Ribosome

  • Article |

    Mass spectrometry and structural studies demonstrate the specific changes in protein composition that accompany the transition of ribosomes in zebrafish and Xenopus eggs from a dormant to an active state during early embryogenesis.

    • Friederike Leesch
    • , Laura Lorenzo-Orts
    •  & Andrea Pauli
  • Article |

    RibosomeST—a ribosome with a specialized nascent polypeptide exit tunnel—cotranslationally regulates the folding of a subset of male germ-cell-specific proteins that are essential for the formation of sperm.

    • Huiling Li
    • , Yangao Huo
    •  & Jiahao Sha
  • Article
    | Open Access

    Cryo-electron tomography is used to reveal the structural dynamics and functional diversity of translating ribosomes in Mycoplasma pneumoniae, providing insight into the translation elongation cycle inside cells and how it is reshaped by antibiotics.

    • Liang Xue
    • , Swantje Lenz
    •  & Julia Mahamid
  • Article |

    Single-molecule spectroscopy and structural studies were used to examine the dynamics of association of eIF1A and eIF5B with the human translation initiation complex and their role in presenting tRNA to the complex to initiate translation.

    • Christopher P. Lapointe
    • , Rosslyn Grosely
    •  & Joseph D. Puglisi
  • Article
    | Open Access

    Structural analysis of the Saccharomyces cerevisiae 80S ribosome trapped in an intermediate translocation state shows stabilization of codon–anticodon interactions by eukaryote-specific elements of the 80S ribosome, eEF2 and tRNA and demonstrates a major role for eEF2 in maintaining the directionality of translocation.

    • Muminjon Djumagulov
    • , Natalia Demeshkina
    •  & Gulnara Yusupova
  • Article |

    A high-resolution map of coding regions in the SARS-CoV-2 genome enables the identification of 23 unannotated open reading frames and quantification of the expression of canonical viral open reading frames.

    • Yaara Finkel
    • , Orel Mizrahi
    •  & Noam Stern-Ginossar
  • Article |

    Time-resolved cryogenic electron microscopy structures of a ribosome during the delivery of aminoacyl-tRNA by EF-Tu•GTP capture 33 ribosomal states, enabling visualization of the initial selection, proofreading and peptidyl transfer stages.

    • Anna B. Loveland
    • , Gabriel Demo
    •  & Andrei A. Korostelev
  • Article |

    Cryo-EM structures of late intermediates in the assembly of human 40S ribosomal subunits help to define the principles by which immature rRNA conformations and ribosomal biogenesis factors shape the 40S maturation process.

    • Michael Ameismeier
    • , Jingdong Cheng
    •  & Roland Beckmann
  • Article |

    A high-resolution structure of the human ribosome determined by cryo-electron microscopy visualizes numerous RNA modifications that are concentrated at functional sites with an extended shell, and suggests the possibility of designing more specific ribosome-targeting drugs.

    • S. Kundhavai Natchiar
    • , Alexander G. Myasnikov
    •  & Bruno P. Klaholz
  • Analysis |

    The large number of small, similarly sized proteins and the small number of heavy RNA molecules that make up a ribosome reduce the time required for reproduction.

    • Shlomi Reuveni
    • , Måns Ehrenberg
    •  & Johan Paulsson
  • Article |

    Structural ensembles of the 70S ribosome bound to cognate or near-cognate charged tRNAs in complex with EF-Tu illustrate the crucial role of the nucleotide G530 in decoding of mRNA, and demonstrate that translational fidelity results from direct control of GTPase by the decoding centre.

    • Anna B. Loveland
    • , Gabriel Demo
    •  & Andrei A. Korostelev
  • Letter |

    The structure of the bacterial 70S ribosome in complex with ArfA, the release factor RF2, a short non-stop mRNA and a cognate P-site tRNA is presented, revealing how ArfA and RF2 facilitate alternative translation termination of the non-stop ribosomal complex using a stop-codon surrogate mechanism.

    • Chengying Ma
    • , Daisuke Kurita
    •  & Ning Gao
  • Article |

    The structures of several states on the pathway of SelB-mediated delivery of selenocysteine-specific tRNA to the ribosome in Escherichia coli reveal the mechanism of UGA stop codon recoding to selenocysteine and show how codon recognition triggers activation of translational GTPases.

    • Niels Fischer
    • , Piotr Neumann
    •  & Holger Stark
  • Letter |

    Here, the selection of substrates by the protein–RNA complex known as the signal recognition particle (SRP) is investigated in the bacterium Escherichia coli, revealing that the SRP has a strong preference for hydrophobic transmembrane domains of inner membrane proteins.

    • Daniela Schibich
    • , Felix Gloge
    •  & Günter Kramer
  • Letter |

    A translation complex sequencing approach has been developed enabling intermediates of all mRNA-associated processes of translation to be isolated and localized across the transcriptome; the results support longstanding models of initiation and termination and offer new mechanistic insights.

