51
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Bi F, Ment D, Luria N, Meng X, Prusky D. Mutation of AREA affects growth, sporulation, nitrogen regulation, and pathogenicity in Colletotrichum gloeosporioides. Fungal Genet Biol 2016; 99:29-39. [PMID: 28027951 DOI: 10.1016/j.fgb.2016.12.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 12/09/2016] [Accepted: 12/16/2016] [Indexed: 01/09/2023]
Abstract
The GATA transcription factor AreA is a global nitrogen regulator that restricts the utilization of complex and poor nitrogen sources in the presence of good nitrogen sources in microorganisms. In this study, we report the biological function of an AreA homolog (the CgareA gene) in the fruit postharvest pathogen Colletotrichum gloeosporioides. Targeted gene deletion mutants of areA exhibited significant reductions in vegetative growth, increases in conidia production, and slight decreases in conidial germination rates. Quantitative RT-PCR (qRT-PCR) analysis revealed that the expression of AreA was highly induced under nitrogen-limiting conditions. Moreover, compared to wild-type and complemented strains, nitrogen metabolism-related genes were misregulated in ΔareA mutant strains. Pathogenicity assays indicated that the virulence of ΔareA mutant strains were affected by the nitrogen content, but not the carbon content, of fruit hosts. Taken together, our results indicate that CgareA plays a critical role in fungal development, conidia production, regulation of nitrogen metabolism and virulence in Colletotrichum gloeosporioides.
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Affiliation(s)
- Fangcheng Bi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou 510640, China; Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Province, Guangzhou 510640, China; Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel
| | - Dana Ment
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel
| | - Neta Luria
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel
| | - Xiangchun Meng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou 510640, China; Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Province, Guangzhou 510640, China.
| | - Dov Prusky
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel.
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52
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Honigberg SM. Similar environments but diverse fates: Responses of budding yeast to nutrient deprivation. MICROBIAL CELL 2016; 3:302-328. [PMID: 27917388 PMCID: PMC5134742 DOI: 10.15698/mic2016.08.516] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Diploid budding yeast (Saccharomyces cerevisiae) can adopt one
of several alternative differentiation fates in response to nutrient limitation,
and each of these fates provides distinct biological functions. When different
strain backgrounds are taken into account, these various fates occur in response
to similar environmental cues, are regulated by the same signal transduction
pathways, and share many of the same master regulators. I propose that the
relationships between fate choice, environmental cues and signaling pathways are
not Boolean, but involve graded levels of signals, pathway activation and
master-regulator activity. In the absence of large differences between
environmental cues, small differences in the concentration of cues may be
reinforced by cell-to-cell signals. These signals are particularly essential for
fate determination within communities, such as colonies and biofilms, where fate
choice varies dramatically from one region of the community to another. The lack
of Boolean relationships between cues, signaling pathways, master regulators and
cell fates may allow yeast communities to respond appropriately to the wide
range of environments they encounter in nature.
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Affiliation(s)
- Saul M Honigberg
- Division of Cell Biology and Biophysics, University of Missouri-Kansas City, 5007 Rockhill Rd, Kansas City MO 64110, USA
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53
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Braunsdorf C, Mailänder-Sánchez D, Schaller M. Fungal sensing of host environment. Cell Microbiol 2016; 18:1188-200. [DOI: 10.1111/cmi.12610] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/02/2016] [Accepted: 05/05/2016] [Indexed: 12/13/2022]
Affiliation(s)
- C. Braunsdorf
- Department of Dermatology; University Hospital Tübingen; Liebermeisterstr. 25 Tübingen Germany
| | - D. Mailänder-Sánchez
- Department of Internal Medicine I; University Hospital Tübingen; Otfried-Müller-Straße 10 72076 Tübingen
| | - M. Schaller
- Department of Dermatology; University Hospital Tübingen; Liebermeisterstr. 25 Tübingen Germany
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Calabrese S, Pérez-Tienda J, Ellerbeck M, Arnould C, Chatagnier O, Boller T, Schüßler A, Brachmann A, Wipf D, Ferrol N, Courty PE. GintAMT3 - a Low-Affinity Ammonium Transporter of the Arbuscular Mycorrhizal Rhizophagus irregularis. FRONTIERS IN PLANT SCIENCE 2016; 7:679. [PMID: 27252708 PMCID: PMC4879785 DOI: 10.3389/fpls.2016.00679] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 05/02/2016] [Indexed: 05/05/2023]
Abstract
Nutrient acquisition and transfer are essential steps in the arbuscular mycorrhizal (AM) symbiosis, which is formed by the majority of land plants. Mineral nutrients are taken up by AM fungi from the soil and transferred to the plant partner. Within the cortical plant root cells the fungal hyphae form tree-like structures (arbuscules) where the nutrients are released to the plant-fungal interface, i.e., to the periarbuscular space, before being taken up by the plant. In exchange, the AM fungi receive carbohydrates from the plant host. Besides the well-studied uptake of phosphorus (P), the uptake and transfer of nitrogen (N) plays a crucial role in this mutualistic interaction. In the AM fungus Rhizophagus irregularis (formerly called Glomus intraradices), two ammonium transporters (AMT) were previously described, namely GintAMT1 and GintAMT2. Here, we report the identification and characterization of a newly identified R. irregularis AMT, GintAMT3. Phylogenetic analyses revealed high sequence similarity to previously identified AM fungal AMTs and a clear separation from other fungal AMTs. Topological analysis indicated GintAMT3 to be a membrane bound pore forming protein, and GFP tagging showed it to be highly expressed in the intraradical mycelium of a fully established AM symbiosis. Expression of GintAMT3 in yeast successfully complemented the yeast AMT triple deletion mutant (MATa ura3 mep1Δ mep2Δ::LEU2 mep3Δ::KanMX2). GintAMT3 is characterized as a low affinity transport system with an apparent Km of 1.8 mM and a V max of 240 nmol(-1) min(-1) 10(8) cells(-1), which is regulated by substrate concentration and carbon supply.
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Affiliation(s)
- Silvia Calabrese
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of BaselBasel, Switzerland
| | - Jacob Pérez-Tienda
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Matthias Ellerbeck
- Faculty of Biology, Genetics, Ludwig-Maximilians-University MunichPlanegg-Martinsried, Germany
| | - Christine Arnould
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Bourgogne Franche-ComtéDijon, France
| | - Odile Chatagnier
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Bourgogne Franche-ComtéDijon, France
| | - Thomas Boller
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of BaselBasel, Switzerland
| | - Arthur Schüßler
- Faculty of Biology, Genetics, Ludwig-Maximilians-University MunichPlanegg-Martinsried, Germany
| | - Andreas Brachmann
- Faculty of Biology, Genetics, Ludwig-Maximilians-University MunichPlanegg-Martinsried, Germany
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Bourgogne Franche-ComtéDijon, France
| | - Nuria Ferrol
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Pierre-Emmanuel Courty
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of BaselBasel, Switzerland
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Boeckstaens M. [From the discovery of microbial Mep-Amt ammonium transporters to human Rhesus factors]. Med Sci (Paris) 2016; 32:394-400. [PMID: 27137697 DOI: 10.1051/medsci/20163204018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Ammonium, ubiquitous on Earth, plays major and distinct roles in most organisms. While it can be a nitrogen source for many microorganisms and plants, it is a cytotoxic metabolic product actively detoxified by the liver in animals. Furthermore, in the latter, ammonium synthesis in the kidney is involved in acid/base homeostasis. Ammonium transport is ensured by a family of proteins, called Mep-Amt-Rh. This family is conserved in all domains of life and comprises the human Rh factors, notably known in transfusional medicine. While the study of bacterial, fungal and vegetal Mep-Amt transporters reveals a fine-tuned and rapid regulation of these proteins in function of environmental changes, the regulation of animal Rh proteins has been poorly addressed. This review notably highlights the importance of the yeast model in the study of the regulation of these proteins as well as in the functional characterization of Mep-Amt-Rh members of diverse origins.
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Affiliation(s)
- Mélanie Boeckstaens
- Laboratoire de biologie du transport membranaire, IBMM, université Libre de Bruxelles, 12, rue des Professeurs Jeener et Brachet, 6041 Gosselies, Belgique
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56
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van den Berg B, Chembath A, Jefferies D, Basle A, Khalid S, Rutherford JC. Structural basis for Mep2 ammonium transceptor activation by phosphorylation. Nat Commun 2016; 7:11337. [PMID: 27088325 PMCID: PMC4852598 DOI: 10.1038/ncomms11337] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 03/14/2016] [Indexed: 11/18/2022] Open
Abstract
Mep2 proteins are fungal transceptors that play an important role as ammonium sensors in fungal development. Mep2 activity is tightly regulated by phosphorylation, but how this is achieved at the molecular level is not clear. Here we report X-ray crystal structures of the Mep2 orthologues from Saccharomyces cerevisiae and Candida albicans and show that under nitrogen-sufficient conditions the transporters are not phosphorylated and present in closed, inactive conformations. Relative to the open bacterial ammonium transporters, non-phosphorylated Mep2 exhibits shifts in cytoplasmic loops and the C-terminal region (CTR) to occlude the cytoplasmic exit of the channel and to interact with His2 of the twin-His motif. The phosphorylation site in the CTR is solvent accessible and located in a negatively charged pocket ∼30 Å away from the channel exit. The crystal structure of phosphorylation-mimicking Mep2 variants from C. albicans show large conformational changes in a conserved and functionally important region of the CTR. The results allow us to propose a model for regulation of eukaryotic ammonium transport by phosphorylation.
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Affiliation(s)
- Bert van den Berg
- Institute for Cell and Molecular Biosciences, The Medical
School, Newcastle University, Newcastle upon Tyne
NE2 4HH, UK
| | - Anupama Chembath
- Institute for Cell and Molecular Biosciences, The Medical
School, Newcastle University, Newcastle upon Tyne
NE2 4HH, UK
| | - Damien Jefferies
- School of Chemistry, University of Southampton,
Highfield Campus, Southampton
SO17 1BJ, UK
| | - Arnaud Basle
- Institute for Cell and Molecular Biosciences, The Medical
School, Newcastle University, Newcastle upon Tyne
NE2 4HH, UK
| | - Syma Khalid
- School of Chemistry, University of Southampton,
Highfield Campus, Southampton
SO17 1BJ, UK
| | - Julian C. Rutherford
- Institute for Cell and Molecular Biosciences, The Medical
School, Newcastle University, Newcastle upon Tyne
NE2 4HH, UK
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57
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van Heerden A, Mouton M, Postma F, van Wyk PWJ, Lerm B, Van Zyl WH, Borstlap CJ, Botha A. The microcyclic conidial stage of Coniochaeta pulveracea and its effect on selected biological interactions. Folia Microbiol (Praha) 2015; 61:319-28. [PMID: 26658947 DOI: 10.1007/s12223-015-0441-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/01/2015] [Indexed: 12/20/2022]
Abstract
Coniochaeta pulveracea is a dimorphic lignicolous fungus that has mostly been isolated from decaying wood. However, relatively little work was conducted on the conditions for the dimorphic switch or the biological interactions of the fungus in its yeast-like microcyclic growth phase. Therefore, in this study, the microcyclic conidiation of C. pulveracea strains and representatives of the closely related species, Coniochaeta boothii and Coniochaeta subcorticalis, was studied under different environmental conditions. The strains were found to exhibit hyphal growth on solid substrates and underwent a dimorphic switch to produce microcycle conidiation upon transfer to a liquid medium which differed in physico-chemical composition compared to the original solid medium. Factors that were found to contribute to this dimorphic switch were temperature, pH and the presence of complex nitrogen sources such as casamino acids and peptone in the medium. However, C. pulveracea showed intraspecific differences with regard to its response to changes in the physico-chemical environment. The interactions of microcyclic Coniochaeta strains with selected yeasts, such as representatives of Meyerozyma guilliermondii and Cryptococcus neoformans, were subsequently studied in complex liquid media and it was found that, depending on medium composition, the microcyclic Coniochaeta exerted different effects on the different yeasts strains. In some co-cultures, a positive effect on yeast growth was observed, whilst in other cases microcyclic Coniochaeta inhibited yeast growth.
