1
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Warner BR, Fredrick K. Contribution of an alternative 16S rRNA helix to biogenesis of the 30S subunit of the ribosome. RNA (NEW YORK, N.Y.) 2024; 30:770-778. [PMID: 38570183 PMCID: PMC11182017 DOI: 10.1261/rna.079960.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/23/2024] [Indexed: 04/05/2024]
Abstract
30S subunits become inactive upon exposure to low Mg2+ concentration, because of a reversible conformational change that entails nucleotides (nt) in the neck helix (h28) and 3' tail of 16S rRNA. This active-to-inactive transition involves partial unwinding of h28 and repairing of nt 921-923 with nt 1532-1534, which requires flipping of the 3' tail by ∼180°. Growing evidence suggests that immature 30S particles adopt the inactive conformation in the cell, and transition to the active state occurs at a late stage of maturation. Here, we target nucleotides that form the alternative helix (hALT) of the inactive state. Using an orthogonal ribosome system, we find that disruption of hALT decreases translation activity in the cell modestly, by approximately twofold, without compromising ribosome fidelity. Ribosomes carrying substitutions at positions 1532-1533 support the growth of Escherichia coli strain Δ7 prrn (which carries a single rRNA operon), albeit at rates 10%-20% slower than wild-type ribosomes. These mutant Δ7 prrn strains accumulate free 30S particles and precursor 17S rRNA, indicative of biogenesis defects. Analysis of purified control and mutant subunits suggests that hALT stabilizes the inactive state by 1.2 kcal/mol with little-to-no impact on the active state or the transition state of conversion.
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Affiliation(s)
- Benjamin R Warner
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Kurt Fredrick
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
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2
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Webster MW, Chauvier A, Rahil H, Graziadei A, Charles K, Takacs M, Saint-André C, Rappsilber J, Walter NG, Weixlbaumer A. Molecular basis of mRNA delivery to the bacterial ribosome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585789. [PMID: 38562847 PMCID: PMC10983998 DOI: 10.1101/2024.03.19.585789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Protein synthesis begins with the formation of a ribosome-mRNA complex. In bacteria, the 30S ribosomal subunit is recruited to many mRNAs through base pairing with the Shine Dalgarno (SD) sequence and RNA binding by ribosomal protein bS1. Translation can initiate on nascent mRNAs and RNA polymerase (RNAP) can promote recruitment of the pioneering 30S subunit. Here we examined ribosome recruitment to nascent mRNAs using cryo-EM, single-molecule fluorescence co-localization, and in-cell crosslinking mass spectrometry. We show that bS1 delivers the mRNA to the ribosome for SD duplex formation and 30S subunit activation. Additionally, bS1 mediates the stimulation of translation initiation by RNAP. Together, our work provides a mechanistic framework for how the SD duplex, ribosomal proteins and RNAP cooperate in 30S recruitment to mRNAs and establish transcription-translation coupling.
