1
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Westbrook ER, Lenn T, Chubb JR, Antolović V. Collective signalling drives rapid jumping between cell states. Development 2023; 150:dev201946. [PMID: 37921687 PMCID: PMC10730084 DOI: 10.1242/dev.201946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023]
Abstract
Development can proceed in 'fits and starts', with rapid transitions between cell states involving concerted transcriptome-wide changes in gene expression. However, it is not clear how these transitions are regulated in complex cell populations, in which cells receive multiple inputs. We address this issue using Dictyostelium cells undergoing development in their physiological niche. A continuous single cell transcriptomics time series identifies a sharp 'jump' in global gene expression marking functionally different cell states. By simultaneously imaging the physiological dynamics of transcription and signalling, we show the jump coincides with the onset of collective oscillations of cAMP. Optogenetic control of cAMP pulses shows that different jump genes respond to distinct dynamic features of signalling. Late jump gene expression changes are almost completely dependent on cAMP, whereas transcript changes at the onset of the jump require additional input. The coupling of collective signalling with gene expression is a potentially powerful strategy to drive robust cell state transitions in heterogeneous signalling environments. Based on the context of the jump, we also conclude that sharp gene expression transitions may not be sufficient for commitment.
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Affiliation(s)
- Elizabeth R. Westbrook
- UCL Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Tchern Lenn
- UCL Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Jonathan R. Chubb
- UCL Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Vlatka Antolović
- UCL Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
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2
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van Steijn L, Wondergem JAJ, Schakenraad K, Heinrich D, Merks RMH. Deformability and collision-induced reorientation enhance cell topotaxis in dense microenvironments. Biophys J 2023; 122:2791-2807. [PMID: 37291829 PMCID: PMC10397819 DOI: 10.1016/j.bpj.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 04/21/2023] [Accepted: 06/02/2023] [Indexed: 06/10/2023] Open
Abstract
In vivo, cells navigate through complex environments filled with obstacles such as other cells and the extracellular matrix. Recently, the term "topotaxis" has been introduced for navigation along topographic cues such as obstacle density gradients. Experimental and mathematical efforts have analyzed topotaxis of single cells in pillared grids with pillar density gradients. A previous model based on active Brownian particles (ABPs) has shown that ABPs perform topotaxis, i.e., drift toward lower pillar densities, due to decreased effective persistence lengths at high pillar densities. The ABP model predicted topotactic drifts of up to 1% of the instantaneous speed, whereas drifts of up to 5% have been observed experimentally. We hypothesized that the discrepancy between the ABP and the experimental observations could be in 1) cell deformability and 2) more complex cell-pillar interactions. Here, we introduce a more detailed model of topotaxis based on the cellular Potts model (CPM). To model persistent cells we use the Act model, which mimics actin-polymerization-driven motility, and a hybrid CPM-ABP model. Model parameters were fitted to simulate the experimentally found motion of Dictyostelium discoideum on a flat surface. For starved D. discoideum, the topotactic drifts predicted by both CPM variants are closer to the experimental results than the previous ABP model due to a larger decrease in persistence length. Furthermore, the Act model outperformed the hybrid model in terms of topotactic efficiency, as it shows a larger reduction in effective persistence time in dense pillar grids. Also pillar adhesion can slow down cells and decrease topotaxis. For slow and less-persistent vegetative D. discoideum cells, both CPMs predicted a similar small topotactic drift. We conclude that deformable cell volume results in higher topotactic drift compared with ABPs, and that feedback of cell-pillar collisions on cell persistence increases drift only in highly persistent cells.
