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Mars JC, Culjkovic-Kraljacic B, Borden KL. eIF4E orchestrates mRNA processing, RNA export and translation to modify specific protein production. Nucleus 2024; 15:2360196. [PMID: 38880976 PMCID: PMC11185188 DOI: 10.1080/19491034.2024.2360196] [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: 02/12/2024] [Accepted: 05/22/2024] [Indexed: 06/18/2024] Open
Abstract
The eukaryotic translation initiation factor eIF4E acts as a multifunctional factor that simultaneously influences mRNA processing, export, and translation in many organisms. Its multifactorial effects are derived from its capacity to bind to the methyl-7-guanosine cap on the 5'end of mRNAs and thus can act as a cap chaperone for transcripts in the nucleus and cytoplasm. In this review, we describe the multifactorial roles of eIF4E in major mRNA-processing events including capping, splicing, cleavage and polyadenylation, nuclear export and translation. We discuss the evidence that eIF4E acts at two levels to generate widescale changes to processing, export and ultimately the protein produced. First, eIF4E alters the production of components of the mRNA processing machinery, supporting a widescale reprogramming of multiple mRNA processing events. In this way, eIF4E can modulate mRNA processing without physically interacting with target transcripts. Second, eIF4E also physically interacts with both capped mRNAs and components of the RNA processing or translation machineries. Further, specific mRNAs are sensitive to eIF4E only in particular mRNA processing events. This selectivity is governed by the presence of cis-acting elements within mRNAs known as USER codes that recruit relevant co-factors engaging the appropriate machinery. In all, we describe the molecular bases for eIF4E's multifactorial function and relevant regulatory pathways, discuss the basis for selectivity, present a compendium of ~80 eIF4E-interacting factors which play roles in these activities and provide an overview of the relevance of its functions to its oncogenic potential. Finally, we summarize early-stage clinical studies targeting eIF4E in cancer.
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Affiliation(s)
- Jean-Clément Mars
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
| | - Biljana Culjkovic-Kraljacic
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
| | - Katherine L.B. Borden
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
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2
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Wu P, Zhang Q, Zhong P, Chai L, Luo Q, Jia C. Development of a prognostic risk model of uveal melanoma based on N7-methylguanosine-related regulators. Hereditas 2024; 161:22. [PMID: 38987843 PMCID: PMC11234703 DOI: 10.1186/s41065-024-00324-0] [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: 12/19/2022] [Accepted: 06/12/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND Uveal melanoma (UVM) stands as the predominant type of primary intraocular malignancy among adults. The clinical significance of N7-methylguanosine (m7G), a prevalent RNA modifications, in UVM remains unclear. METHODS Primary information from 80 UVM patients were analyzed as the training set, incorporating clinical information, mutation annotations and mRNA expression obtained from The Cancer Genome Atlas (TCGA) website. The validation set was carried out using Gene Expression Omnibus (GEO) database GSE22138 and GSE84976. Kaplan-Meier and Cox regression of univariate analyses were subjected to identify m7G-related regulators as prognostic genes. RESULT A prognostic risk model comprising EIF4E2, NUDT16, SNUPN and WDR4 was established through Cox regression of LASSO. Evaluation of the model's predictability for UVM patients' prognosis by Receiver Operating Characteristic (ROC) curves in the training set, demonstrated excellent performance Area Under the Curve (AUC) > 0.75. The high-risk prognosis within the TCGA cohort exhibit a notable worse outcome. Additionally, an independent correlation between the risk score and overall survival (OS) among UVM patients were identified. External validation of this model was carried out using the validation sets (GSE22138 and GSE84976). Immune-related analysis revealed that patients with high score of m7G-related risk model exhibited elevated level of immune infiltration and immune checkpoint gene expression. CONCLUSION We have developed a risk prediction model based on four m7G-related regulators, facilitating effective estimate UVM patients' survival by clinicians. Our findings shed novel light on essential role of m7G-related regulators in UVM and suggest potential novel targets for the diagnosis, prognosis and therapy of UVM.
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Affiliation(s)
- Pingfan Wu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
- Department of Plastic and Aesthetic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Qian Zhang
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
- Institute of Nuclear Medicine, Tongji University School of Medicine, Shanghai, 200072, China
| | - Peng Zhong
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Li Chai
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
- Institute of Nuclear Medicine, Tongji University School of Medicine, Shanghai, 200072, China
| | - Qiong Luo
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
- Institute of Nuclear Medicine, Tongji University School of Medicine, Shanghai, 200072, China
| | - Chengyou Jia
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China.
- Institute of Nuclear Medicine, Tongji University School of Medicine, Shanghai, 200072, China.
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3
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Mahé M, Rios-Fuller T, Katsara O, Schneider RJ. Non-canonical mRNA translation initiation in cell stress and cancer. NAR Cancer 2024; 6:zcae026. [PMID: 38828390 PMCID: PMC11140632 DOI: 10.1093/narcan/zcae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/08/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024] Open
Abstract
The now well described canonical mRNA translation initiation mechanism of m7G 'cap' recognition by cap-binding protein eIF4E and assembly of the canonical pre-initiation complex consisting of scaffolding protein eIF4G and RNA helicase eIF4A has historically been thought to describe all cellular mRNA translation. However, the past decade has seen the discovery of alternative mechanisms to canonical eIF4E mediated mRNA translation initiation. Studies have shown that non-canonical alternate mechanisms of cellular mRNA translation initiation, whether cap-dependent or independent, serve to provide selective translation of mRNAs under cell physiological and pathological stress conditions. These conditions typically involve the global downregulation of canonical eIF4E1/cap-mediated mRNA translation, and selective translational reprogramming of the cell proteome, as occurs in tumor development and malignant progression. Cancer cells must be able to maintain physiological plasticity to acquire a migratory phenotype, invade tissues, metastasize, survive and adapt to severe microenvironmental stress conditions that involve inhibition of canonical mRNA translation initiation. In this review we describe the emerging, important role of non-canonical, alternate mechanisms of mRNA translation initiation in cancer, particularly in adaptation to stresses and the phenotypic cell fate changes involved in malignant progression and metastasis. These alternate translation initiation mechanisms provide new targets for oncology therapeutics development.
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Affiliation(s)
- Mélanie Mahé
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Tiffany Rios-Fuller
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Olga Katsara
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Robert J Schneider
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
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Hernández G, Vazquez-Pianzola P. eIF4E as a molecular wildcard in metazoans RNA metabolism. Biol Rev Camb Philos Soc 2023; 98:2284-2306. [PMID: 37553111 DOI: 10.1111/brv.13005] [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: 02/09/2023] [Revised: 07/01/2023] [Accepted: 07/25/2023] [Indexed: 08/10/2023]
Abstract
The evolutionary origin of eukaryotes spurred the transition from prokaryotic-like translation to a more sophisticated, eukaryotic translation. During this process, successive gene duplication of a single, primordial eIF4E gene encoding the mRNA cap-binding protein eukaryotic translation initiation factor 4E (eIF4E) gave rise to a plethora of paralog genes across eukaryotes that underwent further functional diversification in RNA metabolism. The ability to take different roles is due to eIF4E promiscuity in binding many partner proteins, rendering eIF4E a highly versatile and multifunctional player that functions as a molecular wildcard. Thus, in metazoans, eIF4E paralogs are involved in various processes, including messenger RNA (mRNA) processing, export, translation, storage, and decay. Moreover, some paralogs display differential expression in tissues and developmental stages and show variable biochemical properties. In this review, we discuss recent advances shedding light on the functional diversification of eIF4E in metazoans. We emphasise humans and two phylogenetically distant species which have become paradigms for studies on development, namely the fruit fly Drosophila melanogaster and the roundworm Caenorhabditis elegans.
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Affiliation(s)
- Greco Hernández
- mRNA and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (Instituto Nacional de Cancerología, INCan), 22 San Fernando Ave., Tlalpan, Mexico City, 14080, Mexico
| | - Paula Vazquez-Pianzola
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Berne, 3012, Switzerland
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5
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Korneeva N, Khalil MI, Ghosh I, Fan R, Arnold T, De Benedetti A. SARS-CoV-2 viral protein Nsp2 stimulates translation under normal and hypoxic conditions. Virol J 2023; 20:55. [PMID: 36998012 PMCID: PMC10060939 DOI: 10.1186/s12985-023-02021-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
AbstractWhen viruses like SARS-CoV-2 infect cells, they reprogram the repertoire of cellular and viral transcripts that are being translated to optimize their strategy of replication, often targeting host translation initiation factors, particularly eIF4F complex consisting of eIF4E, eIF4G and eIF4A. A proteomic analysis of SARS-CoV-2/human proteins interaction revealed viral Nsp2 and initiation factor eIF4E2, but a role of Nsp2 in regulating translation is still controversial. HEK293T cells stably expressing Nsp2 were tested for protein synthesis rates of synthetic and endogenous mRNAs known to be translated via cap- or IRES-dependent mechanism under normal and hypoxic conditions. Both cap- and IRES-dependent translation were increased in Nsp2-expressing cells under normal and hypoxic conditions, especially mRNAs that require high levels of eIF4F. This could be exploited by the virus to maintain high translation rates of both viral and cellular proteins, particularly in hypoxic conditions as may arise in SARS-CoV-2 patients with poor lung functioning.
