Phosphorelays provide tunable signal processing capabilities for the cell

PLoS Comput Biol. 2013;9(11):e1003322. doi: 10.1371/journal.pcbi.1003322. Epub 2013 Nov 7.

Abstract

Achieving a complete understanding of cellular signal transduction requires deciphering the relation between structural and biochemical features of a signaling system and the shape of the signal-response relationship it embeds. Using explicit analytical expressions and numerical simulations, we present here this relation for four-layered phosphorelays, which are signaling systems that are ubiquitous in prokaryotes and also found in lower eukaryotes and plants. We derive an analytical expression that relates the shape of the signal-response relationship in a relay to the kinetic rates of forward, reverse phosphorylation and hydrolysis reactions. This reveals a set of mathematical conditions which, when satisfied, dictate the shape of the signal-response relationship. We find that a specific topology also observed in nature can satisfy these conditions in such a way to allow plasticity among hyperbolic and sigmoidal signal-response relationships. Particularly, the shape of the signal-response relationship of this relay topology can be tuned by altering kinetic rates and total protein levels at different parts of the relay. These findings provide an important step towards predicting response dynamics of phosphorelays, and the nature of subsequent physiological responses that they mediate, solely from topological features and few composite measurements; measuring the ratio of reverse and forward phosphorylation rate constants could be sufficient to determine the shape of the signal-response relationship the relay exhibits. Furthermore, they highlight the potential ways in which selective pressures on signal processing could have played a role in the evolution of the observed structural and biochemical characteristic in phosphorelays.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology
  • Hydrolysis
  • Models, Biological*
  • Phosphorylation / physiology*
  • Signal Transduction / physiology*

Grants and funding

EF is supported by a postdoctoral grant “Beatriu de Pinós” from the Generalitat de Catalunya and the project MTM2009-14163-C02-01 from the Spanish government. CW is supported by the Carlsberg Foundation, Denmark and Lundbeck Foundation, Denmark. VBK is the recipient of Dorothy Hodgkin Studentship funded by EPSRC and Microsoft Research. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.