tRNAs articles within Nature Communications

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  • Article
    | Open Access

    Genetic code expansion is limited by the degeneracy of the 61 sense codons which encode for only 20 amino acids. Here, the authors show that by combining hyperaccurate ribosomes and in vitro transcribed tRNAs, dramatic and extensive breaking of sense codon degeneracy can be achieved.

    • Clinton A. L. McFeely
    • , Bipasana Shakya
    •  & Matthew C. T. Hartman

  • Article
    | Open Access

    Aminoacyl-tRNA synthetases catalyze the ligation of amino acids to their cognate tRNAs. Here the authors report the cryo-EM structure of a human mitochondrial seryl-tRNA synthetase•mtRNASer complex showing how strong mutation pressure on mtRNA genes drove a rewiring of intermolecular recognition rules.

    • Bernhard Kuhle
    • , Marscha Hirschi
    •  & Paul Schimmel

  • Article
    | Open Access

    Peptidyl-tRNAs (pep-tRNAs) frequently dissociate from ribosome, called as pep-tRNA drop-off. But, its function remained unclear. The authors proposed a new quality control mechanism of protein synthesis by active rejection of miscoded pep-tRNAs in the early stage of translation.

    • Asuteka Nagao
    • , Yui Nakanishi
    •  & Tsutomu Suzuki

  • Article
    | Open Access

    Viruses completely depend on the host translational machinery, but their genomes are often enriched in rare codons and therefore should be translated with poor efficiency. Here, Jungfleisch et al. apply Ribo-Seq and RNASeq to provide a global view on the translational changes occurring during Chikungunya virus (CHIKV) infection. CHIKV infection induces a codon-specific reprogramming of the host translation machinery to favor the translation of viral RNA genomes over host mRNAs via tRNA modification.

    • Jennifer Jungfleisch
    • , René Böttcher
    •  & Juana Díez

  • Article
    | Open Access

    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

  • 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

    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

    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

    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

    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

    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 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

    Bilaterian mitochondria-encoded tRNA genes accumulate mutations at higher rates than their cytoplasmic tRNA counterparts, resulting in idiosyncratic structures. Here the authors suggest an evolutionary basis for the observed mutational freedom of mitochondrial (mt) tRNAs and reveal the associated co-adaptive structural and functional changes in mt aminoacyl-tRNA synthetases.

    • Bernhard Kuhle
    • , Joseph Chihade
    •  & Paul Schimmel

  • Article
    | Open Access

    E. coli and human tRNAs contain 3-(3-amino-3-carboxypropyl)uridine (acp3U) modification. Here the authors identify E. coli TapT and human DTWD1/2 as tRNA aminocarboxypropyltransferases responsible for acp3U formation. Inhibition of acp3U modification results in genome instability in heat-stressed E. coli and growth defects in human cells.

    • Mayuko Takakura
    • , Kensuke Ishiguro
    •  & Tsutomu Suzuki

  • Article
    | Open Access

    The biosynthesis of N6-threonylcarbamoylated adenosine 37 in tRNA (t6A) involves the YRDC enzyme and the KEOPS complex. Here, the authors report mutations in YRDC and the KEOPS component GON7 in Galloway-Mowat syndrome and determine the crystal structure of a GON7-containg subcomplex that suggests a role in KEOPS complex stability.

    • Christelle Arrondel
    • , Sophia Missoury
    •  & Géraldine Mollet

  • Article
    | Open Access

    MazF endoribonucleases are thought to arrest growth of Mycobacterium tuberculosis by global translation inhibition. Here, Barth et al. show that MazF-mt9 cleaves a specific tRNA, leading to ribosome stalling at AAA codons and thus selective mRNA degradation and changes in transcriptome and proteome.

    • Valdir C. Barth
    • , Ju-Mei Zeng
    •  & Nancy A. Woychik

  • Article
    | Open Access

    Adenovirus Virus-Associated (VA) noncoding RNAs interfere with the host system by mimicking double stranded RNAs. Here, the authors report a 2.7 Å crystal structure of VA-I RNA providing an understanding of its function.