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6
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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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7
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Wang F, Zhang J, Lin X, Yang L, Zhou Q, Mi X, Li Q, Wang S, Li D, Liu XM, Zhou J. METTL16 promotes translation and lung tumorigenesis by sequestering cytoplasmic eIF4E2. Cell Rep 2023; 42:112150. [PMID: 36840945 DOI: 10.1016/j.celrep.2023.112150] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/21/2022] [Accepted: 02/08/2023] [Indexed: 02/26/2023] Open
Abstract
N6-methyladenosine (m6A) plays crucial roles in regulating RNA metabolisms. METTL16 identified as a single-component methyltransferase catalyzes m6A formation in the nucleus; whether it regulates cytoplasmic RNA fate remains unknown. Here, we detected the dual localization of METTL16 in the nucleus and cytoplasm. METTL16 depletion attenuates protein synthesis, but the methyltransferase activity is not required for its translation-promoting function. Mechanistically, we identified an interactor of METTL16, eIF4E2, which represses translation by acting as a competitor of eIF4E. The METTL16-eIF4E2 interaction impedes the recruitment of eIF4E2 to 5' cap structure, promoting the cap recognition by eIF4E and selective protein synthesis. Depletion of METTL16 suppresses lung tumorigenesis by downregulating the translation of key oncogenes. Collectively, our study reports a role of METTL16 in modulating translation and provides a therapeutic target for lung cancer treatment.
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Affiliation(s)
- Fei Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Jun Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Xianrong Lin
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Lu Yang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Qi Zhou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Xue Mi
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Qiujie Li
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Shen Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Dawei Li
- Center for Translational Medicine, The Affiliated Zhangjiagang Hospital of Soochow University, 68 Jiyang West Road, 215600, Suzhou, China
| | - Xiao-Min Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China; Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 21009, China.
| | - Jun Zhou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu 210009, China; Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 21009, 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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Wei W, Liu C, Wang M, Jiang W, Wang C, Zhang S. Prognostic Signature and Tumor Immune Landscape of N7-Methylguanosine-Related lncRNAs in Hepatocellular Carcinoma. Front Genet 2022; 13:906496. [PMID: 35938009 PMCID: PMC9354608 DOI: 10.3389/fgene.2022.906496] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/20/2022] [Indexed: 01/15/2023] Open
Abstract
Despite great advances in the treatment of liver hepatocellular carcinoma (LIHC), such as immunotherapy, the prognosis remains extremely poor, and there is an urgent need to develop novel diagnostic and prognostic markers. Recently, RNA methylation-related long non-coding RNAs (lncRNAs) have been demonstrated to be novel potential biomarkers for tumor diagnosis and prognosis as well as immunotherapy response, such as N6-methyladenine (m6A) and 5-methylcytosine (m5C). N7-Methylguanosine (m7G) is a widespread RNA modification in eukaryotes, but the relationship between m7G-related lncRNAs and prognosis of LIHC patients as well as tumor immunotherapy response is still unknown. In this study, based on the LIHC patients’ clinical and transcriptomic data from TCGA database, a total of 992 m7G-related lncRNAs that co-expressed with 22 m7G regulatory genes were identified using Pearson correlation analysis. Univariate regression analysis was used to screen prognostic m7G-related lncRNAs, and the least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression were applied to construct a 9-m7G-related-lncRNA risk model. The m7G-related lncRNA risk model was validated to exhibit good prognostic performance through Kaplan–Meier analysis and ROC analysis. Together with the clinicopathological features, the m7G-related lncRNA risk score was found to be an independent prognostic factor for LIHC. Furthermore, the high-risk group of LIHC patients was unveiled to have a higher tumor mutation burden (TMB), and their tumor microenvironment was more prone to the immunosuppressive state and exhibited a lower response rate to immunotherapy. In addition, 47 anti-cancer drugs were identified to exhibit a difference in drug sensitivity between the high-risk and low-risk groups. Taken together, the m7G-related lncRNA risk model might display potential value in predicting prognosis, immunotherapy response, and drug sensitivity in LIHC patients.
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Affiliation(s)
- Wei Wei
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Chao Liu
- Department of Vascular Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Meng Wang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Wei Jiang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Caihong Wang
- Department of Pathology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Shuqun Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Shuqun Zhang,
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10
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Hernández-Alvarez L, Oliveira AB, Hernández-González JE, Chahine J, Pascutti PG, de Araujo AS, de Souza FP. Computational study on the allosteric mechanism of Leishmania major IF4E-1 by 4E-interacting protein-1: Unravelling the determinants of m 7GTP cap recognition. Comput Struct Biotechnol J 2021; 19:2027-2044. [PMID: 33995900 PMCID: PMC8085901 DOI: 10.1016/j.csbj.2021.03.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 02/07/2023] Open
Abstract
Atomistic details on perturbations induced by Lm4E-IP1 binding are described. The modulation of LmIF4E-1 affinity for the cap is confirmed by energetic analyses. Signaling paths between the allosteric and othosteric sites of LmIF4E-1 are predicted. Lm4E-IP1 binding increases the side-chain entropy of W83 and R172 of LmIF4E-1. A mechanism of dynamic allostery is proposed for the regulation mediated by Lm4E-IP1.
During their life cycle, Leishmania parasites display a fine-tuned regulation of the mRNA translation through the differential expression of isoforms of eukaryotic translation initiation factor 4E (LeishIF4Es). The interaction between allosteric modulators such as 4E-interacting proteins (4E-IPs) and LeishIF4E affects the affinity of this initiation factor for the mRNA cap. Here, several computational approaches were employed to elucidate the molecular bases of the previously-reported allosteric modulation in L. major exerted by 4E-IP1 (Lm4E-IP1) on eukaryotic translation initiation factor 4E 1 (LmIF4E-1). Molecular dynamics (MD) simulations and accurate binding free energy calculations (ΔGbind) were combined with network-based modeling of residue-residue correlations. We also describe the differences in internal motions of LmIF4E-1 apo form, cap-bound, and Lm4E-IP1-bound systems. Through community network calculations, the differences in the allosteric pathways of allosterically-inhibited and active forms of LmIF4E-1 were revealed. The ΔGbind values show significant differences between the active and inhibited systems, which are in agreement with the available experimental data. Our study thoroughly describes the dynamical perturbations of LmIF4E-1 cap-binding site triggered by Lm4E-IP1. These findings are not only essential for the understanding of a critical process of trypanosomatids’ gene expression but also for gaining insight into the allostery of eukaryotic IF4Es, which could be useful for structure-based design of drugs against this protein family.
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Affiliation(s)
- Lilian Hernández-Alvarez
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| | - Antonio B Oliveira
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil.,Center for Theoretical Biological Physics, Rice University, Huston, TX, United States
| | - Jorge Enrique Hernández-González
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil.,Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jorge Chahine
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| | - Pedro Geraldo Pascutti
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Suman de Araujo
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| | - Fátima Pereira de Souza
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
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11
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Pelletier J, Schmeing TM, Sonenberg N. The multifaceted eukaryotic cap structure. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1636. [PMID: 33300197 DOI: 10.1002/wrna.1636] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/16/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022]
Abstract
The 5' cap structure is added onto RNA polymerase II transcripts soon after initiation of transcription and modulates several post-transcriptional regulatory events involved in RNA maturation. It is also required for stimulating translation initiation of many cytoplasmic mRNAs and serves to protect mRNAs from degradation. These functional properties of the cap are mediated by several cap binding proteins (CBPs) involved in nuclear and cytoplasmic gene expression steps. The role that CBPs play in gene regulation, as well as the biophysical nature by which they recognize the cap, is quite intricate. Differences in mechanisms of capping as well as nuances in cap recognition speak to the potential of targeting these processes for drug development. In this review, we focus on recent findings concerning the cap epitranscriptome, our understanding of cap binding by different CBPs, and explore therapeutic targeting of CBP-cap interaction. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > Capping and 5' End Modifications Translation > Translation Mechanisms.
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Affiliation(s)
- Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Department of Oncology, McGill University, Montreal, Quebec, Canada.,Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada.,Centre de Recherche en Biologie Structurale, McGill University, Montreal, Quebec, Canada
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Centre de Recherche en Biologie Structurale, McGill University, Montreal, Quebec, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
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12
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Liu L, Lu JY, Li F, Xing X, Li T, Yang X, Shen X. IDH1 fine-tunes cap-dependent translation initiation. J Mol Cell Biol 2020; 11:816-828. [PMID: 31408165 PMCID: PMC6884706 DOI: 10.1093/jmcb/mjz082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 06/02/2019] [Accepted: 06/18/2019] [Indexed: 12/15/2022] Open
Abstract
The metabolic enzyme isocitrate dehydrogenase 1 (IDH1) catalyzes the oxidative decarboxylation of isocitrate to α-ketoglutarate (α-KG). Its mutation often leads to aberrant gene expression in cancer. IDH1 was reported to bind thousands of RNA transcripts in a sequence-dependent manner; yet, the functional significance of this RNA-binding activity remains elusive. Here, we report that IDH1 promotes mRNA translation via direct associations with polysome mRNA and translation machinery. Comprehensive proteomic analysis in embryonic stem cells (ESCs) revealed striking enrichment of ribosomal proteins and translation regulators in IDH1-bound protein interactomes. We performed ribosomal profiling and analyzed mRNA transcripts that are associated with actively translating polysomes. Interestingly, knockout of IDH1 in ESCs led to significant downregulation of polysome-bound mRNA in IDH1 targets and subtle upregulation of ribosome densities at the start codon, indicating inefficient translation initiation upon loss of IDH1. Tethering IDH1 to a luciferase mRNA via the MS2-MBP system promotes luciferase translation, independently of the catalytic activity of IDH1. Intriguingly, IDH1 fails to enhance luciferase translation driven by an internal ribosome entry site. Together, these results reveal an unforeseen role of IDH1 in fine-tuning cap-dependent translation via the initiation step.
