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Peguero-Sanchez E, Pardo-Lopez L, Merino E. IRES-dependent translated genes in fungi: computational prediction, phylogenetic conservation and functional association. BMC Genomics 2015; 16:1059. [PMID: 26666532 PMCID: PMC4678720 DOI: 10.1186/s12864-015-2266-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 12/01/2015] [Indexed: 01/17/2023] Open
Abstract
Background The initiation of translation via cellular internal ribosome entry sites plays an important role in the stress response and certain physiological conditions in which canonical cap-dependent translation initiation is compromised. Currently, only a limited number of these regulatory elements have been experimentally identified. Notably, cellular internal ribosome entry sites lack conservation of both the primary sequence and mRNA secondary structure, rendering their identification difficult. Despite their biological importance, the currently available computational strategies to predict them have had limited success. We developed a bioinformatic method based on a support vector machine for the prediction of internal ribosome entry sites in fungi using the 5’-UTR sequences of 20 non-redundant fungal organisms. Additionally, we performed a comparative analysis and characterization of the functional relationships among the gene products predicted to be translated by this cap-independent mechanism. Results Using our method, we predicted 6,532 internal ribosome entry sites in 20 non-redundant fungal organisms. Some orthologous groups were enriched with our positive predictions. This is the case of the HSP70 chaperone family, which remarkably has two verified internal ribosome entry sites, one in humans and the other in flies. A second example is the orthologous group of the eIF4G repression protein Sbp1p, which has two homologous genes known to be translated by this cap-independent mechanism, one in mice and the other in yeast. These examples emphasize the wide conservation of these regulatory elements as a result of selective pressure. In addition, we performed a protein-protein interaction network characterization of the gene products of our positive predictions using Saccharomyces cerevisiae as a model, which revealed a highly connected and modular topology, suggesting a functional association. A remarkable example of this functional association is our prediction of internal ribosome entry sites elements in three components of the RNA polymerase II mediator complex. Conclusions We developed a method for the prediction of cellular internal ribosome entry sites that may guide experimental and bioinformatic analyses to increase our understanding of protein translation regulation. Our analysis suggests that fungi show evolutionary conservation and functional association of proteins translated by this cap-independent mechanism. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2266-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Esteban Peguero-Sanchez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Cuernavaca, Morelos, CP 62210, Mexico.
| | - Liliana Pardo-Lopez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Cuernavaca, Morelos, CP 62210, Mexico.
| | - Enrique Merino
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Cuernavaca, Morelos, CP 62210, Mexico.
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252
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Kinoshita T, Fujita M. Biosynthesis of GPI-anchored proteins: special emphasis on GPI lipid remodeling. J Lipid Res 2015; 57:6-24. [PMID: 26563290 DOI: 10.1194/jlr.r063313] [Citation(s) in RCA: 178] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Indexed: 02/06/2023] Open
Abstract
Glycosylphosphatidylinositols (GPIs) act as membrane anchors of many eukaryotic cell surface proteins. GPIs in various organisms have a common backbone consisting of ethanolamine phosphate (EtNP), three mannoses (Mans), one non-N-acetylated glucosamine, and inositol phospholipid, whose structure is EtNP-6Manα-2Manα-6Manα-4GlNα-6myoinositol-P-lipid. The lipid part is either phosphatidylinositol of diacyl or 1-alkyl-2-acyl form, or inositol phosphoceramide. GPIs are attached to proteins via an amide bond between the C-terminal carboxyl group and an amino group of EtNP. Fatty chains of inositol phospholipids are inserted into the outer leaflet of the plasma membrane. More than 150 different human proteins are GPI anchored, whose functions include enzymes, adhesion molecules, receptors, protease inhibitors, transcytotic transporters, and complement regulators. GPI modification imparts proteins with unique characteristics, such as association with membrane microdomains or rafts, transient homodimerization, release from the membrane by cleavage in the GPI moiety, and apical sorting in polarized cells. GPI anchoring is essential for mammalian embryogenesis, development, neurogenesis, fertilization, and immune system. Mutations in genes involved in remodeling of the GPI lipid moiety cause human diseases characterized by neurological abnormalities. Yeast Saccharomyces cerevisiae has >60 GPI-anchored proteins (GPI-APs). GPI is essential for growth of yeast. In this review, we discuss biosynthesis of GPI-APs in mammalian cells and yeast with emphasis on the lipid moiety.
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Affiliation(s)
- Taroh Kinoshita
- WPI Immunology Frontier Research Center and Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Morihisa Fujita
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
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253
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Formosa C, Dague E. Imaging Living Yeast Cells and Quantifying Their Biophysical Properties by Atomic Force Microscopy. Fungal Biol 2015. [DOI: 10.1007/978-3-319-22437-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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254
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Schiavone M, Sieczkowski N, Castex M, Dague E, Marie François J. Effects of the strain background and autolysis process on the composition and biophysical properties of the cell wall from two different industrial yeasts. FEMS Yeast Res 2015; 15:fou012. [PMID: 25762053 DOI: 10.1093/femsyr/fou012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The Saccharomyces cerevisiae cell surface is endowed with some relevant technological properties, notably antimicrobial and biosorption activities. For these purposes, yeasts are usually processed and packaged in an 'autolysed/dried' formula, which may have some impacts on cell surface properties. In this report, we showed using a combination of biochemical, biophysical and molecular methods that the composition of the cell wall of two wine yeast strains was not altered by the autolysis process. In contrast, this process altered the nanomechanical properties as shown by a 2- to 4-fold increased surface roughness and to a higher adhesion to the atomic force microscope tips of the autolysed cells as compared to live yeast cells. Besides, we found that the two strains harboured differences in biomechanical properties that could be due in part to higher levels of mannan in one of them, and to the fact that the surface of this mannan-enriched strain is decorated with highly adhesive patches forming nanodomains. The presence of these nanodomains could be correlated with the upregulation of flocculin encoding FLO11 as well as to higher expression of few other genes encoding cell wall mannoproteins in this mannan-enriched strain as compared to the other strain.
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Affiliation(s)
- Marion Schiavone
- Université de Toulouse, INSA, UPS, INP, 135 Avenue de Rangueil, F-31077 Toulouse, France INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France CNRS, UMR5504, F-31400 Toulouse, France CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France Lallemand SAS, 19 Rue des Briquetiers, 31702 Blagnac, France
| | | | - Mathieu Castex
- Lallemand SAS, 19 Rue des Briquetiers, 31702 Blagnac, France
| | - Etienne Dague
- Université de Toulouse, INSA, UPS, INP, 135 Avenue de Rangueil, F-31077 Toulouse, France CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France
| | - Jean Marie François
- Université de Toulouse, INSA, UPS, INP, 135 Avenue de Rangueil, F-31077 Toulouse, France INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France CNRS, UMR5504, F-31400 Toulouse, France
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255
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Kabeche R, Howard L, Moseley JB. Eisosomes provide membrane reservoirs for rapid expansion of the yeast plasma membrane. J Cell Sci 2015; 128:4057-62. [PMID: 26403204 DOI: 10.1242/jcs.176867] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/17/2015] [Indexed: 12/22/2022] Open
Abstract
Cell surface area rapidly increases during mechanical and hypoosmotic stresses. Such expansion of the plasma membrane requires 'membrane reservoirs' that provide surface area and buffer membrane tension, but the sources of this membrane remain poorly understood. In principle, the flattening of invaginations and buds within the plasma membrane could provide this additional surface area, as recently shown for caveolae in animal cells. Here, we used microfluidics to study the rapid expansion of the yeast plasma membrane in protoplasts, which lack the rigid cell wall. To survive hypoosmotic stress, yeast cell protoplasts required eisosomes, protein-based structures that generate long invaginations at the plasma membrane. Both budding yeast and fission yeast protoplasts lacking eisosomes were unable to expand like wild-type protoplasts during hypoosmotic stress, and subsequently lysed. By performing quantitative fluorescence microscopy on single protoplasts, we also found that eisosomes disassembled as surface area increased. During this process, invaginations generated by eisosomes at the plasma membrane became flattened, as visualized by scanning electron microscopy. We propose that eisosomes serve as tension-dependent membrane reservoirs for expansion of yeast cells in an analogous manner to caveolae in animal cells.
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Affiliation(s)
- Ruth Kabeche
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Louisa Howard
- Electron Microscope Facility, Dartmouth College, Hanover, NH 03755, USA
| | - James B Moseley
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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256
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Rong Y, Nakamura S, Hirata T, Motooka D, Liu YS, He ZA, Gao XD, Maeda Y, Kinoshita T, Fujita M. Genome-Wide Screening of Genes Required for Glycosylphosphatidylinositol Biosynthesis. PLoS One 2015; 10:e0138553. [PMID: 26383639 PMCID: PMC4575048 DOI: 10.1371/journal.pone.0138553] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/01/2015] [Indexed: 01/16/2023] Open
Abstract
Glycosylphosphatidylinositol (GPI) is synthesized and transferred to proteins in the endoplasmic reticulum (ER). GPI-anchored proteins are then transported from the ER to the plasma membrane through the Golgi apparatus. To date, at least 17 steps have been identified to be required for the GPI biosynthetic pathway. Here, we aimed to establish a comprehensive screening method to identify genes involved in GPI biosynthesis using mammalian haploid screens. Human haploid cells were mutagenized by the integration of gene trap vectors into the genome. Mutagenized cells were then treated with a bacterial pore-forming toxin, aerolysin, which binds to GPI-anchored proteins for targeting to the cell membrane. Cells that showed low surface expression of CD59, a GPI-anchored protein, were further enriched for. Gene trap insertion sites in the non-selected population and in the enriched population were determined by deep sequencing. This screening enriched 23 gene regions among the 26 known GPI biosynthetic genes, which when mutated are expected to decrease the surface expression of GPI-anchored proteins. Our results indicate that the forward genetic approach using haploid cells is a useful and powerful technique to identify factors involved in phenotypes of interest.
