1
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Meyer J, Payr M, Duss O, Hennig J. Exploring the dynamics of messenger ribonucleoprotein-mediated translation repression. Biochem Soc Trans 2024; 52:2267-2279. [PMID: 39601754 DOI: 10.1042/bst20231240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 10/14/2024] [Accepted: 10/21/2024] [Indexed: 11/29/2024]
Abstract
Translational control is crucial for well-balanced cellular function and viability of organisms. Different mechanisms have evolved to up- and down-regulate protein synthesis, including 3' untranslated region (UTR)-mediated translation repression. RNA binding proteins or microRNAs interact with regulatory sequence elements located in the 3' UTR and interfere most often with the rate-limiting initiation step of translation. Dysregulation of post-transcriptional gene expression leads to various kinds of diseases, emphasizing the significance of understanding the mechanisms of these processes. So far, only limited mechanistic details about kinetics and dynamics of translation regulation are understood. This mini-review focuses on 3' UTR-mediated translational regulation mechanisms and demonstrates the potential of using single-molecule fluorescence-microscopy for kinetic and dynamic studies of translation regulation in vivo and in vitro.
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Affiliation(s)
- Julia Meyer
- Department of Biochemistry IV - Biophysical Chemistry, University of Bayreuth, 95447 Bayreuth, Germany
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Marco Payr
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Candidate for Joint PhD Degree From EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Olivier Duss
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Janosch Hennig
- Department of Biochemistry IV - Biophysical Chemistry, University of Bayreuth, 95447 Bayreuth, Germany
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
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2
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Wiechert F, Unbehaun A, Sprink T, Seibel H, Bürger J, Loerke J, Mielke T, Diebolder CA, Schacherl M, Spahn CMT. Visualizing the modification landscape of the human 60S ribosomal subunit at close to atomic resolution. Nucleic Acids Res 2024:gkae1191. [PMID: 39658079 DOI: 10.1093/nar/gkae1191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 11/09/2024] [Accepted: 11/18/2024] [Indexed: 12/12/2024] Open
Abstract
Chemical modifications of ribosomal RNAs (rRNAs) and proteins expand their topological repertoire, and together with the plethora of bound ligands, fine-tune ribosomal function. Detailed knowledge of this natural composition provides important insights into ribosome genesis and function and clarifies some aspects of ribosomopathies. The discovery of new structural properties and functional aspects of ribosomes has gone hand in hand with cryo-electron microscopy (cryo-EM) and its technological development. In line with the ability to visualize atomic details - a prerequisite for identifying chemical modifications and ligands in cryo-EM maps - in this work we present the structure of the 60S ribosomal subunit from HeLa cells at the very high global resolution of 1.78 Å. We identified 113 rRNA modifications and four protein modifications including uL2-Hisβ-ox216, which stabilizes the local structure near the peptidyl transferase centre via an extended hydrogen-bonding network. We can differentiate metal ions Mg2+ and K+, polyamines spermine, spermidine and putrescine and identify thousands of water molecules binding to the 60S subunit. Approaching atomic resolution cryo-EM has become a powerful tool to examine fine details of macromolecular structures that will expand our knowledge about translation and other biological processes in the future and assess the variability of the chemical space due to differences between species/tissues or varying physicochemical environment.
