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Brito Querido J, Díaz-López I, Ramakrishnan V. The molecular basis of translation initiation and its regulation in eukaryotes. Nat Rev Mol Cell Biol 2024; 25:168-186. [PMID: 38052923 DOI: 10.1038/s41580-023-00624-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2023] [Indexed: 12/07/2023]
Abstract
The regulation of gene expression is fundamental for life. Whereas the role of transcriptional regulation of gene expression has been studied for several decades, it has been clear over the past two decades that post-transcriptional regulation of gene expression, of which translation regulation is a major part, can be equally important. Translation can be divided into four main stages: initiation, elongation, termination and ribosome recycling. Translation is controlled mainly during its initiation, a process which culminates in a ribosome positioned with an initiator tRNA over the start codon and, thus, ready to begin elongation of the protein chain. mRNA translation has emerged as a powerful tool for the development of innovative therapies, yet the detailed mechanisms underlying the complex process of initiation remain unclear. Recent studies in yeast and mammals have started to shed light on some previously unclear aspects of this process. In this Review, we discuss the current state of knowledge on eukaryotic translation initiation and its regulation in health and disease. Specifically, we focus on recent advances in understanding the processes involved in assembling the 43S pre-initiation complex and its recruitment by the cap-binding complex eukaryotic translation initiation factor 4F (eIF4F) at the 5' end of mRNA. In addition, we discuss recent insights into ribosome scanning along the 5' untranslated region of mRNA and selection of the start codon, which culminates in joining of the 60S large subunit and formation of the 80S initiation complex.
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Affiliation(s)
- Jailson Brito Querido
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Irene Díaz-López
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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2
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Ochkasova A, Arbuzov G, Malygin A, Graifer D. Two "Edges" in Our Knowledge on the Functions of Ribosomal Proteins: The Revealed Contributions of Their Regions to Translation Mechanisms and the Issues of Their Extracellular Transport by Exosomes. Int J Mol Sci 2023; 24:11458. [PMID: 37511213 PMCID: PMC10380927 DOI: 10.3390/ijms241411458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Ribosomal proteins (RPs), the constituents of the ribosome, belong to the most abundant proteins in the cell. A highly coordinated network of interactions implicating RPs and ribosomal RNAs (rRNAs) forms the functionally competent structure of the ribosome, enabling it to perform translation, the synthesis of polypeptide chain on the messenger RNA (mRNA) template. Several RPs contact ribosomal ligands, namely, those with transfer RNAs (tRNAs), mRNA or translation factors in the course of translation, and the contribution of a number of these particular contacts to the translation process has recently been established. Many ribosomal proteins also have various extra-ribosomal functions unrelated to translation. The least-understood and -discussed functions of RPs are those related to their participation in the intercellular communication via extracellular vesicles including exosomes, etc., which often carry RPs as passengers. Recently reported data show that such a kind of communication can reprogram a receptor cell and change its phenotype, which is associated with cancer progression and metastasis. Here, we review the state-of-art ideas on the implications of specific amino acid residues of RPs in the particular stages of the translation process in higher eukaryotes and currently available data on the transport of RPs by extracellular vesicles and its biological effects.
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Affiliation(s)
- Anastasia Ochkasova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Grigory Arbuzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alexey Malygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Dmitri Graifer
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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3
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Ikeuchi K, Ivic N, Buschauer R, Cheng J, Fröhlich T, Matsuo Y, Berninghausen O, Inada T, Becker T, Beckmann R. Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2. Nat Commun 2023; 14:2730. [PMID: 37169754 PMCID: PMC10175282 DOI: 10.1038/s41467-023-38161-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 04/19/2023] [Indexed: 05/13/2023] Open
Abstract
In actively translating 80S ribosomes the ribosomal protein eS7 of the 40S subunit is monoubiquitinated by the E3 ligase Not4 and deubiquitinated by Otu2 upon ribosomal subunit recycling. Despite its importance for translation efficiency the exact role and structural basis for this translational reset is poorly understood. Here, structural analysis by cryo-electron microscopy of native and reconstituted Otu2-bound ribosomal complexes reveals that Otu2 engages 40S subunits mainly between ribosome recycling and initiation stages. Otu2 binds to several sites on the intersubunit surface of the 40S that are not occupied by any other 40S-binding factors. This binding mode explains the discrimination against 80S ribosomes via the largely helical N-terminal domain of Otu2 as well as the specificity for mono-ubiquitinated eS7 on 40S. Collectively, this study reveals mechanistic insights into the Otu2-driven deubiquitination steps for translational reset during ribosome recycling/(re)initiation.
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Affiliation(s)
- Ken Ikeuchi
- Department of Biochemistry, Gene Center, Feodor-Lynen-Str. 25, University of Munich, 81377, Munich, Germany
| | - Nives Ivic
- Division of Physical Chemistry, Rudjer Boskovic Institute, Bijenicka cesta 54, 10000, Zagreb, Croatia
| | - Robert Buschauer
- Department of Biochemistry, Gene Center, Feodor-Lynen-Str. 25, University of Munich, 81377, Munich, Germany
| | - Jingdong Cheng
- Department of Biochemistry, Gene Center, Feodor-Lynen-Str. 25, University of Munich, 81377, Munich, Germany
- Institutes of biomedical science, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan university, Dong'an Road 131, 200032, Shanghai, China
| | - Thomas Fröhlich
- LAFUGA, Laboratory for Functional Genome Analysis, Gene Center, Feodor-Lynen-Str. 25, University of Munich, 81377, Munich, Germany
| | - Yoshitaka Matsuo
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-ku, 108-8639, Japan
| | - Otto Berninghausen
- Department of Biochemistry, Gene Center, Feodor-Lynen-Str. 25, University of Munich, 81377, Munich, Germany
| | - Toshifumi Inada
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-ku, 108-8639, Japan
| | - Thomas Becker
- Department of Biochemistry, Gene Center, Feodor-Lynen-Str. 25, University of Munich, 81377, Munich, Germany.
| | - Roland Beckmann
- Department of Biochemistry, Gene Center, Feodor-Lynen-Str. 25, University of Munich, 81377, Munich, Germany.
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Zhang D, Zhu L, Wang F, Li P, Wang Y, Gao Y. Molecular mechanisms of eukaryotic translation fidelity and their associations with diseases. Int J Biol Macromol 2023; 242:124680. [PMID: 37141965 DOI: 10.1016/j.ijbiomac.2023.124680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Abstract
Converting genetic information into functional proteins is a complex, multi-step process, with each step being tightly regulated to ensure the accuracy of translation, which is critical to cellular health. In recent years, advances in modern biotechnology, especially the development of cryo-electron microscopy and single-molecule techniques, have enabled a clearer understanding of the mechanisms of protein translation fidelity. Although there are many studies on the regulation of protein translation in prokaryotes, and the basic elements of translation are highly conserved in prokaryotes and eukaryotes, there are still great differences in the specific regulatory mechanisms. This review describes how eukaryotic ribosomes and translation factors regulate protein translation and ensure translation accuracy. However, a certain frequency of translation errors does occur in translation, so we describe diseases that arise when the rate of translation errors reaches or exceeds a threshold of cellular tolerance.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
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5
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Zhuo W, Chen J, Jiang S, Zheng J, Huang H, Xie P, Li W, Lei M, Yin J, Gao Y, Liu Z. Proteomic profiling of eIF3a conditional knockout mice. Front Mol Biosci 2023; 10:1160063. [PMID: 37152897 PMCID: PMC10154561 DOI: 10.3389/fmolb.2023.1160063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/30/2023] [Indexed: 05/09/2023] Open
Abstract
Eukaryotic translation initiation factor 3 subunit A (eIF3a) is the largest subunit of the eukaryotic translation initiation factor 3 (eIF3). eIF3a plays an integral role in protein biosynthesis, hence impacting the onset, development, and treatment of tumors. The proteins regulated by eIF3a are still being explored in vivo. In this study, a Cre-loxP system was used to generate eIF3a conditional knockout mice. Tandem mass tag (TMT) labeling with LC-MS/MS analysis was used to identify differentially expressed proteins (DEPs) in fat, lungs, skin, and spleen tissue of the eIF3a knockout mice and controls. Bioinformatics analysis was then used to explore the functions and molecular signaling pathways of these protein landscapes. It was observed that eIF3a is essential for life sustenance. Abnormal tissue pathology was found in the lungs, fat, skin, spleen, and thymus. In total, 588, 210, 324, and 944 DEPs were quantified in the lungs, fat, skin, and spleen, respectively, of the eIF3a knockout mice as compared to the control. The quantified differentially expressed proteins were tissue-specific, except for eight proteins shared by the four tissues. A broad range of functions for eIF3a, including cellular signaling pathway, immune response, metabolism, defense response, phagocytes, and DNA replication, has been revealed using bioinformatics analysis. Herein, several pathways related to oxidative stress in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, including nitrogen metabolism, peroxisome, cytochrome P450 drug metabolism, pyruvate metabolism, PPAR signaling pathway, phospholipase D signaling pathway, B-cell receptor signaling pathway, ferroptosis, and focal adhesion, have been identified. Collectively, this study shows that eIF3a is an essential gene for sustaining life, and its downstream proteins are involved in diverse novel functions beyond mRNA translational regulation.
