The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling

Interaction between the nascent polypeptide chain and the ribosomal exit tunnel can modulate the rate of translation and induce translational arrest to regulate expression of downstream genes. The ribosomal tunnel also provides a protected environment for initial protein folding events. Here, we present a 2.9 Å cryo-electron microscopy structure of a ribosome stalled during translation of the extremely compacted VemP nascent chain. The nascent chain forms two α-helices connected by an α-turn and a loop, enabling a total of 37 amino acids to be observed within the first 50–55 Å of the exit tunnel. The structure reveals how α-helix formation directly within the peptidyltransferase center of the ribosome interferes with aminoacyl-tRNA accommodation, suggesting that during canonical translation, a major role of the exit tunnel is to prevent excessive secondary structure formation that can interfere with the peptidyltransferase activity of the ribosome. DOI: http://dx.doi.org/10.7554/eLife.25642.001

• Publication year

  2017

• Venue

  eLife

• Publication date

  2017-05-30

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.7554/eLife.25642PMID 28556777PMCID 5449182
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Cotranslational folding of spectrin domains via partially structured states

  2017cited by this paper
• Insights into Cotranslational Nascent Protein Behavior from Computer Simulations.

  2016cited by this paper
• A structural ensemble of a ribosome-nascent chain complex during co-translational protein folding

  2016cited by this paper
• Translation regulation via nascent polypeptide-mediated ribosome stalling.

  2016cited by this paper
• The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis

  2016cited by this paper
• The pathway to GTPase activation of elongation factor SelB on the ribosome

  2016cited by this paper
• A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest

  2016cited by this paper
• Small protein domains fold inside the ribosome exit tunnel

  2016cited by this paper
• Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling

  2015influential reference
• Cotranslational protein folding on the ribosome monitored in real time

  2015cited by this paper
• CTFFIND4: Fast and accurate defocus estimation from electron micrographs

  2015cited by this paper
• Nascent chain-monitored remodeling of the Sec machinery for salinity adaptation of marine bacteria

  2015influential reference
• Structure of a human translation termination complex

  2015influential reference
• Cotranslational Protein Folding inside the Ribosome Exit Tunnel

  2015cited by this paper
• Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

  2015cited by this paper
• FX cloning: a simple and robust high-throughput cloning method for protein expression.

  2014cited by this paper
• Transmembrane segments form tertiary hairpins in the folding vestibule of the ribosome.

  2014influential reference
• Molecular basis for the ribosome functioning as an L-tryptophan sensor.

  2014influential reference
• The Local Resolution of Cryo-EM Density Maps

  2013cited by this paper
• Electron counting and beam-induced motion correction enable near atomic resolution single particle cryoEM

  2013influential reference
• Arrest peptides: cis-acting modulators of translation.

  2013influential reference
• A biphasic pulling force acts on transmembrane helices during translocon-mediated membrane integration

  2012influential reference
• RELION: Implementation of a Bayesian approach to cryo-EM structure determination

  2012cited by this paper
• Cotranslational protein folding within the ribosome tunnel influences trigger-factor recruitment.

  2012cited by this paper
• SecM-Stalled Ribosomes Adopt an Altered Geometry at the Peptidyl Transferase Center

  2011cited by this paper
• Structural basis for translational stalling by human cytomegalovirus and fungal arginine attenuator peptide.

  2010influential reference
• α-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel

  2010influential reference
• A ribosome–nascent chain sensor of membrane protein biogenesis in Bacillus subtilis

  2009influential reference
• Enzymatic assembly of DNA molecules up to several hundred kilobases

  2009cited by this paper
• MolProbity: all-atom structure validation for macromolecular crystallography

  2009cited by this paper
• Tertiary Interactions within the Ribosomal Exit Tunnel

  2009cited by this paper
• Structural Insight into Nascent Polypeptide Chain–Mediated Translational Stalling

  2009cited by this paper
• A construct with fluorescent indicators for conditional expression of miRNA

  2008cited by this paper
• Sharpening high resolution information in single particle electron cryomicroscopy.

  2008cited by this paper
• An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol

  2008cited by this paper
• An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA

  2005influential reference
• Folding zones inside the ribosomal exit tunnel

  2005cited by this paper
• The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release.

  2004influential reference
• REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use.

  2004cited by this paper
• Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins.

  2004cited by this paper
• Coot: model-building tools for molecular graphics.

  2004cited by this paper
• UCSF Chimera—A visualization system for exploratory research and analysis

  2004influential reference
• Review: protein secondary structure prediction continues to rise.

  2001cited by this paper
• Secretion monitor, SecM, undergoes self-translation arrest in the cytosol.

  2001influential reference
• Correspondence e-mail:

  2000cited by this paper
• Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 A resolution.

  1989cited by this paper
• Electronic Reprint Biological Crystallography Phenix : a Comprehensive Python-based System for Macromolecular Structure Solution

  year unknowninfluential reference
• Figures and Figure Supplements Mechanisms of Ribosome Stalling by Secm at Multiple Elongation Steps

  year unknowninfluential reference

• Hydrogen/deuterium exchange mass spectrometry analysis of ribosome-nascent chain complexes to study protein biogenesis at the peptide level.

