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Magliozzi JO, Rands TJ, Shrestha S, Simke WC, Hase NE, Juanes MA, Kelley JB, Goode BL. The roles of yeast formins and their regulators Bud6 and Bil2 in the pheromone response. Mol Biol Cell 2024; 35:ar85. [PMID: 38656798 PMCID: PMC11238086 DOI: 10.1091/mbc.e23-11-0459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
In response to pheromone Saccharomyces cerevisiae extend a mating projection. This process depends on the formation of polarized actin cables which direct secretion to the mating tip and translocate the nucleus for karyogamy. Here, we demonstrate that proper mating projection formation requires the formin Bni1, as well as the actin nucleation promoting activities of Bud6, but not the formin Bnr1. Further, Bni1 is required for pheromone gradient tracking. Our work also reveals unexpected new functions for Bil2 in the pheromone response. Previously we identified Bil2 as a direct inhibitor of Bnr1 during vegetative cell growth. Here, we show that Bil2 has Bnr1-independent functions in spatially focusing Bni1-GFP at mating projection tips, and in vitro Bil2 and its binding partner Bud6 organize Bni1 into clusters that nucleate actin assembly. bil2∆ cells also display entangled Bni1-generated actin cable arrays and defects in secretory vesicle transport and nuclear positioning. At low pheromone concentrations, bil2∆ cells are delayed in establishing a polarity axis, and at high concentrations they prematurely form a second and a third mating projection. Together, these results suggest that Bil2 promotes the proper formation and timing of mating projections by organizing Bni1 and maintaining a persistent axis of polarized growth.
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Affiliation(s)
| | - Thomas J Rands
- Department of Biology, Brandeis University, Waltham, MA 02454
| | - Sudati Shrestha
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469
| | - William C Simke
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469
| | - Niklas E Hase
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469
| | - M Angeles Juanes
- Department of Biology, Brandeis University, Waltham, MA 02454
- Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain
| | - Joshua B Kelley
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469
| | - Bruce L Goode
- Department of Biology, Brandeis University, Waltham, MA 02454
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2
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Srikant S, Gaudet R, Murray AW. Extending the reach of homology by using successive computational filters to find yeast pheromone genes. Curr Biol 2023; 33:4098-4110.e3. [PMID: 37699395 PMCID: PMC10592104 DOI: 10.1016/j.cub.2023.08.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 07/04/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023]
Abstract
The mating of fungi depends on pheromones that mediate communication between two mating types. Most species use short peptides as pheromones, which are either unmodified (e.g., α-factor in Saccharomyces cerevisiae) or C-terminally farnesylated (e.g., a-factor in S. cerevisiae). Peptide pheromones have been found by genetics or biochemistry in a small number of fungi, but their short sequences and modest conservation make it impossible to detect homologous sequences in most species. To overcome this problem, we used a four-step computational pipeline to identify candidate a-factor genes in sequenced genomes of the Saccharomycotina, the fungal clade that contains most of the yeasts: we require that candidate genes have a C-terminal prenylation motif, are shorter than 100 amino acids long, and contain a proteolytic-processing motif upstream of the potential mature pheromone sequence and that closely related species contain highly conserved homologs of the potential mature pheromone sequence. Additional manual curation exploits the observation that many species carry more than one a-factor gene, encoding identical or nearly identical pheromones. From 332 Saccharomycotina genomes, we identified strong candidate pheromone genes in 241 genomes, covering 13 clades that are each separated from each other by at least 100 million years, the time required for evolution to remove detectable sequence homology among small pheromone genes. For one small clade, the Yarrowia, we demonstrated that our algorithm found the a-factor genes: deleting all four related genes in the a-mating type of Yarrowia lipolytica prevents mating.
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Affiliation(s)
- Sriram Srikant
- Department of Molecular and Cellular Biology, Harvard University, Oxford Street, Cambridge, MA 02138, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Oxford Street, Cambridge, MA 02138, USA
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard University, Oxford Street, Cambridge, MA 02138, USA.
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3
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Bernoff AJ, Jilkine A, Navarro Hernández A, Lindsay AE. Single-cell directional sensing from just a few receptor binding events. Biophys J 2023; 122:3108-3116. [PMID: 37355773 PMCID: PMC10432224 DOI: 10.1016/j.bpj.2023.06.015] [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: 04/11/2023] [Revised: 06/08/2023] [Accepted: 06/20/2023] [Indexed: 06/26/2023] Open
Abstract
Identifying the directionality of signaling sources from noisy input to membrane receptors is an essential task performed by many cell types. A variety of models have been proposed to explain directional sensing in cells. However, many of these require significant computational and memory capacities for the cell. We propose and analyze a simple mechanism in which a cell adopts the direction associated with the first few membrane binding events. This model yields an accurate angular estimate to the source long before steady state is reached in biologically relevant scenarios. Our proposed mechanism allows for reliable estimates of the directionality of external signals using temporal information and assumes minimal computational capacities of the cell.
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Affiliation(s)
- Andrew J Bernoff
- Department of Mathematics, Harvey Mudd College, Claremont, California
| | - Alexandra Jilkine
- Department of Applied & Computational Mathematics & Statistics, University of Notre Dame, South Bend, Indiana
| | - Adrián Navarro Hernández
- Department of Applied & Computational Mathematics & Statistics, University of Notre Dame, South Bend, Indiana
| | - Alan E Lindsay
- Department of Applied & Computational Mathematics & Statistics, University of Notre Dame, South Bend, Indiana.
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4
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Seike T, Niki H. Pheromone Response and Mating Behavior in Fission Yeast. Microbiol Mol Biol Rev 2022; 86:e0013022. [PMID: 36468849 PMCID: PMC9769774 DOI: 10.1128/mmbr.00130-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Most ascomycete fungi, including the fission yeast Schizosaccharomyces pombe, secrete two peptidyl mating pheromones: C-terminally modified and unmodified peptides. S. pombe has two mating types, plus and minus, which secrete two different pheromones, P-factor (unmodified) and M-factor (modified), respectively. These pheromones are specifically recognized by receptors on the cell surface of cells of opposite mating types, which trigger a pheromone response. Recognition between pheromones and their corresponding receptors is important for mate discrimination; therefore, genetic changes in pheromone or receptor genes affect mate recognition and cause reproductive isolation that limits gene flow between populations. Such genetic variation in recognition via the pheromone/receptor system may drive speciation. Our recent studies reported that two pheromone receptors in S. pombe might have different stringencies in pheromone recognition. In this review, we focus on the molecular mechanism of pheromone response and mating behavior, emphasizing pheromone diversification and its impact on reproductive isolation in S. pombe and closely related fission yeast species. We speculate that the "asymmetric" system might allow flexible adaptation to pheromone mutational changes while maintaining stringent recognition of mating partners. The loss of pheromone activity results in the extinction of an organism's lineage. Therefore, genetic changes in pheromones and their receptors may occur gradually and/or coincidently before speciation. Our findings suggest that the M-factor plays an important role in partner discrimination, whereas P-factor communication allows flexible adaptation to create variations in S. pombe. Our inferences provide new insights into the evolutionary mechanisms underlying pheromone diversification.
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Affiliation(s)
- Taisuke Seike
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Hironori Niki
- Microbial Physiology Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka, Japan
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5
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Jensen ED, Deichmann M, Ma X, Vilandt RU, Schiesaro G, Rojek MB, Lengger B, Eliasson L, Vento JM, Durmusoglu D, Hovmand SP, Al'Abri I, Zhang J, Crook N, Jensen MK. Engineered cell differentiation and sexual reproduction in probiotic and mating yeasts. Nat Commun 2022; 13:6201. [PMID: 36261657 PMCID: PMC9582028 DOI: 10.1038/s41467-022-33961-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 10/10/2022] [Indexed: 12/24/2022] Open
Abstract
G protein-coupled receptors (GPCRs) enable cells to sense environmental cues and are indispensable for coordinating vital processes including quorum sensing, proliferation, and sexual reproduction. GPCRs comprise the largest class of cell surface receptors in eukaryotes, and for more than three decades the pheromone-induced mating pathway in baker's yeast Saccharomyces cerevisiae has served as a model for studying heterologous GPCRs (hGPCRs). Here we report transcriptome profiles following mating pathway activation in native and hGPCR-signaling yeast and use a model-guided approach to correlate gene expression to morphological changes. From this we demonstrate mating between haploid cells armed with hGPCRs and endogenous biosynthesis of their cognate ligands. Furthermore, we devise a ligand-free screening strategy for hGPCR compatibility with the yeast mating pathway and enable hGPCR-signaling in the probiotic yeast Saccharomyces boulardii. Combined, our findings enable new means to study mating, hGPCR-signaling, and cell-cell communication in a model eukaryote and yeast probiotics.
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Affiliation(s)
- Emil D Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark.
| | - Marcus Deichmann
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Xin Ma
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Rikke U Vilandt
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Giovanni Schiesaro
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Marie B Rojek
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Bettina Lengger
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Line Eliasson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Justin M Vento
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Deniz Durmusoglu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Sandie P Hovmand
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Ibrahim Al'Abri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jie Zhang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark.
