1
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Huang JH, Chen Y, Huang WYC, Tabatabaee S, Ferrell JE. Robust trigger wave speed in Xenopus cytoplasmic extracts. Nat Commun 2024; 15:5782. [PMID: 38987269 PMCID: PMC11237086 DOI: 10.1038/s41467-024-50119-0] [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: 12/19/2023] [Accepted: 07/01/2024] [Indexed: 07/12/2024] Open
Abstract
Self-regenerating trigger waves can spread rapidly through the crowded cytoplasm without diminishing in amplitude or speed, providing consistent, reliable, long-range communication. The macromolecular concentration of the cytoplasm varies in response to physiological and environmental fluctuations, raising the question of how or if trigger waves can robustly operate in the face of such fluctuations. Using Xenopus extracts, we find that mitotic and apoptotic trigger wave speeds are remarkably invariant. We derive a model that accounts for this robustness and for the eventual slowing at extremely high and low cytoplasmic concentrations. The model implies that the positive and negative effects of cytoplasmic concentration (increased reactant concentration vs. increased viscosity) are nearly precisely balanced. Accordingly, artificially maintaining a constant cytoplasmic viscosity during dilution abrogates this robustness. The robustness in trigger wave speeds may contribute to the reliability of the extremely rapid embryonic cell cycle.
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Affiliation(s)
- Jo-Hsi Huang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Yuping Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - William Y C Huang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Saman Tabatabaee
- 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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2
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Co HKC, Wu CC, Lee YC, Chen SH. Emergence of large-scale cell death through ferroptotic trigger waves. Nature 2024:10.1038/s41586-024-07623-6. [PMID: 38987590 DOI: 10.1038/s41586-024-07623-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 05/29/2024] [Indexed: 07/12/2024]
Abstract
Large-scale cell death is commonly observed during organismal development and in human pathologies1-5. These cell death events extend over great distances to eliminate large populations of cells, raising the question of how cell death can be coordinated in space and time. One mechanism that enables long-range signal transmission is trigger waves6, but how this mechanism might be used for death events in cell populations remains unclear. Here we demonstrate that ferroptosis, an iron- and lipid-peroxidation-dependent form of cell death, can propagate across human cells over long distances (≥5 mm) at constant speeds (around 5.5 μm min-1) through trigger waves of reactive oxygen species (ROS). Chemical and genetic perturbations indicate a primary role of ROS feedback loops (Fenton reaction, NADPH oxidase signalling and glutathione synthesis) in controlling the progression of ferroptotic trigger waves. We show that introducing ferroptotic stress through suppression of cystine uptake activates these ROS feedback loops, converting cellular redox systems from being monostable to being bistable and thereby priming cell populations to become bistable media over which ROS propagate. Furthermore, we demonstrate that ferroptosis and its propagation accompany the massive, yet spatially restricted, cell death events during muscle remodelling of the embryonic avian limb, substantiating its use as a tissue-sculpting strategy during embryogenesis. Our findings highlight the role of ferroptosis in coordinating global cell death events, providing a paradigm for investigating large-scale cell death in embryonic development and human pathologies.
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Affiliation(s)
- Hannah K C Co
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan
- Laboratory for Cell Dynamics, Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Chia-Chou Wu
- Laboratory for Cell Dynamics, Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- National Center for Theoretical Sciences, Physics Division, Taipei, Taiwan
| | - Yi-Chen Lee
- Laboratory for Cell Dynamics, Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Sheng-Hong Chen
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan.
- Laboratory for Cell Dynamics, Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
- National Center for Theoretical Sciences, Physics Division, Taipei, Taiwan.
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan.
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3
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Zhou Y, Fichman Y, Zhang S, Mittler R, Chen SJ. Modeling the reactive oxygen species (ROS) wave in Chlamydomonas reinhardtii colonies. Free Radic Biol Med 2024; 222:165-172. [PMID: 38851517 DOI: 10.1016/j.freeradbiomed.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/10/2024]
Abstract
Reactive oxygen species (ROS) play a crucial role as signaling molecules in both plant and animal cells, enabling rapid responses to various stimuli. Among the many cellular mechanisms used to generate and transduce ROS signals, ROS-induced-ROS release (RIRR) is emerging as an important pathway involved in the responses of various multicellular and unicellular organisms to environmental stresses. In RIRR, one cellular compartment, organelle, or cell generates or releases ROS, triggering an increased ROS production and release by another compartment, organelle, or cell, thereby giving rise to a fast propagating ROS wave. This RIRR-based signal relay has been demonstrated to facilitate mitochondria-to-mitochondria communication in animal cells and long-distance systemic signaling in plants in response to biotic and abiotic stresses. More recently, it has been discovered that different unicellular microorganism communities also exhibit a RIRR cell-to-cell signaling process triggered by a localized stress treatment. However, the precise mechanism underlying the propagation of the ROS signal among cells within these unicellular communities remained elusive. In this study, we employed a reaction-diffusion model incorporating the RIRR mechanism to analyze the propagation of ROS-mediated signals. By effectively balancing production and scavenging processes, our model successfully reproduces the experimental ROS signal velocities observed in unicellular green algae (Chlamydomonas reinhardtii) colonies grown on agar plates, furthering our understanding of intercellular ROS communication.
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Affiliation(s)
- Yuanzhe Zhou
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, 65211, USA.
| | - Yosef Fichman
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel.
| | - Sicheng Zhang
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, 65211, USA.
| | - Ron Mittler
- Division of Plant Science and Technology, College of Agriculture, Food and Natural Resources and Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St, Columbia, MO, 65211, USA; Department of Surgery, School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St, Columbia, MO, 65211, USA.
| | - Shi-Jie Chen
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, 65211, USA; Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA.
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4
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Schindler-Johnson M, Petridou NI. Collective effects of cell cleavage dynamics. Front Cell Dev Biol 2024; 12:1358971. [PMID: 38559810 PMCID: PMC10978805 DOI: 10.3389/fcell.2024.1358971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
A conserved process of early embryonic development in metazoans is the reductive cell divisions following oocyte fertilization, termed cell cleavages. Cell cleavage cycles usually start synchronously, lengthen differentially between the embryonic cells becoming asynchronous, and cease before major morphogenetic events, such as germ layer formation and gastrulation. Despite exhibiting species-specific characteristics, the regulation of cell cleavage dynamics comes down to common controllers acting mostly at the single cell/nucleus level, such as nucleus-to-cytoplasmic ratio and zygotic genome activation. Remarkably, recent work has linked cell cleavage dynamics to the emergence of collective behavior during embryogenesis, including pattern formation and changes in embryo-scale mechanics, raising the question how single-cell controllers coordinate embryo-scale processes. In this review, we summarize studies across species where an association between cell cleavages and collective behavior was made, discuss the underlying mechanisms, and propose that cell-to-cell variability in cell cleavage dynamics can serve as a mechanism of long-range coordination in developing embryos.
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Affiliation(s)
- Magdalena Schindler-Johnson
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Nicoletta I. Petridou
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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5
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Rinaldin M, Kickuth A, Dalton B, Xu Y, Di Talia S, Brugués J. Robust cytoplasmic partitioning by solving an intrinsic cytoskeletal instability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584684. [PMID: 38559072 PMCID: PMC10980089 DOI: 10.1101/2024.03.12.584684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Early development across vertebrates and insects critically relies on robustly reorganizing the cytoplasm of fertilized eggs into individualized cells. This intricate process is orchestrated by large microtubule structures that traverse the embryo, partitioning the cytoplasm into physically distinct and stable compartments. Despite the robustness of embryonic development, here we uncover an intrinsic instability in cytoplasmic partitioning driven by the microtubule cytoskeleton. We reveal that embryos circumvent this instability through two distinct mechanisms: either by matching the cell cycle duration to the time needed for the instability to unfold or by limiting microtubule nucleation. These regulatory mechanisms give rise to two possible strategies to fill the cytoplasm, which we experimentally demonstrate in zebrafish and Drosophila embryos, respectively. In zebrafish embryos, unstable microtubule waves fill the geometry of the entire embryo from the first division. Conversely, in Drosophila embryos, stable microtubule asters resulting from reduced microtubule nucleation gradually fill the cytoplasm throughout multiple divisions. Our results indicate that the temporal control of microtubule dynamics could have driven the evolutionary emergence of species-specific mechanisms for effective cytoplasmic organization. Furthermore, our study unveils a fundamental synergy between physical instabilities and biological clocks, uncovering universal strategies for rapid, robust, and efficient spatial ordering in biological systems.
