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Kazan R, Bourgeois G, Lazennec-Schurdevin C, Coureux PD, Mechulam Y, Schmitt E. Structural insights into the evolution of late steps of translation initiation in the three domains of life. Biochimie 2024; 217:31-41. [PMID: 36773835 DOI: 10.1016/j.biochi.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. These two factors are also orthologous to the bacterial IF2 and IF1 proteins, respectively. Recent cryo-EM studies showed how e/aIF5B and e/aIF1A cooperate on the small ribosomal subunit to favor the binding of the large ribosomal subunit and the formation of a ribosome competent for elongation. In this review, pioneering studies and recent biochemical and structural results providing new insights into the role of a/eIF5B in archaea and eukaryotes will be presented. Recent structures will also be compared to orthologous bacterial initiation complexes to highlight domain-specific features and the evolution of initiation mechanisms.
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Affiliation(s)
- Ramy Kazan
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Gabrielle Bourgeois
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Christine Lazennec-Schurdevin
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Pierre-Damien Coureux
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France.
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Kazan R, Bourgeois G, Carisetti D, Florea I, Larquet E, Maurice JL, Mechulam Y, Ozanam F, Schmitt E, Coureux PD. Grid batch-dependent tuning of glow discharge parameters. Front Mol Biosci 2022; 9:910218. [PMID: 36060254 PMCID: PMC9436422 DOI: 10.3389/fmolb.2022.910218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/12/2022] [Indexed: 11/16/2022] Open
Abstract
Sample preparation on cryo-EM grids can give various results, from very thin ice and homogeneous particle distribution (ideal case) to unwanted behavior such as particles around the “holes” or complexes that do not entirely correspond to the one in solution (real life). We recently run into such a case and finally found out that variations in the 3D reconstructions were systematically correlated with the grid batches that were used. We report the use of several techniques to investigate the grids' characteristics, namely TEM, SEM, Auger spectroscopy and Infrared Interferometry. This allowed us to diagnose the origin of grid preparation problems and to adjust glow discharge parameters. The methods used for each approach are described and the results obtained on a common specific case are reported.
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Affiliation(s)
- Ramy Kazan
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, IP Paris, Palaiseau, France
| | - Gabrielle Bourgeois
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, IP Paris, Palaiseau, France
| | | | - Ileana Florea
- Laboratoire de Physique des Interfaces et Couches Minces (LPICM), CNRS-UMR 7647, Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Eric Larquet
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, IP Paris, Palaiseau, France
| | - Jean-Luc Maurice
- Laboratoire de Physique des Interfaces et Couches Minces (LPICM), CNRS-UMR 7647, Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, IP Paris, Palaiseau, France
| | - François Ozanam
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, IP Paris, Palaiseau, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, IP Paris, Palaiseau, France
| | - Pierre-Damien Coureux
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, IP Paris, Palaiseau, France
- *Correspondence: Pierre-Damien Coureux,
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Kazan R, Bourgeois G, Lazennec-Schurdevin C, Larquet E, Mechulam Y, Coureux PD, Schmitt E. Role of aIF5B in archaeal translation initiation. Nucleic Acids Res 2022; 50:6532-6548. [PMID: 35694843 PMCID: PMC9226500 DOI: 10.1093/nar/gkac490] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 01/22/2023] Open
Abstract
In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established and structural data showing eIF5B bound to the full ribosome were obtained. To achieve its function, eIF5B collaborates with eIF1A. However, structural data illustrating how these two factors interact on the small ribosomal subunit have long been awaited. The role of the archaeal counterparts, aIF5B and aIF1A, remains to be extensively addressed. Here, we study the late steps of Pyrococcus abyssi translation initiation. Using in vitro reconstituted initiation complexes and light scattering, we show that aIF5B bound to GTP accelerates subunit joining without the need for GTP hydrolysis. We report the crystallographic structures of aIF5B bound to GDP and GTP and analyze domain movements associated to these two nucleotide states. Finally, we present the cryo-EM structure of an initiation complex containing 30S bound to mRNA, Met-tRNAiMet, aIF5B and aIF1A at 2.7 Å resolution. Structural data shows how archaeal 5B and 1A factors cooperate to induce a conformation of the initiator tRNA favorable to subunit joining. Archaeal and eukaryotic features of late steps of translation initiation are discussed.