    • Iris V. Hood
    • , Jackson M. Gordon
    •  & Jinwei Zhang

  • Article
    | Open Access

    5-carboxymethoxyuridine (cmo5U) is one of the RNA modifications found in bacterial tRNA anticodons. Here the authors show that the first step of cmo5U biosynthesis from uridine is mediated by either one of two parallel factors, TrhP or TrhO, and that cmo5U modification is required for efficient translation.

    • Yusuke Sakai
    • , Satoshi Kimura
    •  & Tsutomu Suzuki

  • Article
    | Open Access

    The genetic code for amino acids is nearly universal, and among eukaryotic nuclear genomes the only known reassignments are of codon CUG in yeasts. Here, the authors identify a third independent CUG transition in budding yeasts that is still ongoing with alternative tRNAs present in the genome.

    • Tadeusz Krassowski
    • , Aisling Y. Coughlan
    •  & Kenneth H. Wolfe

  • Article
    | Open Access

    The number of tRNA isodecoders has expanded significantly during evolution, which has resulted in ambiguity in tRNA selection by synthetases. Here the authors identify and characterize a dedicated proofreading factor that eliminates errors caused by ambiguity in tRNA selection by eukaryotic tRNA synthetases.

    • Santosh Kumar Kuncha
    • , Mohd Mazeed
    •  & Rajan Sankaranarayanan

  • Article
    | Open Access

    tRNA-dependent cysteine biosynthesis is catalyzed by the transsulfursome protein complex. Here, the authors use a multidisciplinary approach to structurally characterize the archaeal transsulfursome and propose a model for tRNA channeling in the complex.

    • Meirong Chen
    • , Koji Kato
    •  & Min Yao

  • 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

    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 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 |

    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

    EF-G enhances the rate of tRNA–mRNA translocation on the ribosome. Here the authors use single-molecule FRET to follow tRNA translocation in real time, identifying new chimeric intermediates and suggesting how EF-G binding and GTP hydrolysis change the energetic landscape of translocation to accelerate forward tRNA movement.

    • Sarah Adio
    • , Tamara Senyushkina
    •  & Marina V. Rodnina

  • Article
    | Open Access

    Borrelidin is an antibiotic with antimicrobial, antifungal, antimalarial and immunosuppressive activity that targets threonyl-tRNA synthetase. Here the authors show that borrelidin functions by preventing binding of all three ThrRS substrates and inducing a distinct, non-productive, conformation of the enzyme.

    • Pengfei Fang
    • , Xue Yu
    •  & Min Guo

  • Article |

    Agrobacterium radiobacter strain K84 generates an antibiotic targeting pathogenic strains of Agrobacterium tumefaciens, enabling its use as a biocontrol to prevent infection of crops. Here the authors show that this antibiotic inhibits leucyl-tRNA synthetases via an unusual mechanism that depends on binding of tRNALeu.

    • Shaileja Chopra
    • , Andrés Palencia
    •  & John S. Reader

  • Article
    | Open Access

    RNase P is a key enzyme implicated in transfer RNA maturation that removes the 5′-leader sequences from transfer RNA precursors. In this study, a biophysical characterization of a novel protein-only variant of RNase P, known as PRORP (PROteinaceous RNase P), reveals that transfer RNA recognition by PRORP is similar to that by ribonucleoprotein RNase P.

    • Anthony Gobert
    • , Franziska Pinker
    •  & Philippe Giegé

  • Article |

    Uridines at the wobble position of transfer RNA anticodons are usually modified to allow efficient decoding of messenger RNA codons. In this study, ALKBH8 is shown to be a bifunctional transfer RNA modification enzyme required for the formation of a novel diastereomeric pair of modified wobble uridines.

    • Erwin van den Born
    • , Cathrine B. Vågbø
    •  & Pål Ø. Falnes

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