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Affiliation(s)
- Melissa Rinaldin
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, 01307 Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307 Germany
- Center for Systems Biology Dresden, 01307 Germany
| | - Alison Kickuth
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, 01307 Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307 Germany
- Center for Systems Biology Dresden, 01307 Germany
| | - Benjamin Dalton
- Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Yitong Xu
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710 USA
| | - Stefano Di Talia
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710 USA
| | - Jan Brugués
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, 01307 Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307 Germany
- Center for Systems Biology Dresden, 01307 Germany
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6
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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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7
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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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8
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Scheibner C, Ori H, Cohen AE, Vitelli V. Spiking at the edge: Excitability at interfaces in reaction-diffusion systems. Proc Natl Acad Sci U S A 2024; 121:e2307996120. [PMID: 38215183 PMCID: PMC10801884 DOI: 10.1073/pnas.2307996120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/25/2023] [Indexed: 01/14/2024] Open
Abstract
Excitable media, ranging from bioelectric tissues and chemical oscillators to forest fires and competing populations, are nonlinear, spatially extended systems capable of spiking. Most investigations of excitable media consider situations where the amplifying and suppressing forces necessary for spiking coexist at every point in space. In this case, spikes arise due to local bistabilities, which require a fine-tuned ratio between local amplification and suppression strengths. But, in nature and engineered systems, these forces can be segregated in space, forming structures like interfaces and boundaries. Here, we show how boundaries can generate and protect spiking when the reacting components can spread out: Even arbitrarily weak diffusion can cause spiking at the edge between two non-excitable media. This edge spiking arises due to a global bistability, which can occur even if amplification and suppression strengths do not allow spiking when mixed. We analytically derive a spiking phase diagram that depends on two parameters: i) the ratio between the system size and the characteristic diffusive length-scale and ii) the ratio between the amplification and suppression strengths. Our analysis explains recent experimental observations of action potentials at the interface between two non-excitable bioelectric tissues. Beyond electrophysiology, we highlight how edge spiking emerges in predator-prey dynamics and in oscillating chemical reactions. Our findings provide a theoretical blueprint for a class of interfacial excitations in reaction-diffusion systems, with potential implications for spatially controlled chemical reactions, nonlinear waveguides and neuromorphic computation, as well as spiking instabilities, such as cardiac arrhythmias, that naturally occur in heterogeneous biological media.
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Affiliation(s)
- Colin Scheibner
- Department of Physics and The James Franck Institute, The University of Chicago, Chicago, IL60637
- Kadanoff Center for Theoretical Physics, The University of Chicago, Chicago, IL60637
| | - Hillel Ori
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
| | - Adam E. Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
- Department of Physics, Harvard University, Cambridge, MA02138
| | - Vincenzo Vitelli
- Department of Physics and The James Franck Institute, The University of Chicago, Chicago, IL60637
- Kadanoff Center for Theoretical Physics, The University of Chicago, Chicago, IL60637
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL60637
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9
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Wang X, Zhang H, Guo Z, Wang J, Lu C, Wang J, Jin R, Mo Z. SNRPB promotes the progression of hepatocellular carcinoma via regulating cell cycle, oxidative stress, and ferroptosis. Aging (Albany NY) 2024; 16:348-366. [PMID: 38189879 PMCID: PMC10817389 DOI: 10.18632/aging.205371] [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] [Received: 08/22/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024]
Abstract
Small Nuclear Ribonucleoprotein Polypeptides B and B1 (SNRPB) have been linked to multiple human cancers. However, the mechanism of SNRPB in hepatocellular carcinoma (HCC) and whether SNRPB has a synergistic effect with sorafenib in the treatment of HCC remain unclear. In this study, bioinformatic analysis found that SNRPB was an independent prognostic factor for HCC that exerted a critical effect on the progression of HCC. SNRPB was linked with immune checkpoints, cell cycle, oxidative stress and ferroptosis in HCC. Single cell sequencing analysis found that HCC cell subset with high expression of SNRPB, accounted for a higher proportion in HCC cells with higher stages, had higher expression levels of the genes which promote cell cycle, inhibit oxidative stress and ferroptosis, and had higher cell cycle score, lower oxidative stress score and ferroptosis score. Single-sample gene set enrichment analysis (ssGSEA) analysis found that 17 oxidative stress pathways and 68 oxidative stress-ferroptosis related genes were significantly correlated with SNRPB risk scores. SNRPB knockdown induced cell cycle G2/M arrest and restrained cell proliferation, while downregulated the expression of CDK1, CDK4, and CyclinB1. The combined treatment (SNRPB knockdown+sorafenib) significantly inhibited tumor growth. In addition, the expression of SLC7A11, which is closely-related to ferroptosis, decreased significantly in vitro and in vivo. Therefore, SNRPB may promote HCC progression by regulating immune checkpoints, cell cycle, oxidative stress and ferroptosis, while its downregulation inhibits cell proliferation, which enhances the therapeutic effect of sorafenib, providing a novel basis for the development of HCC therapies.
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Affiliation(s)
- Xiaoyan Wang
- Department of Experimental Teaching Center, School of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin 541199, Guangxi, China
- Key Laboratory of Biochemistry and Molecular Biology, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, Guilin 541199, Guangxi, China
| | - Hao Zhang
- Key Laboratory of Biochemistry and Molecular Biology, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, Guilin 541199, Guangxi, China
- Department of Biomedical Engineering, School of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin 541199, Guangxi, China
| | - Zehao Guo
- Key Laboratory of Biochemistry and Molecular Biology, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, Guilin 541199, Guangxi, China
- Department of Biomedical Engineering, School of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin 541199, Guangxi, China
| | - Junyuan Wang
- Department of Biomedical Engineering, School of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin 541199, Guangxi, China
| | - Chuntao Lu
- Department of Biomedical Engineering, School of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin 541199, Guangxi, China
| | - Junhua Wang
- Department of Biomedical Engineering, School of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin 541199, Guangxi, China
| | - Rongzhong Jin
- Department of Biochemistry, School of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin 541199, Guangxi, China
| | - Zhijing Mo
- Key Laboratory of Biochemistry and Molecular Biology, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, Guilin 541199, Guangxi, China
- Department of Biochemistry, School of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin 541199, Guangxi, China
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10
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Huang JH, Chen Y, Huang WYC, Tabatabaee S, Ferrell JE. Robust trigger wave speed in Xenopus cytoplasmic extracts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573127. [PMID: 38187567 PMCID: PMC10769400 DOI: 10.1101/2023.12.22.573127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Self-regenerating trigger waves can spread rapidly through the crowded cytoplasm without diminishing in amplitude or speed, providing consistent, reliable, long-range communication. The macromolecular concentration of the cytoplasm varies in response to physiological and environmental fluctuations, raising the question of how or if trigger waves can robustly operate in the face of such fluctuations. Using Xenopus extracts, we found that mitotic and apoptotic trigger wave speeds are remarkably invariant. We derived a model that accounts for this robustness and for the eventual slowing at extremely high and low cytoplasmic concentrations. The model implies that the positive and negative effects of cytoplasmic concentration (increased reactant concentration vs. increased viscosity) are nearly precisely balanced. Accordingly, artificially maintaining a constant cytoplasmic viscosity during dilution abrogates this robustness. The robustness in trigger wave speeds may contribute to the reliability of the extremely rapid embryonic cell cycle.
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Affiliation(s)
- Jo-Hsi Huang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305-5174, USA
- These authors contributed equally
| | - Yuping Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305-5174, USA
- These authors contributed equally
| | - William Y C Huang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305-5174, USA
| | - Saman Tabatabaee
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305-5174, USA
| | - James E Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305-5174, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 943055307, USA
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11
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Meyer K, Lammers NC, Bugaj LJ, Garcia HG, Weiner OD. Optogenetic control of YAP reveals a dynamic communication code for stem cell fate and proliferation. Nat Commun 2023; 14:6929. [PMID: 37903793 PMCID: PMC10616176 DOI: 10.1038/s41467-023-42643-2] [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: 02/17/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
YAP is a transcriptional regulator that controls pluripotency, cell fate, and proliferation. How cells ensure the selective activation of YAP effector genes is unknown. This knowledge is essential to rationally control cellular decision-making. Here we leverage optogenetics, live-imaging of transcription, and cell fate analysis to understand and control gene activation and cell behavior. We reveal that cells decode the steady-state concentrations and timing of YAP activation to control proliferation, cell fate, and expression of the pluripotency regulators Oct4 and Nanog. While oscillatory YAP inputs induce Oct4 expression and proliferation optimally at frequencies that mimic native dynamics, cellular differentiation requires persistently low YAP levels. We identify the molecular logic of the Oct4 dynamic decoder, which acts through an adaptive change sensor. Our work reveals how YAP levels and dynamics enable multiplexing of information transmission for the regulation of developmental decision-making and establishes a platform for the rational control of these behaviors.