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Affiliation(s)
- Yao Rong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Shota Nakamura
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Tetsuya Hirata
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565–0871, Japan
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Daisuke Motooka
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Yi-Shi Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Zeng-An He
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- * E-mail: (XDG); (MF)
| | - Yusuke Maeda
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565–0871, Japan
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Taroh Kinoshita
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565–0871, Japan
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Morihisa Fujita
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- * E-mail: (XDG); (MF)
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257
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Transcriptomic response of Saccharomyces cerevisiae for its adaptation to sulphuric acid-induced stress. Antonie van Leeuwenhoek 2015; 108:1147-60. [DOI: 10.1007/s10482-015-0568-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 08/20/2015] [Indexed: 01/13/2023]
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258
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García R, Botet J, Rodríguez-Peña JM, Bermejo C, Ribas JC, Revuelta JL, Nombela C, Arroyo J. Genomic profiling of fungal cell wall-interfering compounds: identification of a common gene signature. BMC Genomics 2015; 16:683. [PMID: 26341223 PMCID: PMC4560923 DOI: 10.1186/s12864-015-1879-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 08/25/2015] [Indexed: 01/01/2023] Open
Abstract
Background The fungal cell wall forms a compact network whose integrity is essential for cell morphology and viability. Thus, fungal cells have evolved mechanisms to elicit adequate adaptive responses when cell wall integrity (CWI) is compromised. Functional genomic approaches provide a unique opportunity to globally characterize these adaptive mechanisms. To provide a global perspective on these CWI regulatory mechanisms, we developed chemical-genomic profiling of haploid mutant budding yeast cells to systematically identify in parallel those genes required to cope with stresses interfering the cell wall by different modes of action: β-1,3 glucanase and chitinase activities (zymolyase), inhibition of β-1,3 glucan synthase (caspofungin) and binding to chitin (Congo red). Results Measurement of the relative fitness of the whole collection of 4786 haploid budding yeast knock-out mutants identified 222 mutants hypersensitive to caspofungin, 154 mutants hypersensitive to zymolyase, and 446 mutants hypersensitive to Congo red. Functional profiling uncovered both common and specific requirements to cope with different cell wall damages. We identified a cluster of 43 genes highly important for the integrity of the cell wall as the common “signature of cell wall maintenance (CWM)”. This cluster was enriched in genes related to vesicular trafficking and transport, cell wall remodeling and morphogenesis, transcription and chromatin remodeling, signal transduction and RNA metabolism. Although the CWI pathway is the main MAPK pathway regulating cell wall integrity, the collaboration with other signal transduction pathways like the HOG pathway and the invasive growth pathway is also required to cope with the cell wall damage depending on the nature of the stress. Finally, 25 mutant strains showed enhanced caspofungin resistance, including 13 that had not been previously identified. Only three of them, wsc1Δ, elo2Δ and elo3Δ, showed a significant decrease in β-1,3-glucan synthase activity. Conclusions This work provides a global perspective about the mechanisms involved in cell wall stress adaptive responses and the cellular functions required for cell wall integrity. The results may be useful to uncover new potential antifungal targets and develop efficient antifungal strategies by combination of two drugs, one targeting the cell wall and the other interfering with the adaptive mechanisms. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1879-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Raúl García
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, 28040, Madrid, Spain.
| | - Javier Botet
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
| | - José Manuel Rodríguez-Peña
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, 28040, Madrid, Spain.
| | - Clara Bermejo
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, 28040, Madrid, Spain.
| | - Juan Carlos Ribas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain. .,Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC) / Universidad de Salamanca, 37007, Salamanca, Spain.
| | - José Luis Revuelta
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
| | - César Nombela
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, 28040, Madrid, Spain.
| | - Javier Arroyo
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, 28040, Madrid, Spain.
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259
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Biochemical characterization of Arabidopsis APYRASE family reveals their roles in regulating endomembrane NDP/NMP homoeostasis. Biochem J 2015; 472:43-54. [PMID: 26338998 DOI: 10.1042/bj20150235] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 09/03/2015] [Indexed: 12/27/2022]
Abstract
Plant apyrases are nucleoside triphosphate (NTP) diphosphohydrolases (NTPDases) and have been implicated in an array of functions within the plant including the regulation of extracellular ATP. Arabidopsis encodes a family of seven membrane bound apyrases (AtAPY1-7) that comprise three distinct clades, all of which contain the five conserved apyrase domains. With the exception of AtAPY1 and AtAPY2, the biochemical and the sub-cellular characterization of the other members are currently unavailable. In this research, we have shown all seven Arabidopsis apyrases localize to internal membranes comprising the cis-Golgi, endoplasmic reticulum (ER) and endosome, indicating an endo-apyrase classification for the entire family. In addition, all members, with the exception of AtAPY7, can function as endo-apyrases by complementing a yeast double mutant (Δynd1Δgda1) which lacks apyrase activity. Interestingly, complementation of the mutant yeast using well characterized human apyrases could only be accomplished by using a functional ER endo-apyrase (NTPDase6), but not the ecto-apyrase (NTPDase1). Furthermore, the substrate specificity analysis for the Arabidopsis apyrases AtAPY1-6 indicated that each member has a distinct set of preferred substrates covering various NDPs (nucleoside diphosphates) and NTPs. Combining the biochemical analysis and sub-cellular localization of the Arabidopsis apyrases family, the data suggest their possible roles in regulating endomembrane NDP/NMP (nucleoside monophosphate) homoeostasis.
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260
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Kalebina TS, Sokolov SS, Selyakh IO, Vanichkina DP, Severin FF. Amiodarone induces cell wall channel formation in yeast Hansenula polymorpha. SPRINGERPLUS 2015; 4:453. [PMID: 26322259 PMCID: PMC4549368 DOI: 10.1186/s40064-015-1185-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 07/27/2015] [Indexed: 11/17/2022]
Abstract
The yeast cell wall is constantly remodeled to enable cell growth and division. In this study, we describe a novel type of cell wall modification. We report that the drug amiodarone induces rapid channel formation within the cell wall of the yeast Hansenula polymorpha. Light microscopy shows that shortly after adding amiodarone, spherical structures, which can be stained with DNA binding dyes, form on the cell surface. Electron microphotographs show that amiodarone induces the formation of channels 50–80 nm in diameter in the cell wall that appear to be filled with intracellular material. Using fluorescent microscopy, we demonstrate MitoTracker-positive DNA-containing structures visibly extruded from the cells through these channels. We speculate that the observed channel formation acts to enable the secretion of mitochondrial material from the cell under stressful conditions, thus enabling adaptive changes to the extracellular environment.
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Affiliation(s)
- Tatyana S Kalebina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, Moscow, 119992 Russia
| | - Sviatoslav S Sokolov
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1-40 Leninskie Gory, Moscow, 119992 Russia
| | - Irina O Selyakh
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, Moscow, 119992 Russia
| | - Darya P Vanichkina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, Moscow, 119992 Russia ; Institute for Molecular Bioscience, University of Queensland, Queensland, Australia
| | - Fedor F Severin
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1-40 Leninskie Gory, Moscow, 119992 Russia
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261
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Ramirez-Hernandez A, Rupnow J, Hutkins RW. Adherence Reduction of Campylobacter jejuni and Campylobacter coli Strains to HEp-2 Cells by Mannan Oligosaccharides and a High-Molecular-Weight Component of Cranberry Extract. J Food Prot 2015; 78:1496-505. [PMID: 26219363 DOI: 10.4315/0362-028x.jfp-15-087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Campylobacter infections are a leading cause of human bacterial gastroenteritis in the United States and are a major cause of diarrheal disease throughout the world. Colonization and subsequent infection and invasion of Campylobacter require that the bacteria adhere to the surface of host cells. Agents that inhibit adherence could be used prophylactically to reduce Campylobacter carriage and infection. Mannan oligosaccharides (MOS) have been used as a feed supplement in livestock animals to improve performance and to replace growth-promoting antibiotics. However, MOS and other nondigestible oligosaccharides may also prevent pathogen colonization by inhibiting adherence in the gastrointestinal tract. In addition, plant extracts, including those derived from cranberries, have been shown to have antiadherence activity against pathogens. The goal of this study was to assess the ability of MOS and cranberry fractions to serve as antiadherence agents against strains of Campylobacter jejuni and Campylobacter coli. Adherence experiments were performed using HEp-2 cells. Significant reductions in adherence of C. jejuni 29438, C. jejuni 700819, C. jejuni 3329, and C. coli 43485 were observed in the presence of MOS (up to 40 mg/ml) and with a high-molecular-weight fraction of cranberry extract (up to 3 mg/ml). However, none of the tested materials reduced adherence of C. coli BAA-1061. No additive effect in adherence inhibition was observed for an MOS-cranberry blend. These results suggest that both components, MOS and cranberry, could be used to reduce Campylobacter colonization and carriage in livestock animals and potentially limit human exposure to this pathogen.
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Affiliation(s)
- Alejandra Ramirez-Hernandez
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska 68583-0919, USA
| | - John Rupnow
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska 68583-0919, USA
| | - Robert W Hutkins
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska 68583-0919, USA.
