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Rácz HV, Mukhtar F, Imre A, Rádai Z, Gombert AK, Rátonyi T, Nagy J, Pócsi I, Pfliegler WP. How to characterize a strain? Clonal heterogeneity in industrial Saccharomyces influences both phenotypes and heterogeneity in phenotypes. Yeast 2021; 38:453-470. [PMID: 33844327 DOI: 10.1002/yea.3562] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/15/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022] Open
Abstract
Populations of microbes are constantly evolving heterogeneity that selection acts upon, yet heterogeneity is nontrivial to assess methodologically. The necessary practice of isolating single-cell colonies and thus subclone lineages for establishing, transferring, and using a strain results in single-cell bottlenecks with a generally neglected effect on the characteristics of the strain itself. Here, we present evidence that various subclone lineages for industrial yeasts sequenced for recent genomic studies show considerable differences, ranging from loss of heterozygosity to aneuploidies. Subsequently, we assessed whether phenotypic heterogeneity is also observable in industrial yeast, by individually testing subclone lineages obtained from products. Phenotyping of industrial yeast samples and their newly isolated subclones showed that single-cell bottlenecks during isolation can indeed considerably influence the observable phenotype. Next, we decoupled fitness distributions on the level of individual cells from clonal interference by plating single-cell colonies and quantifying colony area distributions. We describe and apply an approach using statistical modeling to compare the heterogeneity in phenotypes across samples and subclone lineages. One strain was further used to show how individual subclonal lineages are remarkably different not just in phenotype but also in the level of heterogeneity in phenotype. With these observations, we call attention to the fact that choosing an initial clonal lineage from an industrial yeast strain may vastly influence downstream performances and observations on karyotype, on phenotype, and also on heterogeneity.
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Affiliation(s)
- Hanna Viktória Rácz
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary.,Doctoral School of Nutrition and Food Sciences, University of Debrecen, Debrecen, Hungary
| | - Fezan Mukhtar
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary
| | - Alexandra Imre
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary.,Kálmán Laki Doctoral School of Biomedical and Clinical Sciences, University of Debrecen, Debrecen, Hungary
| | - Zoltán Rádai
- MTA-ÖK Lendület Seed Ecology Research Group, Institute of Ecology and Botany, Centre for Ecological Research, Vácrátót, Hungary
| | | | - Tamás Rátonyi
- Institute of Land Use, Technology and Regional Development, University of Debrecen, Debrecen, Hungary
| | - János Nagy
- Institute of Land Use, Technology and Regional Development, University of Debrecen, Debrecen, Hungary
| | - István Pócsi
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary
| | - Walter P Pfliegler
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary
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Váchová L, Palková Z. How structured yeast multicellular communities live, age and die? FEMS Yeast Res 2019; 18:4950397. [PMID: 29718174 DOI: 10.1093/femsyr/foy033] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/20/2018] [Indexed: 12/28/2022] Open
Abstract
Yeasts, like other microorganisms, create numerous types of multicellular communities, which differ in their complexity, cell differentiation and in the occupation of different niches. Some of the communities, such as colonies and some types of biofilms, develop by division and subsequent differentiation of cells growing on semisolid or solid surfaces to which they are attached or which they can penetrate. Aggregation of individual cells is important for formation of other community types, such as multicellular flocs, which sediment to the bottom or float to the surface of liquid cultures forming flor biofilms, organized at the border between liquid and air under specific circumstances. These examples together with the existence of more obscure communities, such as stalks, demonstrate that multicellularity is widespread in yeast. Despite this fact, identification of mechanisms and regulations involved in complex multicellular behavior still remains one of the challenges of microbiology. Here, we briefly discuss metabolic differences between particular yeast communities as well as the presence and functions of various differentiated cells and provide examples of the ability of these cells to develop different ways to cope with stress during community development and aging.
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Affiliation(s)
- Libuše Váchová
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, 252 50 Vestec, Czech Republic
| | - Zdena Palková
- Faculty of Science, Charles University, BIOCEV, 252 50 Vestec, Czech Republic
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3
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Palková Z, Váchová L. Yeast cell differentiation: Lessons from pathogenic and non-pathogenic yeasts. Semin Cell Dev Biol 2016; 57:110-119. [PMID: 27084693 DOI: 10.1016/j.semcdb.2016.04.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 04/10/2016] [Accepted: 04/11/2016] [Indexed: 11/29/2022]
Abstract
Yeasts, historically considered to be single-cell organisms, are able to activate different differentiation processes. Individual yeast cells can change their life-styles by processes of phenotypic switching such as the switch from yeast-shaped cells to filamentous cells (pseudohyphae or true hyphae) and the transition among opaque, white and gray cell-types. Yeasts can also create organized multicellular structures such as colonies and biofilms, and the latter are often observed as contaminants on surfaces in industry and medical care and are formed during infections of the human body. Multicellular structures are formed mostly of stationary-phase or slow-growing cells that diversify into specific cell subpopulations that have unique metabolic properties and can fulfill specific tasks. In addition to the development of multiple protective mechanisms, processes of metabolic reprogramming that reflect a changed environment help differentiated individual cells and/or community cell constituents to survive harmful environmental attacks and/or to escape the host immune system. This review aims to provide an overview of differentiation processes so far identified in individual yeast cells as well as in multicellular communities of yeast pathogens of the Candida and Cryptococcus spp. and the Candida albicans close relative, Saccharomyces cerevisiae. Molecular mechanisms and extracellular signals potentially involved in differentiation processes are also briefly mentioned.
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Affiliation(s)
- Zdena Palková
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 44 Prague 2, Czech Republic.
| | - Libuše Váchová
- Institute of Microbiology of the CAS, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic.