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Affiliation(s)
- Ramy Kazan
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Gabrielle Bourgeois
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Christine Lazennec-Schurdevin
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Eric Larquet
- Laboratoire de Physique de la Matière Condensée, PMC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Pierre-Damien Coureux
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
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Biou V, Adaixo RJD, Chami M, Coureux PD, Laurent B, Enguéné VYN, de Amorim GC, Izadi-Pruneyre N, Malosse C, Chamot-Rooke J, Stahlberg H, Delepelaire P. Structural and molecular determinants for the interaction of ExbB from Serratia marcescens and HasB, a TonB paralog. Commun Biol 2022; 5:355. [PMID: 35418619 PMCID: PMC9008036 DOI: 10.1038/s42003-022-03306-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 03/22/2022] [Indexed: 01/20/2023] Open
Abstract
ExbB and ExbD are cytoplasmic membrane proteins that associate with TonB to convey the energy of the proton-motive force to outer membrane receptors in Gram-negative bacteria for iron uptake. The opportunistic pathogen Serratia marcescens (Sm) possesses both TonB and a heme-specific TonB paralog, HasB. ExbBSm has a long periplasmic extension absent in other bacteria such as E. coli (Ec). Long ExbB's are found in several genera of Alphaproteobacteria, most often in correlation with a hasB gene. We investigated specificity determinants of ExbBSm and HasB. We determined the cryo-EM structures of ExbBSm and of the ExbB-ExbDSm complex from S. marcescens. ExbBSm alone is a stable pentamer, and its complex includes two ExbD monomers. We showed that ExbBSm extension interacts with HasB and is involved in heme acquisition and we identified key residues in the membrane domain of ExbBSm and ExbBEc, essential for function and likely involved in the interaction with TonB/HasB. Our results shed light on the class of inner membrane energy machinery formed by ExbB, ExbD and HasB.
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Affiliation(s)
- Valérie Biou
- grid.508487.60000 0004 7885 7602Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, UMR 7099 CNRS, F-75005 Paris, France ,grid.450875.b0000 0004 0643 538XInstitut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Ricardo Jorge Diogo Adaixo
- grid.6612.30000 0004 1937 0642Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Mohamed Chami
- grid.6612.30000 0004 1937 0642Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Pierre-Damien Coureux
- grid.10877.390000000121581279Laboratoire de Biologie Structurale de la Cellule, BIOC, UMR7654 CNRS/Ecole polytechnique, Palaiseau, France
| | - Benoist Laurent
- grid.450875.b0000 0004 0643 538XInstitut de Biologie Physico-Chimique, F-75005 Paris, France ,grid.508487.60000 0004 7885 7602Plateforme de Bioinformatique, Université de Paris, FRC 550 CNRS, F-75005 Paris, France
| | - Véronique Yvette Ntsogo Enguéné
- grid.508487.60000 0004 7885 7602Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, UMR 7099 CNRS, F-75005 Paris, France ,grid.450875.b0000 0004 0643 538XInstitut de Biologie Physico-Chimique, F-75005 Paris, France ,grid.5335.00000000121885934Present Address: Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Gisele Cardoso de Amorim
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur, CNRS UMR3528, CNRS, USR3756 Paris, France ,grid.8536.80000 0001 2294 473XPresent Address: Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ Brasil
| | - Nadia Izadi-Pruneyre
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur, CNRS UMR3528, CNRS, USR3756 Paris, France
| | - Christian Malosse
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR 2000, Institut Pasteur, 75015 Paris, France
| | - Julia Chamot-Rooke
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR 2000, Institut Pasteur, 75015 Paris, France
| | - Henning Stahlberg
- grid.6612.30000 0004 1937 0642Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland ,grid.9851.50000 0001 2165 4204Present Address: Centre d’imagerie Dubochet UNIL-EPFL-UNIGE & Laboratoire de microscopie électronique biologique UNIL-EPFL, Lausanne, Switzerland
| | - Philippe Delepelaire
- grid.508487.60000 0004 7885 7602Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, UMR 7099 CNRS, F-75005 Paris, France ,grid.450875.b0000 0004 0643 538XInstitut de Biologie Physico-Chimique, F-75005 Paris, France
