1
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González L, Mugler A. Collective effects in flow-driven cell migration. Phys Rev E 2023; 108:054406. [PMID: 38115469 DOI: 10.1103/physreve.108.054406] [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: 05/05/2023] [Accepted: 10/17/2023] [Indexed: 12/21/2023]
Abstract
Autologous chemotaxis is the process in which cells secrete and detect molecules to determine the direction of fluid flow. Experiments and theory suggest that autologous chemotaxis fails at high cell densities because molecules from other cells interfere with a given cell's signal. We investigate autologous chemotaxis using a three-dimensional Monte Carlo-based motility simulation that couples spatial and temporal gradient sensing with cell-cell repulsion. Surprisingly, we find that when temporal gradient sensing dominates, high-density clusters chemotax faster than individual cells. To explain this observation, we propose a mechanism by which temporal gradient sensing allows cells to form a collective sensory unit. We demonstrate using computational fluid mechanics that that this mechanism indeed allows a cluster of cells to outperform single cells in terms of the detected anisotropy of the signal, a finding that we demonstrate with analytic scaling arguments. Our work suggests that collective autologous chemotaxis at high cell densities is possible and requires only known, ubiquitous cell capabilities.
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Affiliation(s)
- Louis González
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Andrew Mugler
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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2
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Li F, Chu Q, Hu Z, Lu Z, Fang C, Han G, Fu Y, Li X. An Inter-Cooperative Biohybrid Platform to Enable Tumor Ablation and Immune Activation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207194. [PMID: 37314157 PMCID: PMC10427385 DOI: 10.1002/advs.202207194] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/03/2023] [Indexed: 06/15/2023]
Abstract
A biohybrid therapeutic system, consisting of responsive materials and living microorganisms with inter-cooperative effects, is designed and investigated for tumor treatment. In this biohybrid system, S2 O3 2- -intercalated CoFe layered double hydroxides (LDH) are integrated at the surface of Baker's yeasts. Under the tumor microenvironment, functional interactions between yeast and LDH are effectively triggered, resulting in S2 O3 2- release, H2 S production, and in-situ generation of highly catalytic agents. Meanwhile, the degradation of LDH in the tumor microenvironment induces the exposure of the surface antigen of yeast, leading to effective immune activation at the tumor site. By virtue of the inter-cooperative phenomena, this biohybrid system exhibits significant efficacy in tumor ablation and strong inhibition of recurrence. This study has potentially offered an alternative concept by utilizing the metabolism of living microorganisms and materials in exploring effective tumor therapeutics.
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Affiliation(s)
- Feiyu Li
- State Key Laboratory of Silicon and Advanced Semiconductor MaterialsSchool of Materials Science and EngineeringZhejiang UniversityHangzhou310027China
- ZJU‐Hangzhou Global Science and Technology Innovation CenterZhejiang UniversityHangzhou311215China
| | - Qiang Chu
- Tea Research InstituteCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Zefeng Hu
- State Key Laboratory of Silicon and Advanced Semiconductor MaterialsSchool of Materials Science and EngineeringZhejiang UniversityHangzhou310027China
- ZJU‐Hangzhou Global Science and Technology Innovation CenterZhejiang UniversityHangzhou311215China
| | - Zijie Lu
- State Key Laboratory of Silicon and Advanced Semiconductor MaterialsSchool of Materials Science and EngineeringZhejiang UniversityHangzhou310027China
| | - Chao Fang
- State Key Laboratory of Silicon and Advanced Semiconductor MaterialsSchool of Materials Science and EngineeringZhejiang UniversityHangzhou310027China
| | - Gaorong Han
- State Key Laboratory of Silicon and Advanced Semiconductor MaterialsSchool of Materials Science and EngineeringZhejiang UniversityHangzhou310027China
| | - Yike Fu
- State Key Laboratory of Silicon and Advanced Semiconductor MaterialsSchool of Materials Science and EngineeringZhejiang UniversityHangzhou310027China
- ZJU‐Hangzhou Global Science and Technology Innovation CenterZhejiang UniversityHangzhou311215China
| | - Xiang Li
- State Key Laboratory of Silicon and Advanced Semiconductor MaterialsSchool of Materials Science and EngineeringZhejiang UniversityHangzhou310027China
- ZJU‐Hangzhou Global Science and Technology Innovation CenterZhejiang UniversityHangzhou311215China
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3
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Clark-Cotton MR, Henderson NT, Pablo M, Ghose D, Elston TC, Lew DJ. Exploratory polarization facilitates mating partner selection in Saccharomyces cerevisiae. Mol Biol Cell 2021; 32:1048-1063. [PMID: 33689470 PMCID: PMC8101489 DOI: 10.1091/mbc.e21-02-0068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Yeast decode pheromone gradients to locate mating partners, providing a model for chemotropism. How yeast polarize toward a single partner in crowded environments is unclear. Initially, cells often polarize in unproductive directions, but then they relocate the polarity site until two partners’ polarity sites align, whereupon the cells “commit” to each other by stabilizing polarity to promote fusion. Here we address the role of the early mobile polarity sites. We found that commitment by either partner failed if just one partner was defective in generating, orienting, or stabilizing its mobile polarity sites. Mobile polarity sites were enriched for pheromone receptors and G proteins, and we suggest that such sites engage in an exploratory search of the local pheromone landscape, stabilizing only when they detect elevated pheromone levels. Mobile polarity sites were also enriched for pheromone secretion factors, and simulations suggest that only focal secretion at polarity sites would produce high pheromone concentrations at the partner’s polarity site, triggering commitment.
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Affiliation(s)
| | - Nicholas T Henderson
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708
| | - Michael Pablo
- Department of Chemistry, Chapel Hill, NC 27599.,Program in Molecular and Cellular Biophysics, Chapel Hill, NC 27599
| | - Debraj Ghose
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708
| | - Timothy C Elston
- Department of Pharmacology and Computational Medicine Program, UNC Chapel Hill, Chapel Hill, NC 27599
| | - Daniel J Lew
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708
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4
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Masiulionis VE, Pagnocca FC. In vitro study of volatile organic compounds produced by the mutualistic fungus of leaf-cutter ants and the antagonist Escovopsis. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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5
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Shams DP, Yang X, Mehta P, Schwab DJ. Spatial gradient sensing and chemotaxis via excitability in Dictyostelium discoideum. Phys Rev E 2020; 101:062410. [PMID: 32688583 DOI: 10.1103/physreve.101.062410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/13/2019] [Indexed: 11/07/2022]
Abstract
The social amoeba Dictyostelium discoideum performs chemotaxis under starvation conditions, aggregating towards clusters of cells following waves of the signaling molecule cAMP. Cells sense extracellular cAMP and produce internal caches of cAMP to be released, relaying the signal. These events lead to traveling waves of cAMP washing over the population of cells. While much research has been performed to understand the functioning of the chemotaxis network in D. discoideum, limited work has been done to link the operation of the signal relay network with the chemotaxis network to provide a holistic view of the system. We take inspiration from D. discoideum and propose a model that directly links the relaying of a chemical message to the directional sensing of that signal. Utilizing an excitable dynamical systems model that has been previously validated experimentally, we show that it is possible to have both signal amplification and perfect adaptation in a single module. We show that noise plays a vital role in chemotaxing to static gradients, where stochastic tunneling of transient bursts biases the system towards accurate gradient sensing. Moreover, this model also automatically matches its internal time scale of adaptation to the naturally occurring periodicity of the traveling chemical waves generated in the population. Numerical simulations were performed to study the qualitative phenomenology of the system and explore how the system responds to diverse dynamic spatiotemporal stimuli. Finally, we address dynamical instabilities that impede chemotactic ability in a continuum version of the model.
