Intrinsic disorder is an essential characteristic of components in the conserved circadian circuit

Abstract

Introduction The circadian circuit, a roughly 24 h molecular feedback loop, or clock, is conserved from bacteria to animals and allows for enhanced organismal survival by facilitating the anticipation of the day/night cycle. With circadian regulation reportedly impacting as high as 80% of protein coding genes in higher eukaryotes, the protein-based circadian clock broadly regulates physiology and behavior. Due to the extensive interconnection between the clock and other cellular systems, chronic disruption of these molecular rhythms leads to a decrease in organismal fitness as well as an increase of disease rates in humans. Importantly, recent research has demonstrated that proteins comprising the circadian clock network display a significant amount of intrinsic disorder. Main body In this work, we focus on the extent of intrinsic disorder in the circadian clock and its potential mechanistic role in circadian timing. We highlight the conservation of disorder by quantifying the extent of computationally-predicted protein disorder in the core clock of the key eukaryotic circadian model organisms Drosophila melanogaster, Neurospora crassa, and Mus musculus. We further examine previously published work, as well as feature novel experimental evidence, demonstrating that the core negative arm circadian period drivers FREQUENCY (Neurospora crassa) and PERIOD-2 (PER2) (Mus musculus), possess biochemical characteristics of intrinsically disordered proteins. Finally, we discuss the potential contributions of the inherent biophysical principals of intrinsically disordered proteins that may explain the vital mechanistic roles they play in the clock to drive their broad evolutionary conservation in circadian timekeeping. Conclusion The pervasive conservation of disorder amongst the clock in the crown eukaryotes suggests that disorder is essential for optimal circadian timing from fungi to animals, providing vital homeostatic cellular maintenance and coordinating organismal physiology across phylogenetic kingdoms. Graphical abstract

PRD-2 directly regulates casein kinase I and counteracts nonsense-mediated decay in the Neurospora circadian clock

“…The codons composing the frq transcript are non-optimal, which improves FRQ’s co-translational folding ( Zhou et al, 2013 ), and FRQ’s disordered protein structure is also stabilized by its binding partner FRH ( Hurley et al, 2013 ). Mammalian PER2 is also largely intrinsically disordered, and indeed circadian clock proteins across species have large stretches of intrinsic disorder which are in the early stages of functional characterization ( Pelham et al, 2020 ; Pelham et al, 2018 ) (reviewed in: Partch, 2020 ). These data document the complexity of post-transcriptional regulation of clock components, and this study demonstrates that even non-rhythmic clock transcripts such as CKI are under tight regulation that is essential for normal clock function.…”

“…Indeed, in both animals and fungi, the negative arm components are regulated at the RNA and protein levels to maintain circadian phase and period, and many of the molecular details of this regulation, the focus of this paper, are conserved. Negative arm components FRQ and PER are regulated by anti-sense transcription ( Koike et al, 2012 ; Kramer et al, 2003 ), by thermally regulated splicing ( Colot et al, 2005 ; Majercak et al, 1999 ), and display characteristics of intrinsically disordered proteins ( Pelham et al, 2020 ). Another highly conserved feature of fungal, insect, and mammalian negative arm components is progressive phosphorylation leading to their inactivation ( Baker et al, 2009 ; Ode et al, 2017 ; Vanselow et al, 2006 ) (reviewed in: Dunlap and Loros, 2018 ).…”

Circadian Interactomics: How Research Into Protein-Protein Interactions Beyond the Core Clock Has Influenced the Model of Circadian Timekeeping

“…Wang et al, 2017;Hurley et al, 2018;Collins et al, 2021). In addition, recent investigations have demonstrated that the core proteins of the circadian clock are either intrinsically disordered proteins or proteins with intrinsically disordered regions, a class of proteins that exists in a heterogeneous ensemble of conformations and has a large, transient, interactome (Partch et al, 2005;Tompa, 2012;Hurley et al, 2013;Oldfield and Dunker, 2014;Gustafson and Partch, 2015;Pelham et al, 2018Pelham et al, , 2020. All of the above have led many circadian researchers to shift their studies to the macromolecular protein complexes of the core clock proteins.…”

The pathogen-encoded signaling receptor Tir exploits host-like intrinsic disorder to assist infection

“…They do not adopt well-defined structures but exist as dynamic conformational ensembles that display unique properties complementary to globular proteins (2,3). IDPs/IDRs play essential roles in virtually all signaling pathways in the cell (4), including cell cycle (5), circadian circuits (6), post-transcriptional regulation (7), and protein degradation (8).…”

“…They do not adopt well-defined structures but exist as dynamic conformational ensembles that display unique properties complementary to globular proteins (2, 3). IDPs/IDRs play essential roles in signaling pathways (4), including cell cycle (4), circadian circuits (5), post-transcriptional regulation (6), and protein degradation (7). Given their ubiquitous relevance in cellular signaling, the onset of several human diseases, including cancer and neurodegeneration, are linked to dysfunctional disordered proteins (8).…”