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Cited by 184RNA and protein synthesis mechanismsAdvanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and Function

Visualizing translation dynamics at atomic detail inside a bacterial cell

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Xue, Liang, Lenz, Swantje, Zimmermann-Kogadeeva, Maria, Tegunov, Dimitry, Cramer, Patrick, Bork, Peer, Rappsilber, Juri, Mahamid, Julia·2022·Nature
DOI 10.1038/s41586-022-05255-2PMC PMC9534751

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Abstract

Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells 1 . Here we use advances in cryo-electron tomography and sub-tomogram analysis 2,3 to visualize the structural dynamics of translation inside the bacterium Mycoplasma pneumoniae . To interpret the functional states in detail, we first obtain a high-resolution in-cell average map of all translating ribosomes and build an atomic model for the M. pneumoniae ribosome that reveals distinct extensions of ribosomal proteins. Classification then resolves 13 ribosome states that differ in their conformation and composition. These recapitulate major states that were previously resolved in vitro, and reflect intermediates during active translation. On the basis of these states, we animate translation elongation inside native cells and show how antibiotics reshape the cellular translation landscapes. During translation elongation, ribosomes often assemble in defined three-dimensional arrangements to form polysomes 4 . By mapping the intracellular organization of translating ribosomes, we show that their association into polysomes involves a local coordination mechanism that is mediated by the ribosomal protein L9. We propose that an extended conformation of L9 within polysomes mitigates collisions to facilitate translation fidelity. Our work thus demonstrates the feasibility of visualizing molecular processes at atomic detail inside cells.

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  • Cryo-ET of M. pneumoniae shows a distinct membrane-associated attachment organelle.

    “In contrast, cryo-ET of M. pneumoniae shows a distinct membrane-associated attachment organelle.45”

    From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [45]

    The Fig. 1a caption in the In-cell structure section identifies an attachment organelle in a cryo-ET slice of an M. pneumoniae cell and also labels the plasma membrane. The text does not state that the organelle is membrane-associated, so that part of the claim is not established by our copy. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

  • In situ cryo-EM/cryo-ET remains technically limited to relatively small or thin biological specimens.

    “However, in situ cryo-EM/cryo-ET remains technically limited to relatively small or thin biological specimens, such as bacteria5, yeast6, or peripheral regions of larger eukaryotic cells7.”

    From Ghost Neuron preparation unlocks high-resolution structural mapping of intracellular architecture in axons (2026) · cites this paper as [5]

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Authors
Xue, L., Lenz, S., Zimmermann-Kogadeeva, M., Tegunov, D., Cramer, P., Bork, P., Rappsilber, J., & Mahamid, J.
Affiliations
  • Heidelberg University (DE)
  • Technische Universität Berlin (DE)
  • Max Planck Institute for Biophysical Chemistry (DE)
  • Wellcome Centre for Cell Biology (GB)
  • European Molecular Biology Laboratory (DE)
Corresponding author
Mahamid, Julia
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2022-09-28
Volume
610
Issue
7930
Pages
205-211
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/s41586-022-05255-2
PMC
PMC9534751
OpenAlex
W4297497481
Cited by
184
References
4
Citations by year
2026: 38 · 2025: 50 · 2024: 49 · 2023: 37 · 2022: 10
FWCI
11.92
Type
journal article
Language
en
Update notices
correction (2022-11-10)
Open access
Licence
Locations
  • Nature (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion, cc-by)
  • Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
Funders
  • Wellcome Trust (103139)
  • Deutsche Forschungsgemeinschaft (426290502)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords
translation elongation, Mycoplasma pneumoniae, ribosome structure, ribosomal protein L9, polysome assembly, ribosome collisions, translation fidelity, antibiotics
MeSH terms
Anti-Bacterial Agents, Mycoplasma pneumoniae, Peptide Chain Elongation, Translational, Polyribosomes, Ribosomal Proteins, Ribosomes, Protein Biosynthesis, Cryoelectron Microscopy

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