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4
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Faria-Oliveira F, Carvalho J, Ferreira C, Hernáez ML, Gil C, Lucas C. Quantitative differential proteomics of yeast extracellular matrix: there is more to it than meets the eye. BMC Microbiol 2015; 15:271. [PMID: 26608260 PMCID: PMC4660637 DOI: 10.1186/s12866-015-0550-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/12/2015] [Indexed: 11/16/2022] Open
Abstract
Background Saccharomyces cerevisiae multicellular communities are sustained by a scaffolding extracellular matrix, which provides spatial organization, and nutrient and water availability, and ensures group survival. According to this tissue-like biology, the yeast extracellular matrix (yECM) is analogous to the higher Eukaryotes counterpart for its polysaccharide and proteinaceous nature. Few works focused on yeast biofilms, identifying the flocculin Flo11 and several members of the HSP70 in the extracellular space. Molecular composition of the yECM, is therefore mostly unknown. The homologue of yeast Gup1 protein in high Eukaryotes (HHATL) acts as a regulator of Hedgehog signal secretion, therefore interfering in morphogenesis and cell-cell communication through the ECM, which mediates but is also regulated by this signalling pathway. In yeast, the deletion of GUP1 was associated with a vast number of diverse phenotypes including the cellular differentiation that accompanies biofilm formation. Methods S. cerevisiae W303-1A wt strain and gup1∆ mutant were used as previously described to generate biofilm-like mats in YPDa from which the yECM proteome was extracted. The proteome from extracellular medium from batch liquid growing cultures was used as control for yECM-only secreted proteins. Proteins were separated by SDS-PAGE and 2DE. Identification was performed by HPLC, LC-MS/MS and MALDI-TOF/TOF. The protein expression comparison between the two strains was done by DIGE, and analysed by DeCyder Extended Data Analysis that included Principal Component Analysis and Hierarchical Cluster Analysis. Results The proteome of S. cerevisiae yECM from biofilm-like mats was purified and analysed by Nano LC-MS/MS, 2D Difference Gel Electrophoresis (DIGE), and MALDI-TOF/TOF. Two strains were compared, wild type and the mutant defective in GUP1. As controls for the identification of the yECM-only proteins, the proteome from liquid batch cultures was also identified. Proteins were grouped into distinct functional classes, mostly Metabolism, Protein Fate/Remodelling and Cell Rescue and Defence mechanisms, standing out the presence of heat shock chaperones, metalloproteinases, broad signalling cross-talkers and other putative signalling proteins. The data has been deposited to the ProteomeXchange with identifier PXD001133. Conclusions yECM, as the mammalian counterpart, emerges as highly proteinaceous. As in higher Eukaryotes ECM, numerous proteins that could allow dynamic remodelling, and signalling events to occur in/and via yECM were identified. Importantly, large sets of enzymes encompassing full antagonistic metabolic pathways, suggest that mats develop into two metabolically distinct populations, suggesting that either extensive moonlighting or actual metabolism occurs extracellularly. The gup1∆ showed abnormally loose ECM texture. Accordingly, the correspondent differences in proteome unveiled acetic and citric acid producing enzymes as putative players in structural integrity maintenance.
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Affiliation(s)
- Fábio Faria-Oliveira
- CBMA - Centro de Biologia Molecular e Ambiental, Departamento de Biologia, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Joana Carvalho
- CBMA - Centro de Biologia Molecular e Ambiental, Departamento de Biologia, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Célia Ferreira
- CBMA - Centro de Biologia Molecular e Ambiental, Departamento de Biologia, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Maria Luisa Hernáez
- Unidad de Proteómica, Universidad Complutense de Madrid - Parque Científico de Madrid (UCM-PCM), Madrid, Spain
| | - Concha Gil
- Unidad de Proteómica, Universidad Complutense de Madrid - Parque Científico de Madrid (UCM-PCM), Madrid, Spain.,Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Cândida Lucas
- CBMA - Centro de Biologia Molecular e Ambiental, Departamento de Biologia, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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A Gβ protein and the TupA Co-Regulator Bind to Protein Kinase A Tpk2 to Act as Antagonistic Molecular Switches of Fungal Morphological Changes. PLoS One 2015; 10:e0136866. [PMID: 26334875 PMCID: PMC4559445 DOI: 10.1371/journal.pone.0136866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/09/2015] [Indexed: 11/19/2022] Open
Abstract
The human pathogenic fungus Paracoccidioides brasiliensis (Pb) undergoes a morphological transition from a saprobic mycelium to pathogenic yeast that is controlled by the cAMP-signaling pathway. There is a change in the expression of the Gβ-protein PbGpb1, which interacts with adenylate cyclase, during this morphological transition. We exploited the fact that the cAMP-signaling pathway of Saccharomyces cerevisiae does not include a Gβ-protein to probe the functional role of PbGpb1. We present data that indicates that PbGpb1 and the transcriptional regulator PbTupA both bind to the PKA protein PbTpk2. PbTPK2 was able to complement a TPK2Δ strain of S. cerevisiae, XPY5a/α, which was defective in pseudohyphal growth. Whilst PbGPB1 had no effect on the parent S. cerevisiae strain, MLY61a/α, it repressed the filamentous growth of XPY5a/α transformed with PbTPK2, behaviour that correlated with a reduced expression of the floculin FLO11. In vitro, PbGpb1 reduced the kinase activity of PbTpk2, suggesting that inhibition of PbTpk2 by PbGpb1 reduces the level of expression of Flo11, antagonizing the filamentous growth of the cells. In contrast, expressing the co-regulator PbTUPA in XPY5a/α cells transformed with PbTPK2, but not untransformed cells, induced hyperfilamentous growth, which could be antagonized by co-transforming the cells with PbGPB1. PbTUPA was unable to induce the hyperfilamentous growth of a FLO8Δ strain, suggesting that PbTupA functions in conjunction with the transcription factor Flo8 to control Flo11 expression. Our data indicates that P. brasiliensis PbGpb1 and PbTupA, both of which have WD/β-propeller structures, bind to PbTpk2 to act as antagonistic molecular switches of cell morphology, with PbTupA and PbGpb1 inducing and repressing filamentous growth, respectively. Our findings define a potential mechanism for controlling the morphological switch that underpins the virulence of dimorphic fungi.
