine-phenylalanine) proteins 2 (GIGYF2) and eukaryotic translation initiation factor 4E (eIF4E) homologous protein 4EHP to selectively repress the translation of transcripts such as Ifnb1, which encodes the antiviral cytokine interferon-β (IFN-β). Herein, we reveal that GIGYF1, a paralog of GIGYF2, robustly represses cellular mRNA translation through a distinct 4EHP-independent mechanism. Upon recruitment to a target mRNA, GIGYF1 binds to subunits of eukaryotic translation initiation factor 3 (eIF3) at the eIF3-eIF4G1 interaction interface. This interaction disrupts the eIF3 binding to eIF4G1, resulting in transcript-specific translational repression. Depletion of GIGYF1 induces a robust immune response by derepressing IFN-β production. Our study highlights a unique mechanism of translational regulation by GIGYF1 that involves sequestering eIF3 and abrogating its binding to eIF4G1. This mechanism has profound implications for the host response to viral infections.
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Affiliation(s)
- Jung-Hyun Choi
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Jun Luo
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Geoffrey G. Hesketh
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Shuyue Guo
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Angelos Pistofidis
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Reese Jalal Ladak
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Yuxin An
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Parisa Naeli
- Patrick G. Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK
| | - Tommy Alain
- Department of Biochemistry, Microbiology and Immunology, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - T. Martin Schmeing
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Anne-Claude Gingras
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Thomas Duchaine
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Xu Zhang
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Nahum Sonenberg
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Seyed Mehdi Jafarnejad
- Patrick G. Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK
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2
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Ding Z, Huang G, Wang T, Duan W, Li H, Wang Y, Jia H, Yang Z, Wang K, Chu X, Kurtz-Nelson EC, Ahlers K, Earl RK, Han Y, Feliciano P, Chung WK, Eichler EE, Jiang M, Xiong B. Genetic Ablation of GIGYF1, Associated With Autism, Causes Behavioral and Neurodevelopmental Defects in Zebrafish and Mice. Biol Psychiatry 2023; 94:769-779. [PMID: 36924980 PMCID: PMC10502190 DOI: 10.1016/j.biopsych.2023.02.993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 02/01/2023] [Accepted: 02/16/2023] [Indexed: 03/18/2023]
Abstract
BACKGROUND Autism spectrum disorder is characterized by deficits in social communication and restricted or repetitive behaviors. Due to the extremely high genetic and phenotypic heterogeneity, it is critical to pinpoint the genetic factors for understanding the pathology of these disorders. METHODS We analyzed the exomes generated by the SPARK (Simons Powering Autism Research) project and performed a meta-analysis with previous data. We then generated 1 zebrafish knockout model and 3 mouse knockout models to examine the function of GIGYF1 in neurodevelopment and behavior. Finally, we performed whole tissue and single-nucleus transcriptome analysis to explore the molecular and cellular function of GIGYF1. RESULTS GIGYF1 variants are significantly associated with various neurodevelopmental disorder phenotypes, including autism, global developmental delay, intellectual disability, and sleep disturbance. Loss of GIGYF1 causes similar behavioral effects in zebrafish and mice, including elevated levels of anxiety and reduced social engagement, which is reminiscent of the behavioral deficits in human patients carrying GIGYF1 variants. Moreover, excitatory neuron-specific Gigyf1 knockout mice recapitulate the increased repetitive behaviors and impaired social memory, suggesting a crucial role of Gigyf1 in excitatory neurons, which correlates with the observations in single-nucleus RNA sequencing. We also identified a series of downstream target genes of GIGYF1 that affect many aspects of the nervous system, especially synaptic transmission. CONCLUSIONS De novo variants of GIGYF1 are associated with neurodevelopmental disorders, including autism spectrum disorder. GIGYF1 is involved in neurodevelopment and animal behavior, potentially through regulating hippocampal CA2 neuronal numbers and disturbing synaptic transmission.
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Affiliation(s)
- Zijiao Ding
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Department of Pathology, School of Basic Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Guiyang Huang
- Department of Neurobiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tianyun Wang
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, Beijing, China; Neuroscience Research Institute, Peking University, Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, Beijing, China; Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Weicheng Duan
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hua Li
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yirong Wang
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Huiting Jia
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ziqian Yang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Kang Wang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xufeng Chu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | | | - Kaitlyn Ahlers
- Department of Psychiatry & Behavioral Sciences, University of Washington, Seattle, Washington
| | - Rachel K Earl
- Department of Psychiatry & Behavioral Sciences, University of Washington, Seattle, Washington
| | - Yunyun Han
- Department of Neurobiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | | | - Wendy K Chung
- Simons Foundation, New York; Department of Pediatrics, Columbia University, New York
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington; Howard Hughes Medical Institute, University of Washington, Seattle, Washington
| | - Man Jiang
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Bo Xiong
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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Naeli P, Zhang X, Snell PH, Chatterjee S, Kamran M, Ladak RJ, Orr N, Duchaine T, Sonenberg N, Jafarnejad SM. The SARS-CoV-2 protein NSP2 enhances microRNA-mediated translational repression. J Cell Sci 2023; 136:jcs261286. [PMID: 37732428 PMCID: PMC10617620 DOI: 10.1242/jcs.261286] [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: 04/26/2023] [Accepted: 09/08/2023] [Indexed: 09/22/2023] Open
Abstract
Viruses use microRNAs (miRNAs) to impair the host antiviral response and facilitate viral infection by expressing their own miRNAs or co-opting cellular miRNAs. miRNAs inhibit translation initiation of their target mRNAs by recruiting the GIGYF2-4EHP (or EIF4E2) translation repressor complex to the mRNA 5'-cap structure. We recently reported that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-encoded non-structural protein 2 (NSP2) interacts with GIGYF2. This interaction is critical for blocking translation of the Ifnb1 mRNA that encodes the cytokine interferon β, and thereby impairs the host antiviral response. However, it is not known whether NSP2 also affects miRNA-mediated silencing. Here, we demonstrate the pervasive augmentation of miRNA-mediated translational repression of cellular mRNAs by NSP2. We show that NSP2 interacts with argonaute 2 (AGO2), the core component of the miRNA-induced silencing complex (miRISC), via GIGYF2 and enhances the translational repression mediated by natural miRNA-binding sites in the 3' untranslated region of cellular mRNAs. Our data reveal an additional layer of the complex mechanism by which SARS-CoV-2 and likely other coronaviruses manipulate the host gene expression program by co-opting the host miRNA-mediated silencing machinery.
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Affiliation(s)
- Parisa Naeli
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Xu Zhang
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, H3A 1A3, Canada
| | - Patric Harris Snell
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Susanta Chatterjee
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Muhammad Kamran
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Reese Jalal Ladak
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, H3A 1A3, Canada
| | - Nick Orr
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Thomas Duchaine
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, H3A 1A3, Canada
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, H3A 1A3, Canada
| | - Seyed Mehdi Jafarnejad
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7AE, UK
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4
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Niu F, Li Z, Ren Y, Li Z, Guan H, Li Y, Zhang Y, Li Y, Yang J, Qian L, Shi W, Fan X, Li J, Shi L, Yu Y, Xiong Y. Aberrant hyper-expression of the RNA binding protein GIGYF2 in endothelial cells modulates vascular aging and function. Redox Biol 2023; 65:102824. [PMID: 37517320 PMCID: PMC10400931 DOI: 10.1016/j.redox.2023.102824] [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: 05/26/2023] [Revised: 07/13/2023] [Accepted: 07/23/2023] [Indexed: 08/01/2023] Open
Abstract
Vascular endothelial cells (ECs) senescence plays a crucial role in vascular aging that promotes the initiation and progression of cardiovascular disease. The mutation of Grb10-interacting GYF protein 2 (GIGYF2) is strongly associated with the pathogenesis of aging-related diseases, whereas its role in regulating ECs senescence and dysfunction still remains elusive. In this study, we found aberrant hyperexpression of GIGYF2 in senescent human ECs and aortas of old mice. Silencing GIGYF2 in senescent ECs suppressed eNOS-uncoupling, senescence, and endothelial dysfunction. Conversely, in nonsenescent cells, overexpressing GIGYF2 promoted eNOS-uncoupling, cellular senescence, endothelial dysfunction, and activation of the mTORC1-SK61 pathway, which were ablated by rapamycin or antioxidant N-Acetyl-l-cysteine (NAC). Transcriptome analysis revealed that staufen double-stranded RNA binding protein 1 (STAU1) is remarkably downregulated in the GIGYF2-depleted ECs. STAU1 depletion significantly attenuated GIGYF2-induced cellular senescence, dysfunction, and inflammation in young ECs. Furthermore, we disclosed that GIGYF2 acting as an RNA binding protein (RBP) enhances STAU1 mRNA stability, and that the intron region of the late endosomal/lysosomal adaptor MAPK and mTOR activator 4 (LAMTOR4) could bind to STAU1 protein to upregulate LAMTOR4 expression. Immunofluorescence staining showed that GIGYF2 overexpression promoted the translocation of mTORC1 to lysosome. In the mice model, GIGYF2flox/flox Cdh-Cre+ mice protected aged mice from aging-associated vascular endothelium-dependent relaxation and arterial stiffness. Our work discloses that GIGYF2 serving as an RBP enhances the mRNA stability of STAU1 that upregulates LAMTOR4 expression through binding with its intron region, which activates the mTORC1-S6K1 signaling via recruitment of mTORC1 to the lysosomal membrane, ultimately leading to ECs senescence, dysfunction, and vascular aging. Disrupting the GIGYF2-STAU1-mTORC1 signaling cascade may represent a promising therapeutic approach against vascular aging and aging-related cardiovascular diseases.
