51
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Chen H, Good MC. Nuclear sizER in Early Development. Dev Cell 2021; 54:297-298. [PMID: 32781022 DOI: 10.1016/j.devcel.2020.06.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In this issue of Developmental Cell, Mukherjee et al. (2020) investigate control of nuclear growth by live imaging of early embryogenesis, perturbations of blastomere dimensions, and reconstitution in vitro. The authors uncover new mechanisms of nuclear size scaling by the amount of inherited perinuclear ER and duration of interphase.
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Affiliation(s)
- Hui Chen
- Department of Cell and Developmental Biology, University of Pennsylvania, 421 Curie Blvd., 1151 BRB II/III, Philadelphia, PA 19104, USA
| | - Matthew C Good
- Department of Cell and Developmental Biology, University of Pennsylvania, 421 Curie Blvd., 1151 BRB II/III, Philadelphia, PA 19104, USA; Department of Bioengineering, University of Pennsylvania, 421 Curie Blvd., 1151 BRB II/III, Philadelphia, PA 19104, USA.
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52
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Ishihara K, Decker F, Caldas P, Pelletier JF, Loose M, Brugués J, Mitchison TJ. Spatial variation of microtubule depolymerization in large asters. Mol Biol Cell 2021; 32:869-879. [PMID: 33439671 PMCID: PMC8108532 DOI: 10.1091/mbc.e20-11-0723] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Microtubule plus-end depolymerization rate is a potentially important target of physiological regulation, but it has been challenging to measure, so its role in spatial organization is poorly understood. Here we apply a method for tracking plus ends based on time difference imaging to measure depolymerization rates in large interphase asters growing in Xenopus egg extract. We observed strong spatial regulation of depolymerization rates, which were higher in the aster interior compared with the periphery, and much less regulation of polymerization or catastrophe rates. We interpret these data in terms of a limiting component model, where aster growth results in lower levels of soluble tubulin and microtubule-associated proteins (MAPs) in the interior cytosol compared with that at the periphery. The steady-state polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the aster interior. We propose that the limiting component for microtubule assembly is a MAP that inhibits depolymerization, and that egg asters are tuned to low microtubule density.
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Affiliation(s)
- Keisuke Ishihara
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, 01307 Dresden, Germany.,Center for Systems Biology Dresden, 01307 Dresden, Germany.,Cluster of Excellence Physics of Life, TU Dresden, 01307 Dresden, Germany
| | - Franziska Decker
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, 01307 Dresden, Germany.,Center for Systems Biology Dresden, 01307 Dresden, Germany.,Cluster of Excellence Physics of Life, TU Dresden, 01307 Dresden, Germany
| | - Paulo Caldas
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - James F Pelletier
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115.,Cell Division Group, Marine Biological Laboratory, Woods Hole, MA 02543.,Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Martin Loose
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Jan Brugués
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, 01307 Dresden, Germany.,Center for Systems Biology Dresden, 01307 Dresden, Germany.,Cluster of Excellence Physics of Life, TU Dresden, 01307 Dresden, Germany
| | - Timothy J Mitchison
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115.,Cell Division Group, Marine Biological Laboratory, Woods Hole, MA 02543
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53
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Siedlik MJ, Yang Z, Kadam PS, Eberwine J, Issadore D. Micro- and Nano-Devices for Studying Subcellular Biology. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2005793. [PMID: 33345457 PMCID: PMC8258219 DOI: 10.1002/smll.202005793] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/20/2020] [Indexed: 05/27/2023]
Abstract
Cells are complex machines whose behaviors arise from their internal collection of dynamically interacting organelles, supramolecular complexes, and cytoplasmic chemicals. The current understanding of the nature by which subcellular biology produces cell-level behaviors is limited by the technological hurdle of measuring the large number (>103 ) of small-sized (<1 μm) heterogeneous organelles and subcellular structures found within each cell. In this review, the emergence of a suite of micro- and nano-technologies for studying intracellular biology on the scale of organelles is described. Devices that use microfluidic and microelectronic components for 1) extracting and isolating subcellular structures from cells and lysate; 2) analyzing the physiology of individual organelles; and 3) recreating subcellular assembly and functions in vitro, are described. The authors envision that the continued development of single organelle technologies and analyses will serve as a foundation for organelle systems biology and will allow new insight into fundamental and clinically relevant biological questions.
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Affiliation(s)
- Michael J Siedlik
- Department of Bioengineering, 335 Skirkanich Hall, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA, 19104, USA
| | - Zijian Yang
- Department of Mechanical Engineering and Applied Science, 335 Skirkanich Hall, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA, 19104, USA
| | - Parnika S Kadam
- Systems Pharmacology and Translational Therapeutics, 38 John Morgan Building, University of Pennsylvania, 3620 Hamilton Walk, Philadelphia, PA, 19104, USA
| | - James Eberwine
- Systems Pharmacology and Translational Therapeutics, 38 John Morgan Building, University of Pennsylvania, 3620 Hamilton Walk, Philadelphia, PA, 19104, USA
| | - David Issadore
- Department of Bioengineering, 335 Skirkanich Hall, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA, 19104, USA
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54
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Geisterfer ZM, Oakey J, Gatlin JC. Microfluidic encapsulation of Xenopus laevis cell-free extracts using hydrogel photolithography. STAR Protoc 2020; 1:100221. [PMID: 33377113 PMCID: PMC7757658 DOI: 10.1016/j.xpro.2020.100221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Cell-free extract derived from the eggs of the African clawed frog Xenopus laevis is a well-established model system that has been used historically in bulk aliquots. Here, we describe a microfluidic approach for isolating discrete, biologically relevant volumes of cell-free extract, with more expansive and precise control of extract shape compared with extract-oil emulsions. This approach is useful for investigating the mechanics of intracellular processes affected by cell geometry or cytoplasmic volume, including organelle scaling and positioning mechanisms. For complete details on the use and execution of this protocol, please refer to Geisterfer et al. (2020). Xenopus laevis cell-free extracts can be isolated as discreet volumes typical of cells Approach provides enhanced control over the shape and position of encapsulated extract Improved signal-to-noise during fluorescence imaging versus oil-emulsion extract droplets
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Affiliation(s)
- Zachary M Geisterfer
- Department of Molecular Biology, University of Wyoming, 1000 E. University Ave., Laramie, WY 82070, USA
| | - John Oakey
- Department of Chemical Engineering, University of Wyoming, 1000 E. University Ave., Laramie, WY 82070, USA.,Cell Organization & Division Group, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA
| | - Jesse C Gatlin
- Department of Molecular Biology, University of Wyoming, 1000 E. University Ave., Laramie, WY 82070, USA.,Cell Organization & Division Group, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA
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55
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Dynamic optima in cell sizes during early development enable normal gastrulation in zebrafish embryos. Dev Biol 2020; 468:26-40. [DOI: 10.1016/j.ydbio.2020.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 11/21/2022]
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56
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Datta A, Harbage D, Kondev J. Control of filament length by a depolymerizing gradient. PLoS Comput Biol 2020; 16:e1008440. [PMID: 33275598 PMCID: PMC7744062 DOI: 10.1371/journal.pcbi.1008440] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 12/16/2020] [Accepted: 10/12/2020] [Indexed: 11/19/2022] Open
Abstract
Cells assemble microns-long filamentous structures from protein monomers that are nanometers in size. These structures are often highly dynamic, yet in order for them to function properly, cells maintain them at a precise length. Here we investigate length-dependent depolymerization as a mechanism of length control. This mechanism has been recently proposed for flagellar length control in the single cell organisms Chlamydomonas and Giardia. Length dependent depolymerization can arise from a concentration gradient of a depolymerizing protein, such as kinesin-13 in Giardia, along the length of the flagellum. Two possible scenarios are considered: a linear and an exponential gradient of depolymerizing proteins. We compute analytically the probability distributions of filament lengths for both scenarios and show how these distributions are controlled by key biochemical parameters through a dimensionless number that we identify. In Chlamydomonas cells, the assembly dynamics of its two flagella are coupled via a shared pool of molecular components that are in limited supply, and so we investigate the effect of a limiting monomer pool on the length distributions. Finally, we compare our calculations to experiments. While the computed mean lengths are consistent with observations, the noise is two orders of magnitude smaller than the observed length fluctuations.
