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| Open AccessCombinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
The authors develop an RNA sequencing-based platform, PERSIST-seq, to simultaneously delineate in-cell mRNA stability, ribosome load, and in-solution stability of a diverse mRNA library to derive design principles for improved mRNA therapeutics.
- Kathrin Leppek
- , Gun Woo Byeon
- & Rhiju Das
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Article
| Open AccessSingle-molecule imaging of microRNA-mediated gene silencing in cells
For decades, miRNAs have been studied primarily by ensemble methods, where a bulk collection of molecules is measured outside cells. Here, Kobayashi and Singer report methods to image miRNA function at the single-molecule level inside cells.
- Hotaka Kobayashi
- & Robert H. Singer
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Article
| Open AccessRNA G-quadruplex in TMPRSS2 reduces SARS-CoV-2 infection
Understanding the mechanisms of SARS-CoV-2 infection is important to control the pandemic. Here the authors show the biological and pathological role of RNA G-quadruplex structure in both SARS-CoV-2 genome and host factors, particularly TMPRSS2.
- Geng Liu
- , Wenya Du
- & Xianghui Fu
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Article
| Open AccessCo-translational assembly orchestrates competing biogenesis pathways
The biogenesis of nuclear pores imposes a logistic challenge for cells. Here, the authors investigate structural motifs for co-translational interactions in nucleoporins and find that co-translational assembly events differ between paralogous assembly pathways thus contributing to faithful assembly.
- Maximilian Seidel
- , Anja Becker
- & Martin Beck
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Article
| Open AccessATF-4 and hydrogen sulfide signalling mediate longevity in response to inhibition of translation or mTORC1
The authors showed that, in C. elegans, inhibition of translation or mTORC1 increases ATF-4 expression independently of ISR signalling. ATF-4 promotes longevity by increasing hydrogen sulfide production by the enzyme CTH-2.
- Cyril Statzer
- , Jin Meng
- & Collin Y. Ewald
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Article
| Open AccessA late-stage assembly checkpoint of the human mitochondrial ribosome large subunit
Rebelo-Guiomar et al. unveil late stage assembly intermediates of the human mitochondrial ribosome by inactivating the methyltransferase MRM2 in cells. Absence of MRM2 impairs organismal homeostasis, while its catalytic activity is dispensable for mitoribosomal biogenesis.
- Pedro Rebelo-Guiomar
- , Simone Pellegrino
- & Michal Minczuk
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Article
| Open AccessCyclin B/CDK1 and Cyclin A/CDK2 phosphorylate DENR to promote mitotic protein translation and faithful cell division
The cell cycle regulates translation during mitosis by controlling DENR stability. Here, the authors show the non-canonical translation initiation complex DENR·MCTS1 is phosphorylated during mitosis by CDK1 and 2, enabling the translation of genes needed for proper mitotic progression.
- Katharina Clemm von Hohenberg
- , Sandra Müller
- & Aurelio A. Teleman
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Article
| Open AccessAlteration of ribosome function upon 5-fluorouracil treatment favors cancer cell drug-tolerance
Different mechanisms have been reported to explain resistance to chemotherapy in cancer. Here, the authors show that the chemotherapeutic drug 5-fluorouracil alters the function of ribosomes to promote pro-survival gene translation leading to chemotherapy resistance.
- Gabriel Therizols
- , Zeina Bash-Imam
- & Jean-Jacques Diaz
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Article
| Open AccessMutations in Hcfc1 and Ronin result in an inborn error of cobalamin metabolism and ribosomopathy
Combined methylmalonic acidemia (MMA) and hyperhomocysteinemias are inborn errors of vitamin B12 metabolism, and mutations in the transcriptional regulators HCFC1 and RONIN (THAP11) underlie some forms of these disorders. Here the authors generated mouse models of a human syndrome due to mutations in RONIN (THAP11) and HCFC1, and show that this syndrome is both an inborn error of vitamin B12 metabolism and displays some features of ribosomopathy.