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Affiliation(s)
- Lichao Liu
- Tsinghua-Peking Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - J Yuyang Lu
- Tsinghua-Peking Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fajin Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xudong Xing
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tong Li
- Tsinghua-Peking Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xuerui Yang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohua Shen
- Tsinghua-Peking Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
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13
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Abstract
The stage at which ribosomes are recruited to messenger RNAs (mRNAs) is an elaborate and highly regulated phase of protein synthesis. Upon completion of this step, a ribosome is positioned at an appropriate initiation codon and primed to synthesize the encoded polypeptide product. In most circumstances, this step commits the ribosome to translate the mRNA. We summarize the knowledge regarding the initiation factors implicated in this activity as well as review different mechanisms by which this process is conducted.
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Affiliation(s)
- Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada; , .,Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec H3A 1A3, Canada.,Department of Oncology, McGill University, Montreal, Quebec H4A 3T2, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada; , .,Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec H3A 1A3, Canada
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14
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Borden KLB, Volpon L. The diversity, plasticity, and adaptability of cap-dependent translation initiation and the associated machinery. RNA Biol 2020; 17:1239-1251. [PMID: 32496897 PMCID: PMC7549709 DOI: 10.1080/15476286.2020.1766179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Translation initiation is a critical facet of gene expression with important impacts that underlie cellular responses to stresses and environmental cues. Its dysregulation in many diseases position this process as an important area for the development of new therapeutics. The gateway translation factor eIF4E is typically considered responsible for ‘global’ or ‘canonical’ m7G cap-dependent translation. However, eIF4E impacts translation of specific transcripts rather than the entire translatome. There are many alternative cap-dependent translation mechanisms that also contribute to the translation capacity of the cell. We review the diversity of these, juxtaposing more recently identified mechanisms with eIF4E-dependent modalities. We also explore the multiplicity of functions played by translation factors, both within and outside protein synthesis, and discuss how these differentially contribute to their ultimate physiological impacts. For comparison, we discuss some modalities for cap-independent translation. In all, this review highlights the diverse mechanisms that engage and control translation in eukaryotes.
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Affiliation(s)
- Katherine L B Borden
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal , Montreal, Québec, Canada
| | - Laurent Volpon
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal , Montreal, Québec, Canada
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15
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Reolon LW, Vichier-Guerre S, de Matos BM, Dugué L, Assunção TRDS, Zanchin NIT, Pochet S, Guimarães BG. Crystal structure of the Trypanosoma cruzi EIF4E5 translation factor homologue in complex with mRNA cap-4. Nucleic Acids Res 2019; 47:5973-5987. [PMID: 31066441 PMCID: PMC6582342 DOI: 10.1093/nar/gkz339] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/18/2019] [Accepted: 04/24/2019] [Indexed: 12/20/2022] Open
Abstract
Association of the initiation factor eIF4E with the mRNA cap structure is a key step for translation. Trypanosomatids present six eIF4E homologues, showing a low conservation and also differing significantly from the IF4Es of multicellular eukaryotes. On the mRNA side, while in most eukaryotes the mRNA contains cap-0 (7-methyl-GTP), the trypanosomatid mRNA features a cap-4, which is formed by a cap-0, followed by the AACU sequence containing 2′-O-ribose methylations and base methylations on nucleotides 1 and 4. The studies on eIF4E-cap-4 interaction have been hindered by the difficulty to synthesize this rather elaborated cap-4 sequence. To overcome this problem, we applied a liquid-phase oligonucleotide synthesis strategy and describe for the first time the crystal structure of a trypanosomatid eIF4E (T. cruzi EIF4E5) in complex with cap-4. The TcEIF4E5-cap-4 structure allowed a detailed description of the binding mechanism, revealing the interaction mode for the AACU sequence, with the bases packed in a parallel stacking conformation and involved, together with the methyl groups, in hydrophobic contacts with the protein. This binding mechanism evidences a distinct cap interaction mode in comparison with previously described eIF4E structures and may account for the difference of TcEIF4E5-cap-4 dissociation constant in comparison with other eIF4E homologues.
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Affiliation(s)
- Lidia Watanabe Reolon
- Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ-PR, Curitiba, Paraná 81350-010, Brazil.,Biochemistry Postgraduate Program, Federal University of Parana, Curitiba, Paraná 81530-000, Brazil
| | | | - Bruno Moisés de Matos
- Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ-PR, Curitiba, Paraná 81350-010, Brazil.,Biochemistry Postgraduate Program, Federal University of Parana, Curitiba, Paraná 81530-000, Brazil
| | - Laurence Dugué
- Unité de Chimie et Biocatalyse, Institut Pasteur, UMR3523 CNRS, Paris 75015, France
| | | | - Nilson Ivo Tonin Zanchin
- Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ-PR, Curitiba, Paraná 81350-010, Brazil
| | - Sylvie Pochet
- Unité de Chimie et Biocatalyse, Institut Pasteur, UMR3523 CNRS, Paris 75015, France
| | - Beatriz Gomes Guimarães
- Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ-PR, Curitiba, Paraná 81350-010, Brazil.,Biochemistry Postgraduate Program, Federal University of Parana, Curitiba, Paraná 81530-000, Brazil
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16
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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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17
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Kores K, Lešnik S, Bren U, Janežič D, Konc J. Discovery of Novel Potential Human Targets of Resveratrol by Inverse Molecular Docking. J Chem Inf Model 2019; 59:2467-2478. [PMID: 30883115 DOI: 10.1021/acs.jcim.8b00981] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Resveratrol is a polyphenol known for its antioxidant and anti-inflammatory properties, which support its use as a treatment for variety of diseases. There are already known connections of resveratrol to chemoprevention of cancer because of its ability to prevent tumor initiation and inhibit tumor promotion and progression. Resveratrol is also believed to be important in cardiovascular diseases and neurological disorders, such as Alzheimer's disease. Using an inverse molecular docking approach, we sought to find new potential targets of resveratrol. Docking of resveratrol into each ProBiS predicted binding site of >38 000 protein structures from the Protein Data Bank was examined, and a number of novel potential targets into which resveratrol was docked successfully were found. These explain known actions or predict new effects of resveratrol. The results included three human proteins that are already known to bind resveratrol. A majority of proteins discovered however have no already described connections with resveratrol. We report new potential target human proteins and proteins connected with different organisms into which resveratrol can dock. Our results reveal previously unknown potential target human proteins, whose connection with cardiovascular and neurological disorders could lead to new potential treatments for variety of diseases. We believe that our research could help in future experimental studies on revestratol bioactivity in humans.
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Affiliation(s)
- Katarina Kores
- University of Maribor , Faculty for Chemistry and Chemical Technology Maribor , Smetanova ulica 17 , SI-2000 Maribor , Slovenia
| | - Samo Lešnik
- National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia
| | - Urban Bren
- University of Maribor , Faculty for Chemistry and Chemical Technology Maribor , Smetanova ulica 17 , SI-2000 Maribor , Slovenia.,National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,University of Primorska , Faculty of Mathematics, Natural Sciences and Information Technology , Glagoljaška 8 , SI-6000 Koper , Slovenia
| | - Dušanka Janežič
- University of Primorska , Faculty of Mathematics, Natural Sciences and Information Technology , Glagoljaška 8 , SI-6000 Koper , Slovenia
| | - Janez Konc
- National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,University of Primorska , Faculty of Mathematics, Natural Sciences and Information Technology , Glagoljaška 8 , SI-6000 Koper , Slovenia
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18
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A threonyl-tRNA synthetase-mediated translation initiation machinery. Nat Commun 2019; 10:1357. [PMID: 30902983 PMCID: PMC6430810 DOI: 10.1038/s41467-019-09086-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 02/13/2019] [Indexed: 12/13/2022] Open
Abstract
A fundamental question in biology is how vertebrates evolved and differ from invertebrates, and little is known about differences in the regulation of translation in the two systems. Herein, we identify a threonyl-tRNA synthetase (TRS)-mediated translation initiation machinery that specifically interacts with eIF4E homologous protein, and forms machinery that is structurally analogous to the eIF4F-mediated translation initiation machinery via the recruitment of other translation initiation components. Biochemical and RNA immunoprecipitation analyses coupled to sequencing suggest that this machinery emerged as a gain-of-function event in the vertebrate lineage, and it positively regulates the translation of mRNAs required for vertebrate development. Collectively, our findings demonstrate that TRS evolved to regulate vertebrate translation initiation via its dual role as a scaffold for the assembly of initiation components and as a selector of target mRNAs. This work highlights the functional significance of aminoacyl-tRNA synthetases in the emergence and control of higher order organisms. The initiation of translation is a highly regulated process that contributes to specific gene expression programs. Here the authors find that, in vertebrate, threonyl-tRNA synthetase (TRS) can act as a scaffold for the initiation machinery to stimulate the translation of a specific set of mRNAs.
