1
|
Bernard M, Bergès T, Sebille S, Régnacq M. Calcineurin activation improves cell survival during amino acid starvation in lipid droplet-deficient yeasts. Biochem Biophys Res Commun 2024; 735:150670. [PMID: 39276520 DOI: 10.1016/j.bbrc.2024.150670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 08/23/2024] [Accepted: 09/05/2024] [Indexed: 09/17/2024]
Abstract
Lipid droplets (LD) are storage sites for neutral lipids that can be used as a source of energy during nutrient starvation, but also function as hubs for fatty acid (FA) trafficking between organelles. In the yeast Saccharomyces cerevisiae, the absence of LD causes a severe disorganization of the endomembrane network during starvation. Here we show that cells devoid of LD respond to amino acid (AA) starvation by activating the serine/threonine phosphatase calcineurin and the nuclear translocation of its target protein Crz1. This activation was inhibited by treatments that restore a normal endomembrane organization, i.e. inhibition of FA synthesis with cerulenin or deletion of the inhibitory transcription factor Opi1. Activation of calcineurin increased the lifespan of LD-deficient cells during AA starvation. Indeed, deletion of its regulatory or catalytic subunits accelerated cell death. Surprisingly, calcineurin activation appeared to be calcium-independent. An increase in intracellular calcium was observed in LD-deficient cells during AA starvation, but its inhibition by genetic deletion of MID1 or YVC1 did not affect calcineurin activity. In contrast, calcineurin activation required the direct regulator of calcineurin Rcn1 and its activating (GSK-3)-related protein kinase Mck1.
Collapse
Affiliation(s)
| | - Thierry Bergès
- Laboratoire PRéTI, UR 24184, Université de Poitiers, France
| | | | | |
Collapse
|
2
|
Gupta S, Kumar A, Tamuli R. CRZ1 transcription factor is involved in cell survival, stress tolerance, and virulence in fungi. J Biosci 2022. [DOI: 10.1007/s12038-022-00294-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
3
|
Yang Y, Xie P, Li Y, Bi Y, Prusky DB. Updating Insights into the Regulatory Mechanisms of Calcineurin-Activated Transcription Factor Crz1 in Pathogenic Fungi. J Fungi (Basel) 2022; 8:1082. [PMID: 36294647 PMCID: PMC9604740 DOI: 10.3390/jof8101082] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022] Open
Abstract
Ca2+, as a second messenger in cells, enables organisms to adapt to different environmental stresses by rapidly sensing and responding to external stimuli. In recent years, the Ca2+ mediated calcium signaling pathway has been studied systematically in various mammals and fungi, indicating that the pathway is conserved among organisms. The pathway consists mainly of complex Ca2+ channel proteins, calcium pumps, Ca2+ transporters and many related proteins. Crz1, a transcription factor downstream of the calcium signaling pathway, participates in regulating cell survival, ion homeostasis, infection structure development, cell wall integrity and virulence. This review briefly summarizes the Ca2+ mediated calcium signaling pathway and regulatory roles in plant pathogenic fungi. Based on discussing the structure and localization of transcription factor Crz1, we focus on the regulatory role of Crz1 on growth and development, stress response, pathogenicity of pathogenic fungi and its regulatory mechanisms. Furthermore, we explore the cross-talk between Crz1 and other signaling pathways. Combined with the important role and pathogenic mechanism of Crz1 in fungi, the new strategies in which Crz1 may be used as a target to explore disease control in practice are also discussed.
Collapse
Affiliation(s)
- Yangyang Yang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, China
| | - Pengdong Xie
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, China
| | - Yongcai Li
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, China
| | - Yang Bi
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, China
| | - Dov B. Prusky
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
| |
Collapse
|
4
|
CRISPR-Cas9 approach confirms Calcineurin-responsive zinc finger 1 (Crz1) transcription factor as a promising therapeutic target in echinocandin-resistant Candida glabrata. PLoS One 2022; 17:e0265777. [PMID: 35303047 PMCID: PMC8932611 DOI: 10.1371/journal.pone.0265777] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 03/07/2022] [Indexed: 11/19/2022] Open
Abstract
Invasive fungal infections, which kill more than 1.6 million patients each year worldwide, are difficult to treat due to the limited number of antifungal drugs (azoles, echinocandins, and polyenes) and the emergence of antifungal resistance. The transcription factor Crz1, a key regulator of cellular stress responses and virulence, is an attractive therapeutic target because this protein is absent in human cells. Here, we used a CRISPR-Cas9 approach to generate isogenic crz1Δ strains in two clinical isolates of caspofungin-resistant C. glabrata to analyze the role of this transcription factor in susceptibility to echinocandins, stress tolerance, biofilm formation, and pathogenicity in both non-vertebrate (Galleria mellonella) and vertebrate (mice) models of candidiasis. In these clinical isolates, CRZ1 disruption restores the susceptibility to echinocandins in both in vitro and in vivo models, and affects their oxidative stress response, biofilm formation, cell size, and pathogenicity. These results strongly suggest that Crz1 inhibitors may play an important role in the development of novel therapeutic agents against fungal infections considering the emergence of antifungal resistance and the low number of available antifungal drugs.
Collapse
|
5
|
Cells under pressure: how yeast cells respond to mechanical forces. Trends Microbiol 2022; 30:495-510. [PMID: 35000797 DOI: 10.1016/j.tim.2021.11.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/31/2021] [Accepted: 11/08/2021] [Indexed: 11/23/2022]
Abstract
In their natural habitats, unicellular fungal microbes are exposed to a myriad of mechanical cues such as shear forces from fluid flow, osmotic changes, and contact forces arising from microbial expansion in confined niches. While the rigidity of the cell wall is critical to withstand such external forces and balance high internal turgor pressure, it poses mechanical challenges during physiological processes such as cell growth, division, and mating that require cell wall remodeling. Thus, even organisms as simple as yeast have evolved complex signaling networks to sense and respond to intrinsic and extrinsic mechanical forces. In this review, we summarize the type and origin of mechanical forces experienced by unicellular yeast and discuss how these forces reorganize cell polarity and how pathogenic fungi exploit polarized assemblies to track weak spots in host tissues for successful penetration. We then describe mechanisms of force-sensing by conserved sets of mechanosensors. Finally, we elaborate downstream mechanotransduction mechanisms that orchestrate appropriate cellular responses, leading to improved mechanical fitness.
Collapse
|
6
|
Vellanki S, Billmyre RB, Lorenzen A, Campbell M, Turner B, Huh EY, Heitman J, Lee SC. A Novel Resistance Pathway for Calcineurin Inhibitors in the Human-Pathogenic Mucorales Mucor circinelloides. mBio 2020; 11:e02949-19. [PMID: 31992620 PMCID: PMC6989107 DOI: 10.1128/mbio.02949-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/16/2019] [Indexed: 12/24/2022] Open
Abstract
Mucormycosis is an emerging lethal fungal infection in immunocompromised patients. Mucor circinelloides is a causal agent of mucormycosis and serves as a model system to understand genetics in Mucorales. Calcineurin is a conserved virulence factor in many pathogenic fungi, and calcineurin inhibition or deletion of the calcineurin regulatory subunit (CnbR) in Mucor results in a shift from hyphal to yeast growth. We analyzed 36 calcineurin inhibitor-resistant or bypass mutants that exhibited hyphal growth in the presence of calcineurin inhibitors or in the yeast-locked cnbRΔ mutant background without carrying any mutations in known calcineurin components. We found that a majority of the mutants had altered sequence in a gene, named here bycA (bypass of calcineurin). bycA encodes an amino acid permease. We verified that both the bycAΔ single mutant and the bycAΔ cnbRΔ double mutant are resistant to calcineurin inhibitor FK506, thereby demonstrating a novel mechanism of resistance against calcineurin inhibitors. We also found that the level of expression of bycA was significantly higher in the wild-type strain treated with FK506 and in the cnbRΔ mutants but was significantly lower in the wild-type strain without FK506 treatment. These findings suggest that bycA is a negative regulator of hyphal growth and/or a positive regulator of yeast growth in Mucor and that calcineurin suppresses expression of the bycA gene at the mRNA level to promote hyphal growth. BycA is involved in the Mucor hypha-yeast transition as our data demonstrate positive correlations among bycA expression, protein kinase A activity, and Mucor yeast growth. Also, calcineurin, independently of its role in morphogenesis, contributes to virulence traits, including phagosome maturation blockade, host cell damages, and proangiogenic growth factor induction during interactions with hosts.IMPORTANCEMucor is intrinsically resistant to most known antifungals, which makes mucormycosis treatment challenging. Calcineurin is a serine/threonine phosphatase that is widely conserved across eukaryotes. When calcineurin function is inhibited in Mucor, growth shifts to a less virulent yeast growth form, which makes calcineurin an attractive target for development of new antifungal drugs. Previously, we identified two distinct mechanisms through which Mucor can become resistant to calcineurin inhibitors involving Mendelian mutations in the gene for FKBP12, including mechanisms corresponding to calcineurin A or B subunits and epimutations silencing the FKBP12 gene. Here, we identified a third novel mechanism where loss-of-function mutations in the amino acid permease corresponding to the bycA gene contribute to resistance against calcineurin inhibitors. When calcineurin activity is absent, BycA can activate protein kinase A (PKA) to promote yeast growth via a cAMP-independent pathway. Our data also show that calcineurin activity contributes to host-pathogen interactions primarily in the pathogenesis of Mucor.
