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Desroches Altamirano C, Kang MK, Jordan MA, Borianne T, Dilmen I, Gnädig M, von Appen A, Honigmann A, Franzmann TM, Alberti S. eIF4F is a thermo-sensing regulatory node in the translational heat shock response. Mol Cell 2024; 84:1727-1741.e12. [PMID: 38547866 DOI: 10.1016/j.molcel.2024.02.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 12/18/2023] [Accepted: 02/29/2024] [Indexed: 05/05/2024]
Abstract
Heat-shocked cells prioritize the translation of heat shock (HS) mRNAs, but the underlying mechanism is unclear. We report that HS in budding yeast induces the disassembly of the eIF4F complex, where eIF4G and eIF4E assemble into translationally arrested mRNA ribonucleoprotein particles (mRNPs) and HS granules (HSGs), whereas eIF4A promotes HS translation. Using in vitro reconstitution biochemistry, we show that a conformational rearrangement of the thermo-sensing eIF4A-binding domain of eIF4G dissociates eIF4A and promotes the assembly with mRNA into HS-mRNPs, which recruit additional translation factors, including Pab1p and eIF4E, to form multi-component condensates. Using extracts and cellular experiments, we demonstrate that HS-mRNPs and condensates repress the translation of associated mRNA and deplete translation factors that are required for housekeeping translation, whereas HS mRNAs can be efficiently translated by eIF4A. We conclude that the eIF4F complex is a thermo-sensing node that regulates translation during HS.
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Affiliation(s)
- Christine Desroches Altamirano
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Moo-Koo Kang
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Mareike A Jordan
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Tom Borianne
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Irem Dilmen
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Maren Gnädig
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Alexander von Appen
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Alf Honigmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Titus M Franzmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Simon Alberti
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany.
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2
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Gentry RC, Ide NA, Comunale VM, Hartwick EW, Kinz-Thompson CD, Gonzalez RL. The mechanism of mRNA activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.15.567265. [PMID: 38014128 PMCID: PMC10680758 DOI: 10.1101/2023.11.15.567265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
During translation initiation, messenger RNA molecules must be identified and activated for loading into a ribosome. In this rate-limiting step, the heterotrimeric protein eukaryotic initiation factor eIF4F must recognize and productively interact with the 7-methylguanosine cap at the 5' end of the messenger RNA and subsequently activate the message. Despite its fundamental, regulatory role in gene expression, the molecular events underlying cap recognition and messenger RNA activation remain mysterious. Here, we generate a unique, single-molecule fluorescence imaging system to interrogate the dynamics with which eIF4F discriminates productive and non-productive locations on full-length, native messenger RNA molecules. At the single-molecule level, we observe stochastic sampling of eIF4F along the length of the messenger RNA and identify allosteric communication between the eIF4F subunits which ultimately drive cap-recognition and subsequent activation of the message. Our experiments uncover novel functions for each subunit of eIF4F and we conclude by presenting a model for messenger RNA activation which precisely defines the composition of the activated message. This model provides a general framework for understanding how messenger RNA molecules may be discriminated from one another, and how other RNA-binding proteins may control the efficiency of translation initiation.
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Affiliation(s)
- Riley C Gentry
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Nicholas A Ide
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | | | - Erik W Hartwick
- Department of Chemistry, Columbia University, New York, NY, USA
- Current Address: BioChemistry Krios Electron Microscopy Facility, Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Colin D Kinz-Thompson
- Department of Chemistry, Columbia University, New York, NY, USA
- Current Address: Department of Chemistry, Rutgers University-Newark, Newark, NJ 07102
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3
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Huang J, Zhang L, Yang R, Yao L, Gou J, Cao D, Pan Z, Li D, Pan Y, Zhang W. Eukaryotic translation initiation factor 4A1 in the pathogenesis and treatment of cancers. Front Mol Biosci 2023; 10:1289650. [PMID: 38028556 PMCID: PMC10666758 DOI: 10.3389/fmolb.2023.1289650] [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: 09/06/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Abnormal translate regulation is an important phenomenon in cancer initiation and progression. Eukaryotic translation initiation factor 4A1 (eIF4A1) protein is an ATP-dependent Ribonucleic Acid (RNA) helicase, which is essential for translation and has bidirectional RNA unwinders function. In this review, we discuss the levels of expression, regulatory mechanisms and protein functions of eIF4A1 in different human tumors. eIF4A1 is often involved as a target of microRNAs or long non-coding RNAs during the epithelial-mesenchymal transition, associating with the proliferation and metastasis of tumor cells. eIF4A1 protein exhibits the promising biomarker for rapid diagnosis of pre-cancer lesions, histological phenotypes, clinical staging diagnosis and outcome prediction, which provides a novel strategy for precise medical care and target therapy for patients with tumors at the same time, relevant small molecule inhibitors have also been applied in clinical practice, providing reliable theoretical support and clinical basis for the development of this gene target.
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Affiliation(s)
- Jinghong Huang
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Lei Zhang
- Clinical Laboratory, First Affiliated Hospital of Shihezi University, Shihezi, Xinjiang, China
| | - Rui Yang
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Lixia Yao
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Jinming Gou
- Troops of the People’s Liberation Army, Urumqi, Xinjiang, China
| | - Dongdong Cao
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Zeming Pan
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Dongmei Li
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Yuanming Pan
- Cancer Research Center, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, China
| | - Wei Zhang
- Shihezi People’s Hospital, Shihezi, Xinjiang, China
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4
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Song J, Ge Y, Dong M, Guan Q, Ju M, Song X, Han J, Zhao L. Molecular interplay between EIF4 family and circular RNAs in cancer: Mechanisms and therapeutics. Eur J Pharmacol 2023:175867. [PMID: 37369297 DOI: 10.1016/j.ejphar.2023.175867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
The eukaryotic translation initiation factor 4 (EIF4) family is a major contributor to the recruitment of mRNAs to ribosomes during the initial translation stage in eukaryotes, whose dysregulation either allows for cancer transformation or prevents disordered cancerous cell growth. Circular RNAs (circRNAs), which exhibit distinctive structures and are widely expressed in eukaryotes, are anticipated to be a clinical diagnostic biomarker for cancer therapy. There is considerable evidence that EIF4s can influence the biogenesis, transport, and function of circRNAs and, in turn, circRNAs can control the expressions of EIF4s through certain molecular pathways. Herein, we primarily review the emerging studies of the EIF4 family and pinpoint the roles of dysregulated EIF4s in cancer. We also evaluate the patterns of intricate interactions between circRNAs and EIF4s and discuss the potential utility of circRNA-based therapeutics targeting EIF4s in clinical cancer research.
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Affiliation(s)
- Jia Song
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, PR China.
| | - Yuexin Ge
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, PR China.
| | - Mingyan Dong
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, PR China.
| | - Qiutong Guan
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, PR China.
| | - Mingyi Ju
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, PR China.
| | - Xueyi Song
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, PR China.
| | - Jiali Han
- Department of Otolaryngology, The First Hospital of China Medical University, Shenyang, Liaoning, 110001, PR China.
| | - Lin Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, PR China.
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5
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Schmidt T, Dabrowska A, Waldron JA, Hodge K, Koulouras G, Gabrielsen M, Munro J, Tack DC, Harris G, McGhee E, Scott D, Carlin L, Huang D, Le Quesne J, Zanivan S, Wilczynska A, Bushell M. eIF4A1-dependent mRNAs employ purine-rich 5'UTR sequences to activate localised eIF4A1-unwinding through eIF4A1-multimerisation to facilitate translation. Nucleic Acids Res 2023; 51:1859-1879. [PMID: 36727461 PMCID: PMC9976904 DOI: 10.1093/nar/gkad030] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/20/2022] [Accepted: 01/11/2023] [Indexed: 02/03/2023] Open
Abstract
Altered eIF4A1 activity promotes translation of highly structured, eIF4A1-dependent oncogene mRNAs at root of oncogenic translational programmes. It remains unclear how these mRNAs recruit and activate eIF4A1 unwinding specifically to facilitate their preferential translation. Here, we show that single-stranded RNA sequence motifs specifically activate eIF4A1 unwinding allowing local RNA structural rearrangement and translation of eIF4A1-dependent mRNAs in cells. Our data demonstrate that eIF4A1-dependent mRNAs contain AG-rich motifs within their 5'UTR which specifically activate eIF4A1 unwinding of local RNA structure to facilitate translation. This mode of eIF4A1 regulation is used by mRNAs encoding components of mTORC-signalling and cell cycle progression, and renders these mRNAs particularly sensitive to eIF4A1-inhibition. Mechanistically, we show that binding of eIF4A1 to AG-rich sequences leads to multimerization of eIF4A1 with eIF4A1 subunits performing distinct enzymatic activities. Our structural data suggest that RNA-binding of multimeric eIF4A1 induces conformational changes in the RNA resulting in an optimal positioning of eIF4A1 proximal to the RNA duplex enabling efficient unwinding. Our data proposes a model in which AG-motifs in the 5'UTR of eIF4A1-dependent mRNAs specifically activate eIF4A1, enabling assembly of the helicase-competent multimeric eIF4A1 complex, and positioning these complexes proximal to stable localised RNA structure allowing ribosomal subunit scanning.
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Affiliation(s)
- Tobias Schmidt
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Adrianna Dabrowska
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
- Department of Urology, University of California, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph A Waldron
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Kelly Hodge
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Grigorios Koulouras
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Mads Gabrielsen
- MVLS Structural Biology and Biophysical Characterisation Facility, University of Glasgow, University Avenue, Glasgow G12 8QQ, UK
| | - June Munro
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - David C Tack
- Spectrum Health Office of Research and Education, Spectrum Health System, 15 Michigan Street NE, Grand Rapids, MI 49503, USA
| | - Gemma Harris
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0FA, UK
| | - Ewan McGhee
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - David Scott
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0FA, UK
- ISIS Spallation Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Campus, DidcotOX11 0QX, UK
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington LE12 5RD, UK
| | - Leo M Carlin
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Danny Huang
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - John Le Quesne
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Sara Zanivan
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Ania Wilczynska
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
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6
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Izidoro MS, Sokabe M, Villa N, Merrick WC, Fraser CS. Human eukaryotic initiation factor 4E (eIF4E) and the nucleotide-bound state of eIF4A regulate eIF4F binding to RNA. J Biol Chem 2022; 298:102368. [PMID: 35963437 PMCID: PMC9483636 DOI: 10.1016/j.jbc.2022.102368] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022] Open
Abstract
During translation initiation, the underlying mechanism by which the eukaryotic initiation factor (eIF) 4E, eIF4A, and eIF4G components of eIF4F coordinate their binding activities to regulate eIF4F binding to mRNA is poorly defined. Here, we used fluorescence anisotropy to generate thermodynamic and kinetic frameworks for the interaction of uncapped RNA with human eIF4F. We demonstrate that eIF4E binding to an autoinhibitory domain in eIF4G generates a high-affinity binding conformation of the eIF4F complex for RNA. In addition, we show that the nucleotide-bound state of the eIF4A component further regulates uncapped RNA binding by eIF4F, with a four-fold decrease in the equilibrium dissociation constant observed in the presence versus the absence of ATP. Monitoring uncapped RNA dissociation in real time reveals that ATP reduces the dissociation rate constant of RNA for eIF4F by ∼4-orders of magnitude. Thus, release of ATP from eIF4A places eIF4F in a dynamic state that has very fast association and dissociation rates from RNA. Monitoring the kinetic framework for eIF4A binding to eIF4G revealed two different rate constants that likely reflect two conformational states of the eIF4F complex. Furthermore, we determined that the eIF4G autoinhibitory domain promotes a more stable, less dynamic, eIF4A-binding state, which is overcome by eIF4E binding. Overall, our data support a model whereby eIF4E binding to eIF4G/4A stabilizes a high-affinity RNA-binding state of eIF4F and enables eIF4A to adopt a more dynamic interaction with eIF4G. This dynamic conformation may contribute to the ability of eIF4F to rapidly bind and release mRNA during scanning.