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Affiliation(s)
- Wei Zhuo
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Juan Chen
- Departments of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Shilong Jiang
- Departments of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Juyan Zheng
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Hanxue Huang
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Pan Xie
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Wei Li
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Mengrong Lei
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Jiye Yin
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Ying Gao
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Departments of Gerontology, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Zhaoqian Liu, ; Ying Gao,
| | - Zhaoqian Liu
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
- *Correspondence: Zhaoqian Liu, ; Ying Gao,
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Song Z, Lin J, Su R, Ji Y, Jia R, Li S, Shan G, Huang C. eIF3j inhibits translation of a subset of circular RNAs in eukaryotic cells. Nucleic Acids Res 2022; 50:11529-11549. [PMID: 36330957 PMCID: PMC9723666 DOI: 10.1093/nar/gkac980] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/04/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Increasing studies have revealed that a subset of circular RNAs (circRNAs) harbor an open reading frame and can act as protein-coding templates to generate functional proteins that are closely associated with multiple physiological and disease-relevant processes, and thus proper regulation of synthesis of these circRNA-derived proteins is a fundamental cellular process required for homeostasis maintenance. However, how circRNA translation initiation is coordinated by different trans-acting factors remains poorly understood. In particular, the impact of different eukaryotic translation initiation factors (eIFs) on circRNA translation and the physiological relevance of this distinct regulation have not yet been characterized. In this study, we screened all 43 Drosophila eIFs and revealed the conflicting functions of eIF3 subunits in the translational control of the translatable circRNA circSfl: eIF3 is indispensable for circSfl translation, while the eIF3-associated factor eIF3j is the most potent inhibitor. Mechanistically, the binding of eIF3j to circSfl promotes the disassociation of eIF3. The C-terminus of eIF3j and an RNA regulon within the circSfl untranslated region (UTR) are essential for the inhibitory effect of eIF3j. Moreover, we revealed the physiological relevance of eIF3j-mediated circSfl translation repression in response to heat shock. Finally, additional translatable circRNAs were identified to be similarly regulated in an eIF3j-dependent manner. Altogether, our study provides a significant insight into the field of cap-independent translational regulation and undiscovered functions of eIF3.
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Affiliation(s)
| | | | - Rui Su
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Yu Ji
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ruirui Jia
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Shi Li
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ge Shan
- School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chuan Huang
- To whom correspondence should be addressed. Tel: +86 19956025374;
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Friedrich D, Marintchev A, Arthanari H. The metaphorical swiss army knife: The multitude and diverse roles of HEAT domains in eukaryotic translation initiation. Nucleic Acids Res 2022; 50:5424-5442. [PMID: 35552740 PMCID: PMC9177959 DOI: 10.1093/nar/gkac342] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 11/24/2022] Open
Abstract
Biomolecular associations forged by specific interaction among structural scaffolds are fundamental to the control and regulation of cell processes. One such structural architecture, characterized by HEAT repeats, is involved in a multitude of cellular processes, including intracellular transport, signaling, and protein synthesis. Here, we review the multitude and versatility of HEAT domains in the regulation of mRNA translation initiation. Structural and cellular biology approaches, as well as several biophysical studies, have revealed that a number of HEAT domain-mediated interactions with a host of protein factors and RNAs coordinate translation initiation. We describe the basic structural architecture of HEAT domains and briefly introduce examples of the cellular processes they dictate, including nuclear transport by importin and RNA degradation. We then focus on proteins in the translation initiation system featuring HEAT domains, specifically the HEAT domains of eIF4G, DAP5, eIF5, and eIF2Bϵ. Comparative analysis of their remarkably versatile interactions, including protein–protein and protein–RNA recognition, reveal the functional importance of flexible regions within these HEAT domains. Here we outline how HEAT domains orchestrate fundamental aspects of translation initiation and highlight open mechanistic questions in the area.
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Affiliation(s)
- Daniel Friedrich
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Assen Marintchev
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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8
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Xu C, Shen Y, Shi Y, Zhang M, Zhou L. Eukaryotic translation initiation factor 3 subunit B promotes head and neck cancer via CEBPB translation. Cancer Cell Int 2022; 22:161. [PMID: 35459206 PMCID: PMC9034523 DOI: 10.1186/s12935-022-02578-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/08/2022] [Indexed: 11/22/2022] Open
Abstract
Background Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer type worldwide. Deregulation of mRNA translation is a frequent feature of cancer. Eukaryotic translation initiation factor 3 subunit B (EIF3B) has been reported as an oncogene; however, its role in HNSCC has yet to be fully elucidated. Methods In this study, the clinical significance of EIF3B expression was analyzed based on TCGA datasets. Then, EIF3B expression was knocked down and its role in HNSCC was revealed. To explore the molecular mechanisms of EIF3B, we applied RNA sequencing and proteomics and acquired deregulated pathways. RNA immunoprecipitation (RIP) sequencing was conducted to reveal the target mRNAs of EIF3B, and TCGA datasets were used to validate potential targets of EIF3B. Results Elevated expression of EIF3B was observed in the HNSCC cancer samples. The expression of EIF3B was significantly correlated with the patient’s sex, age, HPV infection status, T stage, N stage, perineural invasion status and survival status. EIF3B serves as a marker of an unfavorable HNSCC prognosis. EIF3B-silenced Fadu and Cal27 cells exhibited reduced cell numbers, and EIF3B knockdown induced apoptosis in both cell lines. The EIF3B-silenced cells demonstrated decreased invasion and migration capabilities, and the EIF3B knockdown group mice showed significantly decreased tumor volumes. The results show that EIF3B promotes CEBPB translation and activates the MAPK pathway and revealed that IL6R and CCNG2 are targets of EIF3B-regulated CEBPB translation. Conclusion In summary, the results indicated that EIF3B is a novel oncogene in HNSCC that promotes CEBPB translation and IL6R expression, and these findings provide a link between the molecular basis and pathogenesis of HNSCC. Graphical Abstract ![]()
EIF3B is a prognostic biomarker for HNSCC risk; EIF3B promotes HNSCC progression in vitro and in vivo; EIF3B promotes CEBPB translation and activates the MAPK pathway; IL6R and CCNG2 are targets of EIF3B-regulated CEBPB translation.
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Affiliation(s)
- Chengzhi Xu
- Department of Otolaryngology-Head and Neck Surgery, Eye Ear Nose and Throat Hospital, Fudan University, No. 83 Fenyang Road, Shanghai, 200031, China
| | - Yupeng Shen
- Department of Otolaryngology-Head and Neck Surgery, The First Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Yong Shi
- Department of Otolaryngology-Head and Neck Surgery, Eye Ear Nose and Throat Hospital, Fudan University, No. 83 Fenyang Road, Shanghai, 200031, China
| | - Ming Zhang
- Department of Otolaryngology-Head and Neck Surgery, Eye Ear Nose and Throat Hospital, Fudan University, No. 83 Fenyang Road, Shanghai, 200031, China
| | - Liang Zhou
- Department of Otolaryngology-Head and Neck Surgery, Eye Ear Nose and Throat Hospital, Fudan University, No. 83 Fenyang Road, Shanghai, 200031, China.
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Abstract
Accurate protein synthesis (translation) relies on translation factors that rectify ribosome fluctuations into a unidirectional process. Understanding this process requires structural characterization of the ribosome and translation-factor dynamics. In the 2000s, crystallographic studies determined high-resolution structures of ribosomes stalled with translation factors, providing a starting point for visualizing translation. Recent progress in single-particle cryogenic electron microscopy (cryo-EM) has enabled near-atomic resolution of numerous structures sampled in heterogeneous complexes (ensembles). Ensemble and time-resolved cryo-EM have now revealed unprecedented views of ribosome transitions in the three principal stages of translation: initiation, elongation, and termination. This review focuses on how translation factors help achieve high accuracy and efficiency of translation by monitoring distinct ribosome conformations and by differentially shifting the equilibria of ribosome rearrangements for cognate and near-cognate substrates. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA;
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10
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Stanciu A, Luo J, Funes L, Galbokke Hewage S, Kulkarni SD, Aitken CE. eIF3 and Its mRNA-Entry-Channel Arm Contribute to the Recruitment of mRNAs With Long 5′-Untranslated Regions. Front Mol Biosci 2022; 8:787664. [PMID: 35087868 PMCID: PMC8787345 DOI: 10.3389/fmolb.2021.787664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/13/2021] [Indexed: 01/21/2023] Open
Abstract
Translation initiation in eukaryotes is a multi-step pathway and the most regulated phase of translation. Eukaryotic initiation factor 3 (eIF3) is the largest and most complex of the translation initiation factors, and it contributes to events throughout the initiation pathway. In particular, eIF3 appears to play critical roles in mRNA recruitment. More recently, eIF3 has been implicated in driving the selective translation of specific classes of mRNAs. However, unraveling the mechanism of these diverse contributions—and disentangling the roles of the individual subunits of the eIF3 complex—remains challenging. We employed ribosome profiling of budding yeast cells expressing two distinct mutations targeting the eIF3 complex. These mutations either disrupt the entire complex or subunits positioned near the mRNA-entry channel of the ribosome and which appear to relocate during or in response to mRNA binding and start-codon recognition. Disruption of either the entire eIF3 complex or specific targeting of these subunits affects mRNAs with long 5′-untranslated regions and whose translation is more dependent on eIF4A, eIF4B, and Ded1 but less dependent on eIF4G, eIF4E, and PABP. Disruption of the entire eIF3 complex further affects mRNAs involved in mitochondrial processes and with structured 5′-untranslated regions. Comparison of the suite of mRNAs most sensitive to both mutations with those uniquely sensitive to disruption of the entire complex sheds new light on the specific roles of individual subunits of the eIF3 complex.
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Affiliation(s)
- Andrei Stanciu
- Computer Science Department, Vassar College, Poughkeepsie, NY, United States
| | - Juncheng Luo
- Biochemistry Program, Vassar College, Poughkeepsie, NY, United States
| | - Lucy Funes
- Biology Department, Vassar College, Poughkeepsie, NY, United States
| | | | - Shardul D. Kulkarni
- Department of Biochemistry and Molecular Biology, Penn State Eberly College of Medicine, University Park, PA, United States
| | - Colin Echeverría Aitken
- Biochemistry Program, Vassar College, Poughkeepsie, NY, United States
- Biology Department, Vassar College, Poughkeepsie, NY, United States
- *Correspondence: Colin Echeverría Aitken,
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11
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Gamble N, Paul EE, Anand B, Marintchev A. Regulation of the interactions between human eIF5 and eIF1A by the CK2 kinase. Curr Res Struct Biol 2022; 4:308-319. [PMID: 36164648 PMCID: PMC9508154 DOI: 10.1016/j.crstbi.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/26/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Translation initiation in eukaryotes relies on a complex network of interactions that are continuously reorganized throughout the process. As more information becomes available about the structure of the ribosomal preinitiation complex (PIC) at various points in translation initiation, new questions arise about which interactions occur when, their roles, and regulation. The eukaryotic translation factor (eIF) 5 is the GTPase-activating protein (GAP) for the GTPase eIF2, which brings the initiator Met-tRNAi to the PIC. eIF5 also plays a central role in PIC assembly and remodeling through interactions with other proteins, including eIFs 1, 1A, and 3c. Phosphorylation by casein kinase 2 (CK2) significantly increases the eIF5 affinity for eIF2. The interaction between eIF5 and eIF1A was reported to be mediated by the eIF5 C-terminal domain (CTD) and the eIF1A N-terminal tail. Here, we report a new contact interface, between eIF5-CTD and the oligonucleotide/oligosaccharide-binding fold (OB) domain of eIF1A, which contributes to the overall affinity between the two proteins. We also show that the interaction is modulated by dynamic intramolecular interactions within both eIF5 and eIF1A. CK2 phosphorylation of eIF5 increases its affinity for eIF1A, offering new insights into the mechanisms by which CK2 stimulates protein synthesis and cell proliferation. eIF5-CTD interacts with both the N-terminal tail and the OB domain of eIF1A. The OB domain contacts stabilize the overall interaction. The eIF1A C-terminal tail and the eIF5 DWEAR motif interfere with OB domain binding. CK2 phosphorylation of eIF5 increases its affinity for eIF1A.
