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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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Chen Y, Huang JH, Phong C, Ferrell JE. Viscosity-dependent control of protein synthesis and degradation. Nat Commun 2024; 15:2149. [PMID: 38459041 PMCID: PMC10923802 DOI: 10.1038/s41467-024-46447-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 02/28/2024] [Indexed: 03/10/2024] Open
Abstract
It has been proposed that the concentration of proteins in the cytoplasm maximizes the speed of important biochemical reactions. Here we have used Xenopus egg extracts, which can be diluted or concentrated to yield a range of cytoplasmic protein concentrations, to test the effect of cytoplasmic concentration on mRNA translation and protein degradation. We find that protein synthesis rates are maximal in ~1x cytoplasm, whereas protein degradation continues to rise to a higher optimal concentration of ~1.8x. We show that this difference in optima can be attributed to a greater sensitivity of translation to cytoplasmic viscosity. The different concentration optima could produce a negative feedback homeostatic system, where increasing the cytoplasmic protein concentration above the 1x physiological level increases the viscosity of the cytoplasm, which selectively inhibits translation and drives the system back toward the 1x set point.
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Affiliation(s)
- Yuping Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Jo-Hsi Huang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Connie Phong
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - James E Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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Puls O, Ruiz-Reynés D, Tavella F, Jin M, Kim Y, Gelens L, Yang Q. Mitotic waves in frog egg extracts: Transition from phase waves to trigger waves. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576267. [PMID: 38496576 PMCID: PMC10942321 DOI: 10.1101/2024.01.18.576267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Cyclin-dependent kinase 1 (Cdk1) activity rises and falls throughout the cell cycle, a cell-autonomous process known as mitotic oscillations. These oscillators can synchronize when spatially coupled, providing a crucial foundation for rapid synchronous divisions in large early embryos like Drosophila (~ 0.5 mm) and Xenopus (~ 1.2 mm). While diffusion alone cannot achieve such long-range coordination, recent studies have proposed two types of mitotic waves, phase and trigger waves, to explain the phenomena. How the waves establish over time for efficient spatial coordination remains unclear. Using Xenopus laevis egg extracts and a Cdk1 FRET sensor, we observe a transition from phase waves to a trigger wave regime in an initially homogeneous cytosol. Adding nuclei accelerates such transition. Moreover, the system transitions almost immediately to this regime when externally driven by metaphase-arrested extracts from the boundary. Employing computational modeling, we pinpoint how wave nature, including speed-period relation, depends on transient dynamics and oscillator properties, suggesting that phase waves appear transiently due to the time required for trigger waves to entrain the system and that spatial heterogeneity promotes entrainment. Therefore, we show that both waves belong to a single biological process capable of coordinating the cell cycle over long distances.
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Affiliation(s)
- Owen Puls
- Department of Physics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel Ruiz-Reynés
- Laboratory of Dynamics in Biological Systems, KU Leuven, Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
- IFISC (CSIC-UIB). Instituto de Física Interdisciplinar y Sistemas Complejos, E-07122 Palma de Mallorca, Spain
| | - Franco Tavella
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Minjun Jin
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yeonghoon Kim
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lendert Gelens
- Laboratory of Dynamics in Biological Systems, KU Leuven, Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
| | - Qiong Yang
- Department of Physics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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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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Liu J, Zhang C. Xenopus cell-free extracts and their applications in cell biology study. BIOPHYSICS REPORTS 2023; 9:195-205. [PMID: 38516620 PMCID: PMC10951473 DOI: 10.52601/bpr.2023.230016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/05/2023] [Indexed: 03/23/2024] Open
Abstract
Xenopus has proven to be a remarkably versatile model organism in the realm of biological research for numerous years, owing to its straightforward maintenance in laboratory settings and its abundant provision of ample-sized oocytes, eggs, and embryos. The cell cycle of these oocytes, eggs, and early embryos exhibits synchrony, and extracts derived from these cells serve various research purposes. Many fundamental concepts in biochemistry, cell biology, and development have been elucidated through the use of cell-free extracts derived from Xenopus cells. Over the past few decades, a wide array of cell-free extracts has been prepared from oocytes, eggs, and early embryos of different Xenopus species at varying cell cycle stages. Each of these extracts possesses distinct characteristics. This review provides a concise overview of the Xenopus species employed in laboratory research, the diverse types of cell-free extracts available, and their respective properties. Furthermore, this review delves into the extensive investigation of spindle assembly in Xenopus egg extracts, underscoring the versatility and potency of these cell-free systems in the realm of cell biology.