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Affiliation(s)
- Franziska Wiechert
- Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Anett Unbehaun
- Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Thiemo Sprink
- Core Facility for Cryo-Electron Microscopy (CFcryoEM), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Robert-Rössle-Str. 10, 13125 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Cryo-EM, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Helena Seibel
- Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jörg Bürger
- Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Justus Loerke
- Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Christoph A Diebolder
- Core Facility for Cryo-Electron Microscopy (CFcryoEM), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Robert-Rössle-Str. 10, 13125 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Cryo-EM, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Magdalena Schacherl
- Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Christian M T Spahn
- Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
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3
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Brodersen P, Arribas-Hernández L. The m 6A-YTH regulatory system in plants: A status. CURRENT OPINION IN PLANT BIOLOGY 2024; 82:102650. [PMID: 39488190 DOI: 10.1016/j.pbi.2024.102650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 09/17/2024] [Accepted: 09/17/2024] [Indexed: 11/04/2024]
Abstract
Plants use mRNA methylation to regulate gene expression. As in other eukaryotes, the only abundant methylated nucleotide in plant mRNA bodies is N6-methyladenosine (m6A). The conserved core components of m6A-based genetic control are a multi-subunit nuclear methyltransferase, and a set of nuclear and cytoplasmic RNA-binding proteins consisting of an m6A recognition module, the YT521-B homology (YTH) domain, and long intrinsically disordered regions (IDRs). In plants, this system is essential for growth during embryonic and post-embryonic development, but emerging evidence also points to key functions in plant-virus interactions and stimulus-dependent gene regulation. Cytoplasmic YTH-domain proteins are particularly important for these functions, and recent progress has identified two elements of the underlying molecular mechanisms: IDR-mediated phase separation and conserved short linear motifs mediating interactions with other key mRNA-binding proteins.
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Affiliation(s)
- Peter Brodersen
- University of Copenhagen, Copenhagen Plant Science Center, Department of Biology, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark.
| | - Laura Arribas-Hernández
- University of Copenhagen, Copenhagen Plant Science Center, Department of Biology, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark; Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' (IHSM), 29750 Algarrobo-Costa, Málaga, Spain.
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4
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Song P, Tian E, Cai Z, Chen X, Chen S, Yu K, Bian H, He K, Jia G. Methyltransferase ATMETTL5 writes m 6A on 18S ribosomal RNA to regulate translation in Arabidopsis. THE NEW PHYTOLOGIST 2024; 244:571-587. [PMID: 39188077 DOI: 10.1111/nph.20034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 07/15/2024] [Indexed: 08/28/2024]
Abstract
Aberrant RNA modifications can lead to dysregulated gene expression and impeded growth in plants. Ribosomal RNA (rRNA) constitutes a substantial portion of total RNA, while the precise functions and molecular mechanisms underlying rRNA modifications in plants remain largely elusive. Here, we elucidated the exclusive occurrence of the canonical RNA modification N6-methyladenosine (m6A) solely 18S rRNA, but not 25S rRNA. We identified a completely uncharacterized protein, ATMETTL5, as an Arabidopsis m6A methyltransferase responsible for installing m6A methylation at the 1771 site of the 18S rRNA. ATMETTL5 is ubiquitously expressed and localized in both nucleus and cytoplasm, mediating rRNA m6A methylation. Mechanistically, the loss of ATMETTL5-mediated methylation results in attenuated translation. Furthermore, we uncovered the role of ATMETTL5-mediated methylation in coordinating blue light-mediated hypocotyl growth by regulating the translation of blue light-related messenger RNAs (mRNAs), specifically HYH and PRR9. Our findings provide mechanistic insights into how rRNA modification regulates ribosome function in mRNA translation and the response to blue light, thereby advancing our understanding of the role of epigenetic modifications in precisely regulating mRNA translation in plants.