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Affiliation(s)
- Fanglin Niu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Zhuozhuo Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Yuanyuan Ren
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Zi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Hua Guan
- Shaanxi Key Laboratory of Ischemic Cardiovascular Diseases & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, Shaanxi, 710018, PR China
| | - Yang Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Yan Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Yirong Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Junle Yang
- Department of Radiology, Xi' an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, PR China
| | - Lu Qian
- Department of Endocrinology, Xi' an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, PR China; Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, PR China
| | - Wenzhen Shi
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, PR China; Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, PR China
| | - Xiaobin Fan
- Department of Obstetrics and Gynecology, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, PR China
| | - Jinli Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Lele Shi
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Yi Yu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China.
| | - Yuyan Xiong
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China; Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, PR China.
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Huang YH, Han JQ, Ma B, Cao WQ, Li XK, Xiong Q, Zhao H, Zhao R, Zhang X, Zhou Y, Wei W, Tao JJ, Zhang WK, Qian W, Chen SY, Yang C, Yin CC, Zhang JS. A translational regulator MHZ9 modulates ethylene signaling in rice. Nat Commun 2023; 14:4674. [PMID: 37542048 PMCID: PMC10403538 DOI: 10.1038/s41467-023-40429-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 07/27/2023] [Indexed: 08/06/2023] Open
Abstract
Ethylene plays essential roles in rice growth, development and stress adaptation. Translational control of ethylene signaling remains unclear in rice. Here, through analysis of an ethylene-response mutant mhz9, we identified a glycine-tyrosine-phenylalanine (GYF) domain protein MHZ9, which positively regulates ethylene signaling at translational level in rice. MHZ9 is localized in RNA processing bodies. The C-terminal domain of MHZ9 interacts with OsEIN2, a central regulator of rice ethylene signaling, and the N-terminal domain directly binds to the OsEBF1/2 mRNAs for translational inhibition, allowing accumulation of transcription factor OsEIL1 to activate the downstream signaling. RNA-IP seq and CLIP-seq analyses reveal that MHZ9 associates with hundreds of RNAs. Ribo-seq analysis indicates that MHZ9 is required for the regulation of ~ 90% of genes translationally affected by ethylene. Our study identifies a translational regulator MHZ9, which mediates translational regulation of genes in response to ethylene, facilitating stress adaptation and trait improvement in rice.
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Affiliation(s)
- Yi-Hua Huang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jia-Qi Han
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Biao Ma
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Wu-Qiang Cao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin-Kai Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Xiong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - He Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rui Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xun Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Wei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian-Jun Tao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wan-Ke Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenfeng Qian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shou-Yi Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chao Yang
- MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
| | - Cui-Cui Yin
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jin-Song Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Construction of a Diagnostic m7G Regulator-Mediated Scoring Model for Identifying the Characteristics and Immune Landscapes of Osteoarthritis. Biomolecules 2023; 13:biom13030539. [PMID: 36979474 PMCID: PMC10046530 DOI: 10.3390/biom13030539] [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] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
With the increasingly serious burden of osteoarthritis (OA) on modern society, it is urgent to propose novel diagnostic biomarkers and differentiation models for OA. 7-methylguanosine (m7G), as one of the most common base modification forms in post transcriptional regulation, through which the seventh position N of guanine (G) of messenger RNA is modified by methyl under the action of methyltransferase; it has been found that it plays a crucial role in different diseases. Therefore, we explored the relationship between OA and m7G. Based on the expression level of 18 m7G-related regulators, we identified nine significant regulators. Then, via a series of methods of machine learning, such as support vector machine recursive feature elimination, random forest and lasso-cox regression analysis, a total of four significant regulators were further identified (DCP2, EIF4E2, LARP1 and SNUPN). Additionally, according to the expression level of the above four regulators, two different m7G-related clusters were divided via consensus cluster analysis. Furthermore, via immune infiltration, differential expression analysis and enrichment analysis, we explored the characteristic of the above two different clusters. An m7G-related scoring model was constructed via the PCA algorithm. Meanwhile, there was a different immune status and correlation for immune checkpoint inhibitors between the above two clusters. The expression difference of the above four regulators was verified via real-time quantitative polymerase chain reaction. Overall, a total of four biomarkers were identified and two different m7G-related subsets of OA with different immune microenvironment were obtained. Meanwhile, the construction of m7G-related Scoring model may provide some new strategies and insights for the therapy and diagnosis of OA patients.
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Zhang X, Qin L, Lu J, Xia Y, Tang X, Lu X, Xia S. Genome-Wide Identification of GYF-Domain Encoding Genes in Three Brassica Species and Their Expression Responding to Sclerotinia sclerotiorum in Brassica napus. Genes (Basel) 2023; 14:224. [PMID: 36672966 PMCID: PMC9858701 DOI: 10.3390/genes14010224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
GYF (glycine-tyrosine-phenylalanine)-domain-containing proteins, which were reported to participate in many aspects of biological processes in yeast and animals, are highly conserved adaptor proteins existing in almost all eukaryotes. Our previous study revealed that GYF protein MUSE11/EXA1 is involved in nucleotide-binding leucine-rich repeat (NLR) receptor-mediated defense in Arabidopsis thaliana. However, the GYF-domain encoding homologous genes are still not clear in other plants. Here, we performed genome-wide identification of GYF-domain encoding genes (GYFs) from Brassica napus and its parental species, Brassica rapa and Brassica oleracea. As a result, 26 GYFs of B. napus (BnaGYFs), 11 GYFs of B. rapa (BraGYFs), and 14 GYFs of B. oleracea (BolGYFs) together with 10 A. thaliana (AtGYFs) were identified, respectively. We, then, conducted gene structure, motif, cis-acting elements, duplication, chromosome localization, and phylogenetic analysis of these genes. Gene structure analysis indicated the diversity of the exon numbers of these genes. We found that the defense and stress responsiveness element existed in 23 genes and also identified 10 motifs in these GYF proteins. Chromosome localization exhibited a similar distribution of BnaGYFs with BraGYFs or BolGYFs in their respective genomes. The phylogenetic and gene collinearity analysis showed the evolutionary conservation of GYFs among B. napus and its parental species as well as Arabidopsis. These 61 identified GYF domain proteins can be classified into seven groups according to their sequence similarity. Expression of BnaGYFs induced by Sclerotinia sclerotiorum provided five highly upregulated genes and five highly downregulated genes, which might be candidates for further research of plant-fungal interaction in B. napus.
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Affiliation(s)
- Xiaobo Zhang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Lei Qin
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Junxing Lu
- College of Life Science, Chongqing Normal University, Chongqing 400047, China
| | - Yunong Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Xianyu Tang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Xun Lu
- Agricultural Science Academy of Xiangxi Tujia and Miao Autonomous Prefecture, Xiangxi 416000, China
| | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
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8
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Christie M, Igreja C. eIF4E-homologous protein (4EHP): a multifarious cap-binding protein. FEBS J 2023; 290:266-285. [PMID: 34758096 DOI: 10.1111/febs.16275] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/29/2021] [Accepted: 11/09/2021] [Indexed: 02/05/2023]
Abstract
The cap-binding protein 4EHP/eIF4E2 has been a recent object of interest in the field of post-transcriptional gene regulation and translational control. From ribosome-associated quality control, to RNA decay and microRNA-mediated gene silencing, this member of the eIF4E protein family regulates gene expression through numerous pathways. Low in abundance but ubiquitously expressed, 4EHP interacts with different binding partners to form multiple protein complexes that regulate translation in a variety of biological contexts. Documented functions of 4EHP primarily relate to its role as a translational repressor, but recent findings indicate that it might also participate in the activation of translation in specific settings. In this review, we discuss the known functions, properties and mechanisms that involve 4EHP in the control of gene expression. We also discuss our current understanding of how 4EHP processes are regulated in eukaryotic cells, and the diseases implicated with dysregulation of 4EHP-mediated translational control.