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Affiliation(s)
- Michael W. Webster
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France
- Université de Strasbourg, 67404 Illkirch Cedex, France
- CNRS UMR7104, 67404 Illkirch Cedex, France
- INSERM U1258, 67404 Illkirch Cedex, France
| | - Adrien Chauvier
- Single Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Huma Rahil
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France
- Université de Strasbourg, 67404 Illkirch Cedex, France
- CNRS UMR7104, 67404 Illkirch Cedex, France
- INSERM U1258, 67404 Illkirch Cedex, France
| | - Andrea Graziadei
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Kristine Charles
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Maria Takacs
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France
- Université de Strasbourg, 67404 Illkirch Cedex, France
- CNRS UMR7104, 67404 Illkirch Cedex, France
- INSERM U1258, 67404 Illkirch Cedex, France
| | - Charlotte Saint-André
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France
- Université de Strasbourg, 67404 Illkirch Cedex, France
- CNRS UMR7104, 67404 Illkirch Cedex, France
- INSERM U1258, 67404 Illkirch Cedex, France
| | - Juri Rappsilber
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Nils G. Walter
- Single Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Albert Weixlbaumer
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France
- Université de Strasbourg, 67404 Illkirch Cedex, France
- CNRS UMR7104, 67404 Illkirch Cedex, France
- INSERM U1258, 67404 Illkirch Cedex, France
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3
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Teran D, Zhang Y, Korostelev AA. Endogenous trans-translation structure visualizes the decoding of the first tmRNA alanine codon. Front Microbiol 2024; 15:1369760. [PMID: 38500588 PMCID: PMC10944890 DOI: 10.3389/fmicb.2024.1369760] [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: 01/12/2024] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
Ribosomes stall on truncated or otherwise damaged mRNAs. Bacteria rely on ribosome rescue mechanisms to replenish the pool of ribosomes available for translation. Trans-translation, the main ribosome-rescue pathway, uses a circular hybrid transfer-messenger RNA (tmRNA) to restart translation and label the resulting peptide for degradation. Previous studies have visualized how tmRNA and its helper protein SmpB interact with the stalled ribosome to establish a new open reading frame. As tmRNA presents the first alanine codon via a non-canonical mRNA path in the ribosome, the incoming alanyl-tRNA must rearrange the tmRNA molecule to read the codon. Here, we describe cryo-EM analyses of an endogenous Escherichia coli ribosome-tmRNA complex with tRNAAla accommodated in the A site. The flexible adenosine-rich tmRNA linker, which connects the mRNA-like domain with the codon, is stabilized by the minor groove of the canonically positioned anticodon stem of tRNAAla. This ribosome complex can also accommodate a tRNA near the E (exit) site, bringing insights into the translocation and dissociation of the tRNA that decoded the defective mRNA prior to tmRNA binding. Together, these structures uncover a key step of ribosome rescue, in which the ribosome starts translating the tmRNA reading frame.
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Affiliation(s)
| | | | - Andrei A. Korostelev
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, United States
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4
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Dimitrova-Paternoga L, Kasvandik S, Beckert B, Granneman S, Tenson T, Wilson DN, Paternoga H. Structural basis of ribosomal 30S subunit degradation by RNase R. Nature 2024; 626:1133-1140. [PMID: 38326618 PMCID: PMC10901742 DOI: 10.1038/s41586-024-07027-6] [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: 03/03/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024]
Abstract
Protein synthesis is a major energy-consuming process of the cell that requires the controlled production1-3 and turnover4,5 of ribosomes. Although the past few years have seen major advances in our understanding of ribosome biogenesis, structural insight into the degradation of ribosomes has been lacking. Here we present native structures of two distinct small ribosomal 30S subunit degradation intermediates associated with the 3' to 5' exonuclease ribonuclease R (RNase R). The structures reveal that RNase R binds at first to the 30S platform to facilitate the degradation of the functionally important anti-Shine-Dalgarno sequence and the decoding-site helix 44. RNase R then encounters a roadblock when it reaches the neck region of the 30S subunit, and this is overcome by a major structural rearrangement of the 30S head, involving the loss of ribosomal proteins. RNase R parallels this movement and relocates to the decoding site by using its N-terminal helix-turn-helix domain as an anchor. In vitro degradation assays suggest that head rearrangement poses a major kinetic barrier for RNase R, but also indicate that the enzyme alone is sufficient for complete degradation of 30S subunits. Collectively, our results provide a mechanistic basis for the degradation of 30S mediated by RNase R, and reveal that RNase R targets orphaned 30S subunits using a dynamic mechanism involving an anchored switching of binding sites.