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6
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Richter F, Bindschedler S, Calonne-Salmon M, Declerck S, Junier P, Stanley CE. Fungi-on-a-Chip: microfluidic platforms for single-cell studies on fungi. FEMS Microbiol Rev 2022; 46:6674677. [PMID: 36001464 PMCID: PMC9779915 DOI: 10.1093/femsre/fuac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 01/07/2023] Open
Abstract
This review highlights new advances in the emerging field of 'Fungi-on-a-Chip' microfluidics for single-cell studies on fungi and discusses several future frontiers, where we envisage microfluidic technology development to be instrumental in aiding our understanding of fungal biology. Fungi, with their enormous diversity, bear essential roles both in nature and our everyday lives. They inhabit a range of ecosystems, such as soil, where they are involved in organic matter degradation and bioremediation processes. More recently, fungi have been recognized as key components of the microbiome in other eukaryotes, such as humans, where they play a fundamental role not only in human pathogenesis, but also likely as commensals. In the food sector, fungi are used either directly or as fermenting agents and are often key players in the biotechnological industry, where they are responsible for the production of both bulk chemicals and antibiotics. Although the macroscopic fruiting bodies are immediately recognizable by most observers, the structure, function, and interactions of fungi with other microbes at the microscopic scale still remain largely hidden. Herein, we shed light on new advances in the emerging field of Fungi-on-a-Chip microfluidic technologies for single-cell studies on fungi. We discuss the development and application of microfluidic tools in the fields of medicine and biotechnology, as well as in-depth biological studies having significance for ecology and general natural processes. Finally, a future perspective is provided, highlighting new frontiers in which microfluidic technology can benefit this field.
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Affiliation(s)
- Felix Richter
- Department of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Saskia Bindschedler
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Maryline Calonne-Salmon
- Laboratory of Mycology, Université catholique de Louvain, Place Croix du Sud 2, B-1348 Louvain-la-Neuve, Belgium
| | - Stéphane Declerck
- Laboratory of Mycology, Université catholique de Louvain, Place Croix du Sud 2, B-1348 Louvain-la-Neuve, Belgium
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Claire E Stanley
- Corresponding author: Department of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, United Kingdom. E-mail:
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7
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Recent Progress in the Development of Droplet-based Microfluidic Technologies for Phenotypic Screening using Cell-cell Interactions. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0081-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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8
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Jacobs KC, Gorman O, Lew DJ. Mechanism of commitment to a mating partner in Saccharomyces cerevisiae. Mol Biol Cell 2022; 33:ar112. [PMID: 35947501 DOI: 10.1091/mbc.e22-02-0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Many cells detect and follow gradients of chemical signals to perform their functions. Yeast cells use gradients of extracellular pheromones to locate mating partners, providing a tractable model to understand how cells decode the spatial information in gradients. To mate, yeast cells must orient polarity toward the mating partner. Polarity sites are mobile, exploring the cell cortex until they reach the proper position, where they stop moving and "commit" to the partner. A simple model to explain commitment posits that a high concentration of pheromone is only detected upon alignment of partner cells' polarity sites, and causes polarity site movement to stop. Here we explore how yeast cells respond to partners that make different amounts of pheromone. Commitment was surprisingly robust to varying pheromone levels, ruling out the simple model. We also tested whether adaptive pathways were responsible for the robustness of commitment, but our results show that cells lacking those pathways were still able to accommodate changes in pheromone. To explain this robustness, we suggest that the steep pheromone gradients near each mating partner's polarity site trap the polarity site in place.
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Affiliation(s)
- Katherine C Jacobs
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708
| | - Olivia Gorman
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708
| | - Daniel J Lew
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708
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9
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Pheromone Guidance of Polarity Site Movement in Yeast. Biomolecules 2022; 12:biom12040502. [PMID: 35454091 PMCID: PMC9027094 DOI: 10.3390/biom12040502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 01/11/2023] Open
Abstract
Cells’ ability to track chemical gradients is integral to many biological phenomena, including fertilization, development, accessing nutrients, and combating infection. Mating of the yeast Saccharomyces cerevisiae provides a tractable model to understand how cells interpret the spatial information in chemical gradients. Mating yeast of the two different mating types secrete distinct peptide pheromones, called a-factor and α-factor, to communicate with potential partners. Spatial gradients of pheromones are decoded to guide mobile polarity sites so that polarity sites in mating partners align towards each other, as a prerequisite for cell-cell fusion and zygote formation. In ascomycetes including S. cerevisiae, one pheromone is prenylated (a-factor) while the other is not (α-factor). The difference in physical properties between the pheromones, combined with associated differences in mechanisms of secretion and extracellular pheromone metabolism, suggested that the pheromones might differ in the spatial information that they convey to potential mating partners. However, as mating appears to be isogamous in this species, it is not clear why any such signaling difference would be advantageous. Here we report assays that directly track movement of the polarity site in each partner as a way to understand the spatial information conveyed by each pheromone. Our findings suggest that both pheromones convey very similar information. We speculate that the different pheromones were advantageous in ancestral species with asymmetric mating systems and may represent an evolutionary vestige in yeasts that mate isogamously.
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10
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11
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Rocha-Gregg B, Huttenlocher A. Signal integration in forward and reverse neutrophil migration: Fundamentals and emerging mechanisms. Curr Opin Cell Biol 2021; 72:124-130. [PMID: 34411839 DOI: 10.1016/j.ceb.2021.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/07/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022]
Abstract
Neutrophils migrate to sites of tissue damage, where they protect the host against pathogens. Often, the cost of these neutrophil defenses is collateral damage to healthy tissues. Thus, the immune system has evolved multiple mechanisms to regulate neutrophil migration. One of these mechanisms is reverse migration - the process whereby neutrophils leave the source of inflammation. In vivo, neutrophils arrive and depart the wound simultaneously - indicating that neutrophils dynamically integrate conflicting signals to engage in forward and reverse migration. This finding is seemingly at odds with the established chemoattractant hierarchy in vitro, which places wound-derived signals at the top. Here we will discuss recent work that has uncovered key players involved in retaining and dispersing neutrophils from wounds. These findings offer the opportunity to integrate established and emerging mechanisms into a holistic model for neutrophil migration in vivo.
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Affiliation(s)
- Briana Rocha-Gregg
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Anna Huttenlocher
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA; Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, USA.
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12
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Ramirez SA, Pablo M, Burk S, Lew DJ, Elston TC. A novel stochastic simulation approach enables exploration of mechanisms for regulating polarity site movement. PLoS Comput Biol 2021; 17:e1008525. [PMID: 34264926 PMCID: PMC8315557 DOI: 10.1371/journal.pcbi.1008525] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 07/27/2021] [Accepted: 06/24/2021] [Indexed: 12/23/2022] Open
Abstract
Cells polarize their movement or growth toward external directional cues in many different contexts. For example, budding yeast cells grow toward potential mating partners in response to pheromone gradients. Directed growth is controlled by polarity factors that assemble into clusters at the cell membrane. The clusters assemble, disassemble, and move between different regions of the membrane before eventually forming a stable polarity site directed toward the pheromone source. Pathways that regulate clustering have been identified but the molecular mechanisms that regulate cluster mobility are not well understood. To gain insight into the contribution of chemical noise to cluster behavior we simulated clustering using the reaction-diffusion master equation (RDME) framework to account for molecular-level fluctuations. RDME simulations are a computationally efficient approximation, but their results can diverge from the underlying microscopic dynamics. We implemented novel concentration-dependent rate constants that improved the accuracy of RDME-based simulations, allowing us to efficiently investigate how cluster dynamics might be regulated. Molecular noise was effective in relocating clusters when the clusters contained low numbers of limiting polarity factors, and when Cdc42, the central polarity regulator, exhibited short dwell times at the polarity site. Cluster stabilization occurred when abundances or binding rates were altered to either lengthen dwell times or increase the number of polarity molecules in the cluster. We validated key results using full 3D particle-based simulations. Understanding the mechanisms cells use to regulate the dynamics of polarity clusters should provide insights into how cells dynamically track external directional cues. Cells localize polarity molecules in a small region of the plasma membrane forming a polarity cluster that directs functions such as migration, reproduction, and growth. Guided by external signals, these clusters move across the membrane allowing cells to reorient growth or motion. The polarity molecules continuously and randomly shuttle between the cluster and the cell cytosol and, as a result, the number and distribution of molecules at the cluster constantly changes. Here we present an improved stochastic simulation algorithm to investigate how such molecular-scale fluctuations induce cluster movement across the cell membrane. Unexpectedly, cluster mobility does not correlate with variations in total molecule abundance within the cluster, but rather with changes in the spatial distribution of molecules that form the cluster. Cluster motion is faster when polarity molecules are scarce and when they shuttle rapidly between the cluster and the cytosol. Our results suggest that cells control cluster mobility by regulating the abundance of polarity molecules and biochemical reactions that affect the time molecules spend at the cluster. We provide insights into how cells harness random molecular behavior to perform functions important for survival, such as detecting the direction of external signals.
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Affiliation(s)
- Samuel A. Ramirez
- Department of Pharmacology and Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (SAR); (TCE)
| | - Michael Pablo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Program in Molecular and Cellular Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sean Burk
- Department of Pharmacology and Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Daniel J. Lew
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, United States of America
| | - Timothy C. Elston
- Department of Pharmacology and Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (SAR); (TCE)
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13
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Abdul-Ganiyu R, Venegas LA, Wang X, Puerner C, Arkowitz RA, Kay BK, Stone DE. Phosphorylated Gβ is a directional cue during yeast gradient tracking. Sci Signal 2021; 14:14/682/eabf4710. [PMID: 33975981 DOI: 10.1126/scisignal.abf4710] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Budding yeast cells interpret shallow pheromone gradients from cells of the opposite mating type, polarize their growth toward the pheromone source, and fuse at the chemotropic growth site. We previously proposed a deterministic, gradient-sensing model that explains how yeast cells switch from the intrinsically positioned default polarity site (DS) to the gradient-aligned chemotropic site (CS) at the plasma membrane. Because phosphorylation of the mating-specific Gβ subunit is thought to be important for this process, we developed a biosensor that bound to phosphorylated but not unphosphorylated Gβ and monitored its spatiotemporal dynamics to test key predictions of our gradient-sensing model. In mating cells, the biosensor colocalized with both Gβ and receptor reporters at the DS and then tracked with them to the CS. The biosensor concentrated on the leading side of the tracking Gβ and receptor peaks and was the first to arrive and stop tracking at the CS. Our data showed that the concentrated localization of phosphorylated Gβ correlated with the tracking direction and final position of the G protein and receptor, consistent with the idea that gradient-regulated phosphorylation and dephosphorylation of Gβ contributes to gradient sensing. Cells expressing a nonphosphorylatable mutant form of Gβ exhibited defects in gradient tracking, orientation toward mating partners, and mating efficiency.