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Affiliation(s)
- Mary Christie
- School of Life and Environmental Sciences, The University of Sydney, NSW, Australia
| | - Cátia Igreja
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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9
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James SW, Palmer J, Keller NP, Brown ML, Dunworth MR, Francisco SG, Watson KG, Titchen B, Achimovich A, Mahoney A, Artemiou JP, Buettner KG, Class M, Sydenstricker AL, Anglin SL. A reciprocal translocation involving Aspergillus nidulans snxAHrb1/Gbp2 and gyfA uncovers a new regulator of the G2-M transition and reveals a role in transcriptional repression for the setBSet2 histone H3-lysine-36 methyltransferase. Genetics 2022; 222:iyac130. [PMID: 36005881 PMCID: PMC9526064 DOI: 10.1093/genetics/iyac130] [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: 06/27/2022] [Accepted: 08/09/2022] [Indexed: 12/24/2022] Open
Abstract
Aspergillus nidulans snxA, an ortholog of Saccharomyces cerevisiae Hrb1/Gbp2 messenger RNA shuttle proteins, is-in contrast to budding yeast-involved in cell cycle regulation, in which snxA1 and snxA2 mutations as well as a snxA deletion specifically suppress the heat sensitivity of mutations in regulators of the CDK1 mitotic induction pathway. snxA mutations are strongly cold sensitive, and at permissive temperature snxA mRNA and protein expression are strongly repressed. Initial attempts to identify the causative snxA mutations revealed no defects in the SNXA protein. Here, we show that snxA1/A2 mutations resulted from an identical chromosome I-II reciprocal translocation with breakpoints in the snxA first intron and the fourth exon of a GYF-domain gene, gyfA. Surprisingly, a gyfA deletion and a reconstructed gyfA translocation allele suppressed the heat sensitivity of CDK1 pathway mutants in a snxA+ background, demonstrating that 2 unrelated genes, snxA and gyfA, act through the CDK1-CyclinB axis to restrain the G2-M transition, and for the first time identifying a role in G2-M regulation for a GYF-domain protein. To better understand snxA1/A2-reduced expression, we generated suppressors of snxA cold sensitivity in 2 genes: (1) loss of the abundant nucleolar protein Nsr1/nucleolin bypassed the requirement for snxA and (2) loss of the Set2 histone H3 lysine36 (H3K36) methyltransferase or a nonmethylatable histone H3K36L mutant rescued hypomorphic snxA mutants by restoring full transcriptional proficiency, indicating that methylation of H3K36 acts normally to repress snxA transcription. These observations are in line with known Set2 functions in preventing excessive and cryptic transcription of active genes.
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Affiliation(s)
- Steven W James
- Department of Biology, Gettysburg College, Gettysburg, PA 17325, USA
| | - Jonathan Palmer
- Data Analytics, Genencor Technology Center, IFF, Palo Alto, CA, 94306, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Morgan L Brown
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew R Dunworth
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
| | - Sarah G Francisco
- Department of Otolaryngology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Katherine G Watson
- School of Medicine, Noorda College of Osteopathic Medicine, Provo, UT 84606, USA
| | - Breanna Titchen
- Department of Biological and Biomedical Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Alecia Achimovich
- Department of Chemistry, Gettysburg College, Gettysburg, PA 17325, USA
| | - Andrew Mahoney
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | | | - Kyra G Buettner
- School of Medicine, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Madelyn Class
- School of Medicine, Temple University, Philadelphia, PA 19140, USA
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10
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SARS-CoV-2 impairs interferon production via NSP2-induced repression of mRNA translation. Proc Natl Acad Sci U S A 2022; 119:e2204539119. [PMID: 35878012 PMCID: PMC9371684 DOI: 10.1073/pnas.2204539119] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A robust antiviral innate immune response is indispensable for combating infections. However, an exacerbated response can result in pathological inflammation and tissue damage. mRNA translational control mechanisms play a crucial role in maintaining the appropriate magnitude and duration of the immune response. We show that the GIGYF2/4EHP translational repressor complex represses translation of Ifnb1 mRNA, which encodes type I interferon β (IFN-β). We also demonstrate that the NSP2 protein encoded by SARS-CoV-2 virus further impedes translation of Ifnb1 mRNA through coopting the GIGYF2/4EHP complex, leading to evasion of a cellular innate immune response. The knowledge of the mechanism of action of NSP2-mediated IFN-β suppression provides valuable information for development of treatments for infections of SARS-CoV-2 and other coronaviruses. Viruses evade the innate immune response by suppressing the production or activity of cytokines such as type I interferons (IFNs). Here we report the discovery of a mechanism by which the SARS-CoV-2 virus coopts an intrinsic cellular machinery to suppress the production of the key immunostimulatory cytokine IFN-β. We reveal that the SARS-CoV-2 encoded nonstructural protein 2 (NSP2) directly interacts with the cellular GIGYF2 protein. This interaction enhances the binding of GIGYF2 to the mRNA cap-binding protein 4EHP, thereby repressing the translation of the Ifnb1 mRNA. Depletion of GIGYF2 or 4EHP significantly enhances IFN-β production, which inhibits SARS-CoV-2 replication. Our findings reveal a target for rescuing the antiviral innate immune response to SARS-CoV-2 and other RNA viruses.
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11
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Zou L, Moch C, Graille M, Chapat C. The SARS-CoV-2 protein NSP2 impairs the silencing capacity of the human 4EHP-GIGYF2 complex. iScience 2022; 25:104646. [PMID: 35756894 PMCID: PMC9213009 DOI: 10.1016/j.isci.2022.104646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/12/2022] [Accepted: 06/15/2022] [Indexed: 01/20/2023] Open
Abstract
There is an urgent need for a molecular understanding of how SARS-CoV-2 influences the machineries of the host cell. Herein, we focused our attention on the capacity of the SARS-CoV-2 protein NSP2 to bind the human 4EHP-GIGYF2 complex, a key factor involved in microRNA-mediated silencing of gene expression. Using in vitro interaction assays, our data demonstrate that NSP2 physically associates with both 4EHP and a central segment in GIGYF2 in the cytoplasm. We also provide functional evidence showing that NSP2 impairs the function of GIGYF2 in mediating translation repression using reporter-based assays. Collectively, these data reveal the potential impact of NSP2 on the post-transcriptional silencing of gene expression in human cells, pointing out 4EHP-GIGYF2 targeting as a possible strategy of SARS-CoV-2 to take over the silencing machinery and to suppress host defenses.
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Affiliation(s)
- Limei Zou
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris. F-91128 Palaiseau, France
| | - Clara Moch
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris. F-91128 Palaiseau, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris. F-91128 Palaiseau, France
| | - Clément Chapat
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris. F-91128 Palaiseau, France
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12
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Elevated GIGYF2 expression suppresses tumor migration and enhances sensitivity to temozolomide in malignant glioma. Cancer Gene Ther 2022; 29:750-757. [PMID: 34059782 DOI: 10.1038/s41417-021-00353-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 05/06/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023]
Abstract
Glioma is a common type of malignant and aggressive tumor in the brain. Despite progress on mechanistic studies, current understanding of the initiation and progression of glioma remains incomplete. GIGYF2 is a critical regulator in neural development and degeneration, however, its contribution in glioma is not yet elucidated. In this study, using an integrative approach spanning bioinformatic analysis and functional approaches, we explored the potential contribution of GIGYF2 in glioma. Bioinformatic data from public database and our cohort showed that GIGYF2 expression was closely associated with low glioma malignancy and better patient survival. Elevation of GIGYF2 expression impaired cell migration and enhanced temozolomide sensitivity of human glioma cells. We further establish its molecular mechanism by demonstrating that GIGYF2 inhibits MMP-9 mediated cell migration pathway and pro-survival AKT/Bax/Caspase-3 signaling. Our work identifies the suppressive role of GIGYF2 in gliomas, and clarifies the relationship between GIGYF2 expression and glioma malignancy, which may provide a potential target for future interventions.
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13
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Mammalian eIF4E2-GSK3β maintains basal phosphorylation of p53 to resist senescence under hypoxia. Cell Death Dis 2022; 13:459. [PMID: 35568694 PMCID: PMC9107480 DOI: 10.1038/s41419-022-04897-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 04/25/2022] [Accepted: 04/29/2022] [Indexed: 12/14/2022]
Abstract
Hypoxia modulates senescence, but their physiological link remains unclear. Here, we found that eIF4E2, a hypoxia-activated translation initiation factor, interacted with GSK3β to maintain phosphorylation of p53, thus resisting senescence under hypoxia. RNA-binding protein RBM38 interacted with eIF4E to inhibit the translation of p53, but GSK3β-mediated Ser195 phosphorylation disrupted the RBM38-eIF4E interaction. Through investigation of RBM38 phosphorylation, we found that the eIF4E2-GSK3β pathway specifically regulated proline-directed serine/threonine phosphorylation (S/T-P). Importantly, peptides e2-I or G3-I that blocking eIF4E2-GSK3β interaction can inhibit the basal S/T-P phosphorylation of p53 at multiple sites, therby inducing senescence through transcriptional inhibition. Additionally, a nanobody was screened via the domain where eIF4E2 bound to GSK3β, and this nanobody inhibited S/T-P phosphorylation to promote senescence. Furthermore, hypoxia inhibited eIF4E2-GSK3β pathway by mediating S-Nitrosylation of GSK3β. Blocking eIF4E2-GSK3β interaction promoted liver senescence under hypoxia, thus leading to liver fibrosis, eventually accelerating N, N-diethylnitrosamine (DEN)-induced tumorigenesis. Interestingly, eIF4E2 isoforms with GSK3β-binding motif exclusively exist in mammals, which protect zebrafish heart against hypoxia. Together, this study reveals a mammalian eIF4E2-GSK3β pathway that prevents senescence by maintaining basal S/T-P phosphorylation of p53, which underlies hypoxia adaptation of tissues.