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Affiliation(s)
- Mario Servulo Izidoro
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA 95616
| | - Masaaki Sokabe
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA 95616
| | - Nancy Villa
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA 95616
| | - William C Merrick
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA 95616
| | - Christopher S Fraser
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA 95616.
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7
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Çetin B, O’Leary SE. mRNA- and factor-driven dynamic variability controls eIF4F-cap recognition for translation initiation. Nucleic Acids Res 2022; 50:8240-8261. [PMID: 35871304 PMCID: PMC9371892 DOI: 10.1093/nar/gkac631] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/29/2022] [Accepted: 07/20/2022] [Indexed: 11/29/2022] Open
Abstract
mRNA 5′ cap recognition by eIF4F is a key element of eukaryotic translational control. Kinetic differences in eIF4F–mRNA interactions have long been proposed to mediate translation-efficiency differences between mRNAs, and recent transcriptome-wide studies have revealed significant heterogeneity in eIF4F engagement with differentially-translated mRNAs. However, detailed kinetic information exists only for eIF4F interactions with short model RNAs. We developed and applied single-molecule fluorescence approaches to directly observe real-time Saccharomyces cerevisiae eIF4F subunit interactions with full-length polyadenylated mRNAs. We found that eIF4E–mRNA association rates linearly anticorrelate with mRNA length. eIF4G–mRNA interaction accelerates eIF4E–mRNA association in proportion to mRNA length, as does an eIF4F-independent activity of eIF4A, though cap-proximal secondary structure still plays an important role in defining the final association rates. eIF4F–mRNA interactions remained dominated by effects of eIF4G, but were modulated to different extents for different mRNAs by the presence of eIF4A and ATP. We also found that eIF4A-catalyzed ATP hydrolysis ejects eIF4E, and likely eIF4E•eIF4G from the mRNA after initial eIF4F•mRNA complex formation, suggesting a mechanism to prepare the mRNA 5′ end for ribosome recruitment. Our results support a role for mRNA-specific, factor-driven eIF4F association rates in kinetically controlling translation.
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Affiliation(s)
- Burak Çetin
- Graduate Program in Cell, Molecular, and Developmental Biology, University of California Riverside , Riverside, CA 92521, USA
| | - Seán E O’Leary
- Graduate Program in Cell, Molecular, and Developmental Biology, University of California Riverside , Riverside, CA 92521, USA
- Department of Biochemistry, University of California Riverside , Riverside, CA 92521, USA
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8
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Krause L, Willing F, Andreou AZ, Klostermeier D. The domains of yeast eIF4G, eIF4E and the cap fine-tune eIF4A activities through an intricate network of stimulatory and inhibitory effects. Nucleic Acids Res 2022; 50:6497-6510. [PMID: 35689631 PMCID: PMC9226541 DOI: 10.1093/nar/gkac437] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/19/2022] [Accepted: 05/23/2022] [Indexed: 12/13/2022] Open
Abstract
Translation initiation in eukaryotes starts with the recognition of the mRNA 5'-cap by eIF4F, a hetero-trimeric complex of eIF4E, the cap-binding protein, eIF4A, a DEAD-box helicase, and eIF4G, a scaffold protein. eIF4G comprises eIF4E- and eIF4A-binding domains (4E-BD, 4A-BD) and three RNA-binding regions (RNA1-RNA3), and interacts with eIF4A, eIF4E, and with the mRNA. Within the eIF4F complex, the helicase activity of eIF4A is increased. We showed previously that RNA3 of eIF4G is important for the stimulation of the eIF4A conformational cycle and its ATPase and helicase activities. Here, we dissect the interplay between the eIF4G domains and the role of the eIF4E/cap interaction in eIF4A activation. We show that RNA2 leads to an increase in the fraction of eIF4A in the closed state, an increased RNA affinity, and faster RNA unwinding. This stimulatory effect is partially reduced when the 4E-BD is present. eIF4E binding to the 4E-BD then further inhibits the helicase activity and closing of eIF4A, but does not affect the RNA-stimulated ATPase activity of eIF4A. The 5'-cap renders the functional interaction of mRNA with eIF4A less efficient. Overall, the activity of eIF4A at the 5'-cap is thus fine-tuned by a delicately balanced network of stimulatory and inhibitory interactions.
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Affiliation(s)
- Linda Krause
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany
| | - Florian Willing
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany
| | - Alexandra Zoi Andreou
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany
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9
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Chakraborty A, Krause L, Klostermeier D. Determination of rate constants for conformational changes of RNA helicases by single-molecule FRET TIRF microscopy. Methods 2022; 204:428-441. [PMID: 35304246 DOI: 10.1016/j.ymeth.2022.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/10/2022] [Accepted: 03/13/2022] [Indexed: 12/18/2022] Open
Abstract
RNA helicases couple nucleotide-driven conformational changes to the unwinding of RNA duplexes. Interaction partners can regulate helicase activity by altering the rate constants of these conformational changes. Single-molecule FRET experiments on donor/acceptor-labeled, immobilized molecules are ideally suited to monitor conformational changes in real time and to extract rate constants for these processes. This article provides guidance on how to design, perform, and analyze single-molecule FRET experiments by TIRF microscopy. It covers the theoretical background of FRET and single-molecule TIRF microscopy, the considerations to prepare proteins of interest for donor/acceptor labeling and surface immobilization, and the principles and procedures of data analysis, including image analysis and the determination of FRET time traces, the extraction of rate constants from FRET time traces, and the general conclusions that can be drawn from these data. A case study, using the DEAD-box protein eIF4A as an example, highlights how single-molecule FRET studies have been instrumental in understanding the role of conformational changes for duplex unwinding and for the regulation of helicase activities. Selected examples illustrate which conclusions can be drawn from the kinetic data obtained, highlight possible pitfalls in data analysis and interpretation, and outline how kinetic models can be related to functionally relevant states.
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Affiliation(s)
| | - Linda Krause
- University of Muenster, Institute for Physical Chemistry, Muenster, Germany
| | - Dagmar Klostermeier
- University of Muenster, Institute for Physical Chemistry, Muenster, Germany.
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10
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Liu X, Moshiri H, He Q, Sahoo A, Walker SE. Deletion of the N-Terminal Domain of Yeast Eukaryotic Initiation Factor 4B Reprograms Translation and Reduces Growth in Urea. Front Mol Biosci 2022; 8:787781. [PMID: 35047555 PMCID: PMC8762332 DOI: 10.3389/fmolb.2021.787781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/03/2021] [Indexed: 11/24/2022] Open
Abstract
The yeast eukaryotic initiation factor 4B binds the 40S subunit in translation preinitiation complexes (PICs), promoting mRNA recruitment. Recent evidence indicates yeast mRNAs have variable dependence on eIF4B under optimal growth conditions. Given the ability of eIF4B to promote translation as a function of nutrient conditions in mammalian cells, we wondered if eIF4B activities in translation could alter phenotypes in yeast through differential mRNA selection for translation. Here we compared the effects of disrupting yeast eIF4B RNA- and 40S-binding motifs under ∼1400 growth conditions. The RNA-Recognition Motif (RRM) was dispensable for stress responses, but the 40S-binding N-terminal Domain (NTD) promoted growth in response to stressors requiring robust cellular integrity. In particular, the NTD conferred a strong growth advantage in the presence of urea, which may be important for pathogenesis of related fungal species. Ribosome profiling indicated that similar to complete eIF4B deletion, deletion of the NTD dramatically reduced translation, particularly of those mRNAs with long and highly structured 5-prime untranslated regions. This behavior was observed both with and without urea exposure, but the specific mRNA pool associated with ribosomes in response to urea differed. Deletion of the NTD led to relative increases in ribosome association of shorter transcripts with higher dependence on eIF4G, as was noted previously for eIF4B deletion. Gene ontology analysis indicated that proteins encoded by eIF4B NTD-dependent transcripts were associated with the cellular membrane system and the cell wall, while NTD-independent transcripts encoded proteins associated with cytoplasmic proteins and protein synthesis. This analysis highlighted the difference in structure content of mRNAs encoding membrane versus cytoplasmic housekeeping proteins and the variable reliance of specific gene ontology classes on various initiation factors promoting otherwise similar functions. Together our analyses suggest that deletion of the eIF4B NTD prevents cellular stress responses by affecting the capacity to translate a diverse mRNA pool.
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Affiliation(s)
- Xiaozhuo Liu
- Department of Biological Sciences, SUNY at Buffalo, Buffalo, NY, United States
| | - Houtan Moshiri
- Department of Biological Sciences, SUNY at Buffalo, Buffalo, NY, United States
| | - Qian He
- Department of Biological Sciences, SUNY at Buffalo, Buffalo, NY, United States
| | - Ansuman Sahoo
- Department of Biological Sciences, SUNY at Buffalo, Buffalo, NY, United States
| | - Sarah E Walker
- Department of Biological Sciences, SUNY at Buffalo, Buffalo, NY, United States
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11
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Analysis of the conformational space and dynamics of RNA helicases by single-molecule FRET in solution and on surfaces. Methods Enzymol 2022; 673:251-310. [DOI: 10.1016/bs.mie.2022.03.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Perroud PF, Demko V, Ako AE, Khanal R, Bokor B, Pavlovič A, Jásik J, Johansen W. The nuclear GUCT domain-containing DEAD-box RNA helicases govern gametophytic and sporophytic development in Physcomitrium patens. PLANT MOLECULAR BIOLOGY 2021; 107:307-325. [PMID: 33886069 PMCID: PMC8648619 DOI: 10.1007/s11103-021-01152-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/06/2021] [Indexed: 05/29/2023]
Abstract
KEY MESSAGE In Physcomitrium patens, PpRH1/PpRH2 are GUCT-domain-containing DEAD-BOX RNA helicases localize to the nucleus. They are implicated in cell and tissue development in all stages of the moss life cycle. ABSTRACT The DEAD-box-containing RNA helicase family encompasses a large and functionally important group of enzymes involved in cellular processes committed to the metabolism of RNA, including its transcription, processing, transport, translation and decay. Studies indicate this protein family has implied roles in plant vegetative and reproductive developmental processes as well as response to environmental stresses such has cold and high salinity. We focus here on a small conserved sub-group of GUCT domain-containing RNA helicase in the moss Physcomitrium patens. Phylogenetic analysis shows that RNA helicases containing the GUCT domain form a distinct conserved clade across the green lineage. In this clade, the P. patens genome possesses two closely related paralogues RNA helicases predicted to be nuclear, PpRH1 and PpRH2. Using in-locus gene fluorescent tagging we show that PpRH1 is localized to the nucleus in protonema. Analysis of PpRH1 and PpRH2 deletions, individually and together, indicates their potential roles in protonema, gametophore and sporophyte cellular and tissue development in P. patens. Additionally, the ultrastructural analysis of phyllid chloroplasts in Δrh2 and Δrh1/2 shows distinct starch granule accumulation under standard growth conditions associated with changes in photosynthetic activity parameters. We could not detect effects of either temperature or stress on protonema growth or PpRH1 and PpRH2 expression. Together, these results suggest that nuclear GUCT-containing RNA helicases play a role primarily in developmental processes directly or indirectly linked to photosynthesis activity in the moss P. patens. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11103-021-01152-w.