Collapse
Affiliation(s)
- Sandeep Vellanki
- South Texas Center for Emerging Infectious Diseases (STCEID), Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - R Blake Billmyre
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Alejandra Lorenzen
- South Texas Center for Emerging Infectious Diseases (STCEID), Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Micaela Campbell
- South Texas Center for Emerging Infectious Diseases (STCEID), Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Broderick Turner
- South Texas Center for Emerging Infectious Diseases (STCEID), Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Eun Young Huh
- South Texas Center for Emerging Infectious Diseases (STCEID), Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Soo Chan Lee
- South Texas Center for Emerging Infectious Diseases (STCEID), Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, USA
| |
Collapse
|
7
|
Ramírez-Montiel F, Mendoza-Macías C, Andrade-Guillén S, Rangel-Serrano Á, Páramo-Pérez I, Rivera-Cuéllar PE, España-Sánchez BL, Luna-Bárcenas G, Anaya-Velázquez F, Franco B, Padilla-Vaca F. Plasma membrane damage repair is mediated by an acid sphingomyelinase in Entamoeba histolytica. PLoS Pathog 2019; 15:e1008016. [PMID: 31461501 PMCID: PMC6713333 DOI: 10.1371/journal.ppat.1008016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 08/02/2019] [Indexed: 12/15/2022] Open
Abstract
Entamoeba histolytica is a pathogen that during its infective process confronts the host defenses, which damages the amoebic plasma membrane (PM), resulting in the loss of viability. However, it is unknown whether amoebic trophozoites are able to repair their PM when it is damaged. Acid sphingomyelinases (aSMases) have been reported in mammalian cells to promote endocytosis and removal of PM lesions. In this work, six predicted amoebic genes encoding for aSMases were found to be transcribed in the HM1:IMSS strain, finding that the EhaSM6 gene is the most transcribed in basal growth conditions and rendered a functional protein. The secreted aSMase activity detected was stimulated by Mg+2 and inhibited by Co+2. Trophozoites that overexpress the EhaSM6 gene (HM1-SM6HA) exhibit an increase of 2-fold in the secreted aSMase activity. This transfectant trophozoites exposed to pore-forming molecules (SLO, Magainin, β-Defensin 2 and human complement) exhibited an increase from 6 to 25-fold in the secreted aSMase activity which correlated with higher amoebic viability in a Ca+2 dependent process. However, other agents that affect the PM such as hydrogen peroxide also induced an increase of secreted aSMase, but to a lesser extent. The aSMase6 enzyme is N- and C-terminal processed. Confocal and transmission electron microscopy showed that trophozoites treated with SLO presented a migration of lysosomes containing the aSMase towards the PM, inducing the formation of membrane patches and endosomes in the control strain. These cellular structures were increased in the overexpressing strain, indicating the involvement of the aSMase6 in the PM injury repair. The pore-forming molecules induced an increase in the expression of EhaSM1, 2, 5 and 6 genes, meanwhile, hydrogen peroxide induced an increase in all of them. In all the conditions evaluated, the EhaSM6 gene exhibited the highest levels of induction. Overall, these novel findings show that the aSMase6 enzyme from E. histolytica promotes the repair of the PM damaged with pore-forming molecules to prevent losing cell integrity. This novel system could act when encountered with the lytic defense systems of the host. The host-amoeba relationship is based on a series of interplays between host defense mechanisms and parasite survival strategies. While host cells elaborate diverse mechanisms for pathogen elimination, Entamoeba histolytica trophozoites have also developed complex strategies to counteract host immune response and facilitate its own survival while confronting host defenses. E. histolytica exposed to pore-forming proteins such as β-Defensin 2, human complement and Streptolysin O (SLO), increases the activity of secreted aSMase, which is related to greater amoebic viability. Other agents that affect plasma membrane (PM) may also increase secreted aSMase but to a lesser extent. SLO form pores in the PM of E. histolytica trophozoites that initiates the uncontrolled entry of Ca2+, recognized as the primary trigger for cell responses which favors the migration of the lysosomes to the periphery of the cell, fuses with the PM and release their content, including aSMase to the external side of the cell. The secreted aSMase favoring the internalization of the lesion for its degradation in phagolysosomes. During the early stages of PM damage, the pores are rapidly blocked by patch-like structures that prevent the lysis of the trophozoite and immediately begin internalizing the lesion. The aSMase6 overexpression favors the repair of the lesion and the survival of E. histolytica trophozoites. Pore-forming proteins induced an increase in the expression of EhaSM1, 2, 5 and 6 genes, meanwhile oxidative stress induced an increase in all of them. Here we report, for the first time, that E. histolytica possess a mechanism for PM damage repair mediated by aSMase similar to the system described in mammalian cells.
Collapse
Affiliation(s)
- Fátima Ramírez-Montiel
- Departmento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
| | - Claudia Mendoza-Macías
- Departmento de Farmacia, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
| | - Sairy Andrade-Guillén
- Departmento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
| | - Ángeles Rangel-Serrano
- Departmento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
| | - Itzel Páramo-Pérez
- Departmento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
| | - Paris E. Rivera-Cuéllar
- Departmento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
| | - B. Liliana España-Sánchez
- CONACYT_Centro de Investigación y Desarrollo en Electroquímica (CIDETEQ) S.C. Parque Tecnológico, San Fandila, Querétaro, México
| | - Gabriel Luna-Bárcenas
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV) Unidad Querétaro, Fracc. Real de Juriquilla, Querétaro, Querétaro, México
| | - Fernando Anaya-Velázquez
- Departmento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
| | - Bernardo Franco
- Departmento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
- * E-mail: (BF); (FPV)
| | - Felipe Padilla-Vaca
- Departmento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
- * E-mail: (BF); (FPV)
| |
Collapse
|
8
|
Shwab EK, Juvvadi PR, Waitt G, Soderblom EJ, Barrington BC, Asfaw YG, Moseley MA, Steinbach WJ. Calcineurin-dependent dephosphorylation of the transcription factor CrzA at specific sites controls conidiation, stress tolerance, and virulence of Aspergillus fumigatus. Mol Microbiol 2019; 112:62-80. [PMID: 30927289 DOI: 10.1111/mmi.14254] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2019] [Indexed: 12/15/2022]
Abstract
Calcium signaling through calcineurin and its major transcription factor (TF), CrzA, is integral to hyphal growth, stress response and virulence of the pathogenic fungus Aspergillus fumigatus, the leading etiology of invasive aspergillosis. Dephosphorylation of CrzA by calcineurin activates the TF, but the specific phosphorylation sites and their roles in the activation/inactivation mechanism are unknown. Mass spectroscopic analysis identified 20 phosphorylation sites, the majority of which were specific to filamentous fungi and distributed throughout the CrzA protein, with particular concentration in a serine-rich region N-terminal to the conserved DNA-binding domain (DBD). Site-directed mutagenesis of phosphorylated residues revealed that CrzA activity during calcium stimulation can only be suppressed by a high degree of phosphorylation in multiple regions of the protein. Our findings further suggest that this regulation is not solely accomplished through control of CrzA nuclear import. Additionally, we demonstrate the importance of the CrzA phosphorylation state in regulating growth, conidiation, calcium and cell wall stress tolerance, and virulence. Finally, we identify two previously undescribed nuclear localization sequences in the DBD. These findings provide novel insight into the phosphoregulation of CrzA which may be exploited to selectively target A. fumigatus.
Collapse
Affiliation(s)
- E Keats Shwab
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Praveen R Juvvadi
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Greg Waitt
- Duke Proteomics and Metabolomics Core Facility, Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Erik J Soderblom
- Duke Proteomics and Metabolomics Core Facility, Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Blake C Barrington
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Yohannes G Asfaw
- Department of Laboratory Animal Resources, Duke University Medical Center, Durham, NC, USA
| | - M Arthur Moseley
- Duke Proteomics and Metabolomics Core Facility, Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - William J Steinbach
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA.,Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| |
Collapse
|
9
|
Ariño J, Ramos J, Sychrova H. Monovalent cation transporters at the plasma membrane in yeasts. Yeast 2018; 36:177-193. [PMID: 30193006 DOI: 10.1002/yea.3355] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/24/2018] [Accepted: 08/29/2018] [Indexed: 01/08/2023] Open
Abstract
Maintenance of proper intracellular concentrations of monovalent cations, mainly sodium and potassium, is a requirement for survival of any cell. In the budding yeast Saccharomyces cerevisiae, monovalent cation homeostasis is determined by the active extrusion of protons through the Pma1 H+ -ATPase (reviewed in another chapter of this issue), the influx and efflux of these cations through the plasma membrane transporters (reviewed in this chapter), and the sequestration of toxic cations into the vacuoles. Here, we will describe the structure, function, and regulation of the plasma membrane transporters Trk1, Trk2, Tok1, Nha1, and Ena1, which play a key role in maintaining physiological intracellular concentrations of Na+ , K+ , and H+ , both under normal growth conditions and in response to stress.
Collapse
Affiliation(s)
- Joaquín Ariño
- Institut de Biotecnologia i Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - José Ramos
- Departamento de Microbiología, Universidad de Córdoba, Córdoba, Spain
| | - Hana Sychrova
- Department of Membrane Transport, Institute of Physiology Czech Academy of Sciences, Prague, Czech Republic
| |
Collapse
|
10
|
MacGilvray ME, Shishkova E, Chasman D, Place M, Gitter A, Coon JJ, Gasch AP. Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response. PLoS Comput Biol 2018; 13:e1006088. [PMID: 29738528 PMCID: PMC5940180 DOI: 10.1371/journal.pcbi.1006088] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 03/13/2018] [Indexed: 11/18/2022] Open
Abstract
Cells respond to stressful conditions by coordinating a complex, multi-faceted response that spans many levels of physiology. Much of the response is coordinated by changes in protein phosphorylation. Although the regulators of transcriptome changes during stress are well characterized in Saccharomyces cerevisiae, the upstream regulatory network controlling protein phosphorylation is less well dissected. Here, we developed a computational approach to infer the signaling network that regulates phosphorylation changes in response to salt stress. We developed an approach to link predicted regulators to groups of likely co-regulated phospho-peptides responding to stress, thereby creating new edges in a background protein interaction network. We then use integer linear programming (ILP) to integrate wild type and mutant phospho-proteomic data and predict the network controlling stress-activated phospho-proteomic changes. The network we inferred predicted new regulatory connections between stress-activated and growth-regulating pathways and suggested mechanisms coordinating metabolism, cell-cycle progression, and growth during stress. We confirmed several network predictions with co-immunoprecipitations coupled with mass-spectrometry protein identification and mutant phospho-proteomic analysis. Results show that the cAMP-phosphodiesterase Pde2 physically interacts with many stress-regulated transcription factors targeted by PKA, and that reduced phosphorylation of those factors during stress requires the Rck2 kinase that we show physically interacts with Pde2. Together, our work shows how a high-quality computational network model can facilitate discovery of new pathway interactions during osmotic stress. Cells sense and respond to stressful environments by utilizing complex signaling networks that integrate diverse signals to coordinate a multi-faceted physiological response. Much of this response is controlled by post-translational protein phosphorylation. Although many regulators that mediate changes in protein phosphorylation are known, how these regulators inter-connect in a single regulatory network that can transmit cellular signals is not known. It is also unclear how regulators that promote growth and regulators that activate the stress response interconnect to reorganize resource allocation during stress. Here, we developed an integrated experimental and computational workflow to infer the signaling network that regulates phosphorylation changes during osmotic stress in the budding yeast Saccharomyces cerevisiae. The workflow integrates data measuring protein phosphorylation changes in response to osmotic stress with known physical interactions between yeast proteins from large-scale datasets, along with other information about how regulators recognize their targets. The resulting network suggested new signaling connections between regulators and pathways, including those involved in regulating growth and defense, and predicted new regulators involved in stress defense. Our work highlights the power of using network inference to deliver new insight on how cells coordinate a diverse adaptive strategy to stress.