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Doyen C, Larquet E, Coureux PD, Frances O, Herman F, Sablé S, Burnouf JP, Sizun C, Lescop E. Nuclear Magnetic Resonance Spectroscopy: A Multifaceted Toolbox to Probe Structure, Dynamics, Interactions, and Real-Time In Situ Release Kinetics in Peptide-Liposome Formulations. Mol Pharm 2021; 18:2521-2539. [PMID: 34151567 DOI: 10.1021/acs.molpharmaceut.1c00037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Liposomal formulations represent attractive biocompatible and tunable drug delivery systems for peptide drugs. Among the tools to analyze their physicochemical properties, nuclear magnetic resonance (NMR) spectroscopy, despite being an obligatory technique to characterize molecular structure and dynamics in chemistry as well as in structural biology, yet appears to be rather sparsely used to study drug-liposome formulations. In this work, we exploited several facets of liquid-state NMR spectroscopy to characterize liposomal delivery systems for the apelin-derived K14P peptide and K14P modified by Nα-fatty acylation. Various liposome compositions and preparation modes were analyzed. Using NMR, in combination with cryo-electron microscopy and dynamic light scattering, we determined structural, dynamic, and self-association properties of these peptides in solution and probed their interactions with liposomes. Using 31P and 1H NMR, we characterized membrane fluidity and thermotropic phase transitions in empty and loaded liposomes. Based on diffusion and 1H NMR experiments, we localized and quantified peptides with respect to the interior/exterior of liposomes and changes over time and upon thermal treatments. Finally, we assessed the release kinetics of several solutes and compared various formulations. Taken together, this work shows that NMR has the potential to assist the design of peptide/liposome systems and more generally drug delivery systems.
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Affiliation(s)
- Camille Doyen
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France.,Sanofi, 13 Quai Jules Guesde, 94403 Vitry sur Seine, France
| | - Eric Larquet
- Laboratoire de Physique de la Matière Condensée (LPMC), Ecole Polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Pierre-Damien Coureux
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Oriane Frances
- Sanofi, 13 Quai Jules Guesde, 94403 Vitry sur Seine, France
| | | | - Serge Sablé
- Sanofi, 13 Quai Jules Guesde, 94403 Vitry sur Seine, France
| | | | - Christina Sizun
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
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Schmitt E, Coureux PD, Kazan R, Bourgeois G, Lazennec-Schurdevin C, Mechulam Y. Recent Advances in Archaeal Translation Initiation. Front Microbiol 2020; 11:584152. [PMID: 33072057 PMCID: PMC7531240 DOI: 10.3389/fmicb.2020.584152] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/24/2020] [Indexed: 12/20/2022] Open
Abstract
Translation initiation (TI) allows accurate selection of the initiation codon on a messenger RNA (mRNA) and defines the reading frame. In all domains of life, translation initiation generally occurs within a macromolecular complex made up of the small ribosomal subunit, the mRNA, a specialized methionylated initiator tRNA, and translation initiation factors (IFs). Once the start codon is selected at the P site of the ribosome and the large subunit is associated, the IFs are released and a ribosome competent for elongation is formed. However, even if the general principles are the same in the three domains of life, the molecular mechanisms are different in bacteria, eukaryotes, and archaea and may also vary depending on the mRNA. Because TI mechanisms have evolved lately, their studies bring important information about the evolutionary relationships between extant organisms. In this context, recent structural data on ribosomal complexes and genome-wide studies are particularly valuable. This review focuses on archaeal translation initiation highlighting its relationships with either the eukaryotic or the bacterial world. Eukaryotic features of the archaeal small ribosomal subunit are presented. Ribosome evolution and TI mechanisms diversity in archaeal branches are discussed. Next, the use of leaderless mRNAs and that of leadered mRNAs having Shine-Dalgarno sequences is analyzed. Finally, the current knowledge on TI mechanisms of SD-leadered and leaderless mRNAs is detailed.