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Faria-Oliveira F, Carvalho J, Belmiro CLR, Ramalho G, Pavão M, Lucas C, Ferreira C. Elemental biochemical analysis of the polysaccharides in the extracellular matrix of the yeastSaccharomyces cerevisiae. J Basic Microbiol 2015; 55:685-94. [DOI: 10.1002/jobm.201400781] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/08/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Fábio Faria-Oliveira
- Centre of Molecular and Environmental Biology (CBMA); Department of Biology; University of Minho; Portugal
| | - Joana Carvalho
- Centre of Molecular and Environmental Biology (CBMA); Department of Biology; University of Minho; Portugal
| | - Celso LR Belmiro
- Laboratory of Glycoconjugates Biochemistry and Cellular Biology; Federal University of Rio de Janeiro; Campus of Macaé RJ Brazil
- Laboratory of Glycoconjugates Biochemistry and Cellular Biology; Institute of Medical Biochemistry; Federal University of Rio de Janeiro; RJ Brazil
| | - Gustavo Ramalho
- Laboratory of Glycoconjugates Biochemistry and Cellular Biology; Institute of Medical Biochemistry; Federal University of Rio de Janeiro; RJ Brazil
| | - Mauro Pavão
- Laboratory of Glycoconjugates Biochemistry and Cellular Biology; Institute of Medical Biochemistry; Federal University of Rio de Janeiro; RJ Brazil
| | - Cândida Lucas
- Centre of Molecular and Environmental Biology (CBMA); Department of Biology; University of Minho; Portugal
| | - Célia Ferreira
- Centre of Molecular and Environmental Biology (CBMA); Department of Biology; University of Minho; Portugal
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Vulin C, Di Meglio JM, Lindner AB, Daerr A, Murray A, Hersen P. Growing yeast into cylindrical colonies. Biophys J 2014; 106:2214-21. [PMID: 24853750 PMCID: PMC4052359 DOI: 10.1016/j.bpj.2014.02.040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 01/28/2014] [Accepted: 02/25/2014] [Indexed: 10/27/2022] Open
Abstract
Microorganisms often form complex multicellular assemblies such as biofilms and colonies. Understanding the interplay between assembly expansion, metabolic yield, and nutrient diffusion within a freely growing colony remains a challenge. Most available data on microorganisms are from planktonic cultures, due to the lack of experimental tools to control the growth of multicellular assemblies. Here, we propose a method to constrain the growth of yeast colonies into simple geometric shapes such as cylinders. To this end, we designed a simple, versatile culture system to control the location of nutrient delivery below a growing colony. Under such culture conditions, yeast colonies grow vertically and only at the locations where nutrients are delivered. Colonies increase in height at a steady growth rate that is inversely proportional to the cylinder radius. We show that the vertical growth rate of cylindrical colonies is not defined by the single-cell division rate, but rather by the colony metabolic yield. This contrasts with cells in liquid culture, in which the single-cell division rate is the only parameter that defines the population growth rate. This method also provides a direct, simple method to estimate the metabolic yield of a colony. Our study further demonstrates the importance of the shape of colonies on setting their expansion. We anticipate that our approach will be a starting point for elaborate studies of the population dynamics, evolution, and ecology of microbial colonies in complex landscapes.
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Affiliation(s)
- Clément Vulin
- Laboratoire Matière et Systèmes Complexes, Centre National de la Recherche Scientifique and Université Paris Diderot, Paris, France
| | - Jean-Marc Di Meglio
- Laboratoire Matière et Systèmes Complexes, Centre National de la Recherche Scientifique and Université Paris Diderot, Paris, France
| | - Ariel B Lindner
- Institut National de la Santé et de la Recherche Médicale, Faculté de Médecine, Université Paris Descartes, Paris, France
| | - Adrian Daerr
- Laboratoire Matière et Systèmes Complexes, Centre National de la Recherche Scientifique and Université Paris Diderot, Paris, France
| | - Andrew Murray
- Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts
| | - Pascal Hersen
- Laboratoire Matière et Systèmes Complexes, Centre National de la Recherche Scientifique and Université Paris Diderot, Paris, France; The Mechanobiology Institute, National University of Singapore, Singapore.
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8
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Faria-Oliveira F, Carvalho J, Belmiro CLR, Martinez-Gomariz M, Hernaez ML, Pavão M, Gil C, Lucas C, Ferreira C. Methodologies to generate, extract, purify and fractionate yeast ECM for analytical use in proteomics and glycomics. BMC Microbiol 2014; 14:244. [PMID: 25344425 PMCID: PMC4219020 DOI: 10.1186/s12866-014-0244-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 09/09/2014] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND In a multicellular organism, the extracellular matrix (ECM) provides a cell-supporting scaffold and helps maintaining the biophysical integrity of tissues and organs. At the same time it plays crucial roles in cellular communication and signalling, with implications in spatial organisation, motility and differentiation. Similarly, the presence of an ECM-like extracellular polymeric substance is known to support and protect bacterial and fungal multicellular aggregates, such as biofilms or colonies. However, the roles and composition of this microbial ECM are still poorly understood. RESULTS This work presents a protocol to produce S. cerevisiae and C. albicans ECM in an equally highly reproducible manner. Additionally, methodologies for the extraction and fractionation into protein and glycosidic analytical pure fractions were improved. These were subjected to analytical procedures, respectively SDS-PAGE, 2-DE, MALDI-TOF-MS and LC-MS/MS, and DAE and FPLC. Additional chemical methods were also used to test for uronic acids and sulphation. CONCLUSIONS The methodologies hereby presented were equally efficiently applied to extract high amounts of ECM material from S. cerevisiae and C. albicans mats, therefore showing their robustness and reproducibility for yECM molecular and structural characterization. yECM from S. cerevisiae and C. albicans displayed a different proteome and glycoside fractions. S. cerevisiae yECM presented two well-defined polysaccharides with different mass/charge, and C. albicans ECM presented a single different one. The chemical methods further suggested the presence of uronic acids, and chemical modification, possibly through sulphate substitution. All taken, the procedures herein described present the first sensible and concise approach to the molecular and chemical characterisation of the yeast ECM, opening the way to the in-depth study of the microbe multicellular aggregates structure and life-style.