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Affiliation(s)
- Junjun Liu
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA 91768, USA
| | - Chuanmao Zhang
- The Academy for Cell and Life Health, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- The Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China
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Morphological growth dynamics, mechanical stability, and active microtubule mechanics underlying spindle self-organization. Proc Natl Acad Sci U S A 2022; 119:e2209053119. [PMID: 36282919 PMCID: PMC9636915 DOI: 10.1073/pnas.2209053119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The spindle is a dynamic intracellular structure self-organized from microtubules and microtubule-associated proteins. The spindle’s bipolar morphology is essential for the faithful segregation of chromosomes during cell division, and it is robustly maintained by multifaceted mechanisms. However, abnormally shaped spindles, such as multipolar spindles, can stochastically arise in a cell population and cause chromosome segregation errors. The physical basis of how microtubules fail in bipolarization and occasionally favor nonbipolar assembly is poorly understood. Here, using live fluorescence imaging and quantitative shape analysis in
Xenopus
egg extracts, we find that spindles of varied shape morphologies emerge through nonrandom, bistable self-organization paths, one leading to a bipolar and the other leading to a multipolar phenotype. The bistability defines the spindle’s unique morphological growth dynamics linked to each shape phenotype and can be promoted by a locally distorted microtubule flow that arises within premature structures. We also find that bipolar and multipolar spindles are stable at the steady-state in bulk but can infrequently switch between the two phenotypes. Our microneedle-based physical manipulation further demonstrates that a transient force perturbation applied near the assembled pole can trigger the phenotypic switching, revealing the mechanical plasticity of the spindle. Together with molecular perturbation of kinesin-5 and augmin, our data propose the physical and molecular bases underlying the emergence of spindle-shape variation, which influences chromosome segregation fidelity during cell division.
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Ems-McClung SC, Walczak CE. Using FLIM-FRET for Characterizing Spatial Interactions in the Spindle. Methods Mol Biol 2022; 2415:221-243. [PMID: 34972958 PMCID: PMC8740612 DOI: 10.1007/978-1-0716-1904-9_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Proper spindle assembly and the attachment of chromosomes to the spindle are key for the accurate segregation of chromosomes to daughter cells. Errors in these processes can lead to aneuploidy, which is a hallmark of cancer. Understanding the mechanisms that drive spindle assembly will provide fundamental insights into how accurate chromosome segregation is achieved. One challenge in elucidating the complexities of spindle assembly is to visualize protein interactions in space and time. The Xenopus egg extract system has been a valuable tool to probe protein function during spindle assembly in vitro. Tagging proteins with fluorescent proteins and utilizing fluorescence-based approaches, such as Förster resonance energy transfer (FRET) and fluorescence lifetime imaging microscopy (FLIM), have provided visual clues about the mechanics of spindle assembly and its regulators. However, elucidating how spindle assembly factors are spatially regulated is still challenging. Combining the egg extract system and visual FRET approaches provides a powerful tool to probe the processes involved in spindle assembly. Here we describe how a FLIM-FRET biosensor can be used to study protein-protein interactions in spindles assembled in Xenopus egg extracts. This approach should be readily adaptable to a wide variety of proteins to allow for new insights into the regulation of spindle assembly.
