Loss of N1-methylation of G37 in tRNA induces ribosome stalling and reprograms gene expression

  1. Isao Masuda
  2. Jae-Yeon Hwang
  3. Thomas Christian
  4. Sunita Maharjan
  5. Fuad Mohammad
  6. Howard Gamper
  7. Allen R Buskirk
  8. Ya-MIng Hou  Is a corresponding author
  1. Thomas Jefferson University, United States
  2. Johns Hopkins University School of medicine, United States
  3. Johns Hopkins University School of Medicine, United States

Abstract

N1-methylation of G37 is required for a subset of tRNAs to maintain the translational reading-frame. While loss of m1G37 increases ribosomal +1 frameshifting, whether it incurs additional translational defects is unknown. Here we address this question by applying ribosome profiling to gain a genome-wide view of the effects of m1G37 deficiency on protein synthesis. Using E. coli as a model, we show that m1G37 deficiency induces ribosome stalling at codons that are normally translated by m1G37-containing tRNAs. Stalling occurs during decoding of affected codons at the ribosomal A site, indicating a distinct mechanism than that of +1 frameshifting, which occurs after the affected codons leave the A site. Enzyme- and cell-based assays show that m1G37 deficiency reduces tRNA aminoacylation and in some cases peptide-bond formation. We observe changes of gene expression in m1G37 deficiency similar to those in the stringent response that is typically induced by deficiency of amino acids. This work demonstrates a previously unrecognized function of m1G37 that emphasizes its role throughout the entire elongation cycle of protein synthesis, providing new insight into its essentiality for bacterial growth and survival.

Data availability

Sequencing data have been deposited in raw FASTQ files at the SRA and processed WIG files at the GEO under accession code GSE165592. Custom Python scripts used to analyze the ribosome profiling and RNA-seq data is freely available athttps://github.com/greenlabjhmi/2021_TrmD.

The following data sets were generated

Article and author information

Author details

  1. Isao Masuda

    Thomas Jefferson University, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9385-4424
  2. Jae-Yeon Hwang

    Johns Hopkins University School of medicine, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Thomas Christian

    Thomas Jefferson University, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Sunita Maharjan

    Thomas Jefferson University, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Fuad Mohammad

    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Howard Gamper

    Thomas Jefferson University, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Allen R Buskirk

    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2720-6896
  8. Ya-MIng Hou

    Thomas Jefferson University, Philadelphia, United States
    For correspondence
    ya-ming.hou@jefferson.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6546-2597

Funding

National Institute of General Medical Sciences (GM134931)

  • Ya-MIng Hou

National Institute of General Medical Sciences (GM110113)

  • Allen R Buskirk

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Alan G Hinnebusch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, United States

Publication history

  1. Received: May 22, 2021
  2. Preprint posted: May 28, 2021 (view preprint)
  3. Accepted: August 9, 2021
  4. Accepted Manuscript published: August 12, 2021 (version 1)
  5. Version of Record published: August 24, 2021 (version 2)

Copyright

© 2021, Masuda et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Isao Masuda
  2. Jae-Yeon Hwang
  3. Thomas Christian
  4. Sunita Maharjan
  5. Fuad Mohammad
  6. Howard Gamper
  7. Allen R Buskirk
  8. Ya-MIng Hou
(2021)
Loss of N1-methylation of G37 in tRNA induces ribosome stalling and reprograms gene expression
eLife 10:e70619.
https://doi.org/10.7554/eLife.70619

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