1
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Seffouh A, Nikolay R, Ortega J. Critical steps in the assembly process of the bacterial 50S ribosomal subunit. Nucleic Acids Res 2024; 52:4111-4123. [PMID: 38554105 PMCID: PMC11077053 DOI: 10.1093/nar/gkae199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 03/02/2024] [Accepted: 03/07/2024] [Indexed: 04/01/2024] Open
Abstract
During assembly, ribosomal particles in bacteria fold according to energy landscapes comprised of multiple parallel pathways. Cryo-electron microscopy studies have identified a critical maturation step that occurs during the late assembly stages of the 50S subunit in Bacillus subtilis. This step acts as a point of convergency for all the parallel assembly pathways of the subunit, where an assembly intermediate accumulates in a 'locked' state, causing maturation to pause. Assembly factors then act on this critical step to 'unlock' the last maturation steps involving the functional sites. Without these factors, the 50S subunit fails to complete its assembly, causing cells to die due to a lack of functional ribosomes to synthesize proteins. In this review, we analyze these findings in B. subtilis and examine other cryo-EM studies that have visualized assembly intermediates in different bacterial species, to determine if convergency points in the ribosome assembly process are a common theme among bacteria. There are still gaps in our knowledge, as these methodologies have not yet been applied to diverse species. However, identifying and characterizing these convergency points can reveal how different bacterial species implement unique mechanisms to regulate critical steps in the ribosome assembly process.
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Affiliation(s)
- Amal Seffouh
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
- Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Rainer Nikolay
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - 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
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2
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Gruffaz C, Smirnov A. GTPase Era at the heart of ribosome assembly. Front Mol Biosci 2023; 10:1263433. [PMID: 37860580 PMCID: PMC10582724 DOI: 10.3389/fmolb.2023.1263433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Ribosome biogenesis is a key process in all organisms. It relies on coordinated work of multiple proteins and RNAs, including an array of assembly factors. Among them, the GTPase Era stands out as an especially deeply conserved protein, critically required for the assembly of bacterial-type ribosomes from Escherichia coli to humans. In this review, we bring together and critically analyze a wealth of phylogenetic, biochemical, structural, genetic and physiological data about this extensively studied but still insufficiently understood factor. We do so using a comparative and, wherever possible, synthetic approach, by confronting observations from diverse groups of bacteria and eukaryotic organelles (mitochondria and chloroplasts). The emerging consensus posits that Era intervenes relatively early in the small subunit biogenesis and is essential for the proper shaping of the platform which, in its turn, is a prerequisite for efficient translation. The timing of Era action on the ribosome is defined by its interactions with guanosine nucleotides [GTP, GDP, (p)ppGpp], ribosomal RNA, and likely other factors that trigger or delay its GTPase activity. As a critical nexus of the small subunit biogenesis, Era is subject to sophisticated regulatory mechanisms at the transcriptional, post-transcriptional, and post-translational levels. Failure of these mechanisms or a deficiency in Era function entail dramatic generalized consequences for the protein synthesis and far-reaching, pleiotropic effects on the organism physiology, such as the Perrault syndrome in humans.
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Affiliation(s)
- Christelle Gruffaz
- UMR7156- Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, Centre National de la Recherche Scientifique (CNRS), Strasbourg, France
| | - Alexandre Smirnov
- UMR7156- Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, Centre National de la Recherche Scientifique (CNRS), Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France
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3
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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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4
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Alobaidallah MSA, García V, De Mets R, Wellner SM, Thomsen LE, Herrero-Fresno A, Olsen JE. Uncovering the Important Genetic Factors for Growth during Cefotaxime-Gentamicin Combination Treatment in blaCTX-M-1 Encoding Escherichia coli. Antibiotics (Basel) 2023; 12:993. [PMID: 37370312 DOI: 10.3390/antibiotics12060993] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Due to the rapid spread of CTX-M type ESBLs, the rate of resistance to third-generation cephalosporin has increased among Gram-negative bacteria, especially in Escherichia coli, and there is a need to find ways to re-sensitize ESBL E. coli to cephalosporin treatment. A previous study showed that genes involved in protein synthesis were significantly up-regulated in the presence of subinhibitory concentration of cefotaxime (CTX) in a CTX-M-1-producing E. coli. In this study, the interaction between CTX and gentamicin (GEN), targeting protein synthesis, was evaluated in MG1655/pTF2, and the MIC of CTX was strongly reduced (128-fold) in the presence of this combnation therapy. Since the underlying mechanism behind this synergy is not known, we constructed a saturated transposon mutant library in MG1655/pTF2::blaCTX-M-1 containing 315,925 unique transposon insertions to measure mutant depletion upon exposure to CTX, GEN, and combination treatment of CTX and GEN by Transposon Directed Insertion-site Sequencing (TraDIS). We identified 57 genes that were depleted (log2FC ≤ -2 and with q.value ≤ 0.01) during exposure to CTX, 18 for GEN, and 31 for combination treatment of CTX and GEN. For validation, we deleted eight genes that were either uniquely identified in combination treatment, overlapped with monotherapy of GEN, or were shared between combination treatment and monotherapy with CTX and GEN. Of these genes, we found that the inactivation of dnaK, mnmA, rsgA, and ybeD increased the efficacy of both CTX and GEN treatment, the inactivation of cpxR and yafN increased the efficacy of only CTX, and the inactivation of mnmA, rsgA, and ybeD resulted in increased synergy between CTX and GEN. Thus, the study points to putative targets for helper drugs that can restore susceptibility to these important drugs, and it indicates that genes involved in protein synthesis are essential for the synergy between these two drugs. In summary, the study identified mutants that sensitize ESBL-producing E. coli to CTX and a combination of CTX and GEN, and it increased our understanding of the mechanism behind synergy between β-lactam and aminoglycoside drugs. This forms a framework for developing new strategies to combat infections caused by resistant bacteria.
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Affiliation(s)
- Mosaed Saleh A Alobaidallah
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Jeddah 21423, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah 22384, Saudi Arabia
| | - Vanesa García
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), 27002 Lugo, Spain
| | - Richard De Mets
- Department of Biomedical Sciences, Core Facility for Integrated Microscopy, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Sandra M Wellner
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Line E Thomsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
- National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
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5
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Gor K, Duss O. Emerging Quantitative Biochemical, Structural, and Biophysical Methods for Studying Ribosome and Protein-RNA Complex Assembly. Biomolecules 2023; 13:biom13050866. [PMID: 37238735 DOI: 10.3390/biom13050866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Ribosome assembly is one of the most fundamental processes of gene expression and has served as a playground for investigating the molecular mechanisms of how protein-RNA complexes (RNPs) assemble. A bacterial ribosome is composed of around 50 ribosomal proteins, several of which are co-transcriptionally assembled on a ~4500-nucleotide-long pre-rRNA transcript that is further processed and modified during transcription, the entire process taking around 2 min in vivo and being assisted by dozens of assembly factors. How this complex molecular process works so efficiently to produce an active ribosome has been investigated over decades, resulting in the development of a plethora of novel approaches that can also be used to study the assembly of other RNPs in prokaryotes and eukaryotes. Here, we review biochemical, structural, and biophysical methods that have been developed and integrated to provide a detailed and quantitative understanding of the complex and intricate molecular process of bacterial ribosome assembly. We also discuss emerging, cutting-edge approaches that could be used in the future to study how transcription, rRNA processing, cellular factors, and the native cellular environment shape ribosome assembly and RNP assembly at large.
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Affiliation(s)
- Kavan Gor
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, 69117 Heidelberg, Germany
| | - Olivier Duss
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
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6
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Giudice E, Georgeault S, Lavigne R, Pineau C, Trautwetter A, Ermel G, Blanco C, Gillet R. Purification and Characterization of Authentic 30S Ribosomal Precursors Induced by Heat Shock. Int J Mol Sci 2023; 24:ijms24043491. [PMID: 36834906 PMCID: PMC9959188 DOI: 10.3390/ijms24043491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Ribosome biogenesis is a complex and multistep process that depends on various assembly factors. To understand this process and identify the ribosome assembly intermediates, most studies have set out to delete or deplete these assembly factors. Instead, we took advantage of the impact of heat stress (45 °C) on the late stages of the biogenesis of the 30S ribosomal subunit to explore authentic precursors. Under these conditions, reduced levels of the DnaK chaperone proteins devoted to ribosome assembly lead to the transient accumulation of 21S ribosomal particles, which are 30S precursors. We constructed strains with different affinity tags on one early and one late 30S ribosomal protein and purified the 21S particles that form under heat shock. A combination of relative quantification using mass spectrometry-based proteomics and cryo-electron microscopy (cryo-EM) was then used to determine their protein contents and structures.