- Tiffany Chern
- , Annita Achilleos
- & Ross A. Poché
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Article
| Open AccessTargeted editing and evolution of engineered ribosomes in vivo by filtered editing
Genome editing methods are limited by the inability to selectively edit repetitive sequences. Here the authors demonstrate precise editing of a repetitive genetic element, a ribosome, while avoiding edits to native sites sharing identical sequence.
- Felix Radford
- , Shane D. Elliott
- & Farren J. Isaacs
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Article
| Open AccessTime-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP
EF-G drives ribosomal translocation along mRNA. Time-resolved cryo-EM captured translocation with EF-G•GTP—without inhibitors—revealing how EF-G uses ribosome fluctuations to drive translocation and GTP hydrolysis to leave at the right moment.
- Christine E. Carbone
- , Anna B. Loveland
- & Andrei A. Korostelev
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Article
| Open AccessThe short isoform of the host antiviral protein ZAP acts as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting
Programmed ribosomal frameshifting (PRF) occurs in many viruses including SARS-CoV-2 to allow the translation of multiple proteins from a single transcript. Here, the authors identify the human short isoform of the zinc-finger antiviral protein (ZAP-S) as a direct regulator of PRF in SARS-CoV-2 that severely impairs SARS-CoV-2 frameshifting in cells and directly interacts with the SARS-CoV-2 RNA; interfering with the folding of the frameshift RNA element.
- Matthias M. Zimmer
- , Anuja Kibe
- & Neva Caliskan
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Article
| Open AccessHow to build a ribosome from RNA fragments in Chlamydomonas mitochondria
Mitoribosomes are remarkably diverse in their structures and compositions. Here the authors combine biochemistry, genetics, single particle cryo-electron microscopy and in situ cryo-electron tomography to reveal the mitochondrial ribosome of Chlamydomonas reinhardtii as an extreme example of evolution and species-specific adaptation.
- Florent Waltz
- , Thalia Salinas-Giegé
- & Yaser Hashem
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Article
| Open AccessStructural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch
Many RNA viruses employ programmed –1 ribosomal frameshifting (PRF) to expand their coding capacity and optimize production of viral proteins. Here, the authors report structural and biophysical analysis of protein 2A from a cardiovirus, with insights into the mechanism of its PRF-stimulatory function.
- Chris H. Hill
- , Lukas Pekarek
- & Ian Brierley
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Article
| Open AccesseIF2B-capturing viral protein NSs suppresses the integrated stress response
Here the authors show that a viral protein interferes with the binding of phosphorylated eIF2 to eIF2B, thereby suppressing the host integrated stress response (ISR). This suppression of the ISR abrogates translational changes of the host and ameliorates neurite degradation under stress.
- Kazuhiro Kashiwagi
- , Yuichi Shichino
- & Takuhiro Ito
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Article
| Open AccessCilia locally synthesize proteins to sustain their ultrastructure and functions
Cilia are microtubule-based organelles containing proteins transported from the cell body. Here, the authors show that the multicilia of mouse ependymal cells contain ribosomal components, tubulin mRNA,18 S rRNA and nascent tubulin peptides, suggesting local translation in the ciliary compartment.
- Kai Hao
- , Yawen Chen
- & Xueliang Zhu
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Article
| Open AccessA DAP5/eIF3d alternate mRNA translation mechanism promotes differentiation and immune suppression by human regulatory T cells
The differentiation of naive T cells to immune suppressing induced regulatory T (iTreg) cells requires TGF-beta-1 and downregulation of mTORC1 activity, which inhibits mRNA translation. Here the authors show that iTreg cell differentiation uses an alternate mRNA translation mechanism involving translation factors DAP5 and eIF3d.