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Affiliation(s)
- Pierre-François Perroud
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, 35043, Marburg, Germany
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Viktor Demko
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 84215, Bratislava, Slovakia
- Plant Science and Biodiversity Center, Slovak Academy of Sciences, Dúbravská cesta 9, 84523, Bratislava, Slovakia
| | - Ako Eugene Ako
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 31, 2318, Hamar, Norway
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Brackenhurst Campus, Southwell, NG25 0QF, Nottinghamshire, UK
| | - Rajendra Khanal
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 31, 2318, Hamar, Norway
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Boris Bokor
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 84215, Bratislava, Slovakia
- Comenius University in Bratislava Science Park, Ilkovicova 8, 84215, Bratislava, Slovakia
| | - Andrej Pavlovič
- Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Ján Jásik
- Plant Science and Biodiversity Center, Slovak Academy of Sciences, Dúbravská cesta 9, 84523, Bratislava, Slovakia
| | - Wenche Johansen
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 31, 2318, Hamar, Norway.
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13
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Donsbach P, Klostermeier D. Regulation of RNA helicase activity: principles and examples. Biol Chem 2021; 402:529-559. [PMID: 33583161 DOI: 10.1515/hsz-2020-0362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/29/2021] [Indexed: 12/16/2022]
Abstract
RNA helicases are a ubiquitous class of enzymes involved in virtually all processes of RNA metabolism, from transcription, mRNA splicing and export, mRNA translation and RNA transport to RNA degradation. Although ATP-dependent unwinding of RNA duplexes is their hallmark reaction, not all helicases catalyze unwinding in vitro, and some in vivo functions do not depend on duplex unwinding. RNA helicases are divided into different families that share a common helicase core with a set of helicase signature motives. The core provides the active site for ATP hydrolysis, a binding site for non-sequence-specific interaction with RNA, and in many cases a basal unwinding activity. Its activity is often regulated by flanking domains, by interaction partners, or by self-association. In this review, we summarize the regulatory mechanisms that modulate the activities of the helicase core. Case studies on selected helicases with functions in translation, splicing, and RNA sensing illustrate the various modes and layers of regulation in time and space that harness the helicase core for a wide spectrum of cellular tasks.
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Affiliation(s)
- Pascal Donsbach
- Institute for Physical Chemistry, University of Münster, Corrensstrasse 30, D-48149Münster, Germany
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Münster, Corrensstrasse 30, D-48149Münster, Germany
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14
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Krause L, Klostermeier D. Probing RNA Helicase Conformational Changes by Single-Molecule FRET Microscopy. Methods Mol Biol 2021; 2209:119-132. [PMID: 33201466 DOI: 10.1007/978-1-0716-0935-4_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Förster resonance energy transfer (FRET) is a versatile tool to study the conformational dynamics of proteins. Here, we describe the use of confocal and total internal reflection fluorescence (TIRF) microscopy to follow the conformational cycling of DEAD-box helicases on the single molecule level, using the eukaryotic translation initiation factor eIF4A as an illustrative example. Confocal microscopy enables the study of donor-acceptor-labeled molecules in solution, revealing the population of different conformational states present. With TIRF microscopy, surface-immobilized molecules can be imaged as a function of time, revealing sequences of conformational states and the kinetics of conformational changes.
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Affiliation(s)
- Linda Krause
- Institute for Physical Chemistry, University of Muenster, Muenster, Germany
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Muenster, Muenster, Germany.
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15
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General and Target-Specific DExD/H RNA Helicases in Eukaryotic Translation Initiation. Int J Mol Sci 2020; 21:ijms21124402. [PMID: 32575790 PMCID: PMC7352612 DOI: 10.3390/ijms21124402] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/19/2022] Open
Abstract
DExD (DDX)- and DExH (DHX)-box RNA helicases, named after their Asp-Glu-x-Asp/His motifs, are integral to almost all RNA metabolic processes in eukaryotic cells. They play myriad roles in processes ranging from transcription and mRNA-protein complex remodeling, to RNA decay and translation. This last facet, translation, is an intricate process that involves DDX/DHX helicases and presents a regulatory node that is highly targetable. Studies aimed at better understanding this family of conserved proteins have revealed insights into their structures, catalytic mechanisms, and biological roles. They have also led to the development of chemical modulators that seek to exploit their essential roles in diseases. Herein, we review the most recent insights on several general and target-specific DDX/DHX helicases in eukaryotic translation initiation.
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16
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Beier DH, Carrocci TJ, van der Feltz C, Tretbar US, Paulson JC, Grabowski N, Hoskins AA. Dynamics of the DEAD-box ATPase Prp5 RecA-like domains provide a conformational switch during spliceosome assembly. Nucleic Acids Res 2020; 47:10842-10851. [PMID: 31712821 PMCID: PMC6846040 DOI: 10.1093/nar/gkz765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 07/29/2019] [Accepted: 08/21/2019] [Indexed: 11/26/2022] Open
Abstract
The DEAD-box family of proteins are ATP-dependent, RNA-binding proteins implicated in many aspects of RNA metabolism. Pre-mRNA splicing in eukaryotes requires three DEAD-box ATPases (Prp5, Prp28 and Sub2), the molecular mechanisms of which are poorly understood. Here, we use single molecule FRET (smFRET) to study the conformational dynamics of yeast Prp5. Prp5 is essential for stable association of the U2 snRNP with the intron branch site (BS) sequence during spliceosome assembly. Our data show that the Prp5 RecA-like domains undergo a large conformational rearrangement only in response to binding of both ATP and RNA. Mutations in Prp5 impact the fidelity of BS recognition and change the conformational dynamics of the RecA-like domains. We propose that BS recognition during spliceosome assembly involves a set of coordinated conformational switches among U2 snRNP components. Spontaneous toggling of Prp5 into a stable, open conformation may be important for its release from U2 and to prevent competition between Prp5 re-binding and subsequent steps in spliceosome assembly.
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Affiliation(s)
- David H Beier
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tucker J Carrocci
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.,Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | | | - U Sandy Tretbar
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua C Paulson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nikolai Grabowski
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.,Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
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17
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Cooperative Analysis of Structural Dynamics in RNA-Protein Complexes by Single-Molecule Förster Resonance Energy Transfer Spectroscopy. Molecules 2020; 25:molecules25092057. [PMID: 32354083 PMCID: PMC7248720 DOI: 10.3390/molecules25092057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/31/2020] [Accepted: 04/13/2020] [Indexed: 12/24/2022] Open
Abstract
RNA-protein complexes (RNPs) are essential components in a variety of cellular processes, and oftentimes exhibit complex structures and show mechanisms that are highly dynamic in conformation and structure. However, biochemical and structural biology approaches are mostly not able to fully elucidate the structurally and especially conformationally dynamic and heterogeneous nature of these RNPs, to which end single molecule Förster resonance energy transfer (smFRET) spectroscopy can be harnessed to fill this gap. Here we summarize the advantages of strategic smFRET studies to investigate RNP dynamics, complemented by structural and biochemical data. Focusing on recent smFRET studies of three essential biological systems, we demonstrate that investigation of RNPs on a single molecule level can answer important functional questions that remained elusive with structural or biochemical approaches alone: The complex structural rearrangements throughout the splicing cycle, unwinding dynamics of the G-quadruplex (G4) helicase RHAU, and aspects in telomere maintenance regulation and synthesis.
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18
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Andreou AZ, Harms U, Klostermeier D. Single-stranded regions modulate conformational dynamics and ATPase activity of eIF4A to optimize 5'-UTR unwinding. Nucleic Acids Res 2019; 47:5260-5275. [PMID: 30997503 PMCID: PMC6547412 DOI: 10.1093/nar/gkz254] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/26/2019] [Accepted: 03/29/2019] [Indexed: 01/14/2023] Open
Abstract
Eukaryotic translation initiation requires unwinding of secondary structures in the 5′-untranslated region of mRNA. The DEAD-box helicase eIF4A is thought to unwind structural elements in the 5′-UTR in conjunction with eIF4G and eIF4B. Both factors jointly stimulate eIF4A activities by modulation of eIF4A conformational cycling between open and closed states. Here we examine how RNA substrates modulate eIF4A activities. The RNAs fall into two classes: Short RNAs only partially stimulate the eIF4A ATPase activity, and closing is rate-limiting for the conformational cycle. By contrast, longer RNAs maximally stimulate ATP hydrolysis and promote closing of eIF4A. Strikingly, the rate constants of unwinding do not correlate with the length of a single-stranded region preceding a duplex, but reach a maximum for RNA with a single-stranded region of six nucleotides. We propose a model in which RNA substrates affect eIF4A activities by modulating the kinetic partitioning of eIF4A between futile, unproductive, and productive cycles.
