Loss of N1-methylation of G37 in tRNA induces ribosome stalling and reprograms gene expression
- Thomas Jefferson University, United States
- Johns Hopkins University School of medicine, United States
- 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.
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Loss of N1-methylation of G37 in tRNA induces ribosome stalling and reprograms gene expressionNCBI Gene Expression Omnibus, GSE165592.
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Author details
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.
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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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