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Affiliation(s)
- Andrea van Heerden
- Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, South Africa
| | - Marnel Mouton
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Stellenbosch, South Africa
| | - Ferdinand Postma
- Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, South Africa
| | - Pieter W J van Wyk
- Centre for Confocal and Electron Microscopy, University of the Free State, P.O. Box 339, Bloemfontein, South Africa
| | - Barbra Lerm
- Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, South Africa
| | - Willem H Van Zyl
- Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, South Africa
| | - Cornelius J Borstlap
- Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, South Africa
| | - Alfred Botha
- Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, South Africa.
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58
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Hou R, Jiang C, Zheng Q, Wang C, Xu JR. The AreA transcription factor mediates the regulation of deoxynivalenol (DON) synthesis by ammonium and cyclic adenosine monophosphate (cAMP) signalling in Fusarium graminearum. MOLECULAR PLANT PATHOLOGY 2015; 16:987-99. [PMID: 25781642 PMCID: PMC6638501 DOI: 10.1111/mpp.12254] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Deoxynivalenol (DON), a trichothecene mycotoxin produced by Fusarium graminearum, is harmful to humans and animals. Because different nitrogen sources are known to have opposite effects on DON production, in this study, we characterized the regulatory mechanisms of the AREA transcription factor in trichothecene biosynthesis. The ΔareA mutant showed significantly reduced vegetative growth and DON production in cultures inoculated with hyphae. Suppression of TRI gene expression and DON production by ammonium were diminished in the ΔareA mutant. The deletion of AREA also affected the stimulatory effects of arginine on DON biosynthesis. The AreA-green fluorescent protein (GFP) fusion complemented the ΔareA mutant, and its localization to the nucleus was enhanced under nitrogen starvation conditions. Site-directed mutagenesis showed that the conserved predicted protein kinase A (PKA) phosphorylation site S874 was important for AreA function, indicating that AreA may be a downstream target of the cyclic adenosine monophosphate (cAMP)-PKA pathway, which is known to regulate DON production. We also showed that AreA interacted with Tri10 in co-immunoprecipitation assays. The interaction of AreA with Tri10 is probably related to its role in the regulation of TRI gene expression. Interestingly, the ΔareA mutant showed significantly reduced PKA activity and expression of all three predicted ammonium permease (MEP) genes, in particular MEP1, under low ammonium conditions. Taken together, our results show that AREA is involved in the regulation of DON production by ammonium suppression and the cAMP-PKA pathway. The AreA transcription factor may interact with Tri10 and control the expression and up-regulation of MEP genes.
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Affiliation(s)
- Rui Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest Agricultural and Forestry University, Yangling, Shaanxi, 712100, China
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Cong Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest Agricultural and Forestry University, Yangling, Shaanxi, 712100, China
| | - Qian Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest Agricultural and Forestry University, Yangling, Shaanxi, 712100, China
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Chenfang Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest Agricultural and Forestry University, Yangling, Shaanxi, 712100, China
| | - Jin-Rong Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest Agricultural and Forestry University, Yangling, Shaanxi, 712100, China
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
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59
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Woods K, Höfken T. The zinc cluster proteins Upc2 and Ecm22 promote filamentation in Saccharomyces cerevisiae by sterol biosynthesis-dependent and -independent pathways. Mol Microbiol 2015; 99:512-27. [PMID: 26448198 DOI: 10.1111/mmi.13244] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2015] [Indexed: 12/31/2022]
Abstract
The transition between a unicellular yeast form to multicellular filaments is crucial for budding yeast foraging and the pathogenesis of many fungal pathogens such as Candida albicans. Here, we examine the role of the related transcription factors Ecm22 and Upc2 in Saccharomyces cerevisiae filamentation. Overexpression of either ECM22 or UPC2 leads to increased filamentation, whereas cells lacking both ECM22 and UPC2 do not exhibit filamentous growth. Ecm22 and Upc2 positively control the expression of FHN1, NPR1, PRR2 and sterol biosynthesis genes. These genes all play a positive role in filamentous growth, and their expression is upregulated during filamentation in an Ecm22/Upc2-dependent manner. Furthermore, ergosterol content increases during filamentous growth. UPC2 expression also increases during filamentation and is inhibited by the transcription factors Sut1 and Sut2. The expression of SUT1 and SUT2 in turn is under negative control of the transcription factor Ste12. We suggest that during filamentation Ste12 becomes activated and reduces SUT1/SUT2 expression levels. This would result in increased UPC2 levels and as a consequence to transcriptional activation of FHN1, NPR1, PRR2 and sterol biosynthesis genes. Higher ergosterol levels in combination with the proteins Fhn1, Npr1 and Prr2 would then mediate the transition to filamentous growth.
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Affiliation(s)
- Kelly Woods
- Division of Biosciences, Brunel University London, Uxbridge, UK
| | - Thomas Höfken
- Division of Biosciences, Brunel University London, Uxbridge, UK
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60
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The TORC1 effector kinase Npr1 fine tunes the inherent activity of the Mep2 ammonium transport protein. Nat Commun 2015; 5:3101. [PMID: 24476960 DOI: 10.1038/ncomms4101] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 12/13/2013] [Indexed: 12/30/2022] Open
Abstract
The TORC1 complex controls cell growth upon integrating nutritional signals including amino-acid availability. TORC1 notably adapts the plasma membrane protein content by regulating arrestin-mediated endocytosis of amino-acid transporters. Here we demonstrate that TORC1 further fine tunes the inherent activity of the ammonium transport protein, Mep2, a yeast homologue of mammalian Rhesus factors, independently of arrestin-mediated endocytosis. The TORC1 effector kinase Npr1 and the upstream TORC1 regulator Npr2 control Mep2 transport activity by phospho-silencing a carboxy-terminal autoinhibitory domain. Under poor nitrogen supply, Npr1 enables Mep2 S457 phosphorylation and thus ammonium transport activity. Supplementation of the preferred nitrogen source glutamine leads to Mep2 inactivation and instant S457 dephosphorylation via plasma membrane Psr1 and Psr2 redundant phosphatases. This study underscores that TORC1 also adjusts nutrient permeability to regulate cell growth in a fast and flexible response to environmental perturbation, establishing a hierarchy in the transporters to be degraded, inactivated or maintained active at the plasma membrane.
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61
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Barbosa C, Mendes-Faia A, Lage P, Mira NP, Mendes-Ferreira A. Genomic expression program of Saccharomyces cerevisiae along a mixed-culture wine fermentation with Hanseniaspora guilliermondii. Microb Cell Fact 2015; 14:124. [PMID: 26314747 PMCID: PMC4552253 DOI: 10.1186/s12934-015-0318-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/14/2015] [Indexed: 02/01/2023] Open
Abstract
Background The introduction of yeast starter cultures consisting in a blend of Saccharomyces cerevisiae and non-Saccharomyces yeast strains is emerging for production of wines with improved complexity of flavor. The rational use of this approach is, however, dependent on knowing the impact that co-inoculation has in the physiology of S. cerevisiae. In this work the transcriptome of S.cerevisiae was monitored throughout a wine fermentation, carried out in single culture or in a consortium with Hanseniasporaguilliermondii, this being the first time that this relevant yeast–yeast interaction is examined at a genomic scale. Results Co-inoculation with H. guilliermondii reduced the overall genome-wide transcriptional response of S. cerevisiae throughout the fermentation, which was attributable to a lower fermentative activity of S. cerevisiae while in the mixed-fermentation. Approximately 350 genes S. cerevisiae genes were found to be differently expressed (FDR < 0.05) in response to the presence of H. guilliermondii in the fermentation medium. Genes involved in biosynthesis of vitamins were enriched among those up-regulated in the mixed-culture fermentation, while genes related with the uptake and biosynthesis of amino acids were enriched among those more expressed in the single-culture. The differences in the aromatic profiles of wines obtained in the single and in the mixed-fermentations correlated with the differential expression of S. cerevisiae genes encoding enzymes required for formation of aroma compounds. Conclusions By integrating results obtained in the transcriptomic analysis performed with physiological data our study provided, for the first time, an integrated view into the adaptive responses of S. cerevisiae to the challenging environment of mixed culture fermentation. The availability of nutrients, in particular, of nitrogen and vitamins, stands out as a factor that may determine population dynamics, fermentative activity and by-product formation. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0318-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Catarina Barbosa
- Escola de Ciências da Vida e Ambiente, Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal.
| | - Arlete Mendes-Faia
- Escola de Ciências da Vida e Ambiente, Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal. .,BioISI-Biosystems and Integrative Sciences Institute, Campo Grande, Lisbon, Portugal.
| | - Patrícia Lage
- Escola de Ciências da Vida e Ambiente, Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal.
| | - Nuno P Mira
- iBB-Institute for Bioengineering and Biosciences, Avenida Rovisco Pais, 1049-001, Lisbon, Portugal. .,Department of Bioengineering, Instituto Superior Técnico, Avenida Rovisco Pais, 1049-001, Lisbon, Portugal.
| | - Ana Mendes-Ferreira
- Escola de Ciências da Vida e Ambiente, Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal. .,BioISI-Biosystems and Integrative Sciences Institute, Campo Grande, Lisbon, Portugal.
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62
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Boeckstaens M, Merhi A, Llinares E, Van Vooren P, Springael JY, Wintjens R, Marini AM. Identification of a Novel Regulatory Mechanism of Nutrient Transport Controlled by TORC1-Npr1-Amu1/Par32. PLoS Genet 2015; 11:e1005382. [PMID: 26172854 PMCID: PMC4501750 DOI: 10.1371/journal.pgen.1005382] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 06/22/2015] [Indexed: 01/12/2023] Open
Abstract
Fine-tuning the plasma-membrane permeability to essential nutrients is fundamental to cell growth optimization. Nutritional signals including nitrogen availability are integrated by the TORC1 complex which notably regulates arrestin-mediated endocytosis of amino-acid transporters. Ammonium is a ubiquitous compound playing key physiological roles in many, if not all, organisms. In yeast, it is a preferred nitrogen source transported by three Mep proteins which are orthologues of the mammalian Rhesus factors. By combining genetic, kinetic, biochemical and cell microscopy analyses, the current study reveals a novel mechanism enabling TORC1 to regulate the inherent activity of ammonium transport proteins, independently of arrestin-mediated endocytosis, identifying the still functional orphan Amu1/Par32 as a selective regulator intermediate. We show that, under poor nitrogen supply, the TORC1 effector kinase' Npr1' promotes phosphorylation of Amu1/Par32 which appears mainly cytosolic while ammonium transport proteins are active. Upon preferred nitrogen supplementation, like glutamine or ammonium addition, TORC1 upregulation enables Npr1 inhibition and Amu1/Par32 dephosphorylation. In these conditions, as in Npr1-lacking cells, hypophosphorylated Amu1/Par32 accumulates at the cell surface and mediates the inhibition of specific ammonium transport proteins. We show that the integrity of a conserved repeated motif of Amu1/Par32 is required for the interaction with these transport proteins. This study underscores the diversity of strategies enabling TORC1-Npr1 to selectively monitor cell permeability to nutrients by discriminating between transporters to be degraded or transiently inactivated and kept stable at the plasma membrane. This study further identifies the function of Amu1/Par32 in acute control of ammonium transport in response to variations in nitrogen availability. Cells have evolved a variety of mechanisms to control the permeability of the plasma membrane to face environmental perturbations. Transcriptional regulation, endocytosis, gating and activity control of channels and transporters enable global or specific responses to stressful conditions and focused variations in nutrient availability. Emerging data from the yeast model reveal that the conserved TORC1 pathway regulates arrestin-mediated endocytosis of amino-acid transporters. We provide genetic and biochemical evidence for a novel mechanism enabling TORC1 to regulate the inherent activity of transport proteins via the Amu1/Par32 regulator intermediate. This low complexity protein mediates inhibition of specific proteins dedicated to the transport of ammonium, a favored nitrogen source, underscoring that TORC1 selects transporters to be degraded or transiently inactivated and preserved at the cell surface according to the environmental situation. The here-revealed mechanism of transport inhibition by Amu/Par32 is reminiscent to the inhibition of prokaryotic ammonium transport proteins mediated by PII-type proteins, key nitrogen signal transducers widespread in bacteria and Archaea.
