Exploring cyclic networks of multisite modification reveals origins of information processing characteristics

Abstract

Multisite phosphorylation (and generally multisite modification) is a basic way of encoding substrate function and circuits/networks of post-translational modifications (PTM) are ubiquitous in cell signalling. The information processing characteristics of PTM systems are a focal point of broad interest. The ordering of modifications is a key aspect of multisite modification, and a broad synthesis of the impact of ordering of modifications is still missing. We focus on a basic class of multisite modification circuits: the cyclic mechanism, which corresponds to the same ordering of phosphorylation and dephosphorylation, and examine multiple variants involving common/separate kinases and common/separate phosphatases. This is of interest both because it is encountered in concrete cellular contexts, and because it serves as a bridge between ordered (sequential) mechanisms (representing one type of ordering) and random mechanisms (which have no ordering). We show that bistability and biphasic dose response curves of the maximally modified phosphoform are ruled out for basic structural reasons independent of parameters, while oscillations can result with even just one shared enzyme. We then examine the effect of relaxing some basic assumptions about the ordering of modification. We show computationally and analytically how bistability, biphasic responses and oscillations can be generated by minimal augmentations to the cyclic mechanism even when these augmentations involved reactions operating in the unsaturated limit. All in all, using this approach we demonstrate (1) how the cyclic mechanism (with single augmentations) represents a modification circuit using minimal ingredients (in terms of shared enzymes and sequestration of enzymes) to generate bistability and oscillations, when compared to other mechanisms, (2) new design principles for rationally designing PTM systems for a variety of behaviour, (3) a basis and a necessary step for understanding the origins and robustness of behaviour observed in basic multisite modification systems.

In distributive phosphorylation catalytic constants enable non-trivial dynamics

“…Networks of cyclic phosphorylation have been studied in Suwanmajo et al. ( 2020 ). The authors study in particular the following mass action network ( 1 ) derived from the reaction scheme of Fig.…”

“…1 a and , , and denote enzyme-substrate complexes): Suwanmajo et al. ( 2020 ) it is shown that for every admissible positive value of the total concentrations and all positive values of the reaction rate constants there exists a unique positive steady state. The authors furthermore provide parameter values where a Hopf bifurcation occurs (with the total amount of kinase as a bifurcation parameter) and sustained oscillations emerge (Suwanmajo et al.…”

“…The authors furthermore provide parameter values where a Hopf bifurcation occurs (with the total amount of kinase as a bifurcation parameter) and sustained oscillations emerge (Suwanmajo et al. 2020 , Fig. 4).…”