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Affiliation(s)
- Arnab Datta
- Department of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - David Harbage
- Department of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Jane Kondev
- Department of Physics, Brandeis University, Waltham, Massachusetts, United States of America
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57
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Rieckhoff EM, Berndt F, Elsner M, Golfier S, Decker F, Ishihara K, Brugués J. Spindle Scaling Is Governed by Cell Boundary Regulation of Microtubule Nucleation. Curr Biol 2020; 30:4973-4983.e10. [DOI: 10.1016/j.cub.2020.10.093] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/11/2020] [Accepted: 10/29/2020] [Indexed: 02/08/2023]
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58
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Groaz A, Moghimianavval H, Tavella F, Giessen TW, Vecchiarelli AG, Yang Q, Liu AP. Engineering spatiotemporal organization and dynamics in synthetic cells. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 13:e1685. [PMID: 33219745 DOI: 10.1002/wnan.1685] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 10/13/2020] [Accepted: 10/30/2020] [Indexed: 12/28/2022]
Abstract
Constructing synthetic cells has recently become an appealing area of research. Decades of research in biochemistry and cell biology have amassed detailed part lists of components involved in various cellular processes. Nevertheless, recreating any cellular process in vitro in cell-sized compartments remains ambitious and challenging. Two broad features or principles are key to the development of synthetic cells-compartmentalization and self-organization/spatiotemporal dynamics. In this review article, we discuss the current state of the art and research trends in the engineering of synthetic cell membranes, development of internal compartmentalization, reconstitution of self-organizing dynamics, and integration of activities across scales of space and time. We also identify some research areas that could play a major role in advancing the impact and utility of engineered synthetic cells. This article is categorized under: Biology-Inspired Nanomaterials > Lipid-Based Structures Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
| | | | | | | | | | - Qiong Yang
- University of Michigan, Ann Arbor, Michigan, USA
| | - Allen P Liu
- University of Michigan, Ann Arbor, Michigan, USA
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59
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Chen H, Qian W, Good MC. Integrating cellular dimensions with cell differentiation during early development. Curr Opin Cell Biol 2020; 67:109-117. [PMID: 33152556 DOI: 10.1016/j.ceb.2020.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/14/2020] [Accepted: 08/03/2020] [Indexed: 11/25/2022]
Abstract
Early embryo development is characterized by alteration of cellular dimensions and fating of blastomeres. An emerging concept is that cell size and shape drive cellular differentiation during early embryogenesis in a variety of model organisms. In this review, we summarize recent advances that elucidate the contribution of the physical dimensions of a cell to major embryonic transitions and cell fate specification in vivo. We also highlight techniques and newly evolving methods for manipulating the sizes and shapes of cells and whole embryos in situ and ex vivo. Finally, we provide an outlook for addressing fundamental questions in the field and more broadly uncovering how changes to cell size control decision making in a variety of biological contexts.
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Affiliation(s)
- Hui Chen
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenchao Qian
- Department of Cell and Developmental Biology, 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.
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60
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Gires PY, Thampi M, Weiss M. Quantifying active diffusion in an agitated fluid. Phys Chem Chem Phys 2020; 22:21678-21684. [PMID: 32966453 DOI: 10.1039/d0cp03629c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Mixing of reactants in microdroplets predominantly relies on diffusional motion due to small Reynolds numbers and the resulting absence of turbulent flows. Enhancing diffusion in microdroplets by an auxiliary noise source is therefore a topical problem. Here we report on how the diffusional motion of tracer beads is enhanced upon agitating the surrounding aqueous fluid with miniaturized magnetic stir bars that are compatible with microdroplets and microfluidic devices. Using single-particle tracking, we demonstrate via a broad palette of measures that local stirring of the fluid at different frequencies leads to an enhanced but apparently normal and homogenous diffusion process, i.e. diffusional steps follow the anticipated Gaussian distribution and no ballistic motion is observed whereas diffusion coefficients are significantly increased. The signature of stirring is, however, visible in the power-spectral density and in the velocity autocorrelation function of trajectories. Our data therefore demonstrate that diffusive mixing can be locally enhanced with miniaturized stir bars while only moderately affecting the ambient noise properties. The latter may also facilitate the controlled addition of nonequilibrium noise to complex fluids in future applications.
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Affiliation(s)
- Pierre-Yves Gires
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany.
| | - Mithun Thampi
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany.
| | - Matthias Weiss
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany.
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61
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Abstract
As cells grow, the size and number of their internal organelles increase in order to keep up with increased metabolic requirements. Abnormal size of organelles is a hallmark of cancer and an important aspect of diagnosis in cytopathology. Most organelles vary in either size or number, or both, as a function of cell size, but the mechanisms that create this variation remain unclear. In some cases, organelle size appears to scale with cell size through processes of relative growth, but in others the size may be set by either active measurement systems or genetic programs that instruct organelle biosynthetic activities to create organelles of a size appropriate to a given cell type.
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Affiliation(s)
- Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA;
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62
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Farhadifar R, Yu CH, Fabig G, Wu HY, Stein DB, Rockman M, Müller-Reichert T, Shelley MJ, Needleman DJ. Stoichiometric interactions explain spindle dynamics and scaling across 100 million years of nematode evolution. eLife 2020; 9:e55877. [PMID: 32966209 PMCID: PMC7511230 DOI: 10.7554/elife.55877] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 08/31/2020] [Indexed: 01/17/2023] Open
Abstract
The spindle shows remarkable diversity, and changes in an integrated fashion, as cells vary over evolution. Here, we provide a mechanistic explanation for variations in the first mitotic spindle in nematodes. We used a combination of quantitative genetics and biophysics to rule out broad classes of models of the regulation of spindle length and dynamics, and to establish the importance of a balance of cortical pulling forces acting in different directions. These experiments led us to construct a model of cortical pulling forces in which the stoichiometric interactions of microtubules and force generators (each force generator can bind only one microtubule), is key to explaining the dynamics of spindle positioning and elongation, and spindle final length and scaling with cell size. This model accounts for variations in all the spindle traits we studied here, both within species and across nematode species spanning over 100 million years of evolution.
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Affiliation(s)
- Reza Farhadifar
- Department of Molecular and Cellular Biology and School of Engineering and Applied Sciences, Harvard UniversityCambridgeUnited States
- Center for Computational Biology, Flatiron InstituteNew YorkUnited States
| | - Che-Hang Yu
- Department of Molecular and Cellular Biology and School of Engineering and Applied Sciences, Harvard UniversityCambridgeUnited States
| | - Gunar Fabig
- Experimental Center, Faculty of Medicine Carl Gustav CarusDresdenGermany
| | - Hai-Yin Wu
- Department of Molecular and Cellular Biology and School of Engineering and Applied Sciences, Harvard UniversityCambridgeUnited States
| | - David B Stein
- Center for Computational Biology, Flatiron InstituteNew YorkUnited States
| | - Matthew Rockman
- Department of Biology and Center for Genomics & Systems Biology, New York UniversityNew YorkUnited States
| | | | - Michael J Shelley
- Center for Computational Biology, Flatiron InstituteNew YorkUnited States
- Courant Institute, New York UniversityNew YorkUnited States
| | - Daniel J Needleman
- Department of Molecular and Cellular Biology and School of Engineering and Applied Sciences, Harvard UniversityCambridgeUnited States
- Center for Computational Biology, Flatiron InstituteNew YorkUnited States
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63
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Carlini L, Brittingham GP, Holt LJ, Kapoor TM. Microtubules Enhance Mesoscale Effective Diffusivity in the Crowded Metaphase Cytoplasm. Dev Cell 2020; 54:574-582.e4. [PMID: 32818469 PMCID: PMC7685229 DOI: 10.1016/j.devcel.2020.07.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 06/10/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022]
Abstract
Mesoscale macromolecular complexes and organelles, tens to hundreds of nanometers in size, crowd the eukaryotic cytoplasm. It is therefore unclear how mesoscale particles remain sufficiently mobile to regulate dynamic processes such as cell division. Here, we study mobility across dividing cells that contain densely packed, dynamic microtubules, comprising the metaphase spindle. In dividing human cells, we tracked 40 nm genetically encoded multimeric nanoparticles (GEMs), whose sizes are commensurate with the inter-filament spacing in metaphase spindles. Unexpectedly, the effective diffusivity of GEMs was similar inside the dense metaphase spindle and the surrounding cytoplasm. Eliminating microtubules or perturbing their polymerization dynamics decreased diffusivity by ~30%, suggesting that microtubule polymerization enhances random displacements to amplify diffusive-like motion. Our results suggest that microtubules effectively fluidize the mitotic cytoplasm to equalize mesoscale mobility across a densely packed, dynamic, non-uniform environment, thus spatially maintaining a key biophysical parameter that impacts biochemistry, ranging from metabolism to the nucleation of cytoskeletal filaments.
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Affiliation(s)
- Lina Carlini
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Gregory P Brittingham
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA.
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64
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Guilloux G, Gibeaux R. Mechanisms of spindle assembly and size control. Biol Cell 2020; 112:369-382. [PMID: 32762076 DOI: 10.1111/boc.202000065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/03/2020] [Accepted: 08/03/2020] [Indexed: 01/09/2023]
Abstract
The spindle is crucial for cell division by allowing the faithful segregation of replicated chromosomes to daughter cells. Proper segregation is ensured only if microtubules (MTs) and hundreds of other associated factors interact to assemble this complex structure with the appropriate architecture and size. In this review, we describe the latest view of spindle organisation as well as the molecular gradients and mechanisms underlying MT nucleation and spindle assembly. We then discuss the overlapping physical and molecular constraints that dictate spindle morphology, concluding with a focus on spindle size regulation.