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Affiliation(s)
- Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Enlin Tian
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Zhihe Cai
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Xu Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Shuyan Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Kemiao Yu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Hanxiao Bian
- Laboratory of Fruit Quality Biology, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Kai He
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Beijing Advanced Center of RNA Biology (BEACON), Peking University, Beijing, 100871, China
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5
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Ting MKY, Gao Y, Barahimipour R, Ghandour R, Liu J, Martinez-Seidel F, Smirnova J, Gotsmann VL, Fischer A, Haydon MJ, Willmund F, Zoschke R. Optimization of ribosome profiling in plants including structural analysis of rRNA fragments. PLANT METHODS 2024; 20:143. [PMID: 39285473 PMCID: PMC11406806 DOI: 10.1186/s13007-024-01267-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 09/02/2024] [Indexed: 09/19/2024]
Abstract
BACKGROUND Ribosome profiling (or Ribo-seq) is a technique that provides genome-wide information on the translational landscape (translatome). Across different plant studies, variable methodological setups have been described which raises questions about the general comparability of data that were generated from diverging methodologies. Furthermore, a common problem when performing Ribo-seq are abundant rRNA fragments that are wastefully incorporated into the libraries and dramatically reduce sequencing depth. To remove these rRNA contaminants, it is common to perform preliminary trials to identify these fragments because they are thought to vary depending on nuclease treatment, tissue source, and plant species. RESULTS Here, we compile valuable insights gathered over years of generating Ribo-seq datasets from different species and experimental setups. We highlight which technical steps are important for maintaining cross experiment comparability and describe a highly efficient approach for rRNA removal. Furthermore, we provide evidence that many rRNA fragments are structurally preserved over diverse nuclease regimes, as well as across plant species. Using a recently published cryo-electron microscopy (cryo-EM) structure of the tobacco 80S ribosome, we show that the most abundant rRNA fragments are spatially derived from the solvent-exposed surface of the ribosome. CONCLUSION The guidelines presented here shall aid newcomers in establishing ribosome profiling in new plant species and provide insights that will help in customizing the methodology for individual research goals.
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Affiliation(s)
- Michael K Y Ting
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
- School of BioSciences, University of Melbourne, VIC, Melbourne, 3010, Australia.
| | - Yang Gao
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Rouhollah Barahimipour
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Rabea Ghandour
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Jinghan Liu
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Federico Martinez-Seidel
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Julia Smirnova
- Charité Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany
| | - Vincent Leon Gotsmann
- Technical University Kaiserslautern, Paul-Ehrlich-Str. 23, 67663, Kaiserslautern, Germany
| | - Axel Fischer
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Michael J Haydon
- School of BioSciences, University of Melbourne, VIC, Melbourne, 3010, Australia
| | - Felix Willmund
- Technical University Kaiserslautern, Paul-Ehrlich-Str. 23, 67663, Kaiserslautern, Germany
- Universität Marburg, Karl-von-Frisch-Str. 14, 35032, Marburg, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
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6
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Holvec S, Barchet C, Lechner A, Fréchin L, De Silva SNT, Hazemann I, Wolff P, von Loeffelholz O, Klaholz BP. The structure of the human 80S ribosome at 1.9 Å resolution reveals the molecular role of chemical modifications and ions in RNA. Nat Struct Mol Biol 2024; 31:1251-1264. [PMID: 38844527 DOI: 10.1038/s41594-024-01274-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 03/14/2024] [Indexed: 08/17/2024]
Abstract
The ribosomal RNA of the human protein synthesis machinery comprises numerous chemical modifications that are introduced during ribosome biogenesis. Here we present the 1.9 Å resolution cryo electron microscopy structure of the 80S human ribosome resolving numerous new ribosomal RNA modifications and functionally important ions such as Zn2+, K+ and Mg2+, including their associated individual water molecules. The 2'-O-methylation, pseudo-uridine and base modifications were confirmed by mass spectrometry, resulting in a complete investigation of the >230 sites, many of which could not be addressed previously. They choreograph key interactions within the RNA and at the interface with proteins, including at the ribosomal subunit interfaces of the fully assembled 80S ribosome. Uridine isomerization turns out to be a key mechanism for U-A base pair stabilization in RNA in general. The structural environment of chemical modifications and ions is primordial for the RNA architecture of the mature human ribosome, hence providing a structural framework to address their role in healthy states and in human diseases.