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Affiliation(s)
- Rashida Abdul-Ganiyu
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Leon A Venegas
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Xin Wang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Charles Puerner
- Université Côte D'Azur, CNRS, INSERM, Institute of Biology Valrose (iBV), Parc Valrose, Nice, France.,Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA
| | - Robert A Arkowitz
- Université Côte D'Azur, CNRS, INSERM, Institute of Biology Valrose (iBV), Parc Valrose, Nice, France
| | - Brian K Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - David E Stone
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
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14
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Ly KL, Hu P, Pham LHP, Luo X. Flow-assembled chitosan membranes in microfluidics: recent advances and applications. J Mater Chem B 2021; 9:3258-3283. [PMID: 33725061 PMCID: PMC8369861 DOI: 10.1039/d1tb00045d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The integration of membranes in microfluidic devices has been extensively exploited for various chemical engineering and bioengineering applications over the past few decades. To augment the applicability of membrane-integrated microfluidic platforms for biomedical and tissue engineering studies, a biologically friendly fabrication process with naturally occurring materials is highly desired. The in situ preparation of membranes involving interfacial reactions between parallel laminar flows in microfluidic networks, known as the flow-assembly technique, is one of the most biocompatible approaches. Membranes of many types with flexible geometries have been successfully assembled inside complex microchannels using this facile and versatile flow-assembly approach. Chitosan is a naturally abundant polysaccharide known for its pronounced biocompatibility, biodegradability, good mechanical stability, ease of modification and processing, and film-forming ability under near-physiological conditions. Chitosan membranes assembled by flows in microfluidics are freestanding, robust, semipermeable, and well-aligned in microstructure, and show high affinity to bioactive reagents and biological components (e.g. biomolecules, nanoparticles, or cells) that provide facile biological functionalization of microdevices. Here, we discuss the recent developments and optimizations in the flow-assembly of chitosan membranes and chitosan-based membranes in microfluidics. Furthermore, we recapitulate the applications of the chitosan membrane-integrated microfluidic platforms dedicated to biology, biochemistry, and drug release fields, and envision the future developments of this important platform with versatile functions.
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Affiliation(s)
- Khanh L Ly
- Department of Biomedical Engineering, The Catholic University of America, Washington, DC 20064, USA
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15
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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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16
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Banavar SP, Trogdon M, Drawert B, Yi TM, Petzold LR, Campàs O. Coordinating cell polarization and morphogenesis through mechanical feedback. PLoS Comput Biol 2021; 17:e1007971. [PMID: 33507956 PMCID: PMC7872284 DOI: 10.1371/journal.pcbi.1007971] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 02/09/2021] [Accepted: 12/21/2020] [Indexed: 12/30/2022] Open
Abstract
Many cellular processes require cell polarization to be maintained as the cell changes shape, grows or moves. Without feedback mechanisms relaying information about cell shape to the polarity molecular machinery, the coordination between cell polarization and morphogenesis, movement or growth would not be possible. Here we theoretically and computationally study the role of a genetically-encoded mechanical feedback (in the Cell Wall Integrity pathway) as a potential coordination mechanism between cell morphogenesis and polarity during budding yeast mating projection growth. We developed a coarse-grained continuum description of the coupled dynamics of cell polarization and morphogenesis as well as 3D stochastic simulations of the molecular polarization machinery in the evolving cell shape. Both theoretical approaches show that in the absence of mechanical feedback (or in the presence of weak feedback), cell polarity cannot be maintained at the projection tip during growth, with the polarization cap wandering off the projection tip, arresting morphogenesis. In contrast, for mechanical feedback strengths above a threshold, cells can robustly maintain cell polarization at the tip and simultaneously sustain mating projection growth. These results indicate that the mechanical feedback encoded in the Cell Wall Integrity pathway can provide important positional information to the molecular machinery in the cell, thereby enabling the coordination of cell polarization and morphogenesis.
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Affiliation(s)
- Samhita P. Banavar
- Department of Physics, University of California, University of California, Santa Barbara, California, United States of America
- California NanoSystems Institute, University of California, Santa Barbara, California, United States of America
| | - Michael Trogdon
- Department of Mechanical Engineering, University of California, Santa Barbara, California, United States of America
| | - Brian Drawert
- Department of Computer Science, University of North Carolina, Asheville, North Carolina, United States of America
| | - Tau-Mu Yi
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, California, United States of America
| | - Linda R. Petzold
- Department of Mechanical Engineering, University of California, Santa Barbara, California, United States of America
- Center for Bioengineering, University of California, Santa Barbara, California, United States of America
| | - Otger Campàs
- California NanoSystems Institute, University of California, Santa Barbara, California, United States of America
- Department of Mechanical Engineering, University of California, Santa Barbara, California, United States of America
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, California, United States of America
- Center for Bioengineering, University of California, Santa Barbara, California, United States of America
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
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17
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Schunke C, Pöggeler S, Nordzieke DE. A 3D Printed Device for Easy and Reliable Quantification of Fungal Chemotropic Growth. Front Microbiol 2020; 11:584525. [PMID: 33224121 PMCID: PMC7669831 DOI: 10.3389/fmicb.2020.584525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/12/2020] [Indexed: 01/19/2023] Open
Abstract
Chemical gradients are surrounding living organisms in all habitats of life. Microorganisms, plants and animals have developed specific mechanisms to sense such gradients. Upon perception, chemical gradients can be categorized either as favorable, like nutrients or hormones, or as disadvantageous, resulting in a clear orientation toward the gradient and avoiding strategies, respectively. Being sessile organisms, fungi use chemical gradients for their orientation in the environment. Integration of this data enables them to successfully explore nutrient sources, identify probable plant or animal hosts, and to communicate during sexual reproduction or early colony development. We have developed a 3D printed device allowing a highly standardized, rapid and low-cost investigation of chemotropic growth processes in fungi. Since the 3D printed device is placed on a microscope slide, detailed microscopic investigations and documentation of the chemotropic process is possible. Using this device, we provide evidence that germlings derived from oval conidia of the hemibiotrophic plant pathogen Colletotrichum graminicola can sense gradients of glucose and reorient their growth toward the nutrient source. We describe in detail the method establishment, probable pitfalls, and provide the original program files for 3D printing to enable broad application of the 3D device in basic, agricultural, medical, and applied fungal science.
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Affiliation(s)
- Carolin Schunke
- Department of Genetics of Eukaryotic Microorganisms, Institute of Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany
| | - Stefanie Pöggeler
- Department of Genetics of Eukaryotic Microorganisms, Institute of Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany
| | - Daniela Elisabeth Nordzieke
- Department of Genetics of Eukaryotic Microorganisms, Institute of Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany
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18
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You JB, Lee B, Choi Y, Lee CS, Peter M, Im SG, Lee SS. Nanoadhesive layer to prevent protein absorption in a poly(dimethylsiloxane) microfluidic device. Biotechniques 2020; 69:404-409. [PMID: 32372656 DOI: 10.2144/btn-2020-0025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Poly(dimethylsiloxane) (PDMS) is widely used as a microfluidics platform material; however, it absorbs various molecules, perturbing specific chemical concentrations in microfluidic channels. We present a simple solution to prevent adsorption into a PDMS microfluidic device. We used a vapor-phase-deposited nanoadhesive layer to seal PDMS microfluidic channels. Absorption of fluorescent molecules into PDMS was efficiently prevented in the nanolayer-treated PDMS device. Importantly, when cultured in a nanolayer-treated PDMS device, yeast cells exhibited the expected concentration-dependent response to a mating pheromone, including mating-specific morphological and gene expression changes, while yeast cultured in an untreated PDMS device did not properly respond to the pheromone. Our method greatly expands microfluidic applications that require precise control of molecule concentrations.
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Affiliation(s)
- Jae Bem You
- Department of Chemical & Materials Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada
| | - Byungjin Lee
- Department of Chemical Engineering & Applied Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Yunho Choi
- Department of Chemical & Biomolecular Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Chang-Soo Lee
- Department of Chemical Engineering & Applied Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Matthias Peter
- Institute for Biochemistry, ETH Zürich, Zürich, CH 8093, Switzerland
| | - Sung Gap Im
- Department of Chemical & Biomolecular Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Sung Sik Lee
- Institute for Biochemistry, ETH Zürich, Zürich, CH 8093, Switzerland.,Scientific Center for Optical & Electron Microscopy (ScopeM), ETH Zürich, Zürich, CH 8093, Switzerland
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19
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Mitotic and pheromone-specific intrinsic polarization cues interfere with gradient sensing in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2020; 117:6580-6589. [PMID: 32152126 DOI: 10.1073/pnas.1912505117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Polarity decisions are central to many processes, including mitosis and chemotropism. In Saccharomyces cerevisiae, budding and mating projection (MP) formation use an overlapping system of cortical landmarks that converges on the small G protein Cdc42. However, pheromone-gradient sensing must override the Rsr1-dependent internal polarity cues used for budding. Using this model system, we asked what happens when intrinsic and extrinsic spatial cues are not aligned. Is there competition, or collaboration? By live-cell microscopy and microfluidics techniques, we uncovered three previously overlooked features of this signaling system. First, the cytokinesis-associated polarization patch serves as a polarity landmark independently of all known cues. Second, the Rax1-Rax2 complex functions as a pheromone-promoted polarity cue in the distal pole of the cells. Third, internal cues remain active during pheromone-gradient tracking and can interfere with this process, biasing the location of MPs. Yeast defective in internal-cue utilization align significantly better than wild type with artificially generated pheromone gradients.