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Affiliation(s)
| | - Sergo Kasvandik
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Bertrand Beckert
- Dubochet Center for Imaging (DCI) at EPFL, EPFL SB IPHYS DCI, Lausanne, Switzerland
| | - Sander Granneman
- Centre for Engineering Biology (SynthSys), University of Edinburgh, Edinburgh, UK
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
| | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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5
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Sun J, Kinman LF, Jahagirdar D, Ortega J, Davis JH. KsgA facilitates ribosomal small subunit maturation by proofreading a key structural lesion. Nat Struct Mol Biol 2023; 30:1468-1480. [PMID: 37653244 PMCID: PMC10710901 DOI: 10.1038/s41594-023-01078-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 07/25/2023] [Indexed: 09/02/2023]
Abstract
Ribosome assembly is orchestrated by many assembly factors, including ribosomal RNA methyltransferases, whose precise role is poorly understood. Here, we leverage the power of cryo-EM and machine learning to discover that the E. coli methyltransferase KsgA performs a 'proofreading' function in the assembly of the small ribosomal subunit by recognizing and partially disassembling particles that have matured but are not competent for translation. We propose that this activity allows inactive particles an opportunity to reassemble into an active state, thereby increasing overall assembly fidelity. Detailed structural quantifications in our datasets additionally enabled the expansion of the Nomura assembly map to highlight rRNA helix and r-protein interdependencies, detailing how the binding and docking of these elements are tightly coupled. These results have wide-ranging implications for our understanding of the quality-control mechanisms governing ribosome biogenesis and showcase the power of heterogeneity analysis in cryo-EM to unveil functionally relevant information in biological systems.
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Affiliation(s)
- Jingyu Sun
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Laurel F Kinman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Dushyant Jahagirdar
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Joaquin Ortega
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada.
- Centre for Structural Biology, McGill University, Montreal, Quebec, Canada.
| | - Joseph H Davis
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA.
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6
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Belinite M, Khusainov I, Marzi S. Staphylococcus aureus 30S Ribosomal Subunit Purification and Its Biochemical and Cryo-EM Analysis. Bio Protoc 2022; 12:e4532. [PMID: 36353712 PMCID: PMC9606446 DOI: 10.21769/bioprotoc.4532] [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: 06/30/2022] [Revised: 08/21/2022] [Accepted: 09/06/2022] [Indexed: 11/06/2022] Open
Abstract
The ribosome is a complex cellular machinery whose solved structure allowed for an incredible leap in structural biology research. Different ions bind to the ribosome, stabilizing inter-subunit interfaces and structurally linking rRNAs, proteins, and ligands. Besides cations such as K + and Mg 2+ , polyamines are known to stabilize the folding of RNA and overall structure. The bacterial ribosome is composed of a small (30S) subunit containing the decoding center and a large (50S) subunit devoted to peptide bond formation. We have previously shown that the small ribosomal subunit of Staphylococcus aureus is sensitive to changes in ionic conditions and polyamines concentration. In particular, its decoding center, where mRNA codons and tRNA anticodons interact, is prone to structural deformations in the absence of spermidine. Here, we report a detailed protocol for the purification of the intact and functional 30S, achieved through specific ionic conditions and the addition of spermidine. Using this protocol, we obtained the cryo-electron microscopy (cryo-EM) structure of the 30S-mRNA complex from S. aureus at 3.6 Å resolution. The 30S-mRNA complex formation was verified by a toeprinting assay. In this article, we also include a description of toeprinting and cryo-EM protocols. The described protocols can be further used to study the process of translation regulation. Graphical abstract.