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12
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Llácer JL, Hussain T, Dong J, Villamayor L, Gordiyenko Y, Hinnebusch AG. Large-scale movement of eIF3 domains during translation initiation modulate start codon selection. Nucleic Acids Res 2021; 49:11491-11511. [PMID: 34648019 PMCID: PMC8599844 DOI: 10.1093/nar/gkab908] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 11/13/2022] Open
Abstract
The eukaryotic initiation factor 3 (eIF3) complex is involved in every step of translation initiation, but there is limited understanding of its molecular functions. Here, we present a single particle electron cryomicroscopy (cryo-EM) reconstruction of yeast 48S ribosomal preinitiation complex (PIC) in an open conformation conducive to scanning, with core subunit eIF3b bound on the 40S interface near the decoding center in contact with the ternary complex eIF2·GTP·initiator tRNA. eIF3b is relocated together with eIF3i from their solvent interface locations observed in other PIC structures, with eIF3i lacking 40S contacts. Re-processing of micrographs of our previous 48S PIC in a closed state also suggests relocation of the entire eIF3b-3i-3g-3a-Cter module during the course of initiation. Genetic analysis indicates that high fidelity initiation depends on eIF3b interactions at the 40S subunit interface that promote the closed PIC conformation, or facilitate the relocation of eIF3b/eIF3i to the solvent interface, on start codon selection.
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Affiliation(s)
- Jose L Llácer
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia 46010, Spain.,Centro para Investigación Biomédica en Red sobre Enfermedades Raras CIBERER-ISCIII, Valencia, Spain
| | - Tanweer Hussain
- Molecular Reproduction, Development and Genetics (MRDG), Biological Sciences Building, Indian Institute of Science, Bangalore 560012, India
| | - Jinsheng Dong
- Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura Villamayor
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia 46010, Spain
| | | | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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13
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Egorova T, Biziaev N, Shuvalov A, Sokolova E, Mukba S, Evmenov K, Zotova M, Kushchenko A, Shuvalova E, Alkalaeva E. eIF3j facilitates loading of release factors into the ribosome. Nucleic Acids Res 2021; 49:11181-11196. [PMID: 34591963 PMCID: PMC8565342 DOI: 10.1093/nar/gkab854] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/23/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022] Open
Abstract
eIF3j is one of the eukaryotic translation factors originally reported as the labile subunit of the eukaryotic translation initiation factor eIF3. The yeast homolog of this protein, Hcr1, has been implicated in stringent AUG recognition as well as in controlling translation termination and stop codon readthrough. Using a reconstituted mammalian in vitro translation system, we showed that the human protein eIF3j is also important for translation termination. We showed that eIF3j stimulates peptidyl-tRNA hydrolysis induced by a complex of eukaryotic release factors, eRF1-eRF3. Moreover, in combination with the initiation factor eIF3, which also stimulates peptide release, eIF3j activity in translation termination increases. We found that eIF3j interacts with the pre-termination ribosomal complex, and eRF3 destabilises this interaction. In the solution, these proteins bind to each other and to other participants of translation termination, eRF1 and PABP, in the presence of GTP. Using a toe-printing assay, we determined the stage at which eIF3j functions – binding of release factors to the A-site of the ribosome before GTP hydrolysis. Based on these data, we assumed that human eIF3j is involved in the regulation of translation termination by loading release factors into the ribosome.
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Affiliation(s)
- Tatiana Egorova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, 119991 Moscow, Russia
| | - Nikita Biziaev
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexey Shuvalov
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, 119991 Moscow, Russia
| | - Elizaveta Sokolova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, 119991 Moscow, Russia
| | - Sabina Mukba
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Konstantin Evmenov
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Maria Zotova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Artem Kushchenko
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ekaterina Shuvalova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, 119991 Moscow, Russia
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14
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Yuan S, Balaji S, Lomakin IB, Xiong Y. Coronavirus Nsp1: Immune Response Suppression and Protein Expression Inhibition. Front Microbiol 2021; 12:752214. [PMID: 34659188 PMCID: PMC8512706 DOI: 10.3389/fmicb.2021.752214] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 08/24/2021] [Indexed: 12/30/2022] Open
Abstract
Coronaviruses have brought severe challenges to public health all over the world in the past 20years. SARS-CoV-2, the causative agent of the COVID-19 pandemic that has led to millions of deaths, belongs to the genus beta-coronavirus. Alpha- and beta-coronaviruses encode a unique protein, nonstructural protein 1 (Nsp1) that both suppresses host immune responses and reduces global gene expression levels in the host cells. As a key pathogenicity factor of coronaviruses, Nsp1 redirects the host translation machinery to increase synthesis of viral proteins. Through multiple mechanisms, coronaviruses impede host protein expression through Nsp1, while escaping inhibition to allow the translation of viral RNA. In this review, we discuss current data about suppression of the immune responses and inhibition of protein synthesis induced by coronavirus Nsp1, as well as the prospect of live-attenuated vaccine development with virulence-attenuated viruses with mutations in Nsp1.
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Affiliation(s)
- Shuai Yuan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Shravani Balaji
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Ivan B Lomakin
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, United States
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
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15
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Alghoul F, Laure S, Eriani G, Martin F. Translation inhibitory elements from Hoxa3 and Hoxa11 mRNAs use uORFs for translation inhibition. eLife 2021; 10:e66369. [PMID: 34076576 PMCID: PMC8172242 DOI: 10.7554/elife.66369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/20/2021] [Indexed: 01/20/2023] Open
Abstract
During embryogenesis, Hox mRNA translation is tightly regulated by a sophisticated molecular mechanism that combines two RNA regulons located in their 5'UTR. First, an internal ribosome entry site (IRES) enables cap-independent translation. The second regulon is a translation inhibitory element or TIE, which ensures concomitant cap-dependent translation inhibition. In this study, we deciphered the molecular mechanisms of mouse Hoxa3 and Hoxa11 TIEs. Both TIEs possess an upstream open reading frame (uORF) that is critical to inhibit cap-dependent translation. However, the molecular mechanisms used are different. In Hoxa3 TIE, we identify an uORF which inhibits cap-dependent translation and we show the requirement of the non-canonical initiation factor eIF2D for this process. The mode of action of Hoxa11 TIE is different, it also contains an uORF but it is a minimal uORF formed by an uAUG followed immediately by a stop codon, namely a 'start-stop'. The 'start-stop' sequence is species-specific and in mice, is located upstream of a highly stable stem loop structure which stalls the 80S ribosome and thereby inhibits cap-dependent translation of Hoxa11 main ORF.
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Affiliation(s)
- Fatima Alghoul
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
| | - Schaeffer Laure
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
| | - Gilbert Eriani
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
| | - Franck Martin
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
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16
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Knockdown of eIF3a attenuated cell growth in K1 human thyroid cancer cells. Genes Genomics 2021; 43:379-388. [PMID: 33595813 DOI: 10.1007/s13258-021-01048-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/08/2021] [Indexed: 01/17/2023]
Abstract
BACKGROUND In ribosome establishment and the initiation of translation, eukaryotic translation initiation factor (eIF) 3a is a pivotal functional subunit of the eIF3 complex. In various cancer types, abnormal eIF3a expression plays an important role in tumorigenesis. OBJECTIVE We aimed to explore the role of eIF3a in human thyroid cancer (TC). MATERIAL AND METHODS The expression of eIF3a was determined in TC tissues by qRT-PCR and immunohistochemistry (IHC) assay, respectively. In addition, the expression of eIF3a in K1 and BCPAP cells were detected by qRT-PCR. Cell proliferation, cell cycle, and cell apoptosis were assessed after eIF3a knockdown in K1 in cell line. RESULTS The expression of eIF3a mRNA was high in TC tissues and cancer cell lines. Moreover, eIF3a expression in TC tissues indicated that high eIF3a level was associated with tumor grade. In addition, eIF3a knockdown resulted in a significantly decrease in cell proliferation and increased the apoptosis of K1 cells. Cell cycle was arrested in both the S and G2/M phase. The levels of phosphorylated ERK1/2 and surviving were decreased after eIF3a knockdown. CONCLUSION Our study suggested that eIF3a contributed to TC cell proliferation. It may be a promising target for gene therapy in human thyroid cancer.
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17
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Lapointe CP, Grosely R, Johnson AG, Wang J, Fernández IS, Puglisi JD. Dynamic competition between SARS-CoV-2 NSP1 and mRNA on the human ribosome inhibits translation initiation. Proc Natl Acad Sci U S A 2021; 118:e2017715118. [PMID: 33479166 PMCID: PMC8017934 DOI: 10.1073/pnas.2017715118] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a beta-CoV that recently emerged as a human pathogen and is the causative agent of the COVID-19 pandemic. A molecular framework of how the virus manipulates host cellular machinery to facilitate infection remains unclear. Here, we focus on SARS-CoV-2 NSP1, which is proposed to be a virulence factor that inhibits protein synthesis by directly binding the human ribosome. We demonstrate biochemically that NSP1 inhibits translation of model human and SARS-CoV-2 messenger RNAs (mRNAs). NSP1 specifically binds to the small (40S) ribosomal subunit, which is required for translation inhibition. Using single-molecule fluorescence assays to monitor NSP1-40S subunit binding in real time, we determine that eukaryotic translation initiation factors (eIFs) allosterically modulate the interaction of NSP1 with ribosomal preinitiation complexes in the absence of mRNA. We further elucidate that NSP1 competes with RNA segments downstream of the start codon to bind the 40S subunit and that the protein is unable to associate rapidly with 80S ribosomes assembled on an mRNA. Collectively, our findings support a model where NSP1 proteins from viruses in at least two subgenera of beta-CoVs associate with the open head conformation of the 40S subunit to inhibit an early step of translation, by preventing accommodation of mRNA within the entry channel.
