Translation articles within Nature

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  • Letter |

    Two proteins are identified in yeast that regulate the timing of pre-ribosome export from the nucleus; Nug2 binds pre-60S particles until they are ready for export, at which time Nug2 is replaced by the export adaptor Nmd3, enabling the export machinery to recognise the pre-ribosome that is ready to be transferred to the cytoplasm.

    • Yoshitaka Matsuo
    • , Sander Granneman
    •  & Ed Hurt

  • Article |

    Three structures of the eukaryotic small ribosomal subunit in complex with initiator tRNA, mRNA and the initiation factors eIF1 and eIF1A have been solved; these structures offer insight into the contributions of the initiation factors, the mechanism by which mRNA is scanned, and the interactions that occur in the ribosome’s P site.

    • Ivan B. Lomakin
    •  & Thomas A. Steitz

  • Letter |

    Members of the SAM-dependent methyltransferase superfamily are involved in the modification of wobble uridine to 5-oxacetyl uridine in Gram-negative bacteria; CmoA converts SAM to carboxy-SAM (Cx-SAM; a metabolite that was unknown previously), and CmoB uses Cx-SAM to convert 5-hydroxyuridine to 5-oxyacetyl uridine in tRNA.

    • Jungwook Kim
    • , Hui Xiao
    •  & Steven C. Almo

  • Article |

    High-resolution cryo-EM density maps are used to present the structures of Drosophila and human 80S ribosomes in complex with eEF2, E-site transfer RNA and Stm1-like proteins, and reveal the presence of two additional structural layers in the ribosomes of metazoan eukaryotes.

    • Andreas M. Anger
    • , Jean-Paul Armache
    •  & Roland Beckmann

  • Letter |

    The frq gene, essential for circadian clock function, is shown to differ from most other genes in Neurospora by exhibiting non-optimal codon usage; by contrast, optimization of codon usage is unexpectedly found to affect the structure and function of the coded protein, subsequently impairing circadian feedback loops.

    • Mian Zhou
    • , Jinhu Guo
    •  & Yi Liu

  • News & Views |

    The discovery of a dramatic structural rearrangement that is stabilized by an RNA scaffold helps to explain how nascent proteins are delivered for export from the cell cytoplasm. See Letter p.271

    • Harris D. Bernstein

  • Article |

    Mice lacking 4E-BP2, an eIF4E repressor, display increased translation of neuroligins; the mice also show autism-related behaviours and alterations in hippocampal synaptic activity, and these are reversed by normalization of eIF4E activity or neuroligin 1 levels.

    • Christos G. Gkogkas
    • , Arkady Khoutorsky
    •  & Nahum Sonenberg

  • Letter |

    Stalled bacterial ribosomes can be rescued by interaction with SmpB protein and a highly structured transfer-messenger RNA, and a cryo-electron microscopy map of this complex now shows how EF-G-dependent translocation of this non-canonical ligand is facilitated by conformational changes in the ribosome and the transfer-messenger RNA.

    • David J. F. Ramrath
    • , Hiroshi Yamamoto
    •  & Christian M. T. Spahn

  • Letter |

    Accumulation of prion protein during prion replication causes persistent translational repression of global protein synthesis, which is mediated by eIF2α-P and is associated with synaptic failure and neuronal loss in prion-diseased mice; promoting translational recovery in hippocampi of prion-infected mice is neuroprotective.

    • Julie A. Moreno
    • , Helois Radford
    •  & Giovanna R. Mallucci

  • News & Views |

    A genome-wide characterization of active translation of messenger RNA following inhibition of mTOR will transform our view of this signalling protein's regulatory role in cancer. See Article p.55 & Letter p.109

    • Antonio Gentilella
    •  & George Thomas

  • Letter |

    mTORC1 is shown to regulate a translational program that requires the rapamycin-resistant 4E-BP family of translational repressors and consists almost entirely of mRNAs containing 5′ terminal oligopyrimidine or related motifs.