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Affiliation(s)
- Gabriel Guilloux
- Univ Rennes, CNRS, IGDR [(Institute of Genetics and Development of Rennes)] - UMR 6290, F-35000 Rennes, France
| | - Romain Gibeaux
- Univ Rennes, CNRS, IGDR [(Institute of Genetics and Development of Rennes)] - UMR 6290, F-35000 Rennes, France
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65
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Miniaturized magnetic stir bars for controlled agitation of aqueous microdroplets. Sci Rep 2020; 10:10911. [PMID: 32616786 PMCID: PMC7331805 DOI: 10.1038/s41598-020-67767-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/08/2020] [Indexed: 12/19/2022] Open
Abstract
Controlled stirring of tiny volumes of aqueous fluids is of particular importance in the life sciences, e.g. in the context of microfluidic and lab-on-chip applications. Local stirring not only accelerates fluid mixing and diffusion-limited processes, but it also allows for adding controlled active noise to the fluid. Here we report on the synthesis and characterization of magnetic nano-stir bars (MNBs) with which these features can be achieved in a straightforward fashion. We also demonstrate the applicability of MNBs to cell extract droplets in microfluidic channels and we show that they can introduce active noise to cell extracts as evidenced by altered fluctuations of ensembles of cytoskeletal filaments.
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66
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Miller KE, Brownlee C, Heald R. The power of amphibians to elucidate mechanisms of size control and scaling. Exp Cell Res 2020; 392:112036. [PMID: 32343955 PMCID: PMC7246146 DOI: 10.1016/j.yexcr.2020.112036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/19/2020] [Accepted: 04/22/2020] [Indexed: 01/26/2023]
Abstract
Size is a fundamental feature of biology that affects physiology at all levels, from the organism to organs and tissues to cells and subcellular structures. How size is determined at these different levels, and how biological structures scale to fit together and function properly are important open questions. Historically, amphibian systems have been extremely valuable to describe scaling phenomena, as they occupy some of the extremes in biological size and are amenable to manipulations that alter genome and cell size. More recently, the application of biochemical, biophysical, and embryological techniques to amphibians has provided insight into the molecular mechanisms underlying scaling of subcellular structures to cell size, as well as how perturbation of normal size scaling impacts other aspects of cell and organism physiology.
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Affiliation(s)
- Kelly E Miller
- Department of Molecular and Cell Biology, University of California, CA, 94720, Berkeley, USA
| | - Christopher Brownlee
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, 11794-8651, USA.
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, CA, 94720, Berkeley, USA.
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67
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Abstract
The size of the intracellular structure that encloses genomic DNA - known as the nucleus in eukaryotes and nucleoid in prokaryotes - is believed to scale according to cell size and genomic content inside them across the tree of life. However, an actual scaling relationship remains largely unexplored across eukaryotic species. Here, I collected a large dataset of nuclear and cell volumes in diverse species across different phyla, including some prokaryotes, from the published literature and assessed the scaling relationship. Although entire inter-species data showed that nuclear volume correlates with cell volume, the quantitative scaling property exhibited differences among prokaryotes, unicellular eukaryotes and multicellular eukaryotes. Additionally, the nuclear volume correlates with genomic content inside the nucleus of multicellular eukaryotes but not of prokaryotes and unicellular eukaryotes. In this Hypothesis, I, thus, propose that the basic concept of nuclear-size scaling is conserved across eukaryotes; however, structural and mechanical properties of nuclear membranes and chromatin can result in different scaling relationships of nuclear volume to cell volume and genomic content among species. In particular, eukaryote-specific properties of the nuclear membrane may contribute to the extreme flexibility of nuclear size with regard to DNA density inside the nucleus.
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Affiliation(s)
- Yuki Hara
- Evolutionary Cell Biology Laboratory, Faculty of Science, Yamaguchi University, Yoshida 1677-1, Yamaguchi city 753-8512, Japan
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68
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Tug-of-war between actomyosin-driven antagonistic forces determines the positioning symmetry in cell-sized confinement. Nat Commun 2020; 11:3063. [PMID: 32541780 PMCID: PMC7295813 DOI: 10.1038/s41467-020-16677-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 05/06/2020] [Indexed: 12/18/2022] Open
Abstract
Symmetric or asymmetric positioning of intracellular structures including the nucleus and mitotic spindle steers various biological processes such as cell migration, division, and embryogenesis. In typical animal cells, both a sparse actomyosin meshwork in the cytoplasm and a dense actomyosin cortex underneath the cell membrane participate in the intracellular positioning. However, it remains unclear how these coexisting actomyosin structures regulate the positioning symmetry. To reveal the potential mechanism, we construct an in vitro model composed of cytoplasmic extracts and nucleus-like clusters confined in droplets. Here we find that periodic centripetal actomyosin waves contract from the droplet boundary push clusters to the center in large droplets, while network percolation of bulk actomyosin pulls clusters to the edge in small droplets. An active gel model quantitatively reproduces molecular perturbation experiments, which reveals that the tug-of-war between two distinct actomyosin networks with different maturation time-scales determines the positioning symmetry.
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69
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Geisterfer ZM, Zhu DY, Mitchison TJ, Oakey J, Gatlin JC. Microtubule Growth Rates Are Sensitive to Global and Local Changes in Microtubule Plus-End Density. Curr Biol 2020; 30:3016-3023.e3. [PMID: 32531285 DOI: 10.1016/j.cub.2020.05.056] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/14/2020] [Accepted: 05/18/2020] [Indexed: 01/02/2023]
Abstract
The microtubule cytoskeleton plays critically important roles in numerous cellular functions in eukaryotes, and it does so across a functionally diverse and morphologically disparate range of cell types [1]. In these roles, microtubule assemblies must adopt distinct morphologies and physical dimensions to perform specific functions [2-5]. As such, these macromolecular assemblies-as well as the dynamics of the individual microtubule polymers from which they are made-must scale and change in accordance with cell size, geometry, and function. Microtubules in cells typically assemble to a steady state in mass, leaving enough of their tubulin subunits soluble to allow rapid growth and turnover. This suggests some negative feedback that limits the extent of assembly, for example, decrease in growth rate, or increase in catastrophe rate, as the soluble subunit pool decreases. Although these ideas have informed the field for decades, they have not been observed experimentally. Here, we describe the application of an experimental approach that combines cell-free extracts with photo-patterned hydrogel micro-enclosures as a means to investigate microtubule dynamics in cytoplasmic volumes of defined size and shape. Our measurements reveal a negative correlation between microtubule plus-end density and microtubule growth rates and suggest that these rates are sensitive to the presence of nearby growing ends.
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Affiliation(s)
- Zachary M Geisterfer
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY 82070, USA.
| | - Daniel Y Zhu
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY 82070, USA
| | - Timothy J Mitchison
- Department of Systems Biology, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Marine Biological Laboratory, Cell Division and Organization Group, 7 MBL Street, Woods Hole, MA 02543, USA
| | - John Oakey
- Marine Biological Laboratory, Cell Division and Organization Group, 7 MBL Street, Woods Hole, MA 02543, USA; Department of Chemical Engineering, University of Wyoming, 1000 E. University Avenue, Laramie, WY 82070, USA
| | - Jesse C Gatlin
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY 82070, USA; Marine Biological Laboratory, Cell Division and Organization Group, 7 MBL Street, Woods Hole, MA 02543, USA.
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70
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Levy DL. Cell Biology: Tubulin Contributes to Spindle Size Scaling. Curr Biol 2020; 30:R637-R639. [PMID: 32516610 DOI: 10.1016/j.cub.2020.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sizes of intracellular structures are important for function, yet mechanisms underlying subcellular size control are largely unexplored. A new study reveals how differences in tubulin populations between two related Xenopus frog species influence microtubule dynamics and spindle length.
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Affiliation(s)
- Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA.
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71
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Abstract
The cell-free molecular synthesis of biochemical systems is a rapidly growing field of research. Advances in the Human Genome Project, DNA synthesis, and other technologies have allowed the in vitro construction of biochemical systems, termed cell-free biology, to emerge as an exciting domain of bioengineering. Cell-free biology ranges from the molecular to the cell-population scales, using an ever-expanding variety of experimental platforms and toolboxes. In this review, we discuss the ongoing efforts undertaken in the three major classes of cell-free biology methodologies, namely protein-based, nucleic acids–based, and cell-free transcription–translation systems, and provide our perspectives on the current challenges as well as the major goals in each of the subfields.