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Affiliation(s)
| | | | - Koen Schakenraad
- Mathematical Institute, Leiden University, Leiden, the Netherlands; Leiden Institute of Physics, Leiden University, Leiden, the Netherlands
| | - Doris Heinrich
- Fraunhofer Institute for Silicate Research ISC, Würzburg, Germany; Institute for Bioprocessing and Analytical Measurement Techniques, Heilbad Heiligenstadt, Germany; Faculty for Mathematics and Natural Sciences, Technische Universität Ilmenau, Ilmenau, Germany
| | - Roeland M H Merks
- Mathematical Institute, Leiden University, Leiden, the Netherlands; Institute of Biology, Leiden University, Leiden, the Netherlands
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3
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Ford HZ, Manhart A, Chubb JR. Controlling periodic long-range signalling to drive a morphogenetic transition. eLife 2023; 12:83796. [PMID: 36856269 PMCID: PMC10027319 DOI: 10.7554/elife.83796] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/28/2023] [Indexed: 03/02/2023] Open
Abstract
Cells use signal relay to transmit information across tissue scales. However, the production of information carried by signal relay remains poorly characterised. To determine how the coding features of signal relay are generated, we used the classic system for long-range signalling: the periodic cAMP waves that drive Dictyostelium collective migration. Combining imaging and optogenetic perturbation of cell signalling states, we find that migration is triggered by an increase in wave frequency generated at the signalling centre. Wave frequency is regulated by cAMP wave circulation, which organises the long-range signal. To determine the mechanisms modulating wave circulation, we combined mathematical modelling, the general theory of excitable media, and mechanical perturbations to test competing models. Models in which cell density and spatial patterning modulate the wave frequency cannot explain the temporal evolution of signalling waves. Instead, our evidence leads to a model where wave circulation increases the ability for cells to relay the signal, causing further increase in the circulation rate. This positive feedback between cell state and signalling pattern regulates the long-range signal coding that drives morphogenesis.
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Affiliation(s)
- Hugh Z Ford
- Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Angelika Manhart
- Department of Mathematics, University College London, London, United Kingdom
- Faculty of Mathematics, University of Vienna, Vienna, Austria
| | - Jonathan R Chubb
- Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, London, United Kingdom
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4
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A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis. Nat Chem Biol 2022; 18:161-170. [PMID: 34931064 PMCID: PMC8810680 DOI: 10.1038/s41589-021-00919-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/12/2021] [Indexed: 12/18/2022]
Abstract
Multi-enzyme assemblies composed of metabolic enzymes catalyzing sequential reactions are being increasingly studied. Here, we report the discovery of a 1.6 megadalton multi-enzyme complex from Bacillus subtilis composed of two enzymes catalyzing opposite ('counter-enzymes') rather than sequential reactions: glutamate synthase (GltAB) and glutamate dehydrogenase (GudB), which make and break glutamate, respectively. In vivo and in vitro studies show that the primary role of complex formation is to inhibit the activity of GudB. Using cryo-electron microscopy, we elucidated the structure of the complex and the molecular basis of inhibition of GudB by GltAB. The complex exhibits unusual oscillatory progress curves and is necessary for both planktonic growth, in glutamate-limiting conditions, and for biofilm growth, in glutamate-rich media. The regulation of a key metabolic enzyme by complexing with its counter enzyme may thus enable cell growth under fluctuating glutamate concentrations.
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5
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Cell dispersal by localized degradation of a chemoattractant. Proc Natl Acad Sci U S A 2021; 118:2008126118. [PMID: 33526658 DOI: 10.1073/pnas.2008126118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chemotaxis, the guided motion of cells by chemical gradients, plays a crucial role in many biological processes. In the social amoeba Dictyostelium discoideum, chemotaxis is critical for the formation of cell aggregates during starvation. The cells in these aggregates generate a pulse of the chemoattractant, cyclic adenosine 3',5'-monophosphate (cAMP), every 6 min to 10 min, resulting in surrounding cells moving toward the aggregate. In addition to periodic pulses of cAMP, the cells also secrete phosphodiesterase (PDE), which degrades cAMP and prevents the accumulation of the chemoattractant. Here we show that small aggregates of Dictyostelium can disperse, with cells moving away from instead of toward the aggregate. This surprising behavior often exhibited oscillatory cycles of motion toward and away from the aggregate. Furthermore, the onset of outward cell motion was associated with a doubling of the cAMP signaling period. Computational modeling suggests that this dispersal arises from a competition between secreted cAMP and PDE, creating a cAMP gradient that is directed away from the aggregate, resulting in outward cell motion. The model was able to predict the effect of PDE inhibition as well as global addition of exogenous PDE, and these predictions were subsequently verified in experiments. These results suggest that localized degradation of a chemoattractant is a mechanism for morphogenesis.
