Ribosome articles within Nature Communications

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  • Article
    | Open Access

    Metelev et al. use single-molecule tracking to study kinetics of translation directly in E. coli cells, and how it is affected by translation inhibitors and rRNA mutations. Their results support widespread 70S re-initiation on mRNAs.

    • Mikhail Metelev
    • , Erik Lundin
    •  & Magnus Johansson

  • Article
    | Open Access

    Jaako et al. discover a conserved tier of translational control that dynamically couples ribosome assembly and recycling. This mechanism is corrupted in an inherited bone marrow failure disorder associated with an increased risk of blood cancer.

    • Pekka Jaako
    • , Alexandre Faille
    •  & Alan J. Warren

  • Article
    | Open Access

    For decades, miRNAs have been studied primarily by ensemble methods, where a bulk collection of molecules is measured outside cells. Here, Kobayashi and Singer report methods to image miRNA function at the single-molecule level inside cells.

    • Hotaka Kobayashi
    •  & Robert H. Singer

  • Article
    | Open Access

    Rebelo-Guiomar et al. unveil late stage assembly intermediates of the human mitochondrial ribosome by inactivating the methyltransferase MRM2 in cells. Absence of MRM2 impairs organismal homeostasis, while its catalytic activity is dispensable for mitoribosomal biogenesis.

    • Pedro Rebelo-Guiomar
    • , Simone Pellegrino
    •  & Michal Minczuk

  • Article
    | Open Access

    Combined methylmalonic acidemia (MMA) and hyperhomocysteinemias are inborn errors of vitamin B12 metabolism, and mutations in the transcriptional regulators HCFC1 and RONIN (THAP11) underlie some forms of these disorders. Here the authors generated mouse models of a human syndrome due to mutations in RONIN (THAP11) and HCFC1, and show that this syndrome is both an inborn error of vitamin B12 metabolism and displays some features of ribosomopathy.

    • Tiffany Chern
    • , Annita Achilleos
    •  & Ross A. Poché

  • Article
    | Open Access

    Genome editing methods are limited by the inability to selectively edit repetitive sequences. Here the authors demonstrate precise editing of a repetitive genetic element, a ribosome, while avoiding edits to native sites sharing identical sequence.

    • Felix Radford
    • , Shane D. Elliott
    •  & Farren J. Isaacs

  • Article
    | Open Access

    EF-G drives ribosomal translocation along mRNA. Time-resolved cryo-EM captured translocation with EF-G•GTP—without inhibitors—revealing how EF-G uses ribosome fluctuations to drive translocation and GTP hydrolysis to leave at the right moment.

    • Christine E. Carbone
    • , Anna B. Loveland
    •  & Andrei A. Korostelev

  • Article
    | Open Access

    Mitoribosomes are remarkably diverse in their structures and compositions. Here the authors combine biochemistry, genetics, single particle cryo-electron microscopy and in situ cryo-electron tomography to reveal the mitochondrial ribosome of Chlamydomonas reinhardtii as an extreme example of evolution and species-specific adaptation.

    • Florent Waltz
    • , Thalia Salinas-Giegé
    •  & Yaser Hashem

  • Article
    | Open Access

    Many RNA viruses employ programmed –1 ribosomal frameshifting (PRF) to expand their coding capacity and optimize production of viral proteins. Here, the authors report structural and biophysical analysis of protein 2A from a cardiovirus, with insights into the mechanism of its PRF-stimulatory function.

    • Chris H. Hill
    • , Lukas Pekarek
    •  & Ian Brierley

  • Article
    | Open Access

    Processing bodies are phase separated compartments enriched in translationally repressed mRNAs. Here, Smith et al. show that, in sensory neurons, eukaryotic elongation factor 2 kinase (eEF2K) plays key roles in the regulation of processing body abundance and the formation of translationally inactive ribosomes.

    • Patrick R. Smith
    • , Sarah Loerch
    •  & Zachary T. Campbell

  • Article
    | Open Access

    Start codon selection is commonly thought to occur through the unidirectional scanning of the mRNA by the 40 S ribosome. Here the authors provide evidence that the pre-initiation complex can backslide on the mRNA to initiate translation at upstream AUG codons.