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Affiliation(s)
- Emmanuel Giudice
- Univ Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, 35000 Rennes, France
| | - Sylvie Georgeault
- Univ Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, 35000 Rennes, France
| | - Régis Lavigne
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)-UMR_S 1085, 35000 Rennes, France
- Univ Rennes, CNRS, Inserm, Biosit UAR 3480 US_S 018, Protim Core Facility, 35000 Rennes, France
| | - Charles Pineau
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)-UMR_S 1085, 35000 Rennes, France
- Univ Rennes, CNRS, Inserm, Biosit UAR 3480 US_S 018, Protim Core Facility, 35000 Rennes, France
| | - Annie Trautwetter
- Univ Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, 35000 Rennes, France
| | - Gwennola Ermel
- Univ Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, 35000 Rennes, France
| | - Carlos Blanco
- Univ Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, 35000 Rennes, France
| | - Reynald Gillet
- Univ Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, 35000 Rennes, France
- Correspondence:
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7
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Cao X, Du X, Jiao H, An Q, Chen R, Fang P, Wang J, Yu B. Carbohydrate-based drugs launched during 2000 -2021. Acta Pharm Sin B 2022; 12:3783-3821. [PMID: 36213536 PMCID: PMC9532563 DOI: 10.1016/j.apsb.2022.05.020] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/18/2022] [Accepted: 05/12/2022] [Indexed: 01/09/2023] Open
Abstract
Carbohydrates are fundamental molecules involved in nearly all aspects of lives, such as being involved in formating the genetic and energy materials, supporting the structure of organisms, constituting invasion and host defense systems, and forming antibiotics secondary metabolites. The naturally occurring carbohydrates and their derivatives have been extensively studied as therapeutic agents for the treatment of various diseases. During 2000 to 2021, totally 54 carbohydrate-based drugs which contain carbohydrate moities as the major structural units have been approved as drugs or diagnostic agents. Here we provide a comprehensive review on the chemical structures, activities, and clinical trial results of these carbohydrate-based drugs, which are categorized by their indications into antiviral drugs, antibacterial/antiparasitic drugs, anticancer drugs, antidiabetics drugs, cardiovascular drugs, nervous system drugs, and other agents.
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Affiliation(s)
- Xin Cao
- Zhongshan Hospital Institute of Clinical Science, Fudan University Shanghai Medical College, Shanghai 200032, China
| | - Xiaojing Du
- Zhongshan Hospital Institute of Clinical Science, Fudan University Shanghai Medical College, Shanghai 200032, China
| | - Heng Jiao
- Zhongshan Hospital Institute of Clinical Science, Fudan University Shanghai Medical College, Shanghai 200032, China
| | - Quanlin An
- Zhongshan Hospital Institute of Clinical Science, Fudan University Shanghai Medical College, Shanghai 200032, China
| | - Ruoxue Chen
- Zhongshan Hospital Institute of Clinical Science, Fudan University Shanghai Medical College, Shanghai 200032, China
| | - Pengfei Fang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jing Wang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Biao Yu
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
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8
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Rabuck-Gibbons JN, Lyumkis D, Williamson JR. Quantitative mining of compositional heterogeneity in cryo-EM datasets of ribosome assembly intermediates. Structure 2022; 30:498-509.e4. [PMID: 34990602 PMCID: PMC9891661 DOI: 10.1016/j.str.2021.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/02/2021] [Accepted: 12/09/2021] [Indexed: 02/03/2023]
Abstract
Single-particle cryoelectron microscopy (cryo-EM) offers a unique opportunity to characterize macromolecular structural heterogeneity by virtue of its ability to place distinct particle populations into different groups through computational classification. However, there is a dearth of tools for surveying the heterogeneity landscape, quantitatively analyzing heterogeneous particle populations after classification, deciding how many unique classes are represented by the data, and accurately cross-comparing reconstructions. Here, we develop a workflow that contains discovery and analysis modules to quantitatively mine cryo-EM data for sets of structures with maximal diversity. This workflow was applied to a dataset of E. coli 50S ribosome assembly intermediates, which are characterized by significant structural heterogeneity. We identified more detailed branchpoints in the assembly process and characterized the interactions of an assembly factor with immature intermediates. While the tools described here were developed for ribosome assembly, they should be broadly applicable to the analysis of other heterogeneous cryo-EM datasets.
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Affiliation(s)
- Jessica N Rabuck-Gibbons
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dmitry Lyumkis
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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9
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Maksimova E, Kravchenko O, Korepanov A, Stolboushkina E. Protein Assistants of Small Ribosomal Subunit Biogenesis in Bacteria. Microorganisms 2022; 10:microorganisms10040747. [PMID: 35456798 PMCID: PMC9032327 DOI: 10.3390/microorganisms10040747] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/16/2022] [Accepted: 03/26/2022] [Indexed: 01/27/2023] Open
Abstract
Ribosome biogenesis is a fundamental and multistage process. The basic steps of ribosome assembly are the transcription, processing, folding, and modification of rRNA; the translation, folding, and modification of r-proteins; and consecutive binding of ribosomal proteins to rRNAs. Ribosome maturation is facilitated by biogenesis factors that include a broad spectrum of proteins: GTPases, RNA helicases, endonucleases, modification enzymes, molecular chaperones, etc. The ribosome assembly factors assist proper rRNA folding and protein–RNA interactions and may sense the checkpoints during the assembly to ensure correct order of this process. Inactivation of these factors is accompanied by severe growth phenotypes and accumulation of immature ribosomal subunits containing unprocessed rRNA, which reduces overall translation efficiency and causes translational errors. In this review, we focus on the structural and biochemical analysis of the 30S ribosomal subunit assembly factors RbfA, YjeQ (RsgA), Era, KsgA (RsmA), RimJ, RimM, RimP, and Hfq, which take part in the decoding-center folding.
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Affiliation(s)
| | | | - Alexey Korepanov
- Correspondence: (A.K.); (E.S.); Tel.: +7-925-7180670 (A.K.); +7-915-4791359 (E.S.)
| | - Elena Stolboushkina
- Correspondence: (A.K.); (E.S.); Tel.: +7-925-7180670 (A.K.); +7-915-4791359 (E.S.)
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10
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YbeY, éminence grise of ribosome biogenesis. Biochem Soc Trans 2021; 49:727-745. [PMID: 33929506 DOI: 10.1042/bst20200669] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/30/2022]
Abstract
YbeY is an ultraconserved small protein belonging to the unique heritage shared by most existing bacteria and eukaryotic organelles of bacterial origin, mitochondria and chloroplasts. Studied in more than a dozen of evolutionarily distant species, YbeY is invariably critical for cellular physiology. However, the exact mechanisms by which it exerts such penetrating influence are not completely understood. In this review, we attempt a transversal analysis of the current knowledge about YbeY, based on genetic, structural, and biochemical data from a wide variety of models. We propose that YbeY, in association with the ribosomal protein uS11 and the assembly GTPase Era, plays a critical role in the biogenesis of the small ribosomal subunit, and more specifically its platform region, in diverse genetic systems of bacterial type.
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11
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Jahagirdar D, Jha V, Basu K, Gomez-Blanco J, Vargas J, Ortega J. Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo-electron microscopy. RNA (NEW YORK, N.Y.) 2020; 26:2017-2030. [PMID: 32989043 PMCID: PMC7668263 DOI: 10.1261/rna.075846.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/22/2020] [Indexed: 05/06/2023]
Abstract
It is only after recent advances in cryo-electron microscopy that it is now possible to describe at high-resolution structures of large macromolecules that do not crystalize. Purified 30S subunits interconvert between an "active" and "inactive" conformation. The active conformation was described by crystallography in the early 2000s, but the structure of the inactive form at high resolution remains unsolved. Here we used cryo-electron microscopy to obtain the structure of the inactive conformation of the 30S subunit to 3.6 Å resolution and study its motions. In the inactive conformation, an alternative base-pairing of three nucleotides causes the region of helix 44, forming the decoding center to adopt an unlatched conformation and the 3' end of the 16S rRNA positions similarly to the mRNA during translation. Incubation of inactive 30S subunits at 42°C reverts these structural changes. The air-water interface to which ribosome subunits are exposed during sample preparation also peel off some ribosomal proteins. Extended exposures to low magnesium concentrations make the ribosomal particles more susceptible to the air-water interface causing the unfolding of large rRNA structural domains. Overall, this study provides new insights about the conformational space explored by the 30S ribosomal subunit when the ribosomal particles are free in solution.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - Josue Gomez-Blanco
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
- Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Javier Vargas
- 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
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12
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Razi A, Davis JH, Hao Y, Jahagirdar D, Thurlow B, Basu K, Jain N, Gomez-Blanco J, Britton RA, Vargas J, Guarné A, Woodson SA, Williamson JR, Ortega J. Role of Era in assembly and homeostasis of the ribosomal small subunit. Nucleic Acids Res 2019; 47:8301-8317. [PMID: 31265110 PMCID: PMC6736133 DOI: 10.1093/nar/gkz571] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/11/2019] [Accepted: 06/27/2019] [Indexed: 01/23/2023] Open
Abstract
Assembly factors provide speed and directionality to the maturation process of the 30S subunit in bacteria. To gain a more precise understanding of how these proteins mediate 30S maturation, it is important to expand on studies of 30S assembly intermediates purified from bacterial strains lacking particular maturation factors. To reveal the role of the essential protein Era in the assembly of the 30S ribosomal subunit, we analyzed assembly intermediates that accumulated in Era-depleted Escherichia coli cells using quantitative mass spectrometry, high resolution cryo-electron microscopy and in-cell footprinting. Our combined approach allowed for visualization of the small subunit as it assembled and revealed that with the exception of key helices in the platform domain, all other 16S rRNA domains fold even in the absence of Era. Notably, the maturing particles did not stall while waiting for the platform domain to mature and instead re-routed their folding pathway to enable concerted maturation of other structural motifs spanning multiple rRNA domains. We also found that binding of Era to the mature 30S subunit destabilized helix 44 and the decoding center preventing binding of YjeQ, another assembly factor. This work establishes Era’s role in ribosome assembly and suggests new roles in maintaining ribosome homeostasis.