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Affiliation(s)
- Daniel P Shams
- Interdisciplinary Biological Sciences, Northwestern University, Evanston, Illinois 60201, USA
| | - Xingbo Yang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Pankaj Mehta
- Department of Physics, Boston University, Boston, Massachusetts 02467, USA
| | - David J Schwab
- Initiative for the Theoretical Sciences, The Graduate Center, City University of New York, New York, New York 10016, USA
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6
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Payne P, Polechová J. Sympatric ecological divergence with coevolution of niche preference. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190749. [PMID: 32654636 PMCID: PMC7423286 DOI: 10.1098/rstb.2019.0749] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Reinforcement, the increase of assortative mating driven by selection against unfit hybrids, is conditional on pre-existing divergence. Yet, for ecological divergence to precede the evolution of assortment, strict symmetries between fitnesses in niches must hold, and/or there must be low gene flow between the nascent species. It has thus been argued that conditions favouring sympatric speciation are rarely met in nature. Indeed, we show that under disruptive selection, violating symmetries in niche sizes and increasing strength of the trade-off in selection between the niches quickly leads to loss of genetic variation, instead of evolution of specialists. The region of the parameter space where polymorphism is maintained further narrows with increasing number of loci encoding the diverging trait and the rate of recombination between them. Yet, evolvable assortment and pre-existing assortment both substantially broaden the parameter space within which polymorphism is maintained. Notably, pre-existing niche preference speeds up further increase of assortment, thus facilitating reinforcement in the later phases of speciation. We conclude that in order for sympatric ecological divergence to occur, niche preference must coevolve throughout the divergence process. Even if populations come into secondary contact, having diverged in isolation, niche preference substantially broadens the conditions for coexistence in sympatry and completion of the speciation process. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Pavel Payne
- Department of Zoology, Charles University, Prague, Czech Republic.,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
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7
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Emmerstorfer-Augustin A, Augustin CM, Shams S, Thorner J. Tracking yeast pheromone receptor Ste2 endocytosis using fluorogen-activating protein tagging. Mol Biol Cell 2018; 29:2720-2736. [PMID: 30207829 PMCID: PMC6249837 DOI: 10.1091/mbc.e18-07-0424] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
To observe internalization of the yeast pheromone receptor Ste2 by fluorescence microscopy in live cells in real time, we visualized only those molecules present at the cell surface at the time of agonist engagement (rather than the total cellular pool) by tagging this receptor at its N-terminus with an exocellular fluorogen-activating protein (FAP). A FAP is a single-chain antibody engineered to bind tightly a nonfluorescent, cell-impermeable dye (fluorogen), thereby generating a fluorescent complex. The utility of FAP tagging to study trafficking of integral membrane proteins in yeast, which possesses a cell wall, had not been examined previously. A diverse set of signal peptides and propeptide sequences were explored to maximize expression. Maintenance of the optimal FAP-Ste2 chimera intact required deletion of two, paralogous, glycosylphosphatidylinositol (GPI)-anchored extracellular aspartyl proteases (Yps1 and Mkc7). FAP-Ste2 exhibited a much brighter and distinct plasma membrane signal than Ste2-GFP or Ste2-mCherry yet behaved quite similarly. Using FAP-Ste2, new information was obtained about the mechanism of its internalization, including novel insights about the roles of the cargo-selective endocytic adaptors Ldb19/Art1, Rod1/Art4, and Rog3/Art7.
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Affiliation(s)
- Anita Emmerstorfer-Augustin
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202
| | - Christoph M Augustin
- Department of Mechanical Engineering, University of California, Berkeley, Berkeley, CA 94720-3202
| | - Shadi Shams
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202
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8
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Microfluidic platform for single cell analysis under dynamic spatial and temporal stimulation. Biosens Bioelectron 2018; 104:58-64. [DOI: 10.1016/j.bios.2017.12.038] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 11/14/2017] [Accepted: 12/22/2017] [Indexed: 11/18/2022]
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9
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Veresoglou SD, Wang D, Andrade-Linares DR, Hempel S, Rillig MC. Fungal Decision to Exploit or Explore Depends on Growth Rate. MICROBIAL ECOLOGY 2018; 75:289-292. [PMID: 28791465 DOI: 10.1007/s00248-017-1053-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/31/2017] [Indexed: 05/28/2023]
Affiliation(s)
- Stavros D Veresoglou
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany.
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany.
| | - Dongwei Wang
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
| | - Diana R Andrade-Linares
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
| | - Stefan Hempel
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
| | - Matthias C Rillig
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
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10
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Azuma SI, Owaki K, Shinohara N, Sugie T. Performance Analysis of Chemotaxis Controllers: Which has Better Chemotaxis Controller, Escherichia coli or Paramecium caudatum? IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 13:730-741. [PMID: 26336141 DOI: 10.1109/tcbb.2015.2474397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Chemotaxis is the biological phenomenon in which organisms move to a more favorable location in an environment with a chemical attractant or repellent. Since chemotaxis is a typical example of the environmental response of organisms, it is a fundamental topic in biology and related fields. We discuss the performance of the internal controllers that generate chemotaxis. We first propose performance indices to evaluate the controllers. Based on these indices, we evaluate the performance of two controller models of Escherichia coli and Paramecium caudatum. As a result, it is disclosed that the E. coli-type controller achieves chemotaxis quickly but roughly, whereas the P. caudatum-type controller achieves it slowly but precisely. This result will be a biological contribution from a control theoretic point of view.
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11
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Sharma R, Roberts E. Gradient sensing by a bistable regulatory motif enhances signal amplification but decreases accuracy in individual cells. Phys Biol 2016; 13:036003. [DOI: 10.1088/1478-3975/13/3/036003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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12
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Sevier SA, Levine H. Properties of cooperatively induced phases in sensing models. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:052707. [PMID: 26066199 DOI: 10.1103/physreve.91.052707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Indexed: 06/04/2023]
Abstract
A large number of eukaryotic cells are able to directly detect external chemical gradients with great accuracy and the ultimate limit to their sensitivity has been a topic of debate for many years. Previous work has been done to understand many aspects of this process but little attention has been paid to the possibility of emergent sensing states. Here we examine how cooperation between sensors existing in a two-dimensional network, as they do on the cell's surface, can both enhance and fundamentally alter the response of the cell to a spatially varying signal. We show that weakly interacting sensors linearly amplify the cell's response to an external gradient while a network of strongly interacting sensors form a collective nonlinear response with two separate domains of active and inactive sensors forming what have called a "1/2-state." In our analysis we examine the cell's ability to sense the direction of a signal and pay special attention to the substantially different behavior realized in the strongly interacting regime.
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Affiliation(s)
- Stuart A Sevier
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| | - Herbert Levine
- Department of Bioengineering, Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
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13
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Analysis of CCR7 mediated T cell transfectant migration using a microfluidic gradient generator. J Immunol Methods 2015; 419:9-17. [PMID: 25733353 DOI: 10.1016/j.jim.2015.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/07/2015] [Accepted: 02/18/2015] [Indexed: 12/11/2022]
Abstract
T lymphocyte migration is crucial for adaptive immunity. Manipulation of signaling molecules controlling cell migration combined with in-vitro cell migration analysis provides a powerful research approach. Microfluidic devices, which can precisely configure chemoattractant gradients and allow quantitative single cell analysis, have been increasingly applied to cell migration and chemotaxis studies. However, there are a very limited number of published studies involving microfluidic migration analysis of genetically manipulated immune cells. In this study, we describe a simple microfluidic method for quantitative analysis of T cells expressing transfected chemokine receptors and other cell migration signaling probes. Using this method, we demonstrated chemotaxis of Jurkat transfectants expressing wild-type or C-terminus mutated CCR7 within a gradient of chemokine CCL19, and characterized the difference in transfectant migration mediated by wild-type and mutant CCR7. The EGFP-tagged CCR7 allows identification of CCR7-expressing transfectants in cell migration analysis and microscopy assessment of CCR7 dynamics. Collectively, our study demonstrated the effective use of the microfluidic method for studying CCR7 mediated T cell transfectant migration. We envision this developed method will provide a useful platform to functionally test various signaling mechanisms at the cell migration level.
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14
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Genetic, structural, and molecular insights into the function of ras of complex proteins domains. ACTA ACUST UNITED AC 2014; 21:809-18. [PMID: 24981771 PMCID: PMC4104024 DOI: 10.1016/j.chembiol.2014.05.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 05/13/2014] [Accepted: 05/28/2014] [Indexed: 11/22/2022]
Abstract
Ras of complex proteins (ROC) domains were identified in 2003 as GTP binding modules in large multidomain proteins from Dictyostelium discoideum. Research into the function of these domains exploded with their identification in a number of proteins linked to human disease, including leucine-rich repeat kinase 2 (LRRK2) and death-associated protein kinase 1 (DAPK1) in Parkinson’s disease and cancer, respectively. This surge in research has resulted in a growing body of data revealing the role that ROC domains play in regulating protein function and signaling pathways. In this review, recent advances in the structural information available for proteins containing ROC domains, along with insights into enzymatic function and the integration of ROC domains as molecular switches in a cellular and organismal context, are explored.
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15
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Chang Q, Zuo L. The biophysical model for accuracy of cellular sensing spatial gradients of multiple chemoattractants. Phys Biol 2013; 10:056014. [PMID: 24104469 DOI: 10.1088/1478-3975/10/5/056014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Spatial gradients of surrounding chemoattractants are the key factors in determining the directionality of eukaryotic cell movement. Thus, it is important for cells to accurately measure the spatial gradients of surrounding chemoattractants. Here, we study the precision of sensing the spatial gradients of multiple chemoattractants using cooperative receptor clusters. Cooperative receptors on cells are modeled as an Ising chain of Monod-Wyman-Changeux clusters subject to multiple chemical-gradient fields to study the physical limits of multiple chemoattractants spatial gradients sensing. We found that eukaryotic cells cannot sense each chemoattractant gradient individually. Instead, cells can only sense a weighted sum of surrounding chemical gradients. Moreover, the precision of sensing one chemical gradient is signicantly affected by coexisting chemoattractant concentrations. These findings can provide a further insight into the role of chemoattractants in immune response and help develop novel treatments for inflammatory diseases.