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6
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Nichols JME, Antolović V, Reich JD, Brameyer S, Paschke P, Chubb JR. Cell and molecular transitions during efficient dedifferentiation. eLife 2020; 9:e55435. [PMID: 32255425 PMCID: PMC7190356 DOI: 10.7554/elife.55435] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/06/2020] [Indexed: 01/16/2023] Open
Abstract
Dedifferentiation is a critical response to tissue damage, yet is not well understood, even at a basic phenomenological level. Developing Dictyostelium cells undergo highly efficient dedifferentiation, completed by most cells within 24 hr. We use this rapid response to investigate the control features of dedifferentiation, combining single cell imaging with high temporal resolution transcriptomics. Gene expression during dedifferentiation was predominantly a simple reversal of developmental changes, with expression changes not following this pattern primarily associated with ribosome biogenesis. Mutation of genes induced early in dedifferentiation did not strongly perturb the reversal of development. This apparent robustness may arise from adaptability of cells: the relative temporal ordering of cell and molecular events was not absolute, suggesting cell programmes reach the same end using different mechanisms. In addition, although cells start from different fates, they rapidly converged on a single expression trajectory. These regulatory features may contribute to dedifferentiation responses during regeneration.
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Affiliation(s)
- John ME Nichols
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Vlatka Antolović
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Jacob D Reich
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | | | - Peggy Paschke
- CRUK Beatson Institute, Garscube Estate, Switchback Road, BearsdenGlasgowUnited Kingdom
| | - Jonathan R Chubb
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
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7
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Nanjundiah V. Many roads lead to Rome: Neutral phenotypes in microorganisms. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 332:339-348. [PMID: 31617664 DOI: 10.1002/jez.b.22909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/10/2019] [Accepted: 09/14/2019] [Indexed: 11/09/2022]
Abstract
John Bonner pointed out that microorganisms differ in several ways, some of which may reflect neutral phenotypic evolution. For making his case, Bonner referred to interspecies differences and morphological traits. Here we consider intraspecies differences and physiological traits. As a case-study, we examine the production of an extracellular cyclic 3 ' ,5 ' monophosphate phosphodiesterase in the cellular slime mold Dictyostelium discoideum. Temporal profiles of phosphodiesterase activity differ significantly between wild-type strains. From that we argue that the inference drawn initially from studies on a single wild-type, namely that the profile displayed by it pointed to an adaptive role, was mistaken. We generalize the conclusion to suggest that physiological differences exhibited by microorganisms of the same species may, but need not, reflect adaptations to different environments. Rather, the differences could be related to the fact that microorganisms live in groups whose composition can vary between homogeneous (clonal) and heterogeneous (polyclonal). More than one physiological profile is consistent with the normal development of the group in a given environment; the alternatives are neutral. When studying microbial physiology and behavior, it is expected that the observations are made on a clonal population; genetic (and so phenotypic) heterogeneity is carefully guarded against. As the example from D. discoideum shows, an unintended consequence of overlooking phenotypic heterogeneity is that one can fall into the trap of accepting a seemingly plausible, but possibly erroneous, adaptive explanation for a "normal" wild-type phenotype.