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Affiliation(s)
- Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Pierre-Damien Coureux
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Ramy Kazan
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Gabrielle Bourgeois
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Christine Lazennec-Schurdevin
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
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Monestier A, Lazennec-Schurdevin C, Coureux PD, Mechulam Y, Schmitt E. Role of aIF1 in Pyrococcus abyssi translation initiation. Nucleic Acids Res 2019; 46:11061-11074. [PMID: 30239976 PMCID: PMC6237735 DOI: 10.1093/nar/gky850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/11/2018] [Indexed: 01/06/2023] Open
Abstract
In archaeal translation initiation, a preinitiation complex (PIC) made up of aIF1, aIF1A, the ternary complex (TC, e/aIF2-GTP-Met-tRNAiMet) and mRNA bound to the small ribosomal subunit is responsible for start codon selection. Many archaeal mRNAs contain a Shine-Dalgarno (SD) sequence allowing the PIC to be prepositioned in the vicinity of the start codon. Nevertheless, cryo-EM studies have suggested local scanning to definitely establish base pairing of the start codon with the tRNA anticodon. Here, using fluorescence anisotropy, we show that aIF1 and mRNA have synergistic binding to the Pyrococcus abyssi 30S. Stability of 30S:mRNA:aIF1 strongly depends on the SD sequence. Further, toeprinting experiments show that aIF1-containing PICs display a dynamic conformation with the tRNA not firmly accommodated in the P site. AIF1-induced destabilization of the PIC is favorable for proofreading erroneous initiation complexes. After aIF1 departure, the stability of the PIC increases reflecting initiator tRNA fully base-paired to the start codon. Altogether, our data support the idea that some of the main events governing start codon selection in eukaryotes and archaea occur within a common structural and functional core. However, idiosyncratic features in loop 1 sequence involved in 30S:mRNA binding suggest adjustments of e/aIF1 functioning in the two domains.
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Affiliation(s)
- Auriane Monestier
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | | | - Pierre-Damien Coureux
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Yves Mechulam
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
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Monestier A, Aleksandrov A, Coureux PD, Panvert M, Mechulam Y, Schmitt E. The structure of an E. coli tRNA fMet A 1-U 72 variant shows an unusual conformation of the A 1-U 72 base pair. RNA 2017; 23:673-682. [PMID: 28143889 PMCID: PMC5393177 DOI: 10.1261/rna.057877.116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 01/26/2017] [Indexed: 06/06/2023]
Abstract
Translation initiation in eukaryotes and archaea involves a methionylated initiator tRNA delivered to the ribosome in a ternary complex with e/aIF2 and GTP. Eukaryotic and archaeal initiator tRNAs contain a highly conserved A1-U72 base pair at the top of the acceptor stem. The importance of this base pair to discriminate initiator tRNAs from elongator tRNAs has been established previously using genetics and biochemistry. However, no structural data illustrating how the A1-U72 base pair participates in the accurate selection of the initiator tRNAs by the translation initiation systems are available. Here, we describe the crystal structure of a mutant E. coli initiator tRNAfMetA1-U72, aminoacylated with methionine, in which the C1:A72 mismatch at the end of the tRNA acceptor stem has been changed to an A1-U72 base pair. Sequence alignments show that the mutant E. coli tRNA is a good mimic of archaeal initiator tRNAs. The crystal structure, determined at 2.8 Å resolution, shows that the A1-U72 pair adopts an unusual arrangement. A1 is in a syn conformation and forms a single H-bond interaction with U72 This interaction requires protonation of the N1 atom of A1 Moreover, the 5' phosphoryl group folds back into the major groove of the acceptor stem and interacts with the N7 atom of G2 A possible role of this unusual geometry of the A1-U72 pair in the recognition of the initiator tRNA by its partners during eukaryotic and archaeal translation initiation is discussed.