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Affiliation(s)
- Qiang Chang
- Chinese Academy of Sciences-Max Plank Society Partner Institute for Computational Biology Shanghai Institute for Biological Sciences, Shanghai 200031, People's Republic of China. Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
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16
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Tan RZ, Ji N, Mentink RA, Korswagen HC, van Oudenaarden A. Deconvolving the roles of Wnt ligands and receptors in sensing and amplification. Mol Syst Biol 2013; 9:631. [PMID: 23295860 PMCID: PMC3564265 DOI: 10.1038/msb.2012.64] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 11/16/2012] [Indexed: 01/09/2023] Open
Abstract
Establishment of cell polarity is crucial for many biological processes including cell migration and asymmetric cell division. The establishment of cell polarity consists of two sequential processes: an external gradient is first sensed and then the resulting signal is amplified and maintained by intracellular signaling networks usually using positive feedback regulation. Generally, these two processes are intertwined and it is challenging to determine which proteins contribute to the sensing or amplification process, particularly in multicellular organisms. Here, we integrated phenomenological modeling with quantitative single-cell measurements to separate the sensing and amplification components of Wnt ligands and receptors during establishment of polarity of the Caenorhabditis elegans P cells. By systematically exploring how P-cell polarity is altered in Wnt ligand and receptor mutants, we inferred that ligands predominantly affect the sensing process, whereas receptors are needed for both sensing and amplification. This integrated approach is generally applicable to other systems and will facilitate decoupling of the different layers of signal sensing and amplification.
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Affiliation(s)
- Rui Zhen Tan
- Harvard University Graduate Biophysics Program, Harvard Medical School, Boston, MA, USA
| | - Ni Ji
- Department of Brian and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Remco A Mentink
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hendrik C Korswagen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Alexander van Oudenaarden
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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17
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Moore TI, Tanaka H, Kim HJ, Jeon NL, Yi TM. Yeast G-proteins mediate directional sensing and polarization behaviors in response to changes in pheromone gradient direction. Mol Biol Cell 2012; 24:521-34. [PMID: 23242998 PMCID: PMC3571874 DOI: 10.1091/mbc.e12-10-0739] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
G-proteins, heterotrimeric and Cdc42, modulate in a ligand-dependent fashion two fundamental cell polarity behaviors (projection bending growth and second projection formation) in response to gradient directional change. Yeast cells polarize by projecting up mating pheromone gradients, a classic cell polarity behavior. However, these chemical gradients may shift direction. We examine how yeast cells sense and respond to a 180o switch in the direction of microfluidically generated pheromone gradients. We identify two behaviors: at low concentrations of α-factor, the initial projection grows by bending, whereas at high concentrations, cells form a second projection toward the new source. Mutations that increase heterotrimeric G-protein activity expand the bending-growth morphology to high concentrations; mutations that increase Cdc42 activity result in second projections at low concentrations. Gradient-sensing projection bending requires interaction between Gβγ and Cdc24, whereas gradient-nonsensing projection extension is stimulated by Bem1 and hyperactivated Cdc42. Of interest, a mutation in Gα affects both bending and extension. Finally, we find a genetic perturbation that exhibits both behaviors. Overexpression of the formin Bni1, a component of the polarisome, makes both bending-growth projections and second projections at low and high α-factor concentrations, suggesting a role for Bni1 downstream of the heterotrimeric G-protein and Cdc42 during gradient sensing and response. Thus we demonstrate that G-proteins modulate in a ligand-dependent manner two fundamental cell-polarity behaviors in response to gradient directional change.
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Affiliation(s)
- Travis I Moore
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
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18
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Freddolino PL, Tavazoie S. Beyond homeostasis: a predictive-dynamic framework for understanding cellular behavior. Annu Rev Cell Dev Biol 2012; 28:363-84. [PMID: 22559263 DOI: 10.1146/annurev-cellbio-092910-154129] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microbial regulatory strategies have long been understood in terms of the homeostatic framework, in which a response is interpreted as a restoring force counteracting the immediate intracellular consequences of a change in the environment. In this review, we summarize the breadth of recent discoveries of cellular behavior extending beyond the homeostatic framework. We argue that the nonrandom structure of native habitats makes environmental fluctuations inherently multidimensional. Beyond its utility for accurate perception of immediate events, the temporal regularity of this multidimensional correlation structure allows microbes to make predictions about the trajectory of their sensory environment. We describe recently discovered examples of such predictive behavior, their physiological benefits, and the underlying evolutionary forces shaping them. These observations compel us to go beyond homeostasis and consider a predictive-dynamic framework in which cellular behavior is orchestrated in response to the meaning of an environmental perturbation, not only its direct and immediate fitness consequences.
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Affiliation(s)
- Peter L Freddolino
- Joint Centers for Systems Biology, Columbia University, New York, New York 10032, USA.
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19
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Ragni E, Piberger H, Neupert C, García-Cantalejo J, Popolo L, Arroyo J, Aebi M, Strahl S. The genetic interaction network of CCW12, a Saccharomyces cerevisiae gene required for cell wall integrity during budding and formation of mating projections. BMC Genomics 2011; 12:107. [PMID: 21320323 PMCID: PMC3049148 DOI: 10.1186/1471-2164-12-107] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 02/14/2011] [Indexed: 01/19/2023] Open
Abstract
Background Mannoproteins construct the outer cover of the fungal cell wall. The covalently linked cell wall protein Ccw12p is an abundant mannoprotein. It is considered as crucial structural cell wall component since in baker's yeast the lack of CCW12 results in severe cell wall damage and reduced mating efficiency. Results In order to explore the function of CCW12, we performed a Synthetic Genetic Analysis (SGA) and identified genes that are essential in the absence of CCW12. The resulting interaction network identified 21 genes involved in cell wall integrity, chitin synthesis, cell polarity, vesicular transport and endocytosis. Among those are PFD1, WHI3, SRN2, PAC10, FEN1 and YDR417C, which have not been related to cell wall integrity before. We correlated our results with genetic interaction networks of genes involved in glucan and chitin synthesis. A core of genes essential to maintain cell integrity in response to cell wall stress was identified. In addition, we performed a large-scale transcriptional analysis and compared the transcriptional changes observed in mutant ccw12Δ with transcriptomes from studies investigating responses to constitutive or acute cell wall damage. We identified a set of genes that are highly induced in the majority of the mutants/conditions and are directly related to the cell wall integrity pathway and cell wall compensatory responses. Among those are BCK1, CHS3, EDE1, PFD1, SLT2 and SLA1 that were also identified in the SGA. In contrast, a specific feature of mutant ccw12Δ is the transcriptional repression of genes involved in mating. Physiological experiments substantiate this finding. Further, we demonstrate that Ccw12p is present at the cell periphery and highly concentrated at the presumptive budding site, around the bud, at the septum and at the tip of the mating projection. Conclusions The combination of high throughput screenings, phenotypic analyses and localization studies provides new insight into the function of Ccw12p. A compensatory response, culminating in cell wall remodelling and transport/recycling pathways is required to buffer the loss of CCW12. Moreover, the enrichment of Ccw12p in bud, septum and mating projection is consistent with a role of Ccw12p in preserving cell wall integrity at sites of active growth. The microarray data produced in this analysis have been submitted to NCBI GEO database and GSE22649 record was assigned.
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Affiliation(s)
- Enrico Ragni
- University of Heidelberg, Centre for Organismal Studies (COS) Heidelberg, Cell Chemistry, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
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Aquino G, Endres RG. Increased accuracy of ligand sensing by receptor diffusion on cell surface. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:041902. [PMID: 21230308 DOI: 10.1103/physreve.82.041902] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Indexed: 05/30/2023]
Abstract
The physical limit with which a cell senses external ligand concentration corresponds to the perfect absorber, where all ligand particles are absorbed and overcounting of same ligand particles does not occur. Here, we analyze how the lateral diffusion of receptors on the cell membrane affects the accuracy of sensing ligand concentration. Specifically, we connect our modeling to neurotransmission in neural synapses where the diffusion of glutamate receptors is already known to refresh synaptic connections. We find that receptor diffusion indeed increases the accuracy of sensing for both the glutamate α-Amino-3-hydroxy-5-Methyl-4-isoxazolePropionic Acid (AMPA) and N-Methyl-D-aspartic Acid (NMDA) receptor, although the NMDA receptor is overall much noisier. We propose that the difference in accuracy of sensing of the two receptors can be linked to their different roles in neurotransmission. Specifically, the high accuracy in sensing glutamate is essential for the AMPA receptor to start membrane depolarization, while the NMDA receptor is believed to work in a second stage as a coincidence detector, involved in long-term potentiation and memory.