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Affiliation(s)
- Aida Razi
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Joseph H Davis
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yumeng Hao
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Dushyant Jahagirdar
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Brett Thurlow
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S4K1, Canada
| | - Kaustuv Basu
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Nikhil Jain
- Department of Molecular Virology and Microbiology, Baylor College of Medicine,Houston, TX 77030, USA.,Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA
| | - Josue Gomez-Blanco
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Robert A Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine,Houston, TX 77030, USA.,Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA
| | - Javier Vargas
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Alba Guarné
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1 Canada
| | - Sarah A Woodson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - James R Williamson
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joaquin Ortega
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
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13
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Bennison DJ, Irving SE, Corrigan RM. The Impact of the Stringent Response on TRAFAC GTPases and Prokaryotic Ribosome Assembly. Cells 2019; 8:cells8111313. [PMID: 31653044 PMCID: PMC6912228 DOI: 10.3390/cells8111313] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/17/2019] [Accepted: 10/23/2019] [Indexed: 12/24/2022] Open
Abstract
Many facets of ribosome biogenesis and function, including ribosomal RNA (rRNA) transcription, 70S assembly and protein translation, are negatively impacted upon induction of a nutrient stress-sensing signalling pathway termed the stringent response. This stress response is mediated by the alarmones guanosine tetra- and penta-phosphate ((p)ppGpp), the accumulation of which leads to a massive cellular response that slows growth and aids survival. The 70S bacterial ribosome is an intricate structure, with assembly both complex and highly modular. Presiding over the assembly process is a group of P-loop GTPases within the TRAFAC (Translation Factor Association) superclass that are crucial for correct positioning of both early and late stage ribosomal proteins (r-proteins) onto the rRNA. Often described as 'molecular switches', members of this GTPase superfamily readily bind and hydrolyse GTP to GDP in a cyclic manner that alters the propensity of the GTPase to carry out a function. TRAFAC GTPases are considered to act as checkpoints to ribosome assembly, involved in binding to immature sections in the GTP-bound state, preventing further r-protein association until maturation is complete. Here we review our current understanding of the impact of the stringent response and (p)ppGpp production on ribosome maturation in prokaryotic cells, focusing on the inhibition of (p)ppGpp on GTPase-mediated subunit assembly, but also touching upon the inhibition of rRNA transcription and protein translation.
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Affiliation(s)
- Daniel J Bennison
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
| | - Sophie E Irving
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
| | - Rebecca M Corrigan
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
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14
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Malhotra S, Träger S, Dal Peraro M, Topf M. Modelling structures in cryo-EM maps. Curr Opin Struct Biol 2019; 58:105-114. [PMID: 31394387 DOI: 10.1016/j.sbi.2019.05.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/23/2019] [Accepted: 05/25/2019] [Indexed: 12/20/2022]
Abstract
Recent advances in structure determination of sub-cellular structures using cryo-electron microscopy and tomography have enabled us to understand their architecture in a more detailed manner and gain insight into their function. The choice of approach to use for atomic model building, fitting, refinement and validation in the 3D map resulting from these experiments depends primarily on the resolution of the map and the prior information on the corresponding model. Here, we survey some of such methods and approaches and highlight their uses in specific recent examples.
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Affiliation(s)
- Sony Malhotra
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom
| | - Sylvain Träger
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Maya Topf
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom.
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15
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Hobbs JK, Boraston AB. (p)ppGpp and the Stringent Response: An Emerging Threat to Antibiotic Therapy. ACS Infect Dis 2019; 5:1505-1517. [PMID: 31287287 DOI: 10.1021/acsinfecdis.9b00204] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In 1969, Cashel and Gallant first observed the presence of (p)ppGpp-the signaling molecule of the stringent response-in starved bacterial cells. Fifty years later, (p)ppGpp and the stringent response have emerged as essential master regulators of not only the bacterial response to stress but also almost all aspects of bacterial physiology, virulence, and immune evasion. More worryingly, a wealth of data now indicate that (p)ppGpp and stringent response activation pose a serious threat to the efficacy and clinical success of antimicrobial therapy. Here, we focus on the central role that (p)ppGpp and the stringent response play in the phenomenon of antibiotic tolerance, as well as the acquisition, development, and expression of antibiotic resistance. We review these consequences of stringent response activation in relation to the main proteins involved in (p)ppGpp production and control, in particular the complex interplay between monofunctional and bifunctional long RelA/SpoT homologues (RSHs) and small alarmone synthetases (SASs). We also review the growing evidence to suggest that there are multiple other indirect pathways of stringent response induction that can affect antibiotic efficacy. Finally, we summarize recent studies that indicate the in vivo and clinical impact of (p)ppGpp production on antibiotic treatment outcomes. We conclude by reviewing the progress to date in the search for novel therapeutics that target the stringent response.
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Affiliation(s)
- Joanne K. Hobbs
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
| | - Alisdair B. Boraston
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
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16
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Janowski M, Zoschke R, Scharff LB, Martinez Jaime S, Ferrari C, Proost S, Ng Wei Xiong J, Omranian N, Musialak-Lange M, Nikoloski Z, Graf A, Schöttler MA, Sampathkumar A, Vaid N, Mutwil M. AtRsgA from Arabidopsis thaliana is important for maturation of the small subunit of the chloroplast ribosome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:404-420. [PMID: 30044525 DOI: 10.1111/tpj.14040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 07/12/2018] [Accepted: 07/17/2018] [Indexed: 05/24/2023]
Abstract
Plastid ribosomes are very similar in structure and function to the ribosomes of their bacterial ancestors. Since ribosome biogenesis is not thermodynamically favorable under biological conditions it requires the activity of many assembly factors. Here we have characterized a homolog of bacterial RsgA in Arabidopsis thaliana and show that it can complement the bacterial homolog. Functional characterization of a strong mutant in Arabidopsis revealed that the protein is essential for plant viability, while a weak mutant produced dwarf, chlorotic plants that incorporated immature pre-16S ribosomal RNA into translating ribosomes. Physiological analysis of the mutant plants revealed smaller, but more numerous, chloroplasts in the mesophyll cells, reduction of chlorophyll a and b, depletion of proplastids from the rib meristem and decreased photosynthetic electron transport rate and efficiency. Comparative RNA sequencing and proteomic analysis of the weak mutant and wild-type plants revealed that various biotic stress-related, transcriptional regulation and post-transcriptional modification pathways were repressed in the mutant. Intriguingly, while nuclear- and chloroplast-encoded photosynthesis-related proteins were less abundant in the mutant, the corresponding transcripts were increased, suggesting an elaborate compensatory mechanism, potentially via differentially active retrograde signaling pathways. To conclude, this study reveals a chloroplast ribosome assembly factor and outlines the transcriptomic and proteomic responses of the compensatory mechanism activated during decreased chloroplast function.
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Affiliation(s)
- Marcin Janowski
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Lars B Scharff
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Silvia Martinez Jaime
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Camilla Ferrari
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Sebastian Proost
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Jonathan Ng Wei Xiong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Nooshin Omranian
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | | | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl- Liebknecht-Strasse 24-25, 14476, Potsdam-Golm, Germany
| | - Alexander Graf
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Mark A Schöttler
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Neha Vaid
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Marek Mutwil
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
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17
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Davis JH, Williamson JR. Structure and dynamics of bacterial ribosome biogenesis. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0181. [PMID: 28138067 DOI: 10.1098/rstb.2016.0181] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 01/28/2023] Open
Abstract
Bacterial ribosome biogenesis has been an active area of research for more than 30 years and has served as a test-bed for the development of new biochemical, biophysical and structural techniques to understand macromolecular assembly generally. Recent work inspecting the process in vivo has advanced our understanding of the role of ribosome biogenesis factors, the co-transcriptional nature of assembly, the kinetics of the process under sub-optimal conditions, and the rRNA folding and ribosome protein binding pathways. Additionally, new structural work enabled by single-particle electron microscopy has helped to connect in vitro ribosomal protein binding maps to the underlying RNA. This review summarizes the state of these in vivo studies, provides a kinetic model for ribosome assembly under sub-optimal conditions, and describes a framework to compare newly emerging assembly intermediate structures.This article is part of the themed issue 'Perspectives on the ribosome'.
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Affiliation(s)
- Joseph H Davis
- Department of Integrative Structural and Computational Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA .,Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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18
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López-Alonso JP, Kaminishi T, Kikuchi T, Hirata Y, Iturrioz I, Dhimole N, Schedlbauer A, Hase Y, Goto S, Kurita D, Muto A, Zhou S, Naoe C, Mills DJ, Gil-Carton D, Takemoto C, Himeno H, Fucini P, Connell SR. RsgA couples the maturation state of the 30S ribosomal decoding center to activation of its GTPase pocket. Nucleic Acids Res 2017; 45:6945-6959. [PMID: 28482099 PMCID: PMC5499641 DOI: 10.1093/nar/gkx324] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 04/19/2017] [Indexed: 01/18/2023] Open
Abstract
During 30S ribosomal subunit biogenesis, assembly factors are believed to prevent accumulation of misfolded intermediate states of low free energy that slowly convert into mature 30S subunits, namely, kinetically trapped particles. Among the assembly factors, the circularly permuted GTPase, RsgA, plays a crucial role in the maturation of the 30S decoding center. Here, directed hydroxyl radical probing and single particle cryo-EM are employed to elucidate RsgA΄s mechanism of action. Our results show that RsgA destabilizes the 30S structure, including late binding r-proteins, providing a structural basis for avoiding kinetically trapped assembly intermediates. Moreover, RsgA exploits its distinct GTPase pocket and specific interactions with the 30S to coordinate GTPase activation with the maturation state of the 30S subunit. This coordination validates the architecture of the decoding center and facilitates the timely release of RsgA to control the progression of 30S biogenesis.