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Affiliation(s)
- Auriane Monestier
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Alexey Aleksandrov
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Pierre-Damien Coureux
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Michel Panvert
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Yves Mechulam
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
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Norais C, Servant P, Bouthier-de-la-Tour C, Coureux PD, Ithurbide S, Vannier F, Guerin PP, Dulberger CL, Satyshur KA, Keck JL, Armengaud J, Cox MM, Sommer S. The Deinococcus radiodurans DR1245 protein, a DdrB partner homologous to YbjN proteins and reminiscent of type III secretion system chaperones. PLoS One 2013; 8:e56558. [PMID: 23441204 PMCID: PMC3575483 DOI: 10.1371/journal.pone.0056558] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 01/04/2013] [Indexed: 11/18/2022] Open
Abstract
The bacterium Deinococcus radiodurans exhibits an extreme resistance to ionizing radiation. A small subset of Deinococcus genus-specific genes were shown to be up-regulated upon exposure to ionizing radiation and to play a role in genome reconstitution. These genes include an SSB-like protein called DdrB. Here, we identified a novel protein encoded by the dr1245 gene as an interacting partner of DdrB. A strain devoid of the DR1245 protein is impaired in growth, exhibiting a generation time approximately threefold that of the wild type strain while radioresistance is not affected. We determined the three-dimensional structure of DR1245, revealing a relationship with type III secretion system chaperones and YbjN family proteins. Thus, DR1245 may display some chaperone activity towards DdrB and possibly other substrates.
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Affiliation(s)
- Cédric Norais
- Department of Biochemistry, University of Wisconsin College of Agriculture and Life Sciences, Madison, Wisconsin, United States of America
- Ecole polytechnique, Laboratoire de Biochimie, Centre national de la recherche scientifique, Palaiseau, France
| | - Pascale Servant
- Univ. Paris-Sud, Institut de Génétique et Microbiologie (Bât. 409), UMR8621, Orsay, France
- Centre national de la recherche scientifique, Orsay, France
| | - Claire Bouthier-de-la-Tour
- Univ. Paris-Sud, Institut de Génétique et Microbiologie (Bât. 409), UMR8621, Orsay, France
- Centre national de la recherche scientifique, Orsay, France
| | - Pierre-Damien Coureux
- Ecole polytechnique, Laboratoire de Biochimie, Centre national de la recherche scientifique, Palaiseau, France
| | - Solenne Ithurbide
- Univ. Paris-Sud, Institut de Génétique et Microbiologie (Bât. 409), UMR8621, Orsay, France
- Centre national de la recherche scientifique, Orsay, France
| | - Françoise Vannier
- Univ. Paris-Sud, Institut de Génétique et Microbiologie (Bât. 409), UMR8621, Orsay, France
- Centre national de la recherche scientifique, Orsay, France
| | - Philippe P. Guerin
- Commissariat à l’énergie atomique et aux énergies alternatives, Direction des Sciences du Vivant, Institut de Biologie Environnementale et Biotechnologie, Lab Biochim System Perturb, Bagnols-sur-Cèze, France
| | - Charles L. Dulberger
- Department of Biochemistry, University of Wisconsin College of Agriculture and Life Sciences, Madison, Wisconsin, United States of America
| | - Kenneth A. Satyshur
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - James L. Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Jean Armengaud
- Commissariat à l’énergie atomique et aux énergies alternatives, Direction des Sciences du Vivant, Institut de Biologie Environnementale et Biotechnologie, Lab Biochim System Perturb, Bagnols-sur-Cèze, France
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin College of Agriculture and Life Sciences, Madison, Wisconsin, United States of America
| | - Suzanne Sommer
- Univ. Paris-Sud, Institut de Génétique et Microbiologie (Bât. 409), UMR8621, Orsay, France
- Centre national de la recherche scientifique, Orsay, France
- * E-mail:
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Schmitt E, Panvert M, Lazennec-Schurdevin C, Coureux PD, Perez J, Thompson A, Mechulam Y. Structure of the ternary initiation complex aIF2-GDPNP-methionylated initiator tRNA. Nat Struct Mol Biol 2012; 19:450-4. [PMID: 22447243 DOI: 10.1038/nsmb.2259] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 02/07/2012] [Indexed: 01/09/2023]
Abstract