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20
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Vo T, Shah SB, Choy JS, Luo X. Chemotropism among populations of yeast cells with spatiotemporal resolution in a biofabricated microfluidic platform. BIOMICROFLUIDICS 2020; 14:014108. [PMID: 32002107 PMCID: PMC6980865 DOI: 10.1063/1.5128739] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 01/07/2020] [Indexed: 05/08/2023]
Abstract
Chemotropism is an essential response of organisms to external chemical gradients that direct the growth of cells toward the gradient source. Chemotropic responses between single cells have been studied using in vitro gradients of synthetically derived signaling molecules and helped to develop a better understanding of chemotropism in multiple organisms. However, dynamic changes including spatial changes to the gradient as well as fluctuations in levels of cell generated signaling molecules can result in the redirection of chemotropic responses, which can be difficult to model with synthetic peptides and single cells. An experimental system that brings together populations of cells to monitor the population-scale chemotropic responses yet retain single cell spatiotemporal resolution would be useful to further inform on models of chemotropism. Here, we describe a microfluidic platform that can measure the chemotropic response between populations of mating yeast A- and α-cells with spatiotemporal programmability and sensitivity by positioning cell populations side by side in calcium alginate hydrogels along semipermeable membranes with micrometer spatial control. The mating phenotypes of the yeast populations were clearly observed over hours. Three distinct responses were observed depending on the distance between the A- and α-cell populations: the cells either continued to divide, arrest, and develop a stereotypical polarized projection termed a "shmoo" toward the cells of opposite mating type or formed shmoos in random directions. The results from our studies of yeast mating suggest that the biofabricated microfluidic platform can be adopted to study population-scale, spatial-sensitive cell-cell signaling behaviors that would be challenging using conventional approaches.
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Affiliation(s)
- Thanh Vo
- Department of Mechanical Engineering, The Catholic University of America, Washington, D.C. 20064, USA
| | - Sameer B. Shah
- Department of Biology, The Catholic University of America, Washington, D.C. 20064, USA
| | - John S. Choy
- Department of Biology, The Catholic University of America, Washington, D.C. 20064, USA
- Authors to whom correspondence should be addressed: and
| | - Xiaolong Luo
- Department of Mechanical Engineering, The Catholic University of America, Washington, D.C. 20064, USA
- Authors to whom correspondence should be addressed: and
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21
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Merrin J. Frontiers in Microfluidics, a Teaching Resource Review. Bioengineering (Basel) 2019; 6:E109. [PMID: 31816954 PMCID: PMC6955790 DOI: 10.3390/bioengineering6040109] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 02/02/2023] Open
Abstract
This is a literature teaching resource review for biologically inspired microfluidics courses or exploring the diverse applications of microfluidics. The structure is around key papers and model organisms. While courses gradually change over time, a focus remains on understanding how microfluidics has developed as well as what it can and cannot do for researchers. As a primary starting point, we cover micro-fluid mechanics principles and microfabrication of devices. A variety of applications are discussed using model prokaryotic and eukaryotic organisms from the set of bacteria (Escherichia coli), trypanosomes (Trypanosoma brucei), yeast (Saccharomyces cerevisiae), slime molds (Physarum polycephalum), worms (Caenorhabditis elegans), flies (Drosophila melangoster), plants (Arabidopsis thaliana), and mouse immune cells (Mus musculus). Other engineering and biochemical methods discussed include biomimetics, organ on a chip, inkjet, droplet microfluidics, biotic games, and diagnostics. While we have not yet reached the end-all lab on a chip, microfluidics can still be used effectively for specific applications.
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Affiliation(s)
- Jack Merrin
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
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22
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Henderson NT, Pablo M, Ghose D, Clark-Cotton MR, Zyla TR, Nolen J, Elston TC, Lew DJ. Ratiometric GPCR signaling enables directional sensing in yeast. PLoS Biol 2019; 17:e3000484. [PMID: 31622333 PMCID: PMC6818790 DOI: 10.1371/journal.pbio.3000484] [Citation(s) in RCA: 19] [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: 06/19/2019] [Revised: 10/29/2019] [Accepted: 09/25/2019] [Indexed: 11/19/2022] Open
Abstract
Accurate detection of extracellular chemical gradients is essential for many cellular behaviors. Gradient sensing is challenging for small cells, which can experience little difference in ligand concentrations on the up-gradient and down-gradient sides of the cell. Nevertheless, the tiny cells of the yeast Saccharomyces cerevisiae reliably decode gradients of extracellular pheromones to find their mates. By imaging the behavior of polarity factors and pheromone receptors, we quantified the accuracy of initial polarization during mating encounters. We found that cells bias the orientation of initial polarity up-gradient, even though they have unevenly distributed receptors. Uneven receptor density means that the gradient of ligand-bound receptors does not accurately reflect the external pheromone gradient. Nevertheless, yeast cells appear to avoid being misled by responding to the fraction of occupied receptors rather than simply the concentration of ligand-bound receptors. Such ratiometric sensing also serves to amplify the gradient of active G protein. However, this process is quite error-prone, and initial errors are corrected during a subsequent indecisive phase in which polarity clusters exhibit erratic mobile behavior. Cells use surface receptors to decode spatial information from chemical gradients, but accurate decoding is hampered by small cell size and the presence of molecular noise. This study shows that yeast cells decode pheromone gradients by measuring the local ratio of bound to unbound receptors. This mechanism corrects for uneven receptor density at the surface and amplifies the gradient transmitted to downstream components.
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Affiliation(s)
- Nicholas T. Henderson
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, United States of America
| | - Michael Pablo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Program in Molecular and Cellular Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Debraj Ghose
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, United States of America
| | - Manuella R. Clark-Cotton
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, United States of America
| | - Trevin R. Zyla
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, United States of America
| | - James Nolen
- Department of Mathematics, Duke University, Durham, North Carolina, United States of America
| | - Timothy C. Elston
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Daniel J. Lew
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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23
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Uehling JK, Entler MR, Meredith HR, Millet LJ, Timm CM, Aufrecht JA, Bonito GM, Engle NL, Labbé JL, Doktycz MJ, Retterer ST, Spatafora JW, Stajich JE, Tschaplinski TJ, Vilgalys RJ. Microfluidics and Metabolomics Reveal Symbiotic Bacterial-Fungal Interactions Between Mortierella elongata and Burkholderia Include Metabolite Exchange. Front Microbiol 2019; 10:2163. [PMID: 31632357 PMCID: PMC6779839 DOI: 10.3389/fmicb.2019.02163] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/03/2019] [Indexed: 01/12/2023] Open
Abstract
We identified two poplar (Populus sp.)-associated microbes, the fungus, Mortierella elongata strain AG77, and the bacterium, Burkholderia strain BT03, that mutually promote each other’s growth. Using culture assays in concert with a novel microfluidic device to generate time-lapse videos, we found growth specific media differing in pH and pre-conditioned by microbial growth led to increased fungal and bacterial growth rates. Coupling microfluidics and comparative metabolomics data results indicated that observed microbial growth stimulation involves metabolic exchange during two ordered events. The first is an emission of fungal metabolites, including organic acids used or modified by bacteria. A second signal of unknown nature is produced by bacteria which increases fungal growth rates. We find this symbiosis is initiated in part by metabolic exchange involving fungal organic acids.
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Affiliation(s)
- Jessie K Uehling
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States.,Department of Biology, Duke University, Durham, NC, United States
| | - Matthew R Entler
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Hannah R Meredith
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States.,Department of Biomedical Engineering, Duke University, Durham, NC, United States
| | - Larry J Millet
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,The Bredesen Center, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Collin M Timm
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jayde A Aufrecht
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Gregory M Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jessy L Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Genome Science & Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Genome Science & Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Scott T Retterer
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | | | - Rytas J Vilgalys
- Department of Biology, Duke University, Durham, NC, United States
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24
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Wang X, Tian W, Banh BT, Statler BM, Liang J, Stone DE. Mating yeast cells use an intrinsic polarity site to assemble a pheromone-gradient tracking machine. J Cell Biol 2019; 218:3730-3752. [PMID: 31570500 PMCID: PMC6829655 DOI: 10.1083/jcb.201901155] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 06/06/2019] [Accepted: 08/08/2019] [Indexed: 12/12/2022] Open
Abstract
The mating of budding yeast depends on chemotropism, a fundamental cellular process. The two yeast mating types secrete peptide pheromones that bind to GPCRs on cells of the opposite type. Cells find and contact a partner by determining the direction of the pheromone source and polarizing their growth toward it. Actin-directed secretion to the chemotropic growth site (CS) generates a mating projection. When pheromone-stimulated cells are unable to sense a gradient, they form mating projections where they would have budded in the next cell cycle, at a position called the default polarity site (DS). Numerous models have been proposed to explain yeast gradient sensing, but none address how cells reliably switch from the intrinsically determined DS to the gradient-aligned CS, despite a weak spatial signal. Here we demonstrate that, in mating cells, the initially uniform receptor and G protein first polarize to the DS, then redistribute along the plasma membrane until they reach the CS. Our data indicate that signaling, polarity, and trafficking proteins localize to the DS during assembly of what we call the gradient tracking machine (GTM). Differential activation of the receptor triggers feedback mechanisms that bias exocytosis upgradient and endocytosis downgradient, thus enabling redistribution of the GTM toward the pheromone source. The GTM stabilizes when the receptor peak centers at the CS and the endocytic machinery surrounds it. A computational model simulates GTM tracking and stabilization and correctly predicts that its assembly at a single site contributes to mating fidelity.