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Affiliation(s)
- Mélanie Boeckstaens
- Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, Gosselies, Belgium
| | - Ahmad Merhi
- Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, Gosselies, Belgium
| | - Elisa Llinares
- Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, Gosselies, Belgium
| | - Pascale Van Vooren
- Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, Gosselies, Belgium
| | | | - René Wintjens
- Laboratoire des Biopolymères et des nanomatériaux supramoléculaires, Université Libre de Bruxelles, Brussels, Belgium
| | - Anna Maria Marini
- Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, Gosselies, Belgium
- * E-mail:
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Chantranupong L, Wolfson RL, Sabatini DM. Nutrient-sensing mechanisms across evolution. Cell 2015; 161:67-83. [PMID: 25815986 DOI: 10.1016/j.cell.2015.02.041] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Indexed: 12/11/2022]
Abstract
For organisms to coordinate their growth and development with nutrient availability, they must be able to sense nutrient levels in their environment. Here, we review select nutrient-sensing mechanisms in a few diverse organisms. We discuss how these mechanisms reflect the nutrient requirements of specific species and how they have adapted to the emergence of multicellularity in eukaryotes.
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Affiliation(s)
- Lynne Chantranupong
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rachel L Wolfson
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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Pfannmüller A, Wagner D, Sieber C, Schönig B, Boeckstaens M, Marini AM, Tudzynski B. The General Amino Acid Permease FfGap1 of Fusarium fujikuroi Is Sorted to the Vacuole in a Nitrogen-Dependent, but Npr1 Kinase-Independent Manner. PLoS One 2015; 10:e0125487. [PMID: 25909858 PMCID: PMC4409335 DOI: 10.1371/journal.pone.0125487] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/14/2015] [Indexed: 12/18/2022] Open
Abstract
The rice pathogenic fungus Fusarium fujikuroi is well known for the production of a broad spectrum of secondary metabolites (SMs) such as gibberellic acids (GAs), mycotoxins and pigments. The biosynthesis of most of these SMs strictly depends on nitrogen availability and of the activity of permeases of nitrogen sources, e.g. the ammonium and amino acid permeases. One of the three ammonium permeases, MepB, was recently shown to act not only as a transporter but also as a nitrogen sensor affecting the production of nitrogen-repressed SMs. Here we describe the identification of a general amino acid permease, FfGap1, among the 99 putative amino acid permeases (AAPs) in the genome of F. fujikuroi. FfGap1 is able to fully restore growth of the yeast gap1∆ mutant on several amino acids including citrulline and tryptophane. In S. cerevisiae, Gap1 activity is regulated by shuttling between the plasma membrane (nitrogen limiting conditions) and the vacuole (nitrogen sufficiency), which we also show for FfGap1. In yeast, the Npr1 serine/threonine kinase stabilizes the Gap1 position at the plasma membrane. Here, we identified and characterized three NPR1-homologous genes, encoding the putative protein kinases FfNpr1-1, FfNpr1-2 and FfNpr1-3 with significant similarity to yeast Npr1. Complementation of the yeast npr1Δ mutant with each of the three F. fujikuroi NPR1 homologues, resulted in partial restoration of ammonium, arginine and proline uptake by FfNPR1-1 while none of the three kinases affect growth on different nitrogen sources and nitrogen-dependent sorting of FfGap1 in F. fujikuroi. However, exchange of the putative ubiquitin-target lysine 9 (K9A) and 15 (K15A) residues of FfGap1 resulted in extended localization to the plasma membrane and increased protein stability independently of nitrogen availability. These data suggest a similar regulation of FfGap1 by nitrogen-dependent ubiquitination, but differences regarding the role of Fusarium Npr1 homologues compared to yeast.
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Affiliation(s)
- Andreas Pfannmüller
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Dominik Wagner
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Christian Sieber
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Birgit Schönig
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Mélanie Boeckstaens
- Laboratoire de Biologie du Transport Membranaire, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, Gosselies, Belgium
| | - Anna Maria Marini
- Laboratoire de Biologie du Transport Membranaire, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, Gosselies, Belgium
| | - Bettina Tudzynski
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Münster, Germany
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65
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Ayadi A, David P, Arrighi JF, Chiarenza S, Thibaud MC, Nussaume L, Marin E. Reducing the genetic redundancy of Arabidopsis PHOSPHATE TRANSPORTER1 transporters to study phosphate uptake and signaling. PLANT PHYSIOLOGY 2015; 167:1511-26. [PMID: 25670816 PMCID: PMC4378149 DOI: 10.1104/pp.114.252338] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/09/2015] [Indexed: 05/18/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) absorbs inorganic phosphate (Pi) from the soil through an active transport process mediated by the nine members of the PHOSPHATE TRANSPORTER1 (PHT1) family. These proteins share a high level of similarity (greater than 61%), with overlapping expression patterns. The resulting genetic and functional redundancy prevents the analysis of their specific roles. To overcome this difficulty, our approach combined several mutations with gene silencing to inactivate multiple members of the PHT1 family, including a cluster of genes localized on chromosome 5 (PHT1;1, PHT1;2, and PHT1;3). Physiological analyses of these lines established that these three genes, along with PHT1;4, are the main contributors to Pi uptake. Furthermore, PHT1;1 plays an important role in translocation from roots to leaves in high phosphate conditions. These genetic tools also revealed that some PHT1 transporters likely exhibit a dual affinity for phosphate, suggesting that their activity is posttranslationally controlled. These lines display significant phosphate deficiency-related phenotypes (e.g. biomass and yield) due to a massive (80%-96%) reduction in phosphate uptake activities. These defects limited the amount of internal Pi pool, inducing compensatory mechanisms triggered by the systemic Pi starvation response. Such reactions have been uncoupled from PHT1 activity, suggesting that systemic Pi sensing is most probably acting downstream of PHT1.
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Affiliation(s)
- Amal Ayadi
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Environnementale et de Biotechnologie, Laboratoire de Biologie du Développement des Plantes, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265 Biologie Végétale and Microbiologie Environnementale, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.); Aix-Marseille Université, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.); andLaboratoire des Symbioses Tropicales et Méditerranéennes, TA A-82/J Campus International de Baillarguet, 34398 Montpellier cedex 5, France (J.-F.A.)
| | - Pascale David
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Environnementale et de Biotechnologie, Laboratoire de Biologie du Développement des Plantes, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265 Biologie Végétale and Microbiologie Environnementale, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.); Aix-Marseille Université, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.); andLaboratoire des Symbioses Tropicales et Méditerranéennes, TA A-82/J Campus International de Baillarguet, 34398 Montpellier cedex 5, France (J.-F.A.)
| | - Jean-François Arrighi
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Environnementale et de Biotechnologie, Laboratoire de Biologie du Développement des Plantes, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265 Biologie Végétale and Microbiologie Environnementale, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.); Aix-Marseille Université, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.); andLaboratoire des Symbioses Tropicales et Méditerranéennes, TA A-82/J Campus International de Baillarguet, 34398 Montpellier cedex 5, France (J.-F.A.)
| | - Serge Chiarenza
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Environnementale et de Biotechnologie, Laboratoire de Biologie du Développement des Plantes, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265 Biologie Végétale and Microbiologie Environnementale, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.); Aix-Marseille Université, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.); andLaboratoire des Symbioses Tropicales et Méditerranéennes, TA A-82/J Campus International de Baillarguet, 34398 Montpellier cedex 5, France (J.-F.A.)
| | - Marie-Christine Thibaud
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Environnementale et de Biotechnologie, Laboratoire de Biologie du Développement des Plantes, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265 Biologie Végétale and Microbiologie Environnementale, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.); Aix-Marseille Université, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.); andLaboratoire des Symbioses Tropicales et Méditerranéennes, TA A-82/J Campus International de Baillarguet, 34398 Montpellier cedex 5, France (J.-F.A.)
| | - Laurent Nussaume
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Environnementale et de Biotechnologie, Laboratoire de Biologie du Développement des Plantes, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265 Biologie Végétale and Microbiologie Environnementale, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.); Aix-Marseille Université, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.); andLaboratoire des Symbioses Tropicales et Méditerranéennes, TA A-82/J Campus International de Baillarguet, 34398 Montpellier cedex 5, France (J.-F.A.)
| | - Elena Marin
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Environnementale et de Biotechnologie, Laboratoire de Biologie du Développement des Plantes, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265 Biologie Végétale and Microbiologie Environnementale, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.); Aix-Marseille Université, F-13108 Saint-Paul-lez-Durance, France (A.A., P.D., S.C., M.-C.T., L.N., E.M.); andLaboratoire des Symbioses Tropicales et Méditerranéennes, TA A-82/J Campus International de Baillarguet, 34398 Montpellier cedex 5, France (J.-F.A.)
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66
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Giehl RFH, von Wirén N. Nitrate signalling: Functions of a nitrate transceptor. NATURE PLANTS 2015; 1:15021. [PMID: 27246888 DOI: 10.1038/nplants.2015.21] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- Ricardo F H Giehl
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Nicolaus von Wirén
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
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67
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Bouguyon E, Brun F, Meynard D, Kubeš M, Pervent M, Leran S, Lacombe B, Krouk G, Guiderdoni E, Zažímalová E, Hoyerová K, Nacry P, Gojon A. Multiple mechanisms of nitrate sensing by Arabidopsis nitrate transceptor NRT1.1. NATURE PLANTS 2015; 1:15015. [PMID: 27246882 DOI: 10.1038/nplants.2015.15] [Citation(s) in RCA: 191] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 01/27/2015] [Indexed: 05/20/2023]
Abstract
In Arabidopsis the plasma membrane nitrate transceptor (transporter/receptor) NRT1.1 governs many physiological and developmental responses to nitrate. Alongside facilitating nitrate uptake, NRT1.1 regulates the expression levels of many nitrate assimilation pathway genes, modulates root system architecture, relieves seed dormancy and protects plants from ammonium toxicity. Here, we assess the functional and phenotypic consequences of point mutations in two key residues of NRT1.1 (P492 and T101). We show that the point mutations differentially affect several of the NRT1.1-dependent responses to nitrate, namely the repression of lateral root development at low nitrate concentrations, and the short-term upregulation of the nitrate-uptake gene NRT2.1, and its longer-term downregulation, at high nitrate concentrations. We also show that these mutations have differential effects on genome-wide gene expression. Our findings indicate that NRT1.1 activates four separate signalling mechanisms, which have independent structural bases in the protein. In particular, we present evidence to suggest that the phosphorylated and non-phosphorylated forms of NRT1.1 at T101 have distinct signalling functions, and that the nitrate-dependent regulation of root development depends on the phosphorylated form. Our findings add to the evidence that NRT1.1 is able to trigger independent signalling pathways in Arabidopsis in response to different environmental conditions.