    • Yifei Gu
    • , Yuanhui Mao
    •  & Shu-Bing Qian

  • Article
    | Open Access

    Alpha-1-antitrypsin (AAT) deficiency results from misfolding-prone AAT variants. Here the authors show that AAT forms co-translational folding intermediates on the ribosome that persist upon release and determine its folding fate. They show too that the ribosome can also modulate misfolding-prone AAT intermediates during their synthesis.

    • Elena Plessa
    • , Lien P. Chu
    •  & Lisa D. Cabrita

  • Article
    | Open Access

    It is increasingly recognised that the spatial localisation of RNA is important for proper cellular function. Here, the authors investigate RNA localisation in skeletal muscle and develop methods to show that global active transport of RNA is required to maintain dispersion of gene products in the large muscle syncytium.

    • Lance T. Denes
    • , Chase P. Kelley
    •  & Eric T. Wang

  • Article
    | Open Access

    Movement of the ribosome along an mRNA requires the universally-conserved translocase (EF-G in bacteria) that couples GTP hydrolysis to directed movement. Here the authors use time-resolved Cryo-EM to visualize the GTPase-powered step on native translocating ribosomes and capture key translocation intermediates.

    • Valentyn Petrychenko
    • , Bee-Zen Peng
    •  & Niels Fischer

  • Article
    | Open Access

    Here, the authors use in vivo site-specific crosslinking to provide molecular-level insight into how the fungal Hsp70 chaperone system — the Ssb:Ssz1:Zuo1 triad — assists the folding process for the nascent peptide chain emerging from the ribosome tunnel.

    • Kanghyun Lee
    • , Thomas Ziegelhoffer
    •  & Elizabeth A. Craig

  • Article
    | Open Access

    Bacteria adjust the expression of some of their metabolic enzymes through metabolite-sensing ribosome nascent chain complexes. Here the authors present a cryo-EM structure of an E. coli ribosome stalled during translation of the TnaC leader peptide and propose a model for L-Trp dependent ribosome stalling where L-Trp competes with release factor 2 for binding to the TnaC-ribosome complex.

    • Anne-Xander van der Stel
    • , Emily R. Gordon
    •  & C. Axel Innis

  • Article
    | Open Access

    Ribosome profiling has become the gold standard to analyze mRNA translation dynamics, and the translation inhibitor cycloheximide (CHX) is often used in its application. Here the authors systematically demonstrate that CHX does not bias the outcome of ribosome profiling experiments in most organisms.

    • Puneet Sharma
    • , Jie Wu
    •  & Sebastian A. Leidel

  • Article
    | Open Access

    Shwachman-Diamond syndrome (SDS) is a leukemia predisposition disorder that is caused by defective release of eIF6 during ribosome assembly. Here the authors show that acquired somatic EIF6 mutations are frequent in the hematopoietic cells from individuals with SDS and provide a selective advantage over non-modified cells.

    • Shengjiang Tan
    • , Laëtitia Kermasson
    •  & Patrick Revy

  • Article
    | Open Access

    Trans-translation, mediated by small protein B (SmpB) and transfer-messenger RNA (tmRNA), enables recycling of the ribosomes stalled on defective mRNAs in bacteria. Here, the authors report structures of the ribosome during trans-translation that reveal a translocation intermediate and elucidate the movements of the tmRNA-SmpB complex in the ribosome.

    • Charlotte Guyomar
    • , Gaetano D’Urso
    •  & Reynald Gillet

  • Article
    | Open Access

    Translational frameshifting is a mechanism that expands the coding capabilities of mRNA. Here, structures of 70S ribosome complexes with GTPase elongation factor G (EF-G), a +1-frameshifting-prone mRNA and tRNAs reveal the cooperation between the ribosome and EF-G to induce +1 frameshifting during the translocation step.

    • Gabriel Demo
    • , Howard B. Gamper
    •  & Andrei A. Korostelev

  • Article
    | Open Access

    Assembly of the mitoribosome requires assistance from numerous specialized factors. Here, structures of the human 39S late assembly intermediates identify several assembly factors which keep the 16S rRNA in immature conformations, and reveal deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly.

    • Jingdong Cheng
    • , Otto Berninghausen
    •  & Roland Beckmann

  • Article
    | Open Access

    Here, the authors report de novo design, optimization and characterization of tRNAs that decode UGA stop codons in E. coli. The structure of the ribosome in a complex with the designed tRNA bound to a UGA stop codon suggests that distinct A-site ligands (tRNAs versus release factors) induce distinct conformation of the stop codon within the mRNA in the decoding center.

