CRYPTOCHROMES promote daily protein homeostasis.

The daily organisation of most mammalian cellular functions is attributed to circadian regulation of clock-controlled protein expression, driven by daily cycles of CRYPTOCHROME-dependent transcriptional feedback repression. To test this, we used quantitative mass spectrometry to compare wild-type and CRY-deficient fibroblasts under constant conditions. In CRY-deficient cells, we found that temporal variation in protein, phosphopeptide, and K+ abundance was at least as great as wild-type controls. Most strikingly, the extent of temporal variation within either genotype was much smaller than overall differences in proteome composition between WT and CRY-deficient cells. This proteome imbalance in CRY-deficient cells and tissues was associated with increased susceptibility to proteotoxic stress, which impairs circadian robustness, and may contribute to the wide-ranging phenotypes of CRY-deficient mice. Rather than generating large-scale daily variation in proteome composition, we suggest it is plausible that the various transcriptional and post-translational functions of CRY proteins ultimately act to maintain protein and osmotic homeostasis against daily perturbation

Compensatory ion transport buffers daily protein rhythms to regulate osmotic balance and cellular physiology

Abstract: Between 6–20% of the cellular proteome is under circadian control and tunes mammalian cell function with daily environmental cycles. For cell viability, and to maintain volume within narrow limits, the daily variation in osmotic potential exerted by changes in the soluble proteome must be counterbalanced. The mechanisms and consequences of this osmotic compensation have not been investigated before. In cultured cells and in tissue we find that compensation involves electroneutral active transport of Na+, K+, and Cl− through differential activity of SLC12A family cotransporters. In cardiomyocytes ex vivo and in vivo, compensatory ion fluxes confer daily variation in electrical activity. Perturbation of soluble protein abundance has commensurate effects on ion composition and cellular function across the circadian cycle. Thus, circadian regulation of the proteome impacts ion homeostasis with substantial consequences for the physiology of electrically active cells such as cardiomyocytes

Cultivated meat as an alternative to traditional animal agriculture

Modern animal agriculture is unsustainable, and is a driver of greenhouse gas emissions and deforestation. There is a rapidly growing interest in alternative proteins as a solution to the increasing demand for food due to an increasing global population. One class of alternative proteins is cultivated meat, where stem cells are grown on an industrial scale to form a wide variety of meat products. Cultivated meat has several advantages over traditional meat, and may be more sustainable. However, the technology is still in its infancy, with many obstacles yet to overcome, including technological hurdles and regulatory development

Daily organisation of cellular physiology by mTOR kinase

Circadian rhythms are self-sustained biological oscillations with a period of approximately 24 hours. They are observed across all levels of biological scale and organise physiology to accommodate the different environmental and energetic demands of day and night. In mammalian cells, the mechanistic target of rapamycin complex (mTORC) activity exhibits daily rhythms both in vivo and in cultured cells. Circadian rhythms are sensitive to changes in mTORC activity, moreover, many circadian-regulated process are directly or indirectly sensitive to changes in mTORC activity e.g., protein synthesis and macromolecular crowding. In my research I have sought to gain insight into the nature of the interaction between circadian regulation and mTORC signalling, in vitro and in vivo. My lab previously observed reciprocal circadian rhythms in the abundance of soluble proteins and ions, which function to maintain cellular osmotic homeostasis and are dependent on mTORC activity. In the first part of this thesis, I explore the consequences of osmotic perturbation on circadian rhythms, and find that acute osmotic perturbations modulate circadian rhythms via mTORC. Next, I sought to understand the generation and function of cell-autonomous soluble protein, and functionally characterise them by quantitative proteomics and phosphoproteomics. I find that, in both cultured cells and in mouse liver, soluble protein rhythms are modulated by mTORC activity. Through pharmacological inhibition of mTORC1 and 2 I explore how circadian regulation of physiological outputs, such as wound healing, is mediated by mTORC activity, as well as the effect of mTORC inhibition on circadian timing in vitro and in vivo. Taken together, this work points to a model where rhythmic mTORC may be sufficient to modulate signalling to and from the circadian timekeeping machinery to drive most rhythmic physiological outputs, both in vitro and in vivo.Medical Research Counci

