Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin

PLoS Comput Biol. 2016 Feb 22;12(2):e1004774. doi: 10.1371/journal.pcbi.1004774. eCollection 2016 Feb.

Abstract

Cellular functions are largely regulated by reversible post-translational modifications of proteins which act as switches. Amongst these, S-palmitoylation is unique in that it confers hydrophobicity. Due to technical difficulties, the understanding of this modification has lagged behind. To investigate principles underlying dynamics and regulation of palmitoylation, we have here studied a key cellular protein, the ER chaperone calnexin, which requires dual palmitoylation for function. Apprehending the complex inter-conversion between single-, double- and non-palmitoylated species required combining experimental determination of kinetic parameters with extensive mathematical modelling. We found that calnexin, due to the presence of two cooperative sites, becomes stably acylated, which not only confers function but also a remarkable increase in stability. Unexpectedly, stochastic simulations revealed that palmitoylation does not occur soon after synthesis, but many hours later. This prediction guided us to find that phosphorylation actively delays calnexin palmitoylation in resting cells. Altogether this study reveals that cells synthesize 5 times more calnexin than needed under resting condition, most of which is degraded. This unused pool can be mobilized by preventing phosphorylation or increasing the activity of the palmitoyltransferase DHHC6.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acylation / genetics*
  • Calnexin* / chemistry
  • Calnexin* / genetics
  • Calnexin* / metabolism
  • Computational Biology
  • Computer Simulation
  • Endoplasmic Reticulum / metabolism
  • HeLa Cells
  • Humans
  • Lipoylation / genetics*
  • Models, Biological*
  • RNA Interference

Substances

  • Calnexin

Grant support

The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement n. 340260 - PalmERa'. This work was also supported by grants from the Swiss National Science Foundation (to FGvdG and to VH), and the Swiss SystemsX.ch initiative evaluated by the Swiss National Science Foundation (LipidX) (to FGvdG and to VH). TD is a recipient of an iPhD fellowship from the Swiss SystemsX.ch initiative. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.