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Affiliation(s)
- Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Allen P. Liu
- Departments of Mechanical Engineering, Biomedical Engineering, Biophysics, and the Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan 48109, USA
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72
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Nolet FE, Vandervelde A, Vanderbeke A, Piñeros L, Chang JB, Gelens L. Nuclei determine the spatial origin of mitotic waves. eLife 2020; 9:e52868. [PMID: 32452767 PMCID: PMC7314552 DOI: 10.7554/elife.52868] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 05/22/2020] [Indexed: 12/11/2022] Open
Abstract
Traveling waves play an essential role in coordinating mitosis over large distances, but what determines the spatial origin of mitotic waves remains unclear. Here, we show that such waves initiate at pacemakers, regions that oscillate faster than their surroundings. In cell-free extracts of Xenopus laevis eggs, we find that nuclei define such pacemakers by concentrating cell cycle regulators. In computational models of diffusively coupled oscillators that account for nuclear import, nuclear positioning determines the pacemaker location. Furthermore, we find that the spatial dimensions of the oscillatory medium change the nuclear positioning and strongly influence whether a pacemaker is more likely to be at a boundary or an internal region. Finally, we confirm experimentally that increasing the system width increases the proportion of pacemakers at the boundary. Our work provides insight into how nuclei and spatial system dimensions can control local concentrations of regulators and influence the emergent behavior of mitotic waves.
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Affiliation(s)
- Felix E Nolet
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU LeuvenLeuvenBelgium
| | - Alexandra Vandervelde
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU LeuvenLeuvenBelgium
| | - Arno Vanderbeke
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU LeuvenLeuvenBelgium
- MeBioS - Biosensors Group, Department of Biosystems, KU LeuvenLeuvenBelgium
| | - Liliana Piñeros
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU LeuvenLeuvenBelgium
| | - Jeremy B Chang
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoUnited States
| | - Lendert Gelens
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU LeuvenLeuvenBelgium
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73
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Hirst WG, Biswas A, Mahalingan KK, Reber S. Differences in Intrinsic Tubulin Dynamic Properties Contribute to Spindle Length Control in Xenopus Species. Curr Biol 2020; 30:2184-2190.e5. [PMID: 32386526 DOI: 10.1016/j.cub.2020.03.067] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/13/2020] [Accepted: 03/26/2020] [Indexed: 01/21/2023]
Abstract
The function of cellular organelles relates not only to their molecular composition but also to their size. However, how the size of dynamic mesoscale structures is established and maintained remains poorly understood [1-3]. Mitotic spindle length, for example, varies several-fold among cell types and among different organisms [4]. Although most studies on spindle size control focus on changes in proteins that regulate microtubule dynamics [5-8], the contribution of the spindle's main building block, the αβ-tubulin heterodimer, has yet to be studied. Apart from microtubule-associated proteins and motors, two factors have been shown to contribute to the heterogeneity of microtubule dynamics: tubulin isoform composition [9, 10] and post-translational modifications [11]. In the past, studying the contribution of tubulin and microtubules to spindle assembly has been limited by the fact that physiologically relevant tubulins were not available. Here, we show that tubulins purified from two closely related frogs, Xenopus laevis and Xenopus tropicalis, have surprisingly different microtubule dynamics in vitro. X. laevis microtubules combine very fast growth and infrequent catastrophes. In contrast, X. tropicalis microtubules grow slower and catastrophe more frequently. We show that spindle length and microtubule mass can be controlled by titrating the ratios of the tubulins from the two frog species. Furthermore, we combine our in vitro reconstitution assay and egg extract experiments with computational modeling to show that differences in intrinsic properties of different tubulins contribute to the control of microtubule mass and therefore set steady-state spindle length.
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Affiliation(s)
- William G Hirst
- IRI Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia; Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Abin Biswas
- IRI Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | | | - Simone Reber
- IRI Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; Marine Biological Laboratory, Woods Hole, MA 02543, USA; University of Applied Sciences Berlin, 13353 Berlin, Germany.
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74
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So C, Seres KB, Steyer AM, Mönnich E, Clift D, Pejkovska A, Möbius W, Schuh M. A liquid-like spindle domain promotes acentrosomal spindle assembly in mammalian oocytes. Science 2020; 364:364/6447/eaat9557. [PMID: 31249032 DOI: 10.1126/science.aat9557] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/02/2019] [Indexed: 12/22/2022]
Abstract
Mammalian oocytes segregate chromosomes with a microtubule spindle that lacks centrosomes, but the mechanisms by which acentrosomal spindles are organized and function are largely unclear. In this study, we identify a conserved subcellular structure in mammalian oocytes that forms by phase separation. This structure, which we term the liquid-like meiotic spindle domain (LISD), permeates the spindle poles and forms dynamic protrusions that extend well beyond the spindle. The LISD selectively concentrates multiple microtubule regulatory factors and allows them to diffuse rapidly within the spindle volume. Disruption of the LISD via different means disperses these factors and leads to severe spindle assembly defects. Our data suggest a model whereby the LISD promotes meiotic spindle assembly by serving as a reservoir that sequesters and mobilizes microtubule regulatory factors in proximity to spindle microtubules.
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Affiliation(s)
- Chun So
- Department of Meiosis, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - K Bianka Seres
- Department of Meiosis, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.,Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.,Bourn Hall Clinic, Cambridge CB23 2TN, UK
| | - Anna M Steyer
- Electron Microscopy Core Unit, Department of Neurogenetics, Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany.,Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), 37073 Göttingen, Germany
| | - Eike Mönnich
- Department of Meiosis, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Dean Clift
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Anastasija Pejkovska
- Department of Meiosis, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Wiebke Möbius
- Electron Microscopy Core Unit, Department of Neurogenetics, Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany.,Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), 37073 Göttingen, Germany
| | - Melina Schuh
- Department of Meiosis, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany. .,Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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75
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Wesley CC, Mishra S, Levy DL. Organelle size scaling over embryonic development. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 9:e376. [PMID: 32003549 DOI: 10.1002/wdev.376] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/19/2019] [Accepted: 01/08/2020] [Indexed: 12/13/2022]
Abstract
Cell division without growth results in progressive cell size reductions during early embryonic development. How do the sizes of intracellular structures and organelles scale with cell size and what are the functional implications of such scaling relationships? Model organisms, in particular Caenorhabditis elegans worms, Drosophila melanogaster flies, Xenopus laevis frogs, and Mus musculus mice, have provided insights into developmental size scaling of the nucleus, mitotic spindle, and chromosomes. Nuclear size is regulated by nucleocytoplasmic transport, nuclear envelope proteins, and the cytoskeleton. Regulators of microtubule dynamics and chromatin compaction modulate spindle and mitotic chromosome size scaling, respectively. Developmental scaling relationships for membrane-bound organelles, like the endoplasmic reticulum, Golgi, mitochondria, and lysosomes, have been less studied, although new imaging approaches promise to rectify this deficiency. While models that invoke limiting components and dynamic regulation of assembly and disassembly can account for some size scaling relationships in early embryos, it will be exciting to investigate the contribution of newer concepts in cell biology such as phase separation and interorganellar contacts. With a growing understanding of the underlying mechanisms of organelle size scaling, future studies promise to uncover the significance of proper scaling for cell function and embryonic development, as well as how aberrant scaling contributes to disease. This article is categorized under: Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Early Embryonic Development > Fertilization to Gastrulation Comparative Development and Evolution > Model Systems.
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Affiliation(s)
- Chase C Wesley
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
| | - Sampada Mishra
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
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76
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Bisht J, LeValley P, Noren B, McBride R, Kharkar P, Kloxin A, Gatlin J, Oakey J. Light-inducible activation of cell cycle progression in Xenopus egg extracts under microfluidic confinement. LAB ON A CHIP 2019; 19:3499-3511. [PMID: 31544194 PMCID: PMC7819639 DOI: 10.1039/c9lc00569b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cell-free Xenopus egg extract is a widely used and biochemically tractable model system that allows recapitulation and elucidation of fundamental cellular processes. Recently, the introduction of microfluidic extract manipulation has enabled compartmentalization of bulk extract and a newfound ability to study organelles on length scales that recapitulate key features of cellular morphology. While the microfluidic confinement of extracts has produced a compelling platform for the in vitro study of cell processes at physiologically-relevant length scales, it also imposes experimental limitations by restricting dynamic control over extract properties. Here, we introduce photodegradable polyethylene glycol (PEG) hydrogels as a vehicle to passively and selectively manipulate extract composition through the release of proteins encapsulated within the hydrogel matrix. Photopatterned PEG hydrogels, passive to both extract and encapsulated proteins, serve as protein depots within microfluidic channels, which are subsequently flooded with extract. Illumination by ultraviolet light (UV) degrades the hydrogel structures and releases encapsulated protein. We show that an engineered fluorescent protein with a nuclear localization signal (GST-GFP-NLS) retains its ability to localize within nearby nuclei following UV-induced release from hydrogel structures. When diffusion is considered, the kinetics of nuclear accumulation are similar to those in experiments utilizing conventional, bulk fluid handling. Similarly, the release of recombinant cyclin B Δ90, a mutant form of the master cell cycle regulator cyclin B which lacks the canonical destruction box, was able to induce the expected cell cycle transition from interphase to mitosis. This transition was confirmed by the observation of nuclear envelope breakdown (NEBD), a phenomenological hallmark of mitosis, and the induction of mitosis-specific biochemical markers. This approach to extract manipulation presents a versatile and customizable route to regulating the spatial and temporal dynamics of cellular events in microfluidically confined cell-free extracts.