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19
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Galloway A, Cowling VH. mRNA cap regulation in mammalian cell function and fate. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2019; 1862:270-279. [PMID: 30312682 PMCID: PMC6414751 DOI: 10.1016/j.bbagrm.2018.09.011] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/13/2018] [Accepted: 09/30/2018] [Indexed: 12/17/2022]
Abstract
In this review we explore the regulation of mRNA cap formation and its impact on mammalian cells. The mRNA cap is a highly methylated modification of the 5' end of RNA pol II-transcribed RNA. It protects RNA from degradation, recruits complexes involved in RNA processing, export and translation initiation, and marks cellular mRNA as "self" to avoid recognition by the innate immune system. The mRNA cap can be viewed as a unique mark which selects RNA pol II transcripts for specific processing and translation. Over recent years, examples of regulation of mRNA cap formation have emerged, induced by oncogenes, developmental pathways and during the cell cycle. These signalling pathways regulate the rate and extent of mRNA cap formation, resulting in changes in gene expression, cell physiology and cell function.
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Affiliation(s)
- Alison Galloway
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Victoria H Cowling
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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20
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Boriack-Sjodin PA, Ribich S, Copeland RA. RNA-modifying proteins as anticancer drug targets. Nat Rev Drug Discov 2018; 17:435-453. [PMID: 29773918 DOI: 10.1038/nrd.2018.71] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
All major biological macromolecules (DNA, RNA, proteins and lipids) undergo enzyme-catalysed covalent modifications that impact their structure, function and stability. A variety of covalent modifications of RNA have been identified and demonstrated to affect RNA stability and translation to proteins; these mechanisms of translational control have been termed epitranscriptomics. Emerging data suggest that some epitranscriptomic mechanisms are altered in human cancers as well as other human diseases. In this Review, we examine the current understanding of RNA modifications with a focus on mRNA methylation, highlight their possible roles in specific cancer indications and discuss the emerging potential of RNA-modifying proteins as therapeutic targets.
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21
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Jafarnejad SM, Chapat C, Matta-Camacho E, Gelbart IA, Hesketh GG, Arguello M, Garzia A, Kim SH, Attig J, Shapiro M, Morita M, Khoutorsky A, Alain T, Gkogkas CG, Stern-Ginossar N, Tuschl T, Gingras AC, Duchaine TF, Sonenberg N. Translational control of ERK signaling through miRNA/4EHP-directed silencing. eLife 2018; 7:e35034. [PMID: 29412140 PMCID: PMC5819943 DOI: 10.7554/elife.35034] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 02/01/2018] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) exert a broad influence over gene expression by directing effector activities that impinge on translation and stability of mRNAs. We recently discovered that the cap-binding protein 4EHP is a key component of the mammalian miRNA-Induced Silencing Complex (miRISC), which mediates gene silencing. However, little is known about the mRNA repertoire that is controlled by the 4EHP/miRNA mechanism or its biological importance. Here, using ribosome profiling, we identify a subset of mRNAs that are translationally controlled by 4EHP. We show that the Dusp6 mRNA, which encodes an ERK1/2 phosphatase, is translationally repressed by 4EHP and a specific miRNA, miR-145. This promotes ERK1/2 phosphorylation, resulting in augmented cell growth and reduced apoptosis. Our findings thus empirically define the integral role of translational repression in miRNA-induced gene silencing and reveal a critical function for this process in the control of the ERK signaling cascade in mammalian cells.
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Affiliation(s)
- Seyed Mehdi Jafarnejad
- Goodman Cancer Research CenterMcGill UniversityMontréalCanada
- Department of BiochemistryMcGill UniversityMontréalCanada
| | - Clément Chapat
- Goodman Cancer Research CenterMcGill UniversityMontréalCanada
- Department of BiochemistryMcGill UniversityMontréalCanada
| | - Edna Matta-Camacho
- Goodman Cancer Research CenterMcGill UniversityMontréalCanada
- Department of BiochemistryMcGill UniversityMontréalCanada
| | - Idit Anna Gelbart
- The Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Geoffrey G Hesketh
- Centre for Systems BiologyLunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | - Meztli Arguello
- Goodman Cancer Research CenterMcGill UniversityMontréalCanada
- Department of BiochemistryMcGill UniversityMontréalCanada
| | - Aitor Garzia
- Laboratory for RNA Molecular BiologyHoward Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
| | - Sung-Hoon Kim
- Goodman Cancer Research CenterMcGill UniversityMontréalCanada
- Department of BiochemistryMcGill UniversityMontréalCanada
| | - Jan Attig
- The Francis Crick InstituteLondonUnited Kingdom
| | - Maayan Shapiro
- Goodman Cancer Research CenterMcGill UniversityMontréalCanada
- Department of BiochemistryMcGill UniversityMontréalCanada
| | - Masahiro Morita
- Goodman Cancer Research CenterMcGill UniversityMontréalCanada
- Department of BiochemistryMcGill UniversityMontréalCanada
| | - Arkady Khoutorsky
- Department of AnesthesiaMcGill UniversityMontréalCanada
- Alan Edwards Centre for Research on PainMcGill UniversityMontréalCanada
| | - Tommy Alain
- Children’s Hospital of Eastern Ontario Research Institute, Department of Biochemistry, Microbiology and ImmunologyUniversity of OttawaOttawaCanada
| | - Christos, G Gkogkas
- Patrick Wild Centre, Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUnited Kingdom
| | - Noam Stern-Ginossar
- The Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Thomas Tuschl
- Laboratory for RNA Molecular BiologyHoward Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
| | - Anne-Claude Gingras
- Centre for Systems BiologyLunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoCanada
| | - Thomas F Duchaine
- Goodman Cancer Research CenterMcGill UniversityMontréalCanada
- Department of BiochemistryMcGill UniversityMontréalCanada
| | - Nahum Sonenberg
- Goodman Cancer Research CenterMcGill UniversityMontréalCanada
- Department of BiochemistryMcGill UniversityMontréalCanada
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22
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Peter D, Weber R, Sandmeir F, Wohlbold L, Helms S, Bawankar P, Valkov E, Igreja C, Izaurralde E. GIGYF1/2 proteins use auxiliary sequences to selectively bind to 4EHP and repress target mRNA expression. Genes Dev 2017; 31:1147-1161. [PMID: 28698298 PMCID: PMC5538437 DOI: 10.1101/gad.299420.117] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 06/01/2017] [Indexed: 01/16/2023]
Abstract
The eIF4E homologous protein (4EHP) is thought to repress translation by competing with eIF4E for binding to the 5' cap structure of specific mRNAs to which it is recruited through interactions with various proteins, including the GRB10-interacting GYF (glycine-tyrosine-phenylalanine domain) proteins 1 and 2 (GIGYF1/2). Despite its similarity to eIF4E, 4EHP does not interact with eIF4G and therefore fails to initiate translation. In contrast to eIF4G, GIGYF1/2 bind selectively to 4EHP but not eIF4E. Here, we present crystal structures of the 4EHP-binding regions of GIGYF1 and GIGYF2 in complex with 4EHP, which reveal the molecular basis for the selectivity of the GIGYF1/2 proteins for 4EHP. Complementation assays in a GIGYF1/2-null cell line using structure-based mutants indicate that 4EHP requires interactions with GIGYF1/2 to down-regulate target mRNA expression. Our studies provide structural insights into the assembly of 4EHP-GIGYF1/2 repressor complexes and reveal that rather than merely facilitating 4EHP recruitment to transcripts, GIGYF1/2 proteins are required for repressive activity.
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Affiliation(s)
- Daniel Peter
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Ramona Weber
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Felix Sandmeir
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Lara Wohlbold
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Sigrun Helms
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Praveen Bawankar
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Eugene Valkov
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Cátia Igreja
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Elisa Izaurralde
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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23
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Zuberek J, Kuchta K, Hernández G, Sonenberg N, Ginalski K. Diverse cap-binding properties of Drosophila eIF4E isoforms. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1292-303. [PMID: 27374989 DOI: 10.1016/j.bbapap.2016.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 06/28/2016] [Indexed: 10/21/2022]
Abstract
The majority of eukaryotic mRNAs are translated in a cap-dependent manner, which requires recognition of the mRNA 5' cap by eIF4E protein. Multiple eIF4E family members have been identified in most eukaryotic organisms. Drosophila melanogaster (Dm) has eight eIF4E related proteins; seven of them belong to Class I and one to Class II. Their biological roles with the exception of Dm eIF4E-1, Dm eIF4E-3 and Dm 4EHP, remain unknown. Here, we compare the molecular basis of Dm eIF4E's interactions with cap and eIF4G peptide by using homology modelling and fluorescence binding assays with various cap analogues. We found that despite the presence of conserved key residues responsible for cap recognition, the differences in binding different cap analogues among Class I Dm eIF4E isoforms are up to 14-fold. The highest affinity for cap analogues was observed for Dm eIF4E-3. We suggest that Dm eIF4E-3 and Dm eIF4E-5 bind the second nucleoside of the cap in an unusual manner via stacking interactions with a histidine or a phenylalanine residue, respectively. Moreover, the analysis of ternary complexes of eIF4G peptide-eIF4E-cap analogue showed cooperativity between eIF4G and cap binding only for Dm eIF4E-4, which exhibits the lowest affinity for cap analogues among all Dm eIF4Es.
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Affiliation(s)
- Joanna Zuberek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw 02-089, Poland.
| | - Krzysztof Kuchta
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland; College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw 02-089, Poland.
| | - Greco Hernández
- Division of Basic Research, National Institute of Cancer (INCan), Tlalpan, Mexico City 14080, Mexico.
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada.
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland.