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Affiliation(s)
- Kirstin Meyer
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Nicholas C Lammers
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Hernan G Garcia
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Orion D Weiner
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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12
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Gagliardi PA, Grädel B, Jacques MA, Hinderling L, Ender P, Cohen AR, Kastberger G, Pertz O, Dobrzyński M. Automatic detection of spatio-temporal signaling patterns in cell collectives. J Cell Biol 2023; 222:e202207048. [PMID: 37516918 PMCID: PMC10374943 DOI: 10.1083/jcb.202207048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 04/24/2023] [Accepted: 06/28/2023] [Indexed: 07/31/2023] Open
Abstract
Increasing experimental evidence points to the physiological importance of space-time correlations in signaling of cell collectives. From wound healing to epithelial homeostasis to morphogenesis, coordinated activation of biomolecules between cells allows the collectives to perform more complex tasks and to better tackle environmental challenges. To capture this information exchange and to advance new theories of emergent phenomena, we created ARCOS, a computational method to detect and quantify collective signaling. We demonstrate ARCOS on cell and organism collectives with space-time correlations on different scales in 2D and 3D. We made a new observation that oncogenic mutations in the MAPK/ERK and PIK3CA/Akt pathways of MCF10A epithelial cells hyperstimulate intercellular ERK activity waves that are largely dependent on matrix metalloproteinase intercellular signaling. ARCOS is open-source and available as R and Python packages. It also includes a plugin for the napari image viewer to interactively quantify collective phenomena without prior programming experience.
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Affiliation(s)
| | - Benjamin Grädel
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Marc-Antoine Jacques
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Lucien Hinderling
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Pascal Ender
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Andrew R. Cohen
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, USA
| | | | - Olivier Pertz
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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13
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Fan Y, Chai C, Li P, Zou X, Ferrell JE, Wang B. Ultrafast distant wound response is essential for whole-body regeneration. Cell 2023; 186:3606-3618.e16. [PMID: 37480850 PMCID: PMC10957142 DOI: 10.1016/j.cell.2023.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 01/11/2023] [Accepted: 06/23/2023] [Indexed: 07/24/2023]
Abstract
Injury induces systemic responses, but their functions remain elusive. Mechanisms that can rapidly synchronize wound responses through long distances are also mostly unknown. Using planarian flatworms capable of whole-body regeneration, we report that injury induces extracellular signal-regulated kinase (Erk) activity waves to travel at a speed 10-100 times faster than those in other multicellular tissues. This ultrafast propagation requires longitudinal body-wall muscles, elongated cells forming dense parallel tracks running the length of the organism. The morphological properties of muscles allow them to act as superhighways for propagating and disseminating wound signals. Inhibiting Erk propagation prevents tissues distant to the wound from responding and blocks regeneration, which can be rescued by a second injury to distal tissues shortly after the first injury. Our findings provide a mechanism for long-range signal propagation in large, complex tissues to coordinate responses across cell types and highlight the function of feedback between spatially separated tissues during whole-body regeneration.
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Affiliation(s)
- Yuhang Fan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Chew Chai
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Pengyang Li
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Xinzhi Zou
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - James E Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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14
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Grodstein J, McMillen P, Levin M. Closing the loop on morphogenesis: a mathematical model of morphogenesis by closed-loop reaction-diffusion. Front Cell Dev Biol 2023; 11:1087650. [PMID: 37645245 PMCID: PMC10461482 DOI: 10.3389/fcell.2023.1087650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 07/31/2023] [Indexed: 08/31/2023] Open
Abstract
Morphogenesis, the establishment and repair of emergent complex anatomy by groups of cells, is a fascinating and biomedically-relevant problem. One of its most fascinating aspects is that a developing embryo can reliably recover from disturbances, such as splitting into twins. While this reliability implies some type of goal-seeking error minimization over a morphogenic field, there are many gaps with respect to detailed, constructive models of such a process. A common way to achieve reliability is negative feedback, which requires characterizing the existing body shape to create an error signal-but measuring properties of a shape may not be simple. We show how cells communicating in a wave-like pattern could analyze properties of the current body shape. We then describe a closed-loop negative-feedback system for creating reaction-diffusion (RD) patterns with high reliability. Specifically, we use a wave to count the number of peaks in a RD pattern, letting us use a negative-feedback controller to create a pattern with N repetitions, where N can be altered over a wide range. Furthermore, the individual repetitions of the RD pattern can be easily stretched or shrunk under genetic control to create, e.g., some morphological features larger than others. This work contributes to the exciting effort of understanding design principles of morphological computation, which can be used to understand evolved developmental mechanisms, manipulate them in regenerative-medicine settings, or engineer novel synthetic morphology constructs with desired robust behavior.
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Affiliation(s)
- Joel Grodstein
- Department of Electrical and Computer Engineering, Tufts University, Medford, MA, United States
| | - Patrick McMillen
- Allen Discovery Center at Tufts University, Medford, MA, United States
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA, United States
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, United States
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15
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Qian W, Good MC. Peeking under the hood of early embryogenesis: Using tools and synthetic biology to understand native control systems and sculpt tissues. Semin Cell Dev Biol 2023; 141:43-49. [PMID: 35525819 PMCID: PMC9633583 DOI: 10.1016/j.semcdb.2022.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/13/2022] [Indexed: 10/18/2022]
Abstract
Early embryogenesis requires rapid division of pluripotent blastomeres, regulated genome activation, precise spatiotemporal signaling to pattern cell fate, and morphogenesis to shape primitive tissue architectures. The complexity of this process has inspired researchers to move beyond simple genetic perturbation into engineered devices and synthetic biology tools to permit temporal and spatial manipulation of the control systems guiding development. By precise alteration of embryo organization, it is now possible to advance beyond basic analytical strategies and directly test the sufficiency of models for developmental regulation. Separately, advances in micropatterning and embryoid culture have facilitated the bottom-up construction of complex embryo tissues allowing ex vivo systems to recapitulate even later stages of development. Embryos fertilized and grown ex vivo offer an excellent opportunity to exogenously perturb fundamental pathways governing embryogenesis. Here we review the technologies developed to thermally modulate the embryo cell cycle, and optically regulate morphogen and signaling pathways in space and time, specifically in the blastula embryo. Additionally, we highlight recent advances in cell patterning in two and three dimensions that have helped reveal the self-organizing properties and gene regulatory networks guiding early embryo organization.
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Affiliation(s)
- Wenchao Qian
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew C. Good
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA,Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Lead Contact,Correspondence: (M.C.G), Address: 421 Curie Blvd, 1151 Biomedical Research Building, Philadelphia PA 19104
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16
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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: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [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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17
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Fan Y, Chai C, Li P, Zou X, Ferrell JE, Wang B. Ultrafast and long-range coordination of wound responses is essential for whole-body regeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532844. [PMID: 36993633 PMCID: PMC10055111 DOI: 10.1101/2023.03.15.532844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Injury induces systemic, global responses whose functions remain elusive. In addition, mechanisms that rapidly synchronize wound responses through long distances across the organismal scale are mostly unknown. Using planarians, which have extreme regenerative ability, we report that injury induces Erk activity to travel in a wave-like manner at an unexpected speed (∼1 mm/h), 10-100 times faster than those measured in other multicellular tissues. This ultrafast signal propagation requires longitudinal body-wall muscles, elongated cells forming dense parallel tracks running the length of the organism. Combining experiments and computational models, we show that the morphological properties of muscles allow them to minimize the number of slow intercellular signaling steps and act as bidirectional superhighways for propagating wound signals and instructing responses in other cell types. Inhibiting Erk propagation prevents cells distant to the wound from responding and blocks regeneration, which can be rescued by a second injury to distal tissues within a narrow time window after the first injury. These results suggest that rapid responses in uninjured tissues far from wounds are essential for regeneration. Our findings provide a mechanism for long-range signal propagation in large and complex tissues to coordinate cellular responses across diverse cell types, and highlights the function of feedback between spatially separated tissues during whole-body regeneration.
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Affiliation(s)
- Yuhang Fan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Chew Chai
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Pengyang Li
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Xinzhi Zou
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - James E. Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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18
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Chen P, Levy DL. Regulation of organelle size and organization during development. Semin Cell Dev Biol 2023; 133:53-64. [PMID: 35148938 PMCID: PMC9357868 DOI: 10.1016/j.semcdb.2022.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/20/2022] [Accepted: 02/01/2022] [Indexed: 12/11/2022]
Abstract
During early embryogenesis, as cells divide in the developing embryo, the size of intracellular organelles generally decreases to scale with the decrease in overall cell size. Organelle size scaling is thought to be important to establish and maintain proper cellular function, and defective scaling may lead to impaired development and disease. However, how the cell regulates organelle size and organization are largely unanswered questions. In this review, we summarize the process of size scaling at both the cell and organelle levels and discuss recently discovered mechanisms that regulate this process during early embryogenesis. In addition, we describe how some recently developed techniques and Xenopus as an animal model can be used to investigate the underlying mechanisms of size regulation and to uncover the significance of proper organelle size scaling and organization.
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Affiliation(s)
- Pan Chen
- Institute of Biochemistry and Molecular Biology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA.