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Affiliation(s)
- E Bouguyon
- Biochimie et Physiologie Moléculaire des Plantes, CNRS/INRA/SupAgro-M/UM, Montpellier 34060, France
| | - F Brun
- Biochimie et Physiologie Moléculaire des Plantes, CNRS/INRA/SupAgro-M/UM, Montpellier 34060, France
| | - D Meynard
- Amélioration Génétique et Adaptation des Plantes, CIRAD/INRA/SupAgro-M, Montpellier, France
| | - M Kubeš
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, v.v.i., Rozvojová 263, Prague 6 - Lysolaje 16502, Czech Republic
| | - M Pervent
- Biochimie et Physiologie Moléculaire des Plantes, CNRS/INRA/SupAgro-M/UM, Montpellier 34060, France
| | - S Leran
- Biochimie et Physiologie Moléculaire des Plantes, CNRS/INRA/SupAgro-M/UM, Montpellier 34060, France
| | - B Lacombe
- Biochimie et Physiologie Moléculaire des Plantes, CNRS/INRA/SupAgro-M/UM, Montpellier 34060, France
| | - G Krouk
- Biochimie et Physiologie Moléculaire des Plantes, CNRS/INRA/SupAgro-M/UM, Montpellier 34060, France
| | - E Guiderdoni
- Amélioration Génétique et Adaptation des Plantes, CIRAD/INRA/SupAgro-M, Montpellier, France
| | - E Zažímalová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, v.v.i., Rozvojová 263, Prague 6 - Lysolaje 16502, Czech Republic
| | - K Hoyerová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, v.v.i., Rozvojová 263, Prague 6 - Lysolaje 16502, Czech Republic
| | - P Nacry
- Biochimie et Physiologie Moléculaire des Plantes, CNRS/INRA/SupAgro-M/UM, Montpellier 34060, France
| | - A Gojon
- Biochimie et Physiologie Moléculaire des Plantes, CNRS/INRA/SupAgro-M/UM, Montpellier 34060, France
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Fine-tuning of histone H3 Lys4 methylation during pseudohyphal differentiation by the CDK submodule of RNA polymerase II. Genetics 2014; 199:435-53. [PMID: 25467068 DOI: 10.1534/genetics.114.172841] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Transcriptional regulation is dependent upon the interactions between the RNA pol II holoenzyme complex and chromatin. RNA pol II is part of a highly conserved multiprotein complex that includes the core mediator and CDK8 subcomplex. In Saccharomyces cerevisiae, the CDK8 subcomplex, composed of Ssn2p, Ssn3p, Ssn8p, and Srb8p, is thought to play important roles in mediating transcriptional control of stress-responsive genes. Also central to transcriptional control are histone post-translational modifications. Lysine methylation, dynamically balanced by lysine methyltransferases and demethylases, has been intensively studied, uncovering significant functions in transcriptional control. A key question remains in understanding how these enzymes are targeted during stress response. To determine the relationship between lysine methylation, the CDK8 complex, and transcriptional control, we performed phenotype analyses of yeast lacking known lysine methyltransferases or demethylases in isolation or in tandem with SSN8 deletions. We show that the RNA pol II CDK8 submodule components SSN8/SSN3 and the histone demethylase JHD2 are required to inhibit pseudohyphal growth-a differentiation pathway induced during nutrient limitation-under rich conditions. Yeast lacking both SSN8 and JHD2 constitutively express FLO11, a major regulator of pseudohyphal growth. Interestingly, deleting known FLO11 activators including FLO8, MSS11, MFG1, TEC1, SNF1, KSS1, and GCN4 results in a range of phenotypic suppression. Using chromatin immunoprecipitation, we found that SSN8 inhibits H3 Lys4 trimethylation independently of JHD2 at the FLO11 locus, suggesting that H3 Lys4 hypermethylation is locking FLO11 into a transcriptionally active state. These studies implicate the CDK8 subcomplex in fine-tuning H3 Lys4 methylation levels during pseudohyphal differentiation.
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69
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Pitts RJ, Derryberry SL, Pulous FE, Zwiebel LJ. Antennal-expressed ammonium transporters in the malaria vector mosquito Anopheles gambiae. PLoS One 2014; 9:e111858. [PMID: 25360676 PMCID: PMC4216128 DOI: 10.1371/journal.pone.0111858] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 10/07/2014] [Indexed: 01/13/2023] Open
Abstract
The principal Afrotropical malaria vector mosquito, Anopheles gambiae remains a significant threat to human health. In this anthropophagic species, females detect and respond to a range of human-derived volatile kairomones such as ammonia, lactic acid, and other carboxylic acids in their quest for blood meals. While the molecular underpinnings of mosquito olfaction and host seeking are becoming better understood, many questions remain unanswered. In this study, we have identified and characterized two candidate ammonium transporter genes, AgAmt and AgRh50 that are expressed in the mosquito antenna and may contribute to physiological and behavioral responses to ammonia, which is an important host kairomone for vector mosquitoes. AgAmt transcripts are highly enhanced in female antennae while a splice variant of AgRh50 appears to be antennal-specific. Functional expression of AgAmt in Xenopus laevis oocytes facilitates inward currents in response to both ammonium and methylammonium, while AgRh50 is able to partially complement a yeast ammonium transporter mutant strain, validating their conserved roles as ammonium transporters. We present evidence to suggest that both AgAmt and AgRh50 are in vivo ammonium transporters that are important for ammonia sensitivity in An. gambiae antennae, either by clearing ammonia from the sensillar lymph or by facilitating sensory neuron responses to environmental exposure. Accordingly, AgAmt and AgRh50 represent new and potentially important targets for the development of novel vector control strategies.
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Affiliation(s)
- R. Jason Pitts
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Institute for Global Health, Nashville, Tennessee, United States of America
| | - Stephen L. Derryberry
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Fadi E. Pulous
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Laurence J. Zwiebel
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Institute for Global Health, Nashville, Tennessee, United States of America
- Department of Pharmacology, Vanderbilt Brain Institute, Program in Developmental Biology and Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- * E-mail:
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70
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Engelberg D, Perlman R, Levitzki A. Transmembrane signaling in Saccharomyces cerevisiae as a model for signaling in metazoans: state of the art after 25 years. Cell Signal 2014; 26:2865-78. [PMID: 25218923 DOI: 10.1016/j.cellsig.2014.09.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 09/02/2014] [Indexed: 02/07/2023]
Abstract
In the very first article that appeared in Cellular Signalling, published in its inaugural issue in October 1989, we reviewed signal transduction pathways in Saccharomyces cerevisiae. Although this yeast was already a powerful model organism for the study of cellular processes, it was not yet a valuable instrument for the investigation of signaling cascades. In 1989, therefore, we discussed only two pathways, the Ras/cAMP and the mating (Fus3) signaling cascades. The pivotal findings concerning those pathways undoubtedly contributed to the realization that yeast is a relevant model for understanding signal transduction in higher eukaryotes. Consequently, the last 25 years have witnessed the discovery of many signal transduction pathways in S. cerevisiae, including the high osmotic glycerol (Hog1), Stl2/Mpk1 and Smk1 mitogen-activated protein (MAP) kinase pathways, the TOR, AMPK/Snf1, SPS, PLC1 and Pkr/Gcn2 cascades, and systems that sense and respond to various types of stress. For many cascades, orthologous pathways were identified in mammals following their discovery in yeast. Here we review advances in the understanding of signaling in S. cerevisiae over the last 25 years. When all pathways are analyzed together, some prominent themes emerge. First, wiring of signaling cascades may not be identical in all S. cerevisiae strains, but is probably specific to each genetic background. This situation complicates attempts to decipher and generalize these webs of reactions. Secondly, the Ras/cAMP and the TOR cascades are pivotal pathways that affect all processes of the life of the yeast cell, whereas the yeast MAP kinase pathways are not essential. Yeast cells deficient in all MAP kinases proliferate normally. Another theme is the existence of central molecular hubs, either as single proteins (e.g., Msn2/4, Flo11) or as multisubunit complexes (e.g., TORC1/2), which are controlled by numerous pathways and in turn determine the fate of the cell. It is also apparent that lipid signaling is less developed in yeast than in higher eukaryotes. Finally, feedback regulatory mechanisms seem to be at least as important and powerful as the pathways themselves. In the final chapter of this essay we dare to imagine the essence of our next review on signaling in yeast, to be published on the 50th anniversary of Cellular Signalling in 2039.
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Affiliation(s)
- David Engelberg
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel; CREATE-NUS-HUJ, Cellular & Molecular Mechanisms of Inflammation Programme, National University of Singapore, 1 CREATE Way, Innovation Wing, #03-09, Singapore 138602, Singapore.
| | - Riki Perlman
- Hematology Division, Hadassah Hebrew University Medical Center, POB 12000, 91120 Jerusalem, Israel
| | - Alexander Levitzki
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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Crépin L, Sanchez I, Nidelet T, Dequin S, Camarasa C. Efficient ammonium uptake and mobilization of vacuolar arginine by Saccharomyces cerevisiae wine strains during wine fermentation. Microb Cell Fact 2014; 13:109. [PMID: 25134990 PMCID: PMC4244049 DOI: 10.1186/s12934-014-0109-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/22/2014] [Indexed: 11/10/2022] Open
Abstract
Background Under N-limiting conditions, Saccharomyces cerevisiae strains display a substantial variability in their biomass yield from consumed nitrogen -in particular wine yeasts exhibit high growth abilities- that is correlated with their capacity to complete alcoholic fermentation, a trait of interest for fermented beverages industries. The aim of the present work was to assess the contribution of nitrogen availability to the strain-specific differences in the ability to efficiently use N-resource for growth and to identify the underlying mechanisms. We compared the profiles of assimilation of several nitrogen sources (mostly ammonium, glutamine, and arginine) for high and low biomass-producing strains in various conditions of nitrogen availability. We also analyzed the intracellular fate of nitrogen compounds. Results Strains clustered into two groups at initial nitrogen concentrations between 85 and 385 mg N.L−1: high biomass producers that included wine strains, were able to complete fermentation of 240 g.L−1 glucose and quickly consume nitrogen, in contrast to low biomass producers. The two classes of strains exhibited distinctive characteristics that contributed to their differential capacity to produce biomass. The contribution of each characteristic varied according to nitrogen availability. In high biomass producers, the high rate of ammonium uptake resulted in an important consumption of this preferred nitrogen source that promoted the growth of these yeasts when nitrogen was provided in excess. Both classes of yeast accumulated poor nitrogen sources, mostly arginine, in vacuoles during the first stages of growth. However, at end of the growth phase when nitrogen had become limiting, high biomass producers more efficiently used this vacuolar nitrogen fraction for protein synthesis and further biomass formation than low biomass producers. Conclusions Overall, we demonstrate that the efficient management of the nitrogen resource, including efficient ammonium uptake and efficient use of the amino acids stored in vacuoles during the late stages of growth, might lead to high biomass production by wine yeasts. Electronic supplementary material The online version of this article (doi:10.1186/s12934-014-0109-0) contains supplementary material, which is available to authorized users.
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Physical and genetic interaction between ammonium transporters and the signaling protein Rho1 in the plant pathogen Ustilago maydis. EUKARYOTIC CELL 2014; 13:1328-36. [PMID: 25128189 DOI: 10.1128/ec.00150-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Dimorphic transitions between yeast-like and filamentous forms occur in many fungi and are often associated with pathogenesis. One of the cues for such a dimorphic switch is the availability of nutrients. Under conditions of nitrogen limitation, fungal cells (such as those of Saccharomyces cerevisiae and Ustilago maydis) switch from budding to pseudohyphal or filamentous growth. Ammonium transporters (AMTs) are responsible for uptake and, in some cases, for sensing the availability of ammonium, a preferred nitrogen source. Homodimer and/or heterodimer formation may be required for regulating the activity of the AMTs. To investigate the potential interactions of Ump1 and Ump2, the AMTs of the maize pathogen U. maydis, we first used the split-ubiquitin system, followed by a modified split-YFP (yellow fluorescent protein) system, to validate the interactions in vivo. This analysis showed the formation of homo- and hetero-oligomers by Ump1 and Ump2. We also demonstrated the interaction of the high-affinity ammonium transporter, Ump2, with the Rho1 GTPase, a central protein in signaling, with roles in controlling polarized growth. This is the first demonstration in eukaryotes of the physical interaction in vivo of an ammonium transporter with the signaling protein Rho1. Moreover, the Ump proteins interact with Rho1 during the growth of cells in low ammonium concentrations, a condition required for the expression of the Umps. Based on these results and the genetic evidence for the interaction of Ump2 with both Rho1 and Rac1, another small GTPase, we propose a model for the role of these interactions in controlling filamentation, a fundamental aspect of development and pathogenesis in U. maydis.