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Affiliation(s)
- Vidyanand Nanjundiah
- Centre for Human Genetics, BioTech Park, Bangalore, India.,Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
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8
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González-Velasco Ó, De Las Rivas J, Lacal J. Proteomic and Transcriptomic Profiling Identifies Early Developmentally Regulated Proteins in Dictyostelium Discoideum. Cells 2019; 8:cells8101187. [PMID: 31581556 PMCID: PMC6830349 DOI: 10.3390/cells8101187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 09/26/2019] [Indexed: 02/06/2023] Open
Abstract
Cyclic AMP acts as a secondary messenger involving different cellular functions in eukaryotes. Here, proteomic and transcriptomic profiling has been combined to identify novel early developmentally regulated proteins in eukaryote cells. These proteomic and transcriptomic experiments were performed in Dictyostelium discoideum given the unique advantages that this organism offers as a eukaryotic model for cell motility and as a nonmammalian model of human disease. By comparing whole-cell proteome analysis of developed (cAMP-pulsed) wild-type AX2 cells and an independent transcriptomic analysis of developed wild-type AX4 cells, our results show that up to 70% of the identified proteins overlap in the two independent studies. Among them, we have found 26 proteins previously related to cAMP signaling and identified 110 novel proteins involved in calcium signaling, adhesion, actin cytoskeleton, the ubiquitin-proteasome pathway, metabolism, and proteins that previously lacked any annotation. Our study validates previous findings, mostly for the canonical cAMP-pathway, and also generates further insight into the complexity of the transcriptomic changes during early development. This article also compares proteomic data between parental and cells lacking glkA, a GSK-3 kinase implicated in substrate adhesion and chemotaxis in Dictyostelium. This analysis reveals a set of proteins that show differences in expression in the two strains as well as overlapping protein level changes independent of GlkA.
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Affiliation(s)
- Óscar González-Velasco
- Bioinformatics and Functional Genomics Research Group. Cancer Research Center (CIC-IBMCC, CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
| | - Javier De Las Rivas
- Bioinformatics and Functional Genomics Research Group. Cancer Research Center (CIC-IBMCC, CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
| | - Jesus Lacal
- Department of Microbiology and Genetics, Faculty of Biology, University of Salamanca, 37007 Salamanca, Spain.
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9
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Wang W, Chen S, Das S, Losert W, Parent CA. Adenylyl cyclase A mRNA localized at the back of cells is actively translated in live chemotaxing Dictyostelium. J Cell Sci 2018; 131:jcs.216176. [PMID: 29618632 DOI: 10.1242/jcs.216176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/26/2018] [Indexed: 11/20/2022] Open
Abstract
Dictyostelium discoideum cells transport adenylyl cyclase A (ACA)-containing vesicles to the back of polarized cells to relay exogenous cAMP signals during chemotaxis. Fluorescence in situ hybridization (FISH) experiments showed that ACA mRNA is also asymmetrically distributed at the back of polarized cells. By using the MS2 bacteriophage system, we now visualize the distribution of ACA mRNA in live chemotaxing cells. We found that the ACA mRNA localization is not dependent on the translation of the protein product and requires multiple cis-acting elements within the ACA-coding sequence. We show that ACA mRNA is associated with actively translating ribosomes and is transported along microtubules towards the back of cells. By monitoring the recovery of ACA-YFP after photobleaching, we observed that local translation of ACA-YFP occurs at the back of cells. These data represent a novel functional role for localized translation in the relay of chemotactic signals during chemotaxis.