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Affiliation(s)
- Fábio Faria-Oliveira
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.
| | - Joana Carvalho
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.
| | - Celso L R Belmiro
- Institute of Medical Biochemistry, Laboratory of Glycoconjugates Biochemistry and Cellular Biology, Federal University of Rio de Janeiro/ Polo de Macaé, Macaé, Brazil.
| | - Montserrat Martinez-Gomariz
- Unidad de Proteómica, Universidad Complutense de Madrid - Parque Científico de Madrid UCM-PCM), Madrid, Spain.
| | - Maria Luisa Hernaez
- Unidad de Proteómica, Universidad Complutense de Madrid - Parque Científico de Madrid UCM-PCM), Madrid, Spain.
| | - Mauro Pavão
- Institute of Medical Biochemistry, Laboratory of Glycoconjugates Biochemistry and Cellular Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Concha Gil
- Unidad de Proteómica, Universidad Complutense de Madrid - Parque Científico de Madrid UCM-PCM), Madrid, Spain. .,Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain.
| | - Cândida Lucas
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.
| | - Célia Ferreira
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.
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Engelberg D, Perlman R, Levitzki A. Transmembrane signaling in Saccharomyces cerevisiae as a model for signaling in metazoans: state of the art after 25 years. Cell Signal 2014; 26:2865-78. [PMID: 25218923 DOI: 10.1016/j.cellsig.2014.09.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 09/02/2014] [Indexed: 02/07/2023]
Abstract
In the very first article that appeared in Cellular Signalling, published in its inaugural issue in October 1989, we reviewed signal transduction pathways in Saccharomyces cerevisiae. Although this yeast was already a powerful model organism for the study of cellular processes, it was not yet a valuable instrument for the investigation of signaling cascades. In 1989, therefore, we discussed only two pathways, the Ras/cAMP and the mating (Fus3) signaling cascades. The pivotal findings concerning those pathways undoubtedly contributed to the realization that yeast is a relevant model for understanding signal transduction in higher eukaryotes. Consequently, the last 25 years have witnessed the discovery of many signal transduction pathways in S. cerevisiae, including the high osmotic glycerol (Hog1), Stl2/Mpk1 and Smk1 mitogen-activated protein (MAP) kinase pathways, the TOR, AMPK/Snf1, SPS, PLC1 and Pkr/Gcn2 cascades, and systems that sense and respond to various types of stress. For many cascades, orthologous pathways were identified in mammals following their discovery in yeast. Here we review advances in the understanding of signaling in S. cerevisiae over the last 25 years. When all pathways are analyzed together, some prominent themes emerge. First, wiring of signaling cascades may not be identical in all S. cerevisiae strains, but is probably specific to each genetic background. This situation complicates attempts to decipher and generalize these webs of reactions. Secondly, the Ras/cAMP and the TOR cascades are pivotal pathways that affect all processes of the life of the yeast cell, whereas the yeast MAP kinase pathways are not essential. Yeast cells deficient in all MAP kinases proliferate normally. Another theme is the existence of central molecular hubs, either as single proteins (e.g., Msn2/4, Flo11) or as multisubunit complexes (e.g., TORC1/2), which are controlled by numerous pathways and in turn determine the fate of the cell. It is also apparent that lipid signaling is less developed in yeast than in higher eukaryotes. Finally, feedback regulatory mechanisms seem to be at least as important and powerful as the pathways themselves. In the final chapter of this essay we dare to imagine the essence of our next review on signaling in yeast, to be published on the 50th anniversary of Cellular Signalling in 2039.
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Affiliation(s)
- David Engelberg
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel; CREATE-NUS-HUJ, Cellular & Molecular Mechanisms of Inflammation Programme, National University of Singapore, 1 CREATE Way, Innovation Wing, #03-09, Singapore 138602, Singapore.
| | - Riki Perlman
- Hematology Division, Hadassah Hebrew University Medical Center, POB 12000, 91120 Jerusalem, Israel
| | - Alexander Levitzki
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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10
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Rapidly developing yeast microcolonies differentiate in a similar way to aging giant colonies. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2013; 2013:102485. [PMID: 23970946 PMCID: PMC3736409 DOI: 10.1155/2013/102485] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 06/25/2013] [Indexed: 12/28/2022]
Abstract
During their development and aging on solid substrates, yeast giant colonies produce ammonia, which acts as a quorum sensing molecule. Ammonia production is connected with alkalization of the surrounding medium and with extensive reprogramming of cell metabolism. In addition, ammonia signaling is important for both horizontal (colony centre versus colony margin) and vertical (upper versus lower cell layers) colony differentiations. The centre of an aging differentiated giant colony is thus composed of two major cell subpopulations, the subpopulation of long-living, metabolically active and stress-resistant cells that form the upper layers of the colony and the subpopulation of stress-sensitive starving cells in the colony interior. Here, we show that microcolonies originating from one cell pass through similar developmental phases as giant colonies. Microcolony differentiation is linked to ammonia signaling, and cells similar to the upper and lower cells of aged giant colonies are formed even in relatively young microcolonies. A comparison of the properties of these cells revealed a number of features that are similar in microcolonies and giant colonies as well as a few that are only typical of chronologically aged giant colonies. These findings show that colony age per se is not crucial for colony differentiation.