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Affiliation(s)
- Alexandra Zoi Andreou
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Ulf Harms
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Dagmar Klostermeier
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, D-48149 Muenster, Germany
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19
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Mishra RK, Datey A, Hussain T. mRNA Recruiting eIF4 Factors Involved in Protein Synthesis and Its Regulation. Biochemistry 2019; 59:34-46. [DOI: 10.1021/acs.biochem.9b00788] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Rishi Kumar Mishra
- Department of Molecular Reproduction, Development and Genetics, Division of Biological Sciences, Indian Institute of Science, Bangalore 560012, India
| | - Ayushi Datey
- Department of Molecular Reproduction, Development and Genetics, Division of Biological Sciences, Indian Institute of Science, Bangalore 560012, India
| | - Tanweer Hussain
- Department of Molecular Reproduction, Development and Genetics, Division of Biological Sciences, Indian Institute of Science, Bangalore 560012, India
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20
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Jiang C, Tang Y, Ding L, Tan R, Li X, Lu J, Jiang J, Cui Z, Tang Z, Li W, Cao Z, Schneider-Poetsch T, Jiang W, Luo C, Ding Y, Liu J, Dang Y. Targeting the N Terminus of eIF4AI for Inhibition of Its Catalytic Recycling. Cell Chem Biol 2019; 26:1417-1426.e5. [DOI: 10.1016/j.chembiol.2019.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 05/26/2019] [Accepted: 07/23/2019] [Indexed: 12/12/2022]
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21
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Migration of Small Ribosomal Subunits on the 5' Untranslated Regions of Capped Messenger RNA. Int J Mol Sci 2019; 20:ijms20184464. [PMID: 31510048 PMCID: PMC6769788 DOI: 10.3390/ijms20184464] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/01/2019] [Accepted: 09/05/2019] [Indexed: 12/12/2022] Open
Abstract
Several control mechanisms of eukaryotic gene expression target the initiation step of mRNA translation. The canonical translation initiation pathway begins with cap-dependent attachment of the small ribosomal subunit (SSU) to the messenger ribonucleic acid (mRNA) followed by an energy-dependent, sequential ‘scanning’ of the 5′ untranslated regions (UTRs). Scanning through the 5′UTR requires the adenosine triphosphate (ATP)-dependent RNA helicase eukaryotic initiation factor (eIF) 4A and its efficiency contributes to the specific rate of protein synthesis. Thus, understanding the molecular details of the scanning mechanism remains a priority task for the field. Here, we studied the effects of inhibiting ATP-dependent translation and eIF4A in cell-free translation and reconstituted initiation reactions programmed with capped mRNAs featuring different 5′UTRs. An aptamer that blocks eIF4A in an inactive state away from mRNA inhibited translation of capped mRNA with the moderately structured β-globin sequences in the 5′UTR but not that of an mRNA with a poly(A) sequence as the 5′UTR. By contrast, the nonhydrolysable ATP analogue β,γ-imidoadenosine 5′-triphosphate (AMP-PNP) inhibited translation irrespective of the 5′UTR sequence, suggesting that complexes that contain ATP-binding proteins in their ATP-bound form can obstruct and/or actively block progression of ribosome recruitment and/or scanning on mRNA. Further, using primer extension inhibition to locate SSUs on mRNA (‘toeprinting’), we identify an SSU complex which inhibits primer extension approximately eight nucleotides upstream from the usual toeprinting stop generated by SSUs positioned over the start codon. This ‘−8 nt toeprint’ was seen with mRNA 5′UTRs of different length, sequence and structure potential. Importantly, the ‘−8 nt toeprint’ was strongly stimulated by the presence of the cap on the mRNA, as well as the presence of eIFs 4F, 4A/4B and ATP, implying active scanning. We assembled cell-free translation reactions with capped mRNA featuring an extended 5′UTR and used cycloheximide to arrest elongating ribosomes at the start codon. Impeding scanning through the 5′UTR in this system with elevated magnesium and AMP-PNP (similar to the toeprinting conditions), we visualised assemblies consisting of several SSUs together with one full ribosome by electron microscopy, suggesting direct detection of scanning intermediates. Collectively, our data provide additional biochemical, molecular and physical evidence to underpin the scanning model of translation initiation in eukaryotes.
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22
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Howard CM, Bearss N, Subramaniyan B, Tilley A, Sridharan S, Villa N, Fraser CS, Raman D. The CXCR4-LASP1-eIF4F Axis Promotes Translation of Oncogenic Proteins in Triple-Negative Breast Cancer Cells. Front Oncol 2019; 9:284. [PMID: 31106142 PMCID: PMC6499106 DOI: 10.3389/fonc.2019.00284] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/28/2019] [Indexed: 12/19/2022] Open
Abstract
Triple-negative breast cancer (TNBC) remains clinically challenging as effective targeted therapies are lacking. In addition, patient mortality mainly results from the metastasized lesions. CXCR4 has been identified to be one of the major chemokine receptors involved in breast cancer metastasis. Previously, our lab had identified LIM and SH3 Protein 1 (LASP1) to be a key mediator in CXCR4-driven invasion. To further investigate the role of LASP1 in this process, a proteomic screen was employed and identified a novel protein-protein interaction between LASP1 and components of eukaryotic initiation 4F complex (eIF4F). We hypothesized that activation of the CXCR4-LASP1-eIF4F axis may contribute to the preferential translation of oncogenic mRNAs leading to breast cancer progression and metastasis. To test this hypothesis, we first confirmed that the gene expression of CXCR4, LASP1, and eIF4A are upregulated in invasive breast cancer. Moreover, we demonstrate that LASP1 associated with eIF4A in a CXCL12-dependent manner via a proximity ligation assay. We then confirmed this finding, and the association of LASP1 with eIF4B via co-immunoprecipitation assays. Furthermore, we show that LASP1 can interact with eIF4A and eIF4B through a GST-pulldown approach. Activation of CXCR4 signaling increased the translation of oncoproteins downstream of eIF4A. Interestingly, genetic silencing of LASP1 interrupted the ability of eIF4A to translate oncogenic mRNAs into oncoproteins. This impaired ability of eIF4A was confirmed by a previously established 5′UTR luciferase reporter assay. Finally, lack of LASP1 sensitizes 231S cells to pharmacological inhibition of eIF4A by Rocaglamide A as evident through BIRC5 expression. Overall, our work identified the CXCR4-LASP1 axis to be a novel mediator in oncogenic protein translation. Thus, our axis of study represents a potential target for future TNBC therapies.
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Affiliation(s)
- Cory M Howard
- Department of Cancer Biology, University of Toledo Health Science Campus, Toledo, OH, United States
| | - Nicole Bearss
- Department of Cancer Biology, University of Toledo Health Science Campus, Toledo, OH, United States
| | - Boopathi Subramaniyan
- Department of Cancer Biology, University of Toledo Health Science Campus, Toledo, OH, United States
| | - Augustus Tilley
- Department of Cancer Biology, University of Toledo Health Science Campus, Toledo, OH, United States
| | - Sangita Sridharan
- Department of Cancer Biology, University of Toledo Health Science Campus, Toledo, OH, United States
| | - Nancy Villa
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Christopher S Fraser
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Dayanidhi Raman
- Department of Cancer Biology, University of Toledo Health Science Campus, Toledo, OH, United States
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23
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Chen K, Lin ZW, He SM, Wang CQ, Yang JC, Lu Y, Xie XB, Li Q. Metformin inhibits the proliferation of rheumatoid arthritis fibroblast-like synoviocytes through IGF-IR/PI3K/AKT/m-TOR pathway. Biomed Pharmacother 2019; 115:108875. [PMID: 31028998 DOI: 10.1016/j.biopha.2019.108875] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 03/31/2019] [Accepted: 04/09/2019] [Indexed: 12/11/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disease in which synovial fibroblast-like cells (FLSs) play an important role in RA development and is known to be lack of effective therapy. Thus, novel therapeutic strategies are greatly needed for treatment of RA. Metformin, a first-line drug for the treatment of type 2 diabetes, has been reported to inhibit the proliferation of a variety of tumor cells. In this study, we demonstrated that metformin could inhibit the RA-FLS proliferation in dose- and time-dependent manner. Our cell viability MTT test and 5-ethynyl-2-deoxyuridine incorporation assay showed that metformin inhibited the RA-FLSs proliferation with a time- and concentration-dependent increase. More importantly, metformin induced G2/M cell cycle phase arrest in RA-FLS via the IGF-IR/PI3K/AKT/ m-TOR pathway and inhibited m-TOR phosphorylation through both the IGF-IR/PI3K/AKT signaling pathways thereby further upregulating and down-regulating p70s6k and 4E-BP1 phosphorylation, respectively; however, metformin was found not to induce apoptosis in RA-FLSs. In summary, these results demonstrate that metformin can effectively inhibit RA-FLS proliferation through inducing cell cycle and upregulating and down-regulating p70s6k and 4E-BP1 phosphorylation. Moreover, IGF-IR/PI3K/AKT m-TOR signaling pathway can be regulated by metformin. Our results indicate that metformin may provide a new way of thinking for the treatment of RA.
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Affiliation(s)
- Kun Chen
- Department of Orthopedics, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China; Department of Orthopedics, Huizhou Third People's Hospital, Guangzhou Medical University, Huizhou, Guangdong, 516002, China
| | - Zhao-Wei Lin
- Department of Orthopedics, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
| | - Sheng-Mao He
- Department of orthopedics, The Second Affiliated Hospital, University of South China, Hengyang, Hunan, 421001, China
| | - Cheng-Qiang Wang
- Department of Orthopedics, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
| | - Jian-Cheng Yang
- Department of Orthopedics, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
| | - Yao Lu
- Department of Orthopedics, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
| | - Xiao-Bo Xie
- Department of Orthopedics, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
| | - Qi Li
- Department of Orthopedics, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China.
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24
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Liu X, Schuessler PJ, Sahoo A, Walker SE. Reconstitution and analyses of RNA interactions with eukaryotic translation initiation factors and ribosomal preinitiation complexes. Methods 2019; 162-163:42-53. [PMID: 30926531 DOI: 10.1016/j.ymeth.2019.03.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 11/25/2022] Open
Abstract
Control of translation initiation plays a critical role in the regulation of gene expression in all organisms, yet the mechanics of translation initiation in eukaryotic organisms are not well understood. Confounding studies of translation are the large number and overlapping functions of many initiation factors in cells, and a lack of cap-dependence in many in vitro systems. To shed light on intricate mechanisms that are often obscured in vivo, we use a fully reconstituted translation initiation system for analyzing RNA interactions with eukaryotic translation initiation factors and complexes from the model organism Saccharomyces cerevisiae. This system exhibits strong cap dependence, and dependence on translation factors varies with mRNA 5' UTR sequences as expected from genome-wide studies of translation. Here we provide optimized protocols for purification and analysis of the effects of labeled and unlabeled mRNA recruitment factors on both the rate and factor dependence of mRNA recruitment to the translation preinitiation complex in response to RNA sequence- and structure-changes. In addition to providing streamlined and detailed protocols, we describe a new construct for purification of higher yields of fluorescently labeled and unlabeled full-length eIF4G.
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Affiliation(s)
- Xiaozhuo Liu
- Department of Biological Sciences, The State University of New York at Buffalo, 109 Cooke Hall, Buffalo, NY 14260, United States
| | - Peter J Schuessler
- Department of Biological Sciences, The State University of New York at Buffalo, 109 Cooke Hall, Buffalo, NY 14260, United States
| | - Ansuman Sahoo
- Department of Biological Sciences, The State University of New York at Buffalo, 109 Cooke Hall, Buffalo, NY 14260, United States
| | - Sarah E Walker
- Department of Biological Sciences, The State University of New York at Buffalo, 109 Cooke Hall, Buffalo, NY 14260, United States.
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25
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Aditi, Mason AC, Sharma M, Dawson TR, Wente SR. MAPK- and glycogen synthase kinase 3-mediated phosphorylation regulates the DEAD-box protein modulator Gle1 for control of stress granule dynamics. J Biol Chem 2018; 294:559-575. [PMID: 30429220 DOI: 10.1074/jbc.ra118.005749] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/24/2018] [Indexed: 12/12/2022] Open
Abstract
Rapid expression of critical stress response factors is a key survival strategy for diseased or stressed cells. During cell stress, translation is inhibited, and a pre-existing pool of cytoplasmic mRNA-protein complexes reversibly assembles into cytoplasmic stress granules (SGs). Gle1 is a conserved modulator of RNA-dependent DEAD-box proteins required for mRNA export, translation, and stress responses. Proper Gle1 function is critical as reflected by some human diseases such as developmental and neurodegenerative disorders and some cancers linked to gle1 mutations. However, the mechanism by which Gle1 controls SG formation is incompletely understood. Here, we show that human Gle1 is regulated by phosphorylation during heat shock stress. In HeLa cells, stress-induced Gle1 hyperphosphorylation was dynamic, primarily in the cytoplasmic pool, and followed changes in translation factors. MS analysis identified 14 phosphorylation sites in the Gle1A isoform, six of which clustered in an intrinsically disordered, low-complexity N-terminal region flanking the coil-coiled self-association domain. Of note, two mitogen-activated protein kinases (MAPKs), extracellular signal-regulated kinase (ERK) and c-Jun N-terminal kinase (JNK), phosphorylated the Gle1A N-terminal domain, priming it for phosphorylation by glycogen synthase kinase 3 (GSK3). A phosphomimetic gle1A6D variant (in which six putative Ser/Thr phosphorylation sites were substituted with Asp) perturbed self-association and inhibited DEAD-box helicase 3 (X-linked) (DDX3) ATPase activity. Expression of alanine-substituted, phosphodeficient GFP-gle1A6A promoted SG assembly, whereas GFP-gle1A6D enhanced SG disassembly. We propose that MAPKs and GSK3 phosphorylate Gle1A and thereby coordinate SG dynamics by altering DDX3 function.