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Affiliation(s)
- Jorge Pedro López-Alonso
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Tatsuya Kaminishi
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Takeshi Kikuchi
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Yuya Hirata
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Idoia Iturrioz
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Neha Dhimole
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Andreas Schedlbauer
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Yoichi Hase
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Simon Goto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Akira Muto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Shu Zhou
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Chieko Naoe
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Deryck J Mills
- Max Planck Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - David Gil-Carton
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Chie Takemoto
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Hyouta Himeno
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Paola Fucini
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Sean R Connell
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
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19
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Razi A, Britton RA, Ortega J. The impact of recent improvements in cryo-electron microscopy technology on the understanding of bacterial ribosome assembly. Nucleic Acids Res 2017; 45:1027-1040. [PMID: 28180306 PMCID: PMC5388408 DOI: 10.1093/nar/gkw1231] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/20/2016] [Accepted: 11/25/2016] [Indexed: 01/14/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) had played a central role in the study of ribosome structure and the process of translation in bacteria since the development of this technique in the mid 1980s. Until recently cryo-EM structures were limited to ∼10 Å in the best cases. However, the recent advent of direct electron detectors has greatly improved the resolution of cryo-EM structures to the point where atomic resolution is now achievable. This improved resolution will allow cryo-EM to make groundbreaking contributions in essential aspects of ribosome biology, including the assembly process. In this review, we summarize important insights that cryo-EM, in combination with chemical and genetic approaches, has already brought to our current understanding of the ribosomal assembly process in bacteria using previous detector technology. More importantly, we discuss how the higher resolution structures now attainable with direct electron detectors can be leveraged to propose precise testable models regarding this process. These structures will provide an effective platform to develop new antibiotics that target this fundamental cellular process.
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Affiliation(s)
- Aida Razi
- Department of Biochemistry and Biomedical Sciences and M. G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada
| | - Robert A Britton
- Department of Molecular Virology and Microbiology and Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences and M. G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada
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20
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The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly. Proc Natl Acad Sci U S A 2017; 114:E3396-E3403. [PMID: 28396444 DOI: 10.1073/pnas.1618016114] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent work suggests that bacterial YjeQ (RsgA) participates in the late stages of assembly of the 30S subunit and aids the assembly of the decoding center but also binds the mature 30S subunit with high affinity. To determine the function and mechanisms of YjeQ in the context of the mature subunit, we determined the cryo-EM structure of the fully assembled 30S subunit in complex with YjeQ at 5.8-Å resolution. We found that binding of YjeQ stabilizes helix 44 into a conformation similar to that adopted by the subunit during proofreading. This finding indicates that, along with acting as an assembly factor, YjeQ has a role as a checkpoint protein, consisting of testing the proofreading ability of the 30S subunit. The structure also informs the mechanism by which YjeQ implements the release from the 30S subunit of a second assembly factor, called RbfA. Finally, it reveals how the 30S subunit stimulates YjeQ GTPase activity and leads to release of the protein. Checkpoint functions have been described for eukaryotic ribosome assembly factors; however, this work describes an example of a bacterial assembly factor that tests a specific translation mechanism of the 30S subunit.
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21
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Conserved GTPase LepA (Elongation Factor 4) functions in biogenesis of the 30S subunit of the 70S ribosome. Proc Natl Acad Sci U S A 2017; 114:980-985. [PMID: 28096346 DOI: 10.1073/pnas.1613665114] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The physiological role of LepA, a paralog of EF-G found in all bacteria, has been a mystery for decades. Here, we show that LepA functions in ribosome biogenesis. In cells lacking LepA, immature 30S particles accumulate. Four proteins are specifically underrepresented in these particles-S3, S10, S14, and S21-all of which bind late in the assembly process and contribute to the folding of the 3' domain of 16S rRNA. Processing of 16S rRNA is also delayed in the mutant strain, as indicated by increased levels of precursor 17S rRNA in assembly intermediates. Mutation ΔlepA confers a synthetic growth phenotype in absence of RsgA, another GTPase, well known to act in 30S subunit assembly. Analysis of the ΔrsgA strain reveals accumulation of intermediates that resemble those seen in the absence of LepA. These data suggest that RsgA and LepA play partially redundant roles to ensure efficient 30S assembly.
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22
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Ni X, Davis JH, Jain N, Razi A, Benlekbir S, McArthur AG, Rubinstein JL, Britton RA, Williamson JR, Ortega J. YphC and YsxC GTPases assist the maturation of the central protuberance, GTPase associated region and functional core of the 50S ribosomal subunit. Nucleic Acids Res 2016; 44:8442-55. [PMID: 27484475 PMCID: PMC5041480 DOI: 10.1093/nar/gkw678] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/21/2016] [Indexed: 11/12/2022] Open
Abstract
YphC and YsxC are GTPases in Bacillus subtilis that facilitate the assembly of the 50S ribosomal subunit, however their roles in this process are still uncharacterized. To explore their function, we used strains in which the only copy of the yphC or ysxC genes were under the control of an inducible promoter. Under depletion conditions, they accumulated incomplete ribosomal subunits that we named 45SYphC and 44.5SYsxC particles. Quantitative mass spectrometry analysis and the 5–6 Å resolution cryo-EM maps of the 45SYphC and 44.5SYsxC particles revealed that the two GTPases participate in the maturation of the central protuberance, GTPase associated region and key RNA helices in the A, P and E functional sites of the 50S subunit. We observed that YphC and YsxC bind specifically to the two immature particles, suggesting that they represent either on-pathway intermediates or that their structure has not significantly diverged from that of the actual substrate. These results describe the nature of these immature particles, a widely used tool to study the assembly process of the ribosome. They also provide the first insights into the function of YphC and YsxC in 50S subunit assembly and are consistent with this process occurring through multiple parallel pathways, as it has been described for the 30S subunit.
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Affiliation(s)
- Xiaodan Ni
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S4K1, Canada M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario L8S4K1, Canada
| | - Joseph H Davis
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nikhil Jain
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA
| | - Aida Razi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S4K1, Canada M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario L8S4K1, Canada
| | - Samir Benlekbir
- Molecular Structure and Function Program, The Hospital for Sick Children,Toronto, Ontario M5G 0A4, Canada
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S4K1, Canada M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario L8S4K1, Canada
| | - John L Rubinstein
- Molecular Structure and Function Program, The Hospital for Sick Children,Toronto, Ontario M5G 0A4, Canada Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Robert A Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Williamson
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S4K1, Canada M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario L8S4K1, Canada
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23
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Sharma H, Anand B. Fluorescence bimolecular complementation enables facile detection of ribosome assembly defects in Escherichia coli. RNA Biol 2016; 13:872-82. [PMID: 27388791 DOI: 10.1080/15476286.2016.1207037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Assembly factors promote the otherwise non-spontaneous maturation of ribosome under physiological conditions inside the cell. Systematic identification and characterization of candidate assembly factors are fraught with bottlenecks due to lack of facile assay system to capture assembly defects. Here, we show that bimolecular fluorescence complementation (BiFC) allows detection of assembly defects that are induced by the loss of assembly factors. The fusion of N and C-terminal fragments of Venus fluorescent protein to the ribosomal proteins uS13 and uL5, respectively, in Escherichia coli facilitated the incorporation of the tagged uS13 and uL5 onto the respective ribosomal subunits. When the ribosomal subunits associated to form the 70S particle, the complementary fragments of Venus were brought into proximity and rendered the Venus fluorescent. Assembly defects that inhibit the subunits association were provoked by either the loss of the known assembly factors such as RsgA and SrmB or the presence of small molecule inhibitors of ribosome maturation such as Lamotrigine and several ribosome-targeting antibiotics and these showed abrogation of the fluorescence complementation. This suggests that BiFC can be employed as a surrogate measure to detect ribosome assembly defects proficiently by circumventing the otherwise cumbersome procedures. BiFC thus offers a facile platform not only for systematic screening to validate potential assembly factors but also to discover novel small molecule inhibitors of ribosome assembly toward mapping the complex assembly landscape of ribosome.
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Affiliation(s)
- Himanshu Sharma
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Assam , India
| | - Baskaran Anand
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Assam , India
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24
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Thurlow B, Davis JH, Leong V, Moraes TF, Williamson JR, Ortega J. Binding properties of YjeQ (RsgA), RbfA, RimM and Era to assembly intermediates of the 30S subunit. Nucleic Acids Res 2016; 44:9918-9932. [PMID: 27382067 PMCID: PMC5175332 DOI: 10.1093/nar/gkw613] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 06/26/2016] [Accepted: 06/27/2016] [Indexed: 11/13/2022] Open
Abstract
Our understanding regarding the function of YjeQ (also called RsgA), RbfA, RimM and Era in ribosome biogenesis has been derived in part from the study of immature 30S particles that accumulate in null strains lacking one of these factors. However, their mechanistic details are still unknown. Here, we demonstrate that these immature particles are not dead-end products of assembly, but progress into mature 30S subunits. Mass spectrometry analysis revealed that in vivo the occupancy level of these factors in these immature 30S particles is below 10% and that the concentration of factors does not increase when immature particles accumulate in cells. We measured by microscale thermophoresis that YjeQ and Era binds to the mature 30S subunit with high affinity. However, the binding affinity of these factors to the immature particles and of RimM and RbfA to mature or immature particles was weak, suggesting that binding is not occurring at physiological concentrations. These results suggest that in the absence of these factors, the immature particles evolve into a thermodynamically stable intermediate that exhibits low affinity for the assembly factors. These results imply that the true substrates of YjeQ, RbfA, RimM and Era are immature particles that precede the ribosomal particles accumulating in the knockouts strains.