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11
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Daniels KJ, Pujol C, Srikantha T, Soll DR. The "finger," a unique multicellular morphology of Candida albicans induced by CO2 and dependent upon the Ras1-cyclic AMP pathway. EUKARYOTIC CELL 2012; 11:1257-67. [PMID: 22923045 PMCID: PMC3485925 DOI: 10.1128/ec.00217-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 08/14/2012] [Indexed: 11/20/2022]
Abstract
Most experiments exploring the basic biology of pathogenic microbes are performed in vitro under conditions that do not usually mimic those of their host niche. Hence, developmental programs initiated by specific host cues may be missed in vitro. We have tested the effects of growing low-density agar cultures of the yeast pathogen Candida albicans in concentrations of CO(2) found in the gastrointestinal tract. It is demonstrated that in physiological concentrations of CO(2) at 37°C, yeast cells form a heretofore undescribed multicellular "finger" morphology distinct from a previously described stalk-like structure induced by high doses of UV irradiation that kills more than 99.99% of cells. The finger extends aerially, is uniform in diameter, and is visible to the naked eye, attaining lengths of 3 mm. It is composed of a basal yeast cell monolayer adhering to a semispherical crater formed in the agar and connected to a basal bulb of yeast cells at a fragile interface. The bulb extends into the long shaft. We propose that a single, centrally located hypha extending the length of the shaft forms buds at compartment junctions that serve as the source of the yeast cells in the shaft. A mutational analysis reveals finger formation is dependent upon the pathway Ras1→Cdc35→cyclic AMP (cAMP) (PDE2-|)→Tpk2→Tec1. Because of the mechanically fragile interface and the compactness of bulb and shaft, we suggest that the finger may function as a multicellular dispersal mechanism produced in host niches containing high levels of CO(2).
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Affiliation(s)
- Karla J Daniels
- Developmental Studies Hybridoma Bank, Department of Biology, The University of Iowa, Iowa City, IA, USA
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12
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Yeast colonies: a model for studies of aging, environmental adaptation, and longevity. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2012; 2012:601836. [PMID: 22928081 PMCID: PMC3425895 DOI: 10.1155/2012/601836] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 07/09/2012] [Indexed: 11/18/2022]
Abstract
When growing on solid surfaces, yeast, like other microorganisms, develops organized multicellular populations (colonies and biofilms) that are composed of differentiated cells with specialized functions. Life within these populations is a prevalent form of microbial existence in natural settings that provides the cells with capabilities to effectively defend against environmental attacks as well as efficiently adapt and survive long periods of starvation and other stresses. Under such circumstances, the fate of an individual yeast cell is subordinated to the profit of the whole population. In the past decade, yeast colonies, with their complicated structure and high complexity that are also developed under laboratory conditions, have become an excellent model for studies of various basic cellular processes such as cell interaction, signaling, and differentiation. In this paper, we summarize current knowledge on the processes related to chronological aging, adaptation, and longevity of a colony cell population and of its differentiated cell constituents. These processes contribute to the colony ability to survive long periods of starvation and mostly differ from the survival strategies of individual yeast cells.
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Cáp M, Stěpánek L, Harant K, Váchová L, Palková Z. Cell differentiation within a yeast colony: metabolic and regulatory parallels with a tumor-affected organism. Mol Cell 2012; 46:436-48. [PMID: 22560924 DOI: 10.1016/j.molcel.2012.04.001] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 12/16/2011] [Accepted: 03/23/2012] [Indexed: 12/30/2022]
Abstract
Nutrient sensing and metabolic reprogramming are crucial for metazoan cell aging and tumor growth. Here, we identify metabolic and regulatory parallels between a layered, multicellular yeast colony and a tumor-affected organism. During development, a yeast colony stratifies into U and L cells occupying the upper and lower colony regions, respectively. U cells activate a unique metabolism controlled by the glutamine-induced TOR pathway, amino acid-sensing systems (SPS and Gcn4p) and signaling from mitochondria with lowered respiration. These systems jointly modulate U cell physiology, which adapts to nutrient limitations and utilize the nutrients released from L cells. Stress-resistant U cells share metabolic pathways and other similar characteristics with tumor cells, including the ability to proliferate. L cells behave similarly to stressed and starving cells, which activate degradative mechanisms to provide nutrients to U cells. Our data suggest a nutrient flow between both cell types, resembling the Cori cycle and glutamine-NH(4)(+) shuttle between tumor and healthy metazoan cells.
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Affiliation(s)
- Michal Cáp
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
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14
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Brückner S, Mösch HU. Choosing the right lifestyle: adhesion and development in Saccharomyces cerevisiae. FEMS Microbiol Rev 2011; 36:25-58. [PMID: 21521246 DOI: 10.1111/j.1574-6976.2011.00275.x] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The budding yeast Saccharomyces cerevisiae is a eukaryotic microorganism that is able to choose between different unicellular and multicellular lifestyles. The potential of individual yeast cells to switch between different growth modes is advantageous for optimal dissemination, protection and substrate colonization at the population level. A crucial step in lifestyle adaptation is the control of self- and foreign adhesion. For this purpose, S. cerevisiae contains a set of cell wall-associated proteins, which confer adhesion to diverse biotic and abiotic surfaces. Here, we provide an overview of different aspects of S. cerevisiae adhesion, including a detailed description of known lifestyles, recent insights into adhesin structure and function and an outline of the complex regulatory network for adhesin gene regulation. Our review shows that S. cerevisiae is a model system suitable for studying not only the mechanisms and regulation of cell adhesion, but also the role of this process in microbial development, ecology and evolution.