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73
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Scherz K, Andersen, Bojsen R, Gro L, Rejkjær, Sørensen, Weiss M, Nielsen, Lisby M, Folkesson A, Regenberg B. Genetic basis for Saccharomyces cerevisiae biofilm in liquid medium. G3 (BETHESDA, MD.) 2014; 4:1671-80. [PMID: 25009170 PMCID: PMC4169159 DOI: 10.1534/g3.114.010892] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 06/26/2014] [Indexed: 11/23/2022]
Abstract
Biofilm-forming microorganisms switch between two forms: free-living planktonic and sessile multicellular. Sessile communities of yeast biofilms in liquid medium provide a primitive example of multicellularity and are clinically important because biofilms tend to have other growth characteristics than free-living cells. We investigated the genetic basis for yeast, Saccharomyces cerevisiae, biofilm on solid surfaces in liquid medium by screening a comprehensive deletion mutant collection in the Σ1278b background and found 71 genes that were essential for biofilm development. Quantitative northern blots further revealed that AIM1, ASG1, AVT1, DRN1, ELP4, FLO8, FMP10, HMT1, KAR5, MIT1, MRPL32, MSS11, NCP1, NPR1, PEP5, PEX25, RIM8, RIM101, RGT1, SNF8, SPC2, STB6, STP22, TEC1, VID24, VPS20, VTC3, YBL029W, YBL029C-A, YFL054C, YGR161W-C, YIL014C-A, YIR024C, YKL151C, YNL200C, YOR034C-A, and YOR223W controlled biofilm through FLO11 induction. Almost all deletion mutants that were unable to form biofilms in liquid medium also lost the ability to form surface-spreading biofilm colonies (mats) on agar and 69% also lost the ability to grow invasively. The protein kinase A isoform Tpk3p functioned specifically in biofilm and mat formation. In a tpk3 mutant, transcription of FLO11 was induced three-fold compared with wild-type, but biofilm development and cell-cell adhesion was absent, suggesting that Tpk3p regulates FLO11 positive posttranscriptionally and negative transcriptionally.The study provides a resource of biofilm-influencing genes for additional research on biofilm development and suggests that the regulation of FLO11 is more complex than previously anticipated.
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Affiliation(s)
- Kaj Scherz
- Department of Biology, University of Copenhagen, Copenhagen, Denmark Department of Systems Biology, Technical University of Denmark, Copenhagen, Denmark
| | - Andersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Bojsen
- Department of Systems Biology, Technical University of Denmark, Copenhagen, Denmark
| | - Laura Gro
- Department of Biology, University of Copenhagen, Copenhagen, Denmark Department of Systems Biology, Technical University of Denmark, Copenhagen, Denmark
| | - Rejkjær
- Department of Biology, University of Copenhagen, Copenhagen, Denmark Department of Systems Biology, Technical University of Denmark, Copenhagen, Denmark
| | - Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Weiss
- Department of Biology, University of Copenhagen, Copenhagen, Denmark Department of Systems Biology, Technical University of Denmark, Copenhagen, Denmark
| | - Nielsen
- Department of Systems Biology, Technical University of Denmark, Copenhagen, Denmark
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anders Folkesson
- Department of Systems Biology, Technical University of Denmark, Copenhagen, Denmark
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Dunkel N, Biswas K, Hiller E, Fellenberg K, Satheesh SV, Rupp S, Morschhäuser J. Control of morphogenesis, protease secretion and gene expression in Candida albicans by the preferred nitrogen source ammonium. MICROBIOLOGY-SGM 2014; 160:1599-1608. [PMID: 24841705 DOI: 10.1099/mic.0.078238-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Micro-organisms sense the availability of nutrients in their environment to control cellular behaviour and the expression of transporters and enzymes that are required for the utilization of these nutrients. In the pathogenic yeast Candida albicans, the preferred nitrogen source ammonium suppresses the switch from yeast to filamentous growth in response to certain stimuli, and it also represses the secretion of proteases, which are required for the utilization of proteins as an alternative nitrogen source. To investigate whether C. albicans senses the availability of ammonium in the extracellular environment or if ammonium uptake into the cell is required to regulate morphogenesis and gene expression, we compared the behaviour of wild-type cells and ammonium uptake-deficient mutants in the presence and absence of extracellular ammonium. Arginine-induced filamentous growth was suppressed by ammonium in the wild-type, but not in mutants lacking the ammonium permeases Mep1 and Mep2. Similarly, ammonium suppressed protease secretion and extracellular protein degradation in the wild-type, but not in mutants lacking the ammonium transporters. By comparing the gene expression profiles of C. albicans grown in the presence of low or high ammonium concentrations, we identified a set of genes whose expression is controlled by nitrogen availability. The repression of genes involved in the utilization of alternative nitrogen sources, which occurred under ammonium-replete conditions in the wild-type, was abrogated in mep1Δ mep2Δ mutants. These results demonstrate that C. albicans does not respond to the presence of sufficient amounts of the preferred nitrogen source ammonium by sensing its availability in the environment. Instead, ammonium has to be taken up into the cell to control morphogenesis, protease secretion and gene expression.
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Affiliation(s)
- Nico Dunkel
- Institut für Molekulare Infektionsbiologie, Universität Würzburg, Josef-Schneider-Str. 2, D-97080 Würzburg, Germany
| | - Kajal Biswas
- Institut für Molekulare Infektionsbiologie, Universität Würzburg, Josef-Schneider-Str. 2, D-97080 Würzburg, Germany
| | - Ekkehard Hiller
- Fraunhofer-Institut für Grenzflächen- und Bioverfahrenstechnik, Nobelstrasse 12, D-70569 Stuttgart, Germany
| | - Kurt Fellenberg
- Forschungszentrum Borstel, Parkallee 30, D-23845 Borstel, Germany
| | - Somisetty V Satheesh
- Institut für Molekulare Infektionsbiologie, Universität Würzburg, Josef-Schneider-Str. 2, D-97080 Würzburg, Germany
| | - Steffen Rupp
- Fraunhofer-Institut für Grenzflächen- und Bioverfahrenstechnik, Nobelstrasse 12, D-70569 Stuttgart, Germany
| | - Joachim Morschhäuser
- Institut für Molekulare Infektionsbiologie, Universität Würzburg, Josef-Schneider-Str. 2, D-97080 Würzburg, Germany
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75
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Bai L, Ma X, Zhang G, Song S, Zhou Y, Gao L, Miao Y, Song CP. A Receptor-Like Kinase Mediates Ammonium Homeostasis and Is Important for the Polar Growth of Root Hairs in Arabidopsis. THE PLANT CELL 2014; 26:1497-1511. [PMID: 24769480 PMCID: PMC4036567 DOI: 10.1105/tpc.114.124586] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 03/30/2014] [Accepted: 04/09/2014] [Indexed: 05/19/2023]
Abstract
Ammonium (NH4+) is both a necessary nutrient and an important signal in plants, but can be toxic in excess. Ammonium sensing and regulatory mechanisms in plant cells have not been fully elucidated. To decipher the complex network of NH4+ signaling, we analyzed [Ca2+]cyt-associated protein kinase (CAP) genes, which encode signaling components that undergo marked changes in transcription levels in response to various stressors. We demonstrated that CAP1, a tonoplast-localized receptor-like kinase, regulates root hair tip growth by maintaining cytoplasmic Ca2+ gradients. A CAP1 knockout mutant (cap1-1) produced elevated levels of cytoplasmic NH4+. Furthermore, root hair growth of cap1-1 was inhibited on Murashige and Skoog medium, but NH4+ depletion reestablished the Ca2+ gradient necessary for normal growth. The lower net NH4+ influx across the vacuolar membrane and relatively alkaline cytosolic pH of cap1-1 root hairs implied that mutation of CAP1 increased NH4+ accumulation in the cytoplasm. Furthermore, CAP1 functionally complemented the npr1 (nitrogen permease reactivator protein) kinase yeast mutant, which is defective in high-affinity NH4+ uptake via MEP2 (methylammonium permease 2), distinguishing CAP1 as a cytosolic modulator of NH4+ levels that participates in NH4+ homeostasis-regulated root hair growth by modulating tip-focused cytoplasmic Ca2+ gradients.
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Affiliation(s)
- Ling Bai
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Xiaonan Ma
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Guozeng Zhang
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Shufei Song
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Yun Zhou
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Lijie Gao
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Yuchen Miao
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Chun-Peng Song
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
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76
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Rck1 up-regulates pseudohyphal growth by activating the Ras2 and MAP kinase pathways independently in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2014; 444:656-61. [DOI: 10.1016/j.bbrc.2014.01.127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 01/25/2014] [Indexed: 12/24/2022]
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77
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Vaudano E, Noti O, Costantini A, Garcia-Moruno E. Effect of additives on the rehydration ofSaccharomyces cerevisiaewine strains in active dry form: influence on viability and performance in the early fermentation phase. JOURNAL OF THE INSTITUTE OF BREWING 2014. [DOI: 10.1002/jib.114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Enrico Vaudano
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura (Centro di Ricerca per l'Enologia); Via Pietro Micca 35 14100 Asti Italy
| | - Olta Noti
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura (Centro di Ricerca per l'Enologia); Via Pietro Micca 35 14100 Asti Italy
| | - Antonella Costantini
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura (Centro di Ricerca per l'Enologia); Via Pietro Micca 35 14100 Asti Italy
| | - Emilia Garcia-Moruno
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura (Centro di Ricerca per l'Enologia); Via Pietro Micca 35 14100 Asti Italy
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78
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Bai L, Zhou Y, Ma X, Gao L, Song CP. Arabidopsis CAP1-mediated ammonium sensing required reactive oxygen species in plant cell growth. PLANT SIGNALING & BEHAVIOR 2014; 9:e29582. [PMID: 25763633 PMCID: PMC4205142 DOI: 10.4161/psb.29582] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 06/13/2014] [Accepted: 06/13/2014] [Indexed: 05/24/2023]
Abstract
[Ca(2+)]cyt-associated protein kinase (CAP) gene 1 is a receptor-like kinase that belongs to CrRLK1L (Catharanthus roseus Receptor like kinase) subfamily. CAP1 has been identified as a novel modulator of NH4(+) in the tonoplast, which regulates root hair growth by maintaining the cytoplasmic Ca(2+) gradients. Different expression pattern of tonoplast intrinsic protein (TIP2;3) in the CAP1 knock out mutant and wild type on Murashige and Skoog (MS) medium suggested that CAP1 influences transport activity to regulate the compartmentalization of NH4(+) into vacuole. Lower expression level of Oxidative Signal-Inducible1(OXI1) in the cap1-1 root and the abnormal reactive oxygen species (ROS) gradient in root hair of cap1-1 on MS medium indicated that ROS signaling involve in CAP1-regulated root hair growth. Wild-type-like ROS distribution pattern in the cap1-1 root hair can be reestablished in seedlings grown on NH4(+) deficient medium, which indicated that CAP1 functions as a sensor for NH4(+) signaling in maintaining tip-focused ROS gradient in root hairs polar growth.
