Translation articles within Nature Communications

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  • Article
    | Open Access

    The GTP-bound form of initiation factor 2 (IF2) promotes translation initiation by accelerating 50S ribosomal subunit joining the 30S ribosomal initiation complex (30S IC). Here the authors use single-molecule FRET and ensemble rapid kinetic methods to uncover the mechanism behind IF2-mediated subunit joining.

    • Kelvin Caban
    • , Michael Pavlov
    •  & Ruben L. Gonzalez Jr

  • Article
    | Open Access

    The eukaryotic release factor eRF1 is able to recognize the three stop codons UAA, UAG and UGA with high accuracy, while discriminating against near-cognate codons. Here the authors use molecular dynamic simulation to provide insight into the molecular basis behind the remarkable codon specificity of eRF1.

    • Christoffer Lind
    • , Ana Oliveira
    •  & Johan Åqvist

  • Article
    | Open Access

    The yeast Hsp70 homolog Ssb is a chaperone that binds translating ribosomes where it is thought to function primarily by promoting nascent peptide folding. Here the authors find that the ribosome biogenesis defect associated with the loss of Ssb is attributable to a specific disruption in TORC1 signaling rather than defects in ribosomal protein folding.

    • Kaivalya Mudholkar
    • , Edith Fitzke
    •  & Sabine Rospert

  • Article
    | Open Access

    Ribosome biogenesis is a dynamic process that involves the ordered assembly of ribosomal proteins and numerous RNA structural rearrangements. Here the authors apply ChemModSeq, a high-throughput RNA structure probing method, to quantitatively measure changes in RNA flexibility during the nucleolar stages of 60S assembly in yeast.

    • Elena Burlacu
    • , Fredrik Lackmann
    •  & Sander Granneman

  • Article
    | Open Access

    When bacteria enter the stationary growth phase, protein translation is suppressed via the dimerization of 70S ribosomes into inactive complexes. Here the authors provide a structural basis for how the dual domain hibernation promotion factor promotes ribosome dimerization and hibernation in bacteria.

    • Linda E. Franken
    • , Gert T. Oostergetel
    •  & Albert Guskov

  • Article
    | Open Access

    Under conditions of nutrient limitation, bacterial ribosomes undergo dimerization, forming a 100S complex that is translationally inactive. Here the authors present the structural basis for formation of the 100S complexes in Gram-positive bacteria, shedding light on the mechanism of translation suppression by the ribosome-silencing factors.

    • Donna Matzov
    • , Shintaro Aibara
    •  & Ada E. Yonath

  • Article
    | Open Access

    Subcellular localization of RNAs and proteins is important for polarized cells such as neurons. Here the authors differentiate mouse embryonic stem cells into neurons, and analyze the local transcriptome, proteome, and translated transcriptome in their cell bodies and neurites, providing a unique resource for future studies on neuronal polarity.

    • Alessandra Zappulo
    • , David van den Bruck
    •  & Marina Chekulaeva

  • Article
    | Open Access

    The transcription factor Gcn4 is known to regulate yeast amino acid synthesis. Here, the authors show that Gcn4 also acts as a repressor of protein biosynthesis in a range of conditions that enhance yeast lifespan, such as ribosomal protein knockout, calorie restriction or mTOR inhibition.

    • Nitish Mittal
    • , Joao C. Guimaraes
    •  & Mihaela Zavolan

  • Article
    | Open Access

    Several protein quality control mechanisms are in place to trigger the rapid degradation of aberrant polypeptides and mRNAs. Here the authors describe a mechanism of ribosome-mediated quality control that involves the ubiquitination of ribosomal proteins by the E3 ubiquitin ligase Hel2/RQT1.

    • Yoshitaka Matsuo
    • , Ken Ikeuchi
    •  & Toshifumi Inada

  • Article
    | Open Access

    Programmed −1 ribosomal frameshifting (−1 PRF) is a mechanism whereby specific signals within mRNAs direct ribosomes to shift into an alternative reading frame. Here the authors describe a mechanism of −1 PRF that is temporally regulated by a viral protein over the course of the virus replicative cycle.

    • Sawsan Napthine
    • , Roger Ling
    •  & Andrew E. Firth

  • Article
    | Open Access

    Membrane proteins are inserted co-transnationally through the association between ribosome, the signal recognition particle and its receptor, and the membrane-bound translocon. Here the authors present a cryo-EM reconstruction of this quaternary complex in the activated state and propose a model for signal sequence transfer to the translocon.

    • Ahmad Jomaa
    • , Yu-Hsien Hwang Fu
    •  & Nenad Ban

  • Article
    | Open Access

    Mistranslation results in amino acid changes in proteins known as phenotypic mutations and these occur at a much higher rate than DNA mutations. Here, the authors show that mistranslation can increase the response to directional selection by exacerbating the fitness effects of deleterious DNA mutations.