    • Suki Albers
    • , Bertrand Beckert
    •  & Zoya Ignatova

  • Article
    | Open Access

    Mitochondrial ribosomes (mitoribosomes) are characterized by a distinct architecture and thus biogenesis pathway. Here, cryo-EM structures of mitoribosome large subunit assembly intermediates elucidate final steps of 16 S rRNA folding, methylation and peptidyl transferase centre (PTC) completion, as well as functions of several mitoribosome assembly factors.

    • Miriam Cipullo
    • , Genís Valentín Gesé
    •  & Joanna Rorbach

  • Article
    | Open Access

    Maturation of the ribosomal peptidyl transferase center (PTC) is mediated by universally conserved GTPases. Here, cryo-EM structures of mitochondrial ribosomal large subunit assembly intermediates and of mature ribosomes offer insight into the roles of several assembly factors, including GTPBP6’s role in both ribosome biogenesis and recycling.

    • Hauke S. Hillen
    • , Elena Lavdovskaia
    •  & Ricarda Richter-Dennerlein

  • Article
    | Open Access

    Mammalian mitoribosomes feature dramatically reduced ribosomal RNAs and follow mitochondria specific assembly pathways. Here the authors describe the process of human mitochondrial ribosome maturation that results in the formation of the ribosomal active site region, including the peptidyl transferase loop and the two tRNA-binding loops.

    • Tea Lenarčič
    • , Mateusz Jaskolowski
    •  & Nenad Ban

  • Article
    | Open Access

    High-resolution cryo-EM structures and biochemical analyses of the human mitoribosome, in complex with mitochondria-specific factors mediating mitoribosome recycling, RRFmt and EF-G2mt, offer insight into mechanisms of mitoribosome recycling and resistance to antibiotic fusidic acid.

    • Ravi Kiran Koripella
    • , Ayush Deep
    •  & Rajendra K. Agrawal

  • Article
    | Open Access

    Mitochondrial ribosomes (mitoribosomes) are characterized by a distinct architecture and thus biogenesis pathway. Here, cryo-EM structures of mitoribosome large subunit assembly intermediates elucidate final steps of 16 S rRNA folding, methylation and peptidyl transferase centre (PTC) completion, as well as functions of several mitoribosome assembly factors.

    • Caillan Crowe-McAuliffe
    • , Victoriia Murina
    •  & Daniel N. Wilson

  • Article
    | Open Access

    22G-RNAs are single-stranded antisense small RNAs that are expressed in C. elegans germline. Here the authors show that CSR-1 dependent 22G-RNAs are produced in the cytosol on mRNAs actively engaged in translation and that codon usage of an mRNA regulates the biogenesis of CSR-1 dependent 22G-RNAs.

    • Meetali Singh
    • , Eric Cornes
    •  & Germano Cecere

  • Article
    | Open Access

    Macrolide antibiotics inhibit bacterial translation in a context-specific manner, arresting ribosomes at defined sites within mRNAs and selectively inhibiting synthesis of only a subset of cellular proteins. Here the authors provide a structural basis for the context-specific activity of macrolides on the eukaryotic ribosome.

    • Maxim S. Svetlov
    • , Timm O. Koller
    •  & Alexander S. Mankin

  • Article
    | Open Access

    Aminoglycoside antibiotics target the ribosome and induce misreading, yet which translation errors induce bacterial cell death is unclear. Here authors use quantitative mass spectrometry and show that bactericidal aminoglycosides induce clusters of errors in full-length proteins in vivo with as many as four amino acid substitutions in a row.

    • Ingo Wohlgemuth
    • , Raffaella Garofalo
    •  & Marina V. Rodnina

  • Article
    | Open Access

    Antibiotic-resistant bacterial pathogens pose a substantial threat to human health. Here, aided by structural analyses, the authors describe the molecular mechanism behind the activity of a series of compounds that inhibit trans-translation and are effective in eradicating N. gonorrhoeae infection in mice.

    • Zachary D. Aron
    • , Atousa Mehrani
    •  & Kenneth C. Keiler

  • Article
    | Open Access

    The ribosome undergoes multiple large-scale structural rearrangements during protein elongation. Here the authors present an all-atom model of the ribosome to study the energetics of P/E hybrid-state formation, an early conformational rearrangement occurring during translocation.

