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Akhtar K, Ain NU, Prasad PVV, Naz M, Aslam MM, Djalovic I, Riaz M, Ahmad S, Varshney RK, He B, Wen R. Physiological, molecular, and environmental insights into plant nitrogen uptake, and metabolism under abiotic stresses. THE PLANT GENOME 2024; 17:e20461. [PMID: 38797919 DOI: 10.1002/tpg2.20461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/27/2024] [Accepted: 04/09/2024] [Indexed: 05/29/2024]
Abstract
Nitrogen (N) as an inorganic macronutrient is inevitable for plant growth, development, and biomass production. Many external factors and stresses, such as acidity, alkalinity, salinity, temperature, oxygen, and rainfall, affect N uptake and metabolism in plants. The uptake of ammonium (NH4 +) and nitrate (NO3 -) in plants mainly depends on soil properties. Under the sufficient availability of NO3 - (>1 mM), low-affinity transport system is activated by gene network NRT1, and under low NO3 - availability (<1 mM), high-affinity transport system starts functioning encoded by NRT2 family of genes. Further, under limited N supply due to edaphic and climatic factors, higher expression of the AtNRT2.4 and AtNRT2.5T genes of the NRT2 family occur and are considered as N remobilizing genes. The NH4 + ion is the final form of N assimilated by cells mediated through the key enzymes glutamine synthetase and glutamate synthase. The WRKY1 is a major transcription factor of the N regulation network in plants. However, the transcriptome and metabolite profiles show variations in N assimilation metabolites, including glycine, glutamine, and aspartate, under abiotic stresses. The overexpression of NO3 - transporters (OsNRT2.3a and OsNRT1.1b) can significantly improve the biomass and yield of various crops. Altering the expression levels of genes could be a valuable tool to improve N metabolism under the challenging conditions of soil and environment, such as unfavorable temperature, drought, salinity, heavy metals, and nutrient stress.
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Affiliation(s)
- Kashif Akhtar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Noor Ul Ain
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - P V Vara Prasad
- Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification, Kansas State University, Manhattan, Kansas, USA
| | - Misbah Naz
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Mehtab Muhammad Aslam
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences & Technology, University of Missouri, Columbia, Missouri, USA
| | - Ivica Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Novi Sad, Serbia
| | - Muhammad Riaz
- Department of Environmental Sciences and Engineering, Government College University Faisalabad, Faisalabad, Pakistan
| | - Shakeel Ahmad
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Bing He
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, China
| | - Ronghui Wen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Life Science and Technology, Guangxi University, Nanning, China
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Cruz-Leite VRM, Moreira ALE, Silva LOS, Inácio MM, Parente-Rocha JA, Ruiz OH, Weber SS, Soares CMDA, Borges CL. Proteomics of Paracoccidioides lutzii: Overview of Changes Triggered by Nitrogen Catabolite Repression. J Fungi (Basel) 2023; 9:1102. [PMID: 37998907 PMCID: PMC10672198 DOI: 10.3390/jof9111102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
Members of the Paracoccidioides complex are the causative agents of Paracoccidioidomycosis (PCM), a human systemic mycosis endemic in Latin America. Upon initial contact with the host, the pathogen needs to uptake micronutrients. Nitrogen is an essential source for biosynthetic pathways. Adaptation to nutritional stress is a key feature of fungi in host tissues. Fungi utilize nitrogen sources through Nitrogen Catabolite Repression (NCR). NCR ensures the scavenging, uptake and catabolism of alternative nitrogen sources, when preferential ones, such as glutamine or ammonium, are unavailable. The NanoUPLC-MSE proteomic approach was used to investigate the NCR response of Paracoccidioides lutzii after growth on proline or glutamine as a nitrogen source. A total of 338 differentially expressed proteins were identified. P. lutzii demonstrated that gluconeogenesis, β-oxidation, glyoxylate cycle, adhesin-like proteins, stress response and cell wall remodeling were triggered in NCR-proline conditions. In addition, within macrophages, yeast cells trained under NCR-proline conditions showed an increased ability to survive. In general, this study allows a comprehensive understanding of the NCR response employed by the fungus to overcome nutritional starvation, which in the human host is represented by nutritional immunity. In turn, the pathogen requires rapid adaptation to the changing microenvironment induced by macrophages to achieve successful infection.