    • Sinisa Bratulic
    • , Macarena Toll-Riera
    •  & Andreas Wagner

  • Article
    | Open Access

    PTEN is a potent tumour suppressor involved in cell growth, proliferation and survival. Here the authors identify an N-terminal extended isoform of PTEN, termed PTENβ that negatively regulates ribosomal DNA transcription and cell proliferation, expanding the pleiotropic functions of the PTEN family.

    • Hui Liang
    • , Xi Chen
    •  & Yuxin Yin

  • Article
    | Open Access

    Fragile X syndrome (FXS) is a leading cause of autism and neurons lacking FMRP show aberrant mRNA translation and intracellular signalling. Here, the authors show that neurons from Fmr1 knockout mice have increased levels of ADCY1 protein, producing abnormal ERK1/2 signalling, dysregulated protein synthesis and behavioural symptoms associated with FXS.

    • Ferzin Sethna
    • , Wei Feng
    •  & Hongbing Wang

  • Article
    | Open Access

    Translocation of the tRNA on the ribosome is associated with large-scale molecular movements of the ribosomal L1 stalk. Here the authors identify the key determinants that allow these dramatic movements, and suggest they represent general strategies used to enable large-scale motions in functional RNAs.

    • Srividya Mohan
    •  & Harry F Noller

  • Article
    | Open Access

    Nonsense-mediated mRNA decay (NMD) is a quality control pathway that recognizes and degrades transcripts harbouring nonsense mutations. Here the authors show that the ATPase activity of UPF1 mediates functional interactions between the NMD machinery and ribosomes required for efficient ribosome release at premature termination codons.

    • Lucas D. Serdar
    • , DaJuan L. Whiteside
    •  & Kristian E. Baker

  • Article
    | Open Access

    mRNA surveillance is essential to maintain homeostasis in eukaryotes and is activated by mRNAs lacking a stop codon. Here the authors describe a high resolution cryo-EM structure of a nonstop complex that shows how arrested ribosome recognition is achieved during Dom34-mediated mRNA surveillance.

    • Tarek Hilal
    • , Hiroshi Yamamoto
    •  & Christian M.T. Spahn

  • Article
    | Open Access

    The correct folding of proteins often requires the intervention molecular chaperones, which can occur co-translationally. Here the authors identify elements of yeast Ssb (Hsp70) that mediate ribosomal binding, and suggest a mechanism that directs efficient interaction of Ssb with the nascent chain.

    • Marie A. Hanebuth
    • , Roman Kityk
    •  & Elke Deuerling

  • Article
    | Open Access

    Epithelial-to-mesenchymal transition is a key process in tumorigenesis but little is known about the molecular mechanism regulating such process at the translational level. Here, the authors identify a subset of mRNAs important for this process that are specifically modulated by the RNA-binding protein CELF1.

    • Arindam Chaudhury
    • , Shebna Cheema
    •  & Joel R. Neilson

  • Article
    | Open Access

    Mycobacteria can adapt to the stress of human infection by entering a dormant state. Here the authors show that hypoxia-induced dormancy in M. bovisBCG involves the reprogramming of tRNA wobble modifications and copy numbers, coupled with biased use of synonymous codons in survival genes.

    • Yok Hian Chionh
    • , Megan McBee
    •  & Peter C. Dedon

  • Article
    | Open Access

    Ribosome recycling orchestrated by ABCE1 connects translation termination and mRNA surveillance mechanisms with re-initiation. Using a cross-linking and mass spectrometry approach, Kiosze-Becker et al. provide new information on the large conformational rearrangements that occur during ribosome recycling.

    • Kristin Kiosze-Becker
    • , Alessandro Ori
    •  & Robert Tampé

  • Article
    | Open Access

    Initiation factor eIF2, common to eukaryotes and archaea, is a central actor in translation initiation. Here the authors describe two cryo-EM structures of archaeal 30S initiation complexes that provide a novel view of the central role that e/aIF2 plays in start codon selection.

    • Pierre-Damien Coureux
    • , Christine Lazennec-Schurdevin
    •  & Yves Mechulam

  • Article
    | Open Access

    The translation of mRNA by the ribosome is governed by a series of large-scale conformational transitions. Here the authors use MD simulations to demonstrate how the rate of dissociation of elongation factor Tu affects the dynamics of tRNA accommodation and proofreading.

    • Jeffrey K. Noel
    •  & Paul C. Whitford

  • Article
    | Open Access

    Leishmania donovani is a protozoan parasite that can cause fatal infections in humans. Here the authors present a high resolution cryoEM structure of the L. donovani80S ribosome and compare it to its human counterpart to provide insight into the basis for drug selectivity towards this eukaryotic parasite.

    • Xing Zhang
    • , Mason Lai
    •  & Z. Hong Zhou

  • Article
    | Open Access

    Prokaryotic translation initiation involves mRNA-ribosomal RNA base pairing interactions. Here, the authors provide evidence for a similar base pairing interactions occurring between the human h4 mRNA and helix 16 of the small subunit rRNA to position the correct AUG codon in the decoding site.