Collapse
Affiliation(s)
- Matthew E. MacGilvray
- Laboratory of Genetics, University of Wisconsin—Madison, Madison, WI, United States of America
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin—Madison, Madison, WI, United States of America
| | - Deborah Chasman
- Wisconsin Institute for Discovery, University of Wisconsin–Madison, Madison, WI, United States of America
| | - Michael Place
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin -Madison, Madison, WI, United States of America
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin—Madison, Madison, WI, United States of America
- Morgridge Institute for Research, Madison, WI, United States of America
- Department of Chemistry, University of Wisconsin -Madison, Madison, WI, United States of America
- Genome Center of Wisconsin, Madison, WI, United States of America
| | - Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin—Madison, Madison, WI, United States of America
- Department of Chemistry, University of Wisconsin -Madison, Madison, WI, United States of America
- * E-mail:
| |
Collapse
|
11
|
Sherrington SL, Kumwenda P, Kousser C, Hall RA. Host Sensing by Pathogenic Fungi. ADVANCES IN APPLIED MICROBIOLOGY 2017; 102:159-221. [PMID: 29680125 DOI: 10.1016/bs.aambs.2017.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ability to cause disease extends from the ability to grow within the host environment. The human host provides a dynamic environment to which fungal pathogens must adapt to in order to survive. The ability to grow under a particular condition (i.e., the ability to grow at mammalian body temperature) is considered a fitness attribute and is essential for growth within the human host. On the other hand, some environmental conditions activate signaling mechanisms resulting in the expression of virulence factors, which aid pathogenicity. Therefore, pathogenic fungi have evolved fitness and virulence attributes to enable them to colonize and infect humans. This review highlights how some of the major pathogenic fungi respond and adapt to key environmental signals within the human host.
Collapse
Affiliation(s)
- Sarah L Sherrington
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Pizga Kumwenda
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Courtney Kousser
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Rebecca A Hall
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom.
| |
Collapse
|
12
|
Niedzwiecka K, Tisi R, Penna S, Lichocka M, Plochocka D, Kucharczyk R. Two mutations in mitochondrial ATP6 gene of ATP synthase, related to human cancer, affect ROS, calcium homeostasis and mitochondrial permeability transition in yeast. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1865:117-131. [PMID: 28986220 DOI: 10.1016/j.bbamcr.2017.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 09/15/2017] [Accepted: 10/02/2017] [Indexed: 02/06/2023]
Abstract
The relevance of mitochondrial DNA (mtDNA) mutations in cancer process is still unknown. Since the mutagenesis of mitochondrial genome in mammals is not possible yet, we have exploited budding yeast S. cerevisiae as a model to study the effects of tumor-associated mutations in the mitochondrial MTATP6 gene, encoding subunit 6 of ATP synthase, on the energy metabolism. We previously reported that four mutations in this gene have a limited impact on the production of cellular energy. Here we show that two mutations, Atp6-P163S and Atp6-K90E (human MTATP6-P136S and MTATP6-K64E, found in prostate and thyroid cancer samples, respectively), increase sensitivity of yeast cells both to compounds inducing oxidative stress and to high concentrations of calcium ions in the medium, when Om45p, the component of porin complex in outer mitochondrial membrane (OM), was fused to GFP. In OM45-GFP background, these mutations affect the activation of yeast permeability transition pore (yPTP, also called YMUC, yeast mitochondrial unspecific channel) upon calcium induction. Moreover, we show that calcium addition to isolated mitochondria heavily induced the formation of ATP synthase dimers and oligomers, recently proposed to form the core of PTP, which was slower in the mutants. We show the genetic evidence for involvement of mitochondrial ATP synthase in calcium homeostasis and permeability transition in yeast. This paper is a first to show, although in yeast model organism, that mitochondrial ATP synthase mutations, which accumulate during carcinogenesis process, may be significant for cancer cell escape from apoptosis.
Collapse
Affiliation(s)
- Katarzyna Niedzwiecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Renata Tisi
- Dept. Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy; Milan Center for Neuroscience, Milan, Italy
| | - Sara Penna
- Dept. Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Malgorzata Lichocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Danuta Plochocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| |
Collapse
|
13
|
Leonov A, Feldman R, Piano A, Arlia-Ciommo A, Lutchman V, Ahmadi M, Elsaser S, Fakim H, Heshmati-Moghaddam M, Hussain A, Orfali S, Rajen H, Roofigari-Esfahani N, Rosanelli L, Titorenko VI. Caloric restriction extends yeast chronological lifespan via a mechanism linking cellular aging to cell cycle regulation, maintenance of a quiescent state, entry into a non-quiescent state and survival in the non-quiescent state. Oncotarget 2017; 8:69328-69350. [PMID: 29050207 PMCID: PMC5642482 DOI: 10.18632/oncotarget.20614] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/14/2017] [Indexed: 12/22/2022] Open
Abstract
A yeast culture grown in a nutrient-rich medium initially containing 2% glucose is not limited in calorie supply. When yeast cells cultured in this medium consume glucose, they undergo cell cycle arrest at a checkpoint in late G1 and differentiate into quiescent and non-quiescent cell populations. Studies of such differentiation have provided insights into mechanisms of yeast chronological aging under conditions of excessive calorie intake. Caloric restriction is an aging-delaying dietary intervention. Here, we assessed how caloric restriction influences the differentiation of chronologically aging yeast cultures into quiescent and non-quiescent cells, and how it affects their properties. We found that caloric restriction extends yeast chronological lifespan via a mechanism linking cellular aging to cell cycle regulation, maintenance of quiescence, entry into a non-quiescent state and survival in this state. Our findings suggest that caloric restriction delays yeast chronological aging by causing specific changes in the following: 1) a checkpoint in G1 for cell cycle arrest and entry into a quiescent state; 2) a growth phase in which high-density quiescent cells are committed to become low-density quiescent cells; 3) the differentiation of low-density quiescent cells into low-density non-quiescent cells; and 4) the conversion of high-density quiescent cells into high-density non-quiescent cells.
Collapse
Affiliation(s)
- Anna Leonov
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Rachel Feldman
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Amanda Piano
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | | | - Vicky Lutchman
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Masoumeh Ahmadi
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Sarah Elsaser
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Hana Fakim
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | | | - Asimah Hussain
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Sandra Orfali
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | | | | | - Leana Rosanelli
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | | |
Collapse
|
14
|
Matsuo Y, Kawamukai M. cAMP-dependent protein kinase involves calcium tolerance through the regulation of Prz1 in Schizosaccharomyces pombe. Biosci Biotechnol Biochem 2017; 81:231-241. [DOI: 10.1080/09168451.2016.1246171] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Abstract
The cAMP-dependent protein kinase Pka1 is known as a regulator of glycogenesis, meiosis, and stress responses in Schizosaccharomyces pombe. We demonstrated that Pka1 is responsible for calcium tolerance. Loss of functional components of the PKA pathway such as Git3, Gpa2, Cyr1, and Pka1 yields a CaCl2-sensitive phenotype, while loss of Cgs1, a regulatory subunit of PKA, results in CaCl2 tolerance. Cytoplasmic distribution of Cgs1 and Pka1 is increased by the addition of CaCl2, suggesting that CaCl2 induces dissociation of Cgs1 and Pka1. The expression of Prz1, a transcriptional regulator in calcium homeostasis, is elevated in a pka1∆ strain and in a wild type strain under glucose-limited conditions. Accordingly, higher expression of Prz1 in the wild type strain results in a CaCl2-sensitive phenotype. These findings suggest that Pka1 is essential for tolerance to exogenous CaCl2, probably because the expression level of Prz1 needs to be properly regulated by Pka1.
Collapse
Affiliation(s)
- Yasuhiro Matsuo
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
| | - Makoto Kawamukai
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
| |
Collapse
|
15
|
Raguz Nakic Z, Seisenbacher G, Posas F, Sauer U. Untargeted metabolomics unravels functionalities of phosphorylation sites in Saccharomyces cerevisiae. BMC SYSTEMS BIOLOGY 2016; 10:104. [PMID: 27846849 PMCID: PMC5109706 DOI: 10.1186/s12918-016-0350-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 11/03/2016] [Indexed: 01/08/2023]
Abstract
Background Coordinated through a complex network of kinases and phosphatases, protein phosphorylation regulates essentially all cellular processes in eukaryotes. Recent advances in proteomics enable detection of thousands of phosphorylation sites (phosphosites) in single experiments. However, functionality of the vast majority of these sites remains unclear and we lack suitable approaches to evaluate functional relevance at a pace that matches their detection. Results Here, we assess functionality of 26 phosphosites by introducing phosphodeletion and phosphomimic mutations in 25 metabolic enzymes and regulators from the TOR and HOG signaling pathway in Saccharomyces cerevisiae by phenotypic analysis and untargeted metabolomics. We show that metabolomics largely outperforms growth analysis and recovers 10 out of the 13 previously characterized phosphosites and suggests functionality for several novel sites, including S79 on the TOR regulatory protein Tip41. We analyze metabolic profiles to identify consequences underlying regulatory phosphorylation events and detecting glycerol metabolism to have a so far unknown influence on arginine metabolism via phosphoregulation of the glycerol dehydrogenases. Further, we also find S508 in the MAPKK Pbs2 as a potential link for cross-talking between HOG signaling and the cell wall integrity pathway. Conclusions We demonstrate that metabolic profiles can be exploited for gaining insight into regulatory consequences and biological roles of phosphosites. Altogether, untargeted metabolomics is a fast, sensitive and informative approach appropriate for future large-scale functional analyses of phosphosites. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0350-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zrinka Raguz Nakic
- Institute of Molecular Systems Biology, ETH Zürich, Auguste-Piccard-Hof 1, Zürich, Switzerland.,PhD Program on Systems Biology, Life Science Zürich, Zürich, Switzerland
| | - Gerhard Seisenbacher
- Cell signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesc Posas
- Cell signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Auguste-Piccard-Hof 1, Zürich, Switzerland.
| |
Collapse
|
16
|
Hernández-Ortiz P, Espeso EA. Spatiotemporal dynamics of the calcineurin target CrzA. Cell Signal 2016; 29:168-180. [PMID: 27832964 DOI: 10.1016/j.cellsig.2016.11.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/26/2016] [Accepted: 11/05/2016] [Indexed: 01/23/2023]
Abstract
The response of Aspergilli to elevated concentrations of extracellular calcium and manganese, or environmental alkalinization is mediated by CrzA, a calcineurin-responsive transcription factor (TF). CrzA is the effector of a signaling pathway which includes the apical protein's calmodulin and calcineurin, and the protein kinases GskA and CkiA. Preferentially located in the cytoplasm, CrzA is the only element of the pathway modifying its localization under those stress conditions, being imported into nuclei. Remarkably, there is a direct relationship between the nature/intensity of the stimulus and the pace of nuclear import and time of nuclear permanence of CrzA. Alkalinity caused a transient nuclear accumulation of CrzA while high Ca2+ and Mn2+ concentrations generated a long-lasting accumulation. Furthermore, Ca2+ concentrations (below 5mM) that are non-toxic for a crzAΔ mutant promoted full signaling of CrzA. However, micromolar concentrations or a mutation disrupting the interaction of CrzA with the phosphatase complex calcineurin, permitted the visualization of a transient and polarized nuclear accumulation of the TF in a tip-to-base gradient. Overall, these results support a model in which nucleo-cytoplasmic dynamics and transcriptional activity of CrzA are driven by apical signals transmitted by calmodulin and calcineurin. This communication is essential to understand Ca+2-induced stress response in fungi.