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Affiliation(s)
- Aditi
- From the Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37240-7935
| | - Aaron C Mason
- From the Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37240-7935
| | - Manisha Sharma
- From the Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37240-7935
| | - T Renee Dawson
- From the Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37240-7935
| | - Susan R Wente
- From the Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37240-7935
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Borsari C, Quotadamo A, Ferrari S, Venturelli A, Cordeiro-da-Silva A, Santarem N, Costi MP. Scaffolds and Biological Targets Avenue to Fight Against Drug Resistance in Leishmaniasis. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2018. [DOI: 10.1016/bs.armc.2018.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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27
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Harigua-Souiai E, Abdelkrim YZ, Bassoumi-Jamoussi I, Zakraoui O, Bouvier G, Essafi-Benkhadir K, Banroques J, Desdouits N, Munier-Lehmann H, Barhoumi M, Tanner NK, Nilges M, Blondel A, Guizani I. Identification of novel leishmanicidal molecules by virtual and biochemical screenings targeting Leishmania eukaryotic translation initiation factor 4A. PLoS Negl Trop Dis 2018; 12:e0006160. [PMID: 29346371 PMCID: PMC5790279 DOI: 10.1371/journal.pntd.0006160] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/30/2018] [Accepted: 12/11/2017] [Indexed: 01/25/2023] Open
Abstract
Leishmaniases are neglected parasitic diseases in spite of the major burden they inflict on public health. The identification of novel drugs and targets constitutes a research priority. For that purpose we used Leishmania infantum initiation factor 4A (LieIF), an essential translation initiation factor that belongs to the DEAD-box proteins family, as a potential drug target. We modeled its structure and identified two potential binding sites. A virtual screening of a diverse chemical library was performed for both sites. The results were analyzed with an in-house version of the Self-Organizing Maps algorithm combined with multiple filters, which led to the selection of 305 molecules. Effects of these molecules on the ATPase activity of LieIF permitted the identification of a promising hit (208) having a half maximal inhibitory concentration (IC50) of 150 ± 15 μM for 1 μM of protein. Ten chemical analogues of compound 208 were identified and two additional inhibitors were selected (20 and 48). These compounds inhibited the mammalian eIF4I with IC50 values within the same range. All three hits affected the viability of the extra-cellular form of L. infantum parasites with IC50 values at low micromolar concentrations. These molecules showed non-significant toxicity toward THP-1 macrophages. Furthermore, their anti-leishmanial activity was validated with experimental assays on L. infantum intramacrophage amastigotes showing IC50 values lower than 4.2 μM. Selected compounds exhibited selectivity indexes between 19 to 38, which reflects their potential as promising anti-Leishmania molecules.
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Affiliation(s)
- Emna Harigua-Souiai
- Laboratory of Molecular Epidemiology and Experimental Pathology – LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, Tunisia
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Yosser Zina Abdelkrim
- Laboratory of Molecular Epidemiology and Experimental Pathology – LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, Tunisia
- Laboratory of Microbial Gene Expression (EGM), CNRS UMR8261/Université Paris Diderot P7, Sorbonne Paris Cité & PSL, Institut de Biologie Physico-Chimique, Paris, France
- Faculté des Sciences de Bizerte, Université de Carthage, Tunis, Tunisia
| | - Imen Bassoumi-Jamoussi
- Laboratory of Molecular Epidemiology and Experimental Pathology – LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, Tunisia
| | - Ons Zakraoui
- Laboratory of Molecular Epidemiology and Experimental Pathology – LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, Tunisia
| | - Guillaume Bouvier
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Khadija Essafi-Benkhadir
- Laboratory of Molecular Epidemiology and Experimental Pathology – LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, Tunisia
| | - Josette Banroques
- Laboratory of Microbial Gene Expression (EGM), CNRS UMR8261/Université Paris Diderot P7, Sorbonne Paris Cité & PSL, Institut de Biologie Physico-Chimique, Paris, France
| | - Nathan Desdouits
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Hélène Munier-Lehmann
- Institut Pasteur, Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, Paris, France
- Unité Mixte de Recherche 3523, Centre National de la Recherche Scientifique, Paris, France
| | - Mourad Barhoumi
- Laboratory of Molecular Epidemiology and Experimental Pathology – LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, Tunisia
| | - N. Kyle Tanner
- Laboratory of Microbial Gene Expression (EGM), CNRS UMR8261/Université Paris Diderot P7, Sorbonne Paris Cité & PSL, Institut de Biologie Physico-Chimique, Paris, France
| | - Michael Nilges
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Arnaud Blondel
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Ikram Guizani
- Laboratory of Molecular Epidemiology and Experimental Pathology – LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, Tunisia
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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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Huen J, Lin CL, Golzarroshan B, Yi WL, Yang WZ, Yuan HS. Structural Insights into a Unique Dimeric DEAD-Box Helicase CshA that Promotes RNA Decay. Structure 2017; 25:469-481. [PMID: 28238534 DOI: 10.1016/j.str.2017.01.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 01/05/2017] [Accepted: 01/29/2017] [Indexed: 11/28/2022]
Abstract
CshA is a dimeric DEAD-box helicase that cooperates with ribonucleases for mRNA turnover. The molecular mechanism for how a dimeric DEAD-box helicase aids in RNA decay remains unknown. Here, we report the crystal structure and small-angle X-ray scattering solution structure of the CshA from Geobacillus stearothermophilus. In contrast to typical monomeric DEAD-box helicases, CshA is exclusively a dimeric protein with the RecA-like domains of each protomer forming a V-shaped structure. We show that the C-terminal domains protruding outward from the tip of the V-shaped structure is critical for mediating strong RNA binding and is crucial for efficient RNA-dependent ATP hydrolysis. We also show that RNA remains bound with CshA during ATP hydrolysis cycles and thus bulk RNAs could be unwound and degraded in a processive manner through cooperation between exoribonucleases and CshA. A dimeric helicase is hence preserved in RNA-degrading machinery for efficient RNA turnover in prokaryotes and eukaryotes.
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Affiliation(s)
- Jennifer Huen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Chia-Liang Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Bagher Golzarroshan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC; Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, ROC; Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan 30013, ROC
| | - Wan-Li Yi
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Wei-Zen Yang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC; Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei, Taiwan 10048, ROC.
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30
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Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae. Genetics 2017; 203:65-107. [PMID: 27183566 DOI: 10.1534/genetics.115.186221] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/24/2016] [Indexed: 12/18/2022] Open
Abstract
In this review, we provide an overview of protein synthesis in the yeast Saccharomyces cerevisiae The mechanism of protein synthesis is well conserved between yeast and other eukaryotes, and molecular genetic studies in budding yeast have provided critical insights into the fundamental process of translation as well as its regulation. The review focuses on the initiation and elongation phases of protein synthesis with descriptions of the roles of translation initiation and elongation factors that assist the ribosome in binding the messenger RNA (mRNA), selecting the start codon, and synthesizing the polypeptide. We also examine mechanisms of translational control highlighting the mRNA cap-binding proteins and the regulation of GCN4 and CPA1 mRNAs.
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31
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Andreou AZ, Harms U, Klostermeier D. eIF4B stimulates eIF4A ATPase and unwinding activities by direct interaction through its 7-repeats region. RNA Biol 2016; 14:113-123. [PMID: 27858515 DOI: 10.1080/15476286.2016.1259782] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Eukaryotic translation initiation starts with binding of the eIF4F complex to the 5'-m7G cap of the mRNA. Recruitment of the 43S pre-initiation complex (PIC), formed by the 40S ribosomal subunit and other translation initiation factors, leads to formation of the 48S PIC that then scans the 5'-untranslated region (5'-UTR) toward the start codon. The eIF4F complex consists of eIF4E, the cap binding protein, eIF4A, a DEAD-box RNA helicase that is believed to unwind secondary structures in the 5'-UTR during scanning, and eIF4G, a scaffold protein that binds to both eIF4E and eIF4A. The ATPase and helicase activities of eIF4A are jointly stimulated by eIF4G and the translation initiation factor eIF4B. Yeast eIF4B mediates recruitment of the 43S PIC to the cap-bound eIF4F complex by interacting with the 40S subunit and possibly with eIF4A. However, a direct interaction between yeast eIF4A and eIF4B has not been demonstrated yet. Here we show that eIF4B binds to eIF4A in the presence of RNA and ADPNP, independent of the presence of eIF4G. A stretch of seven moderately conserved repeats, the r1-7 region, is responsible for complex formation, for modulation of the conformational energy landscape of eIF4A by eIF4B, and for stimulating the RNA-dependent ATPase- and ATP-dependent RNA unwinding activities of eIF4A. The isolated r1-7 region only slightly stimulates eIF4A conformational changes and activities, suggesting that communication of the repeats with other regions of eIF4B is required for full stimulation of eIF4A activity, for recruitment of the PIC to the mRNA and for translation initiation.
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Affiliation(s)
| | - Ulf Harms
- a University of Muenster, Institute for Physical Chemistry , Muenster , Germany
| | - Dagmar Klostermeier
- a University of Muenster, Institute for Physical Chemistry , Muenster , Germany
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32
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Hartmann S, Weidlich D, Klostermeier D. Single-Molecule Confocal FRET Microscopy to Dissect Conformational Changes in the Catalytic Cycle of DNA Topoisomerases. Methods Enzymol 2016; 581:317-351. [PMID: 27793284 DOI: 10.1016/bs.mie.2016.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Molecular machines undergo large-scale conformational changes during their catalytic cycles that are linked to their biological functions. DNA topoisomerases are molecular machines that interconvert different DNA topoisomers and resolve torsional stress that is introduced during cellular processes that involve local DNA unwinding. DNA gyrase catalyzes the introduction of negative supercoils into DNA in an ATP-dependent reaction. During its catalytic cycle, gyrase undergoes large-scale conformational changes that drive the supercoiling reaction. These conformational changes can be followed by single-molecule Förster resonance energy transfer (FRET). Here, we use DNA gyrase from Bacillus subtilis as an illustrative example to present strategies for the investigation of conformational dynamics of multisubunit complexes. We provide a brief introduction into single-molecule FRET and confocal microscopy, with a focus on practical considerations in sample preparation and data analysis. Different strategies in the preparation of donor-acceptor-labeled molecules suitable for single-molecule FRET experiments are outlined. The insight into the mechanism of DNA supercoiling by gyrase gained from single-molecule FRET experiment is summarized. The general strategies described here can also be applied to investigate conformational changes and their link to biological function of other multisubunit molecular machines.