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Affiliation(s)
- Margarita Belinite
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, Illkirch, France
,
Architecture et Réactivité de l’ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
,
Institut Européen de Chimie et Biologie (IECB), ARNA U1212, Université de Bordeaux, Pessac, France
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Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Iskander Khusainov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, Illkirch, France
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Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Stefano Marzi
- Architecture et Réactivité de l’ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
,
*For correspondence:
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7
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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] [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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8
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Abstract
Accurate protein synthesis (translation) relies on translation factors that rectify ribosome fluctuations into a unidirectional process. Understanding this process requires structural characterization of the ribosome and translation-factor dynamics. In the 2000s, crystallographic studies determined high-resolution structures of ribosomes stalled with translation factors, providing a starting point for visualizing translation. Recent progress in single-particle cryogenic electron microscopy (cryo-EM) has enabled near-atomic resolution of numerous structures sampled in heterogeneous complexes (ensembles). Ensemble and time-resolved cryo-EM have now revealed unprecedented views of ribosome transitions in the three principal stages of translation: initiation, elongation, and termination. This review focuses on how translation factors help achieve high accuracy and efficiency of translation by monitoring distinct ribosome conformations and by differentially shifting the equilibria of ribosome rearrangements for cognate and near-cognate substrates. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA;
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9
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Wang J, Arantes PR, Ahsan M, Sinha S, Kyro GW, Maschietto F, Allen B, Skeens E, Lisi GP, Batista VS, Palermo G. Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes. Front Mol Biosci 2022; 9:1072733. [PMID: 36699705 PMCID: PMC9868570 DOI: 10.3389/fmolb.2022.1072733] [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: 10/17/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
The CRISPR-associated protein 9 (Cas9) has been engineered as a precise gene editing tool to make double-strand breaks. CRISPR-associated protein 9 binds the folded guide RNA (gRNA) that serves as a binding scaffold to guide it to the target DNA duplex via a RecA-like strand-displacement mechanism but without ATP binding or hydrolysis. The target search begins with the protospacer adjacent motif or PAM-interacting domain, recognizing it at the major groove of the duplex and melting its downstream duplex where an RNA-DNA heteroduplex is formed at nanomolar affinity. The rate-limiting step is the formation of an R-loop structure where the HNH domain inserts between the target heteroduplex and the displaced non-target DNA strand. Once the R-loop structure is formed, the non-target strand is rapidly cleaved by RuvC and ejected from the active site. This event is immediately followed by cleavage of the target DNA strand by the HNH domain and product release. Within CRISPR-associated protein 9, the HNH domain is inserted into the RuvC domain near the RuvC active site via two linker loops that provide allosteric communication between the two active sites. Due to the high flexibility of these loops and active sites, biophysical techniques have been instrumental in characterizing the dynamics and mechanism of the CRISPR-associated protein 9 nucleases, aiding structural studies in the visualization of the complete active sites and relevant linker structures. Here, we review biochemical, structural, and biophysical studies on the underlying mechanism with emphasis on how CRISPR-associated protein 9 selects the target DNA duplex and rejects non-target sequences.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Pablo R Arantes
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Mohd Ahsan
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Souvik Sinha
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Gregory W Kyro
- Department of Chemistry, Yale University, New Haven, CT, United States
| | | | - Brandon Allen
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Erin Skeens
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - George P Lisi
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
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10
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Belinite M, Khusainov I, Soufari H, Marzi S, Romby P, Yusupov M, Hashem Y. Stabilization of Ribosomal RNA of the Small Subunit by Spermidine in Staphylococcus aureus. Front Mol Biosci 2021; 8:738752. [PMID: 34869582 PMCID: PMC8637172 DOI: 10.3389/fmolb.2021.738752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/07/2021] [Indexed: 11/21/2022] Open
Abstract
Cryo-electron microscopy is now used as a method of choice in structural biology for studying protein synthesis, a process mediated by the ribosome machinery. In order to achieve high-resolution structures using this approach, one needs to obtain homogeneous and stable samples, which requires optimization of ribosome purification in a species-dependent manner. This is especially critical for the bacterial small ribosomal subunit that tends to be unstable in the absence of ligands. Here, we report a protocol for purification of stable 30 S from the Gram-positive bacterium Staphylococcus aureus and its cryo-EM structures: in presence of spermidine at a resolution ranging between 3.4 and 3.6 Å and in its absence at 5.3 Å. Using biochemical characterization and cryo-EM, we demonstrate the importance of spermidine for stabilization of the 30 S via preserving favorable conformation of the helix 44.