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Affiliation(s)
- Christopher P Lapointe
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Alex G Johnson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Israel S Fernández
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, NY 10032
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305;
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18
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Lapointe CP, Grosely R, Johnson AG, Wang J, Fernández IS, Puglisi JD. Dynamic competition between SARS-CoV-2 NSP1 and mRNA on the human ribosome inhibits translation initiation. Proc Natl Acad Sci U S A 2021. [PMID: 33479166 DOI: 10.1101/2020.08.20.259770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a beta-CoV that recently emerged as a human pathogen and is the causative agent of the COVID-19 pandemic. A molecular framework of how the virus manipulates host cellular machinery to facilitate infection remains unclear. Here, we focus on SARS-CoV-2 NSP1, which is proposed to be a virulence factor that inhibits protein synthesis by directly binding the human ribosome. We demonstrate biochemically that NSP1 inhibits translation of model human and SARS-CoV-2 messenger RNAs (mRNAs). NSP1 specifically binds to the small (40S) ribosomal subunit, which is required for translation inhibition. Using single-molecule fluorescence assays to monitor NSP1-40S subunit binding in real time, we determine that eukaryotic translation initiation factors (eIFs) allosterically modulate the interaction of NSP1 with ribosomal preinitiation complexes in the absence of mRNA. We further elucidate that NSP1 competes with RNA segments downstream of the start codon to bind the 40S subunit and that the protein is unable to associate rapidly with 80S ribosomes assembled on an mRNA. Collectively, our findings support a model where NSP1 proteins from viruses in at least two subgenera of beta-CoVs associate with the open head conformation of the 40S subunit to inhibit an early step of translation, by preventing accommodation of mRNA within the entry channel.
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Affiliation(s)
- Christopher P Lapointe
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Alex G Johnson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Israel S Fernández
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, NY 10032
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305;
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19
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Yuan S, Peng L, Park JJ, Hu Y, Devarkar SC, Dong MB, Shen Q, Wu S, Chen S, Lomakin IB, Xiong Y. Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA. Mol Cell 2020. [PMID: 33188728 DOI: 10.1101/2020.08.09.243451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The causative virus of the COVID-19 pandemic, SARS-CoV-2, uses its nonstructural protein 1 (Nsp1) to suppress cellular, but not viral, protein synthesis through yet unknown mechanisms. We show here that among all viral proteins, Nsp1 has the largest impact on host viability in the cells of human lung origin. Differential expression analysis of mRNA-seq data revealed that Nsp1 broadly alters the cellular transcriptome. Our cryo-EM structure of the Nsp1-40S ribosome complex shows that Nsp1 inhibits translation by plugging the mRNA entry channel of the 40S. We also determined the structure of the 48S preinitiation complex formed by Nsp1, 40S, and the cricket paralysis virus internal ribosome entry site (IRES) RNA, which shows that it is nonfunctional because of the incorrect position of the mRNA 3' region. Our results elucidate the mechanism of host translation inhibition by SARS-CoV-2 and advance understanding of the impacts from a major pathogenicity factor of SARS-CoV-2.
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MESH Headings
- Animals
- COVID-19/genetics
- COVID-19/metabolism
- COVID-19/pathology
- Chlorocebus aethiops
- Cryoelectron Microscopy
- Humans
- Protein Biosynthesis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Ribosome Subunits, Small, Eukaryotic/genetics
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Ribosome Subunits, Small, Eukaryotic/ultrastructure
- Ribosome Subunits, Small, Eukaryotic/virology
- SARS-CoV-2/genetics
- SARS-CoV-2/metabolism
- SARS-CoV-2/pathogenicity
- SARS-CoV-2/ultrastructure
- Vero Cells
- Viral Nonstructural Proteins/genetics
- Viral Nonstructural Proteins/metabolism
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Affiliation(s)
- Shuai Yuan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Lei Peng
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jonathan J Park
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Yingxia Hu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Swapnil C Devarkar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Matthew B Dong
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Qi Shen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Shenping Wu
- Department of Pharmacology, Yale University, West Haven, CT 06516, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA.
| | - Ivan B Lomakin
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
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20
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Kratzat H, Mackens-Kiani T, Ameismeier M, Potocnjak M, Cheng J, Dacheux E, Namane A, Berninghausen O, Herzog F, Fromont-Racine M, Becker T, Beckmann R. A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes. EMBO J 2020; 40:e105179. [PMID: 33289941 PMCID: PMC7780240 DOI: 10.15252/embj.2020105179] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 09/21/2020] [Accepted: 09/29/2020] [Indexed: 11/24/2022] Open
Abstract
In eukaryotic translation, termination and ribosome recycling phases are linked to subsequent initiation of a new round of translation by persistence of several factors at ribosomal sub‐complexes. These comprise/include the large eIF3 complex, eIF3j (Hcr1 in yeast) and the ATP‐binding cassette protein ABCE1 (Rli1 in yeast). The ATPase is mainly active as a recycling factor, but it can remain bound to the dissociated 40S subunit until formation of the next 43S pre‐initiation complexes. However, its functional role and native architectural context remains largely enigmatic. Here, we present an architectural inventory of native yeast and human ABCE1‐containing pre‐initiation complexes by cryo‐EM. We found that ABCE1 was mostly associated with early 43S, but also with later 48S phases of initiation. It adopted a novel hybrid conformation of its nucleotide‐binding domains, while interacting with the N‐terminus of eIF3j. Further, eIF3j occupied the mRNA entry channel via its ultimate C‐terminus providing a structural explanation for its antagonistic role with respect to mRNA binding. Overall, the native human samples provide a near‐complete molecular picture of the architecture and sophisticated interaction network of the 43S‐bound eIF3 complex and the eIF2 ternary complex containing the initiator tRNA.
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Affiliation(s)
- Hanna Kratzat
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Timur Mackens-Kiani
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Michael Ameismeier
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Mia Potocnjak
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Jingdong Cheng
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Estelle Dacheux
- Génétique des Interactions Macromoléculaires, UMR3525 CNRS, Institut Pasteur, Paris, France
| | - Abdelkader Namane
- Génétique des Interactions Macromoléculaires, UMR3525 CNRS, Institut Pasteur, Paris, France
| | - Otto Berninghausen
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Franz Herzog
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | | | - Thomas Becker
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Roland Beckmann
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
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21
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Brito Querido J, Sokabe M, Kraatz S, Gordiyenko Y, Skehel JM, Fraser CS, Ramakrishnan V. Structure of a human 48 S translational initiation complex. Science 2020; 369:1220-1227. [PMID: 32883864 DOI: 10.1126/science.aba4904] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/07/2020] [Indexed: 12/20/2022]
Abstract
A key step in translational initiation is the recruitment of the 43S preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to form the 48S initiation complex (i.e., the 48S). The 48S then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we used cryo-electron microscopy to determine the structure of a reconstituted human 48S The structure reveals insights into early events of translation initiation complex assembly, as well as how eIF4F interacts with subunits of eIF3 near the mRNA exit channel in the 43S The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests that downstream mRNA is unwound at least in part by being "pulled" through the 40S subunit during scanning.
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Affiliation(s)
| | - Masaaki Sokabe
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA, USA
| | | | | | | | - Christopher S Fraser
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA, USA.
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22
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Yuan S, Peng L, Park JJ, Hu Y, Devarkar SC, Dong MB, Shen Q, Wu S, Chen S, Lomakin IB, Xiong Y. Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA. Mol Cell 2020; 80:1055-1066.e6. [PMID: 33188728 PMCID: PMC7833686 DOI: 10.1016/j.molcel.2020.10.034] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/05/2020] [Accepted: 10/22/2020] [Indexed: 12/22/2022]
Abstract
The causative virus of the COVID-19 pandemic, SARS-CoV-2, uses its nonstructural protein 1 (Nsp1) to suppress cellular, but not viral, protein synthesis through yet unknown mechanisms. We show here that among all viral proteins, Nsp1 has the largest impact on host viability in the cells of human lung origin. Differential expression analysis of mRNA-seq data revealed that Nsp1 broadly alters the cellular transcriptome. Our cryo-EM structure of the Nsp1-40S ribosome complex shows that Nsp1 inhibits translation by plugging the mRNA entry channel of the 40S. We also determined the structure of the 48S preinitiation complex formed by Nsp1, 40S, and the cricket paralysis virus internal ribosome entry site (IRES) RNA, which shows that it is nonfunctional because of the incorrect position of the mRNA 3′ region. Our results elucidate the mechanism of host translation inhibition by SARS-CoV-2 and advance understanding of the impacts from a major pathogenicity factor of SARS-CoV-2.