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79
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Ellerbeck M, Schüßler A, Brucker D, Dafinger C, Loos F, Brachmann A. Characterization of three ammonium transporters of the glomeromycotan fungus Geosiphon pyriformis. EUKARYOTIC CELL 2013; 12:1554-62. [PMID: 24058172 PMCID: PMC3837933 DOI: 10.1128/ec.00139-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 09/15/2013] [Indexed: 11/20/2022]
Abstract
Members of the Glomeromycota form the arbuscular mycorrhiza (AM) symbiosis. They supply plants with inorganic nutrients, including nitrogen, from the soil. To gain insight into transporters potentially facilitating nitrogen transport processes, ammonium transporters (AMTs) of Geosiphon pyriformis, a glomeromycotan fungus forming a symbiosis with cyanobacteria, were studied. Three AMT genes were identified, and all three were expressed in the symbiotic stage. The localization and functional characterization of the proteins in a heterologous yeast system revealed distinct characteristics for each of them. AMT1 of G. pyriformis (GpAMT1) and GpAMT2 were both plasma membrane localized, but only GpAMT1 transported ammonium. Neither protein transported the ammonium analogue methylammonium. Unexpectedly, GpAMT3 was localized in the vacuolar membrane, and it has as-yet-unknown transport characteristics. An unusual cysteine residue in the AMT signature of GpAMT2 and GpAMT3 was identified, and the corresponding residue was demonstrated to play an important role in ammonium transport. Surprisingly, each of the three AMTs of G. pyriformis had very distinct features. The localization of an AMT in the yeast vacuolar membrane is novel, as is the described amino acid residue that clearly influences ammonium transport. The AMT characteristics might reflect adaptations to the lifestyle of glomeromycotan fungi.
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80
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Host-related metabolic cues affect colonization strategies of a root endophyte. Proc Natl Acad Sci U S A 2013; 110:13965-70. [PMID: 23918389 DOI: 10.1073/pnas.1301653110] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The mechanisms underpinning broad compatibility in root symbiosis are largely unexplored. The generalist root endophyte Piriformospora indica establishes long-lasting interactions with morphologically and biochemically different hosts, stimulating their growth, alleviating salt stress, and inducing local and systemic resistance to pathogens. Cytological studies and global investigations of fungal transcriptional responses to colonization of barley and Arabidopsis at different symbiotic stages identified host-dependent colonization strategies and host-specifically induced effector candidates. Here, we show that in Arabidopsis, P. indica establishes and maintains biotrophic nutrition within living epidermal cells, whereas in barley the symbiont undergoes a nutritional switch to saprotrophy that is associated with the production of secondary thinner hyphae in dead cortex cells. Consistent with a diversified trophic behavior and with the occurrence of nitrogen deficiency at the onset of saprotrophy in barley, fungal genes encoding hydrolytic enzymes and nutrient transporters were highly induced in this host but not in Arabidopsis. Silencing of the high-affinity ammonium transporter PiAMT1 gene, whose transcripts are accumulating during nitrogen starvation and in barley, resulted in enhanced colonization of this host, whereas it had no effect on the colonization of Arabidopsis. Increased levels of free amino acids and reduced enzymatic activity for the cell-death marker VPE (vacuolar-processing enzyme) in colonized barley roots coincided with an extended biotrophic lifestyle of P. indica upon silencing of PiAMT1. This suggests that PiAmt1 functions as a nitrogen sensor mediating the signal that triggers the in planta activation of the saprotrophic program. Thus, host-related metabolic cues affect the expression of P. indica's alternative lifestyles.
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81
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Lee HW, Verlander JW, Handlogten ME, Han KH, Cooke PS, Weiner ID. Expression of the rhesus glycoproteins, ammonia transporter family members, RHCG and RHBG in male reproductive organs. Reproduction 2013; 146:283-96. [PMID: 23904565 DOI: 10.1530/rep-13-0154] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The rhesus glycoproteins, Rh B glycoprotein (RHBG) and Rh C glycoprotein (RHCG), are recently identified ammonia transporters. Rhcg expression is necessary for normal male fertility, but its specific cellular expression is unknown, and Rhbg has not been reported to be expressed in the male reproductive tract. This study sought to determine the specific cellular expression of Rhcg, to determine whether Rhbg is expressed in the male reproductive tract, and, if so, to determine which cells express Rhbg using real-time RT-PCR, immunoblot analysis, and immunohistochemistry. Both Rhbg and Rhcg were expressed throughout the male reproductive tract. In the testis, high levels of Rhbg were expressed in Leydig cells, and Rhcg was expressed in spermatids during the later stages of their maturation (steps 13-16) in stages I-VIII of the seminiferous epithelium cycle. In the epididymis, basolateral Rhbg was present in narrow cells in the initial segment, in principal cells in the upper corpus, and in clear cells throughout the epididymis. Apical Rhcg immunolabel was present in principal cells in the caput and upper corpus epididymidis and in clear cells in the middle and lower corpus and cauda epididymidis. In the vas deferens, apical Rhcg immunolabel and basolateral Rhbg immunolabel were present in some principal cells and colocalized with H(+)-ATPase immunolabel. We conclude that both Rhbg and Rhcg are highly expressed in specific cells in the male reproductive tract where they can contribute to multiple components of male fertility.
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Affiliation(s)
- Hyun-Wook Lee
- Department of Medicine, University of Florida College of Medicine, P.O. Box 100224, Gainesville, Florida 32610, USA
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82
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Lee IR, Morrow CA, Fraser JA. Nitrogen regulation of virulence in clinically prevalent fungal pathogens. FEMS Microbiol Lett 2013; 345:77-84. [PMID: 23701678 DOI: 10.1111/1574-6968.12181] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 05/17/2013] [Accepted: 05/18/2013] [Indexed: 11/25/2022] Open
Abstract
The habitats of fungal pathogens range from environmental to commensal, and the nutrient content of these different niches varies considerably. Upon infection of humans, nutrient availability changes significantly depending on the site and pathophysiology of infection. Nonetheless, a common feature enabling successful establishment in these niches is the ability to metabolise available nutrients including sources of nitrogen, carbon and essential metals such as iron. In particular, nitrogen source utilisation influences specific morphological transitions, sexual and asexual sporulation and virulence factor production. All these physiological changes confer selective advantages to facilitate fungal survival, proliferation and colonisation. The three most well-studied components of the nitrogen regulatory circuit that commonly impact fungal pathogenesis are the ammonium permeases (the nitrogen availability sensor candidate), ureases (a nitrogen-scavenging enzyme) and GATA transcription factors (global regulators of nitrogen catabolism). In certain species, the ammonium permease induces a morphological switch from yeast to invasive filamentous growth forms or infectious spores, while in others, urease is a bona fide virulence factor. In all species studied thus far, transcription of the ammonium permease and urease-encoding genes is modulated by GATA factors. Fungal pathogens therefore integrate the expression of different virulence-associated phenotypes into the regulatory network controlling nitrogen catabolism.
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Affiliation(s)
- I Russel Lee
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, Australia
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83
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High-throughput genome sequencing of lichenizing fungi to assess gene loss in the ammonium transporter/ammonia permease gene family. BMC Genomics 2013; 14:225. [PMID: 23557360 PMCID: PMC3663718 DOI: 10.1186/1471-2164-14-225] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 02/13/2013] [Indexed: 11/20/2022] Open
Abstract
Background Horizontal gene transfer has shaped the evolution of the ammonium transporter/ammonia permease gene family. Horizontal transfers of ammonium transporter/ammonia permease genes into the fungi include one transfer from archaea to the filamentous ascomycetes associated with the adaptive radiation of the leotiomyceta. The horizontally transferred gene has subsequently been lost in most of the group but has been selectively retained in lichenizing fungi. However, some groups of lichens appear to have secondarily lost the archaeal ammonium transporter. Definitive assessment of gene loss can only be made via whole genome sequencing. Results Ammonium transporter/ammonia permease gene sequences were recovered from the assembled genomes of eight lichenizing fungi in key clades including the Caliciales, the Peltigerales, the Ostropomycetidae, the Acarosporomycetidae, the Verrucariales, the Arthoniomycetidae and the Lichinales. The genes recovered were included in a refined phylogenetic analysis. The hypothesis that lichens symbiotic with a nitrogen-fixing cyanobacterium as a primary photobiont or lichens living in high nitrogen environments lose the plant-like ammonium transporters was upheld, but did not account for additional losses of ammonium transporters/ammonia permeases in the lichens from the Acarosporomycetidae, Chaetotheriomycetes and Arthoniomycetes. In addition, the four ammonium transporter/ammonia permease genes from Cladonia grayi were shown to be functional by expressing the lichen genes in a strain of Saccharomyces cerevisiae in which all three native ammonium transporters were deleted, and assaying for growth on limiting ammonia as a sole nitrogen source. Conclusions Given sufficient coverage, next-generation sequencing technology can definitively address the loss of a gene in a genome when using environmental DNA isolated from lichen thalli collected from their natural habitats. Lichen-forming fungi have been losing ammonium transporters/ammonia permease genes at a slower rate than the most closely related non-lichenized lineages. These horizontally transferred genes in the Cladonia grayi genome encode functional ammonium transporters/ammonia permeases.
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84
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Shnaiderman C, Miyara I, Kobiler I, Sherman A, Prusky D. Differential activation of ammonium transporters during the accumulation of ammonia by Colletotrichum gloeosporioides and its effect on appressoria formation and pathogenicity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:345-355. [PMID: 23387470 DOI: 10.1094/mpmi-07-12-0170-r] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Ammonium secreted by the post-harvest pathogen Colletotrichum gloeosporioides during host colonization accumulates in the host environment due to enhanced fungal nitrogen metabolism. Two types of ammonium transporter-encoding genes, AMET and MEP, are expressed during pathogenicity. Gene disruption of AMET, a gene modulating ammonia secretion, showed twofold reduced ammonia secretion and 45% less colonization on avocado fruit, suggesting a contribution to pathogenicity. MEPB, a gene modulating ammonium transport, is expressed by C. gloeosporioides during pathogenicity and starvation conditions in culture. Gene disruption of MEPB, the most highly expressed gene of the MEP family, resulted in twofold overexpression of MEPA and MEPC but reduced colonization, suggesting MEPB expression's contribution to pathogenicity. Analysis of internal and external ammonia accumulation by ΔmepB strains in mycelia and germinated spores showed rapid uptake and accumulation, and reduced secretion of ammonia in the mutant versus wild-type (WT) strains. Ammonia uptake by the WT germinating spores but not by the ΔmepB strain with compromised ammonium transport activated cAMP and transcription of PKA subunits PKAR and PKA2. ΔmepB mutants showed 75% less appressorium formation and colonization than the WT, which was partially restored by 10 mM exogenous ammonia. Thus, whereas both AMET and MEPB genes modulate ammonia secretion, only MEPB contributes to ammonia accumulation by mycelia and germinating spores that activate the cAMP pathways, inducing the morphogenetic processes contributing to C. gloeosporioides pathogenicity.
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Affiliation(s)
- Chen Shnaiderman
- Department of Postharvest Science of Fresh Produce, ARO, Bet Dagan, Israel
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85
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Yang DH, Maeng S, Bahn YS. Msi1-Like (MSIL) Proteins in Fungi. MYCOBIOLOGY 2013; 41:1-12. [PMID: 23610533 PMCID: PMC3627964 DOI: 10.5941/myco.2013.41.1.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 03/11/2013] [Indexed: 05/23/2023]
Abstract
Msi1-like (MSIL) proteins, which are eukaryote-specific and contain a series of WD40 repeats, have pleiotropic roles in chromatin assembly, DNA damage repair, and regulation of nutrient/stress-sensing signaling pathways. In the fungal kingdom, the functions of MSIL proteins have been studied most intensively in the budding yeast model Saccharomyces cerevisiae, an ascomycete. Yet their functions are largely unknown in other fungi. Recently, an MSIL protein, Msl1, was discovered and functionally characterized in the pathogenic yeast Cryptococcus neoformans, a basidiomycete. Interestingly, MSIL proteins appear to have redundant and unique roles in both fungi, suggesting that MSIL proteins may have evolutionarily divergent roles in different parts of the fungal kingdom. In this review, we will describe the current findings regarding the role of MSIL proteins in fungi and discuss future directions for research on this topic.
