Ultrasensitivity in phosphorylation-dephosphorylation cycles with little substrate

PLoS Comput Biol. 2013;9(8):e1003175. doi: 10.1371/journal.pcbi.1003175. Epub 2013 Aug 8.

Abstract

Cellular decision-making is driven by dynamic behaviours, such as the preparations for sunrise enabled by circadian rhythms and the choice of cell fates enabled by positive feedback. Such behaviours are often built upon ultrasensitive responses where a linear change in input generates a sigmoidal change in output. Phosphorylation-dephosphorylation cycles are one means to generate ultrasensitivity. Using bioinformatics, we show that in vivo levels of kinases and phosphatases frequently exceed the levels of their corresponding substrates in budding yeast. This result is in contrast to the conditions often required by zero-order ultrasensitivity, perhaps the most well known means for how such cycles become ultrasensitive. We therefore introduce a mechanism to generate ultrasensitivity when numbers of enzymes are higher than numbers of substrates. Our model combines distributive and non-distributive actions of the enzymes with two-stage binding and concerted allosteric transitions of the substrate. We use analytical and numerical methods to calculate the Hill number of the response. For a substrate with [Formula: see text] phosphosites, we find an upper bound of the Hill number of [Formula: see text], and so even systems with a single phosphosite can be ultrasensitive. Two-stage binding, where an enzyme must first bind to a binding site on the substrate before it can access the substrate's phosphosites, allows the enzymes to sequester the substrate. Such sequestration combined with competition for each phosphosite provides an intuitive explanation for the sigmoidal shifts in levels of phosphorylated substrate. Additionally, we find cases for which the response is not monotonic, but shows instead a peak at intermediate levels of input. Given its generality, we expect the mechanism described by our model to often underlay decision-making circuits in eukaryotic cells.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Allosteric Regulation
  • Computational Biology
  • Computer Simulation
  • Models, Biological*
  • Phosphoric Monoester Hydrolases / metabolism*
  • Phosphorylation
  • Phosphotransferases / metabolism*
  • Saccharomyces cerevisiae / enzymology
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / metabolism
  • Substrate Specificity

Substances

  • Saccharomyces cerevisiae Proteins
  • Phosphotransferases
  • Phosphoric Monoester Hydrolases

Grants and funding

BMCM is supported by Scottish Universities Life Sciences Alliance (SULSA) and by fellowship SFRH/BD/33524/2008 from the Fundação para a Ciência e a Tecnologia as part of the Ph.D. Program in Computational Biology of the Instituto Gulbenkian de Ciência, Oeiras, Portugal. The PhD program is also sponsored by Fundação Calouste Gulbenkian and Siemens, SA. PSS is supported by a Scottish Universities Life Sciences Alliance (SULSA) chair in Systems Biology. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.