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Affiliation(s)
- Vanessa Rafaela Milhomem Cruz-Leite
- Department of Biochemistry and Molecular Biology, Institute of Biological Sciences II, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (A.L.E.M.); (L.O.S.S.); (M.M.I.); (J.A.P.-R.); (C.M.d.A.S.)
| | - André Luís Elias Moreira
- Department of Biochemistry and Molecular Biology, Institute of Biological Sciences II, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (A.L.E.M.); (L.O.S.S.); (M.M.I.); (J.A.P.-R.); (C.M.d.A.S.)
| | - Lana O’Hara Souza Silva
- Department of Biochemistry and Molecular Biology, Institute of Biological Sciences II, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (A.L.E.M.); (L.O.S.S.); (M.M.I.); (J.A.P.-R.); (C.M.d.A.S.)
| | - Moises Morais Inácio
- Department of Biochemistry and Molecular Biology, Institute of Biological Sciences II, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (A.L.E.M.); (L.O.S.S.); (M.M.I.); (J.A.P.-R.); (C.M.d.A.S.)
- Estácio de Goiás University Center—FESGO, Goiânia 74063-010, GO, Brazil
| | - Juliana Alves Parente-Rocha
- Department of Biochemistry and Molecular Biology, Institute of Biological Sciences II, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (A.L.E.M.); (L.O.S.S.); (M.M.I.); (J.A.P.-R.); (C.M.d.A.S.)
| | - Orville Hernandez Ruiz
- MICROBA Research Group, Cellular and Molecular Biology Unit, Department of Microbiology, School of Microbiology, University of Antioquia, Medellín 050010, Colombia;
| | - Simone Schneider Weber
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande 79304-902, MS, Brazil;
| | - Célia Maria de Almeida Soares
- Department of Biochemistry and Molecular Biology, Institute of Biological Sciences II, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (A.L.E.M.); (L.O.S.S.); (M.M.I.); (J.A.P.-R.); (C.M.d.A.S.)
| | - Clayton Luiz Borges
- Department of Biochemistry and Molecular Biology, Institute of Biological Sciences II, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (A.L.E.M.); (L.O.S.S.); (M.M.I.); (J.A.P.-R.); (C.M.d.A.S.)
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Amino Acid Sensing and Assimilation by the Fungal Pathogen Candida albicans in the Human Host. Pathogens 2021; 11:pathogens11010005. [PMID: 35055954 PMCID: PMC8781990 DOI: 10.3390/pathogens11010005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/17/2021] [Accepted: 12/19/2021] [Indexed: 01/04/2023] Open
Abstract
Nutrient uptake is essential for cellular life and the capacity to perceive extracellular nutrients is critical for coordinating their uptake and metabolism. Commensal fungal pathogens, e.g., Candida albicans, have evolved in close association with human hosts and are well-adapted to using diverse nutrients found in discrete host niches. Human cells that cannot synthesize all amino acids require the uptake of the “essential amino acids” to remain viable. Consistently, high levels of amino acids circulate in the blood. Host proteins are rich sources of amino acids but their use depends on proteases to cleave them into smaller peptides and free amino acids. C. albicans responds to extracellular amino acids by pleiotropically enhancing their uptake and derive energy from their catabolism to power opportunistic virulent growth. Studies using Saccharomyces cerevisiae have established paradigms to understand metabolic processes in C. albicans; however, fundamental differences exist. The advent of CRISPR/Cas9-based methods facilitate genetic analysis in C. albicans, and state-of-the-art molecular biological techniques are being applied to directly examine growth requirements in vivo and in situ in infected hosts. The combination of divergent approaches can illuminate the biological roles of individual cellular components. Here we discuss recent findings regarding nutrient sensing with a focus on amino acid uptake and metabolism, processes that underlie the virulence of C. albicans.