    • Carson C. Thoreen
    • , Lynne Chantranupong
    •  & David M. Sabatini

  • Letter |

    An integrated mechanism for decoding is proposed, based on six X-ray structures of the 70S ribosome determined at 3.1–3.4 Å resolution, modelling cognate or near-cognate states of the decoding centre at the proofreading step.

    • Natalia Demeshkina
    • , Lasse Jenner
    •  & Gulnara Yusupova

  • News & Views |

    A subtle biochemical alteration can reprogram signals that herald the termination of protein translation into signals encoding amino acids at the level of messenger RNA — and without altering the corresponding DNA. See Letter p.395

    • Adrian R. Ferré-D'Amaré

  • Letter |

    During translation, tRNAs enter the ribosome and then move sequentially through three sites, known as A, P and E, as they transfer their attached amino acids onto the growing peptide chain. How the ribosome facilitates tRNA translocation between the sites remains largely unknown. Now a study uses multiparticle cryoelectron microscopy of a ribosome bound to the translation elongation factor, EF-G, to get information about tRNA movement. It identifies two new substates and sees that translocation is linked to unratcheting of the 30S ribosomal subunit.

    • Andreas H. Ratje
    • , Justus Loerke
    •  & Christian M. T. Spahn

  • Article |

    tRNAs are synthesized in a premature form that requires trimming of the 5′ and 3′ ends and modification of specific nucleotides. RNase P, a complex containing a long catalytic RNA and a protein cofactor, catalyses the cleavage that generates the mature 5′ end. Here, the structure of RNase P bound to mature tRNAPhe is solved. Recognition of the leader sequence and its mechanism of cleavage is determined by soaking an oligonucleotide corresponding to the premature 5′ end into the crystal.

    • Nicholas J. Reiter
    • , Amy Osterman
    •  & Alfonso Mondragón

  • Letter |

    In most bacteria and all archaea, glutamyl-tRNA synthetase (GluRS) glutamylates both tRNAGlu and tRNAGln; Glu-tRNAGln is then converted to Gln-tRNAGln by an amidotransferase. Here the structure is reported of a bacterial complex containing tRNAGln, GluRS and the amidotransferase GatCAB. The structure provides an explanation for how the enzymes work consecutively: only one can assume a productive state at any time. There also seems to be an intermediary state in which neither enzyme is productive.

    • Takuhiro Ito
    •  & Shigeyuki Yokoyama

  • Letter |

    The translation of messenger RNA that lacks stop codons results in the production of aberrant proteins, which may have harmful effects on the cell. It is unclear how eukaryotic cells eliminate these 'non-stop' proteins. Here it is shown that, in Saccharomyces cerevisiae, an E3 ubiquitin ligase called Ltn1 acts in the quality-control pathway. It associates with ribosomes and marks non-stop proteins with ubiquitin, which targets the proteins for degradation.

    • Mario H. Bengtson
    •  & Claudio A. P. Joazeiro

  • Letter |

    Tail-anchored proteins have a single transmembrane domain at their carboxy termini and are post-translationally targeted to the endoplasmic reticulum via the cytosolic ATPase TRC40. These authors identify a conserved protein complex called Bat3 complex that is recruited to ribosomes, interacts with the transmembrane domain of newly released tail-anchored proteins and transfers them to TRC40 for subsequent targeting to the endoplasmic reticulum.

    • Malaiyalam Mariappan
    • , Xingzhe Li
    •  & Ramanujan S. Hegde

  • Letter |

    In the course of characterizing short RNAs from human cells using single-molecule high-throughput sequencing, these authors identify a new short RNA species. The presence of non-genomically encoded poly(U) residues at their 5' ends implies the existence of an unknown RNA copying mechanism in human cells.

    • Philipp Kapranov
    • , Fatih Ozsolak
    •  & Patrice M. Milos

  • Letter |

    LRRK2 activity is dysregulated in Parkinson's disease, but how it contributes to the pathogenesis is unknown. These authors show that Drosophila LRRK2 interacts with the Argonaute component (dAgo1) of the RNA-induced silencing complex. This is associated with reduced levels of dAgo1, interaction between phospho-4E-BP1 and hAgo2, and impairment of microRNA-mediated repression. This leads to overexpression of the cell cycle genes e2f1 and dp, and consequent degeneration of dopaminergic neurons.