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Affiliation(s)
- Gerardo Aquino
- Division of Molecular Biosciences and Centre for Integrative Systems Biology at Imperial College, Imperial College London, SW7 2AZ London, United Kingdom
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21
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Abstract
Chemical gradients of peptide mating pheromones are necessary for directional growth, which is critical for yeast mating. These gradients are generated by cell-type specific secretion or export and specific degradation in receiving cells. Spatial information is sensed by dedicated seven-transmembrane G-protein coupled receptors and yeast cells are able to detect extremely small differences in ligand concentration across their approximately 5-microm cell surface. Here, I will discuss our current knowledge of how cells detect and respond to such shallow chemical gradients and in particular what is known about the proteins that are involved in directional growth and the establishment of the polarity axis during yeast mating.
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Affiliation(s)
- Robert A Arkowitz
- Institute of Developmental Biology and Cancer, Université de Nice-Sophia Antipolis-CNRS UMR6543, Centre de Biochimie, Faculté des Sciences, Parc Valrose, 06108 Nice Cedex 2, France.
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22
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Mora T, Wingreen NS. Limits of sensing temporal concentration changes by single cells. PHYSICAL REVIEW LETTERS 2010; 104:248101. [PMID: 20867338 DOI: 10.1103/physrevlett.104.248101] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Indexed: 05/29/2023]
Abstract
Berg and Purcell [Biophys. J. 20, 193 (1977)] calculated how the accuracy of concentration sensing by single-celled organisms is limited by noise from the small number of counted molecules. Here we generalize their results to the sensing of concentration ramps, which is often the biologically relevant situation (e.g., during bacterial chemotaxis). We calculate lower bounds on the uncertainty of ramp sensing by three measurement devices: a single receptor, an absorbing sphere, and a monitoring sphere. We contrast two strategies, simple linear regression of the input signal versus maximum likelihood estimation, and show that the latter can be twice as accurate as the former. Finally, we consider biological implementations of these two strategies, and identify possible signatures that maximum likelihood estimation is implemented by real biological systems.
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Affiliation(s)
- Thierry Mora
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
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23
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Aquino G, Endres RG. Increased accuracy of ligand sensing by receptor internalization. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:021909. [PMID: 20365597 DOI: 10.1103/physreve.81.021909] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Revised: 12/21/2009] [Indexed: 05/29/2023]
Abstract
Many types of cells can sense external ligand concentrations with cell-surface receptors at extremely high accuracy. Interestingly, ligand-bound receptors are often internalized, a process also known as receptor-mediated endocytosis. While internalization is involved in a vast number of important functions for the life of a cell, it was recently also suggested to increase the accuracy of sensing ligand as the overcounting of the same ligand molecules is reduced. Here we show, by extending simple ligand-receptor models to out-of-equilibrium thermodynamics, that internalization increases the accuracy with which cells can measure ligand concentrations in the external environment. Comparison with experimental rates of real receptors demonstrates that our model has indeed biological significance.
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Affiliation(s)
- Gerardo Aquino
- Division of Molecular Biosciences and Centre for Integrated Systems Biology at Imperial College, Imperial College London, SW7 2AZ London, United Kingdom
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24
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25
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Endres RG, Wingreen NS. Maximum likelihood and the single receptor. PHYSICAL REVIEW LETTERS 2009; 103:158101. [PMID: 19905667 DOI: 10.1103/physrevlett.103.158101] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Indexed: 05/28/2023]
Abstract
The accuracy by which biological cells sense chemical concentration is ultimately limited by the random arrival of particles at the receptors by diffusion. This fundamental physical limit is generally considered to be the Berg-Purcell limit [Biophys. J. 20, 193 (1977)]. Here we derive a lower limit by applying maximum likelihood to the time series of receptor occupancy. The increased accuracy stems from solely considering the unoccupied time intervals--disregarding the occupied time intervals as these do not contain any information about the external particle concentration, and only decrease the accuracy of the concentration estimate. Receptors which minimize the bound time intervals achieve the highest possible accuracy. We discuss how a cell could implement such an optimal sensing strategy by absorbing or degrading bound particles.
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Affiliation(s)
- Robert G Endres
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom.
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26
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Endres RG, Wingreen NS. Accuracy of direct gradient sensing by cell-surface receptors. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2009; 100:33-9. [DOI: 10.1016/j.pbiomolbio.2009.06.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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27
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Patnaik PR. Transient response analysis of the eukaryotic chemosensory system to intra-cellular fluctuations. J Bioinform Comput Biol 2009; 7:93-105. [PMID: 19226662 DOI: 10.1142/s0219720009003960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Revised: 09/30/2008] [Accepted: 10/04/2008] [Indexed: 11/18/2022]
Abstract
Like prokaryotic cells, those of eukaryotes are also subjected to noise from within the cells. While the cells have a built-in mechanism to attenuate the noise, conditions may arise where this is beyond the cell's ability to regulate. Start-up perturbations and those induced by metabolic shifts are examples of such situations. Then, it becomes useful to understand how the cells respond. For a eukaryotic chemosensory system, this has been studied by applying response coefficient analysis to a recent model. With even three dependent variables - an activator, an inhibitor, and a response element - the response coefficients differ widely with time and from one variable to another. These differences are interpreted in terms of the chemosensory mechanism and its robustness. The results complement similar recent studies of Escherichia coli chemotaxis, thus supporting their credibility and versatility.
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Affiliation(s)
- Pratap R Patnaik
- Institute of Microbial Technology (Council of Scientific and Industrial Research), Sector 39-A, Chandigarh-160036, India.
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28
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Abstract
Virtually all eukaryotic cells can grow in a polarized fashion in response to external signals. Cells can respond to gradients of chemoattractants or chemorepellents by directional growth, a process referred to as chemotropism. The budding yeast Saccharomyces cerevisiae undergoes chemotropic growth during mating, in which two haploid cells of opposite mating type grow toward one another. We have shown that mating pheromone gradients are essential for efficient mating in yeast and have examined the chemotropism defects of different yeast mutants. Two methods of assessing the ability of yeast strains to respond to pheromone gradients are presented here.
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Affiliation(s)
- Peter J Follette
- Institute of Developmental Biology and Cancer, CNRS UMR 6543, University of Nice - Sophia Antipolis, Nice, France
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29
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Abstract
Many types of cells are able to accurately sense shallow gradients of chemicals across their diameters, allowing the cells to move toward or away from chemical sources. This chemotactic ability relies on the remarkable capacity of cells to infer gradients from particles randomly arriving at cell-surface receptors by diffusion. Whereas the physical limits of concentration sensing by cells have been explored, there is no theory for the physical limits of gradient sensing. Here, we derive such a theory, using as models a perfectly absorbing sphere and a perfectly monitoring sphere, which, respectively, infer gradients from the absorbed surface particle density or the positions of freely diffusing particles inside a spherical volume. We find that the perfectly absorbing sphere is superior to the perfectly monitoring sphere, both for concentration and gradient sensing, because previously observed particles are never remeasured. The superiority of the absorbing sphere helps explain the presence at the surfaces of cells of signal-degrading enzymes, such as PDE for cAMP in Dictyostelium discoideum (Dicty) and BAR1 for mating factor alpha in Saccharomyces cerevisiae (budding yeast). Quantitatively, our theory compares favorably with recent measurements of Dicty moving up a cAMP gradient, suggesting these cells operate near the physical limits of gradient detection.
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30
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Strickfaden SC, Pryciak PM. Distinct roles for two Galpha-Gbeta interfaces in cell polarity control by a yeast heterotrimeric G protein. Mol Biol Cell 2007; 19:181-97. [PMID: 17978098 DOI: 10.1091/mbc.e07-04-0385] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Saccharomyces cerevisiae mating pheromones trigger dissociation of a heterotrimeric G protein (Galphabetagamma) into Galpha-guanosine triphosphate (GTP) and Gbetagamma. The Gbetagamma dimer regulates both mitogen-activated protein (MAP) kinase cascade signaling and cell polarization. Here, by independently activating the MAP kinase pathway, we studied the polarity role of Gbetagamma in isolation from its signaling role. MAP kinase signaling alone could induce cell asymmetry but not directional growth. Surprisingly, active Gbetagamma, either alone or with Galpha-GTP, could not organize a persistent polarization axis. Instead, following pheromone gradients (chemotropism) or directional growth without pheromone gradients (de novo polarization) required an intact receptor-Galphabetagamma module and GTP hydrolysis by Galpha. Our results indicate that chemoattractant-induced cell polarization requires continuous receptor-Galphabetagamma communication but not modulation of MAP kinase signaling. To explore regulation of Gbetagamma by Galpha, we mutated Gbeta residues in two structurally distinct Galpha-Gbeta binding interfaces. Polarity control was disrupted only by mutations in the N-terminal interface, and not the Switch interface. Incorporation of these mutations into a Gbeta-Galpha fusion protein, which enforces subunit proximity, revealed that Switch interface dissociation regulates signaling, whereas the N-terminal interface may govern receptor-Galphabetagamma coupling. These findings raise the possibility that the Galphabetagamma heterotrimer can function in a partially dissociated state, tethered by the N-terminal interface.