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Silao FGS, Ryman K, Jiang T, Ward M, Hansmann N, Molenaar C, Liu NN, Chen C, Ljungdahl PO. Correction: Glutamate dehydrogenase (Gdh2)-dependent alkalization is dispensable for escape from macrophages and virulence of Candida albicans. PLoS Pathog 2021; 17:e1009877. [PMID: 34460867 PMCID: PMC8405231 DOI: 10.1371/journal.ppat.1009877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.ppat.1008328.].
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Santos FJPDL, García-Ortega LF, Robledo-Márquez K, Guzmán-Moreno J, Riego-Ruiz L. Transcriptome Analysis Unveils Gln3 Role in Amino Acids Assimilation and Fluconazole Resistance in Candida glabrata. J Microbiol Biotechnol 2021; 31:659-666. [PMID: 33879640 PMCID: PMC9705932 DOI: 10.4014/jmb.2012.12034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 12/15/2022]
Abstract
After Candida albicans, Candida glabrata is one of the most common fungal species associated with candidemia in nosocomial infections. Rapid acquisition of nutrients from the host is important for the survival of pathogens which possess the metabolic flexibility to assimilate different carbon and nitrogen compounds. In Saccharomyces cerevisiae, nitrogen assimilation is controlled through a mechanism known as Nitrogen Catabolite Repression (NCR). NCR is coordinated by the action of four GATA factors; two positive regulators, Gat1 and Gln3, and two negative regulators, Gzf3 and Dal80. A mechanism in C. glabrata similar to NCR in S. cerevisiae has not been broadly studied. We previously showed that in C. glabrata, Gln3, and not Gat1, has a major role in nitrogen assimilation as opposed to what has been observed in S. cerevisiae in which both factors regulate NCR-sensitive genes. Here, we expand the knowledge about the role of Gln3 from C. glabrata through the transcriptional analysis of BG14 and gln3Δ strains. Approximately, 53.5% of the detected genes were differentially expressed (DEG). From these DEG, amino acid metabolism and ABC transporters were two of the most enriched KEGG categories in our analysis (Up-DEG and Down-DEG, respectively). Furthermore, a positive role of Gln3 in AAA assimilation was described, as was its role in the transcriptional regulation of ARO8. Finally, an unexpected negative role of Gln3 in the gene regulation of ABC transporters CDR1 and CDR2 and its associated transcriptional regulator PDR1 was found. This observation was confirmed by a decreased susceptibility of the gln3Δ strain to fluconazole.
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Affiliation(s)
- Francisco J. Pérez-de los Santos
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), CINVESTAV, Mexico,División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A. C. (IPICYT), Mexico
| | - Luis Fernando García-Ortega
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), CINVESTAV, Mexico,Departamento de Ingeniería Genética, Centro de Investigación de Estudios Avanzados del IPN (CINVESTAV), Mexico
| | - Karina Robledo-Márquez
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A. C. (IPICYT), Mexico
| | - Jesús Guzmán-Moreno
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A. C. (IPICYT), Mexico
| | - Lina Riego-Ruiz
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A. C. (IPICYT), Mexico,Corresponding author Phone: +52 (444) 8342000 Fax: +52 (444) 8342010. E-mail:
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Glutamate dehydrogenase (Gdh2)-dependent alkalization is dispensable for escape from macrophages and virulence of Candida albicans. PLoS Pathog 2020; 16:e1008328. [PMID: 32936835 PMCID: PMC7521896 DOI: 10.1371/journal.ppat.1008328] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 09/28/2020] [Accepted: 08/14/2020] [Indexed: 11/19/2022] Open
Abstract
Candida albicans cells depend on the energy derived from amino acid catabolism to induce and sustain hyphal growth inside phagosomes of engulfing macrophages. The concomitant