  2026cites this paper
• Structural modification of oxazolidinone antibiotics alters nascent peptide stalling preference and peptide trajectory through the ribosome

  2026influential citation
• Cryo-EM reveals multiple mechanisms of ribosome inhibition by doxycycline

  2025cites this paper
• Structural basis of enhanced stalling efficiency of an engineered ribosome arrest peptide

  2025cites this paper
• Cotranslational protein folding through non-native structural intermediates

  2025cites this paper
• Cotranslational Protein Folding Through Non-Native Structural Intermediates

  2025cites this paper
• Are Bacterial Processes Dependent on Global Ribosome Pausing Affected by tRNA Modification Defects?

  2025cites this paper
• A mini-hairpin shaped nascent peptide blocks translation termination by a distinct mechanism

  2025cites this paper
• The RNA helicase HrpA rescues collided ribosomes in E. coli.

  2025cites this paper
• Mechanism of Ribosome Stalling by the AMD1 C-terminal Tail Arrest Peptide

  2025cites this paper
• Mechanical forces regulate the composition and fate of stalled nascent chains.

  2025cites this paper
• Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding

  2024cites this paper
• A Universal Support for the Solid‐Phase Synthesis of Peptidyl‐tRNA Mimics

  2024cites this paper
• The RNA helicase HrpA rescues collided ribosomes in E. coli

  2024cites this paper
• Translation arrest cancellation of VemP, a secretion monitor in Vibrio, is regulated by multiple cis and trans factors, including SecY

  2024cites this paper
• Single-residue effects on the behavior of a nascent polypeptide chain inside the ribosome exit tunnel

  2024cites this paper
• Mechanochemical forces regulate the composition and fate of stalled nascent chains

  2024cites this paper
• A newly-identified mini-hairpin shaped nascent peptide blocks translation termination by a novel mechanism

  2024cites this paper
• Three Stages of Nascent Protein Translocation Through the Ribosome Exit Tunnel

  2024cites this paper
• The role of molecular chaperone CCT/TRiC in translation elongation: A literature review

  2024cites this paper
• The SecM arrest peptide traps a pre-peptide bond formation state of the ribosome

  2024influential citation
• RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity

  2024cites this paper
• Mapping Protein–Protein Interactions at Birth: Single-Particle Cryo-EM Analysis of a Ribosome–Nascent Globin Complex

  2024cites this paper
• Synthesis of Peptidyl-tRNA Mimics for Structural Biology Applications

  2023cites this paper
• Patchy and widespread distribution of bacterial translation arrest peptides associated with the protein localization machinery

  2023cites this paper
• Assembly landscape for the bacterial large ribosomal subunit

  2023cites this paper
• Practical Synthesis of N-Formylmethionylated Peptidyl-tRNA Mimics

  2023cites this paper
• Molecular basis of eIF5A-dependent CAT tailing in eukaryotic ribosome-associated quality control.

  2023cites this paper
• Nascent chain-mediated translation regulation in bacteria: translation arrest and intrinsic ribosome destabilization.

  2023cites this paper
• The ribosome as a small-molecule sensor.

  2023cites this paper
• How the ribosome shapes cotranslational protein folding.

  2023influential citation
• Ribosomal protein eL39 is important for maturation of the nascent polypeptide exit tunnel and proper protein folding during translation

  2022cites this paper
• Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria

  2022cites this paper
• Insights into the ribosome function from the structures of non-arrested ribosome–nascent chain complexes

  2022influential citation
• A switch from α‐helical to β‐strand conformation during co‐translational protein folding

  2022cites this paper
• Simulation of Complex Biomolecular Systems: The Ribosome Challenge.

  2022cites this paper
• Metabolic Sensing of Extracytoplasmic Copper Availability via Translational Control by a Nascent Exported Protein

  2022cites this paper
• Unsupervised Voxel-based Segmentation reveals a Landscape of Bacterial Ribosome Large Subunit Early Assembly

  2022cites this paper
• Structural basis for the context-specific action of the classic peptidyl transferase inhibitor chloramphenicol

  2022cites this paper
• Binding of the peptide deformylase on the ribosome surface modulates the structure and dynamics of the exit tunnel interior

  2022cites this paper
• The ribosome stabilises partially folded intermediates of a nascent multi-domain protein

  2022cites this paper
• Modulating co-translational protein folding by rational design and ribosome engineering

  2022cites this paper
• Structural basis of l-tryptophan-dependent inhibition of release factor 2 by the TnaC arrest peptide

  2021cites this paper
• Search for translation arrest peptides encoded upstream of genes for components of protein localization pathways

  2021cites this paper
• Nascent polypeptide within the exit tunnel ensures continuous translation elongation by stabilizing the translating ribosome

  2021influential citation
• Ribosome Rescue Pathways in Bacteria

  2021cites this paper
• Structural basis for the tryptophan sensitivity of TnaC-mediated ribosome stalling

  2021cites this paper
• Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel

  2021cites this paper
• The Tunnel.