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19
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Cell cycle: Making waves to coordinate the entry into mitosis. Curr Biol 2022; 32:R1262-R1264. [PMID: 36413966 DOI: 10.1016/j.cub.2022.10.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
How do very large cells coordinate their entry into mitosis? A new study shows that the bistability of the Cdk/Cyclin system allows cells to generate either 'trigger waves' or 'sweep waves' that drive cells into mitosis in different ways with distinct consequences.
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20
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Hayden L, Hur W, Vergassola M, Di Talia S. Manipulating the nature of embryonic mitotic waves. Curr Biol 2022; 32:4989-4996.e3. [PMID: 36332617 PMCID: PMC9691596 DOI: 10.1016/j.cub.2022.10.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/05/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
Early embryogenesis is characterized by rapid and synchronous cleavage divisions, which are often controlled by wave-like patterns of Cdk1 activity. Two mechanisms have been proposed for mitotic waves: sweep and trigger waves.1,2 The two mechanisms give rise to different wave speeds, dependencies on physical and molecular parameters, and spatial profiles of Cdk1 activity: upward sweeping gradients versus traveling wavefronts. Both mechanisms hinge on the transient bistability governing the cell cycle and are differentiated by the speed of the cell-cycle progression: sweep and trigger waves arise for rapid and slow drives, respectively. Here, using quantitative imaging of Cdk1 activity and theory, we illustrate that sweep waves are the dominant mechanism in Drosophila embryos and test two fundamental predictions on the transition from sweep to trigger waves. We demonstrate that sweep waves can be turned into trigger waves if the cell cycle is slowed down genetically or if significant delays in the cell-cycle progression are introduced across the embryo by altering nuclear density. Our genetic experiments demonstrate that Polo kinase is a major rate-limiting regulator of the blastoderm divisions, and genetic perturbations reducing its activity can induce the transition from sweep to trigger waves. Furthermore, we show that changes in temperature cause an essentially uniform slowdown of interphase and mitosis. That results in sweep waves being observed across a wide temperature range despite the cell-cycle durations being significantly different. Collectively, our combination of theory and experiments elucidates the nature of mitotic waves in Drosophila embryogenesis, their control mechanisms, and their mutual transitions.
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Affiliation(s)
- Luke Hayden
- Department of Cell Biology, Research Drive, Duke University School of Medicine, Durham, NC 27710, USA
| | - Woonyung Hur
- Department of Cell Biology, Research Drive, Duke University School of Medicine, Durham, NC 27710, USA
| | - Massimo Vergassola
- Laboratoire de Physique de l'École Normale Supérieure, CNRS, PSL Research University, Sorbonne Université, 24 Rue Lhomond, 75005 Paris, France; Department of Physics, University of California, San Diego, 9500 Gillman Drive, La Jolla, CA 92093, USA.
| | - Stefano Di Talia
- Department of Cell Biology, Research Drive, Duke University School of Medicine, Durham, NC 27710, USA.
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21
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Huang WYC, Cheng X, Ferrell JE. Cytoplasmic organization promotes protein diffusion in Xenopus extracts. Nat Commun 2022; 13:5599. [PMID: 36151204 PMCID: PMC9508076 DOI: 10.1038/s41467-022-33339-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 09/12/2022] [Indexed: 11/25/2022] Open
Abstract
The cytoplasm is highly organized. However, the extent to which this organization influences the dynamics of cytoplasmic proteins is not well understood. Here, we use Xenopus laevis egg extracts as a model system to study diffusion dynamics in organized versus disorganized cytoplasm. Such extracts are initially homogenized and disorganized, and self-organize into cell-like units over the course of tens of minutes. Using fluorescence correlation spectroscopy, we observe that as the cytoplasm organizes, protein diffusion speeds up by about a factor of two over a length scale of a few hundred nanometers, eventually approaching the diffusion time measured in organelle-depleted cytosol. Even though the ordered cytoplasm contained organelles and cytoskeletal elements that might interfere with diffusion, the convergence of protein diffusion in the cytoplasm toward that in organelle-depleted cytosol suggests that subcellular organization maximizes protein diffusivity. The effect of organization on diffusion varies with molecular size, with the effects being largest for protein-sized molecules, and with the time scale of the measurement. These results show that cytoplasmic organization promotes the efficient diffusion of protein molecules in a densely packed environment. Cytoplasmic organization is a hallmark of living cells. Here, the authors make use of self-organizing cell extracts to examine how the emergence of large-scale organizations influences the microscopic diffusion of protein molecules in the cytoplasm.
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Affiliation(s)
- William Y C Huang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Xianrui Cheng
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, 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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22
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Chen X, Xu Y, Lou K, Peng Y, Zhou C, Zhang HP, Wang W. Programmable, Spatiotemporal Control of Colloidal Motion Waves via Structured Light. ACS NANO 2022; 16:12755-12766. [PMID: 35857820 DOI: 10.1021/acsnano.2c04596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Traveling waves in a reaction-diffusion system are essential for long-range communication in living organisms and inspire biomimetic materials of similar capabilities. One recent example is the traveling motion waves among photochemically oscillating, silver (Ag)-containing colloids. Being able to manipulate these colloidal waves holds the key for potential applications. Here, we have discovered that these motion waves can be confined by light patterns and that the chemical clocks of silver particles are moved forward by reducing local light intensity. Using these discoveries as design principles, we have applied structured light technology for the precise and programmable control of colloidal motion waves, including their origins, propagation directions, paths, shapes, annihilation, frequency, and speeds. We have also used the controlled propagation of colloidal waves to guide chemical messages along a predefined path to activate a population of micromotors located far from the signal. Our demonstrated capabilities in manipulating colloidal waves in space and time offer physical insights on their operation and expand their usefulness in the fundamental study of reaction-diffusion processes. Moreover, our findings inspire biomimetic strategies for the directional transport of mass, energy, and information at micro- or even nanoscales.
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Affiliation(s)
- Xi Chen
- Sauvage Laboratory for Smart Materials, School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Yankai Xu
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kai Lou
- Guangzhou Kayja-Optics Technology Co., Ltd., Guangzhou 511458, China
| | - Yixin Peng
- Sauvage Laboratory for Smart Materials, School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Chao Zhou
- Sauvage Laboratory for Smart Materials, School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
- Department of Mechanical and Energy Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - H P Zhang
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei Wang
- Sauvage Laboratory for Smart Materials, School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
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23
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Diegmiller R, Nunley H, Shvartsman SY, Imran Alsous J. Quantitative models for building and growing fated small cell networks. Interface Focus 2022; 12:20210082. [PMID: 35865502 PMCID: PMC9184967 DOI: 10.1098/rsfs.2021.0082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/31/2022] [Indexed: 02/07/2023] Open
Abstract
Small cell clusters exhibit numerous phenomena typically associated with complex systems, such as division of labour and programmed cell death. A conserved class of such clusters occurs during oogenesis in the form of germline cysts that give rise to oocytes. Germline cysts form through cell divisions with incomplete cytokinesis, leaving cells intimately connected through intercellular bridges that facilitate cyst generation, cell fate determination and collective growth dynamics. Using the well-characterized Drosophila melanogaster female germline cyst as a foundation, we present mathematical models rooted in the dynamics of cell cycle proteins and their interactions to explain the generation of germline cell lineage trees (CLTs) and highlight the diversity of observed CLT sizes and topologies across species. We analyse competing models of symmetry breaking in CLTs to rationalize the observed dynamics and robustness of oocyte fate specification, and highlight remaining gaps in knowledge. We also explore how CLT topology affects cell cycle dynamics and synchronization and highlight mechanisms of intercellular coupling that underlie the observed collective growth patterns during oogenesis. Throughout, we point to similarities across organisms that warrant further investigation and comment on the extent to which experimental and theoretical findings made in model systems extend to other species.
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Affiliation(s)
- Rocky Diegmiller
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Hayden Nunley
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Stanislav Y. Shvartsman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA,Department of Molecular Biology, Princeton University, Princeton, NJ, USA,Flatiron Institute, Simons Foundation, New York, NY, USA
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24
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JENKINSON F, ZEGERMAN P. Roles of phosphatases in eukaryotic DNA replication initiation control. DNA Repair (Amst) 2022; 118:103384. [DOI: 10.1016/j.dnarep.2022.103384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 11/03/2022]
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25
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Swider ZT, Michaud A, Leda M, Landino J, Goryachev AB, Bement WM. Cell cycle and developmental control of cortical excitability in Xenopus laevis. Mol Biol Cell 2022; 33:ar73. [PMID: 35594176 PMCID: PMC9635278 DOI: 10.1091/mbc.e22-01-0025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Interest in cortical excitability—the ability of the cell cortex to generate traveling waves of protein activity—has grown considerably over the past 20 years. Attributing biological functions to cortical excitability requires an understanding of the natural behavior of excitable waves and the ability to accurately quantify wave properties. Here we have investigated and quantified the onset of cortical excitability in Xenopus laevis eggs and embryos and the changes in cortical excitability throughout early development. We found that cortical excitability begins to manifest shortly after egg activation. Further, we identified a close relationship between wave properties—such as wave frequency and amplitude—and cell cycle progression as well as cell size. Finally, we identified quantitative differences between cortical excitability in the cleavage furrow relative to nonfurrow cortical excitability and showed that these wave regimes are mutually exclusive.
