Structure of frequency-interacting RNA helicase from Neurospora crassa reveals high flexibility in a domain critical for circadian rhythm and RNA surveillance

The Function, Regulation, and Mechanism of Protein Turnover in Circadian Systems in Neurospora and Other Species

Circadian clocks drive a large array of physiological and behavioral activities. At the molecular level, circadian clocks are composed of positive and negative elements that form core oscillators generating the basic circadian rhythms. Over the course of the circadian period, circadian negative proteins undergo progressive hyperphosphorylation and eventually degrade, and their stability is finely controlled by complex post-translational pathways, including protein modifications, genetic codon preference, protein-protein interactions, chaperon-dependent conformation maintenance, degradation, etc. The effects of phosphorylation on the stability of circadian clock proteins are crucial for precisely determining protein function and turnover, and it has been proposed that the phosphorylation of core circadian clock proteins is tightly correlated with the circadian period. Nonetheless, recent studies have challenged this view. In this review, we summarize the research progress regarding the function, regulation, and mechanism of protein stability in the circadian clock systems of multiple model organisms, with an emphasis on Neurospora crassa, in which circadian mechanisms have been extensively investigated. Elucidation of the highly complex and dynamic regulation of protein stability in circadian clock networks would greatly benefit the integrated understanding of the function, regulation, and mechanism of protein stability in a wide spectrum of other biological processes.

Circadian regulation of physiology by disordered protein-protein interactions

Cellular circadian clocks, the molecular timers that coordinate physiology to the day/night cycle across the domains of life, are widely regulated by disordereddisordered protein interactions. Here, we review the disordered-disordered protein interactions in the circadian clock of Neurospora crassa (N. crassa), a filamentous fungus which is a model organism for clocks in higher eukaryotes. We focus on what is known about the interactions between the intrinsically disordered core negative arm protein FREQUENCEY (FRQ), the other proteins comprising the transcription-translation feedback loop, and the proteins that control output. We compare and contrast this model with other models of eukaryotic clocks, illustrating that protein disorder is a conserved and essential mechanism in the maintenance of circadian clock across species.

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

The circadian clock is the broadly conserved, protein-based, timekeeping mechanism that synchronizes biology to the Earth's 24-h light-dark cycle. Studies of the mechanisms of circadian timekeeping have placed great focus on the role that individual protein-protein interactions play in the creation of the timekeeping loop. However, research has shown that clock proteins most commonly act as part of large macromolecular protein complexes to facilitate circadian control over physiology. The formation of these complexes has led to the large-scale study of the proteins that comprise these complexes, termed here "circadian interactomics." Circadian interactomic studies of the macromolecular protein complexes that comprise the circadian clock have uncovered many basic principles of circadian timekeeping as well as mechanisms of circadian control over cellular physiology. In this review, we examine the wealth of knowledge accumulated using circadian interactomics approaches to investigate the macromolecular complexes of the core circadian clock, including insights into the core mechanisms that impart circadian timing and the clock's regulation of many physiological processes. We examine data acquired from the investigation of the macromolecular complexes centered on both the activating and repressing arm of the circadian clock and from many circadian model organisms.

Mtr4 RNA helicase structures and interactions

Mtr4 is a Ski2-like RNA helicase that plays a central role in RNA surveillance and degradation pathways as an activator of the RNA exosome. Multiple crystallographic and cryo-EM studies over the past 10 years have revealed important insight into the Mtr4 structure and interactions with protein and nucleic acid binding partners. These structures place Mtr4 at the center of a dynamic process that recruits RNA substrates and presents them to the exosome. In this review, we summarize the available Mtr4 structures and highlight gaps in our current understanding.

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

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. Video abstract.

Entrainment memories: What does stable mean?

Diurnal environmental factors (zeitgebers) set the circadian clock in an antagonistic way: The body clock is tuned forward in the morning, while the same factor late in the day puts the body clock back to a later time-point: Morning light, for example, reduces the clock-effective light-reception (zeitnehmer² ) by shifting the expression of the circadian, light-processing, molecular machinery more into the late, light-less night. Evening light does the same by a backward-shift, respectively. The balance between these daily back and forth adaptations results in a synchronization of the organismic timing with its environment. Those traditional models are challenged in this study. Using Neurospora as a model, I will explore how the entrainment process follows diverging trajectories depending on zeitgeber structure and strength, and the kind of transition between different entraining situations. The diverging routes of entrainment, systematically becoming earlier and earlier or later and later until eventually settling in distinct entrained phases, point out the existence of a long-range "memory" component. The view of entrainment as a non-acute reaction is very well confirmed in feedback loops, limit cycles, phase-response curves, and so forth. However, the presented findings enhance an extension of those concepts: The processing of zeitgebers by oscillating zeitnehmer modules resulting in a certain temporal inner structuring is not fully established within one repetition along a unique reaction norm. I hypothesize that the long-range, multi-cycle component in entraining requires a third parameter of description additional to current internal phase and zeitgeber condition, which originates from the differential of the two or more consecutive periodic situations. I hypothesize that this differential is represented by a gradient of Gibbs free energy of the entrainment pathways. Low points of free energy identify stable phases of entrainment. The fundamentality of Gibbs energy puts entrainment up for discussion not only as a timer but as an important kind of homeostasis.