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Affiliation(s)
- Margarita Belinite
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, Illkirch, France.,Architecture et Réactivité de l'ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France.,Institut Européen de Chimie et Biologie (IECB), ARNA U1212, Université de Bordeaux, Pessac, France
| | - Iskander Khusainov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, Illkirch, France.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Heddy Soufari
- Institut Européen de Chimie et Biologie (IECB), ARNA U1212, Université de Bordeaux, Pessac, France
| | - Stefano Marzi
- Architecture et Réactivité de l'ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Pascale Romby
- Architecture et Réactivité de l'ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Marat Yusupov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, Illkirch, France.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Yaser Hashem
- Architecture et Réactivité de l'ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France.,Institut Européen de Chimie et Biologie (IECB), ARNA U1212, Université de Bordeaux, Pessac, France
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11
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Stephan NC, Ries AB, Boehringer D, Ban N. Structural basis of successive adenosine modifications by the conserved ribosomal methyltransferase KsgA. Nucleic Acids Res 2021; 49:6389-6398. [PMID: 34086932 PMCID: PMC8216452 DOI: 10.1093/nar/gkab430] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/09/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
Biogenesis of ribosomal subunits involves enzymatic modifications of rRNA that fine-tune functionally important regions. The universally conserved prokaryotic dimethyltransferase KsgA sequentially modifies two universally conserved adenosine residues in helix 45 of the small ribosomal subunit rRNA, which is in proximity of the decoding site. Here we present the cryo-EM structure of Escherichia coli KsgA bound to an E. coli 30S at a resolution of 3.1 Å. The high-resolution structure reveals how KsgA recognizes immature rRNA and binds helix 45 in a conformation where one of the substrate nucleotides is flipped-out into the active site. We suggest that successive processing of two adjacent nucleotides involves base-flipping of the rRNA, which allows modification of the second substrate nucleotide without dissociation of the enzyme. Since KsgA is homologous to the essential eukaryotic methyltransferase Dim1 involved in 40S maturation, these results have also implications for understanding eukaryotic ribosome maturation.
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Affiliation(s)
- Niklas C Stephan
- Institute of Molecular Biology and Biophysics, ETH Zurich (Swiss Federal Institute of Technology), Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
| | - Anne B Ries
- Institute of Molecular Biology and Biophysics, ETH Zurich (Swiss Federal Institute of Technology), Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
| | - Daniel Boehringer
- Institute of Molecular Biology and Biophysics, ETH Zurich (Swiss Federal Institute of Technology), Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
| | - Nenad Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich (Swiss Federal Institute of Technology), Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
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12
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Assembly factors chaperone ribosomal RNA folding by isolating helical junctions that are prone to misfolding. Proc Natl Acad Sci U S A 2021; 118:2101164118. [PMID: 34135123 DOI: 10.1073/pnas.2101164118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
While RNAs are known to misfold, the underlying molecular causes have been mainly studied in fragments of biologically relevant larger RNAs. As these small RNAs are dominated by secondary structures, misfolding of these secondary structures remains the most-explored cause for global RNA misfolding. Conversely, how RNA chaperones function in a biological context to promote native folding beyond duplex annealing remains unknown. Here, in a combination of dimethylsulfate mutational profiling with sequencing (DMS-MaPseq), structural analyses, biochemical experiments, and yeast genetics, we show that three-helix junctions are prone to misfolding during assembly of the small ribosomal subunit in vivo. We identify ubiquitous roles for ribosome assembly factors in chaperoning their folding by preventing the formation of premature tertiary interactions, which otherwise kinetically trap misfolded junctions, thereby blocking further progress in the assembly cascade. While these protein chaperones act indirectly by binding the interaction partners of junctions, our analyses also suggest direct roles for small nucleolar RNAs (snoRNAs) in binding and chaperoning helical junctions during transcription. While these assembly factors do not utilize energy to ameliorate misfolding, our data demonstrate how their dissociation renders reversible folding steps irreversible, thereby driving native folding and assembly and setting up a timer that dictates the propensity of misfolded intermediates to escape quality control. Finally, the data demonstrate that RNA chaperones act locally on individual tertiary interactions, in contrast to protein chaperones, which globally unfold misfolded proteins.