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Affiliation(s)
- Zachary T Swider
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison Madison, WI 53706.,Center for Quantitative Cell Imaging, University of Wisconsin-Madison Madison, WI 53706
| | - Ani Michaud
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison Madison, WI 53706.,Center for Quantitative Cell Imaging, University of Wisconsin-Madison Madison, WI 53706
| | - Marcin Leda
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Jennifer Landino
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan-Ann Arbor, Ann Arbor, MI 48109
| | - Andrew B Goryachev
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - William M Bement
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison Madison, WI 53706.,Center for Quantitative Cell Imaging, University of Wisconsin-Madison Madison, WI 53706.,Department of Integrative Biology, University of Wisconsin-Madison Madison, WI 53706
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26
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Tyson JJ, Csikasz-Nagy A, Gonze D, Kim JK, Santos S, Wolf J. Time-keeping and decision-making in living cells: Part II. Interface Focus 2022. [PMCID: PMC9184961 DOI: 10.1098/rsfs.2022.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- John J. Tyson
- Department of Biological Sciences, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA
| | - Attila Csikasz-Nagy
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, 1088 Budapest, Hungary
| | - Didier Gonze
- Unit of Theoretical Chronobiology, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Jae Kyoung Kim
- Department of Mathematical Sciences, KAIST, Daejeon 34141, South Korea
- Biomedical Mathematics Group, Institute for Basic Science, Daejeon 34126, South Korea
| | - Silvia Santos
- Quantitative Stem Cell Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Jana Wolf
- Mathematical Modeling of Cellular Processes, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
- Department of Mathematics and Computer Science, Free University, 14195 Berlin, Germany
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27
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Zhang X, Yao Z, Xue Z, Wang S, Liu X, Hu Y, Zhang Y, Wang J, Li X, Chen A. Resibufogenin Targets the ATP1A1 Signaling Cascade to Induce G2/M Phase Arrest and Inhibit Invasion in Glioma. Front Pharmacol 2022; 13:855626. [PMID: 35656311 PMCID: PMC9152115 DOI: 10.3389/fphar.2022.855626] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Resibufogenin (RB) is a major active ingredient in the traditional Chinese medicine Chansu and has garnered considerable attention for its efficacy in the treatment of cancer. However, the anticancer effects and underlying mechanisms of RB on glioblastoma (GBM) remain unknown. Here, we found that RB induced G2/M phase arrest and inhibited invasion in a primary GBM cell line, P3#GBM, and two GBM cell lines, U251 and A172. Subsequently, we demonstrated that RB-induced G2/M phase arrest occurred through downregulation of CDC25C and upregulation of p21, which was caused by activation of the MAPK/ERK pathway, and that RB inhibited GBM invasion by elevating intercellular Ca2+ to suppress the Src/FAK/Paxillin focal adhesion pathway. Intriguingly, we confirmed that upon RB binding to ATP1A1, Na+-K+-ATPase was activated as a receptor and then triggered the intracellular MAPK/ERK pathway and Ca2+-mediated Src/FAK/Paxillin focal adhesion pathway, which led to G2/M phase arrest and inhibited the invasion of GBM cells. Taken together, our findings reveal the antitumor mechanism of RB by targeting the ATP1A1 signaling cascade and two key signaling pathways and highlight the potential of RB as a new class of promising anticancer agents.
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Affiliation(s)
- Xun Zhang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling and Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Zhong Yao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling and Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Zhiyi Xue
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling and Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Shuai Wang
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Xuemeng Liu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling and Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Yaotian Hu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling and Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Yan Zhang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling and Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Jian Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling and Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China.,Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Xingang Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling and Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Anjing Chen
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling and Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
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28
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Chen X, Xu Y, Zhou C, Lou K, Peng Y, Zhang HP, Wang W. Unraveling the physiochemical nature of colloidal motion waves among silver colloids. SCIENCE ADVANCES 2022; 8:eabn9130. [PMID: 35613263 PMCID: PMC9132452 DOI: 10.1126/sciadv.abn9130] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Traveling waves are common in biological and synthetic systems, including the recent discovery that silver (Ag) colloids form traveling motion waves in H2O2 and under light. Here, we show that this colloidal motion wave is a heterogeneous excitable system. The Ag colloids generate traveling chemical waves via reaction-diffusion, and either self-propel through self-diffusiophoresis ("ballistic waves") or are advected by diffusio-osmotic flows from gradients of neutral molecules ("swarming waves"). Key results include the experimental observation of traveling waves of OH- with pH-sensitive fluorescent dyes and a Rogers-McCulloch model that qualitatively and quantitatively reproduces the key features of colloidal waves. These results are a step forward in elucidating the Ag-H2O2-light oscillatory system at individual and collective levels. In addition, they pave the way for using colloidal waves either as a platform for studying nonlinear phenomena, or as a tool for colloidal transport and for information transmission in microrobot ensembles.
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Affiliation(s)
- Xi Chen
- Sauvage Laboratory for Smart Materials, School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Yankai Xu
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chao Zhou
- Sauvage Laboratory for Smart Materials, School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Kai Lou
- Guangzhou Kayja-Optics Technology Co. Ltd., Guangzhou 511458, China
| | - Yixin Peng
- Sauvage Laboratory for Smart Materials, School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - H. P. Zhang
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Corresponding author. (W.W.); (H.P.Z.)
| | - Wei Wang
- Sauvage Laboratory for Smart Materials, School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
- Corresponding author. (W.W.); (H.P.Z.)
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29
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Hayden L, Chao A, Deneke VE, Vergassola M, Puliafito A, Di Talia S. Cullin-5 mutants reveal collective sensing of the nucleocytoplasmic ratio in Drosophila embryogenesis. Curr Biol 2022; 32:2084-2092.e4. [PMID: 35334230 PMCID: PMC9090985 DOI: 10.1016/j.cub.2022.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/27/2022] [Accepted: 03/01/2022] [Indexed: 11/28/2022]
Abstract
In most metazoans, early embryonic development is characterized by rapid division cycles that pause before gastrulation at the midblastula transition (MBT).1 These cleavage divisions are accompanied by cytoskeletal rearrangements that ensure proper nuclear positioning. However, the molecular mechanisms controlling nuclear positioning are not fully elucidated. In Drosophila, early embryogenesis unfolds in a multinucleated syncytium. Nuclei rapidly move across the anterior-posterior (AP) axis at cell cycles 4-6 in a process driven by actomyosin contractility and cytoplasmic flows.2,3 In shackleton (shkl) mutants, this axial spreading is impaired.4 Here, we show that shkl mutants carry mutations in the cullin-5 (cul-5) gene. Live imaging experiments show that Cul-5 is downstream of the cell cycle but is required for cortical actomyosin contractility. The nuclear spreading phenotype of cul-5 mutants can be rescued by reducing Src activity, suggesting that a major target of cul-5 is Src kinase. cul-5 mutants display gradients of nuclear density across the AP axis that we exploit to study cell-cycle control as a function of the N/C ratio. We found that the N/C ratio is sensed collectively in neighborhoods of about 100 μm, and such collective sensing is required for a precise MBT, in which all the nuclei in the embryo pause their division cycle. Moreover, we found that the response to the N/C ratio is slightly graded along the AP axis. These two features can be linked to Cdk1 dynamics. Collectively, we reveal a new pathway controlling nuclear positioning and provide a dissection of how nuclear cycles respond to the N/C ratio.
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Affiliation(s)
- Luke Hayden
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Anna Chao
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Victoria E Deneke
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Massimo Vergassola
- Laboratoire de physique de l'École Normale Supérieure, CNRS, PSL Research University, Sorbonne Université, Paris, France; Department of Physics, University of California, San Diego, La Jolla, CA, USA
| | - Alberto Puliafito
- Candiolo Cancer Institute, FPO-IRCCS, Laboratory of Cell Migration, 10060 Candiolo, Italy; Department of Oncology, Università di Torino, 10060 Candiolo, Italy
| | - Stefano Di Talia
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA.
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30
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Abstract
The centrosome is a multifunctional organelle that is known primarily for its microtubule organising function. Centrosomal defects caused by changes in centrosomal structure or number have been associated with human diseases ranging from congenital defects to cancer. We are only beginning to appreciate how the non-microtubule organising roles of the centrosome are related to these clinical conditions. In this review, we will discuss the historical evidence that led to the proposal that the centrosome participates in cell cycle regulation. We then summarize the body of work that describes the involvement of the mammalian centrosome in triggering cell cycle progression and checkpoint signalling. Then we will highlight work from the fission yeast model organism, revealing the molecular details that explain how the spindle pole body (SPB, the yeast functional equivalent of the centrosome), participates in these cell cycle transitions. Importantly, we will discuss some of the emerging questions from recent discoveries related to the role of the centrosome as a cell cycle regulator.