- Viviana Volta
- , Sandra Pérez-Baos
- & Robert J. Schneider
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Article
| Open AccessFunctionally distinct roles for eEF2K in the control of ribosome availability and p-body abundance
Processing bodies are phase separated compartments enriched in translationally repressed mRNAs. Here, Smith et al. show that, in sensory neurons, eukaryotic elongation factor 2 kinase (eEF2K) plays key roles in the regulation of processing body abundance and the formation of translationally inactive ribosomes.
- Patrick R. Smith
- , Sarah Loerch
- & Zachary T. Campbell
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Article
| Open AccessBi-directional ribosome scanning controls the stringency of start codon selection
Start codon selection is commonly thought to occur through the unidirectional scanning of the mRNA by the 40 S ribosome. Here the authors provide evidence that the pre-initiation complex can backslide on the mRNA to initiate translation at upstream AUG codons.
- Yifei Gu
- , Yuanhui Mao
- & Shu-Bing Qian
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Article
| Open AccessAn integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation
To characterize molecular changes during cell type transitions, the authors develop a method to simultaneously measure protein expression and thermal stability changes. They apply this approach to study differences between human pluripotent stem cells, their progenies, parental and allogeneic cells.
- Pierre Sabatier
- , Christian M. Beusch
- & Roman A. Zubarev
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Article
| Open AccessNascent chains can form co-translational folding intermediates that promote post-translational folding outcomes in a disease-causing protein
Alpha-1-antitrypsin (AAT) deficiency results from misfolding-prone AAT variants. Here the authors show that AAT forms co-translational folding intermediates on the ribosome that persist upon release and determine its folding fate. They show too that the ribosome can also modulate misfolding-prone AAT intermediates during their synthesis.
- Elena Plessa
- , Lien P. Chu
- & Lisa D. Cabrita
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Article
| Open AccessMicrotubule-based transport is essential to distribute RNA and nascent protein in skeletal muscle
It is increasingly recognised that the spatial localisation of RNA is important for proper cellular function. Here, the authors investigate RNA localisation in skeletal muscle and develop methods to show that global active transport of RNA is required to maintain dispersion of gene products in the large muscle syncytium.
- Lance T. Denes
- , Chase P. Kelley
- & Eric T. Wang
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Article
| Open AccessStructural mechanism of GTPase-powered ribosome-tRNA movement
Movement of the ribosome along an mRNA requires the universally-conserved translocase (EF-G in bacteria) that couples GTP hydrolysis to directed movement. Here the authors use time-resolved Cryo-EM to visualize the GTPase-powered step on native translocating ribosomes and capture key translocation intermediates.
- Valentyn Petrychenko
- , Bee-Zen Peng
- & Niels Fischer
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Article
| Open AccessMultiplex suppression of four quadruplet codons via tRNA directed evolution
Genetic code expansion strategies are limited to specific codons that can be reassigned to new amino acids. Here the authors show that quadruplet-decoding tRNAs (qtRNAs) can be rapidly discovered and evolved to decode new quadruplet codons, enabling four independent decoding events in a single protein in living cells.
- Erika A. DeBenedictis
- , Gavriela D. Carver
- & Ahmed H. Badran
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Article
| Open AccessPathway of Hsp70 interactions at the ribosome
Here, the authors use in vivo site-specific crosslinking to provide molecular-level insight into how the fungal Hsp70 chaperone system — the Ssb:Ssz1:Zuo1 triad — assists the folding process for the nascent peptide chain emerging from the ribosome tunnel.
- Kanghyun Lee
- , Thomas Ziegelhoffer
- & Elizabeth A. Craig
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Article
| Open AccessDirected evolution of rRNA improves translation kinetics and recombinant protein yield
Ribosome kinetics are rate-limiting for protein synthesis. Here the authors evolve diverse 16S rRNAs for enhanced protein synthesis rates and genetic code expansion efficiencies in vivo.
