Translation

  • 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

    Here, Kim et al. apply various sequencing techniques (RPF-seq, QTI-seq, mRNA-seq, sRNA-seq) to unravel the high-resolution, longitudinal translatome and transcriptome of SARS-CoV-2. They identify a translation initiation site in the leader sequence of all genomic and subgenomic RNAs and show its relevance for the SARS-CoV-2 translatome.

    • Doyeon Kim
    • , Sukjun Kim
    •  & Daehyun Baek
  • 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

    Skeletal muscle stem cells (or satellite cells, SCs) are normally quiescent but activate and expand in response to injury. Here the authors show that induction of DHX36 helicase during SC activation promotes mRNA translation by binding to 5′UTR mRNA G-quadruplexes (rG4) in targets including Gnai2 and unwinding them.

    • Xiaona Chen
    • , Jie Yuan
    •  & Huating Wang
  • 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

    Mutations in 5’ untranslated regions (UTRs) have a functional role in gene expression in cancer. Here, the authors develop a sequencing-based high throughput functional assay named PLUMAGE and show the effects of these mutations on gene expression and their association with clinical outcomes in prostate cancer.

    • Yiting Lim
    • , Sonali Arora
    •  & Andrew C. Hsieh
  • 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

    The activity of translation initiation factor eIF2B is known to be modulated through stress-responsive phosphorylation of its substrate eIF2. Here, the authors uncover the regulation of eIF2B by the binding of sugar phosphates, suggesting a link between nutrient status and the rate of protein synthesis.

    • Qi Hao
    • , Jin-Mi Heo
    •  & Carmela Sidrauski
  • 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

    Senescence-associated secretory phenotype (SASP) involves secretion of factors such as pro-inflammatory cytokines. Here the authors show that MIR31HG regulates the expression and secretion of a subset of SASP components that induce paracrine invasion, through interaction with YBX1 and induction of IL1A translation.

    • Marta Montes
    • , Michal Lubas
    •  & Anders H. Lund
  • Article
    | Open Access

    Wobble uridine (U34) tRNA modifications are important for the decoding of AA-ending codons. Here the authors show that while the U34-codon content of mRNAs are predictive of changes in ribosome translation elongation, the resulting outcome in protein expression also relies on specific hydrophilic motifs-dependent protein aggregation and clearance.

    • Francesca Rapino
    • , Zhaoli Zhou
    •  & Pierre Close
  • 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

    Reveromycin A (RM-A) selectively inhibits eukaryotic cytoplasmic isoleucyltRNA synthetase (IleRS). Herein, the authors show that RM-A molecule occupies the tRNAIle binding site of Saccharomyces cerevisiae IleRS, and that RM-A cooperates with isoleucine or isoleucyl-adenylate for IleRS binding.

    • Bingyi Chen
    • , Siting Luo
    •  & Huihao Zhou
  • Article
    | Open Access

    The significance of translated upstream open reading frames is not well known. Here, the authors investigate genetic variants in these regions, finding that they are under high evolutionary constraint and may contribute to disease.

    • David S. M. Lee
    • , Joseph Park
    •  & Yoseph Barash
  • Article
    | Open Access

    KEOPS is an evolutionary conserved complex with a core of four core subunits—Pcc1, Kae1, Bud32 and Cgi121—that catalyzes the universal and essential tRNA modification N6-threonylcarbamoyl adenosine (t6A). Here the authors describe a Cgi121-tRNA crystal structure and new composite model of the KEOPS holo-enzyme-substrate complex that shed light on the t6A catalytic cycle and its regulation.

    • Jonah Beenstock
    • , Samara Mishelle Ona
    •  & Frank Sicheri
  • Article
    | Open Access

    Translatome remodelling controls stress-adaptive protein output. Here the authors reveal that in response to stimuli, eIF5A functions as a pH-regulated translation factor that responds to fermentation-induced acidosis affecting cellular metabolism.

    • Nathan C. Balukoff
    • , J. J. David Ho
    •  & Stephen Lee
  • 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

    AtaT is a type-II toxin from enterohemorrhagic E. coli, reported to acetylate the aminoacyl-moiety of initiator Met-tRNAfMet, thus inhibiting translation initiation. Biochemical analysis suggests that AtaT has a broader specificity for aminoacyl-tRNAs and inhibits global translation. Structure of AtaT in complex with acetylated Met-tRNAfMet offers insight into the substrate selection by the enzyme.

    • Yuka Yashiro
    • , Yuriko Sakaguchi
    •  & Kozo Tomita
  • Article
    | Open Access

    In vivo experiments and optical tweezers force-spectroscopy measurements assessing the co-translational folding of the G-domain from bacterial elongation factor G reveal a sequential folding pathway initiating from the C-terminus. These results suggest that protein folding and synthesis proceed in opposite directions.

    • Xiuqi Chen
    • , Nandakumar Rajasekaran
    •  & Christian M. Kaiser
  • 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

    Upon stress, translation of ATF4 is induced by reinitiating ribosomes following translation of short upstream open reading frames (uORFs). Here the authors show that translation re-initiation of ATF4 is mediated by the DENR-MCTS1 complex which acts on uORFs containing certain penultimate codons.

    • Jonathan Bohlen
    • , Liza Harbrecht
    •  & Aurelio A. Teleman
  • Article
    | Open Access

    Nonsense-mediated mRNA decay (NMD) was thought to ensue when ribosomes fail to terminate translation properly. However, the authors observe similar ribosome occupancy at stop codons of NMD sensitive and insensitive mRNAs, showing that human NMD is not activated by stable ribosome stalling as previously suggested.

    • Evangelos D. Karousis
    • , Lukas-Adrian Gurzeler
    •  & Oliver Mühlemann
  • 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

    The relative abundance of specific tRNA can impact protein production rate, folding, and messenger RNA stability. Here the authors describe QuantM-tRNA seq — a method to monitor tRNA abundance and sequence variants — and uncover distinctions in isodecoder expression between tissues that are independent of the anticodon pool of each tRNA family.

    • Otis Pinkard
    • , Sean McFarland
    •  & Jeff Coller
  • Article
    | Open Access

    Antibiotics targeting protein translation interact in hard-to-predict ways. Here, Kavčič et al. interpret these interactions in terms of translation bottlenecks, the kinetics of drug uptake and target binding, bacterial growth laws, and a model of queued traffic progression.

    • Bor Kavčič
    • , Gašper Tkačik
    •  & Tobias Bollenbach