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Affiliation(s)
- Jitender Bisht
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
- Cell Organization and Division Group, Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543
| | - Paige LeValley
- Department of Chemical Engineering, University of Wyoming, Laramie, WY 82071
- Cell Organization and Division Group, Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716
| | - Benjamin Noren
- Department of Chemical Engineering, University of Wyoming, Laramie, WY 82071
- Cell Organization and Division Group, Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543
| | - Ralph McBride
- Department of Chemical Engineering, University of Wyoming, Laramie, WY 82071
| | - Prathamesh Kharkar
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716
| | - April Kloxin
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716
| | - Jesse Gatlin
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
- Cell Organization and Division Group, Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543
| | - John Oakey
- Department of Chemical Engineering, University of Wyoming, Laramie, WY 82071
- Cell Organization and Division Group, Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543
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77
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Sun M, Li Z, Wang S, Maryu G, Yang Q. Building Dynamic Cellular Machineries in Droplet-Based Artificial Cells with Single-Droplet Tracking and Analysis. Anal Chem 2019; 91:9813-9818. [PMID: 31284720 PMCID: PMC7260773 DOI: 10.1021/acs.analchem.9b01481] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although the application of droplet microfluidics has grown exponentially in chemistry and biology over the past decades, robust universal platforms for the routine generation and comprehensive analysis of droplet-based artificial cells are still rare. Here we report using microfluidic droplets to reproduce a variety of types of cellular machinery in in vitro artificial cells. In combination with a unique image-based analysis method, the system enables full automation in tracking single droplets with high accuracy, high throughput, and high sensitivity. These powerful performances allow broad applicability evident in three representative droplet-based analytical prototypes that we develop for (i) droplet digital detection, (ii) in vitro transcription and translation reactions, and (iii) spatiotemporal dynamics of cell-cycle oscillations. The capacities of this platform to generate, incubate, track, and analyze individual microdroplets via real-time, long-term imaging unleash its great potential in accelerating cell-free synthetic biology. Moreover, the wide scope covering from digital to analog to morphological detections makes this droplet analysis technique adaptable for many other divergent types of droplet-based chemical and biological assays.
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Affiliation(s)
- Meng Sun
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Zhengda Li
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Shiyuan Wang
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Gembu Maryu
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Qiong Yang
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
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78
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Rieckhoff EM, Ishihara K, Brugués J. How to tune spindle size relative to cell size? Curr Opin Cell Biol 2019; 60:139-144. [PMID: 31377657 DOI: 10.1016/j.ceb.2019.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/17/2019] [Accepted: 06/17/2019] [Indexed: 12/20/2022]
Abstract
Cells need to regulate the size and shape of their organelles for proper function. For example, the mitotic spindle adapts its size to changes in cell size over several orders of magnitude, but we lack a mechanistic understanding of how this is achieved. Here, we review our current knowledge of how small and large spindles assemble and ask which microtubule-based biophysical processes (nucleation, polymerization dynamics, transport) may be responsible for spindle size regulation. Finally, we review possible cell-scale mechanisms that put spindle size under the regulation of cell size.
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Affiliation(s)
- Elisa Maria Rieckhoff
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; Max Planck Institute for the Physics of Complex Systems, Dresden, Germany; Center for Systems Biology Dresden, Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| | - Keisuke Ishihara
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; Max Planck Institute for the Physics of Complex Systems, Dresden, Germany; Center for Systems Biology Dresden, Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| | - Jan Brugués
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; Max Planck Institute for the Physics of Complex Systems, Dresden, Germany; Center for Systems Biology Dresden, Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany.
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79
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Sonnen KF, Merten CA. Microfluidics as an Emerging Precision Tool in Developmental Biology. Dev Cell 2019; 48:293-311. [PMID: 30753835 DOI: 10.1016/j.devcel.2019.01.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/13/2018] [Accepted: 01/10/2019] [Indexed: 12/18/2022]
Abstract
Microfluidics has become a precision tool in modern biology. It enables omics data to be obtained from individual cells, as compared to averaged signals from cell populations, and it allows manipulation of biological specimens in entirely new ways. Cells and organisms can be perturbed at extraordinary spatiotemporal resolution, revealing mechanistic insights that would otherwise remain hidden. In this perspective article, we discuss the current and future impact of microfluidic technology in the field of developmental biology. In addition, we provide detailed information on how to start using this technology even without prior experience.
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Affiliation(s)
| | - Christoph A Merten
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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80
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Ross TD, Lee HJ, Qu Z, Banks RA, Phillips R, Thomson M. Controlling organization and forces in active matter through optically defined boundaries. Nature 2019; 572:224-229. [PMID: 31391558 PMCID: PMC6719720 DOI: 10.1038/s41586-019-1447-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/05/2019] [Indexed: 12/22/2022]
Abstract
Living systems are capable of locomotion, reconfiguration and replication. To perform these tasks, cells spatiotemporally coordinate the interactions of force-generating, 'active' molecules that create and manipulate non-equilibrium structures and force fields of up to millimetre length scales1-3. Experimental active-matter systems of biological or synthetic molecules are capable of spontaneously organizing into structures4,5 and generating global flows6-9. However, these experimental systems lack the spatiotemporal control found in cells, limiting their utility for studying non-equilibrium phenomena and bioinspired engineering. Here we uncover non-equilibrium phenomena and principles of boundary-mediated control by optically modulating structures and fluid flow in an engineered system of active biomolecules. Our system consists of purified microtubules and light-activatable motor proteins that crosslink and organize the microtubules into distinct structures upon illumination. We develop basic operations-defined as sets of light patterns-to create, move and merge the microtubule structures. By combining these operations, we create microtubule networks that span several hundred micrometres in length and contract at speeds up to an order of magnitude higher than the speed of an individual motor protein. We manipulate these contractile networks to generate and sculpt persistent fluid flows. The principles of boundary-mediated control that we uncover may be used to study emergent cellular structures and forces and to develop programmable active-matter devices.
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Affiliation(s)
- Tyler D Ross
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Heun Jin Lee
- Department of Applied Physics, California Institute of Technology, Pasadena, CA, USA
| | - Zijie Qu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rachel A Banks
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rob Phillips
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Applied Physics, California Institute of Technology, Pasadena, CA, USA
- Department of Physics, California Institute of Technology, Pasadena, CA, USA
| | - Matt Thomson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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81
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Kohyama S, Yoshinaga N, Yanagisawa M, Fujiwara K, Doi N. Cell-sized confinement controls generation and stability of a protein wave for spatiotemporal regulation in cells. eLife 2019; 8:e44591. [PMID: 31358115 PMCID: PMC6667215 DOI: 10.7554/elife.44591] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 07/12/2019] [Indexed: 01/10/2023] Open
Abstract
The Min system, a system that determines the bacterial cell division plane, uses changes in the localization of proteins (a Min wave) that emerges by reaction-diffusion coupling. Although previous studies have shown that space sizes and boundaries modulate the shape and speed of Min waves, their effects on wave emergence were still elusive. Here, by using a microsized fully confined space to mimic live cells, we revealed that confinement changes the conditions for the emergence of Min waves. In the microsized space, an increased surface-to-volume ratio changed the localization efficiency of proteins on membranes, and therefore, suppression of the localization change was necessary for the stable generation of Min waves. Furthermore, we showed that the cell-sized space strictly limits parameters for wave emergence because confinement inhibits both the instability and excitability of the system. These results show that confinement of reaction-diffusion systems has the potential to control spatiotemporal patterns in live cells.
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Affiliation(s)
- Shunshi Kohyama
- Department of Biosciences and InformaticsKeio UniversityYokohamaJapan
| | - Natsuhiko Yoshinaga
- Mathematical Science Group, WPI Advanced Institute for Materials Research (WPI-AIMR)Tohoku University KatahiraSendaiJapan
- MathAM-OILAISTSendaiJapan
| | - Miho Yanagisawa
- Department of Basic Science, Komaba Institute for Science, Graduate School of Arts and SciencesThe University of TokyoTokyoJapan
| | - Kei Fujiwara
- Department of Biosciences and InformaticsKeio UniversityYokohamaJapan
| | - Nobuhide Doi
- Department of Biosciences and InformaticsKeio UniversityYokohamaJapan
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82
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Garcia-Jove Navarro M, Kashida S, Chouaib R, Souquere S, Pierron G, Weil D, Gueroui Z. RNA is a critical element for the sizing and the composition of phase-separated RNA-protein condensates. Nat Commun 2019; 10:3230. [PMID: 31324804 PMCID: PMC6642089 DOI: 10.1038/s41467-019-11241-6] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 06/27/2019] [Indexed: 01/01/2023] Open
Abstract
Liquid-liquid phase separation is thought to be a key organizing principle in eukaryotic cells to generate highly concentrated dynamic assemblies, such as the RNP granules. Numerous in vitro approaches have validated this model, yet a missing aspect is to take into consideration the complex molecular mixture and promiscuous interactions found in vivo. Here we report the versatile scaffold ArtiG to generate concentration-dependent RNA-protein condensates within living cells, as a bottom-up approach to study the impact of co-segregated endogenous components on phase separation. We demonstrate that intracellular RNA seeds the nucleation of the condensates, as it provides molecular cues to locally coordinate the formation of endogenous high-order RNP assemblies. Interestingly, the co-segregation of intracellular components ultimately impacts the size of the phase-separated condensates. Thus, RNA arises as an architectural element that can influence the composition and the morphological outcome of the condensate phases in an intracellular context.