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Affiliation(s)
- Weiye Wang
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Song Chen
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.,Department of Pharmacology, Michigan Medicine, Ann Arbor, MI 48109, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Satarupa Das
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Wolfgang Losert
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Carole A Parent
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA .,Department of Pharmacology, Michigan Medicine, Ann Arbor, MI 48109, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
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10
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Lacal Romero J, Shen Z, Baumgardner K, Wei J, Briggs SP, Firtel RA. The Dictyostelium GSK3 kinase GlkA coordinates signal relay and chemotaxis in response to growth conditions. Dev Biol 2018; 435:56-72. [PMID: 29355521 DOI: 10.1016/j.ydbio.2018.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/11/2018] [Accepted: 01/11/2018] [Indexed: 12/21/2022]
Abstract
GSK3 plays a central role in orchestrating key biological signaling pathways, including cell migration. Here, we identify GlkA as a GSK3 family kinase with functions that overlap with and are distinct from those of GskA. We show that GlkA, as previously shown for GskA, regulates the cell's cytoskeleton through MyoII assembly and control of Ras and Rap1 function, leading to aberrant cell migration. However, there are both qualitative and quantitative differences in the regulation of Ras and Rap1 and their downstream effectors, including PKB, PKBR1, and PI3K, with glkA- cells exhibiting a more severe chemotaxis phenotype than gskA- cells. Unexpectedly, the severe glkA- phenotypes, but not those of gskA-, are only exhibited when cells are grown attached to a substratum but not in suspension, suggesting that GlkA functions as a key kinase of cell attachment signaling. Using proteomic iTRAQ analysis we show that there are quantitative differences in the pattern of protein expression depending on the growth conditions in wild-type cells. We find that GlkA expression affects the cell's proteome during vegetative growth and development, with many of these changes depending on whether the cells are grown attached to a substratum or in suspension. These changes include key cytoskeletal and signaling proteins known to be essential for proper chemotaxis and signal relay during the aggregation stage of Dictyostelium development.
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Affiliation(s)
- Jesus Lacal Romero
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0380, USA
| | - Zhouxin Shen
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0380, USA
| | - Kimberly Baumgardner
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0380, USA
| | - Jing Wei
- JadeBio, Inc., 505 Coast Boulevard South Suite 206, La Jolla, CA 92037, USA
| | - Steven P Briggs
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0380, USA
| | - Richard A Firtel
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0380, USA.
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11
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Fold-change detection and scale invariance of cell-cell signaling in social amoeba. Proc Natl Acad Sci U S A 2017; 114:E4149-E4157. [PMID: 28495969 DOI: 10.1073/pnas.1702181114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cell-cell signaling is subject to variability in the extracellular volume, cell number, and dilution that potentially increase uncertainty in the absolute concentrations of the extracellular signaling molecules. To direct cell aggregation, the social amoebae Dictyostelium discoideum collectively give rise to oscillations and waves of cyclic adenosine 3',5'-monophosphate (cAMP) under a wide range of cell density. To date, the systems-level mechanism underlying the robustness is unclear. By using quantitative live-cell imaging, here we show that the magnitude of the cAMP relay response of individual cells is determined by fold change in the extracellular cAMP concentrations. The range of cell density and exogenous cAMP concentrations that support oscillations at the population level agrees well with conditions that support a large fold-change-dependent response at the single-cell level. Mathematical analysis suggests that invariance of the oscillations to density transformation is a natural outcome of combining secrete-and-sense systems with a fold-change detection mechanism.
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12
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Fukujin F, Nakajima A, Shimada N, Sawai S. Self-organization of chemoattractant waves in Dictyostelium depends on F-actin and cell-substrate adhesion. J R Soc Interface 2016; 13:20160233. [PMID: 27358278 PMCID: PMC4938087 DOI: 10.1098/rsif.2016.0233] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/01/2016] [Indexed: 12/25/2022] Open
Abstract
In the social amoeba Dictyostelium discoideum, travelling waves of extracellular cyclic adenosine monophosphate (cAMP) self-organize in cell populations and direct aggregation of individual cells to form multicellular fruiting bodies. In contrast to the large body of studies that addressed how movement of cells is determined by spatial and temporal cues encoded in the dynamic cAMP gradients, how cell mechanics affect the formation of a self-generated chemoattractant field has received less attention. Here, we show, by live cell imaging analysis, that the periodicity of the synchronized cAMP waves increases in cells treated with the actin inhibitor latrunculin. Detail analysis of the extracellular cAMP-induced transients of cytosolic cAMP (cAMP relay response) in well-isolated cells demonstrated that their amplitude and duration were markedly reduced in latrunculin-treated cells. Similarly, in cells strongly adhered to a poly-l-lysine-coated surface, the response was suppressed, and the periodicity of the population-level oscillations was markedly lengthened. Our results suggest that cortical F-actin is dispensable for the basic low amplitude relay response but essential for its full amplification and that this enhanced response is necessary to establish high-frequency signalling centres. The observed F-actin dependence may prevent aggregation centres from establishing in microenvironments that are incompatible with cell migration.