    • Stuart K. Archer
    • , Nikolay E. Shirokikh
    •  & Thomas Preiss
  • Letter |

    Translation termination sequences are occasionally bypassed by the ribosome and the resulting proteins can be detrimental to the cell; here it is shown that cells can prevent such proteins from accumulating through peptides that are encoded within the 3' UTR of genes in both humans and C. elegans.

    • Joshua A. Arribere
    • , Elif S. Cenik
    •  & Andrew Z. Fire
  • Article |

    The genes encoding the subunits of oxidative phosphorylation complexes are split between the nuclear and mitochondrial genomes, but their translation is synchronized by signalling from the cytosol to the mitochondria.

    • Mary T. Couvillion
    • , Iliana C. Soto
    •  & L. Stirling Churchman
  • Letter |

    The structure of a bacterial ribosome–RelA complex reveals that RelA, a protein recruited to the ribosome in the case of scarce amino acids, binds in a different location to translation factors, and that this binding event suppresses auto-inhibition to activate synthesis of the (p)ppGpp secondary messenger, thus initiating stringent control.

    • Alan Brown
    • , Israel S. Fernández
    •  & V. Ramakrishnan
  • Article |

    The cryo-electron microscopy structure of the eukaryotic initiation factor 3 (eIF3) within the larger 43S complex is determined; the improved resolution enables visualization of the secondary structures of the subunits, as well as the contacts between eIF3 and both eIF2 and DHX29.

    • Amedee des Georges
    • , Vidya Dhote
    •  & Yaser Hashem
  • Letter |

    All eukaryotes utilize a single termination factor, eRF1, to halt translation when the ribosome encounters one of three possible stop codons; here electron cryo-microscopy structures of ribosome–eRF1 complexes in the process of recognizing each stop codon reveal how stop codons are discriminated from sense codons.

    • Alan Brown
    • , Sichen Shao
    •  & V. Ramakrishnan
  • Letter |

    A ribosome with tethered subunits, ‘Ribo-T’, is engineered by making a hybrid RNA composed of ribosomal RNA of large and small subunits; Ribo-T can support cell growth in vivo in the absence of wild-type ribosomes, and is used to establish a fully orthogonal ribosome–mRNA system.

    • Cédric Orelle
    • , Erik D. Carlson
    •  & Alexander S. Mankin
  • Article |

    The structure of the human ribosome at high resolution has been solved; by combining single-particle cryo-EM and atomic model building, local resolution of 2.9 Å was achieved within the most stable areas of the structure.

    • Heena Khatter
    • , Alexander G. Myasnikov
    •  & Bruno P. Klaholz
  • Letter |

    A single particle cryo-EM structure of the 70S ribosome in complex with the elongation factor Tu breaks the 3 Å resolution barrier of the technique and locally exceeds the resolution of previous crystallographic studies, revealing all modifications in rRNA and explaining their roles in ribosome function and antibiotic binding.

    • Niels Fischer
    • , Piotr Neumann
    •  & Holger Stark
  • Letter |

    A eukaryotic viral internal ribosome entry site (IRES) element is described that binds both bacterial and eukaryotic ribosomes and initiates translation in both, demonstrating that RNA structure-based initiation can occur in both these domains of life, although in bacteria the element uses a mechanism that differs from that in eukaryotes.

    • Timothy M. Colussi
    • , David A. Costantino
    •  & Jeffrey S. Kieft
  • Article |

    Specialized ribosomes (with a particular protein composition) carry out translation of specific transcripts; analysis of Hox mRNA translation in mice reveals that unique RNA structural elements within their 5′ UTRs, including internal ribosome entry sites and translation inhibitory elements, are responsible for this specialized mode of translation.

    • Shifeng Xue
    • , Siqi Tian
    •  & Maria Barna
  • Letter |

    The structure of the 39S large mitoribosome subunit is solved by cryo-electron microscopy at an impressive 3.4 Å resolution, revealing the location of 50 ribosomal proteins, the peptidyl transferase centre, the tRNAs within this active site, and the nascent peptide chain within the exit tunnel.

    • Basil J. Greber
    • , Daniel Boehringer
    •  & Nenad Ban
  • Article |

    Whereas previous structural investigation of ribosome inhibitors has been done using the prokaryotic ribosome, this work presents X-ray crystal structures of the yeast ribosome in complex with 16 inhibitors including eukaryotic-specific inhibitors; the inhibitors all bind the mRNA or tRNA binding sites, larger molecules appear to target specifically the first elongation cycle.

    • Nicolas Garreau de Loubresse
    • , Irina Prokhorova
    •  & Marat Yusupov
  • Letter |

    To investigate the mechanism of frameshifting during messenger RNA translation, a technique was developed to monitor translation of single molecules in real time using Förster resonance energy transfer (FRET); ribosomes were revealed to pause tenfold longer than usual during elongation at the frameshifting sites.

    • Jin Chen
    • , Alexey Petrov
    •  & Joseph D. Puglisi