    • Stephan Gehrke
    • , Yuzuru Imai
    •  & Bingwei Lu

  • Article |

    During protein synthesis within the ribosome, transfer RNAs (tRNAs) move sequentially through different sites as their attached amino acids are transferred onto the growing protein chain. Large conformational movements accompany this process. Here, a staggering 1.9 million electron cryomicroscopy images of the ribosome have been processed to visualize these changes. The results reveal that the ribosome functions as a Brownian machine that couples spontaneous changes driven by thermal energy to directed movement.

    • Niels Fischer
    • , Andrey L. Konevega
    •  & Holger Stark

  • News & Views |

    Time-resolved electron microscopy can capture structural changes in active macromolecular complexes, but detailed imaging is essential. The dynamics of one step in protein synthesis has been deduced from two million images.

    • Måns Ehrenberg

  • Letter |

    Stop codons in messenger RNA define when a protein sequence has been completely synthesized; such codons bind release factors (RFs), which cause the newly made protein to be released. Structures of RFs alone and in combination with the ribosome have been reported, but the energetics of the reaction in the presence of codons had not been determined. Here, molecular dynamics simulations of 14 termination complexes are used to define how termination is achieved and how the RFs distinguish different sequences.

    • Johan Sund
    • , Martin Andér
    •  & Johan Åqvist

  • Letter |

    The initiation of protein synthesis requires the eukaryotic translation initiation factor (eIF) 2, which uses energy from the hydrolysis of GTP. Another factor, eIF5, accelerates the GTP-hydrolysing activity of eIF2. Here, two other roles for eIF5 have been defined. One involves stabilizing GDP, the product of GTP hydrolysis, on eIF2. In its other role, eIF5 works with phosphorylated eIF2 to inhibit the guanine-nucleotide exchange factor eIF2B. These results clarify our understanding of how the initiation of translation is regulated.

    • Martin D. Jennings
    •  & Graham D. Pavitt

  • Article |

    Single-molecule studies allow biological processes to be examined one molecule at a time, as they occur. Here, zero-mode waveguides have been used to concentrate reactions in zeptolitre-sized volumes, making it possible to study real-time translocation by the ribosome. The binding of transfer RNAs (tRNAs) to the ribosome could be followed; the results show that tRNA release from the exit site is uncoupled from tRNA binding to the aminoacyl-tRNA site.

    • Sotaro Uemura
    • , Colin Echeverría Aitken
    •  & Joseph D. Puglisi

  • News & Views |

    The manufacture of proteins by ribosomes involves complex interactions of diverse nucleic-acid and protein ligands. Single-molecule studies allow us, for the first time, to follow the synthesis of full-length proteins in real time.

    • Susanne Brakmann

  • Letter |

    Evolution from one fitness peak to another must involve either transitions through intermediates of low fitness or skirting round the fitness valley through compensatory mutations elsewhere. Here, the base pairs in mitochondrial tRNA stems is used as a model to show that deep fitness valleys can be traversed. Transitions between AU and GC pairs have occurred during mammalian evolution without help from genetic drift or mutations elsewhere.

    • Margarita V. Meer
    • , Alexey S. Kondrashov
    •  & Fyodor A. Kondrashov

  • Letter |

    Although new amino acids with desirable properties can be devised, only a few have been successfully introduced into proteins by the cellular machinery. Even then, only one type of unnatural amino acid can be added to a given protein. Here, a new system has been designed that could allow the incorporation of up to 200 novel amino acids. The system involves an orthogonal ribosome that uses quadruplet — rather than triplet — codons, as well as orthogonal tRNA synthetase–tRNA pairs.

    • Heinz Neumann
    • , Kaihang Wang
    •  & Jason W. Chin

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