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Affiliation(s)
- Stefan Brückner
- Department of Genetics, Philipps-Universität Marburg, Marburg, Germany
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15
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Abstract
Patterning of different cell types in embryos is a key mechanism in metazoan development. Communities of microorganisms, such as colonies and biofilms also display patterns of cell types. For example, in the yeast S. cerevisiae, sporulated cells and pseudohyphal cells are not uniformly distributed in colonies. The functional importance of patterning and the molecular mechanisms that underlie these patterns are still poorly understood. One challenge with respect to investigating patterns of cell types in fungal colonies is that unlike metazoan tissue, cells in colonies are relatively weakly attached to one another. In particular, fungal colonies do not contain the same extensive level of extracellular matrix found in most tissues . Here we report on a method for embedding and sectioning yeast colonies that reveals the interior patterns of cell types in these colonies. The method can be used to prepare thick sections (0.5 μ) useful for light microscopy and thin sections (0.1 μ) suitable for transmission electron microscopy. Asci and pseudohyphal cells can easily be distinguished from ovoid yeast cells by light microscopy , while the interior structure of these cells can be visualized by EM. The method is based on surrounding colonies with agar, infiltrating them with Spurr's medium, and then sectioning. Colonies with a diameter in the range of 1-2 mm are suitable for this protocol. In addition to visualizing the interior of colonies, the method allows visualization of the region of the colony that invades the underlying agar.
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Affiliation(s)
- Sarah Piccirillo
- School of Biological Sciences, University of Missouri - Kansas City, USA
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16
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Granek JA, Magwene PM. Environmental and genetic determinants of colony morphology in yeast. PLoS Genet 2010; 6:e1000823. [PMID: 20107600 PMCID: PMC2809765 DOI: 10.1371/journal.pgen.1000823] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Accepted: 12/21/2009] [Indexed: 12/30/2022] Open
Abstract
Nutrient stresses trigger a variety of developmental switches in the budding yeast Saccharomyces cerevisiae. One of the least understood of such responses is the development of complex colony morphology, characterized by intricate, organized, and strain-specific patterns of colony growth and architecture. The genetic bases of this phenotype and the key environmental signals involved in its induction have heretofore remained poorly understood. By surveying multiple strain backgrounds and a large number of growth conditions, we show that limitation for fermentable carbon sources coupled with a rich nitrogen source is the primary trigger for the colony morphology response in budding yeast. Using knockout mutants and transposon-mediated mutagenesis, we demonstrate that two key signaling networks regulating this response are the filamentous growth MAP kinase cascade and the Ras-cAMP-PKA pathway. We further show synergistic epistasis between Rim15, a kinase involved in integration of nutrient signals, and other genes in these pathways. Ploidy, mating-type, and genotype-by-environment interactions also appear to play a role in the controlling colony morphology. Our study highlights the high degree of network reuse in this model eukaryote; yeast use the same core signaling pathways in multiple contexts to integrate information about environmental and physiological states and generate diverse developmental outputs.
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Affiliation(s)
- Joshua A. Granek
- Department of Biology and Center for Systems Biology, Duke University, Durham, North Carolina, United States of America
| | - Paul M. Magwene
- Department of Biology and Center for Systems Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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17
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Self-organization in high-density bacterial colonies: efficient crowd control. PLoS Biol 2008; 5:e302. [PMID: 18044986 PMCID: PMC2043048 DOI: 10.1371/journal.pbio.0050302] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Accepted: 09/21/2007] [Indexed: 12/14/2022] Open
Abstract
Colonies of bacterial cells can display complex collective dynamics, frequently culminating in the formation of biofilms and other ordered super-structures. Recent studies suggest that to cope with local environmental challenges, bacterial cells can actively seek out small chambers or cavities and assemble there, engaging in quorum sensing behavior. By using a novel microfluidic device, we showed that within chambers of distinct shapes and sizes allowing continuous cell escape, bacterial colonies can gradually self-organize. The directions of orientation of cells, their growth, and collective motion are mutually correlated and dictated by the chamber walls and locations of chamber exits. The ultimate highly organized steady state is conducive to a more-organized escape of cells from the chambers and increased access of nutrients into and evacuation of waste out of the colonies. Using a computational model, we suggest that the lengths of the cells might be optimized to maximize self-organization while minimizing the potential for stampede-like exit blockage. The self-organization described here may be crucial for the early stage of the organization of high-density bacterial colonies populating small, physically confined growth niches. It suggests that this phenomenon can play a critical role in bacterial biofilm initiation and development of other complex multicellular bacterial super-structures, including those implicated in infectious diseases.
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18
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Wedlich-Soldner R, Li R. Yeast and fungal morphogenesis from an evolutionary perspective. Semin Cell Dev Biol 2008; 19:224-33. [PMID: 18299240 DOI: 10.1016/j.semcdb.2008.01.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Accepted: 01/16/2008] [Indexed: 01/21/2023]
Abstract
Cellular morphogenesis is a complex process and molecular studies in the last few decades have amassed a large amount of information that is difficult to grasp in any completeness. Fungal systems, in particular the budding and fission yeasts, have been important players in unravelling the basic structural and regulatory elements involved in a wide array of cellular processes. In this article, we address the design principles underlying the various processes of yeast and fungal morphogenesis. We attempt to explain the apparent molecular complexity from the perspective of the evolutionary theory of "facilitated variation". Following a summary of some of the most studied morphogenetic phenomena, we discuss, using recent examples, the underlying core processes and their associated "weak" regulatory linkages that bring about variation in morphogenetic phenotypes.
