An investigation of the role of Clockwork Orange (CWO) in circadian rhythms of Drosophila melanogaster: a mathematical modeling study

Abstract

The daily behavioral cycles exhibited by nearly all living organisms, known as circadian rhythms, are a crucial feature of life shaped by the Earth’s rotation and regulated by internal biological clocks. These approximately 24-hour patterns reflect intricate biochemical and physiological processes. The fruit fly, Drosophila melanogaster, has emerged as a pivotal model for studying circadian rhythms, with its genetic and molecular underpinnings extensively characterized. Mathematical modeling is a common tool used to dissect these dynamic systems. This study presents three new models of the circadian pathways of Drosophila melanogaster, each integrating three separate transcriptional feedback loops: the classic PER-TIM and VRI-PDP1 cycles, as well as the newly identified Clockwork Orange loop. These models investigate three possible dual functions of the CWO protein, hypothesizing that it may simultaneously activate and repress key circadian genes. They combine established molecular insights with new hypotheses derived from both in vivo data and CWO’s protein sequence using bioinformatics tools. The models employ a probabilistic ordinary differential equation (ODE) grounded in chemical kinetics to describe how transcription factors bind to and dissociate from their targets. Rather than relying extensively on potentially inconsistent in vitro measurements, the study focuses on developing conceptual models and testing hypotheses. Available data were primarily utilized to refine parameter estimates and assess model validity. This methodological choice provided the flexibility needed to probe the molecular functions of CWO more thoroughly. Model behavior was evaluated and validated using mutant data, and the resulting simulations offer insights into circadian biology by clarifying the role of CWO at the molecular level.