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MESH Headings
- Animals
- COVID-19/genetics
- COVID-19/metabolism
- COVID-19/pathology
- Chlorocebus aethiops
- Cryoelectron Microscopy
- Humans
- Protein Biosynthesis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Ribosome Subunits, Small, Eukaryotic/genetics
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Ribosome Subunits, Small, Eukaryotic/ultrastructure
- Ribosome Subunits, Small, Eukaryotic/virology
- SARS-CoV-2/genetics
- SARS-CoV-2/metabolism
- SARS-CoV-2/pathogenicity
- SARS-CoV-2/ultrastructure
- Vero Cells
- Viral Nonstructural Proteins/genetics
- Viral Nonstructural Proteins/metabolism
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Affiliation(s)
- Shuai Yuan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Lei Peng
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jonathan J Park
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Yingxia Hu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Swapnil C Devarkar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Matthew B Dong
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Qi Shen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Shenping Wu
- Department of Pharmacology, Yale University, West Haven, CT 06516, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA.
| | - Ivan B Lomakin
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
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Young DJ, Guydosh NR. Hcr1/eIF3j Is a 60S Ribosomal Subunit Recycling Accessory Factor In Vivo. Cell Rep 2020; 28:39-50.e4. [PMID: 31269449 DOI: 10.1016/j.celrep.2019.05.111] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/26/2019] [Accepted: 05/30/2019] [Indexed: 02/07/2023] Open
Abstract
Hcr1/eIF3j is a sub-stoichiometric subunit of eukaryotic initiation factor 3 (eIF3) that can dissociate the post-termination 40S ribosomal subunit from mRNA in vitro. We examine this ribosome recycling role in vivo by ribosome profiling and reporter assays and find that loss of Hcr1 leads to reinitiation of translation in 3' UTRs, consistent with a defect in recycling. However, the defect appears to be in the recycling of the 60S subunit, rather than the 40S subunit, because reinitiation does not require an AUG codon and is suppressed by overexpression of the 60S dissociation factor Rli1/ABCE1. Consistent with a 60S recycling role, overexpression of Hcr1 cannot compensate for loss of 40S recycling factors Tma64/eIF2D and Tma20/MCT-1. Intriguingly, loss of Hcr1 triggers greater expression of RLI1 via an apparent feedback loop. These findings suggest Hcr1/eIF3j is recruited to ribosomes at stop codons and may coordinate the transition to a new round of translation.
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Affiliation(s)
- David J Young
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Nicholas R Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA.
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24
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Bohlen J, Fenzl K, Kramer G, Bukau B, Teleman AA. Selective 40S Footprinting Reveals Cap-Tethered Ribosome Scanning in Human Cells. Mol Cell 2020; 79:561-574.e5. [DOI: 10.1016/j.molcel.2020.06.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 04/10/2020] [Accepted: 05/18/2020] [Indexed: 11/27/2022]
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25
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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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26
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Simonetti A, Guca E, Bochler A, Kuhn L, Hashem Y. Structural Insights into the Mammalian Late-Stage Initiation Complexes. Cell Rep 2020; 31:107497. [PMID: 32268096 PMCID: PMC7166083 DOI: 10.1016/j.celrep.2020.03.061] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/17/2020] [Accepted: 03/18/2020] [Indexed: 12/12/2022] Open
Abstract
In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. However, the molecular basis underlying its role remains poorly understood. Here, we present the cryoelectron microscopy (cryo-EM) structures of mammalian late-stage 48S initiation complexes (LS48S ICs) in the presence of two different native mRNA sequences, β-globin and histone 4, at overall resolution of 3 and 3.5 Å, respectively. Our high-resolution structures unravel key interactions from the mRNA to eukaryotic initiation factors (eIFs): 1A, 2, 3, 18S rRNA, and several 40S ribosomal proteins. In addition, we are able to study the structural role of ABCE1 in the formation of native 48S ICs. Our results reveal a comprehensive map of ribosome/eIF-mRNA and ribosome/eIF-tRNA interactions and suggest the impact of mRNA sequence on the structure of the LS48S IC.
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MESH Headings
- ATP-Binding Cassette Transporters/genetics
- ATP-Binding Cassette Transporters/metabolism
- Animals
- Codon, Initiator/genetics
- Codon, Initiator/ultrastructure
- Cryoelectron Microscopy/methods
- Enhancer Elements, Genetic/genetics
- Eukaryotic Initiation Factor-1/genetics
- Eukaryotic Initiation Factor-1/metabolism
- Eukaryotic Initiation Factor-2/genetics
- Eukaryotic Initiation Factor-2/metabolism
- Eukaryotic Initiation Factor-3/genetics
- Eukaryotic Initiation Factor-3/metabolism
- Eukaryotic Initiation Factors/metabolism
- Eukaryotic Initiation Factors/ultrastructure
- Humans
- Mice
- Peptide Chain Initiation, Translational
- Protein Biosynthesis
- RNA, Messenger/metabolism
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- RNA, Transfer/metabolism
- Ribosomal Proteins/metabolism
- Ribosomes/metabolism
- Transcription Initiation, Genetic/physiology
- beta-Globins/genetics
- beta-Globins/ultrastructure
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Affiliation(s)
- Angelita Simonetti
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg 67000, France
| | - Ewelina Guca
- INSERM U1212 Acides nucléiques: Régulations Naturelle et Artificielle (ARNA), Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France
| | - Anthony Bochler
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg 67000, France; INSERM U1212 Acides nucléiques: Régulations Naturelle et Artificielle (ARNA), Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France
| | - Lauriane Kuhn
- Proteomic Platform Strasbourg - Esplanade, Institut de Biologie Moléculaire et Cellulaire, CNRS, Université de Strasbourg, Strasbourg 67000, France
| | - Yaser Hashem
- INSERM U1212 Acides nucléiques: Régulations Naturelle et Artificielle (ARNA), Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France.
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27
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Grad-cryo-EM: Tool to Isolate Translation Initiation Complexes from Rabbit Reticulocyte Lysate Suitable for Structural Studies. Methods Mol Biol 2020. [PMID: 32006323 DOI: 10.1007/978-1-0716-0278-2_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Since its development, single-particle cryogenic electron microscopy (cryo-EM) has played a central role in the study at medium resolution of both bacterial and eukaryotic ribosomal complexes. With the advent of the direct electron detectors and new processing software which allow obtaining structures at atomic resolution, formerly obtained only by X-ray crystallography, cryo-EM has become the method of choice for the structural analysis of the translation machinery. In most of the cases, the ribosomal complexes at different stages of the translation process are assembled in vitro from purified components, which limit the analysis to previously well-characterized complexes with known factors composition. The initiation phase of the protein synthesis is a very dynamic process during which several proteins interact with the translation apparatus leading to the formation of a chronological series of initiation complexes (ICs). Here we describe a method to isolate ICs assembled on natural in vitro transcribed mRNA directly from rabbit reticulocyte lysate (RRL) by sucrose density gradient centrifugation . The Grad-cryo-EM approach allows investigating structures and composition of intermediate ribosomal complexes prepared in near-native condition by cryo-EM and mass spectrometry analyses. This is a powerful approach, which could be used to study translation initiation of any mRNAs, including IRES containing ones, and which could be adapted to different cell extracts.
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28
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Zeman J, Itoh Y, Kukačka Z, Rosůlek M, Kavan D, Kouba T, Jansen ME, Mohammad MP, Novák P, Valášek LS. Binding of eIF3 in complex with eIF5 and eIF1 to the 40S ribosomal subunit is accompanied by dramatic structural changes. Nucleic Acids Res 2019; 47:8282-8300. [PMID: 31291455 PMCID: PMC6735954 DOI: 10.1093/nar/gkz570] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/12/2019] [Accepted: 07/05/2019] [Indexed: 12/31/2022] Open
Abstract
eIF3 is a large multiprotein complex serving as an essential scaffold promoting binding of other eIFs to the 40S subunit, where it coordinates their actions during translation initiation. Perhaps due to a high degree of flexibility of multiple eIF3 subunits, a high-resolution structure of free eIF3 from any organism has never been solved. Employing genetics and biochemistry, we previously built a 2D interaction map of all five yeast eIF3 subunits. Here we further improved the previously reported in vitro reconstitution protocol of yeast eIF3, which we cross-linked and trypsin-digested to determine its overall shape in 3D by advanced mass-spectrometry. The obtained cross-links support our 2D subunit interaction map and reveal that eIF3 is tightly packed with its WD40 and RRM domains exposed. This contrasts with reported cryo-EM structures depicting eIF3 as a molecular embracer of the 40S subunit. Since the binding of eIF1 and eIF5 further fortified the compact architecture of eIF3, we suggest that its initial contact with the 40S solvent-exposed side makes eIF3 to open up and wrap around the 40S head with its extended arms. In addition, we mapped the position of eIF5 to the region below the P- and E-sites of the 40S subunit.
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Affiliation(s)
- Jakub Zeman
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Yuzuru Itoh
- Institute of Genetics and Molecular and Cellular Biology, CNRS UMR7104, INSERM UMR964, Illkirch, France
| | - Zdeněk Kukačka
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Michal Rosůlek
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Daniel Kavan
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Tomáš Kouba
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Myrte E Jansen
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Mahabub P Mohammad
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Petr Novák
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Leoš S Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
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29
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Raabe K, Honys D, Michailidis C. The role of eukaryotic initiation factor 3 in plant translation regulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 145:75-83. [PMID: 31665669 DOI: 10.1016/j.plaphy.2019.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/07/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Regulation of translation represents a critical step in the regulation of gene expression. In plants, the translation regulation plays an important role at all stages of development and, during stress responses, functions as a fast and flexible tool which not only modulates the global translation rate but also controls the production of specific proteins. Regulation of translation is mostly focused on the initiation phase. There, one of essential initiation factors is the large multisubunit protein complex of eukaryotic translation initiation factor 3 (eIF3). In all eukaryotes, the general eIF3 function is to scaffold the formation of the translation initiation complex and to enhance the accuracy of scanning mechanism for start codon selection. Over the past decades, additional eIF3 functions were described as necessary for development in various eukaryotic organisms, including plants. The importance of the eIF3 complex lies not only at the global level of initiation event, but also in the precise translation regulation of specific transcripts. This review gathers the available information on functions of the plant eIF3 complex.
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Affiliation(s)
- Karel Raabe
- Institute of Experimental Botany, The Czech Academy of Sciences, Rozvojová 263, 165 02, Praha 6, Czech Republic
| | - David Honys
- Institute of Experimental Botany, The Czech Academy of Sciences, Rozvojová 263, 165 02, Praha 6, Czech Republic
| | - Christos Michailidis
- Institute of Experimental Botany, The Czech Academy of Sciences, Rozvojová 263, 165 02, Praha 6, Czech Republic.