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14
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Naeli P, Winter T, Hackett AP, Alboushi L, Jafarnejad SM. The intricate balance between microRNA-induced mRNA decay and translational repression. FEBS J 2022; 290:2508-2524. [PMID: 35247033 DOI: 10.1111/febs.16422] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/08/2022] [Accepted: 03/03/2022] [Indexed: 12/23/2022]
Abstract
Post-transcriptional regulation of messenger RNAs (mRNAs) (i.e., mechanisms that control translation, stability and localization) is a critical focal point in spatiotemporal regulation of gene expression in response to changes in environmental conditions. The human genome encodes ~ 2000 microRNAs (miRNAs), each of which could control the expression of hundreds of protein-coding mRNAs by inducing translational repression and/or promoting mRNA decay. While mRNA degradation is a terminal event, translational repression is reversible and can be employed for rapid response to internal or external cues. Recent years have seen significant progress in our understanding of how miRNAs induce degradation or translational repression of the target mRNAs. Here, we review the recent findings that illustrate the cellular machinery that contributes to miRNA-induced silencing, with a focus on the factors that could influence translational repression vs. decay.
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Affiliation(s)
- Parisa Naeli
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
| | - Timothy Winter
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
| | - Angela P Hackett
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
| | - Lilas Alboushi
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
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15
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Falk F, Kamanyi Marucha K, Clayton C. The EIF4E1-4EIP cap-binding complex of Trypanosoma brucei interacts with the terminal uridylyl transferase TUT3. PLoS One 2021; 16:e0258903. [PMID: 34807934 PMCID: PMC8608314 DOI: 10.1371/journal.pone.0258903] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/16/2021] [Indexed: 11/25/2022] Open
Abstract
Most transcription in Trypanosoma brucei is constitutive and polycistronic. Consequently, the parasite relies on post-transcriptional mechanisms, especially affecting translation initiation and mRNA decay, to control gene expression both at steady-state and for adaptation to different environments. The parasite has six isoforms of the cap-binding protein EIF4E as well as five EIF4Gs. EIF4E1 does not bind to any EIF4G, instead being associated with a 4E-binding protein, 4EIP. 4EIP represses translation and reduces the stability of a reporter mRNA when artificially tethered to the 3’-UTR, whether or not EIF4E1 is present. 4EIP is essential during the transition from the mammalian bloodstream form to the procyclic form that lives in the Tsetse vector. In contrast, EIF4E1 is dispensable during differentiation, but is required for establishment of growing procyclic forms. In Leishmania, there is some evidence that EIF4E1 might be active in translation initiation, via direct recruitment of EIF3. However in T. brucei, EIF4E1 showed no detectable association with other translation initiation factors, even in the complete absence of 4EIP. There was some evidence for interactions with NOT complex components, but if these occur they must be weak and transient. We found that EIF4E1is less abundant in the absence of 4EIP, and RNA pull-down results suggested this might occur through co-translational complex assembly. We also report that 4EIP directly recruits the cytosolic terminal uridylyl transferase TUT3 to EIF4E1/4EIP complexes. There was, however, no evidence that TUT3 is essential for 4EIP function.
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Affiliation(s)
- Franziska Falk
- DKFZ-ZMBH Alliance, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Kevin Kamanyi Marucha
- DKFZ-ZMBH Alliance, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Christine Clayton
- DKFZ-ZMBH Alliance, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- * E-mail:
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16
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Weber R, Chung MY, Keskeny C, Zinnall U, Landthaler M, Valkov E, Izaurralde E, Igreja C. 4EHP and GIGYF1/2 Mediate Translation-Coupled Messenger RNA Decay. Cell Rep 2021; 33:108262. [PMID: 33053355 DOI: 10.1016/j.celrep.2020.108262] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 08/26/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
Current models of mRNA turnover indicate that cytoplasmic degradation is coupled with translation. However, our understanding of the molecular events that coordinate ribosome transit with the mRNA decay machinery is still limited. Here, we show that 4EHP-GIGYF1/2 complexes trigger co-translational mRNA decay. Human cells lacking these proteins accumulate mRNAs with prominent ribosome pausing. They include, among others, transcripts encoding secretory and membrane-bound proteins or tubulin subunits. In addition, 4EHP-GIGYF1/2 complexes fail to reduce mRNA levels in the absence of ribosome stalling or upon disruption of their interaction with the cap structure, DDX6, and ZNF598. We further find that co-translational binding of GIGYF1/2 to the mRNA marks transcripts with perturbed elongation to decay. Our studies reveal how a repressor complex linked to neurological disorders minimizes the protein output of a subset of mRNAs.
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Affiliation(s)
- Ramona Weber
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Min-Yi Chung
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Csilla Keskeny
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Ulrike Zinnall
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115 Berlin, Germany; IRI Life Sciences, Institute für Biologie, Humboldt Universität zu Berlin, 10115 Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115 Berlin, Germany; IRI Life Sciences, Institute für Biologie, Humboldt Universität zu Berlin, 10115 Berlin, Germany
| | - Eugene Valkov
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Elisa Izaurralde
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Cátia Igreja
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany.
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17
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Nordgaard C, Tollenaere MAX, Val AMD, Bekker-Jensen DB, Blasius M, Olsen JV, Bekker-Jensen S. Regulation of the Golgi Apparatus by p38 and JNK Kinases during Cellular Stress Responses. Int J Mol Sci 2021; 22:9595. [PMID: 34502507 PMCID: PMC8431686 DOI: 10.3390/ijms22179595] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/20/2021] [Accepted: 08/31/2021] [Indexed: 12/15/2022] Open
Abstract
p38 and c-Jun N-terninal kinase (JNK) are activated in response to acute stress and inflammatory signals. Through modification of a plethora of substrates, these kinases profoundly re-shape cellular physiology for the optimal response to a harmful environment and/or an inflammatory state. Here, we utilized phospho-proteomics to identify several hundred substrates for both kinases. Our results indicate that the scale of signaling from p38 and JNK are of a similar magnitude. Among the many new targets, we highlight the regulation of the transcriptional regulators grb10-interacting GYF protein 1 and 2 (GIGYF1/2) by p38-dependent MAP kinase-activated protein kinase 2 (MK2) phosphorylation and 14-3-3 binding. We also show that the Golgi apparatus contains numerous substrates, and is a major target for regulation by p38 and JNK. When activated, these kinases mediate structural rearrangement of the Golgi apparatus, which positively affects protein flux through the secretory system. Our work expands on our knowledge about p38 and JNK signaling with important biological ramifications.
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Affiliation(s)
- Cathrine Nordgaard
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; (C.N.); (M.A.X.T.); (M.B.)
| | - Maxim A. X. Tollenaere
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; (C.N.); (M.A.X.T.); (M.B.)
- LEO Pharma A/S, Industriparken 55, 2750 Ballerup, Denmark
| | - Ana Martinez Del Val
- Mass Spectrometry for Quantitative Proteomics, Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; (A.M.D.V.); (D.B.B.-J.); (J.V.O.)
| | - Dorte B. Bekker-Jensen
- Mass Spectrometry for Quantitative Proteomics, Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; (A.M.D.V.); (D.B.B.-J.); (J.V.O.)
| | - Melanie Blasius
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; (C.N.); (M.A.X.T.); (M.B.)
| | - Jesper V. Olsen
- Mass Spectrometry for Quantitative Proteomics, Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; (A.M.D.V.); (D.B.B.-J.); (J.V.O.)
| | - Simon Bekker-Jensen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; (C.N.); (M.A.X.T.); (M.B.)