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Affiliation(s)
- Fumihito Fukujin
- Department of Basic Science, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Akihiko Nakajima
- Research Center for Complex Systems Biology, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Nao Shimada
- Department of Basic Science, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Satoshi Sawai
- Department of Basic Science, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan Research Center for Complex Systems Biology, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan PRESTO, Japan Science and Technology Agency, Kawaguchi-shi, Saitama 332-0012, Japan
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13
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Corrigan AM, Tunnacliffe E, Cannon D, Chubb JR. A continuum model of transcriptional bursting. eLife 2016; 5. [PMID: 26896676 PMCID: PMC4850746 DOI: 10.7554/elife.13051] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 02/19/2016] [Indexed: 12/20/2022] Open
Abstract
Transcription occurs in stochastic bursts. Early models based upon RNA hybridisation studies suggest bursting dynamics arise from alternating inactive and permissive states. Here we investigate bursting mechanism in live cells by quantitative imaging of actin gene transcription, combined with molecular genetics, stochastic simulation and probabilistic modelling. In contrast to early models, our data indicate a continuum of transcriptional states, with a slowly fluctuating initiation rate converting the gene between different levels of activity, interspersed with extended periods of inactivity. We place an upper limit of 40 s on the lifetime of fluctuations in elongation rate, with initiation rate variations persisting an order of magnitude longer. TATA mutations reduce the accessibility of high activity states, leaving the lifetime of on- and off-states unchanged. A continuum or spectrum of gene states potentially enables a wide dynamic range for cell responses to stimuli. DOI:http://dx.doi.org/10.7554/eLife.13051.001 Understanding how gene activity is regulated relies on accurate measurements of the output of genes. Proteins are generated from genes via a multi-step process. In the first step, called transcription, the DNA of a gene is copied by complex cell machinery to create molecules of mRNA. Subsequently, these mRNA molecules are ‘translated’ into proteins. Previous studies have assayed gene transcription by measuring mRNA production in millions of cells at the same time. The resulting measurements give the impression that transcription occurs as a continuous, smooth process. However, when individual gene transcription is measured in single cells, mRNA production between cells is unexpectedly variable. This challenged the view that transcription is a continuous process. One idea that explains this variability – the "two-state" or "bursting" model – proposes that genes switch between "on" and "off" states with a certain probability. Thus, at any one time, a gene will be off in many cells and on in others. However, the methods used in these experiments measure mRNA in dead cells, and so the dynamic switching of genes between on and off states was presumed, but not accurately measured. Corrigan et al. have now imaged the transcription of a single gene – a gene for a protein called actin – in living cells of an amoeba called Dictyostelium. Genetic techniques and computational modeling were then used to explore what affects the variability in this gene’s activity. These approaches revealed that transcription occurs across a spectrum of activity, rather than in rigid on or off states. The transcription process itself may also contribute to where a gene’s activity sits on this spectrum. Furthermore, Corrigan et al. found that a specific DNA sequence found at the start of the actin gene, that is also found in many genes in complex life-forms, is required for the gene to reach the highest levels of activity on the spectrum. This spectrum of activity states could allow cells to finely tune their responses to the signals they receive. A future challenge will be to assess how the activity of other genes compare to the actin gene and to discover what underlies the variation in the timing of transcription’s different stages. DOI:http://dx.doi.org/10.7554/eLife.13051.002
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Affiliation(s)
- Adam M Corrigan
- Division of Cell and Developmental Biology, University College London, London, United Kingdom.,Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Edward Tunnacliffe