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Affiliation(s)
- S Hartmann
- Institute for Physical Chemistry, University of Muenster, Muenster, Germany
| | - D Weidlich
- Institute for Physical Chemistry, University of Muenster, Muenster, Germany
| | - D Klostermeier
- Institute for Physical Chemistry, University of Muenster, Muenster, Germany.
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Oliveira LN, Casaletti L, Báo SN, Borges CL, de Sousa Lima P, de Almeida Soares CM. Characterizing the nuclear proteome of Paracoccidioides spp. Fungal Biol 2016; 120:1209-24. [PMID: 27647238 DOI: 10.1016/j.funbio.2016.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/05/2016] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
Abstract
Paracoccidioidomycosis is an endemic disease in Latin America, caused by thermo dimorphic fungi of the genus Paracoccidioides. Although previous proteome analyses of Paracoccidioides spp. have been carried out, the nuclear subproteome of this pathogen has not been described. In this way, we aimed to characterize the nuclear proteome of Paracoccidioides species, in the yeast form. For that, yeast cells were disrupted and submitted to cell fractionation. The purity of the nuclear fraction was confirmed by fluorescence and electron microscopy. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) allowed the identification of 867 proteins. In order to support our enrichment method for nuclear proteins, bioinformatics analysis were applied that allowed the identification of 281 proteins with nuclear localization. The analysis revealed proteins related to DNA maintenance, gene expression, synthesis and processing of messenger and ribosomal RNAs, likewise proteins of nuclear-cytoplasmic traffic. It was also possible to detect some proteins that are poorly expressed, like transcription factors involved in important roles such as resistance to abiotic stress, sporulation, cellular growth and DNA and chromatin maintenance. This is the first descriptive nuclear proteome of Paracoccidioides spp. that can be useful as an important platform base for fungi-specific nuclear processes.
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Affiliation(s)
- Lucas Nojosa Oliveira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, 74690-900, Brazil
| | - Luciana Casaletti
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, 74690-900, Brazil; Escola de Engenharia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, 74605-010, Brazil
| | - Sônia Nair Báo
- Laboratório de Microscopia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Distrito Federal, 70910-900, Brazil
| | - Clayton Luiz Borges
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, 74690-900, Brazil
| | - Patrícia de Sousa Lima
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, 74690-900, Brazil
| | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, 74690-900, Brazil.
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eIF4B stimulates translation of long mRNAs with structured 5' UTRs and low closed-loop potential but weak dependence on eIF4G. Proc Natl Acad Sci U S A 2016; 113:10464-72. [PMID: 27601676 DOI: 10.1073/pnas.1612398113] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
DEAD-box RNA helicases eukaryotic translation initiation factor 4A (eIF4A) and Ded1 promote translation by resolving mRNA secondary structures that impede preinitiation complex (PIC) attachment to mRNA or scanning. Eukaryotic translation initiation factor 4B (eIF4B) is a cofactor for eIF4A but also might function independently of eIF4A. Ribosome profiling of mutants lacking eIF4B or with impaired eIF4A or Ded1 activity revealed that eliminating eIF4B reduces the relative translational efficiencies of many more genes than does inactivation of eIF4A, despite comparable reductions in bulk translation, and few genes display unusually strong requirements for both factors. However, either eliminating eIF4B or inactivating eIF4A preferentially impacts mRNAs with longer, more structured 5' untranslated regions (UTRs). These findings reveal an eIF4A-independent role for eIF4B in addition to its function as eIF4A cofactor in promoting PIC attachment or scanning on structured mRNAs. eIF4B, eIF4A, and Ded1 mutations also preferentially impair translation of longer mRNAs in a fashion mitigated by the ability to form closed-loop messenger ribonucleoprotein particles (mRNPs) via eIF4F-poly(A)-binding protein 1 (Pab1) association, suggesting cooperation between closed-loop assembly and eIF4B/helicase functions. Remarkably, depleting eukaryotic translation initiation factor 4G (eIF4G), the scaffold subunit of eukaryotic translation initiation factor 4F (eIF4F), preferentially impacts short mRNAs with strong closed-loop potential and unstructured 5' UTRs, exactly the opposite features associated with hyperdependence on the eIF4B/helicases. We propose that short, highly efficient mRNAs preferentially depend on the stimulatory effects of eIF4G-dependent closed-loop assembly.
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The molecular choreography of protein synthesis: translational control, regulation, and pathways. Q Rev Biophys 2016; 49:e11. [PMID: 27658712 DOI: 10.1017/s0033583516000056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Translation of proteins by the ribosome regulates gene expression, with recent results underscoring the importance of translational control. Misregulation of translation underlies many diseases, including cancer and many genetic diseases. Decades of biochemical and structural studies have delineated many of the mechanistic details in prokaryotic translation, and sketched the outlines of eukaryotic translation. However, translation may not proceed linearly through a single mechanistic pathway, but likely involves multiple pathways and branchpoints. The stochastic nature of biological processes would allow different pathways to occur during translation that are biased by the interaction of the ribosome with other translation factors, with many of the steps kinetically controlled. These multiple pathways and branchpoints are potential regulatory nexus, allowing gene expression to be tuned at the translational level. As research focus shifts toward eukaryotic translation, certain themes will be echoed from studies on prokaryotic translation. This review provides a general overview of the dynamic data related to prokaryotic and eukaryotic translation, in particular recent findings with single-molecule methods, complemented by biochemical, kinetic, and structural findings. We will underscore the importance of viewing the process through the viewpoints of regulation, translational control, and heterogeneous pathways.
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Michaut M, Chin SF, Majewski I, Severson TM, Bismeijer T, de Koning L, Peeters JK, Schouten PC, Rueda OM, Bosma AJ, Tarrant F, Fan Y, He B, Xue Z, Mittempergher L, Kluin RJ, Heijmans J, Snel M, Pereira B, Schlicker A, Provenzano E, Ali HR, Gaber A, O’Hurley G, Lehn S, Muris JJ, Wesseling J, Kay E, Sammut SJ, Bardwell HA, Barbet AS, Bard F, Lecerf C, O’Connor DP, Vis DJ, Benes CH, McDermott U, Garnett MJ, Simon IM, Jirström K, Dubois T, Linn SC, Gallagher WM, Wessels LF, Caldas C, Bernards R. Integration of genomic, transcriptomic and proteomic data identifies two biologically distinct subtypes of invasive lobular breast cancer. Sci Rep 2016; 6:18517. [PMID: 26729235 PMCID: PMC4700448 DOI: 10.1038/srep18517] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/19/2015] [Indexed: 12/23/2022] Open
Abstract
Invasive lobular carcinoma (ILC) is the second most frequently occurring histological breast cancer subtype after invasive ductal carcinoma (IDC), accounting for around 10% of all breast cancers. The molecular processes that drive the development of ILC are still largely unknown. We have performed a comprehensive genomic, transcriptomic and proteomic analysis of a large ILC patient cohort and present here an integrated molecular portrait of ILC. Mutations in CDH1 and in the PI3K pathway are the most frequent molecular alterations in ILC. We identified two main subtypes of ILCs: (i) an immune related subtype with mRNA up-regulation of PD-L1, PD-1 and CTLA-4 and greater sensitivity to DNA-damaging agents in representative cell line models; (ii) a hormone related subtype, associated with Epithelial to Mesenchymal Transition (EMT), and gain of chromosomes 1q and 8q and loss of chromosome 11q. Using the somatic mutation rate and eIF4B protein level, we identified three groups with different clinical outcomes, including a group with extremely good prognosis. We provide a comprehensive overview of the molecular alterations driving ILC and have explored links with therapy response. This molecular characterization may help to tailor treatment of ILC through the application of specific targeted, chemo- and/or immune-therapies.
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Affiliation(s)
- Magali Michaut
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Suet-Feung Chin
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Ian Majewski
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Tesa M. Severson
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Tycho Bismeijer
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Leanne de Koning
- Translational Research Department, Institut Curie, 26 rue d’Ulm, 75248 Paris cedex 05, France
| | | | - Philip C. Schouten
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Oscar M. Rueda
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Astrid J. Bosma
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Finbarr Tarrant
- Cancer Biology and Therapeutics Laboratory, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
- OncoMark Limited, NovaUCD, Belfield Innovation Park, Dublin 4, Ireland
| | - Yue Fan
- Cancer Biology and Therapeutics Laboratory, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Beilei He
- Translational Research Department, Institut Curie, 26 rue d’Ulm, 75248 Paris cedex 05, France
| | - Zheng Xue
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Lorenza Mittempergher
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Roelof J.C. Kluin
- Genomic Core Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Jeroen Heijmans
- Agendia NV, Science Park 406, 1098 XH Amsterdam, The Netherlands
| | - Mireille Snel
- Agendia NV, Science Park 406, 1098 XH Amsterdam, The Netherlands
| | - Bernard Pereira
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Andreas Schlicker
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Elena Provenzano
- Cambridge Experimental Cancer Medicine Centre (ECMR) and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Cambridge Breast Unit and Cambridge University Hospitals, NHS Foundation Trust, Hills Road, Cambridge CB2 0QQ, UK
| | - Hamid Raza Ali
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Alexander Gaber
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, SE-221 85 Lund, Sweden
| | - Gillian O’Hurley
- OncoMark Limited, NovaUCD, Belfield Innovation Park, Dublin 4, Ireland
| | - Sophie Lehn
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, SE-221 85 Lund, Sweden
| | - Jettie J.F. Muris
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Jelle Wesseling
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Elaine Kay
- Department of Pathology, RCSI ERC, Beaumont Hospital, Dublin 9, Ireland
| | - Stephen John Sammut
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Helen A. Bardwell
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Aurélie S. Barbet
- Translational Research Department, Institut Curie, 26 rue d’Ulm, 75248 Paris cedex 05, France
| | - Floriane Bard
- Translational Research Department, Institut Curie, 26 rue d’Ulm, 75248 Paris cedex 05, France
| | - Caroline Lecerf
- Translational Research Department, Institut Curie, 26 rue d’Ulm, 75248 Paris cedex 05, France
| | - Darran P. O’Connor
- Cancer Biology and Therapeutics Laboratory, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Daniël J. Vis
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Cyril H. Benes
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Mathew J. Garnett
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Iris M. Simon
- Agendia NV, Science Park 406, 1098 XH Amsterdam, The Netherlands
| | - Karin Jirström
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, SE-221 85 Lund, Sweden
| | - Thierry Dubois
- Translational Research Department, Institut Curie, 26 rue d’Ulm, 75248 Paris cedex 05, France
| | - Sabine C. Linn
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Division of Medical Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - William M. Gallagher
- Cancer Biology and Therapeutics Laboratory, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
- OncoMark Limited, NovaUCD, Belfield Innovation Park, Dublin 4, Ireland
| | - Lodewyk F.A. Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Department of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cambridge Experimental Cancer Medicine Centre (ECMR) and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Cambridge Breast Unit and Cambridge University Hospitals, NHS Foundation Trust, Hills Road, Cambridge CB2 0QQ, UK
- Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Rene Bernards
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Agendia NV, Science Park 406, 1098 XH Amsterdam, The Netherlands
- Cancer Genomics Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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Ding H, Guo M, Vidhyasagar V, Talwar T, Wu Y. The Q Motif Is Involved in DNA Binding but Not ATP Binding in ChlR1 Helicase. PLoS One 2015; 10:e0140755. [PMID: 26474416 PMCID: PMC4608764 DOI: 10.1371/journal.pone.0140755] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/30/2015] [Indexed: 01/08/2023] Open
Abstract
Helicases are molecular motors that couple the energy of ATP hydrolysis to the unwinding of structured DNA or RNA and chromatin remodeling. The conversion of energy derived from ATP hydrolysis into unwinding and remodeling is coordinated by seven sequence motifs (I, Ia, II, III, IV, V, and VI). The Q motif, consisting of nine amino acids (GFXXPXPIQ) with an invariant glutamine (Q) residue, has been identified in some, but not all helicases. Compared to the seven well-recognized conserved helicase motifs, the role of the Q motif is less acknowledged. Mutations in the human ChlR1 (DDX11) gene are associated with a unique genetic disorder known as Warsaw Breakage Syndrome, which is characterized by cellular defects in genome maintenance. To examine the roles of the Q motif in ChlR1 helicase, we performed site directed mutagenesis of glutamine to alanine at residue 23 in the Q motif of ChlR1. ChlR1 recombinant protein was overexpressed and purified from HEK293T cells. ChlR1-Q23A mutant abolished the helicase activity of ChlR1 and displayed reduced DNA binding ability. The mutant showed impaired ATPase activity but normal ATP binding. A thermal shift assay revealed that ChlR1-Q23A has a melting point value similar to ChlR1-WT. Partial proteolysis mapping demonstrated that ChlR1-WT and Q23A have a similar globular structure, although some subtle conformational differences in these two proteins are evident. Finally, we found ChlR1 exists and functions as a monomer in solution, which is different from FANCJ, in which the Q motif is involved in protein dimerization. Taken together, our results suggest that the Q motif is involved in DNA binding but not ATP binding in ChlR1 helicase.