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18
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Hoefig KP, Reim A, Gallus C, Wong EH, Behrens G, Conrad C, Xu M, Kifinger L, Ito-Kureha T, Defourny KAY, Geerlof A, Mautner J, Hauck SM, Baumjohann D, Feederle R, Mann M, Wierer M, Glasmacher E, Heissmeyer V. Defining the RBPome of primary T helper cells to elucidate higher-order Roquin-mediated mRNA regulation. Nat Commun 2021; 12:5208. [PMID: 34471108 PMCID: PMC8410761 DOI: 10.1038/s41467-021-25345-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 07/28/2021] [Indexed: 01/01/2023] Open
Abstract
Post-transcriptional gene regulation in T cells is dynamic and complex as targeted transcripts respond to various factors. This is evident for the Icos mRNA encoding an essential costimulatory receptor that is regulated by several RNA-binding proteins (RBP), including Roquin-1 and Roquin-2. Here, we identify a core RBPome of 798 mouse and 801 human T cell proteins by utilizing global RNA interactome capture (RNA-IC) and orthogonal organic phase separation (OOPS). The RBPome includes Stat1, Stat4 and Vav1 proteins suggesting unexpected functions for these transcription factors and signal transducers. Based on proximity to Roquin-1, we select ~50 RBPs for testing coregulation of Roquin-1/2 targets by induced expression in wild-type or Roquin-1/2-deficient T cells. Besides Roquin-independent contributions from Rbms1 and Cpeb4 we also show Roquin-1/2-dependent and target-specific coregulation of Icos by Celf1 and Igf2bp3. Connecting the cellular RBPome in a post-transcriptional context, we find contributions from multiple RBPs to the prototypic regulation of mRNA targets by individual trans-acting factors. An extensive RNA binding protein atlas (RBPome) for primary T cells would be a useful resource. Here the authors use two different methods to characterise the mouse and human T cell RBPome and show regulation of Roquin-1/2 dependent and independent pathways.
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Affiliation(s)
- Kai P Hoefig
- Research Unit Molecular Immune Regulation, Helmholtz Center Munich, Munich, Germany
| | - Alexander Reim
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Munich, Germany
| | - Christian Gallus
- Institute of Diabetes and Obesity, Helmholtz Center Munich, Munich, Germany
| | - Elaine H Wong
- Institute for Immunology, Biomedical Center, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Gesine Behrens
- Research Unit Molecular Immune Regulation, Helmholtz Center Munich, Munich, Germany
| | - Christine Conrad
- Institute for Immunology, Biomedical Center, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Meng Xu
- Research Unit Molecular Immune Regulation, Helmholtz Center Munich, Munich, Germany
| | - Lisa Kifinger
- Institute for Immunology, Biomedical Center, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Taku Ito-Kureha
- Institute for Immunology, Biomedical Center, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Kyra A Y Defourny
- Institute for Immunology, Biomedical Center, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany.,Department of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Arie Geerlof
- Institute of Structural Biology, Helmholtz Center Munich, Neuherberg, Germany
| | - Josef Mautner
- Research Unit Gene Vectors, Helmholtz Center Munich & Children's Hospital, TU Munich, Munich, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Center Munich, Munich, Germany
| | - Dirk Baumjohann
- Institute for Immunology, Biomedical Center, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany.,Medical Clinic III for Oncology, Immuno-Oncology and Rheumatology University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Regina Feederle
- Monoclonal Antibody Core Facility and Research Group, Institute for Diabetes and Obesity, Helmholtz Center Munich, Neuherberg, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Munich, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Munich, Germany. .,Proteomics Research Infrastructure, University of Copenhagen, Copenhagen, Denmark.
| | - Elke Glasmacher
- Institute of Diabetes and Obesity, Helmholtz Center Munich, Munich, Germany. .,Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany.
| | - Vigo Heissmeyer
- Research Unit Molecular Immune Regulation, Helmholtz Center Munich, Munich, Germany. .,Institute for Immunology, Biomedical Center, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany.
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19
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Mayya VK, Flamand MN, Lambert AM, Jafarnejad SM, Wohlschlegel JA, Sonenberg N, Duchaine TF. microRNA-mediated translation repression through GYF-1 and IFE-4 in C. elegans development. Nucleic Acids Res 2021; 49:4803-4815. [PMID: 33758928 PMCID: PMC8136787 DOI: 10.1093/nar/gkab162] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/24/2021] [Accepted: 03/17/2021] [Indexed: 12/11/2022] Open
Abstract
microRNA (miRNA)-mediated gene silencing is enacted through the recruitment of effector proteins that direct translational repression or degradation of mRNA targets, but the relative importance of their activities for animal development remains unknown. Our concerted proteomic surveys identified the uncharacterized GYF-domain encoding protein GYF-1 and its direct interaction with IFE-4, the ortholog of the mammalian translation repressor 4EHP, as key miRNA effector proteins in Caenorhabditis elegans. Recruitment of GYF-1 protein to mRNA reporters in vitro or in vivo leads to potent translation repression without affecting the poly(A) tail or impinging on mRNA stability. Loss of gyf-1 is synthetic lethal with hypomorphic alleles of embryonic miR-35-42 and larval (L4) let-7 miRNAs, which is phenocopied through engineered mutations in gyf-1 that abolish interaction with IFE-4. GYF-1/4EHP function is cascade-specific, as loss of gyf-1 had no noticeable impact on the functions of other miRNAs, including lin-4 and lsy-6. Overall, our findings reveal the first direct effector of miRNA-mediated translational repression in C. elegans and its physiological importance for the function of several, but likely not all miRNAs.
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Affiliation(s)
- Vinay K Mayya
- Goodman Cancer Research Center, McGill University, Montréal H3G 1Y6, Canada.,Department of Biochemistry, McGill University, Montréal H3G 1Y6, Canada
| | - Mathieu N Flamand
- Goodman Cancer Research Center, McGill University, Montréal H3G 1Y6, Canada.,Department of Biochemistry, McGill University, Montréal H3G 1Y6, Canada
| | - Alice M Lambert
- Goodman Cancer Research Center, McGill University, Montréal H3G 1Y6, Canada.,Department of Biochemistry, McGill University, Montréal H3G 1Y6, Canada
| | - Seyed Mehdi Jafarnejad
- Patrick G. Johnston Centre for Cancer Research, Queen's University of Belfast, Belfast BT9 7AE UK
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Nahum Sonenberg
- Goodman Cancer Research Center, McGill University, Montréal H3G 1Y6, Canada.,Department of Biochemistry, McGill University, Montréal H3G 1Y6, Canada
| | - Thomas F Duchaine
- Goodman Cancer Research Center, McGill University, Montréal H3G 1Y6, Canada.,Department of Biochemistry, McGill University, Montréal H3G 1Y6, Canada
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20
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Scheer H, de Almeida C, Ferrier E, Simonnot Q, Poirier L, Pflieger D, Sement FM, Koechler S, Piermaria C, Krawczyk P, Mroczek S, Chicher J, Kuhn L, Dziembowski A, Hammann P, Zuber H, Gagliardi D. The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis. Nat Commun 2021; 12:1298. [PMID: 33637717 PMCID: PMC7910438 DOI: 10.1038/s41467-021-21382-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
Uridylation is a widespread modification destabilizing eukaryotic mRNAs. Yet, molecular mechanisms underlying TUTase-mediated mRNA degradation remain mostly unresolved. Here, we report that the Arabidopsis TUTase URT1 participates in a molecular network connecting several translational repressors/decapping activators. URT1 directly interacts with DECAPPING 5 (DCP5), the Arabidopsis ortholog of human LSM14 and yeast Scd6, and this interaction connects URT1 to additional decay factors like DDX6/Dhh1-like RNA helicases. Nanopore direct RNA sequencing reveals a global role of URT1 in shaping poly(A) tail length, notably by preventing the accumulation of excessively deadenylated mRNAs. Based on in vitro and in planta data, we propose a model that explains how URT1 could reduce the accumulation of oligo(A)-tailed mRNAs both by favoring their degradation and because 3' terminal uridines intrinsically hinder deadenylation. Importantly, preventing the accumulation of excessively deadenylated mRNAs avoids the biogenesis of illegitimate siRNAs that silence endogenous mRNAs and perturb Arabidopsis growth and development.
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Affiliation(s)
- Hélène Scheer
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Caroline de Almeida
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Emilie Ferrier
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Quentin Simonnot
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Laure Poirier
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - David Pflieger
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - François M Sement
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Sandrine Koechler
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Christina Piermaria
- Plateforme Protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Paweł Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Johana Chicher
- Plateforme Protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Lauriane Kuhn
- Plateforme Protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Hélène Zuber
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
| | - Dominique Gagliardi
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
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21
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microRNA-induced translational control of antiviral immunity by the cap-binding protein 4EHP. Mol Cell 2021; 81:1187-1199.e5. [PMID: 33581076 DOI: 10.1016/j.molcel.2021.01.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 12/14/2022]
Abstract
Type I interferons (IFNs) are critical cytokines in the host defense against invading pathogens. Sustained production of IFNs, however, is detrimental to the host, as it provokes autoimmune diseases. Thus, the expression of IFNs is tightly controlled. We report that the mRNA 5' cap-binding protein 4EHP plays a key role in regulating type I IFN concomitant with controlling virus replication, both in vitro and in vivo. Mechanistically, 4EHP suppresses IFN-β production by effecting the miR-34a-induced translational silencing of Ifnb1 mRNA. miR-34a is upregulated by both RNA virus infection and IFN-β induction, prompting a negative feedback regulatory mechanism that represses IFN-β expression via 4EHP. These findings demonstrate the direct involvement of 4EHP in virus-induced host response, underscoring a critical translational silencing mechanism mediated by 4EHP and miR-34a to impede sustained IFN production. This study highlights an intrinsic regulatory function for miRNA and the translation machinery in maintaining host homeostasis.