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30
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Weisser M, Ban N. Extensions, Extra Factors, and Extreme Complexity: Ribosomal Structures Provide Insights into Eukaryotic Translation. Cold Spring Harb Perspect Biol 2019; 11:11/9/a032367. [PMID: 31481454 DOI: 10.1101/cshperspect.a032367] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Although the basic aspects of protein synthesis are preserved in all kingdoms of life, there are many important structural and functional differences between bacterial and the more complex eukaryotic ribosomes. High-resolution cryo-electron microscopy (cryo-EM) and X-ray crystallography structures of eukaryotic ribosomes have revealed the complex architectures of eukaryotic ribosomes and species-specific variations in protein and ribosomal RNA (rRNA) extensions. They also enabled structural studies of a range of eukaryotic ribosomal complexes involved in translation initiation, elongation, and termination, revealing unique mechanistic features of the eukaryotic translation process, especially with respect to the identification and recognition of translation start and stop codons on messenger RNAs (mRNAs). Most recently, structural biology has provided insights into the eukaryotic ribosomal biogenesis pathway by visualizing several of its complex intermediates. This review highlights the past decade's structural work on eukaryotic ribosomes and its implications on our understanding of eukaryotic translation.
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Affiliation(s)
- Melanie Weisser
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Nenad Ban
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
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31
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Tetrapeptide 60-63 of human ribosomal protein uS3 is crucial for translation initiation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194411. [PMID: 31356988 DOI: 10.1016/j.bbagrm.2019.194411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/16/2019] [Accepted: 07/16/2019] [Indexed: 12/14/2022]
Abstract
Conserved ribosomal protein uS3 contains a decapeptide fragment in positions 55-64 (human numbering), which has a very specific ability to cross-link to various RNA derivatives bearing aldehyde groups, likely provided by K62. It has been shown that during translation in the cell-free protein-synthesizing system, uS3 becomes accessible for such cross-linking only after eIF3j leaves the mRNA binding channel of the 40S ribosomal subunit. We studied the functional role of K62 and its nearest neighbors in the ribosomal assembly and translation with the use of HEK293T-derived cell cultures capable of producing FLAG-tagged uS3 (uS3FLAG) or its mutant form with amino acid residues at positions 60-63 replaced with alanines. Analysis of polysome profiles from the respective cells and cytosol lysates showed that the mutation significantly affected the uS3 ability to participate in the assembly of 40S subunits, but it was not essential for their maturation and did not prevent the binding of mRNAs to 40S subunits during translation initiation. The most striking effect of the replacement of amino acid residues in the above uS3 positions was that it almost completely deprived the 40S subunits of their ability to form 80S ribosomes, suggesting that the 48S pre-initiation complexes assembled on these subunits were defective in the binding of 60S subunits. Thus, our results revealed the previously unknown crucial role of the uS3 tetrapeptide 60GEKG63 in translation initiation related to maintaining the proper structure of the 48S complex, most likely via the prevention of premature mRNA loading into the ribosomal channel.
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32
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Eliseev B, Yeramala L, Leitner A, Karuppasamy M, Raimondeau E, Huard K, Alkalaeva E, Aebersold R, Schaffitzel C. Structure of a human cap-dependent 48S translation pre-initiation complex. Nucleic Acids Res 2019; 46:2678-2689. [PMID: 29401259 PMCID: PMC5861459 DOI: 10.1093/nar/gky054] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 01/21/2018] [Indexed: 01/13/2023] Open
Abstract
Eukaryotic translation initiation is tightly regulated, requiring a set of conserved initiation factors (eIFs). Translation of a capped mRNA depends on the trimeric eIF4F complex and eIF4B to load the mRNA onto the 43S pre-initiation complex comprising 40S and initiation factors 1, 1A, 2, 3 and 5 as well as initiator-tRNA. Binding of the mRNA is followed by mRNA scanning in the 48S pre-initiation complex, until a start codon is recognised. Here, we use a reconstituted system to prepare human 48S complexes assembled on capped mRNA in the presence of eIF4B and eIF4F. The highly purified h-48S complexes are used for cross-linking/mass spectrometry, revealing the protein interaction network in this complex. We report the electron cryo-microscopy structure of the h-48S complex at 6.3 Å resolution. While the majority of eIF4B and eIF4F appear to be flexible with respect to the ribosome, additional density is detected at the entrance of the 40S mRNA channel which we attribute to the RNA-recognition motif of eIF4B. The eight core subunits of eIF3 are bound at the 40S solvent-exposed side, as well as the subunits eIF3d, eIF3b and eIF3i. elF2 and initiator-tRNA bound to the start codon are present at the 40S intersubunit side. This cryo-EM structure represents a molecular snap-shot revealing the h-48S complex following start codon recognition.
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Affiliation(s)
- Boris Eliseev
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Lahari Yeramala
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Alexander Leitner
- ETH Zürich, Institute of Molecular Systems Biology, Auguste-Piccard-Hof 1, 8093 Zürich, Switzerland
| | - Manikandan Karuppasamy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Etienne Raimondeau
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Karine Huard
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ruedi Aebersold
- ETH Zürich, Institute of Molecular Systems Biology, Auguste-Piccard-Hof 1, 8093 Zürich, Switzerland.,Faculty of Science, University of Zürich, 8057 Zürich, Switzerland
| | - Christiane Schaffitzel
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France.,School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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33
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Abstract
The eukaryotic translation pathway has been studied for more than four decades, but the molecular mechanisms that regulate each stage of the pathway are not completely defined. This is in part because we have very little understanding of the kinetic framework for the assembly and disassembly of pathway intermediates. Steps of the pathway are thought to occur in the subsecond to second time frame, but most assays to monitor these events require minutes to hours to complete. Understanding translational control in sufficient detail will therefore require the development of assays that can precisely monitor the kinetics of the translation pathway in real time. Here, we describe the translation pathway from the perspective of its kinetic parameters, discuss advances that are helping us move toward the goal of a rigorous kinetic understanding, and highlight some of the challenges that remain.
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34
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Abstract
In the past 4 years, because of the advent of new cameras, many ribosome structures have been solved by cryoelectron microscopy (cryo-EM) at high, often near-atomic resolution, bringing new mechanistic insights into the processes of translation initiation, peptide elongation, termination, and recycling. Thus, cryo-EM has joined X-ray crystallography as a powerful technique in structural studies of translation. The significance of this new development is that structures of ribosomes in complex with their functional binding partners can now be determined to high resolution in multiple states as they perform their work. The aim of this article is to provide an overview of these new studies and assess the contributions they have made toward an understanding of translation and translational control.
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35
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Merrick WC, Pavitt GD. Protein Synthesis Initiation in Eukaryotic Cells. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a033092. [PMID: 29735639 DOI: 10.1101/cshperspect.a033092] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review summarizes our current understanding of the major pathway for the initiation phase of protein synthesis in eukaryotic cells, with a focus on recent advances. We describe the major scanning or messenger RNA (mRNA) m7G cap-dependent mechanism, which is a highly coordinated and stepwise regulated process that requires the combined action of at least 12 distinct translation factors with initiator transfer RNA (tRNA), ribosomes, and mRNAs. We limit our review to studies involving either mammalian or budding yeast cells and factors, as these represent the two best-studied experimental systems, and only include a reference to other organisms where particular insight has been gained. We close with a brief description of what we feel are some of the major unknowns in eukaryotic initiation.
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Affiliation(s)
- William C Merrick
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Graham D Pavitt
- Division of Molecular and Cellular Function, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester M13 9PT, United Kingdom
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36
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Major structural rearrangements of the canonical eukaryotic translation initiation complex. Curr Opin Struct Biol 2018; 53:151-158. [DOI: 10.1016/j.sbi.2018.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 08/28/2018] [Indexed: 12/24/2022]
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37
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Llácer JL, Hussain T, Saini AK, Nanda JS, Kaur S, Gordiyenko Y, Kumar R, Hinnebusch AG, Lorsch JR, Ramakrishnan V. Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition. eLife 2018; 7:e39273. [PMID: 30475211 PMCID: PMC6298780 DOI: 10.7554/elife.39273] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/21/2018] [Indexed: 12/22/2022] Open
Abstract
In eukaryotic translation initiation, AUG recognition of the mRNA requires accommodation of Met-tRNAi in a 'PIN' state, which is antagonized by the factor eIF1. eIF5 is a GTPase activating protein (GAP) of eIF2 that additionally promotes stringent AUG selection, but the molecular basis of its dual function was unknown. We present a cryo-electron microscopy (cryo-EM) reconstruction of a yeast 48S pre-initiation complex (PIC), at an overall resolution of 3.0 Å, featuring the N-terminal domain (NTD) of eIF5 bound to the 40S subunit at the location vacated by eIF1. eIF5 interacts with and allows a more accommodated orientation of Met-tRNAi. Substitutions of eIF5 residues involved in the eIF5-NTD/tRNAi interaction influenced initiation at near-cognate UUG codonsin vivo, and the closed/open PIC conformation in vitro, consistent with direct stabilization of the codon:anticodon duplex by the wild-type eIF5-NTD. The present structure reveals the basis for a key role of eIF5 in start-codon selection.
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Affiliation(s)
- Jose Luis Llácer
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
- Instituto de Biomedicina de Valencia (IBV-CSIC)ValenciaSpain
| | - Tanweer Hussain
- Department of Molecular Reproduction, Development and GeneticsIndian Institute of ScienceBangaloreIndia
| | - Adesh K Saini
- Shoolini University of Biotechnology and Management SciencesHimachal PradeshIndia
| | - Jagpreet Singh Nanda
- Laboratory on the Mechanism and Regulation of Protein SynthesisEunice K Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Sukhvir Kaur
- Shoolini University of Biotechnology and Management SciencesHimachal PradeshIndia
| | | | - Rakesh Kumar
- Shoolini University of Biotechnology and Management SciencesHimachal PradeshIndia
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and DevelopmentEunice K Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Jon R Lorsch
- Laboratory on the Mechanism and Regulation of Protein SynthesisEunice K Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - V Ramakrishnan
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
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38
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Melnikov S, Manakongtreecheep K, Söll D. Revising the Structural Diversity of Ribosomal Proteins Across the Three Domains of Life. Mol Biol Evol 2018; 35:1588-1598. [PMID: 29529322 PMCID: PMC5995209 DOI: 10.1093/molbev/msy021] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Ribosomal proteins are indispensable components of a living cell, and yet their structures are remarkably diverse in different species. Here we use manually curated structural alignments to provide a comprehensive catalog of structural variations in homologous ribosomal proteins from bacteria, archaea, eukaryotes, and eukaryotic organelles. By resolving numerous ambiguities and errors of automated structural and sequence alignments, we uncover a whole new class of structural variations that reside within seemingly conserved segments of ribosomal proteins. We then illustrate that these variations reflect an apparent adaptation of ribosomal proteins to the specific environments and lifestyles of living species. Finally, we show that most of these structural variations reside within nonglobular extensions of ribosomal proteins-protein segments that are thought to promote ribosome biogenesis by stabilizing the proper folding of ribosomal RNA. We show that although the extensions are thought to be the most ancient peptides on our planet, they are in fact the most rapidly evolving and most structurally and functionally diverse segments of ribosomal proteins. Overall, our work illustrates that, despite being long considered as slowly evolving and highly conserved, ribosomal proteins are more complex and more specialized than is generally recognized.