Collapse
Affiliation(s)
- Patricia Hernández-Ortiz
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Eduardo A Espeso
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain.
| |
Collapse
|
17
|
Yenush L. Potassium and Sodium Transport in Yeast. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:187-228. [DOI: 10.1007/978-3-319-25304-6_8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
18
|
Albataineh MT, Kadosh D. Regulatory roles of phosphorylation in model and pathogenic fungi. Med Mycol 2015; 54:333-52. [PMID: 26705834 PMCID: PMC4818690 DOI: 10.1093/mmy/myv098] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 11/01/2015] [Indexed: 12/25/2022] Open
Abstract
Over the past 20 years, considerable advances have been made toward our understanding
of how post-translational modifications affect a wide variety of biological
processes, including morphology and virulence, in medically important fungi.
Phosphorylation stands out as a key molecular switch and regulatory modification that
plays a critical role in controlling these processes. In this article, we first
provide a comprehensive and up-to-date overview of the regulatory roles that both
Ser/Thr and non-Ser/Thr kinases and phosphatases play in model and pathogenic fungi.
Next, we discuss the impact of current global approaches that are being used to
define the complete set of phosphorylation targets (phosphoproteome) in medically
important fungi. Finally, we provide new insights and perspectives into the potential
use of key regulatory kinases and phosphatases as targets for the development of
novel and more effective antifungal strategies.
Collapse
Affiliation(s)
- Mohammad T Albataineh
- Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - David Kadosh
- Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| |
Collapse
|
19
|
A Gβ protein and the TupA Co-Regulator Bind to Protein Kinase A Tpk2 to Act as Antagonistic Molecular Switches of Fungal Morphological Changes. PLoS One 2015; 10:e0136866. [PMID: 26334875 PMCID: PMC4559445 DOI: 10.1371/journal.pone.0136866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/09/2015] [Indexed: 11/19/2022] Open
Abstract
The human pathogenic fungus Paracoccidioides brasiliensis (Pb) undergoes a morphological transition from a saprobic mycelium to pathogenic yeast that is controlled by the cAMP-signaling pathway. There is a change in the expression of the Gβ-protein PbGpb1, which interacts with adenylate cyclase, during this morphological transition. We exploited the fact that the cAMP-signaling pathway of Saccharomyces cerevisiae does not include a Gβ-protein to probe the functional role of PbGpb1. We present data that indicates that PbGpb1 and the transcriptional regulator PbTupA both bind to the PKA protein PbTpk2. PbTPK2 was able to complement a TPK2Δ strain of S. cerevisiae, XPY5a/α, which was defective in pseudohyphal growth. Whilst PbGPB1 had no effect on the parent S. cerevisiae strain, MLY61a/α, it repressed the filamentous growth of XPY5a/α transformed with PbTPK2, behaviour that correlated with a reduced expression of the floculin FLO11. In vitro, PbGpb1 reduced the kinase activity of PbTpk2, suggesting that inhibition of PbTpk2 by PbGpb1 reduces the level of expression of Flo11, antagonizing the filamentous growth of the cells. In contrast, expressing the co-regulator PbTUPA in XPY5a/α cells transformed with PbTPK2, but not untransformed cells, induced hyperfilamentous growth, which could be antagonized by co-transforming the cells with PbGPB1. PbTUPA was unable to induce the hyperfilamentous growth of a FLO8Δ strain, suggesting that PbTupA functions in conjunction with the transcription factor Flo8 to control Flo11 expression. Our data indicates that P. brasiliensis PbGpb1 and PbTupA, both of which have WD/β-propeller structures, bind to PbTpk2 to act as antagonistic molecular switches of cell morphology, with PbTupA and PbGpb1 inducing and repressing filamentous growth, respectively. Our findings define a potential mechanism for controlling the morphological switch that underpins the virulence of dimorphic fungi.
Collapse
|
20
|
Serra-Cardona A, Canadell D, Ariño J. Coordinate responses to alkaline pH stress in budding yeast. MICROBIAL CELL 2015; 2:182-196. [PMID: 28357292 PMCID: PMC5349140 DOI: 10.15698/mic2015.06.205] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Alkalinization of the medium represents a stress condition for the budding yeast Saccharomyces cerevisiae to which this organism responds with profound remodeling of gene expression. This is the result of the modulation of a substantial number of signaling pathways whose participation in the alkaline response has been elucidated within the last ten years. These regulatory inputs involve not only the conserved Rim101/PacC pathway, but also the calcium-activated phosphatase calcineurin, the Wsc1-Pkc1-Slt2 MAP kinase, the Snf1 and PKA kinases and oxidative stress-response pathways. The uptake of many nutrients is perturbed by alkalinization of the environment and, consequently, an impact on phosphate, iron/copper and glucose homeostatic mechanisms can also be observed. The analysis of available data highlights cases in which diverse signaling pathways are integrated in the gene promoter to shape the appropriate response pattern. Thus, the expression of different genes sharing the same signaling network can be coordinated, allowing functional coupling of their gene products.
Collapse
Affiliation(s)
- Albert Serra-Cardona
- Departament de Bioquímica i Biologia Molecular & Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
| | - David Canadell
- Departament de Bioquímica i Biologia Molecular & Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
| | - Joaquín Ariño
- Departament de Bioquímica i Biologia Molecular & Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
| |
Collapse
|
21
|
Ariño J, Aydar E, Drulhe S, Ganser D, Jorrín J, Kahm M, Krause F, Petrezsélyová S, Yenush L, Zimmermannová O, van Heusden GPH, Kschischo M, Ludwig J, Palmer C, Ramos J, Sychrová H. Systems biology of monovalent cation homeostasis in yeast: the translucent contribution. Adv Microb Physiol 2014; 64:1-63. [PMID: 24797924 DOI: 10.1016/b978-0-12-800143-1.00001-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Maintenance of monovalent cation homeostasis (mainly K(+) and Na(+)) is vital for cell survival, and cation toxicity is at the basis of a myriad of relevant phenomena, such as salt stress in crops and diverse human diseases. Full understanding of the importance of monovalent cations in the biology of the cell can only be achieved from a systemic perspective. Translucent is a multinational project developed within the context of the SysMO (System Biology of Microorganisms) initiative and focussed in the study of cation homeostasis using the well-known yeast Saccharomyces cerevisiae as a model. The present review summarize how the combination of biochemical, genetic, genomic and computational approaches has boosted our knowledge in this field, providing the basis for a more comprehensive and coherent vision of the role of monovalent cations in the biology of the cell.
Collapse
Affiliation(s)
- Joaquín Ariño
- Institut de Biotecnologia i Biomedicina & Dept. Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain.
| | - Ebru Aydar
- Faculty of Life Sciences and Computing, London Metropolitan University, London, United Kingdom
| | | | | | - Jesús Jorrín
- Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
| | - Matthias Kahm
- RheinAhrCampus, University of Applied Sciences Koblenz, Remagen, Germany
| | | | - Silvia Petrezsélyová
- Institut de Biotecnologia i Biomedicina & Dept. Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Lynne Yenush
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Olga Zimmermannová
- Department of Membrane Transport, Institute of Physiology Academy of Sciences CR, Prague, Czech Republic
| | | | - Maik Kschischo
- RheinAhrCampus, University of Applied Sciences Koblenz, Remagen, Germany
| | | | - Chris Palmer
- Faculty of Life Sciences and Computing, London Metropolitan University, London, United Kingdom
| | - José Ramos
- Department of Microbiology, University of Córdoba, Córdoba, Spain
| | - Hana Sychrová
- Department of Membrane Transport, Institute of Physiology Academy of Sciences CR, Prague, Czech Republic
| |
Collapse
|
22
|
Coregulated expression of the Na+/phosphate Pho89 transporter and Ena1 Na+-ATPase allows their functional coupling under high-pH stress. Mol Cell Biol 2014; 34:4420-35. [PMID: 25266663 DOI: 10.1128/mcb.01089-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The yeast Saccharomyces cerevisiae has two main high-affinity inorganic phosphate (Pi) transporters, Pho84 and Pho89, that are functionally relevant at acidic/neutral pH and alkaline pH, respectively. Upon Pi starvation, PHO84 and PHO89 are induced by the activation of the PHO regulon by the binding of the Pho4 transcription factor to specific promoter sequences. We show that PHO89 and PHO84 are induced by alkalinization of the medium with different kinetics and that the network controlling Pho89 expression in response to alkaline pH differs from that of other members of the PHO regulon. In addition to Pho4, the PHO89 promoter is regulated by the transcriptional activator Crz1 through the calcium-activated phosphatase calcineurin, and it is under the control of several repressors (Mig2, Nrg1, and Nrg2) coordinately regulated by the Snf1 protein kinase and the Rim101 transcription factor. This network mimics the one regulating expression of the Na(+)-ATPase gene ENA1, encoding a major determinant for Na(+) detoxification. Our data highlight a scenario in which the activities of Pho89 and Ena1 are functionally coordinated to sustain growth in an alkaline environment.
Collapse
|
23
|
Adaptive response and tolerance to sugar and salt stress in the food yeast Zygosaccharomyces rouxii. Int J Food Microbiol 2014; 185:140-57. [DOI: 10.1016/j.ijfoodmicro.2014.05.015] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 04/18/2014] [Accepted: 05/04/2014] [Indexed: 11/21/2022]
|
24
|
Cisneros-Barroso E, Yance-Chávez T, Kito A, Sugiura R, Gómez-Hierro A, Giménez-Zaragoza D, Aligue R. Negative feedback regulation of calcineurin-dependent Prz1 transcription factor by the CaMKK-CaMK1 axis in fission yeast. Nucleic Acids Res 2014; 42:9573-87. [PMID: 25081204 PMCID: PMC4150787 DOI: 10.1093/nar/gku684] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Calcium signals trigger the translocation of the Prz1 transcription factor from the cytoplasm to the nucleus. The process is regulated by the calcium-activated phosphatase calcineurin, which activates Prz1 thereby maintaining active transcription during calcium signalling. When calcium signalling ceases, Prz1 is inactivated by phosphorylation and exported to the cytoplasm. In budding yeast and mammalian cells, different kinases have been reported to counter calcineurin activity and regulate nuclear export. Here, we show that the Ca(2+)/calmodulin-dependent kinase Cmk1 is first phosphorylated and activated by the newly identified kinase CaMKK2 homologue, Ckk2, in response to Ca(2+). Then, active Cmk1 binds, phosphorylates and inactivates Prz1 transcription activity whilst at the same time cmk1 expression is enhanced by Prz1 in response to Ca(2+). Furthermore, Cdc25 phosphatase is also phosphorylated by Cmk1, inducing cell cycle arrest in response to an increase in Ca(2+). Moreover, cmk1 deletion shows a high tolerance to chronic exposure to Ca(2+), due to the lack of cell cycle inhibition and elevated Prz1 activity. This work reveals that Cmk1 kinase activated by the newly identified Ckk2 counteracts calcineurin function by negatively regulating Prz1 activity which in turn is involved in activating cmk1 gene transcription. These results are the first insights into Cmk1 and Ckk2 function in Schizosaccharomyces pombe.