Eukaryotic and archaeal translation initiation factor 2 (e/aIF2) is a heterotrimeric GTPase that has a crucial role in the selection of the correct start codon on messenger RNA. We report the 5-Å resolution crystal structure of the ternary complex formed by archaeal aIF2 from Sulfolobus solfataricus, the GTP analog GDPNP and methionylated initiator tRNA. The 3D model is further supported by solution studies using small-angle X-ray scattering. The tRNA is bound by the α and γ subunits of aIF2. Contacts involve the elbow of the tRNA and the minor groove of the acceptor stem, but not the T-stem minor groove. We conclude that despite considerable structural homology between the core γ subunit of aIF2 and the elongation factor EF1A, these two G proteins of the translation apparatus use very different tRNA-binding strategies.
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Affiliation(s)
- Emmanuelle Schmitt
- Laboratoire de Biochimie, Unité mixte de Recherche 7654, Ecole Polytechnique, Centre National de la Recherche Scientifique, Palaiseau, France.
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Sachse C, Chen JZ, Coureux PD, Stroupe ME, Fändrich M, Grigorieff N. High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus. J Mol Biol 2007; 371:812-35. [PMID: 17585939 PMCID: PMC2025690 DOI: 10.1016/j.jmb.2007.05.088] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Revised: 05/18/2007] [Accepted: 05/30/2007] [Indexed: 10/23/2022]
Abstract
The treatment of helical objects as a string of single particles has become an established technique to resolve their three-dimensional (3D) structure using electron cryo-microscopy. It can be applied to a wide range of helical particles such as viruses, microtubules and helical filaments. We have made improvements to this approach using Tobacco Mosaic Virus (TMV) as a test specimen and obtained a map from 210,000 asymmetric units at a resolution better than 5 A. This was made possible by performing a full correction of the contrast transfer function of the microscope. Alignment of helical segments was helped by constraints derived from the helical symmetry of the virus. Furthermore, symmetrization was implemented by multiple inclusions of symmetry-related views in the 3D reconstruction. We used the density map to build an atomic model of TMV. The model was refined using a real-space refinement strategy that accommodates multiple conformers. The atomic model shows significant deviations from the deposited model for the helical form of TMV at the lower-radius region (residues 88 to 109). This region appears more ordered with well-defined secondary structure, compared with the earlier helical structure. The RNA phosphate backbone is sandwiched between two arginine side-chains, stabilizing the interaction between RNA and coat protein. A cluster of two or three carboxylates is buried in a hydrophobic environment isolating it from neighboring subunits. These carboxylates may represent the so-called Caspar carboxylates that form a metastable switch for viral disassembly. Overall, the observed differences suggest that the new model represents a different, more stable state of the virus, compared with the earlier published model.
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Affiliation(s)
- Carsten Sachse
- Howard Hughes Medical Institute, Brandeis University - MS029, 415 South Street, Waltham, MA 02454, USA
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12
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Coureux PD, Genick UK. Triggering and Monitoring Light‐Sensing Reactions in Protein Crystals. Methods Enzymol 2007; 422:305-37. [PMID: 17628146 DOI: 10.1016/s0076-6879(06)22015-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Many bacterial photoreceptors signal via histidine kinases. The light-activated nature of these proteins provides unique experimental opportunities to study their molecular mechanisms of signal transduction. One of these opportunities is the combined application of X-ray crystallography and optical spectroscopy in protein crystals. By combining these two methods it is possible to correlate protein structure to protein function in a way that is exceedingly difficult or impossible to achieve in most other experimental systems. This chapter is divided into two parts. The first part provides a brief overview of light-regulated histidine kinases and the most important techniques for studying the structure of photocycle intermediates by crystallography. The second part of the chapter is dedicated to practical advice on how to select, mount, activate, and monitor the structural and spectroscopic responses of photoreceptor crystals. This chapter is intended for readers who want to start using these experimental tools themselves or who wish to understand enough about the techniques to critically evaluate the work of others.