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22
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Abstract
A diversity of gene regulatory mechanisms drives the changes in gene expression required for animal development. Here, we discuss the developmental roles of a class of gene regulatory factors composed of a core protein subunit of the Argonaute family and a 21-26-nucleotide RNA cofactor. These represent ancient regulatory complexes, originally evolved to repress genomic parasites such as transposons, viruses and retroviruses. However, over the course of evolution, small RNA-guided pathways have expanded and diversified, and they play multiple roles across all eukaryotes. Pertinent to this review, Argonaute and small RNA-mediated regulation has acquired numerous functions that affect all aspects of animal life. The regulatory function is provided by the Argonaute protein and its interactors, while the small RNA provides target specificity, guiding the Argonaute to a complementary RNA. C. elegans has 19 different, functional Argonautes, defining distinct yet interconnected pathways. Each Argonaute binds a relatively well-defined class of small RNA with distinct molecular properties. A broad classification of animal small RNA pathways distinguishes between two groups: (i) the microRNA pathway is involved in repressing relatively specific endogenous genes and (ii) the other small RNA pathways, which effectively act as a genomic immune system to primarily repress expression of foreign or "non-self" RNA while maintaining correct endogenous gene expression. microRNAs play prominent direct roles in all developmental stages, adult physiology and lifespan. The other small RNA pathways act primarily in the germline, but their impact extends far beyond, into embryogenesis and adult physiology, and even to subsequent generations. Here, we review the mechanisms and developmental functions of the diverse small RNA pathways of C. elegans.
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Affiliation(s)
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
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23
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Hickey KL, Dickson K, Cogan JZ, Replogle JM, Schoof M, D'Orazio KN, Sinha NK, Hussmann JA, Jost M, Frost A, Green R, Weissman JS, Kostova KK. GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control. Mol Cell 2020; 79:950-962.e6. [PMID: 32726578 PMCID: PMC7891188 DOI: 10.1016/j.molcel.2020.07.007] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 12/31/2022]
Abstract
Ribosome-associated quality control (RQC) pathways protect cells from toxicity caused by incomplete protein products resulting from translation of damaged or problematic mRNAs. Extensive work in yeast has identified highly conserved mechanisms that lead to degradation of faulty mRNA and partially synthesized polypeptides. Here we used CRISPR-Cas9-based screening to search for additional RQC strategies in mammals. We found that failed translation leads to specific inhibition of translation initiation on that message. This negative feedback loop is mediated by two translation inhibitors, GIGYF2 and 4EHP. Model substrates and growth-based assays established that inhibition of additional rounds of translation acts in concert with known RQC pathways to prevent buildup of toxic proteins. Inability to block translation of faulty mRNAs and subsequent accumulation of partially synthesized polypeptides could explain the neurodevelopmental and neuropsychiatric disorders observed in mice and humans with compromised GIGYF2 function.
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Affiliation(s)
- Kelsey L Hickey
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kimberley Dickson
- Department of Biology, Lawerence University, Appleton, WI 54911, USA
| | - J Zachery Cogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael Schoof
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Karole N D'Orazio
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Niladri K Sinha
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Marco Jost
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Adam Frost
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Rachel Green
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; Howard Hughes Medical Institute, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Carnegie Institution for Science, Baltimore, MD 21218, USA.
| | - Kamena K Kostova
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA.
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24
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Lai S, Du K, Shi Y, Li C, Wang G, Hu S, Jia X, Wang J, Chen S. Long Non-Coding RNAs in Brown Adipose Tissue. Diabetes Metab Syndr Obes 2020; 13:3193-3204. [PMID: 32982350 PMCID: PMC7507876 DOI: 10.2147/dmso.s264830] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/26/2020] [Indexed: 12/25/2022] Open
Abstract
Obesity has become a widespread disease that is harmful to human health. Fat homeostasis is essentially maintained by fat accumulation and energy expenditure. Studies on brown adipose tissue (BAT) represent a promising opportunity to identify a pharmaceutical intervention against obesity through increased energy expenditure. Long non-coding RNAs (lncRNAs) were thought to be critical regulators in a variety of biological processes. Recent studies have revealed that lncRNAs, including ones that are BAT-specific, conserved, and located at key protein-coding genes, function in brown adipogenesis, white adipose browning (ie, beige adipogenesis), and brown thermogenesis. In this review, we describe lncRNA properties and highlight functional lncRNAs in these biological processes, with the goal of establishing links between lncRNAs and BAT. Based on the advances of lncRNAs in the regulation of BAT, we discussed the advantages of potential lncRNA-based obesity drugs. Further BAT lncRNA-based drug development may provide new exciting approaches to defend obesity by regulation of fat homeostasis.
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Affiliation(s)
- Songjia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu611130, People’s Republic of China
| | - Kun Du
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu611130, People’s Republic of China
| | - Yu Shi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu611130, People’s Republic of China
| | - Cao Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu611130, People’s Republic of China
| | - Guoze Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu611130, People’s Republic of China
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang550025, People’s Republic of China
| | - Shenqiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu611130, People’s Republic of China
| | - Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu611130, People’s Republic of China
| | - Jie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu611130, People’s Republic of China
| | - Shiyi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu611130, People’s Republic of China
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25
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Jain Goyal M, Zhao X, Bozhinova M, Andrade-López K, de Heus C, Schulze-Dramac S, Müller-McNicoll M, Klumperman J, Béthune J. A paralog-specific role of COPI vesicles in the neuronal differentiation of mouse pluripotent cells. Life Sci Alliance 2020; 3:3/9/e202000714. [PMID: 32665377 PMCID: PMC7368096 DOI: 10.26508/lsa.202000714] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 12/03/2022] Open
Abstract
The paralogous COPI coat subunit γ1-COP plays a unique role in promoting neurite outgrowth during the neuronal differentiation of mouse pluripotent cells. Coat protein complex I (COPI)–coated vesicles mediate membrane trafficking between Golgi cisternae as well as retrieval of proteins from the Golgi to the endoplasmic reticulum. There are several flavors of the COPI coat defined by paralogous subunits of the protein complex coatomer. However, whether paralogous COPI proteins have specific functions is currently unknown. Here, we show that the paralogous coatomer subunits γ1-COP and γ2-COP are differentially expressed during the neuronal differentiation of mouse pluripotent cells. Moreover, through a combination of genome editing experiments, we demonstrate that whereas γ-COP paralogs are largely functionally redundant, γ1-COP specifically promotes neurite outgrowth. Our work stresses a role of the COPI pathway in neuronal polarization and provides evidence for distinct functions for coatomer paralogous subunits in this process.
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Affiliation(s)
- Manu Jain Goyal
- Junior Research Group, Cluster of Excellence CellNetworks, Heidelberg, Germany.,Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Xiyan Zhao
- Junior Research Group, Cluster of Excellence CellNetworks, Heidelberg, Germany.,Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Mariya Bozhinova
- Junior Research Group, Cluster of Excellence CellNetworks, Heidelberg, Germany.,Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Karla Andrade-López
- Junior Research Group, Cluster of Excellence CellNetworks, Heidelberg, Germany.,Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Cecilia de Heus
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Sandra Schulze-Dramac
- RNA Regulation Group, Cluster of Excellence "Macromolecular Complexes," Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Michaela Müller-McNicoll
- RNA Regulation Group, Cluster of Excellence "Macromolecular Complexes," Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Julien Béthune
- Junior Research Group, Cluster of Excellence CellNetworks, Heidelberg, Germany .,Heidelberg University Biochemistry Center, Heidelberg, Germany
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26
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GIGYF1/2-Driven Cooperation between ZNF598 and TTP in Posttranscriptional Regulation of Inflammatory Signaling. Cell Rep 2020; 26:3511-3521.e4. [PMID: 30917308 DOI: 10.1016/j.celrep.2019.03.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/03/2019] [Accepted: 02/27/2019] [Indexed: 12/15/2022] Open
Abstract
Inflammatory signaling is restricted through degradation and the translational repression of cytokine mRNAs. A key factor in this regulation is tristetraprolin (TTP), an RNA-binding protein (RBP) that recruits RNA-destabilizing factors and the translation inhibitory complex 4EHP-GIGYF1/2 to AU-rich element (ARE)-containing mRNAs. Here, we show that the RBP ZNF598 contributes to the same regulatory module in a TTP-like manner. Similar to TTP, ZNF598 harbors three proline-rich motifs that bind the GYF domain of GIGYF1. RNA sequencing experiments showed that ZNF598 is required for the regulation of known TTP targets, including IL-8 and CSF2 mRNA. Furthermore, we demonstrate that ZNF598 binds to IL-8 mRNA, but not TNF mRNA. Collectively, our findings highlight that ZNF598 functions as an RBP that buffers the level of a range of mRNAs. We propose that ZNF598 is a TTP-like factor that can contribute to the regulation of the inflammatory potential of cytokine-producing cells.