- Division of Cell and Developmental Biology, University College London, London, United Kingdom.,Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Danielle Cannon
- Division of Cell and Developmental Biology, University College London, London, United Kingdom.,Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Jonathan R Chubb
- Division of Cell and Developmental Biology, University College London, London, United Kingdom.,Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
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14
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Noorbakhsh J, Schwab DJ, Sgro AE, Gregor T, Mehta P. Modeling oscillations and spiral waves in Dictyostelium populations. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:062711. [PMID: 26172740 PMCID: PMC5142844 DOI: 10.1103/physreve.91.062711] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Indexed: 06/04/2023]
Abstract
Unicellular organisms exhibit elaborate collective behaviors in response to environmental cues. These behaviors are controlled by complex biochemical networks within individual cells and coordinated through cell-to-cell communication. Describing these behaviors requires new mathematical models that can bridge scales-from biochemical networks within individual cells to spatially structured cellular populations. Here we present a family of "multiscale" models for the emergence of spiral waves in the social amoeba Dictyostelium discoideum. Our models exploit new experimental advances that allow for the direct measurement and manipulation of the small signaling molecule cyclic adenosine monophosphate (cAMP) used by Dictyostelium cells to coordinate behavior in cellular populations. Inspired by recent experiments, we model the Dictyostelium signaling network as an excitable system coupled to various preprocessing modules. We use this family of models to study spatially unstructured populations of "fixed" cells by constructing phase diagrams that relate the properties of population-level oscillations to parameters in the underlying biochemical network. We then briefly discuss an extension of our model that includes spatial structure and show how this naturally gives rise to spiral waves. Our models exhibit a wide range of novel phenomena. including a density-dependent frequency change, bistability, and dynamic death due to slow cAMP dynamics. Our modeling approach provides a powerful tool for bridging scales in modeling of Dictyostelium populations.
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Affiliation(s)
- Javad Noorbakhsh
- Physics Department, Boston University, Boston, Massachusetts, USA
| | - David J. Schwab
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Allyson E. Sgro
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Thomas Gregor
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Pankaj Mehta
- Physics Department, Boston University, Boston, Massachusetts, USA
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15
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Masaki N, Ishizaki I, Hayasaka T, Fisher GL, Sanada N, Yokota H, Setou M. Three-Dimensional Image of Cleavage Bodies in Nuclei Is Configured Using Gas Cluster Ion Beam with Time-of-Flight Secondary Ion Mass Spectrometry. Sci Rep 2015; 5:10000. [PMID: 25961407 PMCID: PMC4426704 DOI: 10.1038/srep10000] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 03/25/2015] [Indexed: 12/28/2022] Open
Abstract
Structural variations of DNA in nuclei are deeply related with development, aging, and diseases through transcriptional regulation. In order to bare cross sections of samples maintaining sub-micron structures, an Ar2500+-gas cluster ion beam (GCIB) sputter was recently engineered. By introducing GCIB sputter to time-of-flight secondary ion mass spectrometry (TOF-SIMS), we analyzed the 3D configuration and chemical composition of subnuclear structures of pyramidal cells in the CA2 region in mouse brain hippocampus. Depth profiles of chemicals were analyzed as 3D distributions by combining topographic analyses. Signals corresponding to anions such as CN− and PO3− were distributed characteristically in the shape of cell organelles. CN− signals overlapped DAPI fluorescence signals corresponding to nuclei. The clusters shown by PO3− and those of adenine ions were colocalized inside nuclei revealed by the 3D reconstruction. Taking into account their size and their number in each nucleus, those clusters could be in the cleavage bodies, which are a kind of intranuclear structure.