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Affiliation(s)
- Dong-Hoon Yang
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
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86
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Aun A, Tamm T, Sedman J. Dysfunctional mitochondria modulate cAMP-PKA signaling and filamentous and invasive growth of Saccharomyces cerevisiae. Genetics 2013; 193:467-81. [PMID: 23172851 PMCID: PMC3567737 DOI: 10.1534/genetics.112.147389] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 11/05/2012] [Indexed: 01/04/2023] Open
Abstract
Mitochondrial metabolism is targeted by conserved signaling pathways that mediate external information to the cell. However, less is known about whether mitochondrial dysfunction interferes with signaling and thereby modulates the cellular response to environmental changes. In this study, we analyzed defective filamentous and invasive growth of the yeast Saccharomyces cerevisiae strains that have a dysfunctional mitochondrial genome (rho mutants). We found that the morphogenetic defect of rho mutants was caused by specific downregulation of FLO11, the adhesin essential for invasive and filamentous growth, and did not result from general metabolic changes brought about by interorganellar retrograde signaling. Transcription of FLO11 is known to be regulated by several signaling pathways, including the filamentous-growth-specific MAPK and cAMP-activated protein kinase A (cAMP-PKA) pathways. Our analysis showed that the filamentous-growth-specific MAPK pathway retained functionality in respiratory-deficient yeast cells. In contrast, the cAMP-PKA pathway was downregulated, explaining also various phenotypic traits observed in rho mutants. Thus, our results indicate that dysfunctional mitochondria modulate the output of the conserved cAMP-PKA signaling pathway.
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Affiliation(s)
| | | | - Juhan Sedman
- Department of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
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87
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Spang A, Poehlein A, Offre P, Zumbrägel S, Haider S, Rychlik N, Nowka B, Schmeisser C, Lebedeva EV, Rattei T, Böhm C, Schmid M, Galushko A, Hatzenpichler R, Weinmaier T, Daniel R, Schleper C, Spieck E, Streit W, Wagner M. The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environ Microbiol 2012; 14:3122-45. [PMID: 23057602 DOI: 10.1111/j.1462-2920.2012.02893.x] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 09/01/2012] [Indexed: 01/21/2023]
Abstract
The cohort of the ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota is a diverse, widespread and functionally important group of microorganisms in many ecosystems. However, our understanding of their biology is still very rudimentary in part because all available genome sequences of this phylum are from members of the Nitrosopumilus cluster. Here we report on the complete genome sequence of Candidatus Nitrososphaera gargensis obtained from an enrichment culture, representing a different evolutionary lineage of AOA frequently found in high numbers in many terrestrial environments. With its 2.83 Mb the genome is much larger than that of other AOA. The presence of a high number of (active) IS elements/transposases, genomic islands, gene duplications and a complete CRISPR/Cas defence system testifies to its dynamic evolution consistent with low degree of synteny with other thaumarchaeal genomes. As expected, the repertoire of conserved enzymes proposed to be required for archaeal ammonia oxidation is encoded by N. gargensis, but it can also use urea and possibly cyanate as alternative ammonia sources. Furthermore, its carbon metabolism is more flexible at the central pyruvate switch point, encompasses the ability to take up small organic compounds and might even include an oxidative pentose phosphate pathway. Furthermore, we show that thaumarchaeota produce cofactor F420 as well as polyhydroxyalkanoates. Lateral gene transfer from bacteria and euryarchaeota has contributed to the metabolic versatility of N. gargensis. This organisms is well adapted to its niche in a heavy metal-containing thermal spring by encoding a multitude of heavy metal resistance genes, chaperones and mannosylglycerate as compatible solute and has the genetic ability to respond to environmental changes by signal transduction via a large number of two-component systems, by chemotaxis and flagella-mediated motility and possibly even by gas vacuole formation. These findings extend our understanding of thaumarchaeal evolution and physiology and offer many testable hypotheses for future experimental research on these nitrifiers.
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Affiliation(s)
- Anja Spang
- Department of Genetics in Ecology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria
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Pseudohyphal growth of Cryptococcus neoformans is a reversible dimorphic transition in response to ammonium that requires Amt1 and Amt2 ammonium permeases. EUKARYOTIC CELL 2012; 11:1391-8. [PMID: 23002105 DOI: 10.1128/ec.00242-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cryptococcus neoformans is a human-pathogenic basidiomycete that commonly infects HIV/AIDS patients to cause meningoencephalitis (7, 19). C. neoformans grows as a budding yeast during vegetative growth or as hyphae during sexual reproduction. Pseudohyphal growth of C. neoformans has been observed rarely during murine and human infections but frequently during coculture with amoeba; however, the genetics underlying pseudohyphal growth are largely unknown. Our studies found that C. neoformans displays pseudohyphal growth under nitrogen-limiting conditions, especially when a small amount of ammonium is available as a sole nitrogen source. Pseudohyphal growth was observed with Cryptococcus neoformans serotypes A and D and Cryptococcus gattii. C. neoformans pseudohyphae bud to produce yeast cells and normal smooth hemispherical colonies when transferred to complete media, indicating that pseudohyphal growth is a conditional developmental stage. Subsequent analysis revealed that two ammonium permeases encoded by the AMT1 and AMT2 genes are required for pseudohyphal growth. Both amt1 and amt2 mutants are capable of forming pseudohyphae; however, amt1 amt2 double mutants do not form pseudohyphae. Interestingly, C. gattii pseudohypha formation is irreversible and involves a RAM pathway mutation that drives pseudohyphal development. We also found that pseudohyphal growth is related to the invasive growth into the medium. These results demonstrate that pseudohyphal growth is a common reversible growth pattern in C. neoformans but a mutational genetic event in C. gattii and provide new insights into understanding pseudohyphal growth of Cryptococcus.
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89
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Glucose, nitrogen, and phosphate repletion in Saccharomyces cerevisiae: common transcriptional responses to different nutrient signals. G3-GENES GENOMES GENETICS 2012; 2:1003-17. [PMID: 22973537 PMCID: PMC3429914 DOI: 10.1534/g3.112.002808] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 06/20/2012] [Indexed: 01/01/2023]
Abstract
Saccharomyces cerevisiae are able to control growth in response to changes in nutrient availability. The limitation for single macronutrients, including nitrogen (N) and phosphate (P), produces stable arrest in G1/G0. Restoration of the limiting nutrient quickly restores growth. It has been shown that glucose (G) depletion/repletion very rapidly alters the levels of more than 2000 transcripts by at least 2-fold, a large portion of which are involved with either protein production in growth or stress responses in starvation. Although the signals generated by G, N, and P are thought to be quite distinct, we tested the hypothesis that depletion and repletion of any of these three nutrients would affect a common core set of genes as part of a generalized response to conditions that promote growth and quiescence. We found that the response to depletion of G, N, or P produced similar quiescent states with largely similar transcriptomes. As we predicted, repletion of each of the nutrients G, N, or P induced a large (501) common core set of genes and repressed a large (616) common gene set. Each nutrient also produced nutrient-specific transcript changes. The transcriptional responses to each of the three nutrients depended on cAMP and, to a lesser extent, the TOR pathway. All three nutrients stimulated cAMP production within minutes of repletion, and artificially increasing cAMP levels was sufficient to replicate much of the core transcriptional response. The recently identified transceptors Gap1, Mep1, Mep2, and Mep3, as well as Pho84, all played some role in the core transcriptional responses to N or P. As expected, we found some evidence of cross talk between nutrient signals, yet each nutrient sends distinct signals.
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90
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Regulation of amino acid, nucleotide, and phosphate metabolism in Saccharomyces cerevisiae. Genetics 2012; 190:885-929. [PMID: 22419079 DOI: 10.1534/genetics.111.133306] [Citation(s) in RCA: 338] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Ever since the beginning of biochemical analysis, yeast has been a pioneering model for studying the regulation of eukaryotic metabolism. During the last three decades, the combination of powerful yeast genetics and genome-wide approaches has led to a more integrated view of metabolic regulation. Multiple layers of regulation, from suprapathway control to individual gene responses, have been discovered. Constitutive and dedicated systems that are critical in sensing of the intra- and extracellular environment have been identified, and there is a growing awareness of their involvement in the highly regulated intracellular compartmentalization of proteins and metabolites. This review focuses on recent developments in the field of amino acid, nucleotide, and phosphate metabolism and provides illustrative examples of how yeast cells combine a variety of mechanisms to achieve coordinated regulation of multiple metabolic pathways. Importantly, common schemes have emerged, which reveal mechanisms conserved among various pathways, such as those involved in metabolite sensing and transcriptional regulation by noncoding RNAs or by metabolic intermediates. Thanks to the remarkable sophistication offered by the yeast experimental system, a picture of the intimate connections between the metabolomic and the transcriptome is becoming clear.
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91
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Torbensen R, Møller HD, Gresham D, Alizadeh S, Ochmann D, Boles E, Regenberg B. Amino acid transporter genes are essential for FLO11-dependent and FLO11-independent biofilm formation and invasive growth in Saccharomyces cerevisiae. PLoS One 2012; 7:e41272. [PMID: 22844449 PMCID: PMC3406018 DOI: 10.1371/journal.pone.0041272] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Accepted: 06/19/2012] [Indexed: 11/25/2022] Open
Abstract
Amino acids can induce yeast cell adhesion but how amino acids are sensed and signal the modulation of the FLO adhesion genes is not clear. We discovered that the budding yeast Saccharomyces cerevisiae CEN.PK evolved invasive growth ability under prolonged nitrogen limitation. Such invasive mutants were used to identify amino acid transporters as regulators of FLO11 and invasive growth. One invasive mutant had elevated levels of FLO11 mRNA and a Q320STOP mutation in the SFL1 gene that encodes a protein kinase A pathway regulated repressor of FLO11. Glutamine-transporter genes DIP5 and GNP1 were essential for FLO11 expression, invasive growth and biofilm formation in this mutant. Invasive growth relied on known regulators of FLO11 and the Ssy1-Ptr3-Ssy5 complex that controls DIP5 and GNP1, suggesting that Dip5 and Gnp1 operates downstream of the Ssy1-Ptr3-Ssy5 complex for regulation of FLO11 expression in a protein kinase A dependent manner. The role of Dip5 and Gnp1 appears to be conserved in the S. cerevisiae strain ∑1278b since the dip5 gnp1 ∑1278b mutant showed no invasive phenotype. Secondly, the amino acid transporter gene GAP1 was found to influence invasive growth through FLO11 as well as other FLO genes. Cells carrying a dominant loss-of-function PTR3(647::CWNKNPLSSIN) allele had increased transcription of the adhesion genes FLO1, 5, 9, 10, 11 and the amino acid transporter gene GAP1. Deletion of GAP1 caused loss of FLO11 expression and invasive growth. However, deletions of FLO11 and genes encoding components of the mitogen-activated protein kinase pathway or the protein kinase A pathway were not sufficient to abolish invasive growth, suggesting involvement of other FLO genes and alternative pathways. Increased intracellular amino acid pools in the PTR3(647::CWNKNPLSSIN)-containing strain opens the possibility that Gap1 regulates the FLO genes through alteration of the amino acid pool sizes.