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Affiliation(s)
- Marina Garcia-Jove Navarro
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Shunnichi Kashida
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Racha Chouaib
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire de Biologie du Développement, F-75005, Paris, France.,School of Arts and Sciences, Lebanese International University (LIU), Beirut, Lebanon.,Faculty of Sciences, Lebanese University, Beirut, Lebanon
| | - Sylvie Souquere
- CNRS UMR-9196, Institut Gustave Roussy, F-94800, Villejuif, France
| | - Gérard Pierron
- CNRS UMR-9196, Institut Gustave Roussy, F-94800, Villejuif, France
| | - Dominique Weil
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire de Biologie du Développement, F-75005, Paris, France
| | - Zoher Gueroui
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
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83
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Kakebeen A, Wills A. Advancing genetic and genomic technologies deepen the pool for discovery in Xenopus tropicalis. Dev Dyn 2019; 248:620-625. [PMID: 31254427 DOI: 10.1002/dvdy.80] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 12/14/2022] Open
Abstract
Xenopus laevis and Xenopus tropicalis have long been used to drive discovery in developmental, cell, and molecular biology. These dual frog species boast experimental strengths for embryology including large egg sizes that develop externally, well-defined fate maps, and cell-intrinsic sources of nutrients that allow explanted tissues to grow in culture. Development of the Xenopus cell extract system has been used to study cell cycle and DNA replication. Xenopus tadpole tail and limb regeneration have provided fundamental insights into the underlying mechanisms of this processes, and the loss of regenerative competency in adults adds a complexity to the system that can be more directly compared to humans. Moreover, Xenopus genetics and especially disease-causing mutations are highly conserved with humans, making them a tractable system to model human disease. In the last several years, genome editing, expanding genomic resources, and intersectional approaches leveraging the distinct characteristics of each species have generated new frontiers in cell biology. While Xenopus have enduringly represented a leading embryological model, new technologies are generating exciting diversity in the range of discoveries being made in areas from genomics and proteomics to regenerative biology, neurobiology, cell scaling, and human disease modeling.
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Affiliation(s)
- Anneke Kakebeen
- Department of Biochemistry, University of Washington, Seattle, Washington
| | - Andrea Wills
- Department of Biochemistry, University of Washington, Seattle, Washington
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84
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Mohapatra L, Lagny TJ, Harbage D, Jelenkovic PR, Kondev J. The Limiting-Pool Mechanism Fails to Control the Size of Multiple Organelles. Cell Syst 2019; 4:559-567.e14. [PMID: 28544883 DOI: 10.1016/j.cels.2017.04.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/31/2017] [Accepted: 04/26/2017] [Indexed: 10/24/2022]
Abstract
How the size of micrometer-scale cellular structures such as the mitotic spindle, cytoskeletal filaments, the nucleus, the nucleolus, and other non-membrane bound organelles is controlled despite a constant turnover of their constituent parts is a central problem in biology. Experiments have implicated the limiting-pool mechanism: structures grow by stochastic addition of molecular subunits from a finite pool until the rates of subunit addition and removal are balanced, producing a structure of well-defined size. Here, we consider these dynamics when multiple filamentous structures are assembled stochastically from a shared pool of subunits. Using analytical calculations and computer simulations, we show that robust size control can be achieved only when a single filament is assembled. When multiple filaments compete for monomers, filament lengths exhibit large fluctuations. These results extend to three-dimensional structures and reveal the physical limitations of the limiting-pool mechanism of size control when multiple organelles are assembled from a shared pool of subunits.
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Affiliation(s)
| | - Thibaut J Lagny
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, 75005 Paris, France; Institut Curie, PSL Research University, CNRS, UMR 144, 75005 Paris, France
| | - David Harbage
- Department of Physics, Brandeis University, Waltham, MA 02454, USA
| | - Predrag R Jelenkovic
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Jane Kondev
- Department of Physics, Brandeis University, Waltham, MA 02454, USA
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85
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Chen Y, Nam S, Chaudhuri O, Huang HC. The evolution of spindles and their mechanical implications for cancer metastasis. Cell Cycle 2019; 18:1671-1675. [PMID: 31234701 DOI: 10.1080/15384101.2019.1632137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The mitotic spindle has long been known to play a crucial role in mitosis, orchestrating the segregation of chromosomes into two daughter cells during mitosis with high fidelity. Intracellular forces generated by the mitotic spindle are increasingly well understood, and recent work has revealed that the efficiency and the accuracy of mitosis is ensured by the scaling of mitotic spindle size with cell size. However, the role of the spindle in cancer progression has largely been ignored. Two recent studies point toward the role of mitotic spindle evolution in cancer progression through extracellular force generation. Cancer cells with lengthened spindles exhibit highly increased metastatic potential. Further, interpolar spindle elongation drives protrusive extracellular force generation along the mitotic axis to allow mitotic elongation, a morphological change that is required for cell division. Together, these findings open a new research area studying the role of the mitotic spindle evolution in cancer metastasis.
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Affiliation(s)
- Yun Chen
- a Institute of Molecular and Cellular Biology , National Taiwan University , Taipei , Taiwan
| | - Sungmin Nam
- b Department of Mechanical Engineering , Stanford University , Stanford , CA , USA
| | - Ovijit Chaudhuri
- b Department of Mechanical Engineering , Stanford University , Stanford , CA , USA
| | - Hsiao-Chun Huang
- a Institute of Molecular and Cellular Biology , National Taiwan University , Taipei , Taiwan
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86
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Gibeaux R, Heald R. The Use of Cell-Free Xenopus Extracts to Investigate Cytoplasmic Events. Cold Spring Harb Protoc 2019; 2019:pdb.top097048. [PMID: 29980587 DOI: 10.1101/pdb.top097048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Experiments using cytoplasmic extracts prepared from Xenopus eggs have made important contributions to our understanding of the cell cycle, the cytoskeleton, and cytoplasmic membrane systems. Here we introduce the extract system and describe methods for visualizing and manipulating diverse cytoplasmic processes, and for assaying the functions, dynamics, and stability of individual factors. These in vitro approaches uniquely enable investigation of events at specific cell cycle states, including the assembly of actin- and microtubule-based structures, and the formation of the endoplasmic reticulum. Maternal stockpiles in extracts recapitulate diverse processes in the near absence of gene expression, and this biochemical system combined with microscopy empowers a wide range of mechanistic investigations.
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Affiliation(s)
- Romain Gibeaux
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-3200
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-3200
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87
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Fanalista F, Birnie A, Maan R, Burla F, Charles K, Pawlik G, Deshpande S, Koenderink GH, Dogterom M, Dekker C. Shape and Size Control of Artificial Cells for Bottom-Up Biology. ACS NANO 2019; 13:5439-5450. [PMID: 31074603 PMCID: PMC6543616 DOI: 10.1021/acsnano.9b00220] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/10/2019] [Indexed: 05/27/2023]
Abstract
Bottom-up biology is an expanding research field that aims to understand the mechanisms underlying biological processes via in vitro assembly of their essential components in synthetic cells. As encapsulation and controlled manipulation of these elements is a crucial step in the recreation of such cell-like objects, microfluidics is increasingly used for the production of minimal artificial containers such as single-emulsion droplets, double-emulsion droplets, and liposomes. Despite the importance of cell morphology on cellular dynamics, current synthetic-cell studies mainly use spherical containers, and methods to actively shape manipulate these have been lacking. In this paper, we describe a microfluidic platform to deform the shape of artificial cells into a variety of shapes (rods and discs) with adjustable cell-like dimensions below 5 μm, thereby mimicking realistic cell morphologies. To illustrate the potential of our method, we reconstitute three biologically relevant protein systems (FtsZ, microtubules, collagen) inside rod-shaped containers and study the arrangement of the protein networks inside these synthetic containers with physiologically relevant morphologies resembling those found in living cells.
