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Chen Y, Huang JH, Phong C, Ferrell JE. Viscosity-dependent control of protein synthesis and degradation. Nat Commun 2024; 15:2149. [PMID: 38459041 PMCID: PMC10923802 DOI: 10.1038/s41467-024-46447-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 02/28/2024] [Indexed: 03/10/2024] Open
Abstract
It has been proposed that the concentration of proteins in the cytoplasm maximizes the speed of important biochemical reactions. Here we have used Xenopus egg extracts, which can be diluted or concentrated to yield a range of cytoplasmic protein concentrations, to test the effect of cytoplasmic concentration on mRNA translation and protein degradation. We find that protein synthesis rates are maximal in ~1x cytoplasm, whereas protein degradation continues to rise to a higher optimal concentration of ~1.8x. We show that this difference in optima can be attributed to a greater sensitivity of translation to cytoplasmic viscosity. The different concentration optima could produce a negative feedback homeostatic system, where increasing the cytoplasmic protein concentration above the 1x physiological level increases the viscosity of the cytoplasm, which selectively inhibits translation and drives the system back toward the 1x set point.
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Affiliation(s)
- Yuping Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Jo-Hsi Huang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Connie Phong
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - James E Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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Puls O, Ruiz-Reynés D, Tavella F, Jin M, Kim Y, Gelens L, Yang Q. Mitotic waves in frog egg extracts: Transition from phase waves to trigger waves. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576267. [PMID: 38496576 PMCID: PMC10942321 DOI: 10.1101/2024.01.18.576267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Cyclin-dependent kinase 1 (Cdk1) activity rises and falls throughout the cell cycle, a cell-autonomous process known as mitotic oscillations. These oscillators can synchronize when spatially coupled, providing a crucial foundation for rapid synchronous divisions in large early embryos like Drosophila (~ 0.5 mm) and Xenopus (~ 1.2 mm). While diffusion alone cannot achieve such long-range coordination, recent studies have proposed two types of mitotic waves, phase and trigger waves, to explain the phenomena. How the waves establish over time for efficient spatial coordination remains unclear. Using Xenopus laevis egg extracts and a Cdk1 FRET sensor, we observe a transition from phase waves to a trigger wave regime in an initially homogeneous cytosol. Adding nuclei accelerates such transition. Moreover, the system transitions almost immediately to this regime when externally driven by metaphase-arrested extracts from the boundary. Employing computational modeling, we pinpoint how wave nature, including speed-period relation, depends on transient dynamics and oscillator properties, suggesting that phase waves appear transiently due to the time required for trigger waves to entrain the system and that spatial heterogeneity promotes entrainment. Therefore, we show that both waves belong to a single biological process capable of coordinating the cell cycle over long distances.
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Affiliation(s)
- Owen Puls
- Department of Physics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel Ruiz-Reynés
- Laboratory of Dynamics in Biological Systems, KU Leuven, Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
- IFISC (CSIC-UIB). Instituto de Física Interdisciplinar y Sistemas Complejos, E-07122 Palma de Mallorca, Spain
| | - Franco Tavella
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Minjun Jin
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yeonghoon Kim
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lendert Gelens
- Laboratory of Dynamics in Biological Systems, KU Leuven, Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
| | - Qiong Yang
- Department of Physics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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Chen Y, Huang JH, Phong C, Ferrell JE. Protein homeostasis from diffusion-dependent control of protein synthesis and degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538146. [PMID: 37162886 PMCID: PMC10168264 DOI: 10.1101/2023.04.24.538146] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
It has been proposed that the concentration of proteins in the cytoplasm maximizes the speed of important biochemical reactions. Here we have used the Xenopus extract system, which can be diluted or concentrated to yield a range of cytoplasmic protein concentrations, to test the effect of cytoplasmic concentration on mRNA translation and protein degradation. We found that protein synthesis rates are maximal in ~1x cytoplasm, whereas protein degradation continues to rise to an optimal concentration of ~1.8x. This can be attributed to the greater sensitivity of translation to cytoplasmic viscosity, perhaps because it involves unusually large macromolecular complexes like polyribosomes. The different concentration optima sets up a negative feedback homeostatic system, where increasing the cytoplasmic protein concentration above the 1x physiological level increases the viscosity of the cytoplasm, which selectively inhibits translation and drives the system back toward the 1x set point.
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Affiliation(s)
- Yuping Chen
- Dept. of Chemical and Systems Biology, Stanford University School of Medicine, Stanford CA 94305
- These authors contributed equally
- Corresponding authors
| | - Jo-Hsi Huang
- Dept. of Chemical and Systems Biology, Stanford University School of Medicine, Stanford CA 94305
- These authors contributed equally
| | - Connie Phong
- Dept. of Chemical and Systems Biology, Stanford University School of Medicine, Stanford CA 94305
| | - James E. Ferrell
- Dept. of Chemical and Systems Biology, Stanford University School of Medicine, Stanford CA 94305
- Dept. of Biochemistry, Stanford University School of Medicine, Stanford CA 94305
- Corresponding authors
- Lead contact
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Lebrec V, Gavet O. Monitoring Chk1 kinase activity dynamics in live single cell imaging assays. Methods Cell Biol 2023; 182:221-236. [PMID: 38359979 DOI: 10.1016/bs.mcb.2022.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The ATR/Chk1 pathway is an important regulator of cell cycle progression, notably upon genotoxic stress where it can detect a large variety of DNA alterations and induce a transient cell cycle arrest that promotes DNA repair. In addition to its role in DNA damage response (DDR), Chk1 is also active during a non-perturbed S phase and contributes to prevent a premature entry into mitosis with an incompletely replicated genome, meaning the ATR/Chk1 pathway is an integral part of the cell cycle machinery that preserves genome integrity during cell growth. We recently developed a FRET-based Chk1 kinase activity reporter to directly monitor and quantify the kinetics of Chk1 activation in live single cell imaging assays with unprecedented sensitivity and time resolution. This tool allowed us to monitor Chk1 activity dynamics over time during a normal S phase and following genotoxic stress, and to elucidate the underlying mechanisms leading to its activation. Here, we review available fluorescent tools to study the interplay of cell cycle progression, DNA damage and DDR in individual live cells, and present the full protocol and image analysis pipeline to monitor Chk1 activity in two imaging assays.