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Affiliation(s)
- Brett Thurlow
- Department of Biochemistry and Biomedical Sciences and M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada
| | - Joseph H Davis
- Department of Integrative Computational and Structural Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Vivian Leong
- Department of Biochemistry and Biomedical Sciences and M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S1A8, Canada
| | - James R Williamson
- Department of Integrative Computational and Structural Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences and M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada
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ppGpp negatively impacts ribosome assembly affecting growth and antimicrobial tolerance in Gram-positive bacteria. Proc Natl Acad Sci U S A 2016; 113:E1710-9. [PMID: 26951678 DOI: 10.1073/pnas.1522179113] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The stringent response is a survival mechanism used by bacteria to deal with stress. It is coordinated by the nucleotides guanosine tetraphosphate and pentaphosphate [(p)ppGpp], which interact with target proteins to promote bacterial survival. Although this response has been well characterized in proteobacteria, very little is known about the effectors of this signaling system in Gram-positive species. Here, we report on the identification of seven target proteins for the stringent response nucleotides in the Gram-positive bacterium Staphylococcus aureus We demonstrate that the GTP synthesis enzymes HprT and Gmk bind with a high affinity, leading to an inhibition of GTP production. In addition, we identified five putative GTPases--RsgA, RbgA, Era, HflX, and ObgE--as (p)ppGpp target proteins. We show that RsgA, RbgA, Era, and HflX are functional GTPases and that their activity is promoted in the presence of ribosomes but strongly inhibited by the stringent response nucleotides. By characterizing the function of RsgA in vivo, we ascertain that this protein is involved in ribosome assembly, with an rsgA deletion strain, or a strain inactivated for GTPase activity, displaying decreased growth, a decrease in the amount of mature 70S ribosomes, and an increased level of tolerance to antimicrobials. We additionally demonstrate that the interaction of ppGpp with cellular GTPases is not unique to the staphylococci, as homologs from Bacillus subtilis and Enterococcus faecalis retain this ability. Taken together, this study reveals ribosome inactivation as a previously unidentified mechanism through which the stringent response functions in Gram-positive bacteria.
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Jeganathan A, Razi A, Thurlow B, Ortega J. The C-terminal helix in the YjeQ zinc-finger domain catalyzes the release of RbfA during 30S ribosome subunit assembly. RNA (NEW YORK, N.Y.) 2015; 21:1203-1216. [PMID: 25904134 PMCID: PMC4436671 DOI: 10.1261/rna.049171.114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 03/22/2015] [Indexed: 06/04/2023]
Abstract
YjeQ (also called RsgA) and RbfA proteins in Escherichia coli bind to immature 30S ribosome subunits at late stages of assembly to assist folding of the decoding center. A key step for the subunit to enter the pool of actively translating ribosomes is the release of these factors. YjeQ promotes dissociation of RbfA during the final stages of maturation; however, the mechanism implementing this functional interplay has not been elucidated. YjeQ features an amino-terminal oligonucleotide/oligosaccharide binding domain, a central GTPase module and a carboxy-terminal zinc-finger domain. We found that the zinc-finger domain is comprised of two functional motifs: the region coordinating the zinc ion and a carboxy-terminal α-helix. The first motif is essential for the anchoring of YjeQ to the 30S subunit and the carboxy-terminal α-helix facilitates the removal of RbfA once the 30S subunit reaches the mature state. Furthermore, the ability of the mature 30S subunit to stimulate YjeQ GTPase activity also depends on the carboxy-terminal α-helix. Our data are consistent with a model in which YjeQ uses this carboxy-terminal α-helix as a sensor to gauge the conformation of helix 44, an essential motif of the decoding center. According to this model, the mature conformation of helix 44 is sensed by the carboxy-terminal α-helix, which in turn stimulates the YjeQ GTPase activity. Hydrolysis of GTP is believed to assist the release of YjeQ from the mature 30S subunit through a still uncharacterized mechanism. These results identify the structural determinants in YjeQ that implement the functional interplay with RbfA.
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Affiliation(s)
- Ajitha Jeganathan
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Aida Razi
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Brett Thurlow
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada L8S 4K1
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Naganathan A, Wood MP, Moore SD. The large ribosomal subunit protein L9 enables the growth of EF-P deficient cells and enhances small subunit maturation. PLoS One 2015; 10:e0120060. [PMID: 25879934 PMCID: PMC4399890 DOI: 10.1371/journal.pone.0120060] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/03/2015] [Indexed: 01/08/2023] Open
Abstract
The loss of the large ribosomal protein L9 causes a reduction in translation fidelity by an unknown mechanism. To identify pathways affected by L9, we identified mutants of E. coli that require L9 for fitness. In a prior study, we characterized L9-dependent mutations in the essential GTPase Der (EngA). Here, we describe a second class of L9-dependent mutations that either compromise or inactivate elongation factor P (EF-P, eIF5A in eukaryotes). Without L9, Δefp cells are practically inviable. Cell fractionation studies revealed that, in both the Der and EF-P mutant cases, L9's activity reduces immature 16S rRNA in 30S particles and partially restores the abundance of monosomes. Inspired by these findings, we discovered that L9 also enhances 16S maturation in wild-type cells. Surprisingly, although the amount of immature 16S in 30S particles was found to be elevated in ΔrplI cells, the amount in polysomes was low and inversely correlated with the immature 16S abundance. These findings provide an explanation for the observed fitness increases afforded by L9 in these mutants and reveal particular physiological conditions in which L9 becomes critical. Additionally, L9 may affect the partitioning of small subunits containing immature 16S rRNA.
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Affiliation(s)
- Anusha Naganathan
- The Burnett School of Biomedical Sciences, College of Medicine, The University of Central Florida, Orlando, FL, 32816, United States of America
| | - Matthew P. Wood
- Seattle Biomed, 307 Westlake Ave N, Suite 500, Seattle, WA, 98109, United States of America
- Department of Global Health, University of Washington, 1510 N.E. San Juan Road, Seattle, WA, 98195, United States of America
| | - Sean D. Moore
- The Burnett School of Biomedical Sciences, College of Medicine, The University of Central Florida, Orlando, FL, 32816, United States of America
- * E-mail:
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28
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In-cell SHAPE reveals that free 30S ribosome subunits are in the inactive state. Proc Natl Acad Sci U S A 2015; 112:2425-30. [PMID: 25675474 DOI: 10.1073/pnas.1411514112] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
It was shown decades ago that purified 30S ribosome subunits readily interconvert between "active" and "inactive" conformations in a switch that involves changes in the functionally important neck and decoding regions. However, the physiological significance of this conformational change had remained unknown. In exponentially growing Escherichia coli cells, RNA SHAPE probing revealed that 16S rRNA largely adopts the inactive conformation in stably assembled, mature 30S subunits and the active conformation in translating (70S) ribosomes. Inactive 30S subunits bind mRNA as efficiently as active subunits but initiate translation more slowly. Mutations that inhibited interconversion between states compromised translation in vivo. Binding by the small antibiotic paromomycin induced the inactive-to-active conversion, consistent with a low-energy barrier between the two states. Despite the small energetic barrier between states, but consistent with slow translation initiation and a functional role in vivo, interconversion involved large-scale changes in structure in the neck region that likely propagate across the 30S body via helix 44. These findings suggest the inactive state is a biologically relevant alternate conformation that regulates ribosome function as a conformational switch.
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Investigating Bacterial Protein Synthesis Using Systems Biology Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 883:21-40. [PMID: 26621460 DOI: 10.1007/978-3-319-23603-2_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Protein synthesis is essential for bacterial growth and survival. Its study in Escherichia coli helped uncover features conserved among bacteria as well as universally. The pattern of discovery and the identification of some of the longest-known components of the protein synthesis machinery, including the ribosome itself, tRNAs, and translation factors proceeded through many stages of successively more refined biochemical purifications, finally culminating in the isolation to homogeneity, identification, and mapping of the smallest unit required for performing the given function. These early studies produced a wealth of information. However, many unknowns remained. Systems biology approaches provide an opportunity to investigate protein synthesis from a global perspective, overcoming the limitations of earlier ad hoc methods to gain unprecedented insights. This chapter reviews innovative systems biology approaches, with an emphasis on those designed specifically for investigating the protein synthesis machinery in E. coli.
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Sashital DG, Greeman CA, Lyumkis D, Potter CS, Carragher B, Williamson JR. A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli. eLife 2014; 3. [PMID: 25313868 PMCID: PMC4371863 DOI: 10.7554/elife.04491] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 10/13/2014] [Indexed: 12/13/2022] Open
Abstract
Ribosome assembly is a complex process involving the folding and processing of ribosomal RNAs (rRNAs), concomitant binding of ribosomal proteins (r-proteins), and participation of numerous accessory cofactors. Here, we use a quantitative mass spectrometry/electron microscopy hybrid approach to determine the r-protein composition and conformation of 30S ribosome assembly intermediates in Escherichia coli. The relative timing of assembly of the 3' domain and the formation of the central pseudoknot (PK) structure depends on the presence of the assembly factor RimP. The central PK is unstable in the absence of RimP, resulting in the accumulation of intermediates in which the 3'-domain is unanchored and the 5'-domain is depleted for r-proteins S5 and S12 that contact the central PK. Our results reveal the importance of the cofactor RimP in central PK formation, and introduce a broadly applicable method for characterizing macromolecular assembly in cells.