    • Mariana Levi
    • , Kelsey Walak
    •  & Paul C. Whitford

  • Article
    | Open Access

    Alternative rescue factor B (ArfB) is an enzyme that releases peptides from stalled ribosomes to allow ribosome recycling. Here the authors carry-out cryo-EM analyses of 70S ribosomes complexed with ArfB on either a short or longer mRNA to reveal distinct modes of ArfB function.

    • Christine E. Carbone
    • , Gabriel Demo
    •  & Andrei A. Korostelev

  • Article
    | Open Access

    The nascent polypeptide exit tunnel (NPET) is a functional center of the large ribosomal subunit through which the nascent polypeptide chains travel from the peptidyltransferase center (PTC). Here the authors provide structural insight into NPET maturation and how it is linked to other aspects of ribosome biogenesis.

    • Daniel M. Wilson
    • , Yu Li
    •  & John L. Woolford Jr

  • Article
    | Open Access

    The GTPase eIF5B is involved in the correct positioning of the initiator Met-tRNAiMet on the ribosome during the late stages of translation initiation. Here the authors present a cryo-EM structure of the ribosome in complex with eIF5B and Met-tRNAiMet immediately before transition into elongation, providing insight on Met-tRNAiMetdelivery and how the correct reading frame is established.

    • Jinfan Wang
    • , Jing Wang
    •  & Israel S. Fernández

  • Article
    | Open Access

    The drug-like compound PF846 and its derivatives inhibit the translation of specific mRNAs by the human ribosome. Here the authors show how PF846 arrests translation at the stop codon by slowing hydrolysis of the protein nascent chain at the ribosome P-site tRNA by eukaryotic release factor 1 (eRF1).

    • Wenfei Li
    • , Stacey Tsai-Lan Chang
    •  & Jamie H. D. Cate

  • Article
    | Open Access

    Rescue of ribosomes stalled on non-stop mRNA is essential for cell viability, and several rescue systems to resolve stalling exist in bacteria. Here, the authors use rapid kinetics and cryo-EM to reveal the pathway and selectivity mechanism of ArfB-mediated ribosome rescue.

    • Kai-Hsin Chan
    • , Valentyn Petrychenko
    •  & Marina V. Rodnina

  • Article
    | Open Access

    Translation within mitochondria is carried out by specialized mitoribosomes and translational factors. Here the authors describe cryo-EM structures of the human mitochondrial translation elongation factor G1 in complex with human mitoribosomes, revealing distinct mechanism that include conformational changes at the polypeptide exit tunnel.

    • Ravi Kiran Koripella
    • , Manjuli R. Sharma
    •  & Rajendra K. Agrawal

  • Article
    | Open Access

    As assembling 60S subunits transit from the nucleolus to the nucleoplasm, they undergo significant changes in protein composition and structure. Here, the authors provide a structural view of interconnected events during the middle steps of assembly that include the maturation of the central protuberance, the peptidyltransferase center and the nascent polypeptide exit tunnel.

    • Jelena Micic
    • , Yu Li
    •  & John L. Woolford Jr.

  • Article
    | Open Access

    Ribosome biogenesis in eukaryotes is a complex process that involves more than 200 protein factors. Here the authors present a structural analysis of a collection of human pre-60S structures sampled through a nuclear export adaptor NMD3, representing structural snapshots of pre-60S particles immediately before and after passing through nuclear pore complex.

    • Xiaomeng Liang
    • , Mei-Qing Zuo
    •  & Ning Gao

  • Article
    | Open Access

    Translation within mitochondria relies upon specialized mitoribosomes and initiation factors. Here the authors use Cryo-EM and single molecule approaches to describe the early steps leading to translation initiation in human mitochondria, and the roles of mitochondria-specific ribosomal proteins and initiation factors mtIF2 and mtIF3.

    • Anas Khawaja
    • , Yuzuru Itoh
    •  & Joanna Rorbach

  • Article
    | Open Access

    Ribosomes of all organisms have retained 5S rRNA as an autonomous rRNA species. Here the authors engineer a bacterial strain with ribosomes that do not have free 5S rRNA, and carry structural analyses that suggest the evolutionary preservation of 5S rRNA as an independent molecule is based on its role in the dynamic process of ribosome biogenesis.

    • Shijie Huang
    • , Nikolay A. Aleksashin
    •  & Alexander S. Mankin

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