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Volume 613 Issue 7945, 26 January 2023

Stops making sense

When genes are read by ribosomes, stop codons act as punctuation, telling the ribosome when to halt protein synthesis. But in some protozoa, the base sequences that comprise stop codons can also encode amino acids, depending on where in the messenger RNA the codon appears. In this week’s issue, Leoš Shivaya Valášek and his colleagues reveal how these organisms recognize when codons should be read as an instruction to code and when as an order to stop. The researchers focused on a previously undescribed unicellular parasite called Blastocrithidia nonstop. They found that it has fundamental changes associated with the transfer RNA molecules that allow the ribosome to read stop codons as amino acids and so produce full-length proteins.

. Cover: Kelly Krause/Nature; Cover concept: Leoš Shivaya Valášek

This Week

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News in Focus

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  • News & Views

    • Messenger RNA has 64 possible triplet sequences, or codons, three of which usually terminate protein synthesis. But some organisms can use all codons to specify amino acids, thanks in part to a surprising feature of a transfer RNA.

      • Pavel V. Baranov
      • John F. Atkins
      News & Views
    • CRISPR–Cas is a bacterial defence system that can attack invading DNA to protect host cells, or help to insert DNA safely into the genome. Structures of this latter type of CRISPR–Cas system have now been visualized.

      • Orsolya Barabas
      • Phoebe A. Rice
      News & Views
    • The study of how chemical reactions work is key to the design of new reactions, but relies on hard work and expert knowledge. A machine-learning tool has been developed that could change the way this challenge is approached.

      • Danilo M. Lustosa
      • Anat Milo
      News & Views
    • A computational resource can identify candidate protein targets for almost all members of a major class of kinase enzyme in humans, with implications for understanding cell signalling in health and disease.

      • Sean J. Humphrey
      • Elise J. Needham
      News & Views
  • Perspective

  • Articles

    • An experiment is described in which the conversion of a single photon in a multimode cavity into a shower of low-energy photons was attempted, but failed owing to many-body localization and violation of Fermi’s golden rule.

      • Nitish Mehta
      • Roman Kuzmin
      • Vladimir E. Manucharyan
    • By using sub-cycle light transients to induce optical field emission of electron pulses from tungsten nanotips and a weak replica of the same transient, investigation of attosecond emission dynamics in real time is demonstrated.

      • H. Y. Kim
      • M. Garg
      • E. Goulielmakis
      Article Open Access
    • Innovations in device design, material fabrication and deep learning are described, leading to a wearable ultrasound transducer capable of dynamic cardiac imaging in various environments and under different conditions.

      • Hongjie Hu
      • Hao Huang
      • Sheng Xu
      Article Open Access
    • Because open-circuit voltage deficit is greater in wide-bandgap perovskite solar cells, the authors introduce diammonium molecules to modify perovskite surface states and achieve a more uniform spatial distribution of surface potential, enabling record voltage all-perovskite tandem solar cells.

      • Hao Chen
      • Aidan Maxwell
      • Edward H. Sargent
    • Mechanistic elucidation through currently available kinetic analysis is limited by mathematical approximations and human interpretation, here a deep neural network model has been trained to analyse ordinary kinetic data and automatically elucidate the corresponding mechanism class.

      • Jordi Burés
      • Igor Larrosa
    • The authors show that, in a chronic social defeat stress rodent model, a subset of male and female mice avoided social interaction with non-aggressive, same-sex juvenile mice and did not develop context-dependent social reward following these encounters.

      • Long Li
      • Romain Durand-de Cuttoli
      • Scott J. Russo
      Article Open Access
    • 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
    • Members of the DUF368-containing and DedA transmembrane protein families have conditional roles in undecaprenyl phosphate translocation in Gram-negative and Gram-positive bacteria and may have a widely conserved function in the biogenesis of microbial cell surface glycopolymers.

      • Brandon Sit
      • Veerasak Srisuknimit
      • Matthew K. Waldor
      Article Open Access
    • Pre-existing high-affinity antibodies alter germinal centre and memory B cell selection by lowering the activation threshold for B cells and through direct masking of their cognate epitopes, thereby permitting a diverse set of abundant lower-affinity clones targeting alternate epitopes to participate in the immune response.

      • Dennis Schaefer-Babajew
      • Zijun Wang
      • Michel C. Nussenzweig
      Article Open Access
    • Analyses of in-frame stop codons in protein-coding genes of Blastocrithidia nonstop with all three stop codons reassigned reveal a mechanism for UGA reassignment in eukaryotes involving shortening of the tRNA anticodon stem and a mutant eRF1 release factor.

      • Ambar Kachale
      • Zuzana Pavlíková
      • Julius Lukeš
    • Bitopic functionalized ligands based on fentanyl can target the sodium ion-binding site of the mu-opioid receptor and selectively modulate downstream signalling pathways, potentially leading to safer analgesics.

      • Abdelfattah Faouzi
      • Haoqing Wang
      • Susruta Majumdar
    • Structural studies of the CRISPR-associated transposon comprising Cas12k, TnsC, TnsB and TniQ from Scytonema hofmannii using cryo-electron microscopy reveal insights into the architecture and mechanism of RNA-guided DNA transposition.

      • Jung-Un Park
      • Amy Wei-Lun Tsai
      • Elizabeth H. Kellogg
      Article Open Access
    • Structural studies of Escherichia coli transcription intrinsic termination complexes representing distinct intermediates using cryo-electron microscopy provide insights into the steps and mechanism of transcription termination.

      • Linlin You
      • Expery O. Omollo
      • Yu Zhang
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