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Affiliation(s)
- Shelly C Strickfaden
- Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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31
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Wagner A. From bit to it: how a complex metabolic network transforms information into living matter. BMC SYSTEMS BIOLOGY 2007; 1:33. [PMID: 17663759 PMCID: PMC1994685 DOI: 10.1186/1752-0509-1-33] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 07/30/2007] [Indexed: 11/25/2022]
Abstract
BACKGROUND Organisms live and die by the amount of information they acquire about their environment. The systems analysis of complex metabolic networks allows us to ask how such information translates into fitness. A metabolic network transforms nutrients into biomass. The better it uses information on available nutrient availability, the faster it will allow a cell to divide. RESULTS I here use metabolic flux balance analysis to show that the accuracy I (in bits) with which a yeast cell can sense a limiting nutrient's availability relates logarithmically to fitness as indicated by biomass yield and cell division rate. For microbes like yeast, natural selection can resolve fitness differences of genetic variants smaller than 10-6, meaning that cells would need to estimate nutrient concentrations to very high accuracy (greater than 22 bits) to ensure optimal growth. I argue that such accuracies are not achievable in practice. Natural selection may thus face fundamental limitations in maximizing the information processing capacity of cells. CONCLUSION The analysis of metabolic networks opens a door to understanding cellular biology from a quantitative, information-theoretic perspective.
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Affiliation(s)
- Andreas Wagner
- Department of Biochemistry, University of Zurich, Building Y27, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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32
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Andrews BW, Iglesias PA. An information-theoretic characterization of the optimal gradient sensing response of cells. PLoS Comput Biol 2007; 3:e153. [PMID: 17676949 PMCID: PMC1937015 DOI: 10.1371/journal.pcbi.0030153] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 06/18/2007] [Indexed: 12/27/2022] Open
Abstract
Many cellular systems rely on the ability to interpret spatial heterogeneities in chemoattractant concentration to direct cell migration. The accuracy of this process is limited by stochastic fluctuations in the concentration of the external signal and in the internal signaling components. Here we use information theory to determine the optimal scheme to detect the location of an external chemoattractant source in the presence of noise. We compute the minimum amount of mutual information needed between the chemoattractant gradient and the internal signal to achieve a prespecified chemotactic accuracy. We show that more accurate chemotaxis requires greater mutual information. We also demonstrate that a priori information can improve chemotaxis efficiency. We compare the optimal signaling schemes with existing experimental measurements and models of eukaryotic gradient sensing. Remarkably, there is good quantitative agreement between the optimal response when no a priori assumption is made about the location of the existing source, and the observed experimental response of unpolarized Dictyostelium discoideum cells. In contrast, the measured response of polarized D. discoideum cells matches closely the optimal scheme, assuming prior knowledge of the external gradient—for example, through prolonged chemotaxis in a given direction. Our results demonstrate that different observed classes of responses in cells (polarized and unpolarized) are optimal under varying information assumptions. For many cell types, the direction of migration is determined in response to spatial differences in the concentration of chemoattractant, a process known as chemotaxis. Precise chemotaxis—that is, motility with low directional distortion—requires that cells make accurate decisions based on the stochastic fluctuations inherent in cell-surface receptor occupancy. Here, we use rate distortion theory, a branch of information theory, to determine chemotaxis strategies for cells based on this imperfect information about their environment. In engineering, rate distortion theory provides the information processing capabilities required to achieve a desired accuracy. We demonstrate that more accurate chemotaxis requires greater information. We also show that a priori information can improve chemotaxis efficiency. We compare the optimal signaling schemes to existing experimental measurements and models of eukaryotic gradient sensing and demonstrate that different observed types of cellular responses (polarized and unpolarized) are optimal under varying information assumptions. Our results also highlight the constraints that noise places on the performance of cellular systems.
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Affiliation(s)
- Burton W Andrews
- Department of Electrical and Computer Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Pablo A Iglesias
- Department of Electrical and Computer Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail:
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Song L, Nadkarni SM, Bödeker HU, Beta C, Bae A, Franck C, Rappel WJ, Loomis WF, Bodenschatz E. Dictyostelium discoideum chemotaxis: threshold for directed motion. Eur J Cell Biol 2006; 85:981-9. [PMID: 16529846 DOI: 10.1016/j.ejcb.2006.01.012] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The chemotactic response of Dictyostelium discoideum cells to stationary, linear gradients of cyclic adenosine 3',5'-monophosphate (cAMP) was studied using microfluidic devices. In shallow gradients of less than 10(-3) nM/microm, the cells showed no directional response and exhibited a constant basal motility. In steeper gradients, cells moved up the gradient on average. The chemotactic speed and the motility increased with increasing steepness up to a plateau at around 10(-1) nM/microm. In very steep gradients, above 10 nM/microm, the cells lost directionality and the motility returned to the sub-threshold level. In the regime of optimal response the difference in receptor occupancy at the front and back of the cell is estimated to be only about 100 molecules.
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Affiliation(s)
- Loling Song
- Laboratory of Atomic and Solid State Physics, Department of Physics, Cornell University, Ithaca, NY 14853, USA
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Govorunova EG, Sineshchekov OA. Chemotaxis in the green flagellate alga Chlamydomonas. BIOCHEMISTRY (MOSCOW) 2006; 70:717-25. [PMID: 16097934 DOI: 10.1007/s10541-005-0176-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Behavior of the green flagellate alga Chlamydomonas changes in response to a number of chemical stimuli. Specific sensitivity of the cells to different substances might appear only at certain stages of the life cycle. The heterogamous species C. allensworthii demonstrates chemotaxis of male gametes towards pheromones excreted by female gametes. In C. reinhardtii chemotaxis towards tryptone occurs only in gametes, whereas chemotaxis towards ammonium, on the contrary, only in vegetative cells. Chemotaxis to different chemical stimuli might involve different mechanisms of reception and signal transduction, elucidation of which has only recently begun. Indirect evidences show that the cells likely respond to tryptone with changes in the membrane electrical conductance. The recently completed project of sequencing the whole nuclear genome of C. reinhardtii provides the basis for future identification of molecular elements of the chemosensory cascade in this alga.
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Affiliation(s)
- E G Govorunova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
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35
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Hu Z, Potthoff B, Hollenberg CP, Ramezani-Rad M. Mdy2, a ubiquitin-like (UBL)-domain protein, is required for efficient mating in Saccharomyces cerevisiae. J Cell Sci 2006; 119:326-38. [PMID: 16390866 DOI: 10.1242/jcs.02754] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
MDY2, a gene required for efficient mating of the yeast Saccharomyces cerevisiae, was characterized in this study. The gene encodes a protein of 212 amino acids, which contains a ubiquitin-like (UBL) domain (residues 74-149). Deletion of MDY2 is associated with a five- to sevenfold reduction in mating efficiency, mainly due to defects in nuclear migration and karyogamy at the prezygotic stage. However, prior to mating pair fusion, shmoo formation is reduced by 30%, with a concomitant failure to form mating pairs. Strikingly, migration of the nucleus into the shmoo tip is also delayed or fails to occur. In addition, we show that in mdy2 mutants, microtubule bundles, as well as the microtubule end-binding protein Kar9, fail to localize properly to the shmoo tip, suggesting that the nuclear migration defect could be due to aberrant localization of Kar9. Pheromone signal transduction (as measured by FUS1 induction by α-factor) is not affected in mdy2Δ mutants and mitosis is also normal in these cells. MDY2 is not induced by mating pheromone. In vegetatively growing cells, GFP-Mdy2 is localized in the nucleus, and remains nuclear after exposure of cells to α-factor. His-tagged Mdy2 shows no evidence of the C-terminal processing typical of ubiquitin, and also localizes to the nucleus. Thus MDY2 is a novel gene, whose product plays a role in shmoo formation and in nuclear migration in the pre-zygote, possibly by interacting with other UBL-type proteins that possess ubiquitin association (UBA) domains.