    • Franck Martin
    • , Jean-François Ménétret
    •  & Gilbert Eriani

  • Article
    | Open Access

    Eukaryotic ribosome biogenesis involves a large number of maturations factors which are responsible for the stepwise assembly of the ribosomal subunits. Here the authors use an array of biochemical and structural biology methods to investigate the function of the UtpA and UtpB complexes as part of the small subunit processome.

    • Mirjam Hunziker
    • , Jonas Barandun
    •  & Sebastian Klinge

  • Article
    | Open Access

    Mutations in the translational activator of cytochrome c oxidase subunit I (TACO1) causes cytochrome c oxidase deficiency and Leigh Syndrome in patients. Here, the authors characterize mice with a mutation that causes lack of TACO1 expression, identifying a mouse model that could be useful for preclinical trials.

    • Tara R. Richman
    • , Henrik Spåhr
    •  & Aleksandra Filipovska

  • Article
    | Open Access

    Tsr1 is an essential ribosome biogenesis factor that has known similarity to GTPases. Here, the authors report the Tsr1 crystal structure and show that it is similar to GTPases but that active site residues are not conserved; modelling of the structure into the pre-40S maps allows inferences on ribosomal maturation to be drawn.

    • Urszula M. McCaughan
    • , Uma Jayachandran
    •  & Atlanta G. Cook

  • Article
    | Open Access

    The CsrA protein binds to and represses translation of certain bacterial mRNAs. Here, Dugar et al. show for the human pathogen Campylobacter jejunithat the major flagellin mRNA acts as both a target and a regulatory 'sponge' for CsrA, and is localized at the cell poles in a translation-dependent manner.

    • Gaurav Dugar
    • , Sarah L. Svensson
    •  & Cynthia M. Sharma

  • Article
    | Open Access

    Upstream open reading frames (uORFs) can repress gene expression. Here, Guo-Liang Chew and colleagues use bioinformatics approaches to show that conservation of uORF-mediated translational repression is mediated by sequence features in human, mouse and zebrafish genomes.

    • Guo-Liang Chew
    • , Andrea Pauli
    •  & Alexander F. Schier

  • Article
    | Open Access

    The global measurement of ribosome occupancy on mRNAs is commonly used as a proxy in estimating rates of protein synthesis. Here the authors describe Xtail, a computational approach that facilitates the extraction of accurate quantitative insight from ribosome profiling data (Ribo-Seq).

    • Zhengtao Xiao
    • , Qin Zou
    •  & Xuerui Yang

  • Article
    | Open Access

    During protein elongation, the translocation of mRNA and tRNA molecules across the 30S ribosomal subunit is associated with large-scale motions of the 30S head domain. Here the authors carry out MD simulations to probe the associated steric interactions and identify novel tilting motions during the late stages of translocation.

    • Kien Nguyen
    •  & Paul C. Whitford

  • Article
    | Open Access

    The co-translational insertion of proteins into membranes requires interaction between a ribosome-bound signal recognition particle (SRP) and a membrane-bound translocon. Here the authors use cryo-EM and single particle reconstructions to obtain a comprehensive view of the co-translational protein targeting process.

    • Ahmad Jomaa
    • , Daniel Boehringer
    •  & Nenad Ban

  • Article
    | Open Access

    The anticodon loops of almost all tRNAs contain modifications known to be important for their function. Here the authors use crystallography to provide new mechanistic insights into how the modification at the wobble position of the E. coli tRNALysUUUassists in discrimination between cognate and near-cognate codons.

    • Alexey Rozov
    • , Natalia Demeshkina
    •  & Gulnara Yusupova

  • Article
    | Open Access

    In response to intracellular signals, bacterial translational riboswitches embedded in mRNAs can regulate gene expression through inhibition of translation initiation. Here, the authors describe SiM-KARTS, a novel approach for detecting changes in the structure of single RNA molecules in response to a ligand.

    • Arlie J. Rinaldi
    • , Paul E. Lund
    •  & Nils G. Walter

  • Article |

    Toxin–antitoxin systems of the Vap class regulate the growth of several bacterial pathogens including Mycobacterium tuberculosis. Here, the authors show that toxin VapC-mt4 arrests M. tuberculosis growth by specifically cleaving three tRNAs at a single site in their anticodon stem loop, leading to translation inhibition.

    • Jonathan W. Cruz
    • , Jared D. Sharp
    •  & Nancy A. Woychik

  • Article
    | Open Access

    The Hepatitis C virus (HCV) relies on an internal ribosome entry site (IRES) for translation of all the proteins encoded by its single-stranded RNA genome. Here the authors present a near-atomic cryo-EM structure of the HCV IRES bound to the human ribosome, shedding light on the initiation mechanism of HCV's and related IRESs.

    • Nick Quade
    • , Daniel Boehringer
    •  & Nenad Ban

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