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Affiliation(s)
- Samuel Holvec
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, France
- Centre National de la Recherche Scientifique UMR, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Charles Barchet
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, France
- Centre National de la Recherche Scientifique UMR, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Antony Lechner
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, France
- Centre National de la Recherche Scientifique UMR, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
- Architecture et Réactivité de l'ARN, CNRS UPR9002, Institute of Molecular and Cellular Biology, Université de Strasbourg, Strasbourg, France
| | - Léo Fréchin
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, France
- Centre National de la Recherche Scientifique UMR, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - S Nimali T De Silva
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, France
- Centre National de la Recherche Scientifique UMR, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Isabelle Hazemann
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, France
- Centre National de la Recherche Scientifique UMR, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Philippe Wolff
- Architecture et Réactivité de l'ARN, CNRS UPR9002, Institute of Molecular and Cellular Biology, Université de Strasbourg, Strasbourg, France
| | - Ottilie von Loeffelholz
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, France
- Centre National de la Recherche Scientifique UMR, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, France.
- Centre National de la Recherche Scientifique UMR, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France.
- Université de Strasbourg, Strasbourg, France.
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7
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Gentry-Torfer D, Murillo E, Barrington CL, Nie S, Leeming MG, Suwanchaikasem P, Williamson NA, Roessner U, Boughton BA, Kopka J, Martinez-Seidel F. Streamlining Protein Fractional Synthesis Rates Using SP3 Beads and Stable Isotope Mass Spectrometry: A Case Study on the Plant Ribosome. Bio Protoc 2024; 14:e4981. [PMID: 38737506 PMCID: PMC11082790 DOI: 10.21769/bioprotoc.4981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 05/14/2024] Open
Abstract
Ribosomes are an archetypal ribonucleoprotein assembly. Due to ribosomal evolution and function, r-proteins share specific physicochemical similarities, making the riboproteome particularly suited for tailored proteome profiling methods. Moreover, the structural proteome of ribonucleoprotein assemblies reflects context-dependent functional features. Thus, characterizing the state of riboproteomes provides insights to uncover the context-dependent functionality of r-protein rearrangements, as they relate to what has been termed the ribosomal code, a concept that parallels that of the histone code, in which chromatin rearrangements influence gene expression. Compared to high-resolution ribosomal structures, omics methods lag when it comes to offering customized solutions to close the knowledge gap between structure and function that currently exists in riboproteomes. Purifying the riboproteome and subsequent shot-gun proteomics typically involves protein denaturation and digestion with proteases. The results are relative abundances of r-proteins at the ribosome population level. We have previously shown that, to gain insight into the stoichiometry of individual proteins, it is necessary to measure by proteomics bound r-proteins and normalize their intensities by the sum of r-protein abundances per ribosomal complex, i.e., 40S or 60S subunits. These calculations ensure that individual r-protein stoichiometries represent the fraction of each family/paralog relative to the complex, effectively revealing which r-proteins become substoichiometric in specific physiological scenarios. Here, we present an optimized method to profile the riboproteome of any organism as well as the synthesis rates of r-proteins determined by stable isotope-assisted mass spectrometry. Our method purifies the r-proteins in a reversibly denatured state, which offers the possibility for combined top-down and bottom-up proteomics. Our method offers a milder native denaturation of the r-proteome via a chaotropic GuHCl solution as compared with previous studies that use irreversible denaturation under highly acidic conditions to dissociate rRNA and r-proteins. As such, our method is better suited to conserve post-translational modifications (PTMs). Subsequently, our method carefully considers the amino acid composition of r-proteins to select an appropriate protease for digestion. We avoid non-specific protease cleavage by increasing the pH of our standardized r-proteome dilutions that enter the digestion pipeline and by using a digestion buffer that ensures an optimal pH for a reliable protease digestion process. Finally, we provide the R package ProtSynthesis to study the fractional synthesis rates of r-proteins. The package uses physiological parameters as input to determine peptide or protein fractional synthesis rates. Once the physiological parameters are measured, our equations allow a fair comparison between treatments that alter the biological equilibrium state of the system under study. Our equations correct peptide enrichment using enrichments in soluble amino acids, growth rates, and total protein accumulation. As a means of validation, our pipeline fails to find "false" enrichments in non-labeled samples while also filtering out proteins with multiple unique peptides that have different enrichment values, which are rare in our datasets. These two aspects reflect the accuracy of our tool. Our method offers the possibility of elucidating individual r-protein family/paralog abundances, PTM status, fractional synthesis rates, and dynamic assembly into ribosomal complexes if top-down and bottom-up proteomic approaches are used concomitantly, taking one step further into mapping the native and dynamic status of the r-proteome onto high-resolution ribosome structures. In addition, our method can be used to study the proteomes of all macromolecular assemblies that can be purified, although purification is the limiting step, and the efficacy and accuracy of the proteases may be limited depending on the digestion requirements. Key features • Efficient purification of the ribosomal proteome: streamlined procedure for the specific purification of the ribosomal proteome or complex Ome. • Accurate calculation of fractional synthesis rates: robust method for calculating fractional protein synthesis rates in macromolecular complexes under different physiological steady states. • Holistic ribosome methodology focused on plants: comprehensive approach that provides insights into the ribosomes and translational control of plants, demonstrated using cold acclimation [1]. • Tailored strategies for stable isotope labeling in plants: methodology focusing on materials and labeling considerations specific to free and proteinogenic amino acid analysis [2].