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19
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Landry CR, Townsend JP, Hartl DL, Cavalieri D. Ecological and evolutionary genomics of Saccharomyces cerevisiae. Mol Ecol 2006; 15:575-91. [PMID: 16499686 DOI: 10.1111/j.1365-294x.2006.02778.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Saccharomyces cerevisiae, the budding yeast, is the most thoroughly studied eukaryote at the cellular, molecular, and genetic levels. Yet, until recently, we knew very little about its ecology or population and evolutionary genetics. In recent years, it has been recognized that S. cerevisiae occupies numerous habitats and that populations harbour important genetic variation. There is therefore an increasing interest in understanding the evolutionary forces acting on the yeast genome. Several researchers have used the tools of functional genomics to study natural isolates of this unicellular fungus. Here, we review some of these studies, and show not only that budding yeast is a prime model system to address fundamental molecular and cellular biology questions, but also that it is becoming a powerful model species for ecological and evolutionary genomics studies as well.
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Affiliation(s)
- Christian R Landry
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
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20
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Ohad I, Nevo R, Brumfeld V, Reich Z, Tsur T, Yair M, Kaplan A. Inactivation of photosynthetic electron flow during desiccation of desert biological sand crusts and Microcoleus sp.-enriched isolates. Photochem Photobiol Sci 2005; 4:977-82. [PMID: 16307110 DOI: 10.1039/b506300k] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Filamentous cyanobacteria, the main primary producers in biological sand crusts, survive harsh environmental conditions including diurnal desiccation/rehydration cycles. Here we describe the inactivation of photosystem II during dehydration of native crusts (NC) and Microcoleus sp. isolates grown on nitrocellulose filters (NCF). The morphology of NCF cells, visualized by scanning-transmission and atomic-force microscopy, disclosed long bacterial filaments encapsulated in extracellular polysaccharides (EPS) tubes consisting of parallel fibrils (100-400 nm wide and 50-100 nm high) oriented mostly perpendicular to the tube length. Presence of empty EPS tubes indicated a gliding capability of the cells. Desiccation of NC resulted in a rapid decline of F(o) and complete loss of F(v). These changes were accompanied by a decrease of 77 K PSII fluorescence emission relative to that of PSI, when excited at 430 nm, and a significant decrease of energy transfer from phycobilisomes to PSII. Lowering the turgor pressure through the addition of 1.5 M trehalose to natural crusts, reduced F(v)/F(m) by over 50% and was accompanied by a decrease of 77 K PSI fluorescence induced by chlorophyll excitation. Excitation of phycobilisomes resulted in a downshift of the PSI emission wavelength by 8 nm, indicative of reduced energy transfer from LHCI to the core PSI. Decline of F(v)/F(m) in trehalose-incubated NCF cells did not induce significant changes in 77 K fluorescence emission. These results suggest that alterations in energy transfer from antennae to reaction centers may be part of the survival strategy of Microcoleus.
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Affiliation(s)
- Itzhak Ohad
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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21
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Palková Z. Multicellular microorganisms: laboratory versus nature. EMBO Rep 2005; 5:470-6. [PMID: 15184977 PMCID: PMC1299056 DOI: 10.1038/sj.embor.7400145] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2004] [Accepted: 03/15/2004] [Indexed: 11/09/2022] Open
Abstract
Our present in-depth knowledge of the physiology and regulatory mechanisms of microorganisms has arisen from our ability to remove them from their natural, complex ecosystems into pure liquid cultures. These cultures are grown under optimized laboratory conditions and allow us to study microorganisms as individuals. However, microorganisms naturally grow in conditions that are far from optimal, which causes them to become organized into multicellular communities that are better protected against the harmful environment. Moreover, this multicellular existence allows individual cells to differentiate and acquire specific properties, such as forming resistant spores, which benefit the whole population. The relocation of natural microorganisms to the laboratory can result in their adaptation to these favourable conditions, which is accompanied by complex changes that include the repression of some protective mechanisms that are essential in nature. Laboratory microorganisms that have been cultured for long periods under optimized conditions might therefore differ markedly from those that exist in natural ecosystems.
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Affiliation(s)
- Zdena Palková
- Department of Genetics and Microbiology, Charles University, Vinicná 5, 12844 Prague 2, Czech Republic.
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22
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Palková Z, Vachova L. Ammonia signaling in yeast colony formation. INTERNATIONAL REVIEW OF CYTOLOGY 2003; 225:229-72. [PMID: 12696594 DOI: 10.1016/s0074-7696(05)25006-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Multicellular structures formed by microorganisms possess various properties, which make them interesting in terms of processes that occur in tissues of higher eukaryotes. These include processes important for morphogenesis and development of multicellular structures as well as those evoked by stress, starvation, and aging. Investigation of colonies created by simple nonmotile yeast cells revealed the existence of various regulators involved in their development. One of the identified signaling compounds, unprotonated volatile ammonia, is produced by colonies in pulses and seems to represent a long-distance signal notifying the colony population of incoming nutrient starvation. This alarm evokes changes in colonies that are important for their long-term survival. Models of the action of ammonia on yeast cells as well as the routes of its production are proposed. Interestingly, ammonia/ammonium also act as a signaling molecule in other organisms. Ammonia regulates several steps of the multicellular development of Dictyostelium discoideum and evidence indicates that ammonia/ammonium plays a role in neural tissues of higher eukaryotes.
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Affiliation(s)
- Zdena Palková
- Department of Genetics and Microbiology, Charles University, 12844 Prague 2, Czech Republic.
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23
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Breitkreutz A, Boucher L, Breitkreutz BJ, Sultan M, Jurisica I, Tyers M. Phenotypic and Transcriptional Plasticity Directed by a Yeast Mitogen-Activated Protein Kinase Network. Genetics 2003; 165:997-1015. [PMID: 14668360 PMCID: PMC1462838 DOI: 10.1093/genetics/165.3.997] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
The yeast pheromone/filamentous growth MAPK pathway mediates both mating and invasive-growth responses. The interface between this MAPK module and the transcriptional machinery consists of a network of two MAPKs, Fus3 and Kss1; two regulators, Rst1 and Rst2 (a.k.a. Dig1 and Dig2); and two transcription factors, Ste12 and Tec1. Of 16 possible combinations of gene deletions in FUS3, KSS1, RST1, and RST2 in the Σ1278 background, 10 display constitutive invasive growth. Rst1 was the primary negative regulator of invasive growth, while other components either attenuated or enhanced invasive growth, depending on the genetic context. Despite activation of the invasive response by lesions at the same level in the MAPK pathway, transcriptional profiles of different invasive mutant combinations did not exhibit a unified program of gene expression. The distal MAPK regulatory network is thus capable of generating phenotypically similar invasive-growth states (an attractor) from different molecular architectures (trajectories) that can functionally compensate for one another. This systems-level robustness may also account for the observed diversity of signals that trigger invasive growth.
