Distinguishing Feedback Mechanisms in Clock Models

TL;DR

This paper compares models of the Kai circadian clock in cyanobacteria, focusing on feedback mechanisms, and proposes experimental methods to distinguish between positive and negative feedback loops in the system.

Contribution

It introduces a comparative analysis of feedback assumptions in Kai oscillator models and suggests experimental approaches to identify the actual feedback mechanism.

Findings

Models with opposing feedback assumptions can be experimentally distinguished.

Introducing a competitive KaiA-binding protein can reveal the feedback type.

Understanding feedback mechanisms informs on evolutionary clock architectures.

Abstract

Biological oscillators are very diverse but can be classified based on dynamical motifs such as the types of feedback loops present. The S. Elongatus circadian clock is a remarkable phosphorylation-based oscillator that can be reconstituted in vitro with only 3 different purified proteins: the clock proteins KaiA, KaiB, and KaiC. Despite a growing body of knowledge about the biochemistry of the Kai proteins, basic questions about how their interactions lead to sustained oscillations remain unanswered. Here, we compare models of this system that make opposing assumptions about whether KaiA sequestration introduces a positive or a negative feedback loop. We find that the two different feedback mechanisms can be distinguished experimentally by the introduction of a protein that binds competitively with KaiA. Understanding the dynamical mechanism responsible for oscillations in the Kai system may shed light on the broader question of what clock architectures have been selected by evolution and why.