Collapse
Affiliation(s)
- Eugenia Cisneros-Barroso
- Departament de Biologia Cellular, Immunologia i Neurociències, Facultat de Medicina, Universitat de Barcelona, Institute of Biomedical Research August Pi i Sunyer (IDIBAPS), Barcelona 08036, Catalunya, Spain
| | - Tula Yance-Chávez
- Departament de Biologia Cellular, Immunologia i Neurociències, Facultat de Medicina, Universitat de Barcelona, Institute of Biomedical Research August Pi i Sunyer (IDIBAPS), Barcelona 08036, Catalunya, Spain
| | - Ayako Kito
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Kowakae, Higashi-Osaka 577-8502, Japan
| | - Reiko Sugiura
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Kowakae, Higashi-Osaka 577-8502, Japan
| | - Alba Gómez-Hierro
- Departament de Biologia Cellular, Immunologia i Neurociències, Facultat de Medicina, Universitat de Barcelona, Institute of Biomedical Research August Pi i Sunyer (IDIBAPS), Barcelona 08036, Catalunya, Spain
| | - David Giménez-Zaragoza
- Departament de Biologia Cellular, Immunologia i Neurociències, Facultat de Medicina, Universitat de Barcelona, Institute of Biomedical Research August Pi i Sunyer (IDIBAPS), Barcelona 08036, Catalunya, Spain
| | - Rosa Aligue
- Departament de Biologia Cellular, Immunologia i Neurociències, Facultat de Medicina, Universitat de Barcelona, Institute of Biomedical Research August Pi i Sunyer (IDIBAPS), Barcelona 08036, Catalunya, Spain
| |
Collapse
|
25
|
Goldman A, Roy J, Bodenmiller B, Wanka S, Landry CR, Aebersold R, Cyert MS. The calcineurin signaling network evolves via conserved kinase-phosphatase modules that transcend substrate identity. Mol Cell 2014; 55:422-435. [PMID: 24930733 DOI: 10.1016/j.molcel.2014.05.012] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 04/02/2014] [Accepted: 05/07/2014] [Indexed: 10/25/2022]
Abstract
To define a functional network for calcineurin, the conserved Ca(2+)/calmodulin-regulated phosphatase, we systematically identified its substrates in S. cerevisiae using phosphoproteomics and bioinformatics, followed by copurification and dephosphorylation assays. This study establishes new calcineurin functions and reveals mechanisms that shape calcineurin network evolution. Analyses of closely related yeasts show that many proteins were recently recruited to the network by acquiring a calcineurin-recognition motif. Calcineurin substrates in yeast and mammals are distinct due to network rewiring but, surprisingly, are phosphorylated by similar kinases. We postulate that corecognition of conserved substrate features, including phosphorylation and docking motifs, preserves calcineurin-kinase opposition during evolution. One example we document is a composite docking site that confers substrate recognition by both calcineurin and MAPK. We propose that conserved kinase-phosphatase pairs define the architecture of signaling networks and allow other connections between kinases and phosphatases to develop that establish common regulatory motifs in signaling networks.
Collapse
Affiliation(s)
- Aaron Goldman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jagoree Roy
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Bernd Bodenmiller
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Stefanie Wanka
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes, PROTEO, Département de Biologie, Université Laval, Québec G1V 0A6, Canada
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland.,Faculty of Science, University of Zürich, 8057 Zürich, Switzerland
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
26
|
Miyakawa T, Mizunuma M. Physiological Roles of Calcineurin inSaccharomyces cerevisiaewith Special Emphasis on Its Roles in G2/M Cell-Cycle Regulation. Biosci Biotechnol Biochem 2014; 71:633-45. [PMID: 17341827 DOI: 10.1271/bbb.60495] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Calcineurin, a highly conserved Ca(2+)/CaM-dependent protein phosphatase, plays key regulatory roles in diverse biological processes from yeast to humans. Genetic and molecular analyses of the yeast model system have proved successful in dissecting complex regulatory pathways mediated by calcineurin. Saccharomyces cerevisiae calcineurin is not essential for growth under laboratory conditions, but becomes essential for survival under certain stress conditions, and is required for stress-induced expression of the genes for ion transporters and cell-wall synthesis. Yeast calcineurin, in collaboration with a Mpk1 MAP kinase cascade, is also important in G(2) cell-cycle regulation due to its action in a checkpoint-like mechanism. Genetic and molecular analysis of the Ca(2+)-dependent cell-cycle regulation has revealed an elaborate mechanism for the calcineurin-dependent regulation of the G(2)/M transition, in which calcineurin multilaterally activates Swe1, a negative regulator of the Cdc28/Clb complex, at the transcriptional, posttranslational, and degradation levels.
Collapse
Affiliation(s)
- Tokichi Miyakawa
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan.
| | | |
Collapse
|
27
|
Defects in phosphate acquisition and storage influence virulence of Cryptococcus neoformans. Infect Immun 2014; 82:2697-712. [PMID: 24711572 DOI: 10.1128/iai.01607-14] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Nutrient acquisition and sensing are critical aspects of microbial pathogenesis. Previous transcriptional profiling indicated that the fungal pathogen Cryptococcus neoformans, which causes meningoencephalitis in immunocompromised individuals, encounters phosphate limitation during proliferation in phagocytic cells. We therefore tested the hypothesis that phosphate acquisition and polyphosphate metabolism are important for cryptococcal virulence. Deletion of the high-affinity uptake system interfered with growth on low-phosphate medium, perturbed the formation of virulence factors (capsule and melanin), reduced survival in macrophages, and attenuated virulence in a mouse model of cryptococcosis. Additionally, analysis of nutrient sensing functions for C. neoformans revealed regulatory connections between phosphate acquisition and storage and the iron regulator Cir1, cyclic AMP (cAMP)-dependent protein kinase A (PKA), and the calcium-calmodulin-activated protein phosphatase calcineurin. Deletion of the VTC4 gene encoding a polyphosphate polymerase blocked the ability of C. neoformans to produce polyphosphate. The vtc4 mutant behaved like the wild-type strain in interactions with macrophages and in the mouse infection model. However, the fungal load in the lungs was significantly increased in mice infected with vtc4 deletion mutants. In addition, the mutant was impaired in the ability to trigger blood coagulation in vitro, a trait associated with polyphosphate. Overall, this study reveals that phosphate uptake in C. neoformans is critical for virulence and that its regulation is integrated with key signaling pathways for nutrient sensing.
Collapse
|
28
|
Abstract
Calcium ions are ubiquitous intracellular messengers. An increase in the cytosolic Ca(2+) concentration activates many proteins, including calmodulin and the Ca(2+)/calmodulin-dependent protein phosphatase calcineurin. The phosphatase is conserved from yeast to humans (except in plants), and many target proteins of calcineurin have been identified. The most prominent and best-investigated targets, however, are the transcription factors NFAT (nuclear factor of activated T cells) in mammals and Crz1 (calcineurin-responsive zinc finger 1) in yeast. In recent years, many orthologues of Crz1 have been identified and characterized in various species of fungi, amoebae, and other lower eukaryotes. It has been shown that the functions of calcineurin-Crz1 signaling, ranging from ion homeostasis through cell wall biogenesis to the building of filamentous structures, are conserved in the different organisms. Furthermore, frequency-modulated gene expression through Crz1 has been discovered as a striking new mechanism by which cells can coordinate their response to a signal. In this review, I focus on the latest findings concerning calcineurin-Crz1 signaling in fungi, amoebae and other lower eukaryotes. I discuss the potential of Crz1 and its orthologues as putative drug targets, and I also discuss possible parallels with calcineurin-NFAT signaling in mammals.
Collapse
|
29
|
Global LC/MS Metabolomics Profiling of Calcium Stressed and Immunosuppressant Drug Treated Saccharomyces cerevisiae. Metabolites 2013; 3:1102-17. [PMID: 24958268 PMCID: PMC3937837 DOI: 10.3390/metabo3041102] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/20/2013] [Accepted: 11/25/2013] [Indexed: 11/17/2022] Open
Abstract
Previous studies have shown that calcium stressed Saccharomyces cerevisiae, challenged with immunosuppressant drugs FK506 and Cyclosporin A, responds with comprehensive gene expression changes and attenuation of the generalized calcium stress response. Here, we describe a global metabolomics workflow for investigating the utility of tracking corresponding phenotypic changes. This was achieved by efficiently analyzing relative abundance differences between intracellular metabolite pools from wild-type and calcium stressed cultures, with and without prior immunosuppressant drugs exposure. We used pathway database content from WikiPathways and YeastCyc to facilitate the projection of our metabolomics profiling results onto biological pathways. A key challenge was to increase the coverage of the detected metabolites. This was achieved by applying both reverse phase (RP) and aqueous normal phase (ANP) chromatographic separations, as well as electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) sources for detection in both ion polarities. Unsupervised principle component analysis (PCA) and ANOVA results revealed differentiation between wild-type controls, calcium stressed and immunosuppressant/calcium challenged cells. Untargeted data mining resulted in 247 differentially expressed, annotated metabolites, across at least one pair of conditions. A separate, targeted data mining strategy identified 187 differential, annotated metabolites. All annotated metabolites were subsequently mapped onto curated pathways from YeastCyc and WikiPathways for interactive pathway analysis and visualization. Dozens of pathways showed differential responses to stress conditions based on one or more matches to the list of annotated metabolites or to metabolites that had been identified further by MS/MS. The purine salvage, pantothenate and sulfur amino acid pathways were flagged as being enriched, which is consistent with previously published literature for transcriptomics analysis. Thus, broad discovery-based data mining combined with targeted pathway projections can be an important asset for rapidly distilling, testing and evaluating a large amount of information for further investigation.
Collapse
|
30
|
Calcineurin plays key roles in the dimorphic transition and virulence of the human pathogenic zygomycete Mucor circinelloides. PLoS Pathog 2013; 9:e1003625. [PMID: 24039585 PMCID: PMC3764228 DOI: 10.1371/journal.ppat.1003625] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 06/27/2013] [Indexed: 11/19/2022] Open
Abstract
Many pathogenic fungi are dimorphic and switch between yeast and filamentous states. This switch alters host-microbe interactions and is critical for pathogenicity. However, in zygomycetes, whether dimorphism contributes to virulence is a central unanswered question. The pathogenic zygomycete Mucor circinelloides exhibits hyphal growth in aerobic conditions but switches to multi-budded yeast growth under anaerobic/high CO₂ conditions. We found that in the presence of the calcineurin inhibitor FK506, Mucor exhibits exclusively multi-budded yeast growth. We also found that M. circinelloides encodes three calcineurin catalytic A subunits (CnaA, CnaB, and CnaC) and one calcineurin regulatory B subunit (CnbR). Mutations in the latch region of CnbR and in the FKBP12-FK506 binding domain of CnaA result in hyphal growth of Mucor in the presence of FK506. Disruption of the cnbR gene encoding the sole calcineurin B subunit necessary for calcineurin activity yielded mutants locked in permanent yeast phase growth. These findings reveal that the calcineurin pathway plays key roles in the dimorphic transition from yeast to hyphae. The cnbR yeast-locked mutants are less virulent than the wild-type strain in a heterologous host system, providing evidence that hyphae or the yeast-hyphal transition are linked to virulence. Protein kinase A activity (PKA) is elevated during yeast growth under anaerobic conditions, in the presence of FK506, or in the yeast-locked cnbR mutants, suggesting a novel connection between PKA and calcineurin. cnaA mutants lacking the CnaA catalytic subunit are hypersensitive to calcineurin inhibitors, display a hyphal polarity defect, and produce a mixture of yeast and hyphae in aerobic culture. The cnaA mutants also produce spores that are larger than wild-type, and spore size is correlated with virulence potential. Our results demonstrate that the calcineurin pathway orchestrates the yeast-hyphal and spore size dimorphic transitions that contribute to virulence of this common zygomycete fungal pathogen.