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13
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Maksimova EM, Korepanov AP, Kravchenko OV, Baymukhametov TN, Myasnikov AG, Vassilenko KS, Afonina ZA, Stolboushkina EA. RbfA Is Involved in Two Important Stages of 30S Subunit Assembly: Formation of the Central Pseudoknot and Docking of Helix 44 to the Decoding Center. Int J Mol Sci 2021; 22:ijms22116140. [PMID: 34200244 PMCID: PMC8201178 DOI: 10.3390/ijms22116140] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 11/16/2022] Open
Abstract
Ribosome biogenesis is a highly coordinated and complex process that requires numerous assembly factors that ensure prompt and flawless maturation of ribosomal subunits. Despite the increasing amount of data collected, the exact role of most assembly factors and mechanistic details of their operation remain unclear, mainly due to the shortage of high-resolution structural information. Here, using cryo-electron microscopy, we characterized 30S ribosomal particles isolated from an Escherichia coli strain with a deleted gene for the RbfA factor. The cryo-EM maps for pre-30S subunits were divided into six classes corresponding to consecutive assembly intermediates: from the particles with a completely unresolved head domain and unfolded central pseudoknot to almost mature 30S subunits with well-resolved body, platform, and head domains and partially distorted helix 44. The structures of two predominant 30S intermediates belonging to most populated classes obtained at 2.7 Å resolutions indicate that RbfA acts at two distinctive 30S assembly stages: early formation of the central pseudoknot including folding of the head, and positioning of helix 44 in the decoding center at a later stage. Additionally, it was shown that the formation of the central pseudoknot may promote stabilization of the head domain, likely through the RbfA-dependent maturation of the neck helix 28. An update to the model of factor-dependent 30S maturation is proposed, suggesting that RfbA is involved in most of the subunit assembly process.
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Affiliation(s)
- Elena M. Maksimova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.M.); (A.P.K.); (O.V.K.); (Z.A.A.)
| | - Alexey P. Korepanov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.M.); (A.P.K.); (O.V.K.); (Z.A.A.)
| | - Olesya V. Kravchenko
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.M.); (A.P.K.); (O.V.K.); (Z.A.A.)
| | - Timur N. Baymukhametov
- National Research Center, “Kurchatov Institute”, Akademika Kurchatova pl. 1, 123182 Moscow, Russia;
| | - Alexander G. Myasnikov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC “Kurchatov Institute”, 188300 Gatchina, Russia;
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Konstantin S. Vassilenko
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.M.); (A.P.K.); (O.V.K.); (Z.A.A.)
- Correspondence: (K.S.V.); (E.A.S.); Tel.: +7-903-6276710 (K.S.V.); +7-915-4791359 (E.A.S.)
| | - Zhanna A. Afonina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.M.); (A.P.K.); (O.V.K.); (Z.A.A.)
| | - Elena A. Stolboushkina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.M.); (A.P.K.); (O.V.K.); (Z.A.A.)
- Correspondence: (K.S.V.); (E.A.S.); Tel.: +7-903-6276710 (K.S.V.); +7-915-4791359 (E.A.S.)
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14
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Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, López-Alonso JP, Lavin JL, Kaminishi T, Çapuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR. A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit. SCIENCE ADVANCES 2021; 7:7/23/eabf7547. [PMID: 34088665 PMCID: PMC8177701 DOI: 10.1126/sciadv.abf7547] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/20/2021] [Indexed: 05/03/2023]
Abstract
While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high-resolution structural information is still missing. To address this, we used single-particle cryo-electron microscopy to visualize the effects of bacterial ribosome assembly factors RimP, RbfA, RsmA, and RsgA on the conformational landscape of the 30S ribosomal subunit and obtained eight snapshots representing late steps in the folding of the decoding center. Analysis of these structures identifies a conserved secondary structure switch in the 16S ribosomal RNA central to decoding site maturation and suggests both a sequential order of action and molecular mechanisms for the assembly factors in coordinating and controlling this switch. Structural and mechanistic parallels between bacterial and eukaryotic systems indicate common folding features inherent to all ribosomes.