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Affiliation(s)
- Dipali G Sashital
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
| | - Candacia A Greeman
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
| | - Dmitry Lyumkis
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
| | - Clinton S Potter
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
| | - Bridget Carragher
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
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Stokes JM, Davis JH, Mangat CS, Williamson JR, Brown ED. Discovery of a small molecule that inhibits bacterial ribosome biogenesis. eLife 2014; 3:e03574. [PMID: 25233066 PMCID: PMC4371806 DOI: 10.7554/elife.03574] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 09/17/2014] [Indexed: 11/29/2022] Open
Abstract
While small molecule inhibitors of the bacterial ribosome have been instrumental in
understanding protein translation, no such probes exist to study ribosome biogenesis.
We screened a diverse chemical collection that included previously approved drugs for
compounds that induced cold sensitive growth inhibition in the model bacterium
Escherichia coli. Among the most cold sensitive was lamotrigine,
an anticonvulsant drug. Lamotrigine treatment resulted in the rapid accumulation of
immature 30S and 50S ribosomal subunits at 15°C. Importantly, this was not the result
of translation inhibition, as lamotrigine was incapable of perturbing protein
synthesis in vivo or in vitro. Spontaneous suppressor mutations blocking lamotrigine
activity mapped solely to the poorly characterized domain II of translation
initiation factor IF2 and prevented the binding of lamotrigine to IF2 in vitro. This
work establishes lamotrigine as a widely available chemical probe of bacterial
ribosome biogenesis and suggests a role for E. coli IF2 in ribosome
assembly. DOI:http://dx.doi.org/10.7554/eLife.03574.001 Inside cells, molecular machines called ribosomes make proteins from instructions
that are provided by genes. The ribosomes themselves are made up of about 50 proteins
and three RNA molecules that need to be assembled like a 3-D jigsaw. In bacteria, a
group of proteins called ribosome biogenesis factors help to assemble these pieces
correctly. To study how a biological process works, scientists often look at what happens when a
component is missing or not working properly. However, this approach cannot be used
to study how ribosomes are made because stopping protein production entirely will
kill the cell. Another approach is to use chemicals to temporarily stop or slow down
a biological process, but researchers are yet to find a chemical that can do this for
ribosome assembly. To address this problem, Stokes et al. ‘screened’ 30,000 chemicals in an effort to
find one or more that could affect ribosome assembly in bacteria. The screen revealed
that a drug called lamotrigine—which is used to treat epilepsy and other conditions
in humans—could stop the assembly of ribosomes, but did not affect the production of
proteins by completed ribosomes. The experiments also suggest that initiation factor 2, a protein that is involved in
the production of other proteins, may also have a role in ribosome assembly. Another
recent study found that the equivalent of initiation factor 2 in yeast acts as a
quality control checkpoint during ribosome assembly, so the bacterial version may
also perform a similar role. It is also be possible that lamotrigine might be used to help develop a novel
mechanistic class of antibiotics. DOI:http://dx.doi.org/10.7554/eLife.03574.002
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Affiliation(s)
- Jonathan M Stokes
- Michael G DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Joseph H Davis
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
| | - Chand S Mangat
- Michael G DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
| | - Eric D Brown
- Michael G DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
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32
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Gupta N, Culver GM. Multiple in vivo pathways for Escherichia coli small ribosomal subunit assembly occur on one pre-rRNA. Nat Struct Mol Biol 2014; 21:937-43. [PMID: 25195050 PMCID: PMC4355579 DOI: 10.1038/nsmb.2887] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/07/2014] [Indexed: 01/01/2023]
Abstract
Processing of transcribed precursor ribosomal RNA (pre-rRNA) to a mature state is a conserved aspect of ribosome biogenesis in vivo. We developed an affinity-purification system to isolate and analyze in vivo-formed pre-rRNA-containing ribonucleoprotein (RNP) particles (rRNPs) from wild-type E. coli. We observed that the first processing intermediate of pre-small subunit (pre-SSU) rRNA is a platform for biogenesis. These pre-SSU-containing RNPs have differing ribosomal-protein and auxiliary factor association and rRNA folding. Each RNP lacks the proper architecture in functional regions, thus suggesting that checkpoints preclude immature subunits from entering the translational cycle. This work offers in vivo snapshots of SSU biogenesis and reveals that multiple pathways exist for the entire SSU biogenesis process in wild-type E. coli. These findings have implications for understanding SSU biogenesis in vivo and offer a general strategy for analysis of RNP biogenesis.
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Affiliation(s)
- Neha Gupta
- Department of Biology, University of Rochester, Rochester, New York, USA
| | - Gloria M Culver
- 1] Department of Biology, University of Rochester, Rochester, New York, USA. [2] Center for RNA Biology, University of Rochester, Rochester, New York, USA
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Initial bridges between two ribosomal subunits are formed within 9.4 milliseconds, as studied by time-resolved cryo-EM. Proc Natl Acad Sci U S A 2014; 111:9822-7. [PMID: 24958863 DOI: 10.1073/pnas.1406744111] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Association of the two ribosomal subunits during the process of translation initiation is a crucial step of protein synthesis. The two subunits (30S and 50S) of the bacterial 70S ribosome are held together by 12 dynamic bridges involving RNA-RNA, RNA-protein, and protein-protein interactions. The process of bridge formation, such as whether all these bridges are formed simultaneously or in a sequential order, is poorly understood. To understand such processes, we have developed and implemented a class of microfluidic devices that mix two components to completion within 0.4 ms and spray the mixture in the form of microdroplets onto an electron microscopy grid, yielding a minimum reaction time of 9.4 ms before cryofixation. Using these devices, we have obtained cryo-EM data corresponding to reaction times of 9.4 and 43 ms and have determined 3D structures of ribosomal subunit association intermediates. Molecular analyses of the cryo-EM maps reveal that eight intersubunit bridges (bridges B1a, B1b, B2a, B2b, B3, B7a, B7b, and B8) form within 9.4 ms, whereas the remaining four bridges (bridges B2c, B4, B5, and B6) take longer than 43 ms to form, suggesting that bridges are formed in a stepwise fashion. Our approach can be used to characterize sequences of various dynamic functional events on complex macromolecular assemblies such as ribosomes.
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McGinnis JL, Weeks KM. Ribosome RNA assembly intermediates visualized in living cells. Biochemistry 2014; 53:3237-47. [PMID: 24818530 DOI: 10.1021/bi500198b] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In cells, RNAs likely adopt numerous intermediate conformations prior to formation of functional RNA-protein complexes. We used single-nucleotide resolution selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) to probe the structure of Escherichia coli 16S rRNA in healthy growing bacteria. SHAPE-directed modeling indicated that the predominant steady-state RNA conformational ensemble in dividing cells had a base-paired structure different from that expected on the basis of comparative sequence analysis and high-resolution studies of the 30S ribosomal subunit. We identified the major cause of these differences by stopping ongoing in-cell transcription (in essence, an in-cell RNA structure pulse-chase experiment) which caused the RNA to chase into a structure that closely resembled the expected one. Most helices that formed alternate RNA conformations under growth conditions interact directly with tertiary-binding ribosomal proteins and form a C-shape that surrounds the mRNA channel and decoding site. These in-cell experiments lead to a model in which ribosome assembly factors function as molecular struts to preorganize this intermediate and emphasize that the final stages of ribonucleoprotein assembly involve extensive protein-facilitated RNA conformational changes.
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Affiliation(s)
- Jennifer L McGinnis
- Department of Chemistry, University of North Carolina , Chapel Hill, North Carolina 27599-3290, United States
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35
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Yang Z, Guo Q, Goto S, Chen Y, Li N, Yan K, Zhang Y, Muto A, Deng H, Himeno H, Lei J, Gao N. Structural insights into the assembly of the 30S ribosomal subunit in vivo: functional role of S5 and location of the 17S rRNA precursor sequence. Protein Cell 2014; 5:394-407. [PMID: 24671761 PMCID: PMC3996153 DOI: 10.1007/s13238-014-0044-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 02/26/2014] [Indexed: 12/20/2022] Open
Abstract
The in vivo assembly of ribosomal subunits is a highly complex process, with a tight coordination between protein assembly and rRNA maturation events, such as folding and processing of rRNA precursors, as well as modifications of selected bases. In the cell, a large number of factors are required to ensure the efficiency and fidelity of subunit production. Here we characterize the immature 30S subunits accumulated in a factor-null Escherichia coli strain (∆rsgA∆rbfA). The immature 30S subunits isolated with varying salt concentrations in the buffer system show interesting differences on both protein composition and structure. Specifically, intermediates derived under the two contrasting salt conditions (high and low) likely reflect two distinctive assembly stages, the relatively early and late stages of the 3' domain assembly, respectively. Detailed structural analysis demonstrates a mechanistic coupling between the maturation of the 5' end of the 17S rRNA and the assembly of the 30S head domain, and attributes a unique role of S5 in coordinating these two events. Furthermore, our structural results likely reveal the location of the unprocessed terminal sequences of the 17S rRNA, and suggest that the maturation events of the 17S rRNA could be employed as quality control mechanisms on subunit production and protein translation.