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Affiliation(s)
- Zheng Hu
- Institut für Mikrobiologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, Geb. 26.12, 40225 Düsseldorf, Germany
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Tsitolovsky LE. Protection from neuronal damage evoked by a motivational excitation is a driving force of intentional actions. ACTA ACUST UNITED AC 2005; 49:566-94. [PMID: 16269320 DOI: 10.1016/j.brainresrev.2005.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2004] [Revised: 12/16/2004] [Accepted: 02/25/2005] [Indexed: 01/13/2023]
Abstract
Motivation may be understood as an organism's subjective attitude to its current physiological state, which somehow modulates generation of actions until the organism attains an optimal state. How does this subjective attitude arise and how does it modulate generation of actions? Diverse lines of evidence suggest that elemental motivational states (hunger, thirst, fear, drug-dependence, etc.) arise as the result of metabolic disturbances and are related to transient injury, while rewards (food, water, avoidance, drugs, etc.) are associated with the recovery of specific neurons. Just as motivation and the very life of an organism depend on homeostasis, i.e., maintenance of optimum performance, so a neuron's behavior depends on neuronal (i.e., ion) homeostasis. During motivational excitation, the conventional properties of a neuron, such as maintenance of membrane potential and spike generation, are disturbed. Instrumental actions may originate as a consequence of the compensational recovery of neuronal excitability after the excitotoxic damage induced by a motivation. When the extent of neuronal actions is proportional to a metabolic disturbance, the neuron theoretically may choose a beneficial behavior even, if at each instant, it acts by chance. Homeostasis supposedly may be directed to anticipating compensation of the factors that lead to a disturbance of the homeostasis and, as a result, participates in the plasticity of motivational behavior. Following this line of thought, I suggest that voluntary actions arise from the interaction between endogenous compensational mechanisms and excitotoxic damage of specific neurons, and thus anticipate the exogenous compensation evoked by a reward.
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Affiliation(s)
- Lev E Tsitolovsky
- Department of Life Science, Bar-Ilan University, Ramat-Gan 52900, Israel.
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Qi M, Elion EA. Formin-induced actin cables are required for polarized recruitment of the Ste5 scaffold and high level activation of MAPK Fus3. J Cell Sci 2005; 118:2837-48. [PMID: 15961405 DOI: 10.1242/jcs.02418] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Little is known about how a mitogen-activated protein kinase (MAPK) cascade is targeted to specific sites at the plasma membrane during receptor stimulation. In budding yeast, the Ste5 scaffold is recruited to a receptor-coupled G protein during mating pheromone stimulation, allowing the tethered MAPK cascade to be activated by Ste20, a Cdc42-anchored kinase. Here we show that stable recruitment of Ste5 at cortical sites requires the formin Bni1, Bni1-induced actin cables, Rho1 and Myo2. Rho1 directs recruitment of Bni1 via the Rho-binding domain, and Bni1 mediates localization of Ste5 through actin cables and Myo2, which co-immunoprecipitates with Ste5 during receptor stimulation. Bni1 is also required for polarized recruitment and full activation of MAPK Fus3, which must bind Ste5 to be activated, and polarized recruitment of Cdc24, the guanine exchange factor that binds Ste5 and promotes its recruitment to the G protein. In contrast, Bni1 is not important for activation of MAPK Kss1, which can be activated while not bound to Ste5 and does not accumulate at cortical sites. These findings reveal that Bni1 mediates the formation of a Ste5 scaffold/Fus3 MAPK signaling complex at polarized sites, and suggests that a pool of Ste5 may translocate along formin-induced actin cables to the cell cortex.
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Affiliation(s)
- Maosong Qi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, MA 02115, USA
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Lawrence PA, Casal J, Struhl G. Cell interactions and planar polarity in the abdominal epidermis ofDrosophila. Development 2004; 131:4651-64. [PMID: 15329345 DOI: 10.1242/dev.01351] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The integument of the Drosophila adult abdomen bears oriented hairs and bristles that indicate the planar polarity of the epidermal cells. We study four polarity genes, frizzled (fz), prickle (pk), Van gogh/strabismus(Vang/stbm) and starry night/flamingo (stan/fmi),and note what happens when these genes are either removed or overexpressed in clones of cells. The edges of the clones are interfaces between cells that carry different amounts of gene products, interfaces that can cause reversals of planar polarity in the clone and wild-type cells outside them. To explain,we present a model that builds on our earlier picture of a gradient of X, the vector of which specifies planar polarity and depends on two cadherin proteins, Dachsous and Fat. We conjecture that the X gradient is read out,cell by cell, as a scalar value of Fz activity, and that Pk acts in this process, possibly to determine the sign of the Fz activity gradient.We discuss evidence that cells can compare their scalar readout of the level of X with that of their neighbours and can set their own readout towards an average of those. This averaging, when it occurs near the edges of clones,changes the scalar response of cells inside and outside the clones, leading to new vectors that change polarity. The results argue that Stan must be present in both cells being compared and acts as a conduit between them for the transfer of information. And also that Vang assists in the receipt of this information. The comparison between neighbours is crucial, because it gives the vector that orients hairs – these point towards the neighbour cell that has the lowest level of Fz activity.Recently, it has been shown that, for a limited period shortly before hair outgrowth in the wing, the four proteins we study, as well as others, become asymmetrically localised in the cell membrane, and this process is thought to be instrumental in the acquisition of cell polarity. However, some results do not fit with this view – we suggest that these localisations may be more a consequence than a cause of planar polarity.
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Affiliation(s)
- Peter A Lawrence
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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Matheos D, Metodiev M, Muller E, Stone D, Rose MD. Pheromone-induced polarization is dependent on the Fus3p MAPK acting through the formin Bni1p. ACTA ACUST UNITED AC 2004; 165:99-109. [PMID: 15067022 PMCID: PMC2172092 DOI: 10.1083/jcb.200309089] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
During mating, budding yeast cells reorient growth toward the highest concentration of pheromone. Bni1p, a formin homologue, is required for this polarized growth by facilitating cortical actin cable assembly. Fus3p, a pheromone-activated MAP kinase, is required for pheromone signaling and cell fusion. We show that Fus3p phosphorylates Bni1p in vitro, and phosphorylation of Bni1p in vivo during the pheromone response is dependent on Fus3p. fus3 mutants exhibited multiple phenotypes similar to bni1 mutants, including defects in actin and cell polarization, as well as Kar9p and cytoplasmic microtubule localization. Disruption of the interaction between Fus3p and the receptor-associated Gα subunit caused similar mutant phenotypes. After pheromone treatment, Bni1p-GFP and Spa2p failed to localize to the cortex of fus3 mutants, and cell wall growth became completely unpolarized. Bni1p overexpression suppressed the actin assembly, cell polarization, and cell fusion defects. These data suggest a model wherein activated Fus3p is recruited back to the cortex, where it activates Bni1p to promote polarization and cell fusion.
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Affiliation(s)
- Dina Matheos
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, USA
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40
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Wiget P, Shimada Y, Butty AC, Bi E, Peter M. Site-specific regulation of the GEF Cdc24p by the scaffold protein Far1p during yeast mating. EMBO J 2004; 23:1063-74. [PMID: 14988725 PMCID: PMC380978 DOI: 10.1038/sj.emboj.7600123] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2003] [Accepted: 01/19/2004] [Indexed: 11/09/2022] Open
Abstract
Receptor-mediated cell polarization via heterotrimeric G-proteins induces cytoskeletal rearrangements in a variety of organisms. In yeast, Far1p is required for orienting cell growth towards the mating partner by linking activated Gbetagamma to the guanine-nucleotide exchange factor (GEF) Cdc24p, which activates the Rho-type GTPase Cdc42p. Here we investigated the role of Far1p in the regulation of Cdc24p in vivo. Using time-lapse microscopy of mating cells and artificial membrane targeting of Far1p, we show that Far1p is necessary and sufficient to recruit Cdc24p to the plasma membrane. Wild-type Far1p contains a PH-like domain, which is required for its membrane localization in vivo. Interestingly, expression of membrane-targeted Far1p causes toxicity, most likely by activating Cdc42p uniformly at the cell cortex. The ability of full-length Far1p to function as an activator of Cdc24p in vivo requires its interaction with Cdc24p and Gbetagamma. Our results imply that Gbetagamma not only targets Far1p to the correct site but may also trigger a conformational change in Far1p that is required for its ability to activate Cdc24p in vivo.