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Affiliation(s)
- Andreas Schedlbauer
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Idoia Iturrioz
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Borja Ochoa-Lizarralde
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Tammo Diercks
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Jorge Pedro López-Alonso
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | | | - Tatsuya Kaminishi
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
- Department of Genetics, Graduate School of Medicine, Osaka University, Japan
| | - Retina Çapuni
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Neha Dhimole
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Elisa de Astigarraga
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - David Gil-Carton
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Paola Fucini
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Sean R Connell
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
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15
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Abstract
CryoEM has become the method of choice for determining the structure of large macromolecular complexes in multiple conformations, at resolutions where unambiguous atomic models can be built. Two effects that have limited progress in single-particle cryoEM are (i) beam-induced movement during image acquisition and (ii) protein adsorption and denaturation at the air-water interface during specimen preparation. While beam-induced movement now appears to have been resolved by all-gold specimen support grids with very small holes, surface effects at the air-water interface are a persistent problem. Strategies to overcome these effects include the use of alternative support films and new techniques for specimen deposition. We examine the future potential of recording perfect images of biological samples for routine structure determination at atomic resolution.
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16
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Kaur S, Gomez-Blanco J, Khalifa AAZ, Adinarayanan S, Sanchez-Garcia R, Wrapp D, McLellan JS, Bui KH, Vargas J. Local computational methods to improve the interpretability and analysis of cryo-EM maps. Nat Commun 2021; 12:1240. [PMID: 33623015 PMCID: PMC7902670 DOI: 10.1038/s41467-021-21509-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 01/29/2021] [Indexed: 12/13/2022] Open
Abstract
Cryo-electron microscopy (cryo-EM) maps usually show heterogeneous distributions of B-factors and electron density occupancies and are typically B-factor sharpened to improve their contrast and interpretability at high-resolutions. However, 'over-sharpening' due to the application of a single global B-factor can distort processed maps causing connected densities to appear broken and disconnected. This issue limits the interpretability of cryo-EM maps, i.e. ab initio modelling. In this work, we propose 1) approaches to enhance high-resolution features of cryo-EM maps, while preventing map distortions and 2) methods to obtain local B-factors and electron density occupancy maps. These algorithms have as common link the use of the spiral phase transformation and are called LocSpiral, LocBSharpen, LocBFactor and LocOccupancy. Our results, which include improved maps of recent SARS-CoV-2 structures, show that our methods can improve the interpretability and analysis of obtained reconstructions.
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Affiliation(s)
- Satinder Kaur
- Departament of Anatomy and Cell Biology, McGill University 3640 Rue University, Montréal, QC, Canada
| | - Josue Gomez-Blanco
- Departament of Anatomy and Cell Biology, McGill University 3640 Rue University, Montréal, QC, Canada
| | - Ahmad A Z Khalifa
- Departament of Anatomy and Cell Biology, McGill University 3640 Rue University, Montréal, QC, Canada
| | - Swathi Adinarayanan
- Departament of Anatomy and Cell Biology, McGill University 3640 Rue University, Montréal, QC, Canada
| | - Ruben Sanchez-Garcia
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC C/Darwin 3, Cantoblanco, Madrid, Spain
| | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Khanh Huy Bui
- Departament of Anatomy and Cell Biology, McGill University 3640 Rue University, Montréal, QC, Canada
| | - Javier Vargas
- Departmento de Óptica, Universidad Complutense de Madrid, Madrid, Spain.