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31
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Abstract
Embryonic development hinges on effective coordination of molecular events across space and time. Waves have recently emerged as constituting an ubiquitous mechanism that ensures rapid spreading of regulatory signals across embryos, as well as reliable control of their patterning, namely, for the emergence of body plan structures. In this article, we review a selection of recent quantitative work on signaling waves and present an overview of the theory of waves. Our aim is to provide a succinct yet comprehensive guiding reference for the theoretical frameworks by which signaling waves can arise in embryos. We start, then, from reaction-diffusion systems, both static and time dependent; move to excitable dynamics; and conclude with systems of coupled oscillators. We link these theoretical models to molecular mechanisms recently elucidated for the control of mitotic waves in early embryos, patterning of the vertebrate body axis, micropattern cultures, and bone regeneration. Our goal is to inspire experimental work that will advance theory in development and connect its predictions to quantitative biological observations. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Stefano Di Talia
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, USA
| | - Massimo Vergassola
- Laboratoire de physique de l'École Normale Supérieure, CNRS, PSL Research University, Sorbonne Université, Paris, France; .,Department of Physics, University of California, San Diego, California, USA
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32
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In vitro cell cycle oscillations exhibit a robust and hysteretic response to changes in cytoplasmic density. Proc Natl Acad Sci U S A 2022; 119:2109547119. [PMID: 35101974 PMCID: PMC8832984 DOI: 10.1073/pnas.2109547119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 12/25/2022] Open
Abstract
The cytoplasm, where most cellular reactions occur, has a variable density. We currently lack an understanding of how density variations affect cellular functions because of the challenge of controlling it experimentally. Here, we systematically modulate the density of an in vitro cytoplasm using microfluidics and analyze how the cell cycle behaves in turn. We found that mitotic cycles maintain their function across 0.2× to 1.2× of the natural density. Higher densities arrest cell cycles, and dilution recovers oscillations. However, the density at which cycles reappear is lower than the natural density. This behavior suggests a history-dependent mechanism called hysteresis, common in physics, chemistry, and engineering. Our approach paves the way for studying the responses of other processes to density changes. Cells control the properties of the cytoplasm to ensure proper functioning of biochemical processes. Recent studies showed that cytoplasmic density varies in both physiological and pathological states of cells undergoing growth, division, differentiation, apoptosis, senescence, and metabolic starvation. Little is known about how cellular processes cope with these cytoplasmic variations. Here, we study how a cell cycle oscillator comprising cyclin-dependent kinase (Cdk1) responds to changes in cytoplasmic density by systematically diluting or concentrating cycling Xenopus egg extracts in cell-like microfluidic droplets. We found that the cell cycle maintains robust oscillations over a wide range of deviations from the endogenous density: as low as 0.2× to more than 1.22× relative cytoplasmic density (RCD). A further dilution or concentration from these values arrested the system in a low or high steady state of Cdk1 activity, respectively. Interestingly, diluting an arrested cytoplasm of 1.22× RCD recovers oscillations at lower than 1× RCD. Thus, the cell cycle switches reversibly between oscillatory and stable steady states at distinct thresholds depending on the direction of tuning, forming a hysteresis loop. We propose a mathematical model which recapitulates these observations and predicts that the Cdk1/Wee1/Cdc25 positive feedback loops do not contribute to the observed robustness, supported by experiments. Our system can be applied to study how cytoplasmic density affects other cellular processes.
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33
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From the Belousov-Zhabotinsky reaction to biochemical clocks, traveling waves and cell cycle regulation. Biochem J 2022; 479:185-206. [PMID: 35098993 DOI: 10.1042/bcj20210370] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 01/23/2023]
Abstract
In the last 20 years, a growing army of systems biologists has employed quantitative experimental methods and theoretical tools of data analysis and mathematical modeling to unravel the molecular details of biological control systems with novel studies of biochemical clocks, cellular decision-making, and signaling networks in time and space. Few people know that one of the roots of this new paradigm in cell biology can be traced to a serendipitous discovery by an obscure Russian biochemist, Boris Belousov, who was studying the oxidation of citric acid. The story is told here from an historical perspective, tracing its meandering path through glycolytic oscillations, cAMP signaling, and frog egg development. The connections among these diverse themes are drawn out by simple mathematical models (nonlinear differential equations) that share common structures and properties.
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34
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Dey S, Singh A. Diverse role of decoys on emergence and precision of oscillations in a biomolecular clock. Biophys J 2021; 120:5564-5574. [PMID: 34774502 PMCID: PMC8715246 DOI: 10.1016/j.bpj.2021.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 08/11/2021] [Accepted: 11/05/2021] [Indexed: 01/14/2023] Open
Abstract
Biomolecular clocks are key drivers of oscillatory dynamics in diverse biological processes including cell-cycle regulation, circadian rhythms, and pattern formation during development. A minimal clock implementation is based on the classical Goodwin oscillator, in which a repressor protein inhibits its own synthesis via time-delayed negative feedback. Clock motifs, however, do not exist in isolation; its components are open to interacting with the complex environment inside cells. For example, there are ubiquitous high-affinity binding sites along the genome, known as decoys, where transcription factors such as repressor proteins can potentially interact. This binding affects the availability of transcription factors and has often been ignored in theoretical studies. How does such genomic decoy binding impact the clock's robustness and precision? To address this question, we systematically analyze deterministic and stochastic models of the Goodwin oscillator in the presence of reversible binding of the repressor to a finite number of decoy sites. Our analysis reveals that the relative stability of decoy-bound repressors compared to the free repressor plays distinct roles on the emergence and precision of oscillations. Interestingly, active degradation of the bound repressor can induce sustained oscillations that are otherwise absent without decoys. In contrast, decoy abundances can kill oscillation dynamics if the bound repressor is protected from degradation. Taking into account low copy-number fluctuations in clock components, we show that the degradation of the bound repressors enhances precision by attenuating noise in both the amplitude and period of oscillations. Overall, these results highlight the versatile role of otherwise hidden decoys in shaping the stochastic dynamics of biological clocks and emphasize the importance of synthetic decoys in designing robust clocks.
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Affiliation(s)
- Supravat Dey
- Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware,Corresponding author
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware,Department of Biomedical Engineering, University of Delaware, Newark, Delaware
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35
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Bell GRR, Rincón E, Akdoğan E, Collins SR. Optogenetic control of receptors reveals distinct roles for actin- and Cdc42-dependent negative signals in chemotactic signal processing. Nat Commun 2021; 12:6148. [PMID: 34785668 PMCID: PMC8595684 DOI: 10.1038/s41467-021-26371-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/29/2021] [Indexed: 11/09/2022] Open
Abstract
During chemotaxis, neutrophils use cell surface G Protein Coupled Receptors to detect chemoattractant gradients. The downstream signaling system is wired with multiple feedback loops that amplify weak inputs and promote spatial separation of cell front and rear activities. Positive feedback could promote rapid signal spreading, yet information from the receptors is transmitted with high spatial fidelity, enabling detection of small differences in chemoattractant concentration across the cell. How the signal transduction network achieves signal amplification while preserving spatial information remains unclear. The GTPase Cdc42 is a cell-front polarity coordinator that is predictive of cell turning, suggesting an important role in spatial processing. Here we directly measure information flow from receptors to Cdc42 by pairing zebrafish parapinopsina, an optogenetic G Protein Coupled Receptor with reversible ON/OFF control, with a spectrally compatible red/far red Cdc42 Fluorescence Resonance Energy Transfer biosensor. Using this toolkit, we show that positive and negative signals downstream of G proteins shape a rapid, dose-dependent Cdc42 response. Furthermore, F-actin and Cdc42 itself provide two distinct negative signals that limit the duration and spatial spread of Cdc42 activation, maintaining output signals local to the originating receptors.
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Affiliation(s)
- George R R Bell
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Esther Rincón
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Emel Akdoğan
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Sean R Collins
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA.
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36
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Bernardello M, Marsal M, Gualda EJ, Loza-Alvarez P. Light-sheet fluorescence microscopy for the in vivo study of microtubule dynamics in the zebrafish embryo. BIOMEDICAL OPTICS EXPRESS 2021; 12:6237-6254. [PMID: 34745732 PMCID: PMC8547989 DOI: 10.1364/boe.438402] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
During its first hours of development, the zebrafish embryo presents a large microtubule array in the yolk region, essential for its development. Despite of its size and dynamic behavior, this network has been studied only in limited field of views or in fixed samples. We designed and implemented different strategies in Light Sheet Fluorescence microscopy for imaging the entire yolk microtubule (MT) network in vivo. These have allowed us to develop a novel image analysis from which we clearly observe a cyclical re-arrangement of the entire MT network in synchrony with blastoderm mitotic waves. These dynamics also affect a previously unreported microtubule array deep within the yolk, here described. These findings provide a new vision of the zebrafish yolk microtubules arrangement, and offers novel insights in the interaction between mitotic events and microtubules reorganization.