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Affiliation(s)
- Noritaka Masaki
- Dept of Cell Biology and Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | | | - Takahiro Hayasaka
- Dept of Cell Biology and Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Gregory L Fisher
- Physical Electronics, 18725 Lake Drive East, Chanhassen, MN 55317, USA
| | - Noriaki Sanada
- ULVAC-PHI, 370 Enzo, Chigasaki, Kanagawa 253-8522, Japan
| | - Hideo Yokota
- Image Processing Research Team, Center for Advanced Photonics, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mitsutoshi Setou
- Dept of Cell Biology and Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
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16
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Kamide T, Okumura S, Ghosh S, Shinoda Y, Mototani Y, Ohnuki Y, Jin H, Cai W, Suita K, Sato I, Umemura M, Fujita T, Yokoyama U, Sato M, Furutani K, Kitano H, Ishikawa Y. Oscillation of cAMP and Ca(2+) in cardiac myocytes: a systems biology approach. J Physiol Sci 2015; 65:195-200. [PMID: 25585963 PMCID: PMC10717207 DOI: 10.1007/s12576-014-0354-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/18/2014] [Indexed: 12/19/2022]
Abstract
Cyclic adenosine monophosphate (cAMP) and Ca(2+) levels may oscillate in harmony within excitable cells; a mathematical oscillation loop model, the Cooper model, of these oscillations was developed two decades ago. However, in that model all adenylyl cyclase (AC) isoforms were assumed to be inhibited by Ca(2+), and it is now known that the heart expresses multiple AC isoforms, among which the type 5/6 isoforms are Ca(2+)-inhibitable whereas the other five (AC2, 3, 4, 7, and 9) are not. We used a computational systems biology approach with CellDesigner simulation software to develop a comprehensive graphical map and oscillation loop model for cAMP and Ca(2+). This model indicated that Ca(2+)-mediated inhibition of AC is essential to create oscillations of Ca(2+) and cAMP, and the oscillations were not altered by incorporation of phosphodiesterase-mediated cAMP hydrolysis or PKA-mediated inhibition of AC into the model. More importantly, they were created but faded out immediately in the co-presence of Ca(2+)-noninhibitable AC isoforms. Because the subcellular locations of AC isoforms are different, spontaneous cAMP and Ca(2+) oscillations may occur within microdomains containing only Ca(2+)-inhibitable isoforms in cardiac myocytes, which might be necessary for fine tuning of excitation-contraction coupling.
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Affiliation(s)
- Takehisa Kamide
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
| | - Satoshi Okumura
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
- Department of Physiology, Tsurumi University School of Dental Medicine, 2-1-2 Tsurumi, Tsurumi-ku, Yokohama, 230-8501 Japan
| | - Samik Ghosh
- The Systems Biology Institute, Minato, Tokyo, 108-0071 Japan
| | - Yoko Shinoda
- Department of Physiology, Tsurumi University School of Dental Medicine, 2-1-2 Tsurumi, Tsurumi-ku, Yokohama, 230-8501 Japan
| | - Yasumasa Mototani
- Department of Physiology, Tsurumi University School of Dental Medicine, 2-1-2 Tsurumi, Tsurumi-ku, Yokohama, 230-8501 Japan
| | - Yoshiki Ohnuki
- Department of Physiology, Tsurumi University School of Dental Medicine, 2-1-2 Tsurumi, Tsurumi-ku, Yokohama, 230-8501 Japan
| | - Huiling Jin
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
| | - Wenqian Cai
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
| | - Kenji Suita
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
| | - Itaru Sato
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
| | - Masanari Umemura
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
| | - Takayuki Fujita
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
| | - Utako Yokoyama
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
| | - Motohiko Sato
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
- Department of Physiology, Aichi Medical University, Nagakute, Aichi 480-1195 Japan
| | - Kazuharu Furutani
- Department of Pharmacology, Graduate School of Medicine, Osaka University, Osaka, 565-0871 Japan
- Center for Advanced Medical Engineering and Informatics, Osaka University, Osaka, 565-0871 Japan
| | - Hiroaki Kitano
- The Systems Biology Institute, Minato, Tokyo, 108-0071 Japan
- Okinawa Institute of Science and Technology Graduate School, Onna-Son, Okinawa, 904-0412 Japan
- Laboratory for Disease Systems Modeling, Riken Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan
| | - Yoshihiro Ishikawa
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
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