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17
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Jha V, Roy B, Jahagirdar D, McNutt ZA, Shatoff EA, Boleratz BL, Watkins DE, Bundschuh R, Basu K, Ortega J, Fredrick K. Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome. Nucleic Acids Res 2021; 49:547-567. [PMID: 33330920 PMCID: PMC7797042 DOI: 10.1093/nar/gkaa1195] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 11/25/2022] Open
Abstract
Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the Bacteroidetes, fail to recognize the SD sequence of mRNA in vitro. A cryo-electron microscopy structure of the complete 70S ribosome from F. johnsoniae at 2.8 Å resolution reveals that the ASD is sequestered by ribosomal proteins bS21, bS18 and bS6, explaining the basis of ASD inhibition. The structure also uncovers a novel ribosomal protein—bL38. Remarkably, in F. johnsoniae and many other Flavobacteriia, the gene encoding bS21 contains a strong SD, unlike virtually all other genes. A subset of Flavobacteriia have an alternative ASD, and in these organisms the fully complementary sequence lies upstream of the bS21 gene, indicative of natural covariation. In other Bacteroidetes classes, strong SDs are frequently found upstream of the genes for bS21 and/or bS18. We propose that these SDs are used as regulatory elements, enabling bS21 and bS18 to translationally control their own production.
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Affiliation(s)
- Vikash Jha
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada.,Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Bappaditya Roy
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Dushyant Jahagirdar
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada.,Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Zakkary A McNutt
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Elan A Shatoff
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Bethany L Boleratz
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Dean E Watkins
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Department of Physics, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry & Biochemistry, Division of Hematology, The Ohio State University, Columbus, OH 43210, USA
| | - Kaustuv Basu
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada.,Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Joaquin Ortega
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada.,Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Kurt Fredrick
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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18
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Klebl DP, Gravett MSC, Kontziampasis D, Wright DJ, Bon RS, Monteiro DCF, Trebbin M, Sobott F, White HD, Darrow MC, Thompson RF, Muench SP. Need for Speed: Examining Protein Behavior during CryoEM Grid Preparation at Different Timescales. Structure 2020; 28:1238-1248.e4. [PMID: 32814033 PMCID: PMC7652391 DOI: 10.1016/j.str.2020.07.018] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/15/2020] [Accepted: 07/29/2020] [Indexed: 12/18/2022]
Abstract
A host of new technologies are under development to improve the quality and reproducibility of cryoelectron microscopy (cryoEM) grid preparation. Here we have systematically investigated the preparation of three macromolecular complexes using three different vitrification devices (Vitrobot, chameleon, and a time-resolved cryoEM device) on various timescales, including grids made within 6 ms (the fastest reported to date), to interrogate particle behavior at the air-water interface for different timepoints. Results demonstrate that different macromolecular complexes can respond to the thin-film environment formed during cryoEM sample preparation in highly variable ways, shedding light on why cryoEM sample preparation can be difficult to optimize. We demonstrate that reducing time between sample application and vitrification is just one tool to improve cryoEM grid quality, but that it is unlikely to be a generic "silver bullet" for improving the quality of every cryoEM sample preparation.
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Affiliation(s)
- David P Klebl
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Molly S C Gravett
- School of Molecular and Cellular Biology, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Dimitrios Kontziampasis
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Chemical and Process Engineering, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds LS2 9JT, UK; Institute of Business, Industry & Leadership, University of Cumbria, Carlisle CA1 2HH, UK
| | - David J Wright
- School of Medicine, Faculty of Medicine and Health & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - Robin S Bon
- School of Medicine, Faculty of Medicine and Health & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | | | - Martin Trebbin
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA; Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - Frank Sobott
- School of Molecular and Cellular Biology, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; Department of Chemistry, Biomolecular & Analytical Mass Spectrometry Group, University of Antwerp, Antwerp, Belgium
| | - Howard D White
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA, USA
| | | | - Rebecca F Thompson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
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