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24
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Valzania L, Ono H, Ignesti M, Cavaliere V, Bernardi F, Gamberi C, Lasko P, Gargiulo G. Drosophila 4EHP is essential for the larval-pupal transition and required in the prothoracic gland for ecdysone biosynthesis. Dev Biol 2015; 410:14-23. [PMID: 26721418 DOI: 10.1016/j.ydbio.2015.12.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 12/21/2015] [Accepted: 12/21/2015] [Indexed: 10/25/2022]
Abstract
Maternal expression of the translational regulator 4EHP (eIF4E-Homologous Protein) has an established role in generating protein gradients essential for specifying the Drosophila embryonic pattern. We generated a null mutation of 4EHP, which revealed for the first time that it is essential for viability and for completion of development. In fact, 4EHP null larvae, and larvae ubiquitously expressing RNAi targeting 4EHP, are developmentally delayed, fail to grow and eventually die. In addition, we found that expressing RNAi that targets 4EHP specifically in the prothoracic gland disrupted ecdysone biosynthesis, causing a block of the transition from the larval to pupal stages. This phenotype can be rescued by dietary administration of ecdysone. Consistent with this, 4EHP is highly expressed in the prothoracic gland and it is required for wild type expression levels of steroidogenic enzymes. Taken together, these results uncover a novel essential function for 4EHP in regulating ecdysone biosynthesis.
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Affiliation(s)
- Luca Valzania
- Dipartimento di Farmacia e Biotecnologie, Università di Bologna, Via Selmi 3, Bologna, Italy
| | - Hajime Ono
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Marilena Ignesti
- Dipartimento di Farmacia e Biotecnologie, Università di Bologna, Via Selmi 3, Bologna, Italy
| | - Valeria Cavaliere
- Dipartimento di Farmacia e Biotecnologie, Università di Bologna, Via Selmi 3, Bologna, Italy
| | - Fabio Bernardi
- Dipartimento di Farmacia e Biotecnologie, Università di Bologna, Via Selmi 3, Bologna, Italy
| | - Chiara Gamberi
- Department of Biology, McGill University, Montreal, Quebec, Canada H3G 0B1; Department of Biology, Concordia University, Montreal, Quebec, Canada H4B 1R6.
| | - Paul Lasko
- Department of Biology, McGill University, Montreal, Quebec, Canada H3G 0B1.
| | - Giuseppe Gargiulo
- Dipartimento di Farmacia e Biotecnologie, Università di Bologna, Via Selmi 3, Bologna, Italy.
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25
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Tristetraprolin Recruits Eukaryotic Initiation Factor 4E2 To Repress Translation of AU-Rich Element-Containing mRNAs. Mol Cell Biol 2015; 35:3921-32. [PMID: 26370510 DOI: 10.1128/mcb.00845-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/06/2015] [Indexed: 11/20/2022] Open
Abstract
Tristetraprolin (TTP) regulates the expression of AU-rich element-containing mRNAs through promoting the degradation and repressing the translation of target mRNA. While the mechanism for promoting target mRNA degradation has been extensively studied, the mechanism underlying translational repression is not well established. Here, we show that TTP recruits eukaryotic initiation factor 4E2 (eIF4E2) to repress target mRNA translation. TTP interacted with eIF4E2 but not with eIF4E. Overexpression of eIF4E2 enhanced TTP-mediated translational repression, and downregulation of endogenous eIF4E2 or overexpression of a truncation mutant of eIF4E2 impaired TTP-mediated translational repression. Overexpression of an eIF4E2 mutant that lost the cap-binding activity also impaired TTP's activity, suggesting that the cap-binding activity of eIF4E2 is important in TTP-mediated translational repression. We further show that TTP promoted eIF4E2 binding to target mRNA. These results imply that TTP recruits eIF4E2 to compete with eIF4E to repress the translation of target mRNA. This notion is supported by the finding that downregulation of endogenous eIF4E2 increased the production of tumor necrosis factor alpha (TNF-α) protein without affecting the mRNA levels in THP-1 cells. Collectively, these results uncover a novel mechanism by which TTP represses target mRNA translation.
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Liu Y, Yang Y, Fan J, He R, Luo M, Zheng X. The crystal structure of the PB2 cap-binding domain of influenza B virus reveals a novel cap recognition mechanism. J Biol Chem 2015; 290:9141-9. [PMID: 25691568 DOI: 10.1074/jbc.m115.636464] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Indexed: 12/17/2022] Open
Abstract
The influenza RNA-dependent RNA polymerase is a core enzyme required for both transcription and replication of the virus RNA genome, making it a potential drug target for the influenza virus. To detect the feature of cap-dependent transcription of influenza B virus (FluB) polymerase, we determined the crystal structures of the wild-type FluB polymerase PB2 subunit cap-binding domain (PB2cap) with bound GDP and the mutant FluB Q325F PB2cap with bound m(7)GDP or GDP. These structures revealed that, distinct from influenza A virus (FluA) PB2cap, the guanine and ribose moieties of substrates invert in FluB PB2caps. Moreover, we characterized the substrate specificity and affinity of the PB2caps using isothermal titration calorimetry. FluB PB2cap has a weaker affinity for m(7)GDP than FluA PB2cap. Unlike FluA PB2cap that has a preference for m(7)GDP in comparison with GDP, FluB PB2cap shows an analogous affinity for both substrates. Replacement of FluB PB2 Glu(325) by Phe, the corresponding residue of FluA PB2, increased the binding affinity of FluB PB2cap for m(7)GDP to a level approximate to that of FluA PB2cap and caused a significant higher affinity to GDP. This study indicated that FluB PB2cap has a unique cap recognition mechanism compared with FluA PB2cap, providing molecular insight into inhibitor design targeting FluB PB2cap.
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Affiliation(s)
- Yong Liu
- From the State Key Lab of Protein and Plant Gene Research and Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China and
| | - Yongfeng Yang
- From the State Key Lab of Protein and Plant Gene Research and Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China and
| | - Jialin Fan
- From the State Key Lab of Protein and Plant Gene Research and Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China and
| | - Ruina He
- From the State Key Lab of Protein and Plant Gene Research and Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China and
| | - Ming Luo
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302
| | - Xiaofeng Zheng
- From the State Key Lab of Protein and Plant Gene Research and Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China and
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Karaki S, Andrieu C, Ziouziou H, Rocchi P. The Eukaryotic Translation Initiation Factor 4E (eIF4E) as a Therapeutic Target for Cancer. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 101:1-26. [PMID: 26572974 PMCID: PMC7185574 DOI: 10.1016/bs.apcsb.2015.09.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cancer cells depend on cap-dependent translation more than normal tissue. This explains the emergence of proteins involved in the cap-dependent translation as targets for potential anticancer drugs. Cap-dependent translation starts when eIF4E binds to mRNA cap domain. This review will present eIF4E's structure and functions. It will also expose the use of eIF4E as a therapeutic target in cancer.
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Affiliation(s)
- Sara Karaki
- INSERM, U1068, CRCM, Marseille, France,Institut Paoli-Calmettes, Marseille, France,Aix-Marseille University, Marseille, France,CNRS, UMR7258, Marseille, France
| | - Claudia Andrieu
- INSERM, U1068, CRCM, Marseille, France,Institut Paoli-Calmettes, Marseille, France,Aix-Marseille University, Marseille, France,CNRS, UMR7258, Marseille, France
| | - Hajer Ziouziou
- INSERM, U1068, CRCM, Marseille, France,Institut Paoli-Calmettes, Marseille, France,Aix-Marseille University, Marseille, France,CNRS, UMR7258, Marseille, France
| | - Palma Rocchi
- INSERM, U1068, CRCM, Marseille, France,Institut Paoli-Calmettes, Marseille, France,Aix-Marseille University, Marseille, France,CNRS, UMR7258, Marseille, France,Corresponding author:
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Five eIF4E isoforms from Arabidopsis thaliana are characterized by distinct features of cap analogs binding. Biochem Biophys Res Commun 2014; 456:47-52. [PMID: 25446076 DOI: 10.1016/j.bbrc.2014.11.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 11/11/2014] [Indexed: 01/08/2023]
Abstract
The assembly of the ribosome on majority of eukaryotic mRNAs is initiated by the recruitment of eIF4E protein to the mRNA 5' end cap structure. Flowering plants use two eIF4E isoforms, named eIF4E and eIF(iso)4E, as canonical translation initiation factors and possess a homolog of mammalian 4EHP (or eIF4E-2) termed nCBP. Plants from Brassicaceae family additionally conserve a close paralog of eIF4E which in Arabidopsis thaliana has two copies named eIF4E1b and eIF4E1c. In order to assess the efficiency of plant non-canonical (eIF4E1b/1c and nCBP) and canonical (eIF4E and eIF(iso)4E) eIF4E proteins to bind mRNAs we utilized fluorescence titrations to determine accurate binding affinities of five A.thaliana eIF4E isoforms for a series of cap analogs. We found that eIF4E binds cap analogs from 4-fold to 10-fold stronger than eIF(iso)4E, while binding affinities of nCBP and eIF(iso)4E are comparable. Furthermore, eIF4E1c interacts similarly strongly with the cap as eIF4E, but eIF4E1b binds cap analogs ca. 2-fold weaker than eIF4E1c, regardless of the 95% sequence identity between these two proteins. The use of differentially chemically modified cap analogs in binding studies and a detailed analysis of the obtained homology models gave us insight into the molecular characteristic of varying cap-binding abilities of Arabidopsis eIF4E isoforms.
