Identification of the mRNA targets of tRNA-specific regulation using genome-wide simulation of translation

Barbara Gorgoni, Luca Ciandrini, Matthew R. McFarland, M. Carmen Romano, Ian Stansfield

Research output: Contribution to journalArticlepeer-review

9 Citations (Scopus)
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Abstract

tRNA gene copy number is a primary determinant of tRNA abundance and therefore the rate at which each tRNA delivers amino acids to the ribosome during translation. Low-abundance tRNAs decode rare codons slowly, but it is unclear which genes might be subject to tRNA-mediated regulation of expression. Here, those mRNA targets were identified via global simulation of translation. In-silico mRNA translation rates were compared for each mRNA in both wild-type and a tRNAGlnCUGtRNACUGGln sup70-65 mutant, which exhibits a pseudohyphal growth phenotype and a 75% slower CAG codon translation rate. Of 4900 CAG-containing mRNAs, 300 showed significantly reduced in silico translation rates in a simulated tRNA mutant. Quantitative immunoassay confirmed that the reduced translation rates of sensitive mRNAs were tRNAGlnCUGtRNACUGGln concentration-dependent. Translation simulations showed that reduced tRNAGlnCUGtRNACUGGln concentrations triggered ribosome queues, which dissipated at reduced translation initiation rates. To validate this prediction experimentally, constitutive gcn2 kinase mutants were used to reduce in vivo translation initiation rates. This repaired the relative translational rate defect of target mRNAs in the sup70-65 background, and ameliorated sup70-65 pseudohyphal growth phenotypes. We thus validate global simulation of translation as a new tool to identify mRNA targets of tRNA-specific gene regulation.
Original languageEnglish
Pages (from-to)9231-9244
Number of pages14
JournalNucleic Acids Research
Volume44
Issue number19
Early online date12 Jul 2016
DOIs
Publication statusPublished - 2 Nov 2016

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