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Affiliation(s)
- Hao Ding
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada
| | - Manhong Guo
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada
| | - Venkatasubramanian Vidhyasagar
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada
| | - Tanu Talwar
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada
| | - Yuliang Wu
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada
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Lu J, Jiang C, Li X, Jiang L, Li Z, Schneider-Poetsch T, Liu J, Yu K, Liu JO, Jiang H, Luo C, Dang Y. A gating mechanism for Pi release governs the mRNA unwinding by eIF4AI during translation initiation. Nucleic Acids Res 2015; 43:10157-67. [PMID: 26464436 PMCID: PMC4666354 DOI: 10.1093/nar/gkv1033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/30/2015] [Indexed: 01/18/2023] Open
Abstract
Eukaryotic translation initiation factor eIF4AI, the founding member of DEAD-box helicases, undergoes ATP hydrolysis-coupled conformational changes to unwind mRNA secondary structures during translation initiation. However, the mechanism of its coupled enzymatic activities remains unclear. Here we report that a gating mechanism for Pi release controlled by the inter-domain linker of eIF4AI regulates the coupling between ATP hydrolysis and RNA unwinding. Molecular dynamic simulations and experimental results revealed that, through forming a hydrophobic core with the conserved SAT motif of the N-terminal domain and I357 from the C-terminal domain, the linker gated the release of Pi from the hydrolysis site, which avoided futile hydrolysis cycles of eIF4AI. Further mutagenesis studies suggested this linker also plays an auto-inhibitory role in the enzymatic activity of eIF4AI, which may be essential for its function during translation initiation. Overall, our results reveal a novel regulatory mechanism that controls eIF4AI-mediated mRNA unwinding and can guide further mechanistic studies on other DEAD-box helicases.
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Affiliation(s)
- Junyan Lu
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chenxiao Jiang
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xiaojing Li
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Lizhi Jiang
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Zengxia Li
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | | | - Jianwei Liu
- Department of Chemistry, Shanghai Key Lab of Chemical Biology for Protein Research & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Kunqian Yu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jun O Liu
- Department of Pharmacology & Molecular Sciences and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yongjun Dang
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
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García-García C, Frieda KL, Feoktistova K, Fraser CS, Block SM. RNA BIOCHEMISTRY. Factor-dependent processivity in human eIF4A DEAD-box helicase. Science 2015; 348:1486-8. [PMID: 26113725 DOI: 10.1126/science.aaa5089] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
During eukaryotic translation initiation, the small ribosomal subunit, assisted by initiation factors, locates the messenger RNA start codon by scanning from the 5' cap. This process is powered by the eukaryotic initiation factor 4A (eIF4A), a DEAD-box helicase. eIF4A has been thought to unwind structures formed in the untranslated 5' region via a nonprocessive mechanism. Using a single-molecule assay, we found that eIF4A functions instead as an adenosine triphosphate-dependent processive helicase when complexed with two accessory proteins, eIF4G and eIF4B. Translocation occurred in discrete steps of 11 ± 2 base pairs, irrespective of the accessory factor combination. Our findings support a memory-less stepwise mechanism for translation initiation and suggest that similar factor-dependent processivity may be shared by other members of the DEAD-box helicase family.
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Affiliation(s)
| | - Kirsten L Frieda
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Kateryna Feoktistova
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA 95616, USA
| | - Christopher S Fraser
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA 95616, USA
| | - Steven M Block
- Department of Biology, Stanford University, Stanford, CA 94305, USA. Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.
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Browning KS, Bailey-Serres J. Mechanism of cytoplasmic mRNA translation. THE ARABIDOPSIS BOOK 2015; 13:e0176. [PMID: 26019692 PMCID: PMC4441251 DOI: 10.1199/tab.0176] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein synthesis is a fundamental process in gene expression that depends upon the abundance and accessibility of the mRNA transcript as well as the activity of many protein and RNA-protein complexes. Here we focus on the intricate mechanics of mRNA translation in the cytoplasm of higher plants. This chapter includes an inventory of the plant translational apparatus and a detailed review of the translational processes of initiation, elongation, and termination. The majority of mechanistic studies of cytoplasmic translation have been carried out in yeast and mammalian systems. The factors and mechanisms of translation are for the most part conserved across eukaryotes; however, some distinctions are known to exist in plants. A comprehensive understanding of the complex translational apparatus and its regulation in plants is warranted, as the modulation of protein production is critical to development, environmental plasticity and biomass yield in diverse ecosystems and agricultural settings.
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Affiliation(s)
- Karen S. Browning
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas at Austin, Austin TX 78712-0165
- Both authors contributed equally to this work
| | - Julia Bailey-Serres
- Department of Botany and Plant Sciences and Center for Plant Cell Biology, University of California, Riverside, CA, 92521 USA
- Both authors contributed equally to this work
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Fraser CS. Quantitative studies of mRNA recruitment to the eukaryotic ribosome. Biochimie 2015; 114:58-71. [PMID: 25742741 DOI: 10.1016/j.biochi.2015.02.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/20/2015] [Indexed: 12/20/2022]
Abstract
The process of peptide bond synthesis by ribosomes is conserved between species, but the initiation step differs greatly between the three kingdoms of life. This is illustrated by the evolution of roughly an order of magnitude more initiation factor mass found in humans compared with bacteria. Eukaryotic initiation of translation is comprised of a number of sub-steps: (i) recruitment of an mRNA and initiator methionyl-tRNA to the 40S ribosomal subunit; (ii) migration of the 40S subunit along the 5' UTR to locate the initiation codon; and (iii) recruitment of the 60S subunit to form the 80S initiation complex. Although the mechanism and regulation of initiation has been studied for decades, many aspects of the pathway remain unclear. In this review, I will focus discussion on what is known about the mechanism of mRNA selection and its recruitment to the 40S subunit. I will summarize how the 43S preinitiation complex (PIC) is formed and stabilized by interactions between its components. I will discuss what is known about the mechanism of mRNA selection by the eukaryotic initiation factor 4F (eIF4F) complex and how the selected mRNA is recruited to the 43S PIC. The regulation of this process by secondary structure located in the 5' UTR of an mRNA will also be discussed. Finally, I present a possible kinetic model with which to explain the process of mRNA selection and recruitment to the eukaryotic ribosome.
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Affiliation(s)
- Christopher S Fraser
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA.
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Regulation of DEAH/RHA helicases by G-patch proteins. BIOMED RESEARCH INTERNATIONAL 2015; 2015:931857. [PMID: 25692149 PMCID: PMC4322301 DOI: 10.1155/2015/931857] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 10/19/2014] [Accepted: 10/24/2014] [Indexed: 11/20/2022]
Abstract
RNA helicases from the DEAH/RHA family are present in all the processes of RNA metabolism. The function of two helicases from this family, Prp2 and Prp43, is regulated by protein partners containing a G-patch domain. The G-patch is a glycine-rich domain discovered by sequence alignment, involved in protein-protein and protein-nucleic acid interaction. Although it has been shown to stimulate the helicase's enzymatic activities, the precise role of the G-patch domain remains unclear. The role of G-patch proteins in the regulation of Prp43 activity has been studied in the two biological processes in which it is involved: splicing and ribosome biogenesis. Depending on the pathway, the activity of Prp43 is modulated by different G-patch proteins. A particular feature of the structure of DEAH/RHA helicases revealed by the Prp43 structure is the OB-fold domain in C-terminal part. The OB-fold has been shown to be a platform responsible for the interaction with G-patch proteins and RNA. Though there is still no structural data on the G-patch domain, in the current model, the interaction between the helicase, the G-patch protein, and RNA leads to a cooperative binding of RNA and conformational changes of the helicase.
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43
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Uversky VN. Unreported intrinsic disorder in proteins: Building connections to the literature on IDPs. INTRINSICALLY DISORDERED PROTEINS 2014; 2:e970499. [PMID: 28232880 PMCID: PMC5314882 DOI: 10.4161/21690693.2014.970499] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 09/08/2014] [Indexed: 02/07/2023]
Abstract
This review opens a new series entitled “Unreported intrinsic disorder in proteins.” The goal of this series is to bring attention of researchers to an interesting phenomenon of missed (or overlooked, or ignored, or unreported) disorder. This series serves as a companion to “Digested Disorder” which provides a quarterly review of papers on intrinsically disordered proteins (IDPs) found by standard literature searches. The need for this alternative series results from the observation that there are numerous publications that describe IDPs (or hybrid proteins with ordered and disordered regions) yet fail to recognize many of the key discoveries and publications in the IDP field. By ignoring the body of work on IDPs, such publications often fail to relate their findings to prior discoveries or fail to explore the obvious implications of their work. Thus, the goal of this series is not only to review these very interesting and important papers, but also to point out how each paper relates to the IDP field and show how common tools in the IDP field can readily take the findings in new directions or provide a broader context for the reported findings.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa, FL USA; Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Russia; Biology Department; Faculty of Science; King Abdulaziz University; Jeddah, Kingdom of Saudi Arabia
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44
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Gallie DR. The role of the poly(A) binding protein in the assembly of the Cap-binding complex during translation initiation in plants. ACTA ACUST UNITED AC 2014; 2:e959378. [PMID: 26779409 DOI: 10.4161/2169074x.2014.959378] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 05/19/2014] [Accepted: 06/17/2014] [Indexed: 12/30/2022]
Abstract
Translation initiation in eukaryotes requires the involvement of multiple initiation factors (eIFs) that facilitate the binding of the 40 S ribosomal subunit to an mRNA and assemble the 80 S ribosome at the correct initiation codon. eIF4F, composed of eIF4E, eIF4A, and eIF4G, binds to the 5'-cap structure of an mRNA and prepares an mRNA for recruitment of a 40 S subunit. eIF4B promotes the ATP-dependent RNA helicase activity of eIF4A and eIF4F needed to unwind secondary structure present in a 5'-leader that would otherwise impede scanning of the 40 S subunit during initiation. The poly(A) binding protein (PABP), which binds the poly(A) tail, interacts with eIF4G and eIF4B to promote circularization of an mRNA and stimulates translation by promoting 40 S subunit recruitment. Thus, these factors serve essential functions in the early steps of protein synthesis. Their assembly and function requires multiple interactions that are competitive in nature and determine the nature of interactions between the termini of an mRNA. In this review, the domain organization and partner protein interactions are presented for the factors in plants which share similarities with those in animals and yeast but differ in several important respects. The functional consequences of their interactions on factor activity are also discussed.