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Affiliation(s)
- Zhixiu Yang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
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36
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Babu M, Arnold R, Bundalovic-Torma C, Gagarinova A, Wong KS, Kumar A, Stewart G, Samanfar B, Aoki H, Wagih O, Vlasblom J, Phanse S, Lad K, Yeou Hsiung Yu A, Graham C, Jin K, Brown E, Golshani A, Kim P, Moreno-Hagelsieb G, Greenblatt J, Houry WA, Parkinson J, Emili A. Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli. PLoS Genet 2014; 10:e1004120. [PMID: 24586182 PMCID: PMC3930520 DOI: 10.1371/journal.pgen.1004120] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 12/03/2013] [Indexed: 02/02/2023] Open
Abstract
Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI) screens can provide insights into the biological role(s) of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems. Genome-wide genetic interaction (GI) screens have been performed in yeast, but no analogous large-scale studies have yet been reported for bacteria. Here, we have used E. coli synthetic genetic array (eSGA) technology developed by our group to quantitatively map GIs to reveal epistatic dependencies and functional cross-talk among ∼600,000 digenic mutant combinations. By combining this epistasis information with functional modules derived by our group's earlier efforts from proteomic and genomic context (GC)-based methods, we identify several unexpected pathway-level dependencies, functional links between protein complexes, and biological roles of uncharacterized bacterial gene products. As part of the study, two of our pathway predictions from GI screens were validated experimentally, where we confirmed the role of these new components in iron-sulphur biogenesis and ribosome integrity. We also extrapolated the epistatic connectivity diagram of E. coli to 233 distantly related γ-proteobacterial species lacking GI information, and identified co-conserved genes and functional modules important for bacterial pathogenesis. Overall, this study describes the first genome-scale map of GIs in gram-negative bacterium, and through integrative analysis with previously derived protein-protein and GC-based interaction networks presents a number of novel insights into the architecture of bacterial pathways that could not have been discerned through either network alone.
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Affiliation(s)
- Mohan Babu
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
- * E-mail: (MB); (AE)
| | - Roland Arnold
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Cedoljub Bundalovic-Torma
- Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Alla Gagarinova
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Keith S. Wong
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Ashwani Kumar
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | - Geordie Stewart
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Bahram Samanfar
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Hiroyuki Aoki
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | - Omar Wagih
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - James Vlasblom
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | - Sadhna Phanse
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | - Krunal Lad
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | | | - Christopher Graham
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | - Ke Jin
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | - Eric Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Ashkan Golshani
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Philip Kim
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | | | - Jack Greenblatt
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - John Parkinson
- Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Emili
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (MB); (AE)
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37
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Jomaa A, Jain N, Davis JH, Williamson JR, Britton RA, Ortega J. Functional domains of the 50S subunit mature late in the assembly process. Nucleic Acids Res 2013; 42:3419-35. [PMID: 24335279 PMCID: PMC3950693 DOI: 10.1093/nar/gkt1295] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Despite the identification of many factors that facilitate ribosome assembly, the molecular mechanisms by which they drive ribosome biogenesis are poorly understood. Here, we analyze the late stages of assembly of the 50S subunit using Bacillus subtilis cells depleted of RbgA, a highly conserved GTPase. We found that RbgA-depleted cells accumulate late assembly intermediates bearing sub-stoichiometric quantities of ribosomal proteins L16, L27, L28, L33a, L35 and L36. Using a novel pulse labeling/quantitative mass spectrometry technique, we show that this particle is physiologically relevant and is capable of maturing into a complete 50S particle. Cryo-electron microscopy and chemical probing revealed that the central protuberance, the GTPase associating region and tRNA-binding sites in this intermediate are unstructured. These findings demonstrate that key functional sites of the 50S subunit remain unstructured until late stages of maturation, preventing the incomplete subunit from prematurely engaging in translation. Finally, structural and biochemical analysis of a ribosome particle depleted of L16 indicate that L16 binding is necessary for the stimulation of RbgA GTPase activity and, in turn, release of this co-factor, and for conversion of the intermediate to a complete 50S subunit.
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Affiliation(s)
- Ahmad Jomaa
- Department of Biochemistry and Biomedical Sciences and MG. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA and Department of Integrative Structural and Computational Biology, Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nikhil Jain
- Department of Biochemistry and Biomedical Sciences and MG. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA and Department of Integrative Structural and Computational Biology, Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joseph H. Davis
- Department of Biochemistry and Biomedical Sciences and MG. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA and Department of Integrative Structural and Computational Biology, Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James R. Williamson
- Department of Biochemistry and Biomedical Sciences and MG. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA and Department of Integrative Structural and Computational Biology, Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert A. Britton
- Department of Biochemistry and Biomedical Sciences and MG. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA and Department of Integrative Structural and Computational Biology, Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Correspondence may also be addressed to Robert A. Britton. Tel: +1 517 884 5395;
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences and MG. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA and Department of Integrative Structural and Computational Biology, Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- *To whom correspondence should be addressed. Tel: +1 905 525 9140 (ext. 22703); Fax: +1 905 522 9033;
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38
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Clatterbuck Soper SF, Dator RP, Limbach PA, Woodson SA. In vivo X-ray footprinting of pre-30S ribosomes reveals chaperone-dependent remodeling of late assembly intermediates. Mol Cell 2013; 52:506-16. [PMID: 24207057 DOI: 10.1016/j.molcel.2013.09.020] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 08/20/2013] [Accepted: 09/19/2013] [Indexed: 12/27/2022]
Abstract
Assembly of 30S ribosomal subunits from their protein and RNA components requires extensive refolding of the 16S rRNA and is assisted by 10-20 assembly factors in bacteria. We probed the structures of 30S assembly intermediates in E. coli cells, using a synchrotron X-ray beam to generate hydroxyl radical in the cytoplasm. Widespread differences between mature and pre-30S complexes in the absence of assembly factors RbfA and RimM revealed global reorganization of RNA-protein interactions prior to maturation of the 16S rRNA and showed how RimM reduces misfolding of the 16S 3' domain during transcription in vivo. Quantitative (14)N/(15)N mass spectrometry of affinity-purified pre-30S complexes confirmed the absence of tertiary assembly proteins and showed that N-terminal acetylation of proteins S18 and S5 correlates with correct folding of the platform and central pseudoknot. Our results indicate that cellular factors delay specific RNA folding steps to ensure the quality of assembly.
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Affiliation(s)
- Sarah F Clatterbuck Soper
- Cell, Molecular, and Developmental Biology and Biophysics Program, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218-2685, USA
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39
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Leong V, Kent M, Jomaa A, Ortega J. Escherichia coli rimM and yjeQ null strains accumulate immature 30S subunits of similar structure and protein complement. RNA (NEW YORK, N.Y.) 2013; 19:789-802. [PMID: 23611982 PMCID: PMC3683913 DOI: 10.1261/rna.037523.112] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Assembly of the Escherichia coli 30S ribosomal subunits proceeds through multiple parallel pathways. The protein factors RimM, YjeQ, RbfA, and Era work in conjunction to assist at the late stages of the maturation process of the small subunit. However, it is unclear how the functional interplay between these factors occurs in the context of multiple parallel pathways. To understand how these factors work together, we have characterized the immature 30S subunits that accumulate in ΔrimM cells and compared them with immature 30S subunits from a ΔyjeQ strain. The cryo-EM maps obtained from these particles showed that the densities representing helices 44 and 45 in the rRNA were partially missing, suggesting mobility of these motifs. These 30S subunits were also partially depleted in all tertiary ribosomal proteins, particularly those binding in the head domain. Using image classification, we identified four subpopulations of ΔrimM immature 30S subunits differing in the amount of missing density for helices 44 and 45, as well as the amount of density existing in these maps for the underrepresented proteins. The structural defects found in these immature subunits resembled those of the 30S subunits that accumulate in the ΔyjeQ strain. These findings are consistent with an "early convergency model" in which multiple parallel assembly pathways of the 30S subunit converge into a late assembly intermediate, as opposed to the mature state. Functionally related factors will bind to this intermediate to catalyze the last steps of maturation leading to the mature 30S subunit.
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MESH Headings
- Binding Sites
- Cryoelectron Microscopy
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Escherichia coli/metabolism
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- GTP Phosphohydrolases/genetics
- GTP Phosphohydrolases/metabolism
- GTP-Binding Proteins/genetics
- GTP-Binding Proteins/metabolism
- Gene Deletion
- Genes, Bacterial
- Models, Molecular
- Nucleic Acid Conformation
- Phenotype
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosome Subunits, Small, Bacterial/genetics
- Ribosome Subunits, Small, Bacterial/metabolism
- Species Specificity
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40
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Li N, Chen Y, Guo Q, Zhang Y, Yuan Y, Ma C, Deng H, Lei J, Gao N. Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit. Nucleic Acids Res 2013; 41:7073-83. [PMID: 23700310 PMCID: PMC3737534 DOI: 10.1093/nar/gkt423] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ribosome assembly is a process fundamental for all cellular activities. The efficiency and accuracy of the subunit assembly are tightly regulated and closely monitored. In the present work, we characterized, both compositionally and structurally, a set of in vivo 50S subunit precursors (45S), isolated from a mutant bacterial strain. Our qualitative mass spectrometry data indicate that L28, L16, L33, L36 and L35 are dramatically underrepresented in the 45S particles. This protein spectrum shows interesting similarity to many qualitatively analyzed 50S precursors from different genetic background, indicating the presence of global rate-limiting steps in the late-stage assembly of 50S subunit. Our structural data reveal two major intermediate states for the 45S particles. Consistently, both states severally lack those proteins, but they also differ in the stability of the functional centers of the 50S subunit, demonstrating that they are translationally inactive. Detailed analysis indicates that the orientation of H38 accounts for the global conformational differences in these intermediate structures, and suggests that the reorientation of H38 to its native position is rate-limiting during the late-stage assembly. Especially, H38 plays an essential role in stabilizing the central protuberance, through the interaction with the 5S rRNA, and the correctly orientated H38 is likely a prerequisite for further maturation of the 50S subunit.