Collapse
|
31
|
Hernández-Ortiz P, Espeso EA. Phospho-regulation and nucleocytoplasmic trafficking of CrzA in response to calcium and alkaline-pH stress in Aspergillus nidulans. Mol Microbiol 2013; 89:532-51. [PMID: 23772954 DOI: 10.1111/mmi.12294] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2013] [Indexed: 12/20/2022]
Abstract
Tolerance to abiotic stresses by microorganisms require of appropriate signalling and regulatory pathways. Calcineurin phosphatases mediate calcium-dependent signalling pathways which are widely distributed among phylogeny. In Saccharomyces cerevisiae, calcineurin mediates the post-translational modification of downstream effectors, most of them transcription factors, being the best-characterized calcineurin-regulated zinc-finger factor 1, Crz1p. Here we study the signalling process of CrzA, a filamentous fungal Crz orthologue, in response to calcium and ambient-pH alkalinization. In Aspergillus nidulans resting cells CrzA locates in the cytoplasm being excluded from nuclei. CrzA is a phospho-protein and upon calcium, manganese or alkaline-pH stresses, accumulates in nuclei in a calcineurin-dependent manner. Functional analysis of CrzA defined the presence of a nuclear-export and two nuclear-localization signals as well as a PSINVE sequence that constitutes the major calcineurin-docking domain. First 450 amino acids of CrzA contain these functional motifs and in this region is where phosphorylated residues locate. Different phosphorylation steps are identified in CrzA and activities of casein kinase 1 homologue, CkiA, and of glycogen synthase kinase-3β, identified for the first time here as GskA, are involved. The phospho-signalling process and nucleocytoplasmic trafficking of CrzA shows similarities to those described in yeast for Crz1p homologues and of NFATs in mammals.
Collapse
Affiliation(s)
- Patricia Hernández-Ortiz
- Department of Cellular and Molecular Biology, Centro Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, Madrid, 28040, Spain
| | | |
Collapse
|
32
|
Grigoriu S, Bond R, Cossio P, Chen JA, Ly N, Hummer G, Page R, Cyert MS, Peti W. The molecular mechanism of substrate engagement and immunosuppressant inhibition of calcineurin. PLoS Biol 2013; 11:e1001492. [PMID: 23468591 PMCID: PMC3582496 DOI: 10.1371/journal.pbio.1001492] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 01/10/2013] [Indexed: 11/18/2022] Open
Abstract
Ser/thr phosphatases dephosphorylate their targets with high specificity, yet the structural and sequence determinants of phosphosite recognition are poorly understood. Calcineurin (CN) is a conserved Ca(2+)/calmodulin-dependent ser/thr phosphatase and the target of immunosuppressants, FK506 and cyclosporin A (CSA). To investigate CN substrate recognition we used X-ray crystallography, biochemistry, modeling, and in vivo experiments to study A238L, a viral protein inhibitor of CN. We show that A238L competitively inhibits CN by occupying a critical substrate recognition site, while leaving the catalytic center fully accessible. Critically, the 1.7 Å structure of the A238L-CN complex reveals how CN recognizes residues in A238L that are analogous to a substrate motif, "LxVP." The structure enabled modeling of a peptide substrate bound to CN, which predicts substrate interactions beyond the catalytic center. Finally, this study establishes that "LxVP" sequences and immunosuppressants bind to the identical site on CN. Thus, FK506, CSA, and A238L all prevent "LxVP"-mediated substrate recognition by CN, highlighting the importance of this interaction for substrate dephosphorylation. Collectively, this work presents the first integrated structural model for substrate selection and dephosphorylation by CN and lays the groundwork for structure-based development of new CN inhibitors.
Collapse
Affiliation(s)
- Simina Grigoriu
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, United States of America
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Rachel Bond
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Pilar Cossio
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jennifer A. Chen
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Nina Ly
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Gerhard Hummer
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Rebecca Page
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Martha S. Cyert
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Wolfgang Peti
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, United States of America
- Department of Chemistry, Brown University, Providence, Rhode Island, United States of America
| |
Collapse
|
33
|
Gancedo JM. Biological roles of cAMP: variations on a theme in the different kingdoms of life. Biol Rev Camb Philos Soc 2013; 88:645-68. [PMID: 23356492 DOI: 10.1111/brv.12020] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 12/19/2012] [Accepted: 12/20/2012] [Indexed: 12/18/2022]
Abstract
Cyclic AMP (cAMP) plays a key regulatory role in most types of cells; however, the pathways controlled by cAMP may present important differences between organisms and between tissues within a specific organism. Changes in cAMP levels are caused by multiple triggers, most affecting adenylyl cyclases, the enzymes that synthesize cAMP. Adenylyl cyclases form a large and diverse family including soluble forms and others with one or more transmembrane domains. Regulatory mechanisms for the soluble adenylyl cyclases involve either interaction with diverse proteins, as happens in Escherichia coli or yeasts, or with calcium or bicarbonate ions, as occurs in mammalian cells. The transmembrane cyclases can be regulated by a variety of proteins, among which the α subunit and the βγ complex from G proteins coupled to membrane receptors are prominent. cAMP levels also are controlled by the activity of phosphodiesterases, enzymes that hydrolyze cAMP. Phosphodiesterases can be regulated by cAMP, cGMP or calcium-calmodulin or by phosphorylation by different protein kinases. Regulation through cAMP depends on its binding to diverse proteins, its proximal targets, this in turn causing changes in a variety of distal targets. Specifically, binding of cAMP to regulatory subunits of cAMP-dependent protein kinases (PKAs) affects the activity of substrates of PKA, binding to exchange proteins directly activated by cAMP (Epac) regulates small GTPases, binding to transcription factors such as the cAMP receptor protein (CRP) or the virulence factor regulator (Vfr) modifies the rate of transcription of certain genes, while cAMP binding to ion channels modulates their activity directly. Further studies on cAMP signalling will have important implications, not only for advancing fundamental knowledge but also for identifying targets for the development of new therapeutic agents.
Collapse
Affiliation(s)
- Juana M Gancedo
- Department of Metabolism and Cell Signalling, Instituto de Investigaciones Biomédicas Alberto Sols CSIC-UAM, Madrid 28029, Spain.
| |
Collapse
|
34
|
Bodvard K, Jörhov A, Blomberg A, Molin M, Käll M. The yeast transcription factor Crz1 is activated by light in a Ca2+/calcineurin-dependent and PKA-independent manner. PLoS One 2013; 8:e53404. [PMID: 23335962 PMCID: PMC3546054 DOI: 10.1371/journal.pone.0053404] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 11/28/2012] [Indexed: 11/19/2022] Open
Abstract
Light in the visible range can be stressful to non-photosynthetic organisms. The yeast Saccharomyces cerevisiae has earlier been reported to respond to blue light via activation of the stress-regulated transcription factor Msn2p. Environmental changes also induce activation of calcineurin, a Ca(2+)/calmodulin dependent phosphatase, which in turn controls gene transcription by dephosphorylating the transcription factor Crz1p. We investigated the connection between cellular stress caused by blue light and Ca(2+) signalling in yeast by monitoring the nuclear localization dynamics of Crz1p, Msn2p and Msn4p. The three proteins exhibit distinctly different stress responses in relation to light exposure. Msn2p, and to a lesser degree Msn4p, oscillate rapidly between the nucleus and the cytoplasm in an apparently stochastic fashion. Crz1p, in contrast, displays a rapid and permanent nuclear localization induced by illumination, which triggers Crz1p-dependent transcription of its target gene CMK2. Moreover, increased extracellular Ca(2+) levels stimulates the light-induced responses of all three transcription factors, e.g. Crz1p localizes much quicker to the nucleus and a larger fraction of cells exhibits permanent Msn2p nuclear localization at higher Ca(2+) concentration. Studies in mutants lacking Ca(2+) transporters indicate that influx of extracellular Ca(2+) is crucial for the initial stages of light-induced Crz1p nuclear localization, while mobilization of intracellular Ca(2+) stores appears necessary for a sustained response. Importantly, we found that Crz1p nuclear localization is dependent on calcineurin and the carrier protein Nmd5p, while not being affected by increased protein kinase A activity (PKA), which strongly inhibits light-induced nuclear localization of Msn2/4p. We conclude that the two central signalling pathways, cAMP-PKA-Msn2/4 and Ca(2+)-calcineurin-Crz1, are both activated by blue light illumination.
Collapse
Affiliation(s)
- Kristofer Bodvard
- Department of Applied Physics, Chalmers University of Technology, Göteborg, Sweden.
| | | | | | | | | |
Collapse
|
35
|
The calcineurin dependent transcription factor TacA is involved in development and the stress response of Dictyostelium discoideum. Eur J Cell Biol 2012; 91:789-99. [DOI: 10.1016/j.ejcb.2012.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 07/20/2012] [Accepted: 07/24/2012] [Indexed: 11/20/2022] Open
|
36
|
The Ca2+/calcineurin-dependent signaling pathway in the gray mold Botrytis cinerea: the role of calcipressin in modulating calcineurin activity. PLoS One 2012; 7:e41761. [PMID: 22844520 PMCID: PMC3402410 DOI: 10.1371/journal.pone.0041761] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 06/25/2012] [Indexed: 12/31/2022] Open
Abstract
In the gray mold fungus Botrytis cinerea the Gα subunit Bcg1 of a heterotrimeric G protein is an upstream activator of the Ca2+/calmodulin-dependent phosphatase calcineurin. In this study we focused on the functional characterization of the catalytic subunit of calcineurin (BcCnA) and its putative regulator calcipressin (BcRcn1). We deleted the genes encoding both proteins to examine their role concerning growth, differentiation and virulence. The ΔbccnA mutant shows a severe growth defect, does not produce conidia and is avirulent, while the loss of BcRcn1 caused retardation of hyphal growth and delayed infection of host plants, but had no impact on conidiation and sclerotia formation. Expression of several calcineurin-dependent genes and bccnA itself is positively affected by BcRcn1. Complementation of the Δbcrcn1 mutant with a GFP-BcRcn1 fusion construct revealed that BcRcn1 is localized in the cytoplasm and accumulates around the nuclei. Furthermore, we showed that BcCnA physically interacts with BcRcn1 and the regulatory subunit of calcineurin, BcCnB. We investigated the impact of several protein domains characteristic for modulation and activation of BcCnA via BcRcn1, such as the phosphorylation sites and the calcineurin-docking site, by physical interaction studies between BcCnA and wild-type and mutated copies of BcRcn1. Based on the observed phenotypes we conclude that BcRcn1 acts as a positive modulator of BcCnA and the Ca2+/calcineurin-mediated signal transduction in B. cinerea, and that both proteins regulate fungal development and virulence.