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Affiliation(s)
- Sergey Melnikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | | | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
- Department of Chemistry, Yale University, New Haven, CT
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The helicase Ded1p controls use of near-cognate translation initiation codons in 5' UTRs. Nature 2018; 559:130-134. [PMID: 29950728 PMCID: PMC6226265 DOI: 10.1038/s41586-018-0258-0] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/08/2018] [Indexed: 12/21/2022]
Abstract
The conserved and essential DEAD-box RNA helicase Ded1p from yeast and its mammalian orthologue DDX3 are critical for the initiation of translation1. Mutations in DDX3 are linked to tumorigenesis2-4 and intellectual disability5, and the enzyme is targeted by a range of viruses6. How Ded1p and its orthologues engage RNAs during the initiation of translation is unknown. Here we show, by integrating transcriptome-wide analyses of translation, RNA structure and Ded1p-RNA binding, that the effects of Ded1p on the initiation of translation are connected to near-cognate initiation codons in 5' untranslated regions. Ded1p associates with the translation pre-initiation complex at the mRNA entry channel and repressing the activity of Ded1p leads to the accumulation of RNA structure in 5' untranslated regions, the initiation of translation from near-cognate start codons immediately upstream of these structures and decreased protein synthesis from the corresponding main open reading frames. The data reveal a program for the regulation of translation that links Ded1p, the activation of near-cognate start codons and mRNA structure. This program has a role in meiosis, in which a marked decrease in the levels of Ded1p is accompanied by the activation of the alternative translation initiation sites that are seen when the activity of Ded1p is repressed. Our observations indicate that Ded1p affects translation initiation by controlling the use of near-cognate initiation codons that are proximal to mRNA structure in 5' untranslated regions.
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Shirokikh NE, Preiss T. Translation initiation by cap-dependent ribosome recruitment: Recent insights and open questions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1473. [PMID: 29624880 DOI: 10.1002/wrna.1473] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/02/2018] [Accepted: 02/14/2018] [Indexed: 12/14/2022]
Abstract
Gene expression universally relies on protein synthesis, where ribosomes recognize and decode the messenger RNA template by cycling through translation initiation, elongation, and termination phases. All aspects of translation have been studied for decades using the tools of biochemistry and molecular biology available at the time. Here, we focus on the mechanism of translation initiation in eukaryotes, which is remarkably more complex than prokaryotic initiation and is the target of multiple types of regulatory intervention. The "consensus" model, featuring cap-dependent ribosome entry and scanning of mRNA leader sequences, represents the predominantly utilized initiation pathway across eukaryotes, although several variations of the model and alternative initiation mechanisms are also known. Recent advances in structural biology techniques have enabled remarkable molecular-level insights into the functional states of eukaryotic ribosomes, including a range of ribosomal complexes with different combinations of translation initiation factors that are thought to represent bona fide intermediates of the initiation process. Similarly, high-throughput sequencing-based ribosome profiling or "footprinting" approaches have allowed much progress in understanding the elongation phase of translation, and variants of them are beginning to reveal the remaining mysteries of initiation, as well as aspects of translation termination and ribosomal recycling. A current view on the eukaryotic initiation mechanism is presented here with an emphasis on how recent structural and footprinting results underpin axioms of the consensus model. Along the way, we further outline some contested mechanistic issues and major open questions still to be addressed. This article is categorized under: Translation > Translation Mechanisms Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Nikolay E Shirokikh
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
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Gunišová S, Hronová V, Mohammad MP, Hinnebusch AG, Valášek LS. Please do not recycle! Translation reinitiation in microbes and higher eukaryotes. FEMS Microbiol Rev 2018; 42:165-192. [PMID: 29281028 PMCID: PMC5972666 DOI: 10.1093/femsre/fux059] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 12/20/2017] [Indexed: 12/14/2022] Open
Abstract
Protein production must be strictly controlled at its beginning and end to synthesize a polypeptide that faithfully copies genetic information carried in the encoding mRNA. In contrast to viruses and prokaryotes, the majority of mRNAs in eukaryotes contain only one coding sequence, resulting in production of a single protein. There are, however, many exceptional mRNAs that either carry short open reading frames upstream of the main coding sequence (uORFs) or even contain multiple long ORFs. A wide variety of mechanisms have evolved in microbes and higher eukaryotes to prevent recycling of some or all translational components upon termination of the first translated ORF in such mRNAs and thereby enable subsequent translation of the next uORF or downstream coding sequence. These specialized reinitiation mechanisms are often regulated to couple translation of the downstream ORF to various stimuli. Here we review all known instances of both short uORF-mediated and long ORF-mediated reinitiation and present our current understanding of the underlying molecular mechanisms of these intriguing modes of translational control.
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Affiliation(s)
- Stanislava Gunišová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
| | - Vladislava Hronová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
| | - Mahabub Pasha Mohammad
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
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Hashem Y, Frank J. The Jigsaw Puzzle of mRNA Translation Initiation in Eukaryotes: A Decade of Structures Unraveling the Mechanics of the Process. Annu Rev Biophys 2018; 47:125-151. [PMID: 29494255 DOI: 10.1146/annurev-biophys-070816-034034] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Translation initiation in eukaryotes is a highly regulated and rate-limiting process. It results in the assembly and disassembly of numerous transient and intermediate complexes involving over a dozen eukaryotic initiation factors (eIFs). This process culminates in the accommodation of a start codon marking the beginning of an open reading frame at the appropriate ribosomal site. Although this process has been extensively studied by hundreds of groups for nearly half a century, it has been only recently, especially during the last decade, that we have gained deeper insight into the mechanics of the eukaryotic translation initiation process. This advance in knowledge is due in part to the contributions of structural biology, which have shed light on the molecular mechanics underlying the different functions of various eukaryotic initiation factors. In this review, we focus exclusively on the contribution of structural biology to the understanding of the eukaryotic initiation process, a long-standing jigsaw puzzle that is just starting to yield the bigger picture.
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Affiliation(s)
- Yaser Hashem
- INSERM U1212, Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France;
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY 10032, USA;
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43
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Fan H, Conn AB, Williams PB, Diggs S, Hahm J, Gamper HB, Hou YM, O'Leary SE, Wang Y, Blaha GM. Transcription-translation coupling: direct interactions of RNA polymerase with ribosomes and ribosomal subunits. Nucleic Acids Res 2017; 45:11043-11055. [PMID: 28977553 PMCID: PMC5737488 DOI: 10.1093/nar/gkx719] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/09/2017] [Indexed: 11/12/2022] Open
Abstract
In prokaryotes, RNA polymerase and ribosomes can bind concurrently to the same RNA transcript, leading to the functional coupling of transcription and translation. The interactions between RNA polymerase and ribosomes are crucial for the coordination of transcription with translation. Here, we report that RNA polymerase directly binds ribosomes and isolated large and small ribosomal subunits. RNA polymerase and ribosomes form a one-to-one complex with a micromolar dissociation constant. The formation of the complex is modulated by the conformational and functional states of RNA polymerase and the ribosome. The binding interface on the large ribosomal subunit is buried by the small subunit during protein synthesis, whereas that on the small subunit remains solvent-accessible. The RNA polymerase binding site on the ribosome includes that of the isolated small ribosomal subunit. This direct interaction between RNA polymerase and ribosomes may contribute to the coupling of transcription to translation.
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Affiliation(s)
- Haitian Fan
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Adam B Conn
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Preston B Williams
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Stephen Diggs
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Joseph Hahm
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Howard B Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Seán E O'Leary
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Gregor M Blaha
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
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Valášek LS, Zeman J, Wagner S, Beznosková P, Pavlíková Z, Mohammad MP, Hronová V, Herrmannová A, Hashem Y, Gunišová S. Embraced by eIF3: structural and functional insights into the roles of eIF3 across the translation cycle. Nucleic Acids Res 2017; 45:10948-10968. [PMID: 28981723 PMCID: PMC5737393 DOI: 10.1093/nar/gkx805] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/31/2017] [Indexed: 12/31/2022] Open
Abstract
Protein synthesis is mediated via numerous molecules including the ribosome, mRNA, tRNAs, as well as translation initiation, elongation and release factors. Some of these factors play several roles throughout the entire process to ensure proper assembly of the preinitiation complex on the right mRNA, accurate selection of the initiation codon, errorless production of the encoded polypeptide and its proper termination. Perhaps, the most intriguing of these multitasking factors is the eukaryotic initiation factor eIF3. Recent evidence strongly suggests that this factor, which coordinates the progress of most of the initiation steps, does not come off the initiation complex upon subunit joining, but instead it remains bound to 80S ribosomes and gradually falls off during the first few elongation cycles to: (1) promote resumption of scanning on the same mRNA molecule for reinitiation downstream—in case of translation of upstream ORFs short enough to preserve eIF3 bound; or (2) come back during termination on long ORFs to fine tune its fidelity or, if signaled, promote programmed stop codon readthrough. Here, we unite recent structural views of the eIF3–40S complex and discus all known eIF3 roles to provide a broad picture of the eIF3’s impact on translational control in eukaryotic cells.