- Fan Liu
- , Siniša Bratulić
- & Ahmed H. Badran
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Article
| Open AccessStructural basis for the tryptophan sensitivity of TnaC-mediated ribosome stalling
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
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| Open AccessA high-resolution temporal atlas of the SARS-CoV-2 translatome and transcriptome
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
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Article
| Open AccessHumans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments
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
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Article
| Open AccessSomatic genetic rescue of a germline ribosome assembly defect
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
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Article
| Open AccessTranslational control by DHX36 binding to 5′UTR G-quadruplex is essential for muscle stem-cell regenerative functions
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
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Article
| Open AccessStructures of tmRNA and SmpB as they transit through the ribosome
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
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Article
| Open AccessStructural dynamics of single SARS-CoV-2 pseudoknot molecules reveal topologically distinct conformers
The RNA pseudoknot of SARS-CoV-2 promotes -1 programmed ribosomal frameshifting. Here the authors use single molecule force spectroscopy to study the folding of this pseudoknot, showing that it forms at least two different pseudoknot conformers with distinct fold topologies.
- Krishna Neupane
- , Meng Zhao
- & Michael T. Woodside
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Article
| Open AccessThe integrated stress response is tumorigenic and constitutes a therapeutic liability in KRAS-driven lung cancer
The Integrated Stress Response (ISR) is a cytoprotective pathway upregulated in many cancers. Here the authors show that the activation of PERK/p-eIF2α arm of ISR enhances ERK phosphorylation through translation repression of DUSP6, thus resulting in KRAS-driven lung tumorigenesis.
- Nour Ghaddar
- , Shuo Wang
- & Antonis E. Koromilas
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Article
| Open AccessStructural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation
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
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Article
| Open AccessA distinct assembly pathway of the human 39S late pre-mitoribosome
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
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Article
| Open AccessStructural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics
Macrolides and ketolides antibiotics selectively interfere with the translation of a specific subset of proteins. Here the authors show how the macrolide erythromycin and the ketolide telithromycin interplay with the nascent polypeptide chain to arrest translation.
- Bertrand Beckert
- , Elodie C. Leroy
- & Daniel N. Wilson
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Article
| Open AccessMultiplexed functional genomic analysis of 5’ untranslated region mutations across the spectrum of prostate cancer
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
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Article
| Open AccessHigh-throughput 5′ UTR engineering for enhanced protein production in non-viral gene therapies
The engineering of 5′ UTRs that modulate protein expression remains a great challenge. Here we leverage synthetic biology and computational design to develop a high-throughput strategy to design, screen, and optimize 5′ UTRs that enhance protein expression for non-viral gene therapies.
- Jicong Cao
- , Eva Maria Novoa
- & Timothy K. Lu
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Article
| Open AccessRepurposing tRNAs for nonsense suppression
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
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Article
| Open AccessStructural basis for late maturation steps of the human mitoribosomal large subunit
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
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Article
| Open AccessStructural basis of GTPase-mediated mitochondrial ribosome biogenesis and recycling
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
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Article
| Open AccessStepwise maturation of the peptidyl transferase region of human mitoribosomes
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
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Article
| Open AccessDistinct mechanisms of the human mitoribosome recycling and antibiotic resistance
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
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Article
| Open AccessStructural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens
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
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Article
| Open AccessTranslation and codon usage regulate Argonaute slicer activity to trigger small RNA biogenesis
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
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Article
| Open AccessSugar phosphate activation of the stress sensor eIF2B
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
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Article
| Open Access40S ribosome profiling reveals distinct roles for Tma20/Tma22 (MCT-1/DENR) and Tma64 (eIF2D) in 40S subunit recycling
Following the termination of translation at stop codons, the eukaryotic 60S subunit of the ribosome is removed by the ATPase ABCE1. Here using 40S ribosome footprinting the authors provide a direct demonstration that the yeast orthologs of eIF2D, MCT-1, and DENR recycle the 40S subunits.
- David J. Young
- , Sezen Meydan
- & Nicholas R. Guydosh
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Article
| Open AccessContext-specific action of macrolide antibiotics on the eukaryotic ribosome
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