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Affiliation(s)
- Vivianne Lebrec
- Division of Cancer Biology, The Institute of Cancer Research, London, United Kingdom
| | - Olivier Gavet
- Sorbonne Université, Faculté des Sciences et Ingénierie, UFR927, Paris, France; UMR9019 CNRS, Université Paris-Saclay, Villejuif, Cedex, France.
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Marrone JI, Sepulchre JA, Ventura AC. A nested bistable module within a negative feedback loop ensures different types of oscillations in signaling systems. Sci Rep 2023; 13:529. [PMID: 36631477 PMCID: PMC9834387 DOI: 10.1038/s41598-022-27047-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023] Open
Abstract
In this article, we consider a double phosphorylation cycle, a ubiquitous signaling component, having the ability to display bistability, a behavior strongly related to the existence of positive feedback loops. If this component is connected to other signaling elements, it very likely undergoes some sort of protein-protein interaction. In several cases, these interactions result in a non-explicit negative feedback effect, leading to interlinked positive and negative feedbacks. This combination was studied in the literature as a way to generate relaxation-type oscillations. Here, we show that the two feedbacks together ensure two types of oscillations, the relaxation-type ones and a smoother type of oscillations functioning in a very narrow range of frequencies, in such a way that outside that range, the amplitude of the oscillations is severely compromised. Even more, we show that the two feedbacks are essential for both oscillatory types to emerge, and it is their hierarchy what determines the type of oscillation at work. We used bifurcation analyses and amplitude vs. frequency curves to characterize and classify the oscillations. We also applied the same ideas to another simple model, with the goal of generalizing what we learned from signaling models. The results obtained display the wealth of oscillatory dynamics that exists in a system with a bistable module nested within a negative feedback loop, showing how to transition between different types of oscillations and other dynamical behaviors such as excitability. Our work provides a framework for the study of other oscillatory systems based on bistable modules, from simple two-component models to more complex examples like the MAPK cascade and experimental cases like cell cycle oscillators.
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Affiliation(s)
- Juan Ignacio Marrone
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE UBA-CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina-Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | | | - Alejandra C Ventura
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina.
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE UBA-CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina-Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina.
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Maryu G, Yang Q. Nuclear-cytoplasmic compartmentalization of cyclin B1-Cdk1 promotes robust timing of mitotic events. Cell Rep 2022; 41:111870. [PMID: 36577372 DOI: 10.1016/j.celrep.2022.111870] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/15/2022] [Accepted: 12/01/2022] [Indexed: 12/28/2022] Open
Abstract
The cyclin-dependent kinase (Cdk1) oscillator is widely characterized in homogenized cytosolic extracts, leaving unclear the impact of nucleocytoplasmic compartmentalization. Here, by developing a Förster resonance energy transfer (FRET) biosensor, we track Cdk1 spatiotemporal dynamics in reconstituted cells with or without side by side and find compartmentalization significantly modulates clock properties previously found in bulk studies. Although nucleus-absent cells display highly tunable frequency, the nucleus-present cells maintain constant frequency against cyclin B1 variations. Despite high expression variability, cyclin degraded within the same duration, enabling a robust mitotic phase. Moreover, Cdk1 and cyclin B1 cycle rigorously out-of-phase, ensuring wide phase-plane orbits, essential for oscillation robustness. Although Cdk1 in homogeneous extracts is well known for delayed switch-like activation, we find active cyclin B1-Cdk1 accumulates in nuclei, without delay, until the nuclear envelope breakdown (NEB) when another abrupt activation triggers anaphase. Cdk1 biphasic activation and spatial compartmentalization may together coordinate the accurate ordering of different downstream events.
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Affiliation(s)
- Gembu Maryu
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Qiong Yang
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Physics, University of Michigan, Ann Arbor, MI 48109, USA.
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Cadart C, Heald R. Scaling of biosynthesis and metabolism with cell size. Mol Biol Cell 2022; 33:pe5. [PMID: 35862496 PMCID: PMC9582640 DOI: 10.1091/mbc.e21-12-0627] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
Cells adopt a size that is optimal for their function, and pushing them beyond this limit can cause cell aging and death by senescence or reduce proliferative potential. However, by increasing their genome copy number (ploidy), cells can increase their size dramatically and homeostatically maintain physiological properties such as biosynthesis rate. Recent studies investigating the relationship between cell size and rates of biosynthesis and metabolism under normal, polyploid, and pathological conditions are revealing new insights into how cells attain the best function or fitness for their size by tuning processes including transcription, translation, and mitochondrial respiration. A new frontier is to connect single-cell scaling relationships with tissue and whole-organism physiology, which promises to reveal molecular and evolutionary principles underlying the astonishing diversity of size observed across the tree of life.
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Affiliation(s)
- Clotilde Cadart
- Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA 94720-3200
| | - Rebecca Heald
- Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA 94720-3200
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