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Kubacka D, Miguel RN, Minshall N, Darzynkiewicz E, Standart N, Zuberek J. Distinct features of cap binding by eIF4E1b proteins. J Mol Biol 2014; 427:387-405. [PMID: 25463438 PMCID: PMC4306533 DOI: 10.1016/j.jmb.2014.11.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 11/05/2014] [Accepted: 11/10/2014] [Indexed: 02/06/2023]
Abstract
eIF4E1b, closely related to the canonical translation initiation factor 4E (eIF4E1a), cap-binding protein is highly expressed in mouse, Xenopus and zebrafish oocytes. We have previously characterized eIF4E1b as a component of the CPEB mRNP translation repressor complex along with the eIF4E-binding protein 4E-Transporter, the Xp54/DDX6 RNA helicase and additional RNA-binding proteins. eIF4E1b exhibited only very weak interactions with m7GTP-Sepharose and, rather than binding eIF4G, interacted with 4E-T. Here we undertook a detailed examination of both Xenopus and human eIF4E1b interactions with cap analogues using fluorescence titration and homology modeling. The predicted structure of eIF4E1b maintains the α + β fold characteristic of eIF4E proteins and its cap-binding pocket is similarly arranged by critical amino acids: Trp56, Trp102, Glu103, Trp166, Arg112, Arg157 and Lys162 and residues of the C-terminal loop. However, we demonstrate that eIF4E1b is 3-fold less well able to bind the cap than eIF4E1a, both proteins being highly stimulated by methylation at N7 of guanine. Moreover, eIF4E1b proteins are distinguishable from eIF4E1a by a set of conserved amino acid substitutions, several of which are located near to cap-binding residues. Indeed, eIF4E1b possesses several distinct features, namely, enhancement of cap binding by a benzyl group at N7 position of guanine, a reduced response to increasing length of the phosphate chain and increased binding to a cap separated by a linker from Sepharose, suggesting differences in the arrangement of the protein's core. In agreement, mutagenesis of the amino acids differentiating eIF4E1b from eIF4E1a reduces cap binding by eIF4E1a 2-fold, demonstrating their role in modulating cap binding. Sequence analysis of vertebrate eIF4E1a and eIF4E1b proteins identified a set of conserved substitutions, including those near to cap-binding residues. The fluorescence titration assay revealed that human and Xenopus eIF4E1b have 3-fold lower affinity for m7GTP than the eIF4E1a proteins. Additional distinct features of cap binding by eIF4E1b suggest differences in the arrangement of the protein's core and its C-terminal loop. Mutagenesis of the distinguishing amino acids reduced cap binding by eIF4E1a 2-fold, demonstrating their role in modulating affinity to m7GTP.
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Affiliation(s)
- Dorota Kubacka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw 02-089, Poland.
| | - Ricardo Núñez Miguel
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK.
| | - Nicola Minshall
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK.
| | - Edward Darzynkiewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw 02-089, Poland; Centre of New Technologies, University of Warsaw, Warsaw 02-089, Poland.
| | - Nancy Standart
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK.
| | - Joanna Zuberek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw 02-089, Poland.
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Coffman K, Yang B, Lu J, Tetlow AL, Pelliccio E, Lu S, Guo DC, Tang C, Dong MQ, Tamanoi F. Characterization of the Raptor/4E-BP1 interaction by chemical cross-linking coupled with mass spectrometry analysis. J Biol Chem 2014; 289:4723-34. [PMID: 24403073 DOI: 10.1074/jbc.m113.482067] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
mTORC1 plays critical roles in the regulation of protein synthesis, growth, and proliferation in response to nutrients, growth factors, and energy conditions. One of the substrates of mTORC1 is 4E-BP1, whose phosphorylation by mTORC1 reverses its inhibitory action on eIF4E, resulting in the promotion of protein synthesis. Raptor in mTOR complex 1 is believed to recruit 4E-BP1, facilitating phosphorylation of 4E-BP1 by the kinase mTOR. We applied chemical cross-linking coupled with mass spectrometry analysis to gain insight into interactions between mTORC1 and 4E-BP1. Using the cross-linking reagent bis[sulfosuccinimidyl] suberate, we showed that Raptor can be cross-linked with 4E-BP1. Mass spectrometric analysis of cross-linked Raptor-4E-BP1 led to the identification of several cross-linked peptide pairs. Compilation of these peptides revealed that the most N-terminal Raptor N-terminal conserved domain (in particular residues from 89 to 180) of Raptor is the major site of interaction with 4E-BP1. On 4E-BP1, we found that cross-links with Raptor were clustered in the central region (amino acid residues 56-72) we call RCR (Raptor cross-linking region). Intramolecular cross-links of Raptor suggest the presence of two structured regions of Raptor: one in the N-terminal region and the other in the C-terminal region. In support of the idea that the Raptor N-terminal conserved domain and the 4E-BP1 central region are closely located, we found that peptides that encompass the RCR of 4E-BP1 inhibit cross-linking and interaction of 4E-BP1 with Raptor. Furthermore, mutations of residues in the RCR decrease the ability of 4E-BP1 to serve as a substrate for mTORC1 in vitro and in vivo.
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Affiliation(s)
- Kimberly Coffman
- From the Department of Microbiology, Immunology, and Molecular Genetics, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California, Los Angeles, California 90095
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Kubacka D, Kamenska A, Broomhead H, Minshall N, Darzynkiewicz E, Standart N. Investigating the consequences of eIF4E2 (4EHP) interaction with 4E-transporter on its cellular distribution in HeLa cells. PLoS One 2013; 8:e72761. [PMID: 23991149 PMCID: PMC3749138 DOI: 10.1371/journal.pone.0072761] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 07/15/2013] [Indexed: 11/25/2022] Open
Abstract
In addition to the canonical eIF4E cap-binding protein, eukaryotes have evolved sequence–related variants with distinct features, some of which have been shown to negatively regulate translation of particular mRNAs, but which remain poorly characterised. Mammalian eIF4E proteins have been divided into three classes, with class I representing the canonical cap-binding protein eIF4E1. eIF4E1 binds eIF4G to initiate translation, and other eIF4E-binding proteins such as 4E-BPs and 4E-T prevent this interaction by binding eIF4E1 with the same consensus sequence YX 4Lϕ. We investigate here the interaction of human eIF4E2 (4EHP), a class II eIF4E protein, which binds the cap weakly, with eIF4E-transporter protein, 4E-T. We first show that ratios of eIF4E1:4E-T range from 50:1 to 15:1 in HeLa and HEK293 cells respectively, while those of eIF4E2:4E-T vary from 6:1 to 3:1. We next provide evidence that eIF4E2 binds 4E-T in the yeast two hybrid assay, as well as in pull-down assays and by recruitment to P-bodies in mammalian cells. We also show that while both eIF4E1 and eIF4E2 bind 4E-T via the canonical YX 4Lϕ sequence, nearby downstream sequences also influence eIF4E:4E-T interactions. Indirect immunofluorescence was used to demonstrate that eIF4E2, normally homogeneously localised in the cytoplasm, does not redistribute to stress granules in arsenite-treated cells, nor to P-bodies in Actinomycin D-treated cells, in contrast to eIF4E1. Moreover, eIF4E2 shuttles through nuclei in a Crm1-dependent manner, but in an 4E-T–independent manner, also unlike eIF4E1. Altogether we conclude that while both cap-binding proteins interact with 4E-T, and can be recruited by 4E-T to P-bodies, eIF4E2 functions are likely to be distinct from those of eIF4E1, both in the cytoplasm and nucleus, further extending our understanding of mammalian class I and II cap-binding proteins.
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Affiliation(s)
- Dorota Kubacka
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Anastasiia Kamenska
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Helen Broomhead
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Nicola Minshall
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Edward Darzynkiewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Nancy Standart
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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32
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Soto-Rifo R, Rubilar PS, Ohlmann T. The DEAD-box helicase DDX3 substitutes for the cap-binding protein eIF4E to promote compartmentalized translation initiation of the HIV-1 genomic RNA. Nucleic Acids Res 2013; 41:6286-99. [PMID: 23630313 PMCID: PMC3695493 DOI: 10.1093/nar/gkt306] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Here, we show a novel molecular mechanism promoted by the DEAD-box RNA helicase DDX3 for translation of the HIV-1 genomic RNA. This occurs through the adenosine triphosphate-dependent formation of a translation initiation complex that is assembled at the 5′ m7GTP cap of the HIV-1 mRNA. This is due to the property of DDX3 to substitute for the initiation factor eIF4E in the binding of the HIV-1 m7GTP 5′ cap structure where it nucleates the formation of a core DDX3/PABP/eIF4G trimeric complex on the HIV-1 genomic RNA. By using RNA fluorescence in situ hybridization coupled to indirect immunofluorescence, we further show that this viral ribonucleoprotein complex is addressed to compartmentalized cytoplasmic foci where the translation initiation complex is assembled.
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Affiliation(s)
- Ricardo Soto-Rifo
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon 69634, France.