Collapse
|
37
|
Koike A, Kato T, Sugiura R, Ma Y, Tabata Y, Ohmoto K, Sio SO, Kuno T. Genetic screening for regulators of Prz1, a transcriptional factor acting downstream of calcineurin in fission yeast. J Biol Chem 2012; 287:19294-303. [PMID: 22496451 PMCID: PMC3365961 DOI: 10.1074/jbc.m111.310615] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 04/03/2012] [Indexed: 12/18/2022] Open
Abstract
Calcineurin phosphatase plays crucial roles in a wide variety of cell types and organisms. Dephosphorylation of the nuclear factor of activated T-cell (NFAT) family of transcriptional factors by calcineurin is essential for activating immune-responsive genes in mammals. NFAT activity is also regulated by diverse signaling pathways, which affect NFAT kinases and nuclear partner proteins. In fission yeast, calcineurin dephosphorylates and activates Prz1, a C2H2-type zinc finger transcriptional factor. Calcineurin-Prz1 signaling regulates the expression of the Pmc1 Ca(2+) pump. Prz1-overexpressing cells showed extremely slow growth and high transcriptional activity of Prz1 in the absence of stimulation. Here, we isolated seven genes as dosage-dependent suppressors of this slow growth phenotype. These seven genes encode Rad24, Rad25, Pka1, Msn5 (SPAC328.01c), Pac1, Ape2, and Tfs1. All of them decreased the high transcriptional activity caused by Prz1 overexpression. Overexpression of Pka1, Rad24, and Rad25 also repressed the Ca(2+)-induced transcriptional activity in cells with Prz1 expressed at wild-type levels. Knock-out of rad24 or rad25 significantly enhanced the transcriptional activity of Prz1, whereas knock-out or mutation of other genes did not enhance the activity. The 14-3-3 proteins, Rad24 and Rad25, bound Prz1 and the Rad24-binding site located at residues 421-426 of Prz1. In msn5 deletion mutants, GFP-Prz1 localized at nucleus in the absence of Ca(2+) stimulation, suggesting that Msn5 functions as an exportin for Prz1. In summary, our data suggest that Rad24 and Rad25 negatively regulate Prz1 and that Pka1, Msn5, Pac1, Tfs1, and Ape2 also regulate Prz1.
Collapse
Affiliation(s)
- Atsushi Koike
- Division of Molecular Pharmacology and Pharmacogenomics, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kusunoki-cho 6-5-1, Chuo-ku, Kobe 650-0017, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Marquina M, González A, Barreto L, Gelis S, Muñoz I, Ruiz A, Álvarez MC, Ramos J, Ariño J. Modulation of yeast alkaline cation tolerance by Ypi1 requires calcineurin. Genetics 2012; 190:1355-64. [PMID: 22367039 PMCID: PMC3316648 DOI: 10.1534/genetics.112.138370] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 01/29/2012] [Indexed: 12/24/2022] Open
Abstract
Ypi1 was discovered as an essential protein able to act as a regulatory subunit of the Saccharomyces cerevisiae type 1 protein phosphatase Glc7 and play a key role in mitosis. We show here that partial depletion of Ypi1 causes lithium sensitivity and that high levels of this protein confer a lithium-tolerant phenotype to yeast cells. Remarkably, this phenotype was independent of the role of Ypi1 as a Glc7 regulatory subunit. Lithium tolerance in cells overexpressing Ypi1 was caused by a combination of increased efflux of lithium, mediated by augmented expression of the alkaline cation ATPase ENA1, and decreased lithium influx through the Trk1,2 high-affinity potassium transporters. Deletion of CNB1, encoding the regulatory subunit of the calcineurin phosphatase, blocked Ypi1-induced expression of ENA1, normalized Li(+) fluxes, and abolished the Li(+) hypertolerant phenotype of Ypi1-overexpressing cells. These results point to a complex role of Ypi1 on the regulation of cation homeostasis, largely mediated by the calcineurin phosphatase.
Collapse
Affiliation(s)
- Maribel Marquina
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
| | - Asier González
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
| | - Lina Barreto
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
| | - Samuel Gelis
- Departamento de Microbiología, Universidad de Córdoba, Campus Rabanales, 14071 Córdoba, Spain
| | - Iván Muñoz
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
| | - Amparo Ruiz
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
| | - Mari Carmen Álvarez
- Departamento de Microbiología, Universidad de Córdoba, Campus Rabanales, 14071 Córdoba, Spain
| | - José Ramos
- Departamento de Microbiología, Universidad de Córdoba, Campus Rabanales, 14071 Córdoba, Spain
| | - Joaquín Ariño
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
| |
Collapse
|
39
|
|
40
|
Juvvadi PR, Fortwendel JR, Rogg LE, Burns KA, Randell SH, Steinbach WJ. Localization and activity of the calcineurin catalytic and regulatory subunit complex at the septum is essential for hyphal elongation and proper septation in Aspergillus fumigatus. Mol Microbiol 2011; 82:1235-59. [PMID: 22066998 DOI: 10.1111/j.1365-2958.2011.07886.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Calcineurin, a heterodimer composed of the catalytic (CnaA) and regulatory (CnaB) subunits, plays key roles in growth, virulence and stress responses of fungi. To investigate the contribution of CnaA and CnaB to hyphal growth and septation, ΔcnaB and ΔcnaAΔcnaB strains of Aspergillus fumigatus were constructed. CnaA colocalizes to the contractile actin ring early during septation and remains at the centre of the mature septum. While CnaB's septal localization is CnaA-dependent, CnaA's septal localization is CnaB-independent, but CnaB is required for CnaA's function at the septum. Catalytic null mutations in CnaA caused stunted growth despite septal localization of the calcineurin complex, indicating the requirement of calcineurin activity at the septum. Compared to the ΔcnaA and ΔcnaB strains, the ΔcnaAΔcnaB strain displayed more defective growth and aberrant septation. While three Ca(2+) -binding motifs in CnaB were sufficient for its association with CnaA at the septum, the amino-terminal arginine-rich domains (16-RRRR-19 and 44-RLRKR-48) are dispensable for septal localization, yet required for complete functionality. Mutation of the 51-KLDK-54 motif in CnaB causes its mislocalization from the septum to the nucleus, suggesting it is a nuclear export signal sequence. These findings confirm a cooperative role for the calcineurin complex in regulating hyphal growth and septation.
Collapse
Affiliation(s)
- Praveen Rao Juvvadi
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | | | | | | | | | | |
Collapse
|
41
|
Casado C, González A, Platara M, Ruiz A, Ariño J. The role of the protein kinase A pathway in the response to alkaline pH stress in yeast. Biochem J 2011; 438:523-33. [PMID: 21749328 PMCID: PMC3253439 DOI: 10.1042/bj20110607] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2010] [Revised: 07/11/2011] [Accepted: 07/13/2011] [Indexed: 11/17/2022]
Abstract
Exposure of Saccharomyces cerevisiae to alkaline pH provokes a stress condition that generates a compensatory reaction. In the present study we examined a possible role for the PKA (protein kinase A) pathway in this response. Phenotypic analysis revealed that mutations that activate the PKA pathway (ira1 ira2, bcy1) tend to cause sensitivity to alkaline pH, whereas its deactivation enhances tolerance to this stress. We observed that alkalinization causes a transient decrease in cAMP, the main regulator of the pathway. Alkaline pH causes rapid nuclear localization of the PKA-regulated Msn2 transcription factor which, together with Msn4, mediates a general stress response by binding with STRE (stress response element) sequences in many promoters. Consequently, a synthetic STRE-LacZ reporter shows a rapid induction in response to alkaline stress. A msn2 msn4 mutant is sensitive to alkaline pH, and transcriptomic analysis reveals that after 10 min of alkaline stress, the expression of many induced genes (47%) depends, at least in part, on the presence of Msn2 and Msn4. Taken together, these results demonstrate that inhibition of the PKA pathway by alkaline pH represents a substantial part of the adaptive response to this kind of stress and that this response involves Msn2/Msn4-mediated genome expression remodelling. However, the relevance of attenuation of PKA in high pH tolerance is probably not restricted to regulation of Msn2 function.
Collapse
Key Words
- alkaline stress
- gene expression
- msn2
- msn4
- protein kinase a (pka)
- saccharomyces cerevisiae
- transcription factor
- cdre, calcineurin-dependent response element
- cy3, indocarbocyanine
- cy5, indodicarbocyanine
- gap, gtpase activating proteins
- gef, guanine-nucleotide-exchange factor
- gfp, green fluorescent protein
- go, gene ontology
- pka, protein kinase a
- stre, stress response element
- tor, target of rapamycin
Collapse
Affiliation(s)
- Carlos Casado
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra 08193, Barcelona, Spain
| | - Asier González
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra 08193, Barcelona, Spain
| | - Maria Platara
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra 08193, Barcelona, Spain
| | - Amparo Ruiz
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra 08193, Barcelona, Spain
| | - Joaquín Ariño
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra 08193, Barcelona, Spain
| |
Collapse
|
42
|
Shapiro RS, Robbins N, Cowen LE. Regulatory circuitry governing fungal development, drug resistance, and disease. Microbiol Mol Biol Rev 2011; 75:213-67. [PMID: 21646428 PMCID: PMC3122626 DOI: 10.1128/mmbr.00045-10] [Citation(s) in RCA: 384] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Pathogenic fungi have become a leading cause of human mortality due to the increasing frequency of fungal infections in immunocompromised populations and the limited armamentarium of clinically useful antifungal drugs. Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus are the leading causes of opportunistic fungal infections. In these diverse pathogenic fungi, complex signal transduction cascades are critical for sensing environmental changes and mediating appropriate cellular responses. For C. albicans, several environmental cues regulate a morphogenetic switch from yeast to filamentous growth, a reversible transition important for virulence. Many of the signaling cascades regulating morphogenesis are also required for cells to adapt and survive the cellular stresses imposed by antifungal drugs. Many of these signaling networks are conserved in C. neoformans and A. fumigatus, which undergo distinct morphogenetic programs during specific phases of their life cycles. Furthermore, the key mechanisms of fungal drug resistance, including alterations of the drug target, overexpression of drug efflux transporters, and alteration of cellular stress responses, are conserved between these species. This review focuses on the circuitry regulating fungal morphogenesis and drug resistance and the impact of these pathways on virulence. Although the three human-pathogenic fungi highlighted in this review are those most frequently encountered in the clinic, they represent a minute fraction of fungal diversity. Exploration of the conservation and divergence of core signal transduction pathways across C. albicans, C. neoformans, and A. fumigatus provides a foundation for the study of a broader diversity of pathogenic fungi and a platform for the development of new therapeutic strategies for fungal disease.