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Affiliation(s)
- Xin Wang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL
| | - Wei Tian
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL
| | - Bryan T Banh
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL
| | | | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL
| | - David E Stone
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL
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25
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Tian C, Shi Q, Cui X, Guo J, Yang Z, Shi J. Spatiotemporal dynamics of a reaction-diffusion model of pollen tube tip growth. J Math Biol 2019; 79:1319-1355. [PMID: 31280334 DOI: 10.1007/s00285-019-01396-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 06/06/2019] [Indexed: 11/28/2022]
Abstract
A reaction-diffusion model is proposed to describe the mechanisms underlying the spatial distributions of ROP1 and calcium on the pollen tube tip. The model assumes that the plasma membrane ROP1 activates itself through positive feedback loop, while the cytosolic calcium ions inhibit ROP1 via a negative feedback loop. Furthermore it is proposed that lateral movement of molecules on the plasma membrane are depicted by diffusion. It is shown that bistable or oscillatory dynamics could exist even in the non-spatial model, and stationary and oscillatory spatiotemporal patterns are found in the full spatial model which resemble the experimental data of pollen tube tip growth.
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Affiliation(s)
- Chenwei Tian
- Department of Statistics, University of California, Riverside, CA, 92521, USA
| | - Qingyan Shi
- Department of Mathematics, College of William and Mary, Williamsburg, VA, 23187-8795, USA.,School of Mathematical Sciences, Tongji University, Shanghai, 200092, China
| | - Xinping Cui
- Department of Statistics, University of California, Riverside, CA, 92521, USA
| | - Jingzhe Guo
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA, 92521, USA
| | - Zhenbiao Yang
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA, 92521, USA
| | - Junping Shi
- Department of Mathematics, College of William and Mary, Williamsburg, VA, 23187-8795, USA.
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26
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Shellhammer JP, Pomeroy AE, Li Y, Dujmusic L, Elston TC, Hao N, Dohlman HG. Quantitative analysis of the yeast pheromone pathway. Yeast 2019; 36:495-518. [PMID: 31022772 DOI: 10.1002/yea.3395] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/10/2019] [Accepted: 04/16/2019] [Indexed: 01/04/2023] Open
Abstract
The pheromone response pathway of the yeast Saccharomyces cerevisiae is a well-established model for the study of G proteins and mitogen-activated protein kinase (MAPK) cascades. Our longstanding ability to combine sophisticated genetic approaches with established functional assays has provided a thorough understanding of signalling mechanisms and regulation. In this report, we compare new and established methods used to quantify pheromone-dependent MAPK phosphorylation, transcriptional induction, mating morphogenesis, and gradient tracking. These include both single-cell and population-based assays of activity. We describe several technical advances, provide example data for benchmark mutants, highlight important differences between newer and established methodologies, and compare the advantages and disadvantages of each as applied to the yeast model. Quantitative measurements of pathway activity have been used to develop mathematical models and reveal new regulatory mechanisms in yeast. It is our expectation that experimental and computational approaches developed in yeast may eventually be adapted to human systems biology and pharmacology.
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Affiliation(s)
- James P Shellhammer
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Amy E Pomeroy
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Yang Li
- Division of Biological Sciences, University of California San Diego, San Diego, CA, 92093, USA
| | - Lorena Dujmusic
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Timothy C Elston
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Nan Hao
- Division of Biological Sciences, University of California San Diego, San Diego, CA, 92093, USA
| | - Henrik G Dohlman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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27
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Seike T, Maekawa H, Nakamura T, Shimoda C. The asymmetric chemical structures of two mating pheromones reflect their differential roles in mating of fission yeast. J Cell Sci 2019; 132:jcs.230722. [PMID: 31186279 DOI: 10.1242/jcs.230722] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/03/2019] [Indexed: 02/01/2023] Open
Abstract
In the fission yeast Schizosaccharomyces pombe, the mating reaction is controlled by two mating pheromones, M-factor and P-factor, secreted by M- and P-type cells, respectively. M-factor is a C-terminally farnesylated lipid peptide, whereas P-factor is a simple peptide. To examine whether this chemical asymmetry in the two pheromones is essential for conjugation, we constructed a mating system in which either pheromone can stimulate both M- and P-cells, and examined whether the resulting autocrine strains can mate. Autocrine M-cells responding to M-factor successfully mated with P-factor-lacking P-cells, indicating that P-factor is not essential for conjugation; by contrast, autocrine P-cells responding to P-factor were unable to mate with M-factor-lacking M-cells. The sterility of the autocrine P-cells was completely restored by expressing the M-factor receptor. These observations indicate that the different chemical characteristics of the two types of pheromone, a lipid and a simple peptide, are not essential; however, a lipid peptide might be required for successful mating. Our findings allow us to propose a model of the differential roles of M-factor and P-factor in conjugation of S. pombeThis article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Taisuke Seike
- Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Hiromi Maekawa
- Yeast Genetic Resources Laboratory, Graduate School of Engineering, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Taro Nakamura
- Department of Biology, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Chikashi Shimoda
- Department of Biology, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
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Martin SG. Molecular mechanisms of chemotropism and cell fusion in unicellular fungi. J Cell Sci 2019; 132:132/11/jcs230706. [PMID: 31152053 DOI: 10.1242/jcs.230706] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In all eukaryotic phyla, cell fusion is important for many aspects of life, from sexual reproduction to tissue formation. Fungal cells fuse during mating to form the zygote, and during vegetative growth to connect mycelia. Prior to fusion, cells first detect gradients of pheromonal chemoattractants that are released by their partner and polarize growth in their direction. Upon pairing, cells digest their cell wall at the site of contact and merge their plasma membrane. In this Review, I discuss recent work on the chemotropic response of the yeast models Saccharomyces cerevisiae and Schizosaccharomyces pombe, which has led to a novel model of gradient sensing: the cell builds a motile cortical polarized patch, which acts as site of communication where pheromones are released and sensed. Initial patch dynamics serve to correct its position and align it with the gradient from the partner cell. Furthermore, I highlight the transition from cell wall expansion during growth to cell wall digestion, which is imposed by physical and signaling changes owing to hyperpolarization that is induced by cell proximity. To conclude, I discuss mechanisms of membrane fusion, whose characterization remains a major challenge for the future.
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Affiliation(s)
- Sophie G Martin
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
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Seike T, Shimoda C, Niki H. Asymmetric diversification of mating pheromones in fission yeast. PLoS Biol 2019; 17:e3000101. [PMID: 30668560 PMCID: PMC6342294 DOI: 10.1371/journal.pbio.3000101] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 12/19/2018] [Indexed: 01/25/2023] Open
Abstract
In fungi, mating between partners depends on the molecular recognition of two peptidyl mating pheromones by their respective receptors. The fission yeast Schizosaccharomyces pombe (Sp) has two mating types, Plus (P) and Minus (M). The mating pheromones P-factor and M-factor, secreted by P and M cells, are recognized by the receptors mating type auxiliary minus 2 (Mam2) and mating type auxiliary plus 3 (Map3), respectively. Our recent study demonstrated that a few mutations in both M-factor and Map3 can trigger reproductive isolation in S. pombe. Here, we explored the mechanism underlying reproductive isolation through genetic changes of pheromones/receptors in nature. We investigated the diversity of genes encoding the pheromones and their receptor in 150 wild S. pombe strains. Whereas the amino acid sequences of M-factor and Map3 were completely conserved, those of P-factor and Mam2 were very diverse. In addition, the P-factor gene contained varying numbers of tandem repeats of P-factor (4–8 repeats). By exploring the recognition specificity of pheromones between S. pombe and its close relative Schizosaccharomyces octosporus (So), we found that So-M-factor did not have an effect on S. pombe P cells, but So-P-factor had a partial effect on S. pombe M cells. Thus, recognition of M-factor seems to be stringent, whereas that of P-factor is relatively relaxed. We speculate that asymmetric diversification of the two pheromones might be facilitated by the distinctly different specificities of the two receptors. Our findings suggest that M-factor communication plays an important role in defining the species, whereas P-factor communication is able to undergo a certain degree of flexible adaptation–perhaps as a first step toward prezygotic isolation in S. pombe. An asymmetric pheromone/receptor system in the fission yeast Schizosaccharomyces pombe might allow flexible adaptation of pheromones to mutational changes while maintaining stringent recognition for mating partners, perhaps as a first step toward prezygotic mating isolation. The emergence of a new species might occur when two groups can no longer mate. Although such reproductive isolation is considered a key evolutionary process, the mechanisms by which it actually occurs have been confined to conjecture. The two sexes (Plus [P] and Minus [M]) of S. pombe each secrete a pheromone (P-factor and M-factor), which binds to a corresponding receptor (mating type auxiliary minus 2 [Mam2] and mating type auxiliary plus 3 [Map3]) on cells of the opposite sex. The interaction between a pheromone and its receptor is essential for successful mating. Here, we explored conservation of the mating pheromone communication system among 150 wild S. pombe strains of different geographical origins and the closely related species S. octosporus. We found that 1) the M-factor/Map3 interaction was completely conserved, whereas the P-factor/Mam2 interaction was very diverse in the strains investigated, and 2) most of the P-factor variants were functional across species. Thus, we have revealed an asymmetric pheromone/receptor system in fungal mating: namely, whereas M-factor communication operates extremely stringently, P-factor communication has the flexibility to create variations, perhaps facilitating prezygotic isolation in S. pombe.