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262
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A Genetic Screen for Saccharomyces cerevisiae Mutants That Fail to Enter Quiescence. G3-GENES GENOMES GENETICS 2015; 5:1783-95. [PMID: 26068574 PMCID: PMC4528334 DOI: 10.1534/g3.115.019091] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Budding yeast begin the transition to quiescence by prolonging G1 and accumulating limited nutrients. They undergo asymmetric cell divisions, slow cellular expansion, acquire significant stress tolerance and construct elaborate cell walls. These morphologic changes give rise to quiescent (Q) cells, which can be distinguished from three other cell types in a stationary phase culture by flow cytometry. We have used flow cytometry to screen for genes that are required to obtain the quiescent cell fraction. We find that cell wall integrity is critical and these genes may help define quiescence-specific features of the cell wall. Genes required to evade the host innate immune response are common. These may be new targets for antifungal drugs. Acquired thermotolerance is also a common property, and we show that the stress-response transcription factors Msn2 and Msn4 promote quiescence. Many other pathways also contribute, including a subset of genes involved in autophagy, ubiquitin-mediated proteolysis, DNA replication, bud site selection, and cytokinesis.
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263
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Kieliszek M, Błażejak S, Gientka I, Bzducha-Wróbel A. Accumulation and metabolism of selenium by yeast cells. Appl Microbiol Biotechnol 2015; 99:5373-82. [PMID: 26003453 PMCID: PMC4464373 DOI: 10.1007/s00253-015-6650-x] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 04/23/2015] [Accepted: 04/25/2015] [Indexed: 11/30/2022]
Abstract
This paper examines the process of selenium bioaccumulation and selenium metabolism in yeast cells. Yeast cells can bind elements in ionic from the environment and permanently integrate them into their cellular structure. Up to now, Saccharomyces cerevisiae, Candida utilis, and Yarrowia lipolytica yeasts have been used primarily in biotechnological studies to evaluate binding of minerals. Yeast cells are able to bind selenium in the form of both organic and inorganic compounds. The process of bioaccumulation of selenium by microorganisms occurs through two mechanisms: extracellular binding by ligands of membrane assembly and intracellular accumulation associated with the transport of ions across the cytoplasmic membrane into the cell interior. During intracellular metabolism of selenium, oxidation, reduction, methylation, and selenoprotein synthesis processes are involved, as exemplified by detoxification processes that allow yeasts to survive under culture conditions involving the elevated selenium concentrations which were observed. Selenium yeasts represent probably the best absorbed form of this element. In turn, in terms of wide application, the inclusion of yeast with accumulated selenium may aid in lessening selenium deficiency in a diet.
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Affiliation(s)
- Marek Kieliszek
- Department of Biotechnology, Microbiology and Food Evaluation, Faculty of Food Sciences, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159 C, 02-776, Warsaw, Poland,
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264
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Garcia VG, Knoll LR, Longo M, Novaes VCN, Assem NZ, Ervolino E, de Toledo BEC, Theodoro LH. Effect of the probiotic Saccharomyces cerevisiae on ligature-induced periodontitis in rats. J Periodontal Res 2015; 51:26-37. [PMID: 25918871 DOI: 10.1111/jre.12274] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2015] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND OBJECTIVE This study assessed the effects of the local use of Saccharomyces cerevisiae as monotherapy and as an adjuvant to the mechanical treatment of ligature-induced periodontitis in rats. MATERIAL AND METHODS Periodontitis was induced in 72 rats via the installation of a ligature around the mandibular first molar. After 7 d, the ligature was removed and the rats were placed in one of the following groups: no treatment (C; n = 18); scaling and root planing (SRP; n = 18); local irrigation with probiotics (PRO; n = 18); and SRP followed by local irrigation with probiotics (SRP/PRO; n = 18). Six rats from each group were killed at 7, 15 and 30 d. The histological characteristics, alveolar bone loss (ABL) and immunolabeling of tumor necrosis factor alpha (TNF-α), interleukin-1beta (IL-1β), interleukin-10 (IL-10) and TRAP on the furcation area of the first molar were assessed. RESULTS The PRO group showed features of acceleration of the tissue-repair process during the entire experiment. On day 15, there was less ABL in the SRP/PRO group compared with the C group. There were fewer TRAP-positive cells in the SRP and SRP/PRO groups at 30 d. There was less immunostaining for TNF-α in the PRO and SRP/PRO groups and less immunostaining for IL-1β in the PRO group. However, there was more immunostaining for IL-10 in the PRO group on day 15. CONCLUSION Local use of the probiotic did not result in any adverse effects on periodontal tissues. When used as monotherapy or as an adjuvant, the probiotic was effective at controlling periodontitis in rats.
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Affiliation(s)
- V G Garcia
- Group of Research and Study on Laser in Dentistry (GEPLO), Division of Periodontics, Department of Surgery and Integrated Clinic, University Estadual Paulista (UNESP), Araçatuba, Brazil.,Master Course, Barretos Dental School, University Center of the Educational Foundation of Barretos (UNIFEB), Barretos, Brazil
| | - L R Knoll
- Master Course, Barretos Dental School, University Center of the Educational Foundation of Barretos (UNIFEB), Barretos, Brazil
| | - M Longo
- Group of Research and Study on Laser in Dentistry (GEPLO), Division of Periodontics, Department of Surgery and Integrated Clinic, University Estadual Paulista (UNESP), Araçatuba, Brazil
| | - V C N Novaes
- Group of Research and Study on Laser in Dentistry (GEPLO), Division of Periodontics, Department of Surgery and Integrated Clinic, University Estadual Paulista (UNESP), Araçatuba, Brazil
| | - N Z Assem
- Group of Research and Study on Laser in Dentistry (GEPLO), Division of Periodontics, Department of Surgery and Integrated Clinic, University Estadual Paulista (UNESP), Araçatuba, Brazil
| | - E Ervolino
- Department of Basic Science, University Estadual Paulista (UNESP), Araçatuba, Brazil
| | - B E C de Toledo
- Master Course, Barretos Dental School, University Center of the Educational Foundation of Barretos (UNIFEB), Barretos, Brazil
| | - L H Theodoro
- Group of Research and Study on Laser in Dentistry (GEPLO), Division of Periodontics, Department of Surgery and Integrated Clinic, University Estadual Paulista (UNESP), Araçatuba, Brazil
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265
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Kopecká M, Yamaguchi M, Kawamoto S. Effects of the F-actin inhibitor latrunculin A on the budding yeast Saccharomyces cerevisiae. MICROBIOLOGY-SGM 2015; 161:1348-55. [PMID: 25858300 DOI: 10.1099/mic.0.000091] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Our basic cell biology research was aimed at investigating the effect on eukaryotic cells of the sudden loss of the F-actin cytoskeleton. Cells treated with latrunculin A (LA) in yeast extract peptone dextrose (YEPD) medium were examined using phase-contrast and fluorescent microscopy, freeze-substitution, transmission and scanning electron microscopy, counted using a Bürker chamber and their absorbance measured. The cells responded to the presence of LA, an F-actin inhibitor, with the disappearance of actin patches, actin cables and actin rings. This resulted in the formation of larger spherical cells with irregular morphology in the cell walls and ultrastructural disorder of the cell organelles and secretory vesicles. Instead of buds, LA-inhibited cells formed only 'table-mountain-like' wide flattened swellings without apical growth with a thinner glucan cell-wall layer containing β-1,3-glucan microfibrils. The LA-inhibited cells lysed. Actin cables and patches were required for bud formation and bud growth. In addition, actin patches were required for the formation of β-1,3-glucan microfibrils in the bud cell wall. LA has fungistatic, fungicidal and fungilytic effects on the budding yeast Saccharomyces cerevisiae.
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Affiliation(s)
- Marie Kopecká
- 1Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Masashi Yamaguchi
- 2Medical Mycology Research Centre, Chiba University, Chuo-ku, Japan
| | - Susumu Kawamoto
- 2Medical Mycology Research Centre, Chiba University, Chuo-ku, Japan
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266
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Tartakoff AM. Cell biology of yeast zygotes, from genesis to budding. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1702-14. [PMID: 25862405 DOI: 10.1016/j.bbamcr.2015.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/28/2015] [Accepted: 03/31/2015] [Indexed: 12/23/2022]
Abstract
The zygote is the essential intermediate that allows interchange of nuclear, mitochondrial and cytosolic determinants between cells. Zygote formation in Saccharomyces cerevisiae is accomplished by mechanisms that are not characteristic of mitotic cells. These include shifting the axis of growth away from classical cortical landmarks, dramatically reorganizing the cell cortex, remodeling the cell wall in preparation for cell fusion, fusing with an adjacent partner, accomplishing nuclear fusion, orchestrating two steps of septin morphogenesis that account for a delay in fusion of mitochondria, and implementing new norms for bud site selection. This essay emphasizes the sequence of dependent relationships that account for this progression from cell encounters through zygote budding. It briefly summarizes classical studies of signal transduction and polarity specification and then focuses on downstream events.
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Affiliation(s)
- Alan M Tartakoff
- Department of Pathology and Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA.
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267
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Liesche J, Marek M, Günther-Pomorski T. Cell wall staining with Trypan blue enables quantitative analysis of morphological changes in yeast cells. Front Microbiol 2015; 6:107. [PMID: 25717323 PMCID: PMC4324143 DOI: 10.3389/fmicb.2015.00107] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 01/27/2015] [Indexed: 11/13/2022] Open
Abstract
Yeast cells are protected by a cell wall that plays an important role in the exchange of substances with the environment. The cell wall structure is dynamic and can adapt to different physiological states or environmental conditions. For the investigation of morphological changes, selective staining with fluorescent dyes is a valuable tool. Furthermore, cell wall staining is used to facilitate sub-cellular localization experiments with fluorescently-labeled proteins and the detection of yeast cells in non-fungal host tissues. Here, we report staining of Saccharomyces cerevisiae cell wall with Trypan Blue, which emits strong red fluorescence upon binding to chitin and yeast glucan; thereby, it facilitates cell wall analysis by confocal and super-resolution microscopy. The staining pattern of Trypan Blue was similar to that of the widely used UV-excitable, blue fluorescent cell wall stain Calcofluor White. Trypan Blue staining facilitated quantification of cell size and cell wall volume when utilizing the optical sectioning capacity of a confocal microscope. This enabled the quantification of morphological changes during growth under anaerobic conditions and in the presence of chemicals, demonstrating the potential of this approach for morphological investigations or screening assays.