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Affiliation(s)
- Dione Gentry-Torfer
- Applied Metabolome Analysis, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- School of Biosciences, The University of Melbourne, Parkville, Australia
| | - Ester Murillo
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Chloe L. Barrington
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Shuai Nie
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Australia
| | - Michael G. Leeming
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Australia
- School of Chemistry, The University of Melbourne, Parkville, Australia
| | | | - Nicholas A. Williamson
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Australia
| | - Ute Roessner
- School of Biosciences, The University of Melbourne, Parkville, Australia
- Research School of Biology, The Australian National University, Acton, Australia
| | - Berin A. Boughton
- School of Biosciences, The University of Melbourne, Parkville, Australia
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Australia
| | - Joachim Kopka
- Applied Metabolome Analysis, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Federico Martinez-Seidel
- Applied Metabolome Analysis, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- School of Biosciences, The University of Melbourne, Parkville, Australia
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
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8
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Mishra RK, Sharma P, Khaja FT, Uday AB, Hussain T. Cryo-EM structure of wheat ribosome reveals unique features of the plant ribosomes. Structure 2024; 32:562-574.e3. [PMID: 38458197 PMCID: PMC7616111 DOI: 10.1016/j.str.2024.02.006] [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: 08/16/2023] [Revised: 11/16/2023] [Accepted: 02/12/2024] [Indexed: 03/10/2024]
Abstract
Plants being sessile organisms exhibit unique features in ribosomes, which might aid in rapid gene expression and regulation in response to varying environmental conditions. Here, we present high-resolution structures of the 60S and 80S ribosomes from wheat, a monocot staple crop plant (Triticum aestivum). While plant ribosomes have unique plant-specific rRNA modification (Cm1847) in the peptide exit tunnel (PET), the zinc-finger motif in eL34 is absent, and uL4 is extended, making an exclusive interaction network. We note differences in the eL15-helix 11 (25S) interaction, eL6-ES7 assembly, and certain rRNA chemical modifications between monocot and dicot ribosomes. In eukaryotes, we observe highly conserved rRNA modification (Gm75) in 5.8S rRNA and a flipped base (G1506) in PET. These features are likely involved in sensing or stabilizing nascent chain. Finally, we discuss the importance of the universal conservation of three consecutive rRNA modifications in all ribosomes for their interaction with A-site aminoacyl-tRNA.
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Affiliation(s)
- Rishi Kumar Mishra
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India
| | - Prafful Sharma
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India
| | - Faisal Tarique Khaja
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India
| | - Adwaith B Uday
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India
| | - Tanweer Hussain
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India.