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Affiliation(s)
- Taisuke Seike
- Genetics Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, Japan
- * E-mail:
| | - Chikashi Shimoda
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan
| | - Hironori Niki
- Genetics Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, Japan
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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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31
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Giese W, Milicic G, Schröder A, Klipp E. Spatial modeling of the membrane-cytosolic interface in protein kinase signal transduction. PLoS Comput Biol 2018; 14:e1006075. [PMID: 29630597 PMCID: PMC5908195 DOI: 10.1371/journal.pcbi.1006075] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 04/19/2018] [Accepted: 03/07/2018] [Indexed: 02/06/2023] Open
Abstract
The spatial architecture of signaling pathways and the interaction with cell size and morphology are complex, but little understood. With the advances of single cell imaging and single cell biology, it becomes crucial to understand intracellular processes in time and space. Activation of cell surface receptors often triggers a signaling cascade including the activation of membrane-attached and cytosolic signaling components, which eventually transmit the signal to the cell nucleus. Signaling proteins can form steep gradients in the cytosol, which cause strong cell size dependence. We show that the kinetics at the membrane-cytosolic interface and the ratio of cell membrane area to the enclosed cytosolic volume change the behavior of signaling cascades significantly. We suggest an estimate of average concentration for arbitrary cell shapes depending on the cell volume and cell surface area. The normalized variance, known from image analysis, is suggested as an alternative measure to quantify the deviation from the average concentration. A mathematical analysis of signal transduction in time and space is presented, providing analytical solutions for different spatial arrangements of linear signaling cascades. Quantification of signaling time scales reveals that signal propagation is faster at the membrane than at the nucleus, while this time difference decreases with the number of signaling components in the cytosol. Our investigations are complemented by numerical simulations of non-linear cascades with feedback and asymmetric cell shapes. We conclude that intracellular signal propagation is highly dependent on cell geometry and, thereby, conveys information on cell size and shape to the nucleus.
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Affiliation(s)
- Wolfgang Giese
- Mathematical Cell Physiology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Gregor Milicic
- Department of Mathematics, University of Salzburg, Salzburg, Austria
| | - Andreas Schröder
- Department of Mathematics, University of Salzburg, Salzburg, Austria
| | - Edda Klipp
- Theoretische Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
- * E-mail:
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32
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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 towards one another. Mating pheromone gradients are essential for efficient mating in yeast and different yeast mutants are defective in chemotropism. Two methods of assessing the ability of yeast strains to respond to pheromone gradients are presented here.
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Affiliation(s)
- David E Stone
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA.
| | - Robert A Arkowitz
- Institute of Biology Valrose, CNRS/INSERM/Université Nice-Sophia Antipolis, Valrose Parc, 06108, Nice Cedex 2, France.
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Jin SH, Lee SS, Lee B, Jeong SG, Peter M, Lee CS. Programmable Static Droplet Array for the Analysis of Cell–Cell Communication in a Confined Microenvironment. Anal Chem 2017; 89:9722-9729. [DOI: 10.1021/acs.analchem.7b01462] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Si Hyung Jin
- Department
of Chemical Engineering, Chungnam National University, 99 Daehak-ro,
Yuseong-Gu, Daejeon, 34134, Republic of Korea
| | | | - Byungjin Lee
- Department
of Chemical Engineering, Chungnam National University, 99 Daehak-ro,
Yuseong-Gu, Daejeon, 34134, Republic of Korea
| | - Seong-Geun Jeong
- Department
of Chemical Engineering, Chungnam National University, 99 Daehak-ro,
Yuseong-Gu, Daejeon, 34134, Republic of Korea
| | | | - Chang-Soo Lee
- Department
of Chemical Engineering, Chungnam National University, 99 Daehak-ro,
Yuseong-Gu, Daejeon, 34134, Republic of Korea
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34
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Ismael A, Stone DE. Yeast chemotropism: A paradigm shift in chemical gradient sensing. CELLULAR LOGISTICS 2017; 7:e1314237. [PMID: 28702274 DOI: 10.1080/21592799.2017.1314237] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/17/2017] [Accepted: 03/28/2017] [Indexed: 12/25/2022]
Abstract
The ability of cells to direct their movement and growth in response to shallow chemical gradients is essential in the life cycles of all eukaryotic organisms. The signaling mechanisms underlying directional sensing in chemotactic cells have been well studied; however, relatively little is known about how chemotropic cells interpret chemical gradients. Recent studies of chemotropism in budding and fission yeast have revealed 2 quite different mechanisms-biased wandering of the polarity complex, and differential internalization of the receptor and G protein. Each of these mechanisms has been proposed to play a key role in decoding mating pheromone gradients. Here we explore how they may work together as 2 essential components of one gradient sensing machine.
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Affiliation(s)
- Amber Ismael
- Department of Cell and Developmental Biology, University of Colorado, Denver Anschutz Medical Campus, Aurora, CO, USA
| | - David E Stone
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
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35
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Lakhani V, Elston TC. Testing the limits of gradient sensing. PLoS Comput Biol 2017; 13:e1005386. [PMID: 28207738 PMCID: PMC5347372 DOI: 10.1371/journal.pcbi.1005386] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 03/03/2017] [Accepted: 01/27/2017] [Indexed: 02/04/2023] Open
Abstract
The ability to detect a chemical gradient is fundamental to many cellular processes. In multicellular organisms gradient sensing plays an important role in many physiological processes such as wound healing and development. Unicellular organisms use gradient sensing to move (chemotaxis) or grow (chemotropism) towards a favorable environment. Some cells are capable of detecting extremely shallow gradients, even in the presence of significant molecular-level noise. For example, yeast have been reported to detect pheromone gradients as shallow as 0.1 nM/μm. Noise reduction mechanisms, such as time-averaging and the internalization of pheromone molecules, have been proposed to explain how yeast cells filter fluctuations and detect shallow gradients. Here, we use a Particle-Based Reaction-Diffusion model of ligand-receptor dynamics to test the effectiveness of these mechanisms and to determine the limits of gradient sensing. In particular, we develop novel simulation methods for establishing chemical gradients that not only allow us to study gradient sensing under steady-state conditions, but also take into account transient effects as the gradient forms. Based on reported measurements of reaction rates, our results indicate neither time-averaging nor receptor endocytosis significantly improves the cell’s accuracy in detecting gradients over time scales associated with the initiation of polarized growth. Additionally, our results demonstrate the physical barrier of the cell membrane sharpens chemical gradients across the cell. While our studies are motivated by the mating response of yeast, we believe our results and simulation methods will find applications in many different contexts. In order to survive, many organisms must not only be able to detect the presence of a chemical compound, but also in which direction that compound increases or decreases in concentration. For example, bacteria cells prefer to move towards areas with high sugar concentrations. The process by which cells determine the direction of a chemical gradient is called “Gradient Sensing”. Of particular interest is the gradient sensing capability of yeast cells. These cells have been observed detecting the direction of extremely shallow gradients, which produce only a 2% difference in the number of molecules across the cell. Because the molecular-level noise is much larger than this signal, it is unclear what noise-reduction mechanism the cell employs to reduce the noise and detect the signal. We developed a 3D computational simulation platform to calculate and study the exact positions of molecules during this process. Our platform utilizes High Performance Computing clusters and GPGPUs. We find that, of the two prevailing models in the literature, neither time-averaging nor receptor endocytosis sufficiently reduces molecular noise for yeast cells to reliably detect chemical gradients before they initiate polarized growth. This finding implies yeast must possess a mechanism for reorienting the direction of growth after cell polarization has occurred. We also find the cell membrane and similarly, any other physical barrier nearby the cell can improve the cell’s likelihood of detecting the gradient. Our simulation methods and results will be applicable in other areas of research.
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Affiliation(s)
- Vinal Lakhani
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Battelle Center for Mathematical Medicine, Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Timothy C. Elston
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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36
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Atay O, Skotheim JM. Spatial and temporal signal processing and decision making by MAPK pathways. J Cell Biol 2017; 216:317-330. [PMID: 28043970 PMCID: PMC5294789 DOI: 10.1083/jcb.201609124] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/25/2016] [Accepted: 12/12/2016] [Indexed: 01/14/2023] Open
Abstract
Recent studies show that MAPK pathways perform exquisite spatial and temporal signal processing. This review discusses the mechanisms that process dynamic inputs into graded output responses, the role of positive and negative feedbacks, and feedforward regulation. Mitogen-activated protein kinase (MAPK) pathways are conserved from yeast to man and regulate a variety of cellular processes, including proliferation and differentiation. Recent developments show how MAPK pathways perform exquisite spatial and temporal signal processing and underscores the importance of studying the dynamics of signaling pathways to understand their physiological response. The importance of dynamic mechanisms that process input signals into graded downstream responses has been demonstrated in the pheromone-induced and osmotic stress–induced MAPK pathways in yeast and in the mammalian extracellular signal-regulated kinase MAPK pathway. Particularly, recent studies in the yeast pheromone response have shown how positive feedback generates switches, negative feedback enables gradient detection, and coherent feedforward regulation underlies cellular memory. More generally, a new wave of quantitative single-cell studies has begun to elucidate how signaling dynamics determine cell physiology and represents a paradigm shift from descriptive to predictive biology.
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Affiliation(s)
- Oguzhan Atay
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305
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37
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Wang X, Liu Z, Pang Y. Concentration gradient generation methods based on microfluidic systems. RSC Adv 2017. [DOI: 10.1039/c7ra04494a] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Various concentration gradient generation methods based on microfluidic systems are summarized in this paper.