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Affiliation(s)
- Matteo Bernardello
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, 08860, Spain
- equal contribution
| | - Maria Marsal
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, 08860, Spain
- equal contribution
| | - Emilio J. Gualda
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, 08860, Spain
- equal contribution
| | - Pablo Loza-Alvarez
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, 08860, Spain
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37
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Hannum ME, Lin C, Bell K, Toskala A, Koch R, Galaniha T, Nolden A, Reed DR, Joseph P. The genetics of eating behaviors: research in the age of COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.09.03.458854. [PMID: 34518838 DOI: 10.1101/2021.04.03.438340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
How much pleasure we take in eating is more than just how much we enjoy the taste of food. Food involvement - the amount of time we spend on food beyond the immediate act of eating and tasting - is key to the human food experience. We took a biological approach to test whether food-related behaviors, together capturing food involvement, have genetic components and are partly due to inherited variation. We collected data via an internet survey from a genetically informative sample of 419 adult twins (114 monozygotic twin pairs, 31 dizygotic twin pairs, and 129 singletons). Because we conducted this research during the pandemic, we also ascertained how many participants had experienced COVID-19-associated loss of taste and smell. Since these respondents had previously participated in research in person, we measured their level of engagement to evaluate the quality of their online responses. Additive genetics explained 16-44% of the variation in some measures of food involvement, most prominently various aspects of cooking, suggesting some features of the human food experience may be inborn. Other features reflected shared (early) environment, captured by respondents' twin status. About 6% of participants had a history of COVID-19 infection, many with transitory taste and smell loss, but all but one had recovered before the survey. Overall, these results suggest that people may have inborn as well as learned variations in their involvement with food. We also learned to adapt to research during a pandemic by considering COVID-19 status and measuring engagement in online studies of human eating behavior.
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38
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Rombouts J, Gelens L. Analytical approximations for the speed of pacemaker-generated waves. Phys Rev E 2021; 104:014220. [PMID: 34412213 DOI: 10.1103/physreve.104.014220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/25/2021] [Indexed: 11/07/2022]
Abstract
In oscillatory media, waves can be generated by pacemaker regions which oscillate faster than their surroundings. In many chemical and biological systems, such waves can synchronize the whole medium and as such they are a means of transmitting information at a fixed speed over large distances. In this paper, we apply analytical tools to investigate the factors that determine the speed of these waves. More precisely, we apply singular perturbation and phase reduction methods to two types of negative-feedback oscillators, one built on underlying bistability and one including a time delay in the negative feedback. In both systems, we investigate the influence of time-scale separation on the resulting wave speed, as well as the effect of size and frequency of the pacemaker region. We compare our analytical estimates to numerical simulations which we described previously [J. Rombouts and L. Gelens, Phys. Rev. Research 2, 043038 (2020)2643-156410.1103/PhysRevResearch.2.043038].
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Affiliation(s)
- Jan Rombouts
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, University of Leuven (KU Leuven), B-3000 Leuven, Belgium
| | - Lendert Gelens
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, University of Leuven (KU Leuven), B-3000 Leuven, Belgium
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39
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Dieterle PB, Amir A. Diffusive wave dynamics beyond the continuum limit. Phys Rev E 2021; 104:014406. [PMID: 34412293 DOI: 10.1103/physreve.104.014406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/25/2021] [Indexed: 11/07/2022]
Abstract
Scientists have observed and studied diffusive waves in contexts as disparate as population genetics and cell signaling. Often, these waves are propagated by discrete entities or agents, such as individual cells in the case of cell signaling. For a broad class of diffusive waves, we characterize the transition between the collective propagation of diffusive waves, in which the wave speed is well described by continuum theory, and the propagation of diffusive waves by individual agents. We show that this transition depends heavily on the dimensionality of the system in which the wave propagates and that disordered systems yield dynamics largely consistent with lattice systems. In some system dimensionalities, the intuition that closely packed sources more accurately mimic a continuum can be grossly violated.
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Affiliation(s)
- Paul B Dieterle
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Ariel Amir
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
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40
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Wang Q, Zhou C, Huang L, Wang W. "Ballistic" waves among chemically oscillating micromotors. Chem Commun (Camb) 2021; 57:8492-8495. [PMID: 34350918 DOI: 10.1039/d1cc02558a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Coordinating a group of chemically powered micromotors holds great importance in potential applications that involve a large population in a complex environment, yet information transmission at a population scale remains challenging. To this end, we demonstrate how propagating waves emerge among a population of spontaneously oscillating micromotors that dash toward a direction prescribed by their Janus orientations (termed a "ballistic" wave). Moreover, chemical communication among these micromotors enables the tuning of the speed and frequency of individual micromotors and their waves, by varying the population density or the viscosity of the medium.
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Affiliation(s)
- Qizhang Wang
- School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China.
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41
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Abstract
The temporal coordination of events at cellular and tissue scales is essential for the proper development of organisms, and involves cell-intrinsic processes that can be coupled by local cellular signalling and instructed by global signalling, thereby creating spatial patterns of cellular states that change over time. The timing and structure of these patterns determine how an organism develops. Traditional developmental genetic methods have revealed the complex molecular circuits regulating these processes but are limited in their ability to predict and understand the emergent spatio-temporal dynamics. Increasingly, approaches from physics are now being used to help capture the dynamics of the system by providing simplified, generic descriptions. Combined with advances in imaging and computational power, such approaches aim to provide insight into timing and patterning in developing systems.
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42
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Nolet FE, Gelens L. Mitotic waves in an import-diffusion model with multiple nuclei in a shared cytoplasm. Biosystems 2021; 208:104478. [PMID: 34246690 DOI: 10.1016/j.biosystems.2021.104478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 11/29/2022]
Abstract
Nuclei import and export proteins, including cell cycle regulators. These import-export processes are modulated periodically by the cell cycle, for example due to the periodic assembly and breakdown of the nuclear envelope. As such, replicated DNA can be segregated between the two daughter cells and the proteins that were localized in the nucleus are free to diffuse throughout the cytoplasm. Here, we study a mathematical import-diffusion model to show how proteins, i.e. cell cycle regulators, could be redistributed in the cytoplasm by nuclei that periodically toggle between interphase and mitosis. We show that when the cell cycle period depends on the local concentration of regulators, the model exhibits mitotic waves. We discuss how the velocity and spatial origin of these mitotic waves depend on the different model parameters. This work is motivated by recent in vitro experiments reporting on mitotic waves in cycling cell-free extracts made with Xenopus laevis frog eggs, where multiple nuclei share the same cytoplasm. Such experiments have shown that nuclei act as pacemakers for the cell cycle and thus play an important role in collectively defining the spatial origin of mitotic waves.
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Affiliation(s)
- F E Nolet
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Belgium.
| | - L Gelens
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Belgium.
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43
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Abstract
Understanding the mechanisms of embryonic cell cycles is a central goal of developmental biology, as the regulation of the cell cycle must be closely coordinated with other events during early embryogenesis. Quantitative imaging approaches have recently begun to reveal how the cell cycle oscillator is controlled in space and time, and how it is integrated with mechanical signals to drive morphogenesis. Here, we discuss how the Drosophila embryo has served as an excellent model for addressing the molecular and physical mechanisms of embryonic cell cycles, with comparisons to other model systems to highlight conserved and species-specific mechanisms. We describe how the rapid cleavage divisions characteristic of most metazoan embryos require chemical waves and cytoplasmic flows to coordinate morphogenesis across the large expanse of the embryo. We also outline how, in the late cleavage divisions, the cell cycle is inter-regulated with the activation of gene expression to ensure a reliable maternal-to-zygotic transition. Finally, we discuss how precise transcriptional regulation of the timing of mitosis ensures that tissue morphogenesis and cell proliferation are tightly controlled during gastrulation.
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Affiliation(s)
| | - Stefano Di Talia
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27705, USA
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44
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Abstract
The formation of crossovers between homologous chromosomes is key to sexual reproduction. In most species, crossovers are spaced further apart than would be expected if they formed independently, a phenomenon termed crossover interference. Despite more than a century of study, the molecular mechanisms implementing crossover interference remain a subject of active debate. Recent findings of how signaling proteins control the formation of crossovers and about the interchromosomal interface in which crossovers form offer new insights into this process. In this Review, we present a cell biological and biophysical perspective on crossover interference, summarizing the evidence that links interference to the spatial, dynamic, mechanical and molecular properties of meiotic chromosomes. We synthesize this physical understanding in the context of prevailing mechanistic models that aim to explain how crossover interference is implemented.