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27
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Ruscica V, Bawankar P, Peter D, Helms S, Igreja C, Izaurralde E. Direct role for the Drosophila GIGYF protein in 4EHP-mediated mRNA repression. Nucleic Acids Res 2020; 47:7035-7048. [PMID: 31114929 PMCID: PMC6648886 DOI: 10.1093/nar/gkz429] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/02/2019] [Accepted: 05/08/2019] [Indexed: 02/07/2023] Open
Abstract
The eIF4E-homologous protein (4EHP) is a translational repressor that competes with eIF4E for binding to the 5'-cap structure of specific mRNAs, to which it is recruited by protein factors such as the GRB10-interacting GYF (glycine-tyrosine-phenylalanine domain) proteins (GIGYF). Several experimental evidences suggest that GIGYF proteins are not merely facilitating 4EHP recruitment to transcripts but are actually required for the repressor activity of the complex. However, the underlying molecular mechanism is unknown. Here, we investigated the role of the uncharacterized Drosophila melanogaster (Dm) GIGYF protein in post-transcriptional mRNA regulation. We show that, when in complex with 4EHP, Dm GIGYF not only elicits translational repression but also promotes target mRNA decay via the recruitment of additional effector proteins. We identified the RNA helicase Me31B/DDX6, the decapping activator HPat and the CCR4-NOT deadenylase complex as binding partners of GIGYF proteins. Recruitment of Me31B and HPat via discrete binding motifs conserved among metazoan GIGYF proteins is required for downregulation of mRNA expression by the 4EHP-GIGYF complex. Our findings are consistent with a model in which GIGYF proteins additionally recruit decapping and deadenylation complexes to 4EHP-containing RNPs to induce translational repression and degradation of mRNA targets.
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Affiliation(s)
- Vincenzo Ruscica
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Praveen Bawankar
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany.,Institute of Molecular Biology gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Daniel Peter
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany.,European Molecular Biology Laboratory, 71 avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Sigrun Helms
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Cátia Igreja
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Elisa Izaurralde
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
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28
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Nowosad K, Hordyjewska-Kowalczyk E, Tylzanowski P. Mutations in gene regulatory elements linked to human limb malformations. J Med Genet 2019; 57:361-370. [PMID: 31857429 DOI: 10.1136/jmedgenet-2019-106369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/09/2019] [Accepted: 11/03/2019] [Indexed: 01/08/2023]
Abstract
Most of the human genome has a regulatory function in gene expression. The technological progress made in recent years permitted the revision of old and discovery of new mutations outside of the protein-coding regions that do affect human limb morphology. Steadily increasing discovery rate of such mutations suggests that until now the largely neglected part of the genome rises to its well-deserved prominence. In this review, we describe the recent technological advances permitting this unprecedented advance in identifying non-coding mutations. We especially focus on the mutations in cis-regulatory elements such as enhancers, and trans-regulatory elements such as miRNA and long non-coding RNA, linked to hereditary or inborn limb defects. We also discuss the role of chromatin organisation and enhancer-promoter interactions in the aetiology of limb malformations.
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Affiliation(s)
- Karol Nowosad
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland.,The Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Hordyjewska-Kowalczyk
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland.,The Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Przemko Tylzanowski
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland .,Department of Development and Regeneration, Skeletal Biology and Engineering Research Center, University of Leuven, Leuven, Belgium
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29
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Communication Is Key: 5'-3' Interactions that Regulate mRNA Translation and Turnover. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:149-164. [PMID: 31811634 DOI: 10.1007/978-3-030-31434-7_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Most eukaryotic mRNAs maintain a 5' cap structure and 3' poly(A) tail, cis-acting elements that are often separated by thousands of nucleotides. Nevertheless, multiple paradigms exist where mRNA 5' and 3' termini interact with each other in order to regulate mRNA translation and turnover. mRNAs recruit translation initiation factors to their termini, which in turn physically interact with each other. This physical bridging of the mRNA termini is known as the "closed loop" model, with years of genetic and biochemical evidence supporting the functional synergy between the 5' cap and 3' poly(A) tail to enhance mRNA translation initiation. However, a number of examples exist of "non-canonical" 5'-3' communication for cellular and viral RNAs that lack 5' cap structures and/or poly(A) tails. Moreover, in several contexts, mRNA 5'-3' communication can function to repress translation. Overall, we detail how various mRNA 5'-3' interactions play important roles in posttranscriptional regulation, wherein depending on the protein factors involved can result in translational stimulation or repression.
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30
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Valerius O, Asif AR, Beißbarth T, Bohrer R, Dihazi H, Feussner K, Jahn O, Majcherczyk A, Schmidt B, Schmitt K, Urlaub H, Lenz C. Mapping Cellular Microenvironments: Proximity Labeling and Complexome Profiling (Seventh Symposium of the Göttingen Proteomics Forum). Cells 2019; 8:cells8101192. [PMID: 31581721 PMCID: PMC6830108 DOI: 10.3390/cells8101192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 10/01/2019] [Indexed: 11/16/2022] Open
Abstract
Mass spectrometry-based proteomics methods are finding increasing use in structural biology research. Beyond simple interaction networks, information about stable protein-protein complexes or spatially proximal proteins helps to elucidate the biological functions of proteins in a wider cellular context. To shed light on new developments in this field, the Göttingen Proteomics Forum organized a one-day symposium focused on complexome profiling and proximity labeling, two emerging technologies that are gaining significant attention in biomolecular research. The symposium was held in Göttingen, Germany on 23 May, 2019, as part of a series of regular symposia organized by the Göttingen Proteomics Forum.
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Affiliation(s)
- Oliver Valerius
- Institute for Microbiology and Genetics, Georg August University, 37077 Göttingen, Germany.
| | - Abdul R Asif
- Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany.
| | - Tim Beißbarth
- Department of Medical Statistics, University Medical Center Göttingen, 37075 Göttingen, Germany.
| | - Rainer Bohrer
- Gesellschaft für Wissenschaftliche Datenverarbeitung mbH Göttingen, 37077 Göttingen, Germany.
| | - Hassan Dihazi
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, 37075 Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075 Göttingen, Germany.
| | - Kirstin Feussner
- Department of Plant Biochemistry, Albrecht von Haller Institute for Plant Sciences, Georg August University, 37073 Göttingen, Germany.
| | - Olaf Jahn
- Proteomics Group, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany.
| | - Andrzej Majcherczyk
- Büsgen Institute, Section Molecular Wood Biotechnology and Technical Mycology, Georg August University, 37077 Göttingen, Germany.
| | - Bernhard Schmidt
- Institute for Biochemistry, University Medical Center Göttingen, 37075 Göttingen, Germany.
| | - Kerstin Schmitt
- Institute for Microbiology and Genetics, Georg August University, 37077 Göttingen, Germany.
| | - Henning Urlaub
- Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany.
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
- DFG Collaborative Research Centre SFB1190 "Compartmental Gates and Contact Sites in Cells", 37075 Göttingen, Germany.
| | - Christof Lenz
- Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany.
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
- DFG Collaborative Research Centre SFB1190 "Compartmental Gates and Contact Sites in Cells", 37075 Göttingen, Germany.
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31
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Peter D, Ruscica V, Bawankar P, Weber R, Helms S, Valkov E, Igreja C, Izaurralde E. Molecular basis for GIGYF-Me31B complex assembly in 4EHP-mediated translational repression. Genes Dev 2019; 33:1355-1360. [PMID: 31439631 PMCID: PMC6771390 DOI: 10.1101/gad.329219.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/18/2019] [Indexed: 11/24/2022]
Abstract
In this study, Peter et al. provide new insights into how GIGYF proteins function together with DDX6 in the regulation of mRNA expression. They used structural analysis, in vivo expression analysis, and biochemical assays to show that GIGYF contains a motif that is necessary and sufficient for direct interaction with Me31B/DDX6, and their findings advance our understanding of the mechanism and assembly of the 4EHP–GIGYF–DDX6 repressor complex. GIGYF (Grb10-interacting GYF [glycine–tyrosine–phenylalanine domain]) proteins coordinate with 4EHP (eIF4E [eukaryotic initiation factor 4E] homologous protein), the DEAD (Asp–Glu–Ala–Asp)-box helicase Me31B/DDX6, and mRNA-binding proteins to elicit transcript-specific repression. However, the underlying molecular mechanism remains unclear. Here, we report that GIGYF contains a motif necessary and sufficient for direct interaction with Me31B/DDX6. A 2.4 Å crystal structure of the GIGYF–Me31B complex reveals that this motif arranges into a coil connected to a β hairpin on binding to conserved hydrophobic patches on the Me31B RecA2 domain. Structure-guided mutants indicate that 4EHP–GIGYF–DDX6 complex assembly is required for tristetraprolin-mediated down-regulation of an AU-rich mRNA, thus revealing the molecular principles of translational repression.