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Affiliation(s)
- Johannes Liesche
- Department of Plant and Environmental Sciences, University of Copenhagen Copenhagen, Denmark
| | - Magdalena Marek
- Department of Plant and Environmental Sciences, University of Copenhagen Copenhagen, Denmark
| | - Thomas Günther-Pomorski
- Department of Plant and Environmental Sciences, University of Copenhagen Copenhagen, Denmark
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268
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VCP/Cdc48 rescues the growth defect of aGPI10mutant in yeast. FEBS Lett 2015; 589:576-80. [DOI: 10.1016/j.febslet.2015.01.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/09/2015] [Accepted: 01/14/2015] [Indexed: 11/17/2022]
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269
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Mekoue Nguela J, Sieczkowski N, Roi S, Vernhet A. Sorption of grape proanthocyanidins and wine polyphenols by yeasts, inactivated yeasts, and yeast cell walls. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:660-670. [PMID: 25575250 DOI: 10.1021/jf504494m] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Inactivated yeast fractions (IYFs) can be used in enology to improve the stability and mouthfeel of red wines. However, information concerning the mechanisms involved and the impact of the IYF characteristics is scarce. Adsorption isotherms were used to investigate interactions between grape proanthocyanidin fractions (PAs) or wine polyphenols (WP) and a commercial yeast strain (Y), the inactivated yeast (IY), the yeast submitted to autolyzis and inactivation (A-IY), and the cell walls obtained by mechanical disruption (CW). High affinity isotherms and high adsorption capacities were observed for grape PAs and whole cells (Y, IY, and A-IY). Affinity and adsorbed amount were lower with wine PAs, due to chemical changes occurring during winemaking. By contrast to whole cells, grape PAs and WP adsorption on CW remained very low. This raises the issue of the part played by cell walls in the interactions between yeast and proanthocyanidins and suggests the passage of the latter through the wall pores and their interaction with the plasma membrane.
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270
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Blanco N, Sanz AB, Rodríguez-Peña JM, Nombela C, Farkaš V, Hurtado-Guerrero R, Arroyo J. Structural and functional analysis of yeast Crh1 and Crh2 transglycosylases. FEBS J 2015; 282:715-31. [DOI: 10.1111/febs.13176] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 10/28/2014] [Accepted: 12/11/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Noelia Blanco
- Departamento de Microbiología II; Facultad de Farmacia; Universidad Complutense de Madrid; IRYCIS; Spain
| | - Ana B. Sanz
- Departamento de Microbiología II; Facultad de Farmacia; Universidad Complutense de Madrid; IRYCIS; Spain
| | - Jose M. Rodríguez-Peña
- Departamento de Microbiología II; Facultad de Farmacia; Universidad Complutense de Madrid; IRYCIS; Spain
| | - César Nombela
- Departamento de Microbiología II; Facultad de Farmacia; Universidad Complutense de Madrid; IRYCIS; Spain
| | - Vladimír Farkaš
- Department of Glycobiology; Center for Glycomics, Institute of Chemistry; Center for Glycomics; Slovak Academy of Sciences; Bratislava Slovakia
| | - Ramón Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI); University of Zaragoza; BIFI-IQFR (CSIC) Joint Unit; Spain
- Fundacion ARAID; Zaragoza Spain
| | - Javier Arroyo
- Departamento de Microbiología II; Facultad de Farmacia; Universidad Complutense de Madrid; IRYCIS; Spain
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271
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Formosa C, Lachaize V, Galés C, Rols MP, Martin-Yken H, François JM, Duval RE, Dague E. Mapping HA-tagged protein at the surface of living cells by atomic force microscopy. J Mol Recognit 2014; 28:1-9. [DOI: 10.1002/jmr.2407] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 06/20/2014] [Accepted: 06/25/2014] [Indexed: 11/08/2022]
Affiliation(s)
- C. Formosa
- CNRS; LAAS; 7 avenue du Colonel Roche 31400 Toulouse France
- Université de Toulouse; LAAS, ITAV, IPBS; 31400 Toulouse France
- CNRS; UMR 7565, SRSMC; Vandœuvre-lès-Nancy France
- Université de Lorraine; UMR 7565, Faculté de Pharmacie; Nancy France
| | - V. Lachaize
- CNRS; LAAS; 7 avenue du Colonel Roche 31400 Toulouse France
- Université de Toulouse; LAAS, ITAV, IPBS; 31400 Toulouse France
- Institut des Maladies Métaboliques et Cardiovasculaires, Institut National de la Santé et de la Recherche Médicale U1048; Université Toulouse III Paul Sabatier; 31432 Toulouse France
- CNRS; ITAV; 1 Place Pierre Potier 31000 Toulouse France
| | - C. Galés
- Université de Toulouse; LAAS, ITAV, IPBS; 31400 Toulouse France
- Institut des Maladies Métaboliques et Cardiovasculaires, Institut National de la Santé et de la Recherche Médicale U1048; Université Toulouse III Paul Sabatier; 31432 Toulouse France
- CNRS; ITAV; 1 Place Pierre Potier 31000 Toulouse France
| | - M. P. Rols
- Université de Toulouse; LAAS, ITAV, IPBS; 31400 Toulouse France
- CNRS; IPBS, UMR 5089; 205 route de Narbonne 31077 Toulouse France
| | - H. Martin-Yken
- Université de Toulouse; LAAS, ITAV, IPBS; 31400 Toulouse France
- INRA; UMR 972 LISBP; Toulouse France
| | - J. M. François
- Université de Toulouse; LAAS, ITAV, IPBS; 31400 Toulouse France
- INRA; UMR 972 LISBP; Toulouse France
| | - R. E. Duval
- CNRS; UMR 7565, SRSMC; Vandœuvre-lès-Nancy France
- Université de Lorraine; UMR 7565, Faculté de Pharmacie; Nancy France
- ABC Platform®; Nancy France
| | - E. Dague
- CNRS; LAAS; 7 avenue du Colonel Roche 31400 Toulouse France
- Université de Toulouse; LAAS, ITAV, IPBS; 31400 Toulouse France
- CNRS; ITAV; 1 Place Pierre Potier 31000 Toulouse France
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272
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Up against the wall: is yeast cell wall integrity ensured by mechanosensing in plasma membrane microdomains? Appl Environ Microbiol 2014; 81:806-11. [PMID: 25398859 DOI: 10.1128/aem.03273-14] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Yeast cell wall integrity (CWI) signaling serves as a model of the regulation of fungal cell wall synthesis and provides the basis for the development of antifungal drugs. A set of five membrane-spanning sensors (Wsc1 to Wsc3, Mid2, and Mtl1) detect cell surface stress and commence the signaling pathway upon perturbations of either the cell wall structure or the plasma membrane. We here summarize the latest advances in the structure/function relationship primarily of the Wsc1 sensor and critically review the evidence that it acts as a mechanosensor. The relevance and physiological significance of the information obtained for the function of the other CWI sensors, as well as expected future developments, are discussed.
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273
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O'Doherty PJ, Lyons V, Tun NM, Rogers PJ, Bailey TD, Wu MJ. Transcriptomic and biochemical evidence for the role of lysine biosynthesis against linoleic acid hydroperoxide-induced stress in Saccharomyces cerevisiae. Free Radic Res 2014; 48:1454-61. [PMID: 25184342 DOI: 10.3109/10715762.2014.961448] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Amino acid biosynthesis forms part of an integrated stress response against oxidants in Saccharomyces cerevisiae and higher eukaryotes. Here we show an essential protective role of the l-lysine biosynthesis pathway in response to the oxidative stress condition induced by the lipid oxidant-linoleic acid hydroperoxide (LoaOOH), by means of transcriptomic profiling and phenotypic analysis, and using the deletion mutant dal80∆ and lysine auxotroph lys1∆. A comprehensive up-regulation of lysine biosynthetic genes (LYS1, LYS2, LYS4, LYS9, LYS12, LYS20 and LYS21) was revealed in dal80Δ following the oxidant challenge. The lysine auxotroph (lys1∆) exhibited a significant decrease in growth compared with that of BY4743 upon exposure to LoaOOH, albeit with the sufficient provision of lysine in the medium. Furthermore, the growth of wild type BY4743 exposed to LoaOOH was also greatly reduced in lysine-deficient conditions, despite a full complement of lysine biosynthetic genes. Amino acid analysis of LoaOOH-treated yeast showed that the level of cellular lysine remained unchanged throughout oxidant challenge, suggesting that the induced lysine biosynthesis leads to a steady-state metabolism as compared to the untreated yeast cells. Together, these findings demonstrate that lysine availability and its biosynthesis pathway play an important role in protecting the cell from lipid peroxide-induced oxidative stress, which is directly related to understanding environmental stress and industrial yeast management in brewing, wine making and baking.