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Affiliation(s)
- Rasmus Torbensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - David Gresham
- Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
- Department of Biology, New York, New York University, New York, United States of America
| | - Sefa Alizadeh
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Doreen Ochmann
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Eckhard Boles
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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92
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Bojsen RK, Andersen KS, Regenberg B. Saccharomyces cerevisiae— a model to uncover molecular mechanisms for yeast biofilm biology. ACTA ACUST UNITED AC 2012; 65:169-82. [DOI: 10.1111/j.1574-695x.2012.00943.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Revised: 01/06/2012] [Accepted: 02/09/2012] [Indexed: 01/14/2023]
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93
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Abstract
Filamentous growth is a nutrient-regulated growth response that occurs in many fungal species. In pathogens, filamentous growth is critical for host-cell attachment, invasion into tissues, and virulence. The budding yeast Saccharomyces cerevisiae undergoes filamentous growth, which provides a genetically tractable system to study the molecular basis of the response. Filamentous growth is regulated by evolutionarily conserved signaling pathways. One of these pathways is a mitogen activated protein kinase (MAPK) pathway. A remarkable feature of the filamentous growth MAPK pathway is that it is composed of factors that also function in other pathways. An intriguing challenge therefore has been to understand how pathways that share components establish and maintain their identity. Other canonical signaling pathways-rat sarcoma/protein kinase A (RAS/PKA), sucrose nonfermentable (SNF), and target of rapamycin (TOR)-also regulate filamentous growth, which raises the question of how signals from multiple pathways become integrated into a coordinated response. Together, these pathways regulate cell differentiation to the filamentous type, which is characterized by changes in cell adhesion, cell polarity, and cell shape. How these changes are accomplished is also discussed. High-throughput genomics approaches have recently uncovered new connections to filamentous growth regulation. These connections suggest that filamentous growth is a more complex and globally regulated behavior than is currently appreciated, which may help to pave the way for future investigations into this eukaryotic cell differentiation behavior.
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94
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Pichia fermentans dimorphic changes depend on the nitrogen source. Fungal Biol 2012; 116:769-77. [PMID: 22749163 DOI: 10.1016/j.funbio.2012.04.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 04/03/2012] [Accepted: 04/12/2012] [Indexed: 11/24/2022]
Abstract
Pichia fermentans DiSAABA 726 is a biofilm-forming yeast that undergoes dimorphic transition. Under yeast-like morphology it controls brown rot caused by Monilia spp. on apple fruit, while under pseudohyphal form, it shows pathogenic behaviour itself on peach fruit. The present study investigates the nutritional factors that induce and separate yeast-like and pseudohyphal morphologies under laboratory conditions. We show that P. fermentans DiSAABA 726 produces mainly yeast-like cells on media containing millimolar concentrations of urea and diammonium phosphate, and forms pseudohyphae at micromolar concentrations of these two salts. With ammonium sulphate, yeast-like or pseudohyphal morphology depends on the N concentration and the pH of the culture media. Amino acids such as methionine, valine, and phenylalanine invariably induce pseudohyphal morphology irrespective of the N concentration and the pH of the culture media. Methionol, 1-butanol, isobutanol, and isopropanol induce pseudohyphal growth, while phenylethanol and isoamyl alcohol fail to induce the formation of filaments. Thus, the morphogenesis of P. fermentans DiSAABA 726 depends more on the nitrogen source than on the N concentration, and is regulated by the quorum-sensing molecules that are generally produced from amino-acid assimilation under nitrogen starvation.
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95
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Horst RJ, Zeh C, Saur A, Sonnewald S, Sonnewald U, Voll LM. The Ustilago maydis Nit2 homolog regulates nitrogen utilization and is required for efficient induction of filamentous growth. EUKARYOTIC CELL 2012; 11:368-80. [PMID: 22247264 PMCID: PMC3294441 DOI: 10.1128/ec.05191-11] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 12/22/2011] [Indexed: 11/20/2022]
Abstract
Nitrogen catabolite repression (NCR) is a regulatory strategy found in microorganisms that restricts the utilization of complex and unfavored nitrogen sources in the presence of favored nitrogen sources. In fungi, this concept has been best studied in yeasts and filamentous ascomycetes, where the GATA transcription factors Gln3p and Gat1p (in yeasts) and Nit2/AreA (in ascomycetes) constitute the main positive regulators of NCR. The reason why functional Nit2 homologs of some phytopathogenic fungi are required for full virulence in their hosts has remained elusive. We have identified the Nit2 homolog in the basidiomycetous phytopathogen Ustilago maydis and show that it is a major, but not the exclusive, positive regulator of nitrogen utilization. By transcriptome analysis of sporidia grown on artificial media devoid of favored nitrogen sources, we show that only a subset of nitrogen-responsive genes are regulated by Nit2, including the Gal4-like transcription factor Ton1 (a target of Nit2). Ustilagic acid biosynthesis is not under the control of Nit2, while nitrogen starvation-induced filamentous growth is largely dependent on functional Nit2. nit2 deletion mutants show the delayed initiation of filamentous growth on maize leaves and exhibit strongly compromised virulence, demonstrating that Nit2 is required to efficiently initiate the pathogenicity program of U. maydis.
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Affiliation(s)
- Robin J Horst
- Division of Biochemistry, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstr. 5, Erlangen, Germany
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96
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McDonald TR, Dietrich FS, Lutzoni F. Multiple horizontal gene transfers of ammonium transporters/ammonia permeases from prokaryotes to eukaryotes: toward a new functional and evolutionary classification. Mol Biol Evol 2012; 29:51-60. [PMID: 21680869 PMCID: PMC3383101 DOI: 10.1093/molbev/msr123] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The proteins of the ammonium transporter/methylammonium permease/Rhesus factor family (AMT/MEP/Rh family) are responsible for the movement of ammonia or ammonium ions across the cell membrane. Although it has been established that the Rh proteins are distantly related to the other members of the family, the evolutionary history of the AMT/MEP/Rh family remains unclear. Here, we use phylogenetic analysis to infer the evolutionary history of this family of proteins across 191 genomes representing all main lineages of life and to provide a new classification of the proteins in this family. Our phylogenetic analysis suggests that what has heretofore been conceived of as a protein family with two clades (AMT/MEP and Rh) is instead a protein family with three clades (AMT, MEP, and Rh). We show that the AMT/MEP/Rh family illustrates two contrasting modes of gene transmission: The AMT family as defined here exhibits vertical gene transfer (i.e., standard parent-to-offspring inheritance), whereas the MEP family as defined here is characterized by several ancient independent horizontal gene transfers (HGTs). These ancient HGT events include a gene replacement during the early evolution of the fungi, which could be a defining trait for the kingdom Fungi, a gene gain from hyperthermophilic chemoautolithotrophic prokaryotes during the early evolution of land plants (Embryophyta), and an independent gain of this same gene in the filamentous ascomycetes (Pezizomycotina) that was subsequently lost in most lineages but retained in even distantly related lichenized fungi. This recircumscription of the ammonium transporters/ammonia permeases family into MEP and AMT families informs the debate on the mechanism of transport in these proteins and on the nature of the transported molecule because published crystal structures of proteins from the MEP and Rh clades may not be representative of the AMT clade. The clades as depicted in this phylogenetic study appear to correspond to functionally different groups, with AMTs and ammonia permeases forming two distinct and possibly monophyletic groups.
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97
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Pérez-Tienda J, Testillano PS, Balestrini R, Fiorilli V, Azcón-Aguilar C, Ferrol N. GintAMT2, a new member of the ammonium transporter family in the arbuscular mycorrhizal fungus Glomus intraradices. Fungal Genet Biol 2011; 48:1044-55. [DOI: 10.1016/j.fgb.2011.08.003] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 06/27/2011] [Accepted: 08/15/2011] [Indexed: 11/16/2022]
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98
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Zara G, Budroni M, Mannazzu I, Zara S. Air-liquid biofilm formation is dependent on ammonium depletion in a Saccharomyces cerevisiae flor strain. Yeast 2011; 28:809-14. [DOI: 10.1002/yea.1907] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 07/20/2011] [Accepted: 08/30/2011] [Indexed: 11/09/2022] Open
Affiliation(s)
- Giacomo Zara
- Dipartimento di Scienze Ambientali Agrarie e Biotecnologie Agroalimentari, Sezione di Microbiologia Generale ed Applicata; Università degli Studi di Sassari; 07100; Sassari; Italy
| | - Marilena Budroni
- Dipartimento di Scienze Ambientali Agrarie e Biotecnologie Agroalimentari, Sezione di Microbiologia Generale ed Applicata; Università degli Studi di Sassari; 07100; Sassari; Italy
| | - Ilaria Mannazzu
- Dipartimento di Scienze Ambientali Agrarie e Biotecnologie Agroalimentari, Sezione di Microbiologia Generale ed Applicata; Università degli Studi di Sassari; 07100; Sassari; Italy
| | - Severino Zara
- Dipartimento di Scienze Ambientali Agrarie e Biotecnologie Agroalimentari, Sezione di Microbiologia Generale ed Applicata; Università degli Studi di Sassari; 07100; Sassari; Italy
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99
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Van Zeebroeck G, Kimpe M, Vandormael P, Thevelein JM. A split-ubiquitin two-hybrid screen for proteins physically interacting with the yeast amino acid transceptor Gap1 and ammonium transceptor Mep2. PLoS One 2011; 6:e24275. [PMID: 21912684 PMCID: PMC3166329 DOI: 10.1371/journal.pone.0024275] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 08/09/2011] [Indexed: 01/13/2023] Open
Abstract
Several nutrient permeases have been identified in yeast, which combine a transport and receptor function, and are called transceptors. The Gap1 general amino acid permease and the Mep2 ammonium permease mediate rapid activation by amino acids and by ammonium, respectively, of the protein kinase A (PKA) pathway in nitrogen-starved cells. Their mode of action is not well understood. Both proteins are subject to complex controls governing their intracellular trafficking. Using a split-ubiquitin yeast two-hybrid screen with Gap1 or Mep2 as bait, we identified proteins putatively interacting with Gap1 and/or Mep2. They are involved in glycosylation, the secretory pathway, sphingolipid biosynthesis, cell wall biosynthesis and other processes. For several candidate interactors, determination of transport and signaling capacity, as well as localization of Gap1 or Mep2 in the corresponding deletion strains, confirmed a functional interaction with Gap1 and/or Mep2. Also common interacting proteins were identified. Transport and signaling were differentially affected in specific deletion strains, clearly separating the two functions of the transceptors and confirming that signaling does not require transport. We identified two new proteins, Bsc6 and Yir014w, that affect trafficking or downregulation of Gap1. Deletion of EGD2, YNL024c or SPC2 inactivates Gap1 transport and signaling, while its plasma membrane level appears normal.. Vma4 is required for Mep2 expression, while Gup1 appears to be required for proper distribution of Mep2 over the plasma membrane. Some of the interactions were confirmed by GST pull-down assay, using the C-terminal tail of Gap1 or Mep2 expressed in E.coli. Our results reveal the effectiveness of split-ubiquitin two-hybrid screening for identification of proteins functionally interacting with membrane proteins. They provide several candidate proteins involved in the transport and signaling function or in the complex trafficking control of the Gap1 and Mep2 transceptors.
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Affiliation(s)
- Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KULeuven, Flanders, Belgium
- Department of Molecular Microbiology, The Vlaams Instituut voor Biotechnologie, Flanders, Belgium
| | - Marlies Kimpe
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KULeuven, Flanders, Belgium
- Department of Molecular Microbiology, The Vlaams Instituut voor Biotechnologie, Flanders, Belgium
| | - Patrick Vandormael
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KULeuven, Flanders, Belgium
- Department of Molecular Microbiology, The Vlaams Instituut voor Biotechnologie, Flanders, Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KULeuven, Flanders, Belgium
- Department of Molecular Microbiology, The Vlaams Instituut voor Biotechnologie, Flanders, Belgium
- * E-mail:
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100
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