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Affiliation(s)
- Daniel R Gallie
- Department of Biochemistry; University of California ; Riverside, CA USA
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45
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Fluorescence methods in the investigation of the DEAD-box helicase mechanism. ACTA ACUST UNITED AC 2014; 105:161-92. [PMID: 25095995 DOI: 10.1007/978-3-0348-0856-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
DEAD-box proteins catalyze the ATP-dependent unwinding of RNA duplexes and accompany RNA molecules throughout their cellular life. Conformational changes in the helicase core of DEAD-box proteins are intimately linked to duplex unwinding. In the absence of ligands, the two RecA domains of the helicase core are separated. ATP and RNA binding induces a closure of the cleft between the RecA domains that is coupled to the distortion of bound RNA, leading to duplex destabilization and dissociation of one RNA strand. Reopening of the helicase core occurs after ATP hydrolysis and is coupled to phosphate release and dissociation of the second RNA strand.Fluorescence spectroscopy provides an array of approaches to study intermolecular interactions, local structural rearrangements, or large conformational changes of biomolecules. The fluorescence intensity of a fluorophore reports on its environment, and fluorescence anisotropy reflects the size of the molecular entity the fluorophore is part of. Fluorescence intensity and anisotropy are therefore sensitive probes to report on binding and dissociation events. Fluorescence resonance energy transfer (FRET) reports on the distance between two fluorophores and thus on conformational changes. Single-molecule FRET experiments reveal the distribution of conformational states and the kinetics of their interconversion. This chapter summarizes fluorescence approaches for monitoring individual aspects of DEAD-box protein activity, from nucleotide and RNA binding and RNA unwinding to protein and RNA conformational changes in the catalytic cycle, and illustrates exemplarily how fluorescence-based methods have contributed to understanding the mechanism of DEAD-box helicase-catalyzed RNA unwinding.
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46
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Insights from a Paradigm Shift: How the Poly(A)-Binding Protein Brings Translating mRNAs Full Circle. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/873084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In recent years, our thinking of how the initiation of protein synthesis occurs has changed dramatically. Initiation was thought to involve only events occurring at or near the 5′-cap structure, which serves as the binding site for the cap-binding complex, a group of translation initiation factors (eIFs) that facilitate the binding of the 40 S ribosomal subunit to an mRNA. Because the poly(A)-binding protein (PABP) binds the poly(A) tail present at the 3′-terminus of an mRNA, it was long thought to play no role in translation initiation. In this review, I present evidence from my laboratory that has contributed to the paradigm shift in how we think of mRNAs during translation. The depiction of mRNAs as straight molecules in which the poly(A) tail is far from events occurring at the 5′-end has now been replaced by the concept of a circular mRNA where the interaction between PABP and the cap-binding complex bridges the termini of an mRNA and promotes translation initiation. The research from my laboratory supports the new paradigm that translation of most mRNAs requires a functional and physical interaction between the termini of an mRNA.
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West nile virus-induced activation of mammalian target of rapamycin complex 1 supports viral growth and viral protein expression. J Virol 2014; 88:9458-71. [PMID: 24920798 DOI: 10.1128/jvi.01323-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Since its introduction in New York City, NY, in 1999, West Nile virus (WNV) has spread to all 48 contiguous states of the United States and is now the leading cause of epidemic encephalitis in North America. As a member of the family Flaviviridae, WNV is part of a group of clinically important human pathogens, including dengue virus and Japanese encephalitis virus. The members of this family of positive-sense, single-stranded RNA viruses have limited coding capacity and are therefore obligated to co-opt a significant amount of cellular factors to translate their genomes effectively. Our previous work has shown that WNV growth was independent of macroautophagy activation, but the role of the evolutionarily conserved mammalian target of rapamycin (mTOR) pathway during WNV infection was not well understood. mTOR is a serine/threonine kinase that acts as a central cellular censor of nutrient status and exercises control of vital anabolic and catabolic cellular responses such as protein synthesis and autophagy, respectively. We now show that WNV activates mTOR and cognate downstream activators of cap-dependent protein synthesis at early time points postinfection and that pharmacologic inhibition of mTOR (KU0063794) significantly reduced WNV growth. We used an inducible Raptor and Rictor knockout mouse embryonic fibroblast (MEF) system to further define the role of mTOR complexes 1 and 2 in WNV growth and viral protein synthesis. Following inducible genetic knockout of the major mTOR cofactors raptor (TOR complex 1 [TORC1]) and rictor (TORC2), we now show that TORC1 supports flavivirus protein synthesis via cap-dependent protein synthesis pathways and supports subsequent WNV growth. IMPORTANCE Since its introduction in New York City, NY, in 1999, West Nile virus (WNV) has spread to all 48 contiguous states in the United States and is now the leading cause of epidemic encephalitis in North America. Currently, the mechanism by which flaviviruses such as WNV translate their genomes in host cells is incompletely understood. Elucidation of the host mechanisms required to support WNV genome translation will provide broad understanding for the basic mechanisms required to translate capped viral RNAs. We now show that WNV activates mTOR and cognate downstream activators of cap-dependent protein synthesis at early time points postinfection. Following inducible genetic knockout of the major mTOR complex cofactors raptor (TORC1) and rictor (TORC2), we now show that TORC1 supports WNV growth and protein synthesis. This study demonstrates the requirement for TORC1 function in support of WNV RNA translation and provides insight into the mechanisms underlying flaviviral RNA translation in mammalian cells.
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Sun Y, Atas E, Lindqvist LM, Sonenberg N, Pelletier J, Meller A. Single-molecule kinetics of the eukaryotic initiation factor 4AI upon RNA unwinding. Structure 2014; 22:941-8. [PMID: 24909782 DOI: 10.1016/j.str.2014.04.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/06/2014] [Accepted: 04/24/2014] [Indexed: 11/30/2022]
Abstract
The eukaryotic translation initiation factor 4AI (eIF4AI) is the prototypical DEAD-box RNA helicase. It has a "dumbbell" structure consisting of two domains connected by a flexible linker. Previous studies demonstrated that eIF4AI, in conjunction with eIF4H, bind to loop structures and repetitively unwind RNA hairpins. Here, we probe the conformational dynamics of eIF4AI in real time using single-molecule FRET. We demonstrate that eIF4AI/eIF4H complex can repetitively unwind RNA hairpins by transitioning between an eIF4AI "open" and a "closed" conformation using the energy derived from ATP hydrolysis. Our experiments directly track the conformational changes in the catalytic cycle of eIF4AI and eIF4H, and this correlates precisely with the kinetics of RNA unwinding. Furthermore, we show that the small-molecule eIF4A inhibitor hippuristanol locks eIF4AI in the closed conformation, thus efficiently inhibiting RNA unwinding. These results indicate that the large conformational changes undertaken by eIF4A during the helicase catalytic cycle are rate limiting.
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Affiliation(s)
- Yingjie Sun
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Evrim Atas
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Lisa M Lindqvist
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Biochemistry and The Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Nahum Sonenberg
- Department of Biochemistry and The Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Jerry Pelletier
- Department of Biochemistry and The Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Amit Meller
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Faculty of Biomedical Engineering, The Technion, Haifa 32000, Israel.
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49
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Harms U, Andreou AZ, Gubaev A, Klostermeier D. eIF4B, eIF4G and RNA regulate eIF4A activity in translation initiation by modulating the eIF4A conformational cycle. Nucleic Acids Res 2014; 42:7911-22. [PMID: 24848014 PMCID: PMC4081068 DOI: 10.1093/nar/gku440] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Eukaryotic translation initiation factor eIF4A is a DEAD-box helicase that resolves secondary structure elements in the 5'-UTR of mRNAs during ribosome scanning. Its RNA-stimulated ATPase and ATP-dependent helicase activities are enhanced by other translation initiation factors, but the underlying mechanisms are unclear. DEAD-box proteins alternate between open and closed conformations during RNA unwinding. The transition to the closed conformation is linked to duplex destabilization. eIF4A is a special DEAD-box protein that can adopt three different conformations, an open state in the absence of ligands, a half-open state stabilized by the translation initiation factor eIF4G and a closed state in the presence of eIF4G and eIF4B. We show here that eIF4A alone does not measurably sample the closed conformation. The translation initiation factors eIF4B and eIF4G accelerate the eIF4A conformational cycle. eIF4G increases the rate of closing more than the opening rate, and eIF4B selectively increases the closing rate. Strikingly, the rate constants and the effect of eIF4B are different for different RNAs, and are related to the presence of single-stranded regions. Modulating the kinetics of the eIF4A conformational cycle is thus central for the multi-layered regulation of its activity, and for its role as a regulatory hub in translation initiation.
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Affiliation(s)
- Ulf Harms
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Alexandra Zoi Andreou
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Airat Gubaev
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Dagmar Klostermeier
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, D-48149 Muenster, Germany
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50
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Abstract
In eukaryotes, the translation initiation codon is generally identified by the scanning mechanism, wherein every triplet in the messenger RNA leader is inspected for complementarity to the anticodon of methionyl initiator transfer RNA (Met-tRNAi). Binding of Met-tRNAi to the small (40S) ribosomal subunit, in a ternary complex (TC) with eIF2-GTP, is stimulated by eukaryotic initiation factor 1 (eIF1), eIF1A, eIF3, and eIF5, and the resulting preinitiation complex (PIC) joins the 5' end of mRNA preactivated by eIF4F and poly(A)-binding protein. RNA helicases remove secondary structures that impede ribosome attachment and subsequent scanning. Hydrolysis of eIF2-bound GTP is stimulated by eIF5 in the scanning PIC, but completion of the reaction is impeded at non-AUG triplets. Although eIF1 and eIF1A promote scanning, eIF1 and possibly the C-terminal tail of eIF1A must be displaced from the P decoding site to permit base-pairing between Met-tRNAi and the AUG codon, as well as to allow subsequent phosphate release from eIF2-GDP. A second GTPase, eIF5B, catalyzes the joining of the 60S subunit to produce an 80S initiation complex that is competent for elongation.
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Affiliation(s)
- 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, Maryland 20892;
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