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Affiliation(s)
- Xiang Wang
- College of Mechanical Engineering and Applied Electronics Technology
- Beijing University of Technology
- Beijing 100124
- China
| | - Zhaomiao Liu
- College of Mechanical Engineering and Applied Electronics Technology
- Beijing University of Technology
- Beijing 100124
- China
| | - Yan Pang
- College of Mechanical Engineering and Applied Electronics Technology
- Beijing University of Technology
- Beijing 100124
- China
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38
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Drawert B, Hellander S, Trogdon M, Yi TM, Petzold L. A framework for discrete stochastic simulation on 3D moving boundary domains. J Chem Phys 2016; 145:184113. [PMID: 27846706 PMCID: PMC5116030 DOI: 10.1063/1.4967338] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 10/26/2016] [Indexed: 12/20/2022] Open
Abstract
We have developed a method for modeling spatial stochastic biochemical reactions in complex, three-dimensional, and time-dependent domains using the reaction-diffusion master equation formalism. In particular, we look to address the fully coupled problems that arise in systems biology where the shape and mechanical properties of a cell are determined by the state of the biochemistry and vice versa. To validate our method and characterize the error involved, we compare our results for a carefully constructed test problem to those of a microscale implementation. We demonstrate the effectiveness of our method by simulating a model of polarization and shmoo formation during the mating of yeast. The method is generally applicable to problems in systems biology where biochemistry and mechanics are coupled, and spatial stochastic effects are critical.
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Affiliation(s)
- Brian Drawert
- Department of Computer Science, University of California-Santa Barbara, Santa Barbara, California 93106, USA
| | - Stefan Hellander
- Department of Computer Science, University of California-Santa Barbara, Santa Barbara, California 93106, USA
| | - Michael Trogdon
- Department of Mechanical Engineering, University of California-Santa Barbara, Santa Barbara, California 93106, USA
| | - Tau-Mu Yi
- Department of Molecular, Cellular, and Developmental Biology, University of California-Santa Barbara, Santa Barbara, California 93106, USA
| | - Linda Petzold
- Department of Computer Science, University of California-Santa Barbara, Santa Barbara, California 93106, USA
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39
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Jo MC, Qin L. Microfluidic Platforms for Yeast-Based Aging Studies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:5787-5801. [PMID: 27717149 PMCID: PMC5554731 DOI: 10.1002/smll.201602006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/30/2016] [Indexed: 06/06/2023]
Abstract
The budding yeast Saccharomyces cerevisiae has been a powerful model for the study of aging and has enabled significant contributions to our understanding of basic mechanisms of aging in eukaryotic cells. However, the laborious low-throughput nature of conventional methods of performing aging assays limits the pace of discoveries in this field. Some of the technical challenges of conventional aging assay methods can be overcome by use of microfluidic systems coupled to time-lapse microscopy. One of the major advantages is the ability of a microfluidic system to perform long-term cell culture under well-defined environmental conditions while tracking individual yeast. Here, recent advancements in microfluidic platforms for various yeast-based studies including replicative lifespan assay, long-term culture and imaging, gene expression, and cell signaling are discussed. In addition, emerging problems and limitations of current microfluidic approaches are examined and perspectives on the future development of this dynamic field are presented.
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Affiliation(s)
- Myeong Chan Jo
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY, 10065, USA
| | - Lidong Qin
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY, 10065, USA
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40
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Luo X, Vo T, Jambi F, Pham P, Choy JS. Microfluidic partition with in situ biofabricated semipermeable biopolymer membranes for static gradient generation. LAB ON A CHIP 2016; 16:3815-3823. [PMID: 27713976 DOI: 10.1039/c6lc00742b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We report an in situ biofabrication strategy that conveniently partitions microfluidic networks into physically separated while chemically communicating microchannels with semipermeable biopolymer membranes, which enable the facile generation of static gradients for biomedical applications. The biofabrication of parallel biopolymer membranes was initiated with the dissipation of trapped air bubbles in parallel apertures in polydimethylsiloxane (PDMS) microfluidic devices, followed by tunable membrane growth with precise temporal and spatial control to the desired thickness. Static gradients were generated within minutes and well maintained over time by pure diffusion of molecules through the biofabricated semipermeable membranes. As an example application, the static gradient of alpha factor was generated to study the development of the "shmoo" morphology of yeast over time. The in situ biofabrication provides a simple approach to generate static gradients and an ideal platform for biological applications where flow-free static gradients are indispensable.
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Affiliation(s)
- Xiaolong Luo
- Department of Mechanical Engineering, The Catholic University of America, Washington, D.C. 20064, USA.
| | - Thanh Vo
- Department of Mechanical Engineering, The Catholic University of America, Washington, D.C. 20064, USA.
| | - Fahad Jambi
- Department of Mechanical Engineering, The Catholic University of America, Washington, D.C. 20064, USA.
| | - Phu Pham
- Department of Mechanical Engineering, The Catholic University of America, Washington, D.C. 20064, USA.
| | - John S Choy
- Department of Biology, The Catholic University of America, Washington, D.C. 20064, USA
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41
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Single-cell dynamics and variability of MAPK activity in a yeast differentiation pathway. Proc Natl Acad Sci U S A 2016; 113:E5896-E5905. [PMID: 27651485 DOI: 10.1073/pnas.1610081113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In response to pheromones, yeast cells activate a MAPK pathway to direct processes important for mating, including gene induction, cell-cycle arrest, and polarized cell growth. Although a variety of assays have been able to elucidate signaling activities at multiple steps in the pathway, measurements of MAPK activity during the pheromone response have remained elusive, and our understanding of single-cell signaling behavior is incomplete. Using a yeast-optimized FRET-based mammalian Erk-activity reporter to monitor Fus3 and Kss1 activity in live yeast cells, we demonstrate that overall mating MAPK activity exhibits distinct temporal dynamics, rapid reversibility, and a graded dose dependence around the KD of the receptor, where phenotypic transitions occur. The complex dose response was found to be largely a consequence of two feedbacks involving cyclin-mediated scaffold phosphorylation and Fus3 autoregulation. Distinct cell cycle-dependent response patterns comprised a large portion of the cell-to-cell variability at each dose, constituting the major source of extrinsic noise in coupling activity to downstream gene-expression responses. Additionally, we found diverse spatial MAPK activity patterns to emerge over time in cells undergoing default, gradient, and true mating responses. Furthermore, ramping up and rapid loss of activity were closely associated with zygote formation in mating-cell pairs, supporting a role for elevated MAPK activity in successful cell fusion and morphogenic reorganization. Altogether, these findings present a detailed view of spatiotemporal MAPK activity during the pheromone response, elucidating its role in mediating complex long-term developmental fates in a unicellular differentiation system.
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42
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Banderas A, Koltai M, Anders A, Sourjik V. Sensory input attenuation allows predictive sexual response in yeast. Nat Commun 2016; 7:12590. [PMID: 27557894 PMCID: PMC5007329 DOI: 10.1038/ncomms12590] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 07/14/2016] [Indexed: 12/22/2022] Open
Abstract
Animals are known to adjust their sexual behaviour depending on mate competition. Here we report similar regulation for mating behaviour in a sexual unicellular eukaryote, the budding yeast Saccharomyces cerevisiae. We demonstrate that pheromone-based communication between the two mating types, coupled to input attenuation by recipient cells, enables yeast to robustly monitor relative mate abundance (sex ratio) within a mixed population and to adjust their commitment to sexual reproduction in proportion to their estimated chances of successful mating. The mechanism of sex-ratio sensing relies on the diffusible peptidase Bar1, which is known to degrade the pheromone signal produced by mating partners. We further show that such a response to sexual competition within a population can optimize the fitness trade-off between the costs and benefits of mating response induction. Our study thus provides an adaptive explanation for the known molecular mechanism of pheromone degradation in yeast. Cells of the yeast Saccharomyces cerevisiae can mate with other cells of opposite mating type. Here, the authors show that the combination of a pheromone and a pheromone-degrading enzyme allows yeast cells to monitor relative mate abundance within a population and adjust their commitment to sexual reproduction.
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Affiliation(s)
- Alvaro Banderas
- Max Planck Institute for Terrestrial Microbiology &LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, D-35037 Marburg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Mihaly Koltai
- Max Planck Institute for Terrestrial Microbiology &LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, D-35037 Marburg, Germany
| | - Alexander Anders
- Max Planck Institute for Terrestrial Microbiology &LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, D-35037 Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology &LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, D-35037 Marburg, Germany
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Turrà D, Nordzieke D, Vitale S, El Ghalid M, Di Pietro A. Hyphal chemotropism in fungal pathogenicity. Semin Cell Dev Biol 2016; 57:69-75. [PMID: 27150623 DOI: 10.1016/j.semcdb.2016.04.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 04/29/2016] [Accepted: 04/29/2016] [Indexed: 10/21/2022]
Abstract
The ability to grow as filamentous hyphae defines the lifestyle of fungi. Hyphae are exposed to a variety of chemical stimuli such as nutrients or signal molecules from mating partners and host organisms. How fungi sense and process this chemical information to steer hyphal growth is poorly understood. Saccharomyces cerevisiae and Neurospora crassa have served as genetic models for the identification of cellular components functioning in chemotropism. A recent study in the pathogen Fusarium oxysporum revealed distinct MAPK pathways governing hyphal growth towards nutrient sources and sex pheromones or plant signals, suggesting an unanticipated complexity of chemosensing during fungus-host interactions.
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Affiliation(s)
- David Turrà
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Daniela Nordzieke
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Stefania Vitale
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Mennat El Ghalid
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Antonio Di Pietro
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, 14071 Córdoba, Spain.