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Affiliation(s)
- P J O'Doherty
- School of Science and Health, University of Western Sydney , Penrith, New South Wales , Australia
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274
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Kuznets G, Vigonsky E, Weissman Z, Lalli D, Gildor T, Kauffman SJ, Turano P, Becker J, Lewinson O, Kornitzer D. A relay network of extracellular heme-binding proteins drives C. albicans iron acquisition from hemoglobin. PLoS Pathog 2014; 10:e1004407. [PMID: 25275454 PMCID: PMC4183699 DOI: 10.1371/journal.ppat.1004407] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 08/18/2014] [Indexed: 12/14/2022] Open
Abstract
Iron scavenging constitutes a crucial challenge for survival of pathogenic microorganisms in the iron-poor host environment. Candida albicans, like many microbial pathogens, is able to utilize iron from hemoglobin, the largest iron pool in the host's body. Rbt5 is an extracellular glycosylphosphatidylinositol (GPI)-anchored heme-binding protein of the CFEM family that facilitates heme-iron uptake by an unknown mechanism. Here, we characterize an additional C. albicans CFEM protein gene, PGA7, deletion of which elicits a more severe heme-iron utilization phenotype than deletion of RBT5. The virulence of the pga7−/− mutant is reduced in a mouse model of systemic infection, consistent with a requirement for heme-iron utilization for C. albicans pathogenicity. The Pga7 and Rbt5 proteins exhibit distinct cell wall attachment, and discrete localization within the cell envelope, with Rbt5 being more exposed than Pga7. Both proteins are shown here to efficiently extract heme from hemoglobin. Surprisingly, while Pga7 has a higher affinity for heme in vitro, we find that heme transfer can occur bi-directionally between Pga7 and Rbt5, supporting a model in which they cooperate in a heme-acquisition relay. Together, our data delineate the roles of Pga7 and Rbt5 in a cell surface protein network that transfers heme from extracellular hemoglobin to the endocytic pathway, and provide a paradigm for how receptors embedded in the cell wall matrix can mediate nutrient uptake across the fungal cell envelope. Candida albicans, a commensal fungus of human mucosal surfaces in healthy individuals, is a common cause of superficial infections, as well as of life-threatening systemic infections in individuals suffering from a reduced immune function. As a systemic pathogen, it has to cope with a scarcity of specific nutrients in the host environment, chief among them iron. To overcome this iron limitation, C. albicans is able to extract iron from heme and hemoglobin, the largest iron pools in the human body, via a pathway that involves endocytosis into the cell. Here we show that efficient heme uptake relies on a family of extracellularly-anchored proteins that serve as heme receptors, two of which, at least, are required for efficient heme utilization. Our data suggest the existence of a relay system that transfers heme from one protein to the next across the cell envelope, explaining the requirement for multiple heme receptors for efficient heme-iron utilization. This study extends our understanding of the pathway of host heme utilization by fungal pathogens, and provides new insights into the question of how nutrients such as heme cross the fungal cell wall.
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Affiliation(s)
- Galit Kuznets
- B. Rappaport Faculty of Medicine, Technion – I.I.T. and the Rappaport Institute for Research in the Medical Sciences, Haifa, Israel
| | - Elena Vigonsky
- B. Rappaport Faculty of Medicine, Technion – I.I.T. and the Rappaport Institute for Research in the Medical Sciences, Haifa, Israel
| | - Ziva Weissman
- B. Rappaport Faculty of Medicine, Technion – I.I.T. and the Rappaport Institute for Research in the Medical Sciences, Haifa, Israel
| | - Daniela Lalli
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Tsvia Gildor
- B. Rappaport Faculty of Medicine, Technion – I.I.T. and the Rappaport Institute for Research in the Medical Sciences, Haifa, Israel
| | - Sarah J. Kauffman
- Microbiology Department, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Paola Turano
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Jeffrey Becker
- Microbiology Department, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Oded Lewinson
- B. Rappaport Faculty of Medicine, Technion – I.I.T. and the Rappaport Institute for Research in the Medical Sciences, Haifa, Israel
| | - Daniel Kornitzer
- B. Rappaport Faculty of Medicine, Technion – I.I.T. and the Rappaport Institute for Research in the Medical Sciences, Haifa, Israel
- * E-mail:
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275
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Mélida H, Sain D, Stajich JE, Bulone V. Deciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches. Environ Microbiol 2014; 17:1649-62. [DOI: 10.1111/1462-2920.12601] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 08/06/2014] [Accepted: 08/11/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Hugo Mélida
- Division of Glycoscience; School of Biotechnology; Royal Institute of Technology (KTH); AlbaNova University Centre; Stockholm Sweden
| | - Divya Sain
- Department of Plant Pathology and Microbiology; University of California; Riverside CA 92507 USA
| | - Jason E. Stajich
- Department of Plant Pathology and Microbiology; University of California; Riverside CA 92507 USA
| | - Vincent Bulone
- Division of Glycoscience; School of Biotechnology; Royal Institute of Technology (KTH); AlbaNova University Centre; Stockholm Sweden
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276
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Identification of long-lived proteins retained in cells undergoing repeated asymmetric divisions. Proc Natl Acad Sci U S A 2014; 111:14019-26. [PMID: 25228775 DOI: 10.1073/pnas.1416079111] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Long-lived proteins have been implicated in age-associated decline in metazoa, but they have only been identified in extracellular matrices or postmitotic cells. However, the aging process also occurs in dividing cells undergoing repeated asymmetric divisions. It was not clear whether long-lived proteins exist in asymmetrically dividing cells or whether they are involved in aging. Here we identify long-lived proteins in dividing cells during aging using the budding yeast, Saccharomyces cerevisiae. Yeast mother cells undergo a limited number of asymmetric divisions that define replicative lifespan. We used stable-isotope pulse-chase and total proteome mass-spectrometry to identify proteins that were both long-lived and retained in aging mother cells after ∼ 18 cells divisions. We identified ∼ 135 proteins that we designate as long-lived asymmetrically retained proteins (LARPS). Surprisingly, the majority of LARPs appeared to be stable fragments of their original full-length protein. However, 15% of LARPs were full-length proteins and we confirmed several candidates to be long-lived and retained in mother cells by time-lapse microscopy. Some LARPs localized to the plasma membrane and remained robustly in the mother cell upon cell division. Other full-length LARPs were assembled into large cytoplasmic structures that had a strong bias to remain in mother cells. We identified age-associated changes to LARPs that include an increase in their levels during aging because of their continued synthesis, which is not balanced by turnover. Additionally, several LARPs were posttranslationally modified during aging. We suggest that LARPs contribute to age-associated phenotypes and likely exist in other organisms.
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277
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Abstract
The protein kinase Hog1 (high osmolarity glycerol 1) was discovered 20 years ago, being revealed as a central signaling mediator during osmoregulation in the budding yeast Saccharomyces cerevisiae. Homologs of Hog1 exist in all evaluated eukaryotic organisms, and this kinase plays a central role in cellular responses to external stresses and stimuli. Here, we highlight the mechanism by which cells sense changes in extracellular osmolarity, the method by which Hog1 regulates cellular adaptation, and the impacts of the Hog1 pathway upon cellular growth and morphology. Studies that have addressed these issues reveal the influence of the Hog1 signaling pathway on diverse cellular processes.
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Affiliation(s)
- Jay L Brewster
- Natural Science Division, Pepperdine University, 24255 Pacific Coast Highway, Malibu, CA 90263, USA.
| | - Michael C Gustin
- Department of BioSciences, Rice University, 6100 Main Street, Houston, TX 77251, USA
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278
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Dupont S, Rapoport A, Gervais P, Beney L. Survival kit of Saccharomyces cerevisiae for anhydrobiosis. Appl Microbiol Biotechnol 2014; 98:8821-34. [DOI: 10.1007/s00253-014-6028-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/08/2014] [Accepted: 08/10/2014] [Indexed: 01/08/2023]
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279
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Schiavone M, Vax A, Formosa C, Martin-Yken H, Dague E, François JM. A combined chemical and enzymatic method to determine quantitatively the polysaccharide components in the cell wall of yeasts. FEMS Yeast Res 2014; 14:933-47. [PMID: 25041403 DOI: 10.1111/1567-1364.12182] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/02/2014] [Accepted: 07/03/2014] [Indexed: 12/19/2022] Open
Abstract
A reliable method to determine cell wall polysaccharides composition in yeast is presented, which combines acid and enzymatic hydrolysis. Sulphuric acid treatment is used to determine mannans, whereas specific hydrolytic enzymes are employed in a two sequential steps to quantify chitin and the proportion of β-(1,3) and β-(1,6)-glucan in the total β-glucan of the cell wall. In the first step, chitin and β-(1,3)-glucan were hydrolysed into their corresponding monomers N-acetylglucosamine and glucose, respectively, by the combined action of a chitinase from Streptomyces griseus and a pure preparation of endo/exo-β-(1,3)-glucanase from Trichoderma species. This step was followed by addition of recombinant endo-β-(1,6)-glucanase from Trichoderma harzianum with β-glucosidase from Aspergillus niger to hydrolyse the remaining β-glucan. This latter component corresponded to a highly branched β-(1,6)-glucan that contained about 75-80% of linear β-(1,6)-glucose linked units as deduced from periodate oxidation. We validated this novel method by showing that the content of β-(1,3), β-(1,6)-glucan or chitin was dramatically decreased in yeast mutants defective in the biosynthesis of these cell wall components. Moreover, we found that heat shock at 42 °C in Saccharomyces cerevisiae and treatment of this yeast species and Candida albicans with the antifungal drug caspofungin resulted in 2- to 3-fold increase of chitin and in a reduction of β-(1,3)-glucan accompanied by an increase of β-(1,6)-glucan, whereas ethanol stress had apparently no effect on yeast cell wall composition.