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Deolal P, Male G, Mishra K. The challenge of staying in shape: nuclear size matters. Curr Genet 2021; 67:605-612. [PMID: 33779777 DOI: 10.1007/s00294-021-01176-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 10/21/2022]
Abstract
Cellular organelles have unique morphology and the organelle size to cell size ratio is regulated. Nucleus is one of the most prominent, usually round in shape, organelle of a eukaryotic cell that occupies 8-10% of cellular volume. The shape and size of nucleus is known to undergo remodeling during processes such as cell growth, division and certain stresses. Regulation of protein and lipid distribution at the nuclear envelope is crucial for preserving the nuclear morphology and size. As size and morphology are interlinked, altering one influences the other. In this perspective, we discuss the relationship between size and shape regulation of the nucleus.
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Affiliation(s)
- Pallavi Deolal
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Gurranna Male
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Krishnaveni Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India.
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Romano FB, Blok NB, Rapoport TA. Peroxisome protein import recapitulated in Xenopus egg extracts. J Cell Biol 2019; 218:2021-2034. [PMID: 30971414 PMCID: PMC6548129 DOI: 10.1083/jcb.201901152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/17/2019] [Accepted: 03/28/2019] [Indexed: 12/14/2022] Open
Abstract
Peroxisomes import proteins with a C-terminal SKL sequence by a poorly understood mechanism. Romano et al. use Xenopus egg extracts to study peroxisome import in vitro. The novel assay recapitulates import in vivo and provides mechanistic insights. Peroxisomes import their luminal proteins from the cytosol. Most substrates contain a C-terminal Ser-Lys-Leu (SKL) sequence that is recognized by the receptor Pex5. Pex5 binds to peroxisomes via a docking complex containing Pex14, and recycles back into the cytosol following its mono-ubiquitination at a conserved Cys residue. The mechanism of peroxisome protein import remains incompletely understood. Here, we developed an in vitro import system based on Xenopus egg extracts. Import is dependent on the SKL motif in the substrate and on the presence of Pex5 and Pex14, and is sustained by ATP hydrolysis. A protein lacking an SKL sequence can be coimported, providing strong evidence for import of a folded protein. The conserved cysteine in Pex5 is not essential for import or to clear import sites for subsequent rounds of translocation. This new in vitro assay will be useful for further dissecting the mechanism of peroxisome protein import.
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Affiliation(s)
- Fabian B Romano
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Neil B Blok
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA
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Abstract
Cell division involves mechanical processes, such as chromosome transport and centrosome separation. Quantitative micromanipulation-based approaches have been central to dissecting the forces driving these processes. We highlight two biophysical assays that can be employed for such analyses. First, an in vitro "mini-spindle" assay is described that can be used to examine the collective mechanics of mitotic motor proteins cross-linking two microtubules. In the spindle, motor proteins (e.g., kinesin-5, kinesin-14, and dynein) can localize to overlapping microtubules that slide relative to each other, work as an ensemble, and equilibrate between cytoplasm and the microtubules. The "mini-spindle" assay can recapitulate these features and allows measurements of forces generated between adjacent microtubules and their dependence on filament orientation, sliding speed, overlap length, and motor protein density. Second, we describe a force-calibrated microneedle-based "whole-spindle" micromechanics assay. Microneedle-based micromanipulation can be a useful technique to examine cellular scale mechanics, but its use has been restricted by the difficulty in getting probes to penetrate the plasma membrane without disrupting cell physiology. As detailed here, the use of cell-free extracts prepared from metaphase-arrested Xenopus eggs can address this limitation. These micromanipulation studies also benefit from the use of frozen stocks of Xenopus egg extract. Together, these approaches can be used to decipher how micromechanics and biochemical activities ensure successful cell division.
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Affiliation(s)
- Yuta Shimamoto
- Center for Frontier Research, National Institute of Genetics, Mishima, Shizuoka, Japan.
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, United States.
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