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Affiliation(s)
- Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Jakub Zeman
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Susan Wagner
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Petra Beznosková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Zuzana Pavlíková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Mahabub Pasha Mohammad
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Vladislava Hronová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Anna Herrmannová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Yaser Hashem
- CNRS, Architecture et Réactivité de l'ARN UPR9002, Université de Strasbourg, 67084 Strasbourg, France
| | - Stanislava Gunišová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
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45
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Cate JHD. Human eIF3: from 'blobology' to biological insight. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0176. [PMID: 28138064 PMCID: PMC5311922 DOI: 10.1098/rstb.2016.0176] [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] [Accepted: 11/16/2016] [Indexed: 02/06/2023] Open
Abstract
Translation in eukaryotes is highly regulated during initiation, a process impacted by numerous readouts of a cell's state. There are many cases in which cellular messenger RNAs likely do not follow the canonical ‘scanning’ mechanism of translation initiation, but the molecular mechanisms underlying these pathways are still being uncovered. Some RNA viruses such as the hepatitis C virus use highly structured RNA elements termed internal ribosome entry sites (IRESs) that commandeer eukaryotic translation initiation, by using specific interactions with the general eukaryotic translation initiation factor eIF3. Here, I present evidence that, in addition to its general role in translation, eIF3 in humans and likely in all multicellular eukaryotes also acts as a translational activator or repressor by binding RNA structures in the 5′-untranslated regions of specific mRNAs, analogous to the role of the mediator complex in transcription. Furthermore, eIF3 in multicellular eukaryotes also harbours a 5′ 7-methylguanosine cap-binding subunit—eIF3d—which replaces the general cap-binding initiation factor eIF4E in the translation of select mRNAs. Based on results from cell biological, biochemical and structural studies of eIF3, it is likely that human translation initiation proceeds through dozens of different molecular pathways, the vast majority of which remain to be explored. This article is part of the themed issue ‘Perspectives on the ribosome’.
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Affiliation(s)
- Jamie H D Cate
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220, USA .,Lawrence Berkeley National Laboratory, Division of Molecular Biophysics and Integrated Bioimaging, Berkeley, CA 94720, USA
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46
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Aylett CHS, Ban N. Eukaryotic aspects of translation initiation brought into focus. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0186. [PMID: 28138072 DOI: 10.1098/rstb.2016.0186] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 11/12/2022] Open
Abstract
In all organisms, mRNA-directed protein synthesis is catalysed by ribosomes. Although the basic aspects of translation are preserved in all kingdoms of life, important differences are found in the process of translation initiation, which is rate-limiting and the most important step for translation regulation. While great strides had been taken towards a complete structural understanding of the initiation of translation in eubacteria, our understanding of the eukaryotic process, which includes numerous eukaryotic-specific initiation factors, was until recently limited owing to a lack of structural information. In this review, we discuss recent results in the field that provide an increasingly complete molecular description of the eukaryotic initiation process. The structural snapshots obtained using a range of methods now provide insights into the architecture of the initiation complex, start-codon recognition by the initiator tRNA and the process of subunit joining. Future advances will require both higher-resolution insights into previously characterized complexes and mapping of initiation factors that control translation on an additional level by interacting only peripherally or transiently with ribosomal subunits.This article is part of the themed issue 'Perspectives on the ribosome'.
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Affiliation(s)
- Christopher H S Aylett
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
| | - Nenad Ban
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
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47
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Yourik P, Aitken CE, Zhou F, Gupta N, Hinnebusch AG, Lorsch JR. Yeast eIF4A enhances recruitment of mRNAs regardless of their structural complexity. eLife 2017; 6:31476. [PMID: 29192585 PMCID: PMC5726853 DOI: 10.7554/elife.31476] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/23/2017] [Indexed: 12/11/2022] Open
Abstract
eIF4A is a DEAD-box RNA-dependent ATPase thought to unwind RNA secondary structure in the 5'-untranslated regions (UTRs) of mRNAs to promote their recruitment to the eukaryotic translation pre-initiation complex (PIC). We show that eIF4A's ATPase activity is markedly stimulated in the presence of the PIC, independently of eIF4E•eIF4G, but dependent on subunits i and g of the heteromeric eIF3 complex. Surprisingly, eIF4A accelerated the rate of recruitment of all mRNAs tested, regardless of their degree of structural complexity. Structures in the 5'-UTR and 3' of the start codon synergistically inhibit mRNA recruitment in a manner relieved by eIF4A, indicating that the factor does not act solely to melt hairpins in 5'-UTRs. Our findings that eIF4A functionally interacts with the PIC and plays important roles beyond unwinding 5'-UTR structure is consistent with a recent proposal that eIF4A modulates the conformation of the 40S ribosomal subunit to promote mRNA recruitment.
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Affiliation(s)
- Paul Yourik
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Colin Echeverría Aitken
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Fujun Zhou
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Neha Gupta
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Jon R Lorsch
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
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48
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Abstract
The eukaryotic initiation factor 3 (eIF3) is one of the most complex translation initiation factors in mammalian cells, consisting of several subunits (eIF3a to eIF3m). It is crucial in translation initiation and termination, and in ribosomal recycling. Accordingly, deregulated eIF3 expression is associated with different pathological conditions, including cancer. In this manuscript, we discuss the interactome and function of each subunit of the human eIF3 complex. Furthermore, we review how altered levels of eIF3 subunits correlate with neurodegenerative disorders and cancer onset and development; in addition, we evaluate how such misregulation may also trigger infection cascades. A deep understanding of the molecular mechanisms underlying eIF3 role in human disease is essential to develop new eIF3-targeted therapeutic approaches and thus, overcome such conditions.
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Affiliation(s)
- Andreia Gomes-Duarte
- a Department of Human Genetics , Instituto Nacional de Saúde Doutor Ricardo Jorge , Lisbon , Portugal.,b Gene Expression and Regulation Group, Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências , Universidade de Lisboa , Lisbon , Portugal
| | - Rafaela Lacerda
- a Department of Human Genetics , Instituto Nacional de Saúde Doutor Ricardo Jorge , Lisbon , Portugal.,b Gene Expression and Regulation Group, Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências , Universidade de Lisboa , Lisbon , Portugal
| | - Juliane Menezes
- a Department of Human Genetics , Instituto Nacional de Saúde Doutor Ricardo Jorge , Lisbon , Portugal.,b Gene Expression and Regulation Group, Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências , Universidade de Lisboa , Lisbon , Portugal
| | - Luísa Romão
- a Department of Human Genetics , Instituto Nacional de Saúde Doutor Ricardo Jorge , Lisbon , Portugal.,b Gene Expression and Regulation Group, Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências , Universidade de Lisboa , Lisbon , Portugal
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49
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Gross L, Vicens Q, Einhorn E, Noireterre A, Schaeffer L, Kuhn L, Imler JL, Eriani G, Meignin C, Martin F. The IRES5'UTR of the dicistrovirus cricket paralysis virus is a type III IRES containing an essential pseudoknot structure. Nucleic Acids Res 2017; 45:8993-9004. [PMID: 28911115 PMCID: PMC5587806 DOI: 10.1093/nar/gkx622] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 07/07/2017] [Indexed: 02/02/2023] Open
Abstract
Cricket paralysis virus (CrPV) is a dicistrovirus. Its positive-sense single-stranded RNA genome contains two internal ribosomal entry sites (IRESs). The 5′ untranslated region (5′UTR) IRES5′UTR mediates translation of non-structural proteins encoded by ORF1 whereas the well-known intergenic region (IGR) IRESIGR is required for translation of structural proteins from open reading frame 2 in the late phase of infection. Concerted action of both IRES is essential for host translation shut-off and viral translation. IRESIGR has been extensively studied, in contrast the IRES5′UTR remains largely unexplored. Here, we define the minimal IRES element required for efficient translation initiation in drosophila S2 cell-free extracts. We show that IRES5′UTR promotes direct recruitment of the ribosome on the cognate viral AUG start codon without any scanning step, using a Hepatitis-C virus-related translation initiation mechanism. Mass spectrometry analysis revealed that IRES5′UTR recruits eukaryotic initiation factor 3, confirming that it belongs to type III class of IRES elements. Using Selective 2′-hydroxyl acylation analyzed by primer extension and DMS probing, we established a secondary structure model of 5′UTR and of the minimal IRES5′UTR. The IRES5′UTR contains a pseudoknot structure that is essential for proper folding and ribosome recruitment. Overall, our results pave the way for studies addressing the synergy and interplay between the two IRES from CrPV.
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Affiliation(s)
- Lauriane Gross
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Quentin Vicens
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Evelyne Einhorn
- Université de Strasbourg, CNRS, Réponse Immunitaire et Développement chez les Insectes, UPR 9022, F-67000 Strasbourg, France
| | - Audrey Noireterre
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Laure Schaeffer
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Lauriane Kuhn
- Université de Strasbourg, CNRS, Plateforme Protéomique Strasbourg-Esplanade, F-67000 Strasbourg, France
| | - Jean-Luc Imler
- Université de Strasbourg, CNRS, Réponse Immunitaire et Développement chez les Insectes, UPR 9022, F-67000 Strasbourg, France
| | - Gilbert Eriani
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Carine Meignin
- Université de Strasbourg, CNRS, Réponse Immunitaire et Développement chez les Insectes, UPR 9022, F-67000 Strasbourg, France
| | - Franck Martin
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
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50
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Yin JY, Zhang JT, Zhang W, Zhou HH, Liu ZQ. eIF3a: A new anticancer drug target in the eIF family. Cancer Lett 2017; 412:81-87. [PMID: 29031564 DOI: 10.1016/j.canlet.2017.09.055] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 09/12/2017] [Accepted: 09/25/2017] [Indexed: 02/04/2023]
Abstract
eIF3a is the largest subunit of eIF3, which is a key player in all steps of translation initiation. During the past years, eIF3a is recognized as a proto-oncogene, which is an important discovery in this field. It is widely reported to be correlated with cancer occurrence, metastasis, prognosis, and therapeutic response. Recently, the mechanisms of eIF3a action in the carcinogenesis are unveiled gradually. A number of cellular, physiological, and pathological processes involving eIF3a are identified. Most importantly, it is emerging as a new potential drug target in the eIF family, and some small molecule inhibitors are being developed. Thus, we perform a critical review of recent advances in understanding eIF3a physiological and pathological functions, with specific focus on its role in cancer and anticancer drug targets.
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Affiliation(s)
- Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, PR China.
| | - Jian-Ting Zhang
- Department of Pharmacology & Toxicology and IU Cancer Center, Indiana University School of Medicine, Indianapolis IN 46202, USA
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, PR China
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, PR China
| | - Zhao-Qian Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, PR China.
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