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Affiliation(s)
- Lexy von Diezmann
- Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT 84112, USA.,School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Ofer Rog
- Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT 84112, USA.,School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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45
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El Dika M. Use of Xenopus laevis cell-free extracts to study BRCA2 role in chromosome alignment. DNA Repair (Amst) 2021; 100:103053. [PMID: 33550028 DOI: 10.1016/j.dnarep.2021.103053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 01/19/2021] [Accepted: 01/23/2021] [Indexed: 11/18/2022]
Affiliation(s)
- Mohammed El Dika
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, USA; Institut Curie, PSL Research University, CNRS, UMR3348, Orsay, France; Paris Sud University, Paris-Saclay University, CNRS, UMR3348, Orsay, France.
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46
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Shamipour S, Caballero-Mancebo S, Heisenberg CP. Cytoplasm's Got Moves. Dev Cell 2021; 56:213-226. [PMID: 33321104 DOI: 10.1016/j.devcel.2020.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/22/2020] [Accepted: 11/30/2020] [Indexed: 01/01/2023]
Abstract
Cytoplasm is a gel-like crowded environment composed of various macromolecules, organelles, cytoskeletal networks, and cytosol. The structure of the cytoplasm is highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules are restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the crowded nature of the cytoplasm at the microscopic scale, large-scale reorganization of the cytoplasm is essential for important cellular functions, such as cell division and polarization. How such mesoscale reorganization of the cytoplasm is achieved, especially for large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, is only beginning to be understood. In this review, we will discuss recent advances in elucidating the molecular, cellular, and biophysical mechanisms by which the cytoskeleton drives cytoplasmic reorganization across different scales, structures, and species.
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Affiliation(s)
- Shayan Shamipour
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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47
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Rombouts J, Gelens L. Dynamic bistable switches enhance robustness and accuracy of cell cycle transitions. PLoS Comput Biol 2021; 17:e1008231. [PMID: 33411761 PMCID: PMC7817062 DOI: 10.1371/journal.pcbi.1008231] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 01/20/2021] [Accepted: 11/18/2020] [Indexed: 02/06/2023] Open
Abstract
Bistability is a common mechanism to ensure robust and irreversible cell cycle transitions. Whenever biological parameters or external conditions change such that a threshold is crossed, the system abruptly switches between different cell cycle states. Experimental studies have uncovered mechanisms that can make the shape of the bistable response curve change dynamically in time. Here, we show how such a dynamically changing bistable switch can provide a cell with better control over the timing of cell cycle transitions. Moreover, cell cycle oscillations built on bistable switches are more robust when the bistability is modulated in time. Our results are not specific to cell cycle models and may apply to other bistable systems in which the bistable response curve is time-dependent. Many systems in nature show bistability, which means they can evolve to one of two stable steady states under exactly the same conditions. Which state they evolve to depends on where the system comes from. Such bistability underlies the switching behavior that is essential for cells to progress in the cell division cycle. A quick switch happens when the cell jumps from one steady state to another steady state. Typical of this switching behavior is its robustness and irreversibility. In this paper, we expand this viewpoint of the dynamics of the cell cycle by considering bistable switches which themselves are changing in time. This gives the cell an extra layer of control over transitions both in time and in space, and can make those transitions more robust. Such dynamically changing bistability can appear very naturally. We show this in a model of mitotic entry, in which we include a nuclear and cytoplasmic compartment. The activity of a crucial cell cycle protein follows a bistable switch in each compartment, but the shape of its response is changing in time as proteins are imported into and exported from the nucleus.
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Affiliation(s)
- Jan Rombouts
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, University of Leuven (KU Leuven), B-3000 Leuven, Belgium
- * E-mail: (J.R.); (L.G.)
| | - Lendert Gelens
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, University of Leuven (KU Leuven), B-3000 Leuven, Belgium
- * E-mail: (J.R.); (L.G.)
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48
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Kamenz J, Gelens L, Ferrell JE. Bistable, Biphasic Regulation of PP2A-B55 Accounts for the Dynamics of Mitotic Substrate Phosphorylation. Curr Biol 2020; 31:794-808.e6. [PMID: 33357450 PMCID: PMC7904671 DOI: 10.1016/j.cub.2020.11.058] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 10/20/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022]
Abstract
The phosphorylation of mitotic proteins is bistable, which contributes to the decisiveness of the transitions into and out of M phase. The bistability in substrate phosphorylation has been attributed to bistability in the activation of the cyclin-dependent kinase Cdk1. However, more recently it has been suggested that bistability also arises from positive feedback in the regulation of the Cdk1-counteracting phosphatase PP2A-B55. Here, we demonstrate biochemically using Xenopus laevis egg extracts that the Cdk1-counter-acting phosphatase PP2A-B55 functions as a bistable switch, even when the bistability of Cdk1 activation is suppressed. In addition, Cdk1 regulates PP2A-B55 in a biphasic manner; low concentrations of Cdk1 activate PP2A-B55 and high concentrations inactivate it. As a consequence of this incoherent feedforward regulation, PP2A-B55 activity rises concurrently with Cdk1 activity during interphase and suppresses substrate phosphorylation. PP2A-B55 activity is then sharply downregulated at the onset of mitosis. During mitotic exit, Cdk1 activity initially falls with no obvious change in substrate phosphorylation; dephosphorylation then commences once PP2A-B55 spikes in activity. These findings suggest that changes in Cdk1 activity are permissive for mitotic entry and exit but that the changes in PP2A-B55 activity are the ultimate trigger. Mitotic transitions are accompanied by drastic changes in the phosphorylation state of proteins. Kamenz et al. demonstrate biochemically that the major mitotic phosphatase PP2A-B55 is regulated by incoherent feedforward and double-negative feedback loops to promote rapid and switch-like mitotic entry and exit.
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Affiliation(s)
- Julia Kamenz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305-5174, USA.
| | - Lendert Gelens
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305-5174, USA; Laboratory of Dynamics in Biological Systems, KU Leuven, Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
| | - James E Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305-5174, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA.
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49
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Afanzar O, Buss GK, Stearns T, Ferrell JE. The nucleus serves as the pacemaker for the cell cycle. eLife 2020; 9:59989. [PMID: 33284106 PMCID: PMC7755385 DOI: 10.7554/elife.59989] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 12/06/2020] [Indexed: 12/20/2022] Open
Abstract
Mitosis is a dramatic process that affects all parts of the cell. It is driven by an oscillator whose various components are localized in the nucleus, centrosome, and cytoplasm. In principle, the cellular location with the fastest intrinsic rhythm should act as a pacemaker for the process. Here we traced the waves of tubulin polymerization and depolymerization that occur at mitotic entry and exit in Xenopus egg extracts back to their origins. We found that mitosis was commonly initiated at sperm-derived nuclei and their accompanying centrosomes. The cell cycle was ~20% faster at these initiation points than in the slowest regions of the extract. Nuclei produced from phage DNA, which did not possess centrosomes, also acted as trigger wave sources, but purified centrosomes in the absence of nuclei did not. We conclude that the nucleus accelerates mitotic entry and propose that it acts as a pacemaker for cell cycle.
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Affiliation(s)
- Oshri Afanzar
- Department of Chemical and Systems Biology, Stanford Medicine, Stanford, United States
| | - Garrison K Buss
- Department of Molecular and Cellular Physiology, Stanford Medicine, Stanford, United States
| | - Tim Stearns
- Department of Biology, Stanford University, Stanford, United States.,Department of Genetics, Stanford Medicine, Stanford, United States
| | - James E Ferrell
- Department of Chemical and Systems Biology, Stanford Medicine, Stanford, United States.,Department of Biochemistry, Stanford Medicine, Stanford, United States
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50
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Dieterle PB, Min J, Irimia D, Amir A. Dynamics of diffusive cell signaling relays. eLife 2020; 9:61771. [PMID: 33275097 PMCID: PMC7781602 DOI: 10.7554/elife.61771] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/03/2020] [Indexed: 01/22/2023] Open
Abstract
In biological contexts as diverse as development, apoptosis, and synthetic microbial consortia, collections of cells or subcellular components have been shown to overcome the slow signaling speed of simple diffusion by utilizing diffusive relays, in which the presence of one type of diffusible signaling molecule triggers participation in the emission of the same type of molecule. This collective effect gives rise to fast-traveling diffusive waves. Here, in the context of cell signaling, we show that system dimensionality – the shape of the extracellular medium and the distribution of cells within it – can dramatically affect the wave dynamics, but that these dynamics are insensitive to details of cellular activation. As an example, we show that neutrophil swarming experiments exhibit dynamical signatures consistent with the proposed signaling motif. We further show that cell signaling relays generate much steeper concentration profiles than does simple diffusion, which may facilitate neutrophil chemotaxis.
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Affiliation(s)
- Paul B Dieterle
- Department of Physics, Harvard University, Cambridge, United States
| | - Jiseon Min
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Daniel Irimia
- BioMEMS Resource Center and Center for Surgery, Innovation and Bioengineering, Department of Surgery, Massachusetts General Hospital, Boston, United States
| | - Ariel Amir
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, United States
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