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eIF4E3 acts as a tumor suppressor by utilizing an atypical mode of methyl-7-guanosine cap recognition. Proc Natl Acad Sci U S A 2013; 110:3877-82. [PMID: 23431134 DOI: 10.1073/pnas.1216862110] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recognition of the methyl-7-guanosine (m(7)G) cap structure on mRNA is an essential feature of mRNA metabolism and thus gene expression. Eukaryotic translation initiation factor 4E (eIF4E) promotes translation, mRNA export, proliferation, and oncogenic transformation dependent on this cap-binding activity. eIF4E-cap recognition is mediated via complementary charge interactions of the positively charged m(7)G cap between the negative π-electron clouds from two aromatic residues. Here, we demonstrate that a variant subfamily, eIF4E3, specifically binds the m(7)G cap in the absence of an aromatic sandwich, using instead a different spatial arrangement of residues to provide the necessary electrostatic and van der Waals contacts. Contacts are much more extensive between eIF4E3-cap than other family members. Structural analyses of other cap-binding proteins indicate this recognition mode is atypical. We demonstrate that eIF4E3 relies on this cap-binding activity to act as a tumor suppressor, competing with the growth-promoting functions of eIF4E. In fact, reduced eIF4E3 in high eIF4E cancers suggests that eIF4E3 underlies a clinically relevant inhibitory mechanism that is lost in some malignancies. Taken together, there is more structural plasticity in cap recognition than previously thought, and this is physiologically relevant.
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34
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Kinkelin K, Veith K, Grünwald M, Bono F. Crystal structure of a minimal eIF4E-Cup complex reveals a general mechanism of eIF4E regulation in translational repression. RNA (NEW YORK, N.Y.) 2012; 18:1624-34. [PMID: 22832024 PMCID: PMC3425778 DOI: 10.1261/rna.033639.112] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Cup is an eIF4E-binding protein (4E-BP) that plays a central role in translational regulation of localized mRNAs during early Drosophila development. In particular, Cup is required for repressing translation of the maternally contributed oskar, nanos, and gurken mRNAs, all of which are essential for embryonic body axis determination. Here, we present the 2.8 Å resolution crystal structure of a minimal eIF4E-Cup assembly, consisting of the interacting regions of the two proteins. In the structure, two separate segments of Cup contact two orthogonal faces of eIF4E. The eIF4E-binding consensus motif of Cup (YXXXXLΦ) binds the convex side of eIF4E similarly to the consensus of other eIF4E-binding proteins, such as 4E-BPs and eIF4G. The second, noncanonical, eIF4E-binding site of Cup binds laterally and perpendicularly to the eIF4E β-sheet. Mutations of Cup at this binding site were shown to reduce binding to eIF4E and to promote the destabilization of the associated mRNA. Comparison with the binding mode of eIF4G to eIF4E suggests that Cup and eIF4G binding would be mutually exclusive at both binding sites. This shows how a common molecular surface of eIF4E might recognize different proteins acting at different times in the same pathway. The structure provides insight into the mechanism by which Cup disrupts eIF4E-eIF4G interaction and has broader implications for understanding the role of 4E-BPs in translational regulation.
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Affiliation(s)
- Kerstin Kinkelin
- Max-Planck-Institute for Developmental Biology, 71076 Tübingen, Germany
| | - Katharina Veith
- Max-Planck-Institute for Developmental Biology, 71076 Tübingen, Germany
| | - Marlene Grünwald
- Max-Planck-Institute for Developmental Biology, 71076 Tübingen, Germany
| | - Fulvia Bono
- Max-Planck-Institute for Developmental Biology, 71076 Tübingen, Germany
- Corresponding authorE-mail
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35
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Kong J, Lasko P. Translational control in cellular and developmental processes. Nat Rev Genet 2012; 13:383-94. [PMID: 22568971 DOI: 10.1038/nrg3184] [Citation(s) in RCA: 146] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Growing evidence indicates that translational control of specific mRNAs contributes importantly to genetic regulation across the breadth of cellular and developmental processes. Synthesis of protein from a specific mRNA can be controlled by RNA-binding proteins at the level of translational initiation and elongation, and translational control is also sometimes coupled to mRNA localization mechanisms. Recent discoveries from invertebrate and vertebrate systems have uncovered novel modes of translational regulation, have provided new insights into how specific regulators target the general translational machinery and have identified several new links between translational control and human disease.
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Affiliation(s)
- Jian Kong
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec H3G 0T5, Canada
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36
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A novel 4EHP-GIGYF2 translational repressor complex is essential for mammalian development. Mol Cell Biol 2012; 32:3585-93. [PMID: 22751931 DOI: 10.1128/mcb.00455-12] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The binding of the eukaryotic initiation factor 4E (eIF4E) to the mRNA 5' cap structure is a rate-limiting step in mRNA translation initiation. eIF4E promotes ribosome recruitment to the mRNA. In Drosophila, the eIF4E homologous protein (d4EHP) forms a complex with binding partners to suppress the translation of distinct mRNAs by competing with eIF4E for binding the 5' cap structure. This repression mechanism is essential for the asymmetric distribution of proteins and normal embryonic development in Drosophila. In contrast, the physiological role of the mammalian 4EHP (m4EHP) was not known. In this study, we have identified the Grb10-interacting GYF protein 2 (GIGYF2) and the zinc finger protein 598 (ZNF598) as components of the m4EHP complex. GIGYF2 directly interacts with m4EHP, and this interaction is required for stabilization of both proteins. Disruption of the m4EHP-GIGYF2 complex leads to increased translation and perinatal lethality in mice. We propose a model by which the m4EHP-GIGYF2 complex represses translation of a subset of mRNAs during embryonic development, as was previously reported for d4EHP.
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Jia Y, Polunovsky V, Bitterman PB, Wagner CR. Cap-dependent translation initiation factor eIF4E: an emerging anticancer drug target. Med Res Rev 2012; 32:786-814. [PMID: 22495651 PMCID: PMC7168506 DOI: 10.1002/med.21260] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cancer cells tend to be more highly dependent on cap‐dependent translation than normal tissues. Thus, proteins involved in the initiation of cap‐dependent translation have emerged as potential anti‐cancer drug targets. Cap‐dependent translation is initiated by the binding of the factor eIF4E to the cap domain of mRNA. Detailed x‐ray crystal and NMR structures are available for eIF4E in association with cap‐analogs, as well as domains of other initiation factors. This review will summarize efforts to design potential antagonist of eIF4E that could be used as new pharmacological tools and anti‐cancer agents and. Insights drawn from these studies should aid in the design of future inhibitors of eIF4E dependent translation initiation. © 2012 Wiley Periodicals, Inc. Med Res Rev., 32, No. 4, 786‐814, 2012
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Affiliation(s)
- Yan Jia
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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38
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Liu W, Jankowska-Anyszka M, Piecyk K, Dickson L, Wallace A, Niedzwiecka A, Stepinski J, Stolarski R, Darzynkiewicz E, Kieft J, Zhao R, Jones DNM, Davis RE. Structural basis for nematode eIF4E binding an m(2,2,7)G-Cap and its implications for translation initiation. Nucleic Acids Res 2011; 39:8820-32. [PMID: 21965542 PMCID: PMC3203607 DOI: 10.1093/nar/gkr650] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Metazoan spliced leader (SL) trans-splicing generates mRNAs with an m2,2,7G-cap and a common downstream SL RNA sequence. The mechanism for eIF4E binding an m2,2,7G-cap is unknown. Here, we describe the first structure of an eIF4E with an m2,2,7G-cap and compare it to the cognate m7G-eIF4E complex. These structures and Nuclear Magnetic Resonance (NMR) data indicate that the nematode Ascaris suum eIF4E binds the two different caps in a similar manner except for the loss of a single hydrogen bond on binding the m2,2,7G-cap. Nematode and mammalian eIF4E both have a low affinity for m2,2,7G-cap compared with the m7G-cap. Nematode eIF4E binding to the m7G-cap, m2,2,7G-cap and the m2,2,7G-SL 22-nt RNA leads to distinct eIF4E conformational changes. Additional interactions occur between Ascaris eIF4E and the SL on binding the m2,2,7G-SL. We propose interactions between Ascaris eIF4E and the SL impact eIF4G and contribute to translation initiation, whereas these interactions do not occur when only the m2,2,7G-cap is present. These data have implications for the contribution of 5′-UTRs in mRNA translation and the function of different eIF4E isoforms.
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Affiliation(s)
- Weizhi Liu
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
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Liu W, Zhao R, McFarland C, Kieft J, Niedzwiecka A, Jankowska-Anyszka M, Stepinski J, Darzynkiewicz E, Jones DNM, Davis RE. Structural insights into parasite eIF4E binding specificity for m7G and m2,2,7G mRNA caps. J Biol Chem 2009; 284:31336-49. [PMID: 19710013 PMCID: PMC2781531 DOI: 10.1074/jbc.m109.049858] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 08/19/2009] [Indexed: 01/02/2023] Open
Abstract
The eukaryotic translation initiation factor eIF4E recognizes the mRNA cap, a key step in translation initiation. Here we have characterized eIF4E from the human parasite Schistosoma mansoni. Schistosome mRNAs have either the typical monomethylguanosine (m(7)G) or a trimethylguanosine (m(2,2,7)G) cap derived from spliced leader trans-splicing. Quantitative fluorescence titration analyses demonstrated that schistosome eIF4E has similar binding specificity for both caps. We present the first crystal structure of an eIF4E with similar binding specificity for m(7)G and m(2,2,7)G caps. The eIF4E.m(7)GpppG structure demonstrates that the schistosome protein binds monomethyl cap in a manner similar to that of single specificity eIF4Es and exhibits a structure similar to other known eIF4Es. The structure suggests an alternate orientation of a conserved, key Glu-90 in the cap-binding pocket that may contribute to dual binding specificity and a position for mRNA bound to eIF4E consistent with biochemical data. Comparison of NMR chemical shift perturbations in schistosome eIF4E on binding m(7)GpppG and m(2,2,7)GpppG identified key differences between the two complexes. Isothermal titration calorimetry demonstrated significant thermodynamics differences for the binding process with the two caps (m(7)G versus m(2,2,7)G). Overall the NMR and isothermal titration calorimetry data suggest the importance of intrinsic conformational flexibility in the schistosome eIF4E that enables binding to m(2,2,7)G cap.