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Coureux PD, Sweeney HL, Houdusse A. Three myosin V structures delineate essential features of chemo-mechanical transduction. EMBO J 2004; 23:4527-37. [PMID: 15510214 PMCID: PMC533045 DOI: 10.1038/sj.emboj.7600458] [Citation(s) in RCA: 242] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Accepted: 10/05/2004] [Indexed: 11/09/2022] Open
Abstract
The molecular motor, myosin, undergoes conformational changes in order to convert chemical energy into force production. Based on kinetic and structural considerations, we assert that three crystal forms of the myosin V motor delineate the conformational changes that myosin motors undergo upon detachment from actin. First, a motor domain structure demonstrates that nucleotide-free myosin V adopts a specific state (rigor-like) that is not influenced by crystal packing. A second structure reveals an actomyosin state that favors rapid release of ADP, and differs from the rigor-like state by a P-loop rearrangement. Comparison of these structures with a third structure, a 2.0 angstroms resolution structure of the motor bound to an ATP analog, illuminates the structural features that provide communication between the actin interface and nucleotide-binding site. Paramount among these is a region we name the transducer, which is composed of the seven-stranded beta-sheet and associated loops and linkers. Reminiscent of the beta-sheet distortion of the F1-ATPase, sequential distortion of this transducer region likely controls sequential release of products from the nucleotide pocket during force generation.
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Affiliation(s)
| | - H Lee Sweeney
- Department of Physiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
- Department of Physiology, University of Pennsylvania School of Medicine, A700 Richards Bldg, 3700 Hamilton Walk, Philadelphia, PA 19104-6085, USA. Tel.: +1 215 898 0486; Fax: +1 215 898 0475; E-mail:
| | - Anne Houdusse
- Structural Motility, Institut Curie CNRS, UMR144, Paris, France
- Structural Motility, Institut Curie CNRS, UMR 144, 26 rue d'ULM, 75248 Paris Cedex 05, France. Tel.: +33 1 4234 6395; Fax: +33 1 4234 6382; E-mail:
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Coureux PD, Wells AL, Ménétrey J, Yengo CM, Morris CA, Sweeney HL, Houdusse A. A structural state of the myosin V motor without bound nucleotide. Nature 2003; 425:419-23. [PMID: 14508494 DOI: 10.1038/nature01927] [Citation(s) in RCA: 250] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2003] [Accepted: 07/18/2003] [Indexed: 11/09/2022]
Abstract
The myosin superfamily of molecular motors use ATP hydrolysis and actin-activated product release to produce directed movement and force. Although this is generally thought to involve movement of a mechanical lever arm attached to a motor core, the structural details of the rearrangement in myosin that drive the lever arm motion on actin attachment are unknown. Motivated by kinetic evidence that the processive unconventional myosin, myosin V, populates a unique state in the absence of nucleotide and actin, we obtained a 2.0 A structure of a myosin V fragment. Here we reveal a conformation of myosin without bound nucleotide. The nucleotide-binding site has adopted new conformations of the nucleotide-binding elements that reduce the affinity for the nucleotide. The major cleft in the molecule has closed, and the lever arm has assumed a position consistent with that in an actomyosin rigor complex. These changes have been accomplished by relative movements of the subdomains of the molecule, and reveal elements of the structural communication between the actin-binding interface and nucleotide-binding site of myosin that underlie the mechanism of chemo-mechanical transduction.
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Affiliation(s)
- Pierre-Damien Coureux
- Structural Motility, Institut Curie CNRS, UMR144, 26 rue d'Ulm, 75248 Paris cedex 05, France
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