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Affiliation(s)
- Philippe Wiget
- Swiss Federal Institute of Technology Zurich (ETH), Institute of Biochemistry, Zurich, Switzerland
- Swiss Institute for Experimental Cancer Research (ISREC), Chemin des Boveresses 155, Switzerland
| | - Yukiko Shimada
- Swiss Institute for Experimental Cancer Research (ISREC), Chemin des Boveresses 155, Switzerland
| | - Anne-Christine Butty
- Swiss Institute for Experimental Cancer Research (ISREC), Chemin des Boveresses 155, Switzerland
| | - Efrei Bi
- Department of Cell and Developmental Biology, University of Pennsylvania, School of Medicine, Philadelphia, PA, USA
| | - Matthias Peter
- Swiss Federal Institute of Technology Zurich (ETH), Institute of Biochemistry, Zurich, Switzerland
- Swiss Institute for Experimental Cancer Research (ISREC), Chemin des Boveresses 155, Switzerland
- Swiss Federal Institute of Technology Zurich (ETH), Institute of Biochemistry, ETH Hoenggerberg HPM G 6.2, CH-8093 Zurich, Switzerland. Tel.: +41 1 633 6586; Fax: +41 1 633 1228; E-mail:
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Shimada Y, Wiget P, Gulli MP, Bi E, Peter M. The nucleotide exchange factor Cdc24p may be regulated by auto-inhibition. EMBO J 2004; 23:1051-62. [PMID: 14988726 PMCID: PMC380979 DOI: 10.1038/sj.emboj.7600124] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2003] [Accepted: 01/19/2004] [Indexed: 11/09/2022] Open
Abstract
Site-specific activation of the Rho-type GTPase Cdc42p by its guanine-nucleotide exchange factor (GEF) Cdc24p is critical for the establishment of cell polarity. Here we show that binding of Cdc24p to the small GTPase Rsr1p/Bud1p is required for its recruitment to the incipient bud site. Rsr1p/Bud1p binds to the CH-domain of Cdc24p, which is essential for its function in vivo. We have identified a cdc24-mutant allele, which is specifically defective for bud-site selection. Our results suggest that Cdc24p is auto-inhibited by an intramolecular interaction with its carboxy-terminal PB1-domain. Rsr1p/Bud1p appears to activate the GEF activity of Cdc24p in vivo, possibly by triggering a conformational change that dissociates the PB1-domain from its intramolecular binding site. Genetic experiments suggest that Bem1p functions as a positive regulator of Cdc24p by binding to the PB1-domain of Cdc24p, thereby preventing its re-binding to the intramolecular inhibitory site. Taken together, our results support a two-step molecular mechanism for the site-specific activation of Cdc24p, which involves Rsr1p/Bud1p and the adaptor protein Bem1p.
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Affiliation(s)
- Yukiko Shimada
- Swiss Institute for Experimental Cancer Research (ISREC), Epalinges/VD, Switzerland
| | - Philippe Wiget
- Swiss Institute for Experimental Cancer Research (ISREC), Epalinges/VD, Switzerland
- Swiss Federal Institute of Technology Zurich (ETH), Institute of Biochemistry, Zurich, Switzerland
| | - Marie-Pierre Gulli
- Swiss Institute for Experimental Cancer Research (ISREC), Epalinges/VD, Switzerland
| | - Efrei Bi
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthias Peter
- Swiss Federal Institute of Technology Zurich (ETH), Institute of Biochemistry, Zurich, Switzerland
- Swiss Federal Institute of Technology Zurich (ETH), Institute of Biochemistry, ETH Hoenggerberg HPM G 6.2, 8093 Zurich, Switzerland. Tel.: +41 1 632 3134; Fax: +41 1 632 1269; E-mail:
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Mackin NA, Sousou TJ, Erdman SE. The PXL1 gene of Saccharomyces cerevisiae encodes a paxillin-like protein functioning in polarized cell growth. Mol Biol Cell 2004; 15:1904-17. [PMID: 14767053 PMCID: PMC379286 DOI: 10.1091/mbc.e04-01-0004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The Saccharomyces cerevisiae open reading frame YKR090w encodes a predicted protein displaying similarity in organization to paxillin, a scaffolding protein that organizes signaling and actin cytoskeletal regulating activities in many higher eucaryotic cell types. We found that YKR090w functions in a manner analogous to paxillin as a mediator of polarized cell growth; thus, we have named this gene PXL1 (Paxillin-like protein 1). Analyses of pxl1Delta strains show that PXL1 is required for the selection and maintenance of polarized growth sites during vegetative growth and mating. Genetic analyses of strains lacking both PXL1 and the Rho GAP BEM2 demonstrate that such cells display pronounced growth defects in response to different conditions causing Rho1 pathway activation. PXL1 also displays genetic interactions with the Rho1 effector FKS1. Pxl1p may therefore function as a modulator of Rho-GTPase signaling. A GFP::Pxl1 fusion protein localizes to sites of polarized cell growth. Experiments mapping the localization determinants of Pxl1p demonstrate the existence of localization mechanisms conserved between paxillin and Pxl1p and indicate an evolutionarily ancient and conserved role for LIM domain proteins in acting to modulate cell signaling and cytoskeletal organization during polarized growth.
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Affiliation(s)
- Nancy A Mackin
- Department of Biology, Syracuse University, Syracuse, New York 13244, USA
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Wei SH, Parker I, Miller MJ, Cahalan MD. A stochastic view of lymphocyte motility and trafficking within the lymph node. Immunol Rev 2003; 195:136-59. [PMID: 12969316 DOI: 10.1034/j.1600-065x.2003.00076.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Two-photon microscopy is providing literal insight into the cellular dynamics of lymphoid organs and, guided by analysis of three-dimensional images, into mechanisms that underlie cell migration and antigen recognition in vivo. This review describes lymphocyte motility and antigen recognition in the native tissue environment and compares these results with a much more extensive literature on lymphocyte motility, signaling, and chemotaxis in vitro. We discuss the in vitro literature on dynamic aspects of lymphocyte motility, chemotaxis, and the response to antigen and present the view that random migration of lymphocytes may drive a stochastic mechanism of antigen recognition in lymphoid organs, rather than being guided by chemotaxis.
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Affiliation(s)
- Sindy H Wei
- Departments of Physiology and Biophysics, University of California, Irvine, CA 92697-4561, USA
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Affiliation(s)
- Roland Wedlich-Soldner
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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Wedlich-Soldner R, Altschuler S, Wu L, Li R. Spontaneous cell polarization through actomyosin-based delivery of the Cdc42 GTPase. Science 2003; 299:1231-5. [PMID: 12560471 DOI: 10.1126/science.1080944] [Citation(s) in RCA: 301] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Cell polarization can occur in the absence of any spatial cues. To investigate the mechanism of spontaneous cell polarization, we used an assay in yeast where expression of an activated form of Cdc42, a Rho-type guanosine triphosphatase (GTPase) required for cell polarization, could generate cell polarity without any recourse to a preestablished physical cue. The polar distribution of Cdc42 in this assay required targeted secretion directed by the actin cytoskeleton. A mathematical simulation showed that a stable polarity axis could be generated through a positive feedback loop in which a stochastic increase in the local concentration of activated Cdc42 on the plasma membrane enhanced the probability of actin polymerization and increased the probability of further Cdc42 accumulation to that site.
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Korohoda W, Madeja Z, Sroka J. Diverse chemotactic responses of Dictyostelium discoideum amoebae in the developing (temporal) and stationary (spatial) concentration gradients of folic acid, cAMP, Ca(2+) and Mg(2+). CELL MOTILITY AND THE CYTOSKELETON 2002; 53:1-25. [PMID: 12211112 DOI: 10.1002/cm.10052] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The responses of Dictyostelium discoideum amoebae to developing (temporal) and stationary (spatial) gradients of folic acid, cAMP, Ca(2+), and Mg(2+) were studied using the methods of computer-aided image analysis. The results presented demonstrate that the new type of experimental chambers used for the observation of single cells moving within the investigated gradients of chemoattractants permit time lapse recording of single amoebae and determination of the trajectories of moving cells. It was found that, besides folic acid and cAMP (natural chemoattractants for Dictyostelium discoideum amoebae), also extracellular Ca(2+) and Mg(2+) are potent inducers of these cells' chemotaxis, and the amoebae of D. discoideum can respond to various chemoattractants differently. In the positively developing gradients of folic acid, cAMP, Ca(2+), and Mg(2+) oriented locomotion of amoebae directed towards the higher concentration of the tested chemoattractants was observed. However, in the negatively developing (temporal) and stationary linear (spatial) gradients, the univocal chemotaxis of amoebae was recorded only in the case of the Mg(2+) concentration gradient. This demonstrates that amoebae can respond to both developing and stationary gradients, depending upon the nature of the chemoattractant. We also investigated the effects of chosen inhibitors of signalling pathways upon chemotaxis of D. discoideum amoebae in the positively developing (temporal) gradients of tested chemoattractants. Verapamil was found to abolish the chemotaxis of amoebae only in the Ca(2+) gradients. Pertussis toxin suppressed the chemotactic response of cells in the gradients of folic acid and cAMP but did not prevent chemotaxis in those of Ca(2+) and Mg(2+), while quinacrine inhibited chemotaxis in the gradients of folic acid, cAMP, and Ca(2+) but only slightly affected chemotaxis in the Mg(2+) gradient. None of the tested inhibitors causes inhibition of cell random movement, when applied in isotropic solution. Also EDTA and EGTA up to 50 mM concentration did not inhibit locomotion of amoebae in control isotropic solutions.