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Affiliation(s)
- Marion Schiavone
- INSA, UPS, INP, Université de Toulouse, Toulouse, France; UMR792 Ingénierie des Systèmes Biologiques et des Procédés, INRA, Toulouse, France; UMR5504, CNRS, Toulouse, France; Lallemand SAS, Blagnac, France
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280
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Latgé JP, Beauvais A. Functional duality of the cell wall. Curr Opin Microbiol 2014; 20:111-7. [PMID: 24937317 DOI: 10.1016/j.mib.2014.05.009] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 05/13/2014] [Accepted: 05/14/2014] [Indexed: 10/25/2022]
Abstract
The polysaccharide cell wall is the extracellular armour of the fungal cell. Although essential in the protection of the fungal cell against aggressive external stresses, the biosynthesis of the polysaccharide core is poorly understood. For a long time it was considered that this cell wall skeleton was a fixed structure whose role was only to be sensed as non-self by the host and consequently trigger the defence response. It is now known that the cell wall polysaccharide composition and localization continuously change to adapt to their environment and that these modifications help the fungus to escape from the immune system. Moreover, cell wall polysaccharides could function as true virulence factors.
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Affiliation(s)
| | - Anne Beauvais
- Unité des Aspergillus, Institut Pasteur, Paris, France
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281
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Yang YH, Kang HW, Ro HS. Cloning and Molecular Characterization of β-1,3-Glucan Synthase from Sparassis crispa. MYCOBIOLOGY 2014; 42:167-173. [PMID: 25071386 PMCID: PMC4112233 DOI: 10.5941/myco.2014.42.2.167] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 06/07/2014] [Accepted: 06/10/2014] [Indexed: 06/03/2023]
Abstract
A β-glucan synthase gene was isolated from the genomic DNA of polypore mushroom Sparassis crispa, which reportedly produces unusually high amount of soluble β-1,3-glucan (β-glucan). Sequencing and subsequent open reading frame analysis of the isolated gene revealed that the gene (5,502 bp) consisted of 10 exons separated by nine introns. The predicted mRNA encoded a β-glucan synthase protein, consisting of 1,576 amino acid residues. Comparison of the predicted protein sequence with multiple fungal β-glucan synthases estimated that the isolated gene contained a complete N-terminus but was lacking approximately 70 amino acid residues in the C-terminus. Fungal β-glucan synthases are integral membrane proteins, containing the two catalytic and two transmembrane domains. The lacking C-terminal part of S. crispa β-glucan synthase was estimated to include catalytically insignificant transmembrane α-helices and loops. Sequence analysis of 101 fungal β-glucan synthases, obtained from public databases, revealed that the β-glucan synthases with various fungal origins were categorized into corresponding fungal groups in the classification system. Interestingly, mushrooms belonging to the class Agaricomycetes were found to contain two distinct types (Type I and II) of β-glucan synthases with the type-specific sequence signatures in the loop regions. S. crispa β-glucan synthase in this study belonged to Type II family, meaning Type I β-glucan synthase is expected to be discovered in S. crispa. The high productivity of soluble β-glucan was not explained but detailed biochemical studies on the catalytic loop domain in the S. crispa β-glucan synthase will provide better explanations.
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Affiliation(s)
- Yun Hui Yang
- Division of Applied Life Science (BK21Plus) and Research Institute of Life Sciences, Gyeongsang National University, Jinju 660-701, Korea
| | - Hyeon-Woo Kang
- Division of Applied Life Science (BK21Plus) and Research Institute of Life Sciences, Gyeongsang National University, Jinju 660-701, Korea
| | - Hyeon-Su Ro
- Division of Applied Life Science (BK21Plus) and Research Institute of Life Sciences, Gyeongsang National University, Jinju 660-701, Korea
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282
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Teparić R, Mrsa V. Proteins involved in building, maintaining and remodeling of yeast cell walls. Curr Genet 2014; 59:171-85. [PMID: 23959528 DOI: 10.1007/s00294-013-0403-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/27/2013] [Accepted: 08/06/2013] [Indexed: 11/29/2022]
Abstract
The cell wall defines the shape and provides osmotic stability to the yeast cell. It also serves to anchor proteins required for communication of the yeast cell with surrounding molecules and other cells. It is synthesized as a complex structure with β-1,3-glucan chains forming the basic network to which β-1,6-glucan, chitin and a number of mannoproteins are attached. Synthesis, maintaining and remodeling of this complex structure require a set of different synthases, hydrolases and transglycosidases whose concerted activities provide necessary firmness but at the same time flexibility of the wall moiety. The present state of comprehension of the interplay of these proteins in the yeast cell wall is the subject of this article.
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283
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Sørensen DM, Holen HW, Holemans T, Vangheluwe P, Palmgren MG. Towards defining the substrate of orphan P5A-ATPases. Biochim Biophys Acta Gen Subj 2014; 1850:524-35. [PMID: 24836520 DOI: 10.1016/j.bbagen.2014.05.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 05/05/2014] [Accepted: 05/06/2014] [Indexed: 11/16/2022]
Abstract
BACKGROUND P-type ATPases are ubiquitous ion and lipid pumps found in cellular membranes. P5A-ATPases constitute a poorly characterized subfamily of P-type ATPases present in all eukaryotic organisms but for which a transported substrate remains to be identified. SCOPE OF REVIEW This review aims to discuss the available evidence which could lead to identification of possible substrates of P5A-ATPases. MAJOR CONCLUSIONS The complex phenotypes resulting from the loss of P5A-ATPases in model organisms can be explained by a role of the P5A-ATPase in the endoplasmic reticulum (ER), where loss of function leads to broad and unspecific phenotypes related to the impairment of basic ER functions such as protein folding and processing. Genetic interactions in Saccharomyces cerevisiae point to a role of the endogenous P5A-ATPase Spf1p in separation of charges in the ER, in sterol metabolism, and in insertion of tail-anchored proteins in the ER membrane. A role for P5A-ATPases in vesicle formation would explain why sterol transport and distribution are affected in knock out cells, which in turn has a negative impact on the spontaneous insertion of tail-anchored proteins. It would also explain why secretory proteins destined for the Golgi and the cell wall have difficulties in reaching their final destination. Cations and phospholipids could both be transported substrates of P5A-ATPases and as each carry charges, transport of either might explain why a charge difference arises across the ER membrane. GENERAL SIGNIFICANCE Identification of the substrate of P5A-ATPases would throw light on an important general process in the ER that is still not fully understood. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
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Affiliation(s)
- Danny Mollerup Sørensen
- Centre for Membrane Pumps in Cells and Disease-PUMPkin, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Henrik Waldal Holen
- Centre for Membrane Pumps in Cells and Disease-PUMPkin, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Tine Holemans
- Department of Cellular and Molecular Medicine, ON1 Campus Gasthuisberg, Katholieke Universiteit Leuven, Herestraat 49, Box 802, B3000 Leuven, Belgium
| | - Peter Vangheluwe
- Department of Cellular and Molecular Medicine, ON1 Campus Gasthuisberg, Katholieke Universiteit Leuven, Herestraat 49, Box 802, B3000 Leuven, Belgium
| | - Michael G Palmgren
- Centre for Membrane Pumps in Cells and Disease-PUMPkin, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.
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284
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Gyore J, Parameswar AR, Hebbard CFF, Oh Y, Bi E, Demchenko AV, Price NP, Orlean P. 2-Acylamido analogues of N-acetylglucosamine prime formation of chitin oligosaccharides by yeast chitin synthase 2. J Biol Chem 2014; 289:12835-41. [PMID: 24619411 PMCID: PMC4007471 DOI: 10.1074/jbc.m114.550749] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Chitin, a homopolymer of β1,4-linked N-acetylglucosamine (GlcNAc) residues, is a key component of the cell walls of fungi and the exoskeletons of arthropods. Chitin synthases transfer GlcNAc from UDP-GlcNAc to preexisting chitin chains in reactions that are typically stimulated by free GlcNAc. The effect of GlcNAc was probed by using a yeast strain expressing a single chitin synthase, Chs2, by examining formation of chitin oligosaccharides (COs) and insoluble chitin, and by replacing GlcNAc with 2-acylamido analogues of GlcNAc. Synthesis of COs was strongly dependent on inclusion of GlcNAc in chitin synthase incubations, and N,N'-diacetylchitobiose (GlcNAc2) was the major reaction product. Formation of both COs and insoluble chitin was also stimulated by GlcNAc2 and by N-propanoyl-, N-butanoyl-, and N-glycolylglucosamine. MALDI analyses of the COs made in the presence of 2-acylamido analogues of GlcNAc showed they that contained a single GlcNAc analogue and one or more additional GlcNAc residues. These results indicate that Chs2 can use certain 2-acylamido analogues of GlcNAc, and likely free GlcNAc and GlcNAc2 as well, as GlcNAc acceptors in a UDP-GlcNAc-dependent glycosyltransfer reaction. Further, formation of modified disaccharides indicates that CSs can transfer single GlcNAc residues.
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Affiliation(s)
- Jacob Gyore
- From the Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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285
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Unexpected function of the glucanosyltransferase Gas1 in the DNA damage response linked to histone H3 acetyltransferases in Saccharomyces cerevisiae. Genetics 2014; 196:1029-39. [PMID: 24532730 DOI: 10.1534/genetics.113.158824] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Chromatin organization and structure are crucial for transcriptional regulation, DNA replication, and damage repair. Although initially characterized in remodeling cell wall glucans, the β-1,3-glucanosyltransferase Gas1 was recently discovered to regulate transcriptional silencing in a manner separable from its activity at the cell wall. However, the function of Gas1 in modulating chromatin remains largely unexplored. Our genetic characterization revealed that GAS1 had critical interactions with genes encoding the histone H3 lysine acetyltransferases Gcn5 and Sas3. Specifically, whereas the gas1 gcn5 double mutant was synthetically lethal, deletion of both GAS1 and SAS3 restored silencing in Saccharomyces cerevisiae. The loss of GAS1 also led to broad DNA damage sensitivity with reduced Rad53 phosphorylation and defective cell cycle checkpoint activation following exposure to select genotoxins. Deletion of SAS3 in the gas1 background restored both Rad53 phosphorylation and checkpoint activation following exposure to genotoxins that trigger the DNA replication checkpoint. Our analysis thus uncovers previously unsuspected functions for both Gas1 and Sas3 in DNA damage response and cell cycle regulation.