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Affiliation(s)
- Ningning Li
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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41
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Abstract
The ribosome is an RNA- and protein-based macromolecule having multiple functional domains to facilitate protein synthesis, and it is synthesized through multiple steps including transcription, stepwise cleavages of the primary transcript, modifications of ribosomal proteins and RNAs and assemblies of ribosomal proteins with rRNAs. This process requires dozens of trans-acting factors including GTP- and ATP-binding proteins to overcome several energy-consuming steps. Despite accumulation of genetic, biochemical and structural data, the entire process of bacterial ribosome synthesis remains elusive. Here, we review GTPases involved in bacterial ribosome maturation.
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Affiliation(s)
- Simon Goto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
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42
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Guo Q, Goto S, Chen Y, Feng B, Xu Y, Muto A, Himeno H, Deng H, Lei J, Gao N. Dissecting the in vivo assembly of the 30S ribosomal subunit reveals the role of RimM and general features of the assembly process. Nucleic Acids Res 2013; 41:2609-20. [PMID: 23293003 PMCID: PMC3575805 DOI: 10.1093/nar/gks1256] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Ribosome biogenesis is a tightly regulated, multi-stepped process. The assembly of ribosomal subunits is a central step of the complex biogenesis process, involving nearly 30 protein factors in vivo in bacteria. Although the assembly process has been extensively studied in vitro for over 40 years, very limited information is known for the in vivo process and specific roles of assembly factors. Such an example is ribosome maturation factor M (RimM), a factor involved in the late-stage assembly of the 30S subunit. Here, we combined quantitative mass spectrometry and cryo-electron microscopy to characterize the in vivo 30S assembly intermediates isolated from mutant Escherichia coli strains with genes for assembly factors deleted. Our compositional and structural data show that the assembly of the 3′-domain of the 30S subunit is severely delayed in these intermediates, featured with highly underrepresented 3′-domain proteins and large conformational difference compared with the mature 30S subunit. Further analysis indicates that RimM functions not only to promote the assembly of a few 3′-domain proteins but also to stabilize the rRNA tertiary structure. More importantly, this study reveals intriguing similarities and dissimilarities between the in vitro and the in vivo assembly pathways, suggesting that they are in general similar but with subtle differences.
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Affiliation(s)
- Qiang Guo
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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43
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Boehringer D, O'Farrell HC, Rife JP, Ban N. Structural insights into methyltransferase KsgA function in 30S ribosomal subunit biogenesis. J Biol Chem 2012; 287:10453-10459. [PMID: 22308031 DOI: 10.1074/jbc.m111.318121] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The assembly of the ribosomal subunits is facilitated by ribosome biogenesis factors. The universally conserved methyltransferase KsgA modifies two adjacent adenosine residues in the 3'-terminal helix 45 of the 16 S ribosomal RNA (rRNA). KsgA recognizes its substrate adenosine residues only in the context of a near mature 30S subunit and is required for the efficient processing of the rRNA termini during ribosome biogenesis. Here, we present the cryo-EM structure of KsgA bound to a nonmethylated 30S ribosomal subunit. The structure reveals that KsgA binds to the 30S platform with the catalytic N-terminal domain interacting with substrate adenosine residues in helix 45 and the C-terminal domain making extensive contacts to helix 27 and helix 24. KsgA excludes the penultimate rRNA helix 44 from adopting its position in the mature 30S subunit, blocking the formation of the decoding site and subunit joining. We suggest that the activation of methyltransferase activity and subsequent dissociation of KsgA control conformational changes in helix 44 required for final rRNA processing and translation initiation.
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Affiliation(s)
- Daniel Boehringer
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland, and
| | - Heather C O'Farrell
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Jason P Rife
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia 23298.
| | - Nenad Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland, and.
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44
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Abstract
Many RNAs do not directly code proteins but are nonetheless indispensable to cellular function. These strands fold into intricate three-dimensional shapes that are essential structures in protein synthesis, splicing, and many other processes of gene regulation and expression. A variety of biophysical and biochemical methods are now showing, in real time, how ribosomal subunits and other ribonucleoprotein complexes assemble from their molecular components. Footprinting methods are particularly useful for studying the folding of long RNAs: they provide quantitative information about the conformational state of each residue and require little material. Data from footprinting complement the global information available from small-angle X-ray scattering or cryo-electron microscopy, as well as the dynamic information derived from single-molecule Förster resonance energy transfer (FRET) and NMR methods. In this Account, I discuss how we have used hydroxyl radical footprinting and other experimental methods to study pathways of RNA folding and 30S ribosome assembly. Hydroxyl radical footprinting probes the solvent accessibility of the RNA backbone at each residue in as little as 10 ms, providing detailed views of RNA folding pathways in real time. In conjunction with other methods such as solution scattering and single-molecule FRET, time-resolved footprinting of ribozymes showed that stable domains of RNA tertiary structure fold in less than 1 s. However, the free energy landscapes for RNA folding are rugged, and individual molecules kinetically partition into folding pathways that lead through metastable intermediates, stalling the folding or assembly process. Time-resolved footprinting was used to follow the formation of tertiary structure and protein interactions in the 16S ribosomal RNA (rRNA) during the assembly of 30S ribosomes. As previously observed in much simpler ribozymes, assembly occurs in stages, with individual molecules taking different routes to the final complex. Interactions occur concurrently in all domains of the 16S rRNA, and multistage protection of binding sites of individual proteins suggests that initial encounter complexes between the rRNA and ribosomal proteins are remodeled during assembly. Equilibrium footprinting experiments showed that one primary binding protein was sufficient to stabilize the tertiary structure of the entire 16S 5'-domain. The rich detail available from the footprinting data showed that the secondary assembly protein S16 suppresses non-native structures in the 16S 5'-domain. In doing so, S16 enables a conformational switch distant from its own binding site, which may play a role in establishing interactions with other domains of the 30S subunit. Together, the footprinting results show how protein-induced changes in RNA structure are communicated over long distances, ensuring cooperative assembly of even very large RNA-protein complexes such as the ribosome.
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Affiliation(s)
- Sarah A. Woodson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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45
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Jomaa A, Stewart G, Mears JA, Kireeva I, Brown ED, Ortega J. Cryo-electron microscopy structure of the 30S subunit in complex with the YjeQ biogenesis factor. RNA (NEW YORK, N.Y.) 2011; 17:2026-38. [PMID: 21960487 PMCID: PMC3198595 DOI: 10.1261/rna.2922311] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2011] [Accepted: 08/26/2011] [Indexed: 05/22/2023]
Abstract
YjeQ is a protein broadly conserved in bacteria containing an N-terminal oligonucleotide/oligosaccharide fold (OB-fold) domain, a central GTPase domain, and a C-terminal zinc-finger domain. YjeQ binds tightly and stoichiometrically to the 30S subunit, which stimulates its GTPase activity by 160-fold. Despite growing evidence for the involvement of the YjeQ protein in bacterial 30S subunit assembly, the specific function and mechanism of this protein remain unclear. Here, we report the costructure of YjeQ with the 30S subunit obtained by cryo-electron microscopy. The costructure revealed that YjeQ interacts simultaneously with helix 44, the head and the platform of the 30S subunit. This binding location of YjeQ in the 30S subunit suggests a chaperone role in processing of the 3' end of the rRNA as well as in mediating the correct orientation of the main domains of the 30S subunit. In addition, the YjeQ binding site partially overlaps with the interaction site of initiation factors 2 and 3, and upon binding, YjeQ covers three inter-subunit bridges that are important for the association of the 30S and 50S subunits. Hence, our structure suggests that YjeQ may assist in ribosome maturation by preventing premature formation of the translation initiation complex and association with the 50S subunit. Together, these results support a role for YjeQ in the late stages of 30S maturation.
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Affiliation(s)
- Ahmad Jomaa
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, L8N3Z5, Canada
| | - Geordie Stewart
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, L8N3Z5, Canada
| | - Jason A. Mears
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Inga Kireeva
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, L8N3Z5, Canada
| | - Eric D. Brown
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, L8N3Z5, Canada
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, L8N3Z5, Canada
- Corresponding author.E-mail .
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46
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Structural basis for the function of a small GTPase RsgA on the 30S ribosomal subunit maturation revealed by cryoelectron microscopy. Proc Natl Acad Sci U S A 2011; 108:13100-5. [PMID: 21788480 DOI: 10.1073/pnas.1104645108] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The bacterial RsgA, a circularly permutated GTPase, whose GTPase activity is dependent on the 30S ribosomal subunit, is a late-stage ribosome biogenesis factor involved in the 30S subunit maturation. The role of RsgA is to release another 30S biogenesis factor, RbfA, from the mature 30S subunit in a GTP-dependent manner. Using cryoelectron microscopy, we have determined the structure of the 30S subunit bound with RsgA in the presence of GMPPNP at subnanometer resolution. In the structure, RsgA binds to the central part of the 30S subunit, close to the decoding center, in a position that is incompatible with multiple biogenesis factors, all three translation initiation factors, as well as A-, P-site tRNAs and the 50S subunit. Further structural analysis not only provides a structural model for the RsgA-dependent release of RbfA from the nascent 30S subunit, but also indicates RsgA's role in the ribosomal protein assembly, to promote some tertiary binding protein incorporation. Moreover, together with available biochemical and genetic data, our results suggest that RsgA might be a general checkpoint protein in the late stage of the 30S subunit biogenesis, whose function is not only to release biogenesis factors (e.g., RbfA) from the nascent 30S subunit, but also to block the association of initiation factors to the premature 30S subunit.
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