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Affiliation(s)
- Federico Fanalista
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Anthony Birnie
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Renu Maan
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Federica Burla
- Department
of Living Matter, Biological Soft Matter Group, AMOLF, Science Park
104, 1098 XG Amsterdam, The Netherlands
| | - Kevin Charles
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Grzegorz Pawlik
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Siddharth Deshpande
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Gijsje H. Koenderink
- Department
of Living Matter, Biological Soft Matter Group, AMOLF, Science Park
104, 1098 XG Amsterdam, The Netherlands
| | - Marileen Dogterom
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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88
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Abstract
The assembly of the mitotic spindle and the subsequent segregation of sister chromatids are based on the self-organized action of microtubule filaments, motor proteins, and other microtubule-associated proteins, which constitute the fundamental force-generating elements in the system. Many of the components in the spindle have been identified, but until recently it remained unclear how their collective behaviors resulted in such a robust bipolar structure. Here, we review the current understanding of the physics of the metaphase spindle that is only now starting to emerge.
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Affiliation(s)
- David Oriola
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany; .,Max Planck Institute for the Physics of Complex Systems, 01187, Dresden, Germany.,Center for Systems Biology Dresden, 01307, Dresden, Germany
| | - Daniel J Needleman
- School of Engineering and Applied Sciences, Department of Molecular and Cellular Biology, and FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 021382, USA
| | - Jan Brugués
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany; .,Max Planck Institute for the Physics of Complex Systems, 01187, Dresden, Germany.,Center for Systems Biology Dresden, 01307, Dresden, Germany
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89
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Glantz ST, Berlew EE, Chow BY. Synthetic cell-like membrane interfaces for probing dynamic protein-lipid interactions. Methods Enzymol 2019; 622:249-270. [PMID: 31155055 DOI: 10.1016/bs.mie.2019.02.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The ability to rapidly screen interactions between proteins and membrane-like interfaces would aid in establishing the structure-function of protein-lipid interactions, provide a platform for engineering lipid-interacting protein tools, and potentially inform the signaling mechanisms and dynamics of membrane-associated proteins. Here, we describe the preparation and application of water-in-oil (w/o) emulsions with lipid-stabilized droplet interfaces that emulate the plasma membrane inner leaflet with tunable composition. Fluorescently labeled proteins are easily visualized in these synthetic cell-like droplets on an automated inverted fluorescence microscope, thus allowing for both rapid screening of relative binding and spatiotemporally resolved analyses of for example, protein-interface association and dissociation dynamics and competitive interactions, using commonplace instrumentation. We provide protocols for droplet formation, automated imaging assays and analysis, and the production of the positive control protein BcLOV4, a natural photoreceptor with a directly light-regulated interaction with anionic membrane phospholipids that is useful for optogenetic membrane recruitment.
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Affiliation(s)
- Spencer T Glantz
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Erin E Berlew
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Brian Y Chow
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States.
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90
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Krüger LK, Sanchez JL, Paoletti A, Tran PT. Kinesin-6 regulates cell-size-dependent spindle elongation velocity to keep mitosis duration constant in fission yeast. eLife 2019; 8:42182. [PMID: 30806623 PMCID: PMC6391065 DOI: 10.7554/elife.42182] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 02/13/2019] [Indexed: 01/01/2023] Open
Abstract
The length of the mitotic spindle scales with cell size in a wide range of organisms during embryonic development. Interestingly, in C. elegans embryos, this goes along with temporal regulation: larger cells speed up spindle assembly and elongation. We demonstrate that, similarly in fission yeast, spindle length and spindle dynamics adjust to cell size, which allows to keep mitosis duration constant. Since prolongation of mitosis was shown to affect cell viability, this may resemble a mechanism to regulate mitosis duration. We further reveal how the velocity of spindle elongation is regulated: coupled to cell size, the amount of kinesin-6 Klp9 molecules increases, resulting in an acceleration of spindle elongation in anaphase B. In addition, the number of Klp9 binding sites to microtubules increases overproportionally to Klp9 molecules, suggesting that molecular crowding inversely correlates to cell size and might have an impact on spindle elongation velocity control.
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Affiliation(s)
| | | | - Anne Paoletti
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France
| | - Phong Thanh Tran
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, United States
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91
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Xie K, Yang Y, Jiang H. Controlling Cellular Volume via Mechanical and Physical Properties of Substrate. Biophys J 2019; 114:675-687. [PMID: 29414713 DOI: 10.1016/j.bpj.2017.11.3785] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 01/10/2023] Open
Abstract
The mechanical and physical properties of substrate play a crucial role in regulating many cell functions and behaviors. However, how these properties affect cell volume is still unclear. Here, we show that an increase in substrate stiffness, available spread area, or effective adhesion energy density results in a remarkable cell volume decrease (up to 50%), and the dynamic cell spreading process is also accompanied by dramatic cell volume decrease. Further, studies of ion channel inhibition and osmotic shock suggest that these volume decreases are due to the efflux of water and ions. We also show that disrupting cortex contractility leads to bigger cell volume. Collectively, these results reveal the "mechanism of adhesion-induced compression of cells," i.e., stronger interaction between cell and substrate leads to higher actomyosin contractility, expels water and ions, and thus decreases cell volume.
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Affiliation(s)
- Kenan Xie
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, Anhui, China
| | - Yuehua Yang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, Anhui, China
| | - Hongyuan Jiang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, Anhui, China.
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92
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Bao M, Xie J, Katoele N, Hu X, Wang B, Piruska A, Huck WT. Cellular Volume and Matrix Stiffness Direct Stem Cell Behavior in a 3D Microniche. ACS APPLIED MATERIALS & INTERFACES 2019; 11:1754-1759. [PMID: 30584755 PMCID: PMC6343943 DOI: 10.1021/acsami.8b19396] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 12/25/2018] [Indexed: 05/18/2023]
Abstract
The central question addressed in this study is whether cells with different sizes have different responses to matrix stiffness. We used methacrylated hyaluronic acid (MeHA) hydrogels as the matrix to prepare an in vitro 3D microniche in which the single stem cell volume and matrix stiffness can be altered independently from each other. This simple approach enabled us to decouple the effects of matrix stiffness and cell volume in 3D microenvironments. Human mesenchymal stem cells (hMSCs) were cultured in individual 3D microniches with different volumes (2800, 3600, and 6000 μm3) and stiffnesses (5, 12, and 23 kPa). We demonstrated that cell volume affected the cellular response to matrix stiffness. When cells had an optimal volume, cells could form clear stress fibers and focal adhesions on soft, intermediate, or stiff matrix. In small cells, stress fiber formation and YAP/TAZ localization were not affected by stiffness. This study highlights the importance of considering cellular volume and substrate stiffness as important cues governing cell-matrix interactions.
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93
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Brownlee C, Heald R. Importin α Partitioning to the Plasma Membrane Regulates Intracellular Scaling. Cell 2019; 176:805-815.e8. [PMID: 30639102 DOI: 10.1016/j.cell.2018.12.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 09/25/2018] [Accepted: 11/30/2018] [Indexed: 01/05/2023]
Abstract
Early embryogenesis is accompanied by reductive cell divisions requiring that subcellular structures adapt to a range of cell sizes. The interphase nucleus and mitotic spindle scale with cell size through both physical and biochemical mechanisms, but control systems that coordinately scale intracellular structures are unknown. We show that the nuclear transport receptor importin α is modified by palmitoylation, which targets it to the plasma membrane and modulates its binding to nuclear localization signal (NLS)-containing proteins that regulate nuclear and spindle size in Xenopus egg extracts. Reconstitution of importin α targeting to the outer boundary of extract droplets mimicking cell-like compartments recapitulated scaling relationships observed during embryogenesis, which were altered by inhibitors that shift levels of importin α palmitoylation. Modulation of importin α palmitoylation in human cells similarly affected nuclear and spindle size. These experiments identify importin α as a conserved surface area-to-volume sensor that scales intracellular structures to cell size.
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Affiliation(s)
- Christopher Brownlee
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
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94
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Gibeaux R, Miller K, Acker R, Kwon T, Heald R. Xenopus Hybrids Provide Insight Into Cell and Organism Size Control. Front Physiol 2018; 9:1758. [PMID: 30564147 PMCID: PMC6288844 DOI: 10.3389/fphys.2018.01758] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 11/20/2018] [Indexed: 01/08/2023] Open
Abstract
Determining how size is controlled is a fundamental question in biology that is poorly understood at the organismal, cellular, and subcellular levels. The Xenopus species, X. laevis and X. tropicalis differ in size at all three of these levels. Despite these differences, fertilization of X. laevis eggs with X. tropicalis sperm gives rise to viable hybrid animals that are intermediate in size. We observed that although hybrid and X. laevis embryogenesis initiates from the same sized zygote and proceeds synchronously through development, hybrid animals were smaller by the tailbud stage, and a change in the ratio of nuclear size to cell size was observed shortly after zygotic genome activation (ZGA), suggesting that differential gene expression contributes to size differences. Transcriptome analysis at the onset of ZGA identified twelve transcription factors paternally expressed in hybrids. A screen of these X. tropicalis factors by expression in X. laevis embryos revealed that Hes7 and Ventx2 significantly reduced X. laevis body length size by the tailbud stage, although nuclear to cell size scaling relationships were not affected as in the hybrid. Together, these results suggest that transcriptional regulation contributes to biological size control in Xenopus.