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Affiliation(s)
- Włodzimierz Korohoda
- Department of Cell Biology, The J. Zurzycki Institute of Molecular Biology and Biotechnology, Jagiellonian University, Kraków, Poland.
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Butty AC, Perrinjaquet N, Petit A, Jaquenoud M, Segall JE, Hofmann K, Zwahlen C, Peter M. A positive feedback loop stabilizes the guanine-nucleotide exchange factor Cdc24 at sites of polarization. EMBO J 2002; 21:1565-76. [PMID: 11927541 PMCID: PMC125953 DOI: 10.1093/emboj/21.7.1565] [Citation(s) in RCA: 171] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
In Saccharomyces cerevisiae, activation of Cdc42 by its guanine-nucleotide exchange factor Cdc24 triggers polarization of the actin cytoskeleton at bud emergence and in response to mating pheromones. The adaptor protein Bem1 localizes to sites of polarized growth where it interacts with Cdc42, Cdc24 and the PAK-like kinase Cla4. We have isolated Bem1 mutants (Bem1-m), which are specifically defective for binding to Cdc24. The mutations map within the conserved PB1 domain, which is necessary and sufficient to interact with the octicos peptide repeat (OPR) motif of Cdc24. Although Bem1-m mutant proteins localize normally, bem1-m cells are unable to maintain Cdc24 at sites of polarized growth. As a consequence, they are defective for apical bud growth and the formation of mating projections. Localization of Bem1 to the incipient bud site requires activated Cdc42, and conversely, expression of Cdc42-GTP is sufficient to accumulate Bem1 at the plasma membrane. Thus, our results suggest that Bem1 functions in a positive feedback loop: local activation of Cdc24 produces Cdc42-GTP, which recruits Bem1. In turn, Bem1 stabilizes Cdc24 at the site of polarization, leading to apical growth.
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Affiliation(s)
| | | | - Audrey Petit
- Swiss Institute for Experimental Cancer Research, Chemin des Boveresses 155, CH-1066 Epalinges/VD,
Institute of Organic Chemistry, University of Lausanne, CH-1015 Lausanne, Switzerland, Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA and Bioinformatics Group, Memorec Stoffel GmbH, Stöckheimerweg 1, D-50829 Köln, Germany Corresponding author e-mail:
| | | | - Jeffrey E. Segall
- Swiss Institute for Experimental Cancer Research, Chemin des Boveresses 155, CH-1066 Epalinges/VD,
Institute of Organic Chemistry, University of Lausanne, CH-1015 Lausanne, Switzerland, Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA and Bioinformatics Group, Memorec Stoffel GmbH, Stöckheimerweg 1, D-50829 Köln, Germany Corresponding author e-mail:
| | - Kay Hofmann
- Swiss Institute for Experimental Cancer Research, Chemin des Boveresses 155, CH-1066 Epalinges/VD,
Institute of Organic Chemistry, University of Lausanne, CH-1015 Lausanne, Switzerland, Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA and Bioinformatics Group, Memorec Stoffel GmbH, Stöckheimerweg 1, D-50829 Köln, Germany Corresponding author e-mail:
| | - Catherine Zwahlen
- Swiss Institute for Experimental Cancer Research, Chemin des Boveresses 155, CH-1066 Epalinges/VD,
Institute of Organic Chemistry, University of Lausanne, CH-1015 Lausanne, Switzerland, Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA and Bioinformatics Group, Memorec Stoffel GmbH, Stöckheimerweg 1, D-50829 Köln, Germany Corresponding author e-mail:
| | - Matthias Peter
- Swiss Institute for Experimental Cancer Research, Chemin des Boveresses 155, CH-1066 Epalinges/VD,
Institute of Organic Chemistry, University of Lausanne, CH-1015 Lausanne, Switzerland, Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA and Bioinformatics Group, Memorec Stoffel GmbH, Stöckheimerweg 1, D-50829 Köln, Germany Corresponding author e-mail:
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48
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Levchenko A, Iglesias PA. Models of eukaryotic gradient sensing: application to chemotaxis of amoebae and neutrophils. Biophys J 2002; 82:50-63. [PMID: 11751295 PMCID: PMC1302448 DOI: 10.1016/s0006-3495(02)75373-3] [Citation(s) in RCA: 348] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Eukaryotic cells can detect shallow gradients of chemoattractants with exquisite precision and respond quickly to changes in the gradient steepness and direction. Here, we describe a set of models explaining both adaptation to uniform increases in chemoattractant and persistent signaling in response to gradients. We demonstrate that one of these models can be mapped directly onto the biochemical signal-transduction pathways underlying gradient sensing in amoebae and neutrophils. According to this scheme, a locally acting activator (PI3-kinase) and a globally acting inactivator (PTEN or a similar phosphatase) are coordinately controlled by the G-protein activation. This signaling system adapts perfectly to spatially homogeneous changes in the chemoattractant. In chemoattractant gradients, an imbalance between the action of the activator and the inactivator results in a spatially oriented persistent signaling, amplified by a substrate supply-based positive feedback acting through small G-proteins. The amplification is activated only in a continuous presence of the external signal gradient, thus providing the mechanism for sensitivity to gradient alterations. Finally, based on this mapping, we make predictions concerning the dynamics of signaling. We propose that the underlying principles of perfect adaptation and substrate supply-based positive feedback will be found in the sensory systems of other chemotactic cell types.
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Affiliation(s)
- Andre Levchenko
- Divisions of Biology, California Institute of Technology, Pasadena, California 91125, USA
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49
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Abstract
An emerging theme of mitogen-activated protein kinase (MAPK) cascades is that they form molecular assemblies within cells; the spatial organization of which is provided by scaffold proteins. Yeast Ste5p was the first MAPK cascade scaffold to be described. Early work demonstrated that Ste5p selectively tethers the MAPKKK, MAPKK and MAPK of the yeast mating pathway and is essential for efficient activation of the MAPK by the pheromone stimulus. Recent work indicates that Ste5p is not a passive scaffold but plays a direct role in the activation of the MAPKKK by a heterotrimeric G protein and PAK-type kinase. This activation event requires the formation of an active Ste5p oligomer and proper recruitment of Ste5p to a Gβγ dimer at the submembrane of the cell cortex, which suggests that Ste5p forms a stable Ste5p signalosome linked to a G protein. Additional studies underscore the importance of regulated localization of Ste5p to the plasma membrane and have revealed nuclear shuttling as a regulatory device that controls the access of Ste5p to the plasma membrane. A model that links Ste5p oligomerization with stable membrane recruitment is presented. In this model, pathway activation is coordinated with the conversion of a less active closed form of Ste5 containing a protected RING-H2 domain into an active Ste5p dimer that can bind to Gβγ and form a multimeric scaffold lattice upon which the MAPK cascade can assemble.
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Affiliation(s)
- E A Elion
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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50
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Abstract
Haploid cells of the budding yeast Saccharomyces cerevisiae respond to mating pheromones by arresting their cell-division cycle in G1 and differentiating into a cell type capable of locating and fusing with mating partners. Yeast cells undergo chemotactic cell surface growth when pheromones are present above a threshold level for morphogenesis; however, the morphogenetic responses of cells to levels of pheromone below this threshold have not been systematically explored. Here we show that MATa haploid cells exposed to low levels of the alpha-factor mating pheromone undergo a novel cellular response: cells modulate their division patterns and cell shape, forming colonies composed of filamentous chains of cells. Time-lapse analysis of filament formation shows that its dynamics are distinct from that of pseudohyphal growth; during pheromone-induced filament formation, daughter cells are delayed relative to mother cells with respect to the timing of bud emergence. Filament formation requires the RSR1(BUD1), BUD8, SLK1/BCK1, and SPA2 genes and many elements of the STE11/STE7 MAP kinase pathway; this response is also independent of FAR1, a gene involved in orienting cell polarization during the mating response. We suggest that mating yeast cells undergo a complex response to low levels of pheromone that may enhance the ability of cells to search for mating partners through the modification of cell shape and alteration of cell-division patterns.
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Affiliation(s)
- S Erdman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
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