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Affiliation(s)
- Daniel Peter
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany.,European Molecular Biology Laboratory, 38042 Grenoble Cedex 9, France
| | - Vincenzo Ruscica
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Praveen Bawankar
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany.,Institute of Molecular Biology, 55128 Mainz, Germany
| | - Ramona Weber
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Sigrun Helms
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Eugene Valkov
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Cátia Igreja
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Elisa Izaurralde
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
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32
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Terrao M, Marucha KK, Mugo E, Droll D, Minia I, Egler F, Braun J, Clayton C. The suppressive cap-binding complex factor 4EIP is required for normal differentiation. Nucleic Acids Res 2019; 46:8993-9010. [PMID: 30124912 PMCID: PMC6158607 DOI: 10.1093/nar/gky733] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/01/2018] [Indexed: 12/27/2022] Open
Abstract
Trypanosoma brucei live in mammals as bloodstream forms and in the Tsetse midgut as procyclic forms. Differentiation from one form to the other proceeds via a growth-arrested stumpy form with low messenger RNA (mRNA) content and translation. The parasites have six eIF4Es and five eIF4Gs. EIF4E1 pairs with the mRNA-binding protein 4EIP but not with any EIF4G. EIF4E1 and 4EIP each inhibit expression when tethered to a reporter mRNA, but while tethered EIF4E1 suppresses only when 4EIP is present, suppression by tethered 4EIP does not require the interaction with EIF4E1. In growing bloodstream forms, 4EIP is preferentially associated with unstable mRNAs. Bloodstream- or procyclic-form trypanosomes lacking 4EIP have only a marginal growth disadvantage. Bloodstream forms without 4EIP are, however, defective in translation suppression during stumpy-form differentiation and cannot subsequently convert to growing procyclic forms. Intriguingly, the differentiation defect can be complemented by a truncated 4EIP that does not interact with EIF4E1. In contrast, bloodstream forms lacking EIF4E1 have a growth defect, stumpy formation seems normal, but they appear unable to grow as procyclic forms. We suggest that 4EIP and EIF4E1 fine-tune mRNA levels in growing cells, and that 4EIP contributes to translation suppression during differentiation to the stumpy form.
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Affiliation(s)
- Monica Terrao
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Kevin K Marucha
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Elisha Mugo
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Dorothea Droll
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Igor Minia
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Franziska Egler
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Johanna Braun
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Christine Clayton
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
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33
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Volpon L, Osborne MJ, Borden KL. Biochemical and Structural Insights into the Eukaryotic Translation Initiation Factor eIF4E. Curr Protein Pept Sci 2019; 20:525-535. [DOI: 10.2174/1389203720666190110142438] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/26/2018] [Accepted: 01/04/2019] [Indexed: 12/18/2022]
Abstract
A major question in cell and cancer biology is concerned with understanding the flow of
information from gene to protein. Indeed, many studies indicate that the proteome can be decoupled
from the transcriptome. A major source of this decoupling is post-transcriptional regulation. The eukaryotic
translation initiation factor eIF4E serves as an excellent example of a protein that can modulate
the proteome at the post-transcriptional level. eIF4E is elevated in many cancers thus highlighting
the relevance of this mode of control to biology. In this review, we provide a brief overview of various
functions of eIF4E in RNA metabolism e.g. in nuclear-cytoplasmic RNA export, translation,
RNA stability and/or sequestration. We focus on the modalities of eIF4E regulation at the biochemical
and particularly structural level. In this instance, we describe not only the importance for the m7Gcap
eIF4E interaction but also of recently discovered non-traditional RNA-eIF4E interactions as well
as cap-independent activities of eIF4E. Further, we describe several distinct structural modalities used
by the cell and some viruses to regulate or co-opt eIF4E, substantially extending the types of proteins
that can regulate eIF4E from the traditional eIF4E-binding proteins (e.g. 4E-BP1 and eIF4G). Finally,
we provide an overview of the results of targeting eIF4E activity in the clinic.
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Affiliation(s)
- Laurent Volpon
- Institute for Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Universite de Montreal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, Quebec, Canada
| | - Michael J. Osborne
- Institute for Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Universite de Montreal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, Quebec, Canada
| | - Katherine L.B. Borden
- Institute for Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Universite de Montreal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, Quebec, Canada
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34
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Keskeny C, Raisch T, Sgromo A, Igreja C, Bhandari D, Weichenrieder O, Izaurralde E. A conserved CAF40-binding motif in metazoan NOT4 mediates association with the CCR4-NOT complex. Genes Dev 2019; 33:236-252. [PMID: 30692204 PMCID: PMC6362812 DOI: 10.1101/gad.320952.118] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/10/2018] [Indexed: 11/25/2022]
Abstract
The multisubunit CCR4-NOT mRNA deadenylase complex plays important roles in the posttranscriptional regulation of gene expression. The NOT4 E3 ubiquitin ligase is a stable component of the CCR4-NOT complex in yeast but does not copurify with the human or Drosophila melanogaster complex. Here we show that the C-terminal regions of human and D. melanogaster NOT4 contain a conserved sequence motif that directly binds the CAF40 subunit of the CCR4-NOT complex (CAF40-binding motif [CBM]). In addition, nonconserved sequences flanking the CBM also contact other subunits of the complex. Crystal structures of the CBM-CAF40 complex reveal a mutually exclusive binding surface for NOT4 and Roquin or Bag of marbles mRNA regulatory proteins. Furthermore, CAF40 depletion or structure-guided mutagenesis to disrupt the NOT4-CAF40 interaction impairs the ability of NOT4 to elicit decay of tethered reporter mRNAs in cells. Together with additional sequence analyses, our results reveal the molecular basis for the association of metazoan NOT4 with the CCR4-NOT complex and show that it deviates substantially from yeast. They mark the NOT4 ubiquitin ligase as an ancient but nonconstitutive cofactor of the CCR4-NOT deadenylase with potential recruitment and/or effector functions.
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Affiliation(s)
- Csilla Keskeny
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Tobias Raisch
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Annamaria Sgromo
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Cátia Igreja
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Dipankar Bhandari
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Oliver Weichenrieder
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Elisa Izaurralde
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
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35
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Mugridge JS, Coller J, Gross JD. Structural and molecular mechanisms for the control of eukaryotic 5'-3' mRNA decay. Nat Struct Mol Biol 2018; 25:1077-1085. [PMID: 30518847 DOI: 10.1038/s41594-018-0164-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/31/2018] [Indexed: 12/15/2022]
Abstract
5'-3' RNA decay pathways are critical for quality control and regulation of gene expression. Structural and biochemical studies have provided insights into the key nucleases that carry out deadenylation, decapping, and exonucleolysis during 5'-3' decay, but detailed understanding of how these activities are coordinated is only beginning to emerge. Here we review recent mechanistic insights into the control of 5'-3' RNA decay, including coupling between translation and decay, coordination between the complexes and activities that process 5' and 3' RNA termini, conformational control of enzymatic activity, liquid phase separation, and RNA modifications.
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Affiliation(s)
- Jeffrey S Mugridge
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Jeff Coller
- The Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH, USA
| | - John D Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
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36
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Chen YC, Chang YW, Huang YS. Dysregulated Translation in Neurodevelopmental Disorders: An Overview of Autism-Risk Genes Involved in Translation. Dev Neurobiol 2018; 79:60-74. [PMID: 30430754 DOI: 10.1002/dneu.22653] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/17/2018] [Accepted: 10/25/2018] [Indexed: 01/08/2023]
Abstract
Regulated local translation-whereby specific mRNAs are transported and localized in subcellular domains where they are translated in response to regional signals-allows for remote control of gene expression to concentrate proteins in subcellular compartments. Neurons are highly polarized cells with unique features favoring local control for axonal pathfinding and synaptic plasticity, which are key processes involved in constructing functional circuits in the developing brain. Neurodevelopmental disorders are caused by genetic or environmental factors that disturb the nervous system's development during prenatal and early childhood periods. The growing list of genetic mutations that affect mRNA translation raises the question of whether aberrant translatomes in individuals with neurodevelopmental disorders share common molecular features underlying their stereotypical phenotypes and, vice versa, cause a certain degree of phenotypic heterogeneity. Here, we briefly give an overview of the role of local translation during neuronal development. We take the autism-risk gene list and discuss the molecules that (perhaps) are involved in mRNA transport and translation. Both exaggerated and suppressed translation caused by mutations in those genes have been identified or suggested. Finally, we discuss some proof-of-principle regimens for use in autism mouse models to correct dysregulated translation.
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Affiliation(s)
- Yan-Chu Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Wei Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Shuian Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
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