title: Identification of the mRNA targets of tRNA-specific regulation using genome-wide simulation of translation.
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 [Formula: see text] 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 [Formula: see text] concentration-dependent. Translation simulations showed that reduced [Formula: see text] 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.
authors.affiliation: University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK.
authors.forename: Barbara
authors.initials: B
authors.lastname: Gorgoni
authors.affiliation: DIMNP - UMR 5235 & CNRS, Université de Montpellier, 34095 Montpellier, France.|Laboratoire Charles Coulomb UMR5221 & CNRS, Université de Montpellier, 34095 Montpellier, France.
authors.forename: Luca
authors.initials: L
authors.lastname: Ciandrini
authors.affiliation: University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: McFarland
authors.affiliation: University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK.|University of Aberdeen, Institute for Complex Systems and Mathematical Biology, King's College, Aberdeen AB24 3UE, UK.
authors.forename: M Carmen
authors.initials: MC
authors.lastname: Romano
authors.affiliation: University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK i.stansfield@abdn.ac.uk.
authors.forename: Ian
authors.initials: I
authors.lastname: Stansfield
mesh_terms: D000483:Alleles; D000926:Anticodon; D020029:Base Pairing; D003062:Codon; D003198:Computer Simulation; D018628:Gene Dosage; D005786:Gene Expression Regulation; D015966:Gene Expression Regulation, Fungal; D055106:Genome-Wide Association Study; D008954:Models, Biological; D009154:Mutation; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D012343:RNA, Transfer / Q000235:genetics* / Q000378:metabolism; D015003:Yeasts / Q000235:genetics / Q000378:metabolism
chemical_list: D000926:Anticodon; D003062:Codon; D012333:RNA, Messenger; D012343:RNA, Transfer