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Hydrophobin-Based Surface Engineering for Sensitive and Robust Quantification of Yeast Pheromones. SENSORS 2016; 16:s16050602. [PMID: 27128920 PMCID: PMC4883293 DOI: 10.3390/s16050602] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 03/31/2016] [Accepted: 04/20/2016] [Indexed: 02/05/2023]
Abstract
Detection and quantification of small peptides, such as yeast pheromones, are often challenging. We developed a highly sensitive and robust affinity-assay for the quantification of the α-factor pheromone of Saccharomyces cerevisiae based on recombinant hydrophobins. These small, amphipathic proteins self-assemble into highly stable monolayers at hydrophilic-hydrophobic interfaces. Upon functionalization of solid supports with a combination of hydrophobins either lacking or exposing the α-factor, pheromone-specific antibodies were bound to the surface. Increasing concentrations of the pheromone competitively detached the antibodies, thus allowing for quantification of the pheromone. By adjusting the percentage of pheromone-exposing hydrophobins, the sensitivity of the assay could be precisely predefined. The assay proved to be highly robust against changes in sample matrix composition. Due to the high stability of hydrophobin layers, the functionalized surfaces could be repeatedly used without affecting the sensitivity. Furthermore, by using an inverse setup, the sensitivity was increased by three orders of magnitude, yielding a novel kind of biosensor for the yeast pheromone with the lowest limit of detection reported so far. This assay was applied to study the pheromone secretion of diverse yeast strains including a whole-cell biosensor strain of Schizosaccharomyces pombe modulating α-factor secretion in response to an environmental signal.
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Muller N, Piel M, Calvez V, Voituriez R, Gonçalves-Sá J, Guo CL, Jiang X, Murray A, Meunier N. A Predictive Model for Yeast Cell Polarization in Pheromone Gradients. PLoS Comput Biol 2016; 12:e1004795. [PMID: 27077831 PMCID: PMC4831791 DOI: 10.1371/journal.pcbi.1004795] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 02/08/2016] [Indexed: 11/18/2022] Open
Abstract
Budding yeast cells exist in two mating types, a and α, which use peptide pheromones to communicate with each other during mating. Mating depends on the ability of cells to polarize up pheromone gradients, but cells also respond to spatially uniform fields of pheromone by polarizing along a single axis. We used quantitative measurements of the response of a cells to α-factor to produce a predictive model of yeast polarization towards a pheromone gradient. We found that cells make a sharp transition between budding cycles and mating induced polarization and that they detect pheromone gradients accurately only over a narrow range of pheromone concentrations corresponding to this transition. We fit all the parameters of the mathematical model by using quantitative data on spontaneous polarization in uniform pheromone concentration. Once these parameters have been computed, and without any further fit, our model quantitatively predicts the yeast cell response to pheromone gradient providing an important step toward understanding how cells communicate with each other.
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Affiliation(s)
- Nicolas Muller
- MAP5, CNRS UMR 8145, Université Paris Descartes, Paris, France
| | - Matthieu Piel
- Institut Curie, CNRS UMR 144, Paris, France
- * E-mail: (MP); (AM); (NM)
| | - Vincent Calvez
- Unité de Mathématiques Pures et Appliquées, CNRS UMR 5669 and équipe-projet INRIA NUMED, École Normale Supérieure de Lyon, Lyon, France
| | - Raphaël Voituriez
- Laboratoire Jean Perrin and Laboratoire de Physique Théorique de la Matière Condensée, UMR 7600 CNRS /UPMC, Paris, France
| | - Joana Gonçalves-Sá
- Molecular and Cell Biology and FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Chin-Lin Guo
- Molecular and Cell Biology and FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Institute of Physics, Academia Sinica, Taiwan
| | - Xingyu Jiang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, People’s Republic of China
| | - Andrew Murray
- Molecular and Cell Biology and FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail: (MP); (AM); (NM)
| | - Nicolas Meunier
- MAP5, CNRS UMR 8145, Université Paris Descartes, Paris, France
- * E-mail: (MP); (AM); (NM)
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Ismael A, Tian W, Waszczak N, Wang X, Cao Y, Suchkov D, Bar E, Metodiev MV, Liang J, Arkowitz RA, Stone DE. Gβ promotes pheromone receptor polarization and yeast chemotropism by inhibiting receptor phosphorylation. Sci Signal 2016; 9:ra38. [PMID: 27072657 DOI: 10.1126/scisignal.aad4376] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Gradient-directed cell migration (chemotaxis) and growth (chemotropism) are processes that are essential to the development and life cycles of all species. Cells use surface receptors to sense the shallow chemical gradients that elicit chemotaxis and chemotropism. Slight asymmetries in receptor activation are amplified by downstream signaling systems, which ultimately induce dynamic reorganization of the cytoskeleton. During the mating response of budding yeast, a model chemotropic system, the pheromone receptors on the plasma membrane polarize to the side of the cell closest to the stimulus. Although receptor polarization occurs before and independently of actin cable-dependent delivery of vesicles to the plasma membrane (directed secretion), it requires receptor internalization. Phosphorylation of pheromone receptors by yeast casein kinase 1 or 2 (Yck1/2) stimulates their internalization. We showed that the pheromone-responsive Gβγ dimer promotes the polarization of the pheromone receptor by interacting with Yck1/2 and locally inhibiting receptor phosphorylation. We also found that receptor phosphorylation is essential for chemotropism, independently of its role in inducing receptor internalization. A mathematical model supports the idea that the interaction between Gβγ and Yck1/2 results in differential phosphorylation and internalization of the pheromone receptor and accounts for its polarization before the initiation of directed secretion.
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Affiliation(s)
- Amber Ismael
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Wei Tian
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Nicholas Waszczak
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Xin Wang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Youfang Cao
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Dmitry Suchkov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Eli Bar
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Metodi V Metodiev
- School of Biological Sciences, University of Essex, Essex CO4 3SQ, UK
| | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Robert A Arkowitz
- CNRS UMR7277/INSERM UMR1091/Université Nice-Sophia Antipolis, Institute of Biology Valrose, 06108 Nice Cedex 2, France
| | - David E Stone
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
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McClure AW, Minakova M, Dyer JM, Zyla TR, Elston TC, Lew DJ. Role of Polarized G Protein Signaling in Tracking Pheromone Gradients. Dev Cell 2016; 35:471-82. [PMID: 26609960 DOI: 10.1016/j.devcel.2015.10.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 09/30/2015] [Accepted: 10/26/2015] [Indexed: 12/16/2022]
Abstract
Yeast cells track gradients of pheromones to locate mating partners. Intuition suggests that uniform distribution of pheromone receptors over the cell surface would yield optimal gradient sensing. However, yeast cells display polarized receptors. The benefit of such polarization was unknown. During gradient tracking, cell growth is directed by a patch of polarity regulators that wanders around the cortex. Patch movement is sensitive to pheromone dose, with wandering reduced on the up-gradient side of the cell, resulting in net growth in that direction. Mathematical modeling suggests that active receptors and associated G proteins lag behind the polarity patch and act as an effective drag on patch movement. In vivo, the polarity patch is trailed by a G protein-rich domain, and this polarized distribution of G proteins is required to constrain patch wandering. Our findings explain why G protein polarization is beneficial and illuminate a novel mechanism for gradient tracking.
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Affiliation(s)
- Allison W McClure
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Maria Minakova
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jayme M Dyer
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Trevin R Zyla
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Timothy C Elston
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Daniel J Lew
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.
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Sarto-Jackson I, Tomaska L. How to bake a brain: yeast as a model neuron. Curr Genet 2016; 62:347-70. [PMID: 26782173 DOI: 10.1007/s00294-015-0554-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 12/09/2015] [Accepted: 12/10/2015] [Indexed: 12/14/2022]
Abstract
More than 30 years ago Dan Koshland published an inspirational essay presenting the bacterium as a model neuron (Koshland, Trends Neurosci 6:133-137, 1983). In the article he argued that there are several similarities between neurons and bacterial cells in "how signals are processed within a cell or how this processing machinery can be modified to produce plasticity". He then explored the bacterial chemosensory system to emphasize its attributes that are analogous to information processing in neurons. In this review, we wish to expand Koshland's original idea by adding the yeast cell to the list of useful models of a neuron. The fact that yeasts and neurons are specialized versions of the eukaryotic cell sharing all principal components sets the stage for a grand evolutionary tinkering where these components are employed in qualitatively different tasks, but following analogous molecular logic. By way of example, we argue that evolutionarily conserved key components involved in polarization processes (from budding or mating in Saccharomyces cervisiae to neurite outgrowth or spinogenesis in neurons) are shared between yeast and neurons. This orthologous conservation of modules makes S. cervisiae an excellent model organism to investigate neurobiological questions. We substantiate this claim by providing examples of yeast models used for studying neurological diseases.
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Affiliation(s)
- Isabella Sarto-Jackson
- Konrad Lorenz Institute for Evolution and Cognition Research, Martinstraße 12, 3400, Klosterneuburg, Austria.
| | - Lubomir Tomaska
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynska dolina B-1, Ilkovicova 6, 842 15, Bratislava, Slovak Republic.
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Giese W, Eigel M, Westerheide S, Engwer C, Klipp E. Influence of cell shape, inhomogeneities and diffusion barriers in cell polarization models. Phys Biol 2015; 12:066014. [DOI: 10.1088/1478-3975/12/6/066014] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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50
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Turrà D, Di Pietro A. Chemotropic sensing in fungus-plant interactions. CURRENT OPINION IN PLANT BIOLOGY 2015; 26:135-40. [PMID: 26247120 DOI: 10.1016/j.pbi.2015.07.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 07/13/2015] [Accepted: 07/14/2015] [Indexed: 05/14/2023]
Abstract
Growth of fungal hyphae is guided by a variety of chemical gradients, including nutrients, mating pheromones or host compounds. Over 100 years after chemotropism was first reported in fungus-plant interactions, our knowledge on the host signals, fungal receptors and cellular pathways is still rudimentary. Genetic analysis in the model organisms Saccharomyces cerevisiae and Neurospora crassa has provided valuable insights into the chemotropic machinery of the fungal hypha. Moreover, recent studies in the root-infecting pathogen Fusarium oxysporum reveal an unanticipated complexity in chemotropic sensing of nutrient sources, peptide pheromones and host plant signals.
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Affiliation(s)
- David Turrà
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Antonio Di Pietro
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, 14071 Córdoba, Spain.
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