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286
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Wanless AG, Lin Y, Weiss EL. Cell morphogenesis proteins are translationally controlled through UTRs by the Ndr/LATS target Ssd1. PLoS One 2014; 9:e85212. [PMID: 24465507 PMCID: PMC3897418 DOI: 10.1371/journal.pone.0085212] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 11/24/2013] [Indexed: 11/19/2022] Open
Abstract
Eukaryotic cells control their growth and morphogenesis to maintain integrity and viability. Free-living cells are further challenged by their direct interaction with the environment and in many cases maintain a resilient cell wall to stay alive under widely varying conditions. For these organisms, stringent and highly localized control of the cell wall's remodeling and expansion is crucial for cell growth and reproduction. In the budding yeast Saccharomyces cerevisiae the RNA binding protein Ssd1 helps control cell wall remodeling by repressing translation of proteins involved in wall expansion. Ssd1 is itself negatively regulated by the highly conserved Ndr/LATS protein kinase Cbk1. We sought to identify mRNA regions that confer Ssd1-mediated translational control. After validating a GFP reporter system as a readout of Ssd1 activity we found that 3′ untranslated regions of the known Ssd1 targets CTS1, SIM1 and UTH1 are sufficient for Cbk1-regulated translational control. The 5′ untranslated region of UTH1 also facilitated Ssd1-mediated translational control in a heterologous context. The CTS1 and SIM1 3′ untranslated regions confer Ssd1 binding, and the SIM1 3′ untranslated region improves Ssd1 immunoprecipitation of the endogenous SIM1 transcript. However, SIM1's 3′ untranslated region is not essential for Ssd1-regulated control of the message's translation. We propose that Ssd1 regulates translation of its target message primarily through UTRs and the SIM1 message through multiple potential points of interaction, permitting fine translational control in various contexts.
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Affiliation(s)
- Antony G. Wanless
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Yuan Lin
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Eric L. Weiss
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- * E-mail:
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287
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Matsuoka H, Hashimoto K, Saijo A, Takada Y, Kondo A, Ueda M, Ooshima H, Tachibana T, Azuma M. Cell wall structure suitable for surface display of proteins inSaccharomyces cerevisiae. Yeast 2014; 31:67-76. [DOI: 10.1002/yea.2995] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 12/03/2013] [Accepted: 12/09/2013] [Indexed: 11/11/2022] Open
Affiliation(s)
- Hiroyuki Matsuoka
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering; Osaka City University; Japan
| | - Kazuya Hashimoto
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering; Osaka City University; Japan
| | - Aki Saijo
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering; Osaka City University; Japan
| | - Yuki Takada
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering; Osaka City University; Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering; Kobe University; Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture; Kyoto University; Japan
| | - Hiroshi Ooshima
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering; Osaka City University; Japan
| | - Taro Tachibana
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering; Osaka City University; Japan
| | - Masayuki Azuma
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering; Osaka City University; Japan
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288
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A visual screen of protein localization during sporulation identifies new components of prospore membrane-associated complexes in budding yeast. EUKARYOTIC CELL 2014; 13:383-91. [PMID: 24390141 DOI: 10.1128/ec.00333-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
During ascospore formation in Saccharomyces cerevisiae, the secretory pathway is reorganized to create new intracellular compartments, termed prospore membranes. Prospore membranes engulf the nuclei produced by the meiotic divisions, giving rise to individual spores. The shape and growth of prospore membranes are constrained by cytoskeletal structures, such as septin proteins, that associate with the membranes. Green fluorescent protein (GFP) fusions to various proteins that associate with septins at the bud neck during vegetative growth as well as to proteins encoded by genes that are transcriptionally induced during sporulation were examined for their cellular localization during prospore membrane growth. We report localizations for over 100 different GFP fusions, including over 30 proteins localized to the prospore membrane compartment. In particular, the screen identified IRC10 as a new component of the leading-edge protein complex (LEP), a ring structure localized to the lip of the prospore membrane. Localization of Irc10 to the leading edge is dependent on SSP1, but not ADY3. Loss of IRC10 caused no obvious phenotype, but an ady3 irc10 mutant was completely defective in sporulation and displayed prospore membrane morphologies similar to those of an ssp1 strain. These results reveal the architecture of the LEP and provide insight into the evolution of this membrane-organizing complex.
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289
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Yu Q, Sun M, Wang Y, Li M, Liu L. The interaction between lead sulfide nano-dendrites and Saccharomyce cerevisiae is involved in nanotoxicity. RSC Adv 2014. [DOI: 10.1039/c4ra01861c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Interaction between PbS nano-dendrites and yeast cells lead to degradation of dendrites, cell wall damage and ROS accumulation.
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Affiliation(s)
- Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology
- Ministry of Education
- Department of Microbiology
- Nankai University
- Tianjin, PR China
| | - Meiqing Sun
- College of Environmental Science and Engineering
- Nankai University
- Tianjin, China 300071
| | - Yu Wang
- Key Laboratory of Molecular Microbiology and Technology
- Ministry of Education
- Department of Microbiology
- Nankai University
- Tianjin, PR China
| | - Mingchun Li
- Key Laboratory of Molecular Microbiology and Technology
- Ministry of Education
- Department of Microbiology
- Nankai University
- Tianjin, PR China
| | - Lu Liu
- College of Environmental Science and Engineering
- Nankai University
- Tianjin, China 300071
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290
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How carbohydrates sculpt cells: chemical control of morphogenesis in the yeast cell wall. Nat Rev Microbiol 2013; 11:648-55. [PMID: 23949603 DOI: 10.1038/nrmicro3090] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In budding yeast, the neck that connects the mother and daughter cell is the site of essential functions such as organelle trafficking, septum formation and cytokinesis. Therefore, the morphology of this region, which depends on the surrounding cell wall, must be maintained throughout the cell cycle. Growth at the neck is prevented, redundantly, by a septin ring inside the cell membrane and a chitin ring in the cell wall. Here, we describe recent work supporting the hypothesis that attachment of the chitin ring, which forms at the mother-bud neck during budding, to β-1,3-glucan in the cell wall is necessary to stop growth at the neck. Thus, in this scenario, chemistry controls morphogenesis.
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291
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Yun Y, Liu Z, Zhang J, Shim WB, Chen Y, Ma Z. The MAPKK FgMkk1 ofFusarium graminearumregulates vegetative differentiation, multiple stress response, and virulence via the cell wall integrity and high-osmolarity glycerol signaling pathways. Environ Microbiol 2013; 16:2023-37. [DOI: 10.1111/1462-2920.12334] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 11/07/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Yingzi Yun
- Institute of Biotechnology; Zhejiang University; 866 Yuhangtang Road Hangzhou 310058 China
| | - Zunyong Liu
- Institute of Biotechnology; Zhejiang University; 866 Yuhangtang Road Hangzhou 310058 China
| | - Jingze Zhang
- Institute of Biotechnology; Zhejiang University; 866 Yuhangtang Road Hangzhou 310058 China
| | - Won-Bo Shim
- Department of Plant Pathology and Microbiology; Texas A&M University; College Station TX USA
| | - Yun Chen
- Institute of Biotechnology; Zhejiang University; 866 Yuhangtang Road Hangzhou 310058 China
| | - Zhonghua Ma
- Institute of Biotechnology; Zhejiang University; 866 Yuhangtang Road Hangzhou 310058 China
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292
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Mutations in SNF1 complex genes affect yeast cell wall strength. Eur J Cell Biol 2013; 92:383-95. [DOI: 10.1016/j.ejcb.2014.01.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 12/19/2013] [Accepted: 01/02/2014] [Indexed: 01/01/2023] Open
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293
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Okada H, Ohnuki S, Roncero C, Konopka JB, Ohya Y. Distinct roles of cell wall biogenesis in yeast morphogenesis as revealed by multivariate analysis of high-dimensional morphometric data. Mol Biol Cell 2013; 25:222-33. [PMID: 24258022 PMCID: PMC3890343 DOI: 10.1091/mbc.e13-07-0396] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
To better define how cell wall structure affects morphogenesis, the morphology of yeast cells was analyzed quantitatively after treatment with the three drugs that inhibit different aspects of cell wall synthesis. These drugs induced both similar effects, including broader necks and increased morphological variation, and distinct effects. The cell wall of budding yeast is a rigid structure composed of multiple components. To thoroughly understand its involvement in morphogenesis, we used the image analysis software CalMorph to quantitatively analyze cell morphology after treatment with drugs that inhibit different processes during cell wall synthesis. Cells treated with cell wall–affecting drugs exhibited broader necks and increased morphological variation. Tunicamycin, which inhibits the initial step of N-glycosylation of cell wall mannoproteins, induced morphologies similar to those of strains defective in α-mannosylation. The chitin synthase inhibitor nikkomycin Z induced morphological changes similar to those of mutants defective in chitin transglycosylase, possibly due to the critical role of chitin in anchoring the β-glucan network. To define the mode of action of echinocandin B, a 1,3-β-glucan synthase inhibitor, we compared the morphology it induced with mutants of Fks1 that contains the catalytic domain for 1,3-β-glucan synthesis. Echinocandin B exerted morphological effects similar to those observed in some fks1 mutants, with defects in cell polarity and reduced glucan synthesis activity, suggesting that echinocandin B affects not only 1,3-β-glucan synthesis, but also another functional domain. Thus our multivariate analyses reveal discrete functions of cell wall components and increase our understanding of the pharmacology of antifungal drugs.
