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Eiler DR, Wimberly BT, Bilodeau DY, Taliaferro JM, Reigan P, Rissland OS, Kieft JS. The Giardia lamblia ribosome structure reveals divergence in several biological pathways and the mode of emetine function. Structure 2024; 32:400-410.e4. [PMID: 38242118 PMCID: PMC10997490 DOI: 10.1016/j.str.2023.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/23/2023] [Accepted: 12/23/2023] [Indexed: 01/21/2024]
Abstract
Giardia lamblia is a deeply branching protist and a human pathogen. Its unusual biology presents the opportunity to explore conserved and fundamental molecular mechanisms. We determined the structure of the G. lamblia 80S ribosome bound to tRNA, mRNA, and the antibiotic emetine by cryo-electron microscopy, to an overall resolution of 2.49 Å. The structure reveals rapidly evolving protein and nucleotide regions, differences in the peptide exit tunnel, and likely altered ribosome quality control pathways. Examination of translation initiation factor binding sites suggests these interactions are conserved despite a divergent initiation mechanism. Highlighting the potential of G. lamblia to resolve conserved biological principles; our structure reveals the interactions of the translation inhibitor emetine with the ribosome and mRNA, thus providing insight into the mechanism of action for this widely used antibiotic. Our work defines key questions in G. lamblia and motivates future experiments to explore the diversity of eukaryotic gene regulation.
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Affiliation(s)
- Daniel R Eiler
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Brian T Wimberly
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Danielle Y Bilodeau
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA BioScience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA BioScience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Philip Reigan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Olivia S Rissland
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA BioScience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA BioScience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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Sun M, Shen B, Li W, Samir P, Browne CM, Link AJ, Frank J. A Time-Resolved Cryo-EM Study of Saccharomyces cerevisiae 80S Ribosome Protein Composition in Response to a Change in Carbon Source. Proteomics 2020; 21:e2000125. [PMID: 33007145 DOI: 10.1002/pmic.202000125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/31/2020] [Indexed: 12/28/2022]
Abstract
The role of the ribosome in the regulation of gene expression has come into increased focus. It is proposed that ribosomes are catalytic engines capable of changing their protein composition in response to environmental stimuli. Time-resolved cryo-electron microscopy (cryo-EM) techniques are employed to identify quantitative changes in the protein composition and structure of the Saccharomyces cerevisiae 80S ribosomes after shifting the carbon source from glucose to glycerol. Using cryo-EM combined with the computational classification approach, it is found that a fraction of the yeast cells' 80S ribosomes lack ribosomal proteins at the entrance and exit sites for tRNAs, including uL16(RPL10), eS1(RPS1), uS11(RPS14A/B), and eS26(RPS26A/B). This fraction increased after a change from glucose to glycerol medium. The quantitative structural analysis supports the hypothesis that ribosomes are dynamic complexes that alter their composition in response to changes in growth or environmental conditions.
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Affiliation(s)
- Ming Sun
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Bingxin Shen
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Wen Li
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Parimal Samir
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA
| | - Christopher M Browne
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA
| | - Andrew J Link
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA.,Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
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Rahman N, Shamsuzzaman M, Lindahl L. Interaction between the assembly of the ribosomal subunits: Disruption of 40S ribosomal assembly causes accumulation of extra-ribosomal 60S ribosomal protein uL18/L5. PLoS One 2020; 15:e0222479. [PMID: 31986150 PMCID: PMC6984702 DOI: 10.1371/journal.pone.0222479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/07/2020] [Indexed: 12/22/2022] Open
Abstract
Inhibition of the synthesis of an essential ribosomal protein (r-protein) abrogates the assembly of its cognate subunit, while assembly of the other subunit continues. Ribosomal components that are not stably incorporated into ribosomal particles due to the disrupted assembly are rapidly degraded. The 60S protein uL18/L5 is an exception and this protein accumulates extra-ribosomally during inhibition of 60S assembly. Since the r-proteins in each ribosomal subunit are essential only for the formation of their cognate subunit, it would be predicted that accumulation of extra-ribosomal uL18/L5 is specific to restriction of 60S assembly and does not occur abolition of 40S assembly. Contrary to this prediction, we report here that repression of 40S r-protein genes does lead to accumulation of uL18/L5 outside of the ribosome. Furthermore, the effect varies depending on which 40S ribosomal protein is repressed. Our results also show extra-ribosomal uL18/L5 is formed during 60S assembly, not during degradation of mature cytoplasmic 60S subunits. Finally, we propose a model for the accumulation of extra-ribosomal uL18 in response to the abolition of 40S r-proteins.
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Affiliation(s)
- Nusrat Rahman
- Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, Maryland, United States of America
| | - Md Shamsuzzaman
- Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, Maryland, United States of America
| | - Lasse Lindahl
- Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, Maryland, United States of America
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