McFarland2020 - Synthetase sequestration Model:a combined translation and tRNA charging cycle

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Short description
The Synthetase Sequestration Model (SSM) is a simplified translation model that considers explicitly two main steps in the process of tRNA aminoacylation: first, the tRNA is bound by the aminoacyl tRNA synthetase, and in a second step, the amino acid is attached to the tRNA. The tRNA then participates in the translation reaction, becoming deacylated as a result. The tRNA exists in states bound, charged and uncharged. In the bound state, the tRNA is bound to the synthetase but uncharged, i.e., the tRNA is sequestered by the synthetase. The model predicts how the balance between the three different tRNA states (empty, bound and charged) changes depending on aminoacyl tRNA synthetase availability.
Original code
Related Publication
  • The molecular aetiology of tRNA synthetase depletion: induction of a GCN4 amino acid starvation response despite homeostatic maintenance of charged tRNA levels
  • Ian Stansfield, Matthew R McFarland, Corina D Keller, Brandon M Childers, Stephen A Adeniyi, Holly Corrigall, Adélaïde Raguin, M Carmen Romano,
  • Nucleic Acids Research , 1/ 2020 , DOI: 10.1093/nar/gkaa055
  • University of Aberdeen
  • During protein synthesis, charged tRNAs deliver amino acids to translating ribosomes, and are then re-charged by tRNA synthetases (aaRS). In humans, mutant aaRS cause a diversity of neurological disorders, but their molecular aetiologies are incompletely characterised. To understand system responses to aaRS depletion, the yeast glutamine aaRS gene (GLN4) was transcriptionally regulated using doxycycline by tet-off control. Depletion of Gln4p inhibited growth, and induced a GCN4 amino acid starvation response, indicative of uncharged tRNA accumulation and Gcn2 kinase activation. Using a global model of translation that included aaRS recharging, Gln4p depletion was simulated, confirming slowed translation. Modelling also revealed that Gln4p depletion causes negative feedback that matches translational demand for Gln-tRNAGln to aaRS recharging capacity. This maintains normal charged tRNAGln levels despite Gln4p depletion, confirmed experimentally using tRNA Northern blotting. Model analysis resolves the paradox that Gln4p depletion triggers a GCN4 response, despite maintenance of tRNAGln charging levels, revealing that normally, the aaRS population can sequester free, uncharged tRNAs during aminoacylation. Gln4p depletion reduces this sequestration capacity, allowing uncharged tRNAGln to interact with Gcn2 kinase. The study sheds new light on mutant aaRS disease aetiologies, and explains how aaRS sequestration of uncharged tRNAs can prevent GCN4 activation under non-starvation conditions.
Rahuman Sheriff, Ian Stansfield

Metadata information

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Modelling approach(es)

Name Description Size Actions

Model files C representation of a combined translation and tRNA charging cycle (zipped archive) 18.58 KB Preview | Download

Additional files

README-SSM.txt C representation of a combined translation and tRNA charging cycle (readme file) 12.24 KB Preview | Download

  • Model originally submitted by : Ian Stansfield
  • Submitted: 05-Feb-2020 23:39:05
  • Last Modified: 05-Feb-2020 23:39:05
  • Version: 9 public model Download this version
    • Submitted on: 05-Feb-2020 23:39:05
    • Submitted by: Rahuman Sheriff
    • With comment: Edited model metadata online.