Roles of Sulfur Sources in the Formation of Alloyed Cu_2–<i>x</i>S_<i>y</i>Se_1–<i>y</i> Nanocrystals: Controllable Synthesis and Tuning of Plasmonic Resonance Absorption

Ternary alloyed Cu_2–<i>x</i>S_<i>y</i>Se_1–<i>y</i> nanocrystals (NCs) were synthesized by using a simple and phosphine-free colloidal approach, in which sulfur powder and 1-dodecanethiol (DDT) were used as sulfur sources. In both cases, the crystal phase transformed from cubic berzelianite to monoclinic djurleite structure together with the morphology evolution from quasi-triangular to spherical or discal with an increase of sulfur content. Accordingly, the near-infrared (NIR) localized surface plasmon resonance (LSPR) absorption of the as-obtained sulfur-rich NCs exhibited obvious red-shift of wavelength and widening of absorption width. When the sulfur powder was chosen as sulfur sources, the LSPR wavelength of the as-obtained alloyed Cu_2–<i>x</i>S_<i>y</i>Se_1–<i>y</i> NCs could be tuned from 975 to 1230 nm with a decrease of selenium content in the NCs. In contrast, the region of the red-shift could be up to 1250 nm for the alloyed NCs synthesized by incorporation of different DDT dosage into the reaction system. The different sulfur sources and the electron donating effects of the DDT as a ligand played an important role in the LSPR absorption tuning. This deduction could be testified by the post-treating the quasi-triangular Cu_2–<i>x</i>Se NCs with DDT under different temperatures and over different reaction time, which exhibited a red-shift of LSPR wavelength up to 450 nm due to coordination of DDT to Cu atoms on the NC surface while incorporating some sulfur anions into the lattice. This study offers a convenient tool for tuning the LSPR absorption of copper chalcogenide NCs and makes them for application in biological and optoelectronic fields

Circadian regulation of macromolecular complex turnover and proteome renewal.

Acknowledgements: The authors thank all members of O’Neill lab, Rachel Edgar, Manu Hegde and Szymon Juszkiewicz for valuable feedback and discussions, as well as Kathryn Lilley and Holger Kramer for advice on proteomics. The authors also thank biomedical technical staff at Medical Research Council (MRC) Ares facility and LMB facilities for assistance. NMR was supported by the Medical Research Council (MR/S022023/1). JON was supported by the Medical Research Council (MC_UP_1201/4).Although costly to maintain, protein homeostasis is indispensable for normal cellular function and long-term health. In mammalian cells and tissues, daily variation in global protein synthesis has been observed, but its utility and consequences for proteome integrity are not fully understood. Using several different pulse-labelling strategies, here we gain direct insight into the relationship between protein synthesis and abundance proteome-wide. We show that protein degradation varies in-phase with protein synthesis, facilitating rhythms in turnover rather than abundance. This results in daily consolidation of proteome renewal whilst minimising changes in composition. Coupled rhythms in synthesis and turnover are especially salient to the assembly of macromolecular protein complexes, particularly the ribosome, the most abundant species of complex in the cell. Daily turnover and proteasomal degradation rhythms render cells and mice more sensitive to proteotoxic stress at specific times of day, potentially contributing to daily rhythms in the efficacy of proteasomal inhibitors against cancer. Our findings suggest that circadian rhythms function to minimise the bioenergetic cost of protein homeostasis through temporal consolidation of protein turnover

CRYPTOCHROMES confer robustness, not rhythmicity, to circadian timekeeping

Circadian rhythms are a pervasive property of mammalian cells, tissues and behaviour, ensuring physiological adaptation to solar time. Models of cellular timekeeping revolve around transcriptional feedback repression, whereby CLOCK and BMAL1 activate the expression of PERIOD (PER) and CRYPTOCHROME (CRY), which in turn repress CLOCK/BMAL1 activity. CRY proteins are therefore considered essential components of the cellular clock mechanism, supported by behavioural arrhythmicity of CRY-deficient (CKO) mice under constant conditions. Challenging this interpretation, we find locomotor rhythms in adult CKO mice under specific environmental conditions and circadian rhythms in cellular PER2 levels when CRY is absent. CRY-less oscillations are variable in their expression and have shorter periods than wild-type controls. Importantly, we find classic circadian hallmarks such as temperature compensation and period determination by CK1δ/ε activity to be maintained. In the absence of CRY-mediated feedback repression and rhythmic Per2 transcription, PER2 protein rhythms are sustained for several cycles, accompanied by circadian variation in protein stability. We suggest that, whereas circadian transcriptional feedback imparts robustness and functionality onto biological clocks, the core timekeeping mechanism is post-translational