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Neumann SA, Gaspin C, Sáez-Vásquez J. Plant ribosomes as a score to fathom the melody of 2'- O-methylation across evolution. RNA Biol 2024; 21:70-81. [PMID: 39508203 PMCID: PMC11542601 DOI: 10.1080/15476286.2024.2417152] [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: 05/16/2024] [Revised: 10/07/2024] [Accepted: 10/08/2024] [Indexed: 11/08/2024] Open
Abstract
2'-O-ribose methylation (2'-O-Me) is one of the most common RNA modifications detected in ribosomal RNAs (rRNA) from bacteria to eukaryotic cells. 2'-O-Me favours a specific RNA conformation and protects RNA from hydrolysis. Moreover, rRNA 2'-O-Me might stabilize its interactions with messenger RNA (mRNA), transfer RNA (tRNA) or proteins. The extent of rRNA 2'-O-Me fluctuates between species from 3-4 sites in bacteria to tens of sites in archaea, yeast, algae, plants and human. Depending on the organism as well as the rRNA targeting site and position, the 2'-O-Me reaction can be carried out by several site-specific RNA methyltransferases (RMTase) or by a single RMTase associated to specific RNA guides. Here, we review current progresses in rRNA 2'-O-Me (sites/Nm and RMTases) in plants and compare the results with molecular clues from unicellular (bacteria, archaea, algae and yeast) as well as multicellular (human and plants) organisms.
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MESH Headings
- Methylation
- Ribosomes/metabolism
- RNA, Ribosomal/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/chemistry
- Plants/metabolism
- Plants/genetics
- Humans
- Evolution, Molecular
- Methyltransferases/metabolism
- Methyltransferases/genetics
- Methyltransferases/chemistry
- RNA, Plant/metabolism
- RNA, Plant/genetics
- RNA, Plant/chemistry
- Archaea/genetics
- Archaea/metabolism
- RNA, Transfer/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/chemistry
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Affiliation(s)
- Sara Alina Neumann
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, Perpignan, France
- University Perpignan Via Domitia, LGDP, UMR 5096, Perpignan, France
| | - Christine Gaspin
- Université Fédérale de Toulouse, INRAE, MIAT, Castanet-Tolosan, France
- Université Fédérale de Toulouse, INRAE, BioinfOmics, Genotoul Bioinformatics Facility, Castanet-Tolosan, France
| | - Julio Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, Perpignan, France
- University Perpignan Via Domitia, LGDP, UMR 5096, Perpignan, France
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Kravchenko OV, Baymukhametov TN, Afonina ZA, Vassilenko KS. High-Resolution Structure and Internal Mobility of a Plant 40S Ribosomal Subunit. Int J Mol Sci 2023; 24:17453. [PMID: 38139282 PMCID: PMC10743738 DOI: 10.3390/ijms242417453] [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: 11/23/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Ribosome is a major part of the protein synthesis machinery, and analysis of its structure is of paramount importance. However, the structure of ribosomes from only a limited number of organisms has been resolved to date; it especially concerns plant ribosomes and ribosomal subunits. Here, we report a high-resolution cryo-electron microscopy reconstruction of the small subunit of the Triticum aestivum (common wheat) cytoplasmic ribosome. A detailed atomic model was built that includes the majority of the rRNA and some of the protein modifications. The analysis of the obtained data revealed structural peculiarities of the 40S subunit in the monocot plant ribosome. We applied the 3D Flexible Refinement approach to analyze the internal mobility of the 40S subunit and succeeded in decomposing it into four major motions, describing rotations of the head domain and a shift in the massive rRNA expansion segment. It was shown that these motions are almost uncorrelated and that the 40S subunit is flexible enough to spontaneously adopt any conformation it takes as a part of a translating ribosome or ribosomal complex. Here, we introduce the first high-resolution structure of an isolated plant 40S subunit and the first quantitative analysis of the flexibility of small ribosomal subunits, hoping that it will help in studying various aspects of ribosome functioning.
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Affiliation(s)
- Olesya V. Kravchenko
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (O.V.K.)
| | - Timur N. Baymukhametov
- National Research Center, “Kurchatov Institute”, Akademika Kurchatova pl. 1, 123182 Moscow, Russia;
| | - Zhanna A. Afonina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (O.V.K.)
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