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Affiliation(s)
- Weizhi Liu
- From the Departments of Biochemistry and Molecular Genetics and
| | - Rui Zhao
- From the Departments of Biochemistry and Molecular Genetics and
| | - Craig McFarland
- From the Departments of Biochemistry and Molecular Genetics and
| | - Jeffrey Kieft
- From the Departments of Biochemistry and Molecular Genetics and
| | - Anna Niedzwiecka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
- Biological Physics Group, Institute of Physics, Polish Academy of Sciences, 32/46 Lotnikow Avenue, 02-668 Warsaw, Poland
| | | | - Janusz Stepinski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - Edward Darzynkiewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - David N. M. Jones
- **Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
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Bradrick SS, Gromeier M. Identification of gemin5 as a novel 7-methylguanosine cap-binding protein. PLoS One 2009; 4:e7030. [PMID: 19750007 PMCID: PMC2736588 DOI: 10.1371/journal.pone.0007030] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Accepted: 08/14/2009] [Indexed: 01/04/2023] Open
Abstract
Background A unique attribute of RNA molecules synthesized by RNA polymerase II is the presence of a 7-methylguanosine (m7G) cap structure added co-transcriptionally to the 5′ end. Through its association with trans-acting effector proteins, the m7G cap participates in multiple aspects of RNA metabolism including localization, translation and decay. However, at present relatively few eukaryotic proteins have been identified as factors capable of direct association with m7G. Methodology/Principal Findings Employing an unbiased proteomic approach, we identified gemin5, a component of the survival of motor neuron (SMN) complex, as a factor capable of direct and specific interaction with the m7G cap. Gemin5 was readily purified by cap-affinity chromatography in contrast to other SMN complex proteins. Investigating the underlying basis for this observation, we found that purified gemin5 associates with m7G-linked sepharose in the absence of detectable eIF4E, and specifically crosslinks to radiolabeled cap structure after UV irradiation. Deletion analysis revealed that an intact set of WD repeat domains located in the N-terminal half of gemin5 are required for cap-binding. Moreover, using structural modeling and site-directed mutagenesis, we identified two proximal aromatic residues located within the WD repeat region that significantly impact m7G association. Conclusions/Significance This study rigorously identifies gemin5 as a novel cap-binding protein and describes an unprecedented role for WD repeat domains in m7G recognition. The findings presented here will facilitate understanding of gemin5's role in the metabolism of non-coding snRNAs and perhaps other RNA pol II transcripts.
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Affiliation(s)
- Shelton S Bradrick
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America.
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Curry S, Kotik-Kogan O, Conte MR, Brick P. Getting to the end of RNA: structural analysis of protein recognition of 5' and 3' termini. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1789:653-66. [PMID: 19619683 DOI: 10.1016/j.bbagrm.2009.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 07/07/2009] [Accepted: 07/09/2009] [Indexed: 10/20/2022]
Abstract
The specific recognition by proteins of the 5' and 3' ends of RNA molecules is an important facet of many cellular processes, including RNA maturation, regulation of translation initiation and control of gene expression by degradation and RNA interference. The aim of this review is to survey recent structural analyses of protein binding domains that specifically bind to the extreme 5' or 3' termini of RNA. For reasons of space and because their interactions are also governed by catalytic considerations, we have excluded enzymes that modify the 5' and 3' extremities of RNA. It is clear that there is enormous structural diversity among the proteins that have evolved to bind to the ends of RNA molecules. Moreover, they commonly exhibit conformational flexibility that appears to be important for binding and regulation of the interaction. This flexibility has sometimes complicated the interpretation of structural results and presents significant challenges for future investigations.
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Affiliation(s)
- Stephen Curry
- Biophysics Section, Blackett Laboratory, Imperial College, Exhibition Road, London, SW7 2AZ, UK.
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Bjelić S, Jelesarov I. A survey of the year 2007 literature on applications of isothermal titration calorimetry. J Mol Recognit 2008; 21:289-312. [PMID: 18729242 DOI: 10.1002/jmr.909] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Elucidation of the energetic principles of binding affinity and specificity is a central task in many branches of current sciences: biology, medicine, pharmacology, chemistry, material sciences, etc. In biomedical research, integral approaches combining structural information with in-solution biophysical data have proved to be a powerful way toward understanding the physical basis of vital cellular phenomena. Isothermal titration calorimetry (ITC) is a valuable experimental tool facilitating quantification of the thermodynamic parameters that characterize recognition processes involving biomacromolecules. The method provides access to all relevant thermodynamic information by performing a few experiments. In particular, ITC experiments allow to by-pass tedious and (rarely precise) procedures aimed at determining the changes in enthalpy and entropy upon binding by van't Hoff analysis. Notwithstanding limitations, ITC has now the reputation of being the "gold standard" and ITC data are widely used to validate theoretical predictions of thermodynamic parameters, as well as to benchmark the results of novel binding assays. In this paper, we discuss several publications from 2007 reporting ITC results. The focus is on applications in biologically oriented fields. We do not intend a comprehensive coverage of all newly accumulated information. Rather, we emphasize work which has captured our attention with originality and far-reaching analysis, or else has provided ideas for expanding the potential of the method.
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Affiliation(s)
- Sasa Bjelić
- Biochemisches Institut der Universität Zürich, Winterthurerstrasse 190, Zürich, Switzerland
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Characterization of pokeweed antiviral protein binding to mRNA cap analogs: competition with nucleotides and enhancement by translation initiation factor iso4G. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1789:109-16. [PMID: 18935985 DOI: 10.1016/j.bbagrm.2008.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Revised: 09/09/2008] [Accepted: 09/10/2008] [Indexed: 11/23/2022]
Abstract
Pokeweed antiviral protein (PAP) is a type I ribosomal inactivating protein (RIP). PAP binds to and depurinates the sarcin/ricin loop (SRL) of ribosomal RNA resulting in the cessation of protein synthesis. PAP has also been shown to bind to mRNA cap analogs and depurinate mRNA downstream of the cap structure. The biological role of cap binding and its possible role in PAP activity are not known. Here we show the first direct quantitative evidence for PAP binding to the cap analog m(7)GTP. We report a binding affinity of 43.3+/-0.1 nM at 25 degrees C as determined by fluorescence quenching experiments. This is similar to the values reported for wheat cap-binding proteins eIFiso4E and eIFiso4F. van't Hoff analysis of m(7)GTP-PAP equilibrium reveals a binding reaction that is enthalpy driven and entropy favored with TDeltaS degrees contributing 15% to the overall value of DeltaG degrees . This is in contrast to the wheat cap-binding proteins which are enthalpically driven in the DeltaG degrees for binding. Competition experiments indicate that ATP and GTP compete for the cap-binding site on PAP with slightly different affinities. Fluorescence studies of PAP-eIFiso4G binding reveal a protein-protein interaction with a K(d) of 108.4+/-0.3 nM. eIFiso4G was shown to enhance the interaction of PAP with m(7)GTP cap analog by 2.4-fold. These results suggest the involvement of PAP-translation initiation factor complexes in RNA selection and depurination.
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Brown CJ, McNae I, Fischer PM, Walkinshaw MD. Crystallographic and mass spectrometric characterisation of eIF4E with N7-alkylated cap derivatives. J Mol Biol 2007; 372:7-15. [PMID: 17631896 DOI: 10.1016/j.jmb.2007.06.033] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Revised: 06/10/2007] [Accepted: 06/12/2007] [Indexed: 10/23/2022]
Abstract
Structural complexes of the eukaryotic translation initiation factor 4E (eIF4E) with a series of N(7)-alkylated guanosine derivative mRNA cap analogue structures have been characterised. Mass spectrometry was used to determine apparent gas-phase equilibrium dissociation constants (K(d)) values of 0.15 microM, 13.6 microM, and 55.7 microM for eIF4E with 7-methyl-GTP (m(7)GTP), GTP, and GMP, respectively. For tight and specific binding to the eIF4E mononucleotide binding site, there seems to be a clear requirement for guanosine derivatives to possess both the delocalised positive charge of the N(7)-methylated guanine system and at least one phosphate group. We show that the N(7)-benzylated monophosphates 7-benzyl-GMP (Bn(7)GMP) and 7-(p-fluorobenzyl)-GMP (FBn(7)GMP) bind eIF4E substantially more tightly than non-N(7)-alkylated guanosine derivatives (K(d) values of 7.0 microM and 2.0 microM, respectively). The eIF4E complex crystal structures with Bn(7)GMP and FBn(7)GMP show that additional favourable contacts of the benzyl groups with eIF4E contribute binding energy that compensates for loss of the beta and gamma-phosphates. The N(7)-benzyl groups pack into a hydrophobic pocket behind the two tryptophan side-chains that are involved in the cation-pi stacking interaction between the cap and the eIF4E mononucleotide binding site. This pocket is formed by an induced fit in which one of the tryptophan residues involved in cap binding flips through 180 degrees relative to structures with N(7)-methylated cap derivatives. This and other observations made here will be useful in the design of new families of eIF4E inhibitors, which may have potential therapeutic applications in cancer.
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Affiliation(s)
- Christopher J Brown
- Structural Biochemistry, The University of Edinburgh, Michael Swann Building, King's Buildings, Edinburgh, EH9 3JR, Scotland, UK
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