  2021cites this paper
• Mechanisms of Cotranslational Protein Maturation in Bacteria

  2021cites this paper
• Structural basis for the context-specific action of classic peptidyl transferase inhibitors

  2021cites this paper
• Ribosome collisions in bacteria promote ribosome rescue by triggering mRNA cleavage by SmrB

  2021cites this paper
• Nascent polypeptide within the exit tunnel stabilizes the ribosome to counteract risky translation

  2021cites this paper
• A nascent peptide code for translational control of mRNA stability in human cells

  2021cites this paper
• Peptidyl transferase center decompaction and structural constraints during early protein elongation on the ribosome

  2021cites this paper
• Cotranslational Folding of Proteins on the Ribosome

  2020cites this paper
• Ribosome-associated quality control of membrane proteins at the endoplasmic reticulum

  2020cites this paper
• Cysteine oxidation and disulfide formation in the ribosomal exit tunnel

  2020cites this paper
• Force transduction creates long-ranged coupling in ribosomes stalled by arrest peptides

  2020influential citation
• Proteome-wide Capture of Co-translational Protein Dynamics in Bacillus subtilis Using TnDR, a Transposable Protein-Dynamics Reporter.

  2020cites this paper
• Structural insights into assembly of the ribosomal nascent polypeptide exit tunnel

  2020cites this paper
• Selective inhibition of human translation termination by a drug-like compound

  2020cites this paper
• Fine interaction profiling of VemP and mechanisms responsible for its translocation-coupled arrest-cancelation

  2020influential citation
• Gradual compaction of the nascent peptide during cotranslational folding on the ribosome

  2020cites this paper
• Selective inhibition of human translation by a drug-like compound that traps terminated protein nascent chains on the ribosome

  2020cites this paper
• Structural basis for selective stalling of human ribosome nascent chain complexes by a drug-like molecule

  2019cites this paper
• Visualising nascent chain dynamics at the ribosome exit tunnel by cryo-electron microscopy

  2019influential citation
• Exit tunnel modulation as resistance mechanism of S. aureus erythromycin resistant mutant

  2019cites this paper
• Structure of XBP1u-paused ribosome nascent chain complex (post-state)

  2019cites this paper
• Nervous-Like Circuits in the Ribosome Facts, Hypotheses and Perspectives

  2019cites this paper
• Recognition Elements for Elongation Factor P on the Ribosome

  2019cites this paper
• Structural and mutational analysis of the ribosome-arresting human XBP1u

  2019cites this paper
• Structure-based working model of SecDF, a proton-driven bacterial protein translocation factor

  2018cites this paper
• MifM-instructed translation arrest involves nascent chain interactions with the exterior as well as the interior of the ribosome

  2018cites this paper
• Modeling protein folding in vivo

  2018cites this paper
• Monitoring substrate enables real-time regulation of a protein localization pathway.

  2018cites this paper
• Structural basis for selective stalling of human ribosome nascent chain complexes by a drug-like molecule

  2018influential citation
• Non-equilibrium coupling of protein structure and function to translation-elongation kinetics.

  2018cites this paper
• Structure-based working model of SecDF , a proton-driven bacterial protein 3 translocation factor 4 5

  2018cites this paper
• The Folding Pathway of an Ig Domain is Conserved On and Off the Ribosome

  2018cites this paper
• Co-Translational Folding Trajectory of the HemK Helical Domain.

  2018cites this paper
• Pushing the resolution limit by correcting the Ewald sphere effect in single-particle Cryo-EM reconstructions

  2018cites this paper
• Biophysical Analysis of Sec-Mediated Protein Translocation in Nanodiscs

  2018cites this paper
• Identification and characterization of a translation arrest motif in VemP by systematic mutational analysis

  2018cites this paper
• Structural evidence for product stabilization by the ribosomal mRNA helicase

  2018cites this paper
• Transmembrane but not soluble helices fold inside the ribosome tunnel

  2018cites this paper
• Folding pathway of an Ig domain is conserved on and off the ribosome

  2018cites this paper
• Investigating the Effect of Chain Connectivity on the Folding of a Beta-Sheet Protein On and Off the Ribosome

  2018cites this paper
• Effects of protein size, thermodynamic stability, and net charge on cotranslational folding on the ribosome

  2018cites this paper
• Folding up and Moving on-Nascent Protein Folding on the Ribosome.

  2018cites this paper
• Mutational analysis of the human Xbp1 translational arrest peptide and construction of arrest-enhanced variants

  2017cites this paper
• Computational Studies of Protein Synthesis on the Ribosome and Ligand Binding to Riboswitches

  2017cites this paper
• Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P.

  2017cites this paper
• Dynamik des ribosomalen Ausgangstunnels

  2017cites this paper
• Gigadalton-scale shape-programmable DNA assemblies

  2017cites this paper
• Structural and mutational analysis of the ribosome-1 arresting human XBP 1 u 2

  year unknowncites this paper