Macromolecular condensation buffers intracellular water potential

Acknowledgements: The order of the second and corresponding authors is arbitrary and these authors can change the order of their respective names to suit their own interests. This work has been supported by the Medical Research Council, as part of United Kingdom Research and Innovation (MC_UP_1201/13 to E.D.; MC_UP_1201/4 to J.S.O. and MCMB MR/V028669/1 to J.E.C.), the Human Frontier Science Program (Career Development Award CDA00034/2017 to E.D.), a Versus Arthritis Senior Research Fellowship Award (20875 to Q.-J.M.) and an MRC project grant (MR/K019392/1 to Q.-J.M.), a Grifols ‘ALTA’ Alpha-1-Antitrypsin Laurell’s Training Award and an Alpha-1-Foundation (grant number 614939) to J.E.C., and by a Wellcome Trust Sir Henry Dale Fellowship (208790/Z/17/Z to R.S.E.). N.M.R. is supported by a Medical Research Council Clinician Scientist Fellowship (MR/S022023/1). L.K.K. and V.J.P.-H. are recipients of EMBO Postdoctoral fellowships (ALTF 876-2021 and ALTF 577-2018, respectively). K.E.M. is supported by the Wellcome Trust through a Sir Henry Wellcome Postdoctoral Fellowship (220480/Z/20/Z). P.M.M. and J.B. were supported by Volkswagen ‘Life’ grant number 96827 and the DFG Excellence Cluster Physics of Life. We thank H. Andreas for frog maintenance; C. Godlee and M. Kaksonen for the gift of unpublished S. cerevisiae yeast strains and initial discussion of yeast experiments about temperature; P. Tran for S. pombe yeast strains; L. Miller for help with yeast work; A. Bertolotti for the kind gift of SH-SY5Y cells; and C. Russo, F. Jülicher, M. Gonzalez-Gaitan, K. Kruse, L. Blanchoin, J. Löwe, R. Hegde, P. Farrell and P. Crosby for discussion and suggestions; the staff at the companies Cherry Biotech and Elvesys, in particular T. Guérinier, for their help in designing and assembling the custom microfluidics system required for this project; the members of the Electronics and Mechanical workshops of the LMB for key support; the staff at the LMB Mass Spectrometry facility for performing and analysing MS data; and A. Prasad and T. Stevens for sharing the scripts for protein disorder and kinase motif predictions, respectively. Cartoons were created using BioRender. For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any author accepted manuscript version arising.Optimum protein function and biochemical activity critically depends on water availability because solvent thermodynamics drive protein folding and macromolecular interactions1. Reciprocally, macromolecules restrict the movement of ‘structured’ water molecules within their hydration layers, reducing the available ‘free’ bulk solvent and therefore the total thermodynamic potential energy of water, or water potential. Here, within concentrated macromolecular solutions such as the cytosol, we found that modest changes in temperature greatly affect the water potential, and are counteracted by opposing changes in osmotic strength. This duality of temperature and osmotic strength enables simple manipulations of solvent thermodynamics to prevent cell death after extreme cold or heat shock. Physiologically, cells must sustain their activity against fluctuating temperature, pressure and osmotic strength, which impact water availability within seconds. Yet, established mechanisms of water homeostasis act over much slower timescales2, 3; we therefore postulated the existence of a rapid compensatory response. We find that this function is performed by water potential-driven changes in macromolecular assembly, particularly biomolecular condensation of intrinsically disordered proteins. The formation and dissolution of biomolecular condensates liberates and captures free water, respectively, quickly counteracting thermal or osmotic perturbations of water potential, which is consequently robustly buffered in the cytoplasm. Our results indicate that biomolecular condensation constitutes an intrinsic biophysical feedback response that rapidly compensates for intracellular osmotic and thermal fluctuations. We suggest that preserving water availability within the concentrated cytosol is an overlooked evolutionary driver of protein (dis)order and function