Collapse
Affiliation(s)
| | | | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| |
Collapse
|
43
|
Glucose-induced calcium influx in budding yeast involves a novel calcium transport system and can activate calcineurin. Cell Calcium 2011; 49:376-86. [DOI: 10.1016/j.ceca.2011.03.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Revised: 02/15/2011] [Accepted: 03/17/2011] [Indexed: 11/16/2022]
|
44
|
Martínez-Montañés F, Pascual-Ahuir A, Proft M. Toward a genomic view of the gene expression program regulated by osmostress in yeast. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2010; 14:619-27. [PMID: 20726780 DOI: 10.1089/omi.2010.0046] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Osmostress triggers profound adaptive changes in the physiology of the cell with a great impact on gene expression. Saccharomyces cerevisiae has served as an instructive model system to unravel the complexity of the stress response at the transcriptional level. The main signal transduction pathways like the HOG (high osmolarity glycerol) MAP kinase cascade or the protein kinase A pathway regulate multiple specific transcription factors to accomplish large changes in the expression pattern of the genome. Transcription profiling and proteomic studies give us an idea about the impact of osmostress on gene expression and the overall protein composition. Recent genome wide location studies for several transcription factors and signaling kinases involved in the transcriptional stress response shed light on the genomic organization of the osmostress response at the level of the dynamic association of regulators with chromatin. Finally, global surveys of mRNA stability complete our picture of the mechanisms underlying the massive reprogramming of global gene expression, which leads to efficient adaptation to osmotic stress.
Collapse
Affiliation(s)
- Fernando Martínez-Montañés
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia, Consejo Superior de Investigaciones Científicas, Ciudad Politécnica de la Innovación, Ingeniero Fausto Elio s/n, Valencia, Spain
| | | | | |
Collapse
|
45
|
Ariño J. Integrative responses to high pH stress in S. cerevisiae. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2010; 14:517-23. [PMID: 20726779 DOI: 10.1089/omi.2010.0044] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The budding yeast Saccharomyces cerevisiae grows far better at acidic than at neutral or alkaline pH. Consequently, even a modest alkalinization of the medium represents a stressful situation for this yeast. In the past few years, data generated by a combination of genome-wide techniques has demonstrated that adaptive responses of S. cerevisiae to high pH stress involves extensive gene remodeling as a result of the fast activation of a number of stress-related signaling pathways, such as the Rim101, the Wsc1-Pkc1-Slt2 MAP kinase, and the calcium-activated calcineurin pathways. Alkalinization of the environment also disturbs nutrient homeostasis, as deduced from its impact on iron/copper, phosphate, and glucose uptake/utilization pathways. In this review we will examine these responses, their possible interactions, and the role that they play in tolerance to high pH stress.
Collapse
Affiliation(s)
- Joaquín Ariño
- Departament de Bioquímica i Biologia Molecular & Institut de Biotecnologia i Biomedicina, Universitat Autónoma de Barcelona, Barcelona, Spain.
| |
Collapse
|
46
|
Abstract
The maintenance of appropriate intracellular concentrations of alkali metal cations, principally K(+) and Na(+), is of utmost importance for living cells, since they determine cell volume, intracellular pH, and potential across the plasma membrane, among other important cellular parameters. Yeasts have developed a number of strategies to adapt to large variations in the concentrations of these cations in the environment, basically by controlling transport processes. Plasma membrane high-affinity K(+) transporters allow intracellular accumulation of this cation even when it is scarce in the environment. Exposure to high concentrations of Na(+) can be tolerated due to the existence of an Na(+), K(+)-ATPase and an Na(+), K(+)/H(+)-antiporter, which contribute to the potassium balance as well. Cations can also be sequestered through various antiporters into intracellular organelles, such as the vacuole. Although some uncertainties still persist, the nature of the major structural components responsible for alkali metal cation fluxes across yeast membranes has been defined within the last 20 years. In contrast, the regulatory components and their interactions are, in many cases, still unclear. Conserved signaling pathways (e.g., calcineurin and HOG) are known to participate in the regulation of influx and efflux processes at the plasma membrane level, even though the molecular details are obscure. Similarly, very little is known about the regulation of organellar transport and homeostasis of alkali metal cations. The aim of this review is to provide a comprehensive and up-to-date vision of the mechanisms responsible for alkali metal cation transport and their regulation in the model yeast Saccharomyces cerevisiae and to establish, when possible, comparisons with other yeasts and higher plants.
Collapse
|
47
|
Life in the midst of scarcity: adaptations to nutrient availability in Saccharomyces cerevisiae. Curr Genet 2010; 56:1-32. [PMID: 20054690 DOI: 10.1007/s00294-009-0287-1] [Citation(s) in RCA: 163] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 12/18/2009] [Accepted: 12/19/2009] [Indexed: 12/27/2022]
Abstract
Cells of all living organisms contain complex signal transduction networks to ensure that a wide range of physiological properties are properly adapted to the environmental conditions. The fundamental concepts and individual building blocks of these signalling networks are generally well-conserved from yeast to man; yet, the central role that growth factors and hormones play in the regulation of signalling cascades in higher eukaryotes is executed by nutrients in yeast. Several nutrient-controlled pathways, which regulate cell growth and proliferation, metabolism and stress resistance, have been defined in yeast. These pathways are integrated into a signalling network, which ensures that yeast cells enter a quiescent, resting phase (G0) to survive periods of nutrient scarceness and that they rapidly resume growth and cell proliferation when nutrient conditions become favourable again. A series of well-conserved nutrient-sensory protein kinases perform key roles in this signalling network: i.e. Snf1, PKA, Tor1 and Tor2, Sch9 and Pho85-Pho80. In this review, we provide a comprehensive overview on the current understanding of the signalling processes mediated via these kinases with a particular focus on how these individual pathways converge to signalling networks that ultimately ensure the dynamic translation of extracellular nutrient signals into appropriate physiological responses.
Collapse
|
48
|
Egan JD, García-Pedrajas MD, Andrews DL, Gold SE. Calcineurin is an antagonist to PKA protein phosphorylation required for postmating filamentation and virulence, while PP2A is required for viability in Ustilago maydis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2009; 22:1293-1301. [PMID: 19737102 DOI: 10.1094/mpmi-22-10-1293] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Ustilago maydis is a dimorphic basidiomycete and the causal agent of corn smut disease. It serves as a genetic model for understanding dimorphism, pathogenicity, and mating response in filamentous fungi. Previous studies indicated the importance of regulated cAMP-dependent protein kinase A (PKA) for filamentous growth and pathogenicity in U. maydis. The roles of two protein phosphatases that potentially act antagonistically to PKA were assessed. A reverse genetics approach to mutate the catalytic subunits of calcineurin (CN, protein phosphatase [PP]2B) and PP2A in U. maydis was employed. A mutation in the CN catalytic subunit ucn1 caused a dramatic multiple-budding phenotype and mating between two ucn1 mutants was severely reduced. The pathogenicity of ucn1 mutant strains was also severely reduced, even in a solopathogenic haploid strain. Importantly, mutations disrupting protein phosphorylation by PKA were epistatic to ucn1 mutation, indicating a major role of ucn1 as a PKA antagonistic phosphatase. Genetic and inhibitor studies indicated that the U. maydis PP2A catalytic subunit gene (upa2) was essential.
Collapse
Affiliation(s)
- John D Egan
- Department of Plant Pathology, University of Georgia, Athens, GA 30602-7274, USA
| | | | | | | |
Collapse
|
49
|
Jain D, Roy N, Chattopadhyay D. CaZF, a plant transcription factor functions through and parallel to HOG and calcineurin pathways in Saccharomyces cerevisiae to provide osmotolerance. PLoS One 2009; 4:e5154. [PMID: 19365545 PMCID: PMC2664467 DOI: 10.1371/journal.pone.0005154] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2009] [Accepted: 03/13/2009] [Indexed: 01/19/2023] Open
Abstract
Salt-sensitive yeast mutants were deployed to characterize a gene encoding a C2H2 zinc finger protein (CaZF) that is differentially expressed in a drought-tolerant variety of chickpea (Cicer arietinum) and provides salinity-tolerance in transgenic tobacco. In Saccharomyces cerevisiae most of the cellular responses to hyper-osmotic stress is regulated by two interconnected pathways involving high osmolarity glycerol mitogen-activated protein kinase (Hog1p) and Calcineurin (CAN), a Ca(2+)/calmodulin-regulated protein phosphatase 2B. In this study, we report that heterologous expression of CaZF provides osmotolerance in S. cerevisiae through Hog1p and Calcineurin dependent as well as independent pathways. CaZF partially suppresses salt-hypersensitive phenotypes of hog1, can and hog1can mutants and in conjunction, stimulates HOG and CAN pathway genes with subsequent accumulation of glycerol in absence of Hog1p and CAN. CaZF directly binds to stress response element (STRE) to activate STRE-containing promoter in yeast. Transactivation and salt tolerance assays of CaZF deletion mutants showed that other than the transactivation domain a C-terminal domain composed of acidic and basic amino acids is also required for its function. Altogether, results from this study suggests that CaZF is a potential plant salt-tolerance determinant and also provide evidence that in budding yeast expression of HOG and CAN pathway genes can be stimulated in absence of their regulatory enzymes to provide osmotolerance.
Collapse
Affiliation(s)
- Deepti Jain
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Nilanjan Roy
- National Institute for Pharmaceutical Education and Research, SAS Nagar, Punjab, India
| | | |
Collapse
|
50
|
Choi J, Kim Y, Kim S, Park J, Lee YH. MoCRZ1, a gene encoding a calcineurin-responsive transcription factor, regulates fungal growth and pathogenicity of Magnaporthe oryzae. Fungal Genet Biol 2008; 46:243-54. [PMID: 19111943 DOI: 10.1016/j.fgb.2008.11.010] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2008] [Revised: 11/18/2008] [Accepted: 11/27/2008] [Indexed: 11/30/2022]
Abstract
Ca(2+)-dependent signaling plays important roles in cellular development and metabolism in fungi. Pharmacological and molecular evidence clearly indicates that Ca(2+)-dependent signaling is required for infection-related development and pathogenicity in the rice blast fungus Magnaporthe oryzae. However, little information is available on downstream regulators in the Ca(2+)-dependent signaling pathway. To understand the role of a calcineurin-dependent transcription factor in the rice blast fungus, an ortholog of Saccharomyces cerevisiae CRZ1 in M. oryzae, MoCRZ1, was identified and functionally characterized. The Deltamocrz1 mutant exhibited impaired growth in the presence of Ca(2+) ions or cell wall perturbing agents. The Deltamocrz1 mutant also showed reduced conidiation and reduced pathogenicity, which is mainly due to a defect in host penetration. MoCRZ1 fused to EGFP was trans-localized into the nucleus in a Ca(2+)/calcineurin-dependent manner. The MoCRZ1 gene is also required for the calcineurin-dependent transcriptional induction of FKS1, a gene encoding a beta-1,3 glucan synthase, CHS2 and CHS4, genes encoding two chitin synthases, and PMC and PMR gene families encoding P-type ATPases in response to Ca(2+). These results suggest that MoCRZ1 is a downstream regulator in Ca(2+)-dependent signaling for pathogenicity in M. oryzae, and its biochemical mechanisms are well conserved among fungal species.
Collapse
Affiliation(s)
- Jinhee Choi
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, Seoul National University, Seoul, South Korea
| | | | | | | | | |
Collapse
|