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Affiliation(s)
- Romain Gibeaux
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Kelly Miller
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Rachael Acker
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
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95
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Guo X, Ni J, Liang Z, Xue J, Fenech MF, Wang X. The molecular origins and pathophysiological consequences of micronuclei: New insights into an age-old problem. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 779:1-35. [PMID: 31097147 DOI: 10.1016/j.mrrev.2018.11.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 02/07/2023]
Abstract
Micronuclei (MN), the small nucleus-like bodies separated from the primary nucleus, can exist in cells with numerical and/or structural chromosomal aberrations in apparently normal tissues and more so in tumors in humans. While MN have been observed for over 100 years, they were merely and constantly considered as passive indicators of chromosome instability (CIN) for a long time. Relatively little is known about the molecular origins and biological consequences of MN. Rapid technological advances are helping to close these gaps. Very recent studies provide exciting evidence that MN act as key platform for chromothripsis and a trigger of innate immune response, suggesting that MN could affect cellular functions by both genetic and nongenetic means. These previously unappreciated findings have reawakened widespread interests in MN. In this review, the diverse mechanisms leading to MN generation and the complex fate profiles of MN are discussed, together with the evidence for their contribution to CIN, inflammation, senescence and cell death. Moreover, we put this knowledge together into a speculative perspective on how MN may be responsible for cancer development and how their presence may influence the choice of treatment. We suggest that the heterogeneous responses to MN may function physiological to ensure the arrestment, elimination and immune clearance of damaged cells, but pathologically, may enable the survival and oncogenic transformation of cells bearing CIN. These insights not only underscore the complexity of MN biology, but also raise a host of new questions and provide fertile ground for future research.
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Affiliation(s)
- Xihan Guo
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, Yunnan, 650500, China
| | - Juan Ni
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, Yunnan, 650500, China
| | - Ziqing Liang
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, Yunnan, 650500, China
| | - Jinglun Xue
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Michael F Fenech
- University of South Australia, Adelaide, SA, 5000, Australia; Genome Health Foundation, North Brighton, SA, 5048, Australia.
| | - Xu Wang
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, Yunnan, 650500, China.
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96
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Gasic I, Mitchison TJ. Autoregulation and repair in microtubule homeostasis. Curr Opin Cell Biol 2018; 56:80-87. [PMID: 30415186 DOI: 10.1016/j.ceb.2018.10.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/24/2018] [Accepted: 10/21/2018] [Indexed: 10/27/2022]
Abstract
Even in the face of damaging insults, most cells maintain stability over time through multiple homeostatic pathways, including maintenance of the microtubule cytoskeleton that is fundamental to numerous cellular processes. The dynamic instability-perpetual growth and shrinkage-is the best-known microtubule regulatory pathway, which allows rapid rebuilding of the microtubule cytoskeleton in response to internal or external cues. Much less investigated is homeostatic regulation through availability of α-β tubulin heterodimers-microtubules' main building blocks-which influences total mass and dynamic behavior of microtubules. Finally, the most recently discovered is microtubule homeostasis through self-repair, where new GTP-bound tubulin heterodimers replace the lost ones in the microtubule lattice. In this review we try to integrate our current knowledge on how dynamic instability, regulation of tubulin mass, and self-repair work together to achieve microtubule homeostasis.
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Affiliation(s)
- Ivana Gasic
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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97
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98
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Elting MW, Suresh P, Dumont S. The Spindle: Integrating Architecture and Mechanics across Scales. Trends Cell Biol 2018; 28:896-910. [PMID: 30093097 PMCID: PMC6197898 DOI: 10.1016/j.tcb.2018.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/02/2018] [Accepted: 07/09/2018] [Indexed: 01/28/2023]
Abstract
The spindle segregates chromosomes at cell division, and its task is a mechanical one. While we have a nearly complete list of spindle components, how their molecular-scale mechanics give rise to cellular-scale spindle architecture, mechanics, and function is not yet clear. Recent in vitro and in vivo measurements bring new levels of molecular and physical control and shed light on this question. Highlighting recent findings and open questions, we introduce the molecular force generators of the spindle, and discuss how they organize microtubules into diverse architectural modules and give rise to the emergent mechanics of the mammalian spindle. Throughout, we emphasize the breadth of space and time scales at play, and the feedback between spindle architecture, dynamics, and mechanics that drives robust function.
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Affiliation(s)
- Mary Williard Elting
- Department of Cell & Tissue Biology, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA; Department of Physics, Riddick Hall 258A, Box 8202, North Carolina State University, Raleigh, NC 27695, USA; These authors contributed equally
| | - Pooja Suresh
- Department of Cell & Tissue Biology, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA; Biophysics Graduate Program, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA; These authors contributed equally
| | - Sophie Dumont
- Department of Cell & Tissue Biology, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA; Biophysics Graduate Program, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA; Department of Cellular & Molecular Pharmacology, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA.
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99
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Guan Y, Wang S, Jin M, Xu H, Yang Q. Reconstitution of Cell-cycle Oscillations in Microemulsions of Cell-free Xenopus Egg Extracts. J Vis Exp 2018:58240. [PMID: 30320763 PMCID: PMC6235322 DOI: 10.3791/58240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Real-time measurement of oscillations at the single-cell level is important to uncover the mechanisms of biological clocks. Although bulk extracts prepared from Xenopus laevis eggs have been powerful in dissecting biochemical networks underlying the cell-cycle progression, their ensemble average measurement typically leads to a damped oscillation, despite each individual oscillator being sustained. This is due to the difficulty of perfect synchronization among individual oscillators in noisy biological systems. To retrieve the single-cell dynamics of the oscillator, we developed a droplet-based artificial cell system that can reconstitute mitotic cycles in cell-like compartments encapsulating cycling cytoplasmic extracts of Xenopus laevis eggs. These simple cytoplasmic-only cells exhibit sustained oscillations for over 30 cycles. To build more complicated cells with nuclei, we added demembranated sperm chromatin to trigger nuclei self-assembly in the system. We observed a periodic progression of chromosome condensation/decondensation and nuclei envelop breakdown/reformation, like in real cells. This indicates that the mitotic oscillator functions faithfully to drive multiple downstream mitotic events. We simultaneously tracked the dynamics of the mitotic oscillator and downstream processes in individual droplets using multi-channel time-lapse fluorescence microscopy. The artificial cell-cycle system provides a high-throughput framework for quantitative manipulation and analysis of mitotic oscillations with single-cell resolution, which likely provides important insights into the regulatory machinery and functions of the clock.
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Affiliation(s)
- Ye Guan
- Department of Biophysics, University of Michigan, Ann Arbor; Department of Chemistry, University of Michigan, Ann Arbor
| | - Shiyuan Wang
- Department of Biophysics, University of Michigan, Ann Arbor
| | - Minjun Jin
- Department of Chemistry, University of Michigan, Ann Arbor
| | - Haotian Xu
- Department of Computer Science, Wayne State University
| | - Qiong Yang
- Department of Biophysics, University of Michigan, Ann Arbor; Department of Physics, University of Michigan, Ann Arbor;
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Arbach HE, Harland-Dunaway M, Chang JK, Wills AE. Extreme nuclear branching in healthy epidermal cells of the Xenopus tail fin. J Cell Sci 2018; 131:jcs.217513. [PMID: 30131443 DOI: 10.1242/jcs.217513] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/10/2018] [Indexed: 01/09/2023] Open
Abstract
Changes in nuclear morphology contribute to the regulation of complex cell properties, including differentiation and tissue elasticity. Perturbations of nuclear morphology are associated with pathologies that include progeria, cancer and muscular dystrophy. The mechanisms governing nuclear shape changes in healthy cells remain poorly understood, partially because there are few models of nuclear shape variation in healthy cells. Here, we introduce nuclear branching in epidermal fin cells of Xenopus tropicalis as a model for extreme variation of nuclear morphology in a diverse population of healthy cells. We found that nuclear branching arises within these cells and becomes more elaborate during embryonic development. These cells contain broadly distributed marks of transcriptionally active chromatin and heterochromatin, and have active cell cycles. We found that nuclear branches are disrupted by loss of filamentous actin and depend on epidermal expression of the nuclear lamina protein Lamin B1. Inhibition of nuclear branching disrupts fin morphology, suggesting that nuclear branching may be involved in fin development. This study introduces the nuclei of the Xenopus fin as a powerful new model for extreme nuclear morphology in healthy cells to complement studies of nuclear shape variation in pathological contexts.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Hannah E Arbach
- Department of Biochemistry, University of Washington, Seattle, WA 98195-3750, USA
| | | | - Jessica K Chang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Andrea E Wills
- Department of Biochemistry, University of Washington, Seattle, WA 98195-3750, USA
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