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Affiliation(s)
- Hiroki Okada
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8561, Japan Instituto de Biología Funcional y Genómica and Departamento de Microbiología y Genética, CSIC/Universidad de Salamanca, 37007 Salamanca, Spain Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794
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294
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Cell wall-related bionumbers and bioestimates of Saccharomyces cerevisiae and Candida albicans. EUKARYOTIC CELL 2013; 13:2-9. [PMID: 24243791 DOI: 10.1128/ec.00250-13] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bionumbers and bioestimates are valuable tools in biological research. Here we focus on cell wall-related bionumbers and bioestimates of the budding yeast Saccharomyces cerevisiae and the polymorphic, pathogenic fungus Candida albicans. We discuss the linear relationship between cell size and cell ploidy, the correlation between cell size and specific growth rate, the effect of turgor pressure on cell size, and the reason why using fixed cells for measuring cellular dimensions can result in serious underestimation of in vivo values. We further consider the evidence that individual buds and hyphae grow linearly and that exponential growth of the population results from regular formation of new daughter cells and regular hyphal branching. Our calculations show that hyphal growth allows C. albicans to cover much larger distances per unit of time than the yeast mode of growth and that this is accompanied by strongly increased surface expansion rates. We therefore predict that the transcript levels of genes involved in wall formation increase during hyphal growth. Interestingly, wall proteins and polysaccharides seem barely, if at all, subject to turnover and replacement. A general lesson is how strongly most bionumbers and bioestimates depend on environmental conditions and genetic background, thus reemphasizing the importance of well-defined and carefully chosen culture conditions and experimental approaches. Finally, we propose that the numbers and estimates described here offer a solid starting point for similar studies of other cell compartments and other yeast species.
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295
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Miles S, Li L, Davison J, Breeden LL. Xbp1 directs global repression of budding yeast transcription during the transition to quiescence and is important for the longevity and reversibility of the quiescent state. PLoS Genet 2013; 9:e1003854. [PMID: 24204289 PMCID: PMC3814307 DOI: 10.1371/journal.pgen.1003854] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 08/19/2013] [Indexed: 01/03/2023] Open
Abstract
Pure populations of quiescent yeast can be obtained from stationary phase cultures that have ceased proliferation after exhausting glucose and other carbon sources from their environment. They are uniformly arrested in the G1 phase of the cell cycle, and display very high thermo-tolerance and longevity. We find that G1 arrest is initiated before all the glucose has been scavenged from the media. Maintaining G1 arrest requires transcriptional repression of the G1 cyclin, CLN3, by Xbp1. Xbp1 is induced as glucose is depleted and it is among the most abundant transcripts in quiescent cells. Xbp1 binds and represses CLN3 transcription and in the absence of Xbp1, or with extra copies of CLN3, cells undergo ectopic divisions and produce very small cells. The Rad53-mediated replication stress checkpoint reinforces the arrest and becomes essential when Cln3 is overproduced. The XBP1 transcript also undergoes metabolic oscillations under glucose limitation and we identified many additional transcripts that oscillate out of phase with XBP1 and have Xbp1 binding sites in their promoters. Further global analysis revealed that Xbp1 represses 15% of all yeast genes as they enter the quiescent state and over 500 of these transcripts contain Xbp1 binding sites in their promoters. Xbp1-repressed transcripts are highly enriched for genes involved in the regulation of cell growth, cell division and metabolism. Failure to repress some or all of these targets leads xbp1 cells to enter a permanent arrest or senescence with a shortened lifespan. Complex organisms depend on populations of non-dividing quiescent cells for their controlled growth, development and tissue renewal. These quiescent cells are maintained in a resting state, and divide only when stimulated to do so. Unscheduled exit or failure to enter this quiescent state results in uncontrolled proliferation and cancer. Yeast cells also enter a stable, protected and reversible quiescent state. As with higher cells, they exit the cell cycle from G1, reduce growth, conserve and recycle cellular contents. These similarities, and the fact that the mechanisms that start and stop the cell cycle are fundamentally conserved lead us to think that understanding how yeast enter, maintain and reverse quiescence could give important leads into the same processes in complex organisms. We show that yeast cells maintain G1 arrest by expressing a transcription factor that represses conserved activators (cyclins) and hundreds of other genes that are important for cell division and cell growth. Failure to repress some or all of these targets leads to extra cell divisions, prevents reversible arrest and shortens life span. Many Xbp1 targets are conserved cell cycle regulators and may also be actively repressed in the quiescent cells of more complex organisms.
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Affiliation(s)
- Shawna Miles
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Lihong Li
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jerry Davison
- Computational Biology, Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Linda L. Breeden
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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296
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A novel fluorescence assay and catalytic properties of Crh1 and Crh2 yeast cell wall transglycosylases. Biochem J 2013; 455:307-18. [DOI: 10.1042/bj20130354] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A fluorescence assay was devised for the determination of transglycosylating activities of Crh1 and Crh2 yeast cell wall mannoproteins. Both proteins use chitin derivatives as donors and oligosaccharides derived from chitin, β-(1,3)-glucan and β-(1,6)-glucan as acceptors in vitro and in vivo.
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297
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Rodríguez-Peña JM, Díez-Muñiz S, Bermejo C, Nombela C, Arroyo J. Activation of the yeast cell wall integrity MAPK pathway by zymolyase depends on protease and glucanase activities and requires the mucin-like protein Hkr1 but not Msb2. FEBS Lett 2013; 587:3675-80. [DOI: 10.1016/j.febslet.2013.09.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 09/17/2013] [Accepted: 09/17/2013] [Indexed: 12/24/2022]
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298
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Francois JM, Formosa C, Schiavone M, Pillet F, Martin-Yken H, Dague E. Use of atomic force microscopy (AFM) to explore cell wall properties and response to stress in the yeast Saccharomyces cerevisiae. Curr Genet 2013; 59:187-96. [PMID: 24071902 DOI: 10.1007/s00294-013-0411-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 09/12/2013] [Accepted: 09/18/2013] [Indexed: 11/30/2022]
Abstract
Over the past 20 years, the yeast cell wall has been thoroughly investigated by genetic and biochemical methods, leading to remarkable advances in the understanding of its biogenesis and molecular architecture as well as to the mechanisms by which this organelle is remodeled in response to environmental stresses. Being a dynamic structure that constitutes the frontier between the cell interior and its immediate surroundings, imaging cell surface, measuring mechanical properties of cell wall or probing cell surface proteins for localization or interaction with external biomolecules are among the most burning questions that biologists wished to address in order to better understand the structure-function relationships of yeast cell wall in adhesion, flocculation, aggregation, biofilm formation, interaction with antifungal drugs or toxins, as well as response to environmental stresses, such as temperature changes, osmotic pressure, shearing stress, etc. The atomic force microscopy (AFM) is nowadays the most qualified and developed technique that offers the possibilities to address these questions since it allows working directly on living cells to explore and manipulate cell surface properties at nanometer resolution and to analyze cell wall proteins at the single molecule level. In this minireview, we will summarize the most recent contributions made by AFM in the analysis of the biomechanical and biochemical properties of the yeast cell wall and illustrate the power of this tool to unravel unexpected effects caused by environmental stresses and antifungal agents on the surface of living yeast cells.
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Affiliation(s)
- Jean Marie Francois
- Université de Toulouse, INSA, UPS, INP, 135 avenue de Rangueil, 31077, Toulouse, France,
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Lin CPC, Kim C, Smith SO, Neiman AM. A highly redundant gene network controls assembly of the outer spore wall in S. cerevisiae. PLoS Genet 2013; 9:e1003700. [PMID: 23966878 PMCID: PMC3744438 DOI: 10.1371/journal.pgen.1003700] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 06/20/2013] [Indexed: 12/01/2022] Open
Abstract
The spore wall of Saccharomyces cerevisiae is a multilaminar extracellular structure that is formed de novo in the course of sporulation. The outer layers of the spore wall provide spores with resistance to a wide variety of environmental stresses. The major components of the outer spore wall are the polysaccharide chitosan and a polymer formed from the di-amino acid dityrosine. Though the synthesis and export pathways for dityrosine have been described, genes directly involved in dityrosine polymerization and incorporation into the spore wall have not been identified. A synthetic gene array approach to identify new genes involved in outer spore wall synthesis revealed an interconnected network influencing dityrosine assembly. This network is highly redundant both for genes of different activities that compensate for the loss of each other and for related genes of overlapping activity. Several of the genes in this network have paralogs in the yeast genome and deletion of entire paralog sets is sufficient to severely reduce dityrosine fluorescence. Solid-state NMR analysis of partially purified outer spore walls identifies a novel component in spore walls from wild type that is absent in some of the paralog set mutants. Localization of gene products identified in the screen reveals an unexpected role for lipid droplets in outer spore wall formation. The cell wall of fungi is a complex extracellular matrix and an important target for antifungal drugs. Assembly of the wall during spore formation in baker's yeast is a useful model for fungal wall development. The outermost layers of the spore wall are composed of a polymer of dityrosine connected to an underlying polysaccharide layer. The assembly pathway of this dityrosine polymer is not known. Using a genetic approach we reveal a network of genes that function redundantly to control dityrosine layer synthesis. Solid state NMR analysis of spore walls from wild-type and mutant cells reveals a novel constituent of the spore wall that may link the dityrosine to the underlying polysaccharides and a role for lipid droplets in the incorporation of this new component into the spore wall.
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Affiliation(s)
- Coney Pei-Chen Lin
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Carey Kim
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Steven O. Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Aaron M. Neiman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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