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Affiliation(s)
- Ashton Breitkreutz
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
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24
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Kuthan M, Devaux F, Janderová B, Slaninová I, Jacq C, Palková Z. Domestication of wild Saccharomyces cerevisiae is accompanied by changes in gene expression and colony morphology. Mol Microbiol 2003; 47:745-54. [PMID: 12535073 DOI: 10.1046/j.1365-2958.2003.03332.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Although colonies from Saccharomyces cerevisiae laboratory strains are smooth, those isolated from nature exhibit a structured fluffy pattern. Environmental scanning electron microscopy shows that the cells within wild fluffy colonies are connected by extracellular matrix (ECM) material. This material contains a protein of about 200 kDa unrelated to the flocculins, proteins involved in cell-cell adhesion in liquid media. The matrix material binds to concanavalin A. Within a few passages on rich agar medium, the wild strains switch from the fluffy to the smooth colony morphology. This domestication is accompanied by loss of the ECM and by extensive changes in gene expression as detected by DNA microarrays. The expression of about 320 genes was changed in smooth colonies. The major changes comprise carbohydrate metabolism, cell wall, water channels, Ty-transposons and subtelomeric genes, iron homeostasis, vitamin metabolism and cell cycle and polarity. The growth in fluffy colonies may represent a metabolic strategy for survival of yeast under unfavourable conditions that is switched off under felicitous laboratory conditions.
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Affiliation(s)
- Martin Kuthan
- Department of Genetics and Microbiology, Charles University, Vinicná 5, 12844 Prague 2, Czech Republic
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25
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Scherz R, Shinder V, Engelberg D. Anatomical analysis of Saccharomyces cerevisiae stalk-like structures reveals spatial organization and cell specialization. J Bacteriol 2001; 183:5402-13. [PMID: 11514526 PMCID: PMC95425 DOI: 10.1128/jb.183.18.5402-5413.2001] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recently we reported an unusual multicellular organization in yeast that we termed stalk-like structures. These structures are tall (0.5 to 3 cm long) and narrow (1 to 3 mm in diameter). They are formed in response to UV radiation of cultures spread on high agar concentrations. Here we present an anatomical analysis of the stalks. Microscopic inspection of cross sections taken from stalks revealed that stalks are composed of an inner core in which cells are dense and vital and a layer of cells (four to six rows) that surrounds the core. This outer layer is physically separated from the core and contains many dead cells. The outer layer may form a protective shell for the core cells. Through electron microscopy analysis we observed three types of cells within the stalk population: (i) cells containing many unusual vesicles, which might be undergoing some kind of cell death; (ii) cells containing spores (usually one or two spores only); and (iii) familiar rounded cells. We suggest that stalk cells are not only spatially organized but may undergo processes that induce a certain degree of cell specialization. We also show that high agar concentration alone, although not sufficient to induce stalk formation, induces dramatic changes in a colony's morphology. Most striking among the agar effects is the induction of growth into the agar, forming peg-like structures. Colonies grown on 4% agar or higher are reminiscent of stalks in some aspects. The agar concentration effects are mediated in part by the Ras pathway and are related to the invasive-growth phenomenon.
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Affiliation(s)
- R Scherz
- Department of Biological Chemistry, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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26
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Stanhill A, Schick N, Engelberg D. The yeast ras/cyclic AMP pathway induces invasive growth by suppressing the cellular stress response. Mol Cell Biol 1999; 19:7529-38. [PMID: 10523641 PMCID: PMC84760 DOI: 10.1128/mcb.19.11.7529] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Haploid yeast cells are capable of invading agar when grown on rich media. Cells of the Sigma1278b genetic background manifest this property, whereas other laboratory strains are incapable of invasive growth. We show that disruption of the RAS2 gene in the Sigma1278b background significantly reduces invasive growth but that expression of a constitutively active Ras2p (Ras2(Val19)p) in this strain has a minimal effect on its invasiveness. On the other hand, expression of Ras2(Val19)p in another laboratory strain, SP1, rendered it invasive. These results suggest that a hyperactive Ras2 pathway induces invasive growth and that this pathway might be overactive in the Sigma1278b genetic background. Indeed, cells of the Sigma1278b are defective in the induction of stress-responsive genes, while their Gcn4 target genes are constitutively transcribed. This pattern of gene expression was previously shown to be associated with an active Ras/cyclic AMP (cAMP) pathway. We show that suppression of stress-related genes in Sigma1278b cells is a result of their inability to activate transcription through the stress response element (STRE). Disruption of RAS2, which abolished invasiveness, induced an increase in STRE activity. Further, in the SP1 genetic background, disruption of either the MSN2/4 genes (encoding activators of STRE) or the yAP-1 gene was sufficient to restore invasive growth in ras2Delta cells. We conclude that Ras2-mediated suppression of the stress response is sufficient to induce invasiveness. Accordingly, the fact that the stress response is suppressed in Sigma1278b background explains its invasiveness. It seems that invasiveness is a phenotype related to unregulated growth and is therefore manifested by cells harboring an overactive Ras/cAMP cascade. In this respect, invasiveness in yeast is reminiscent of the property of ras-transformed fibroblasts to invade soft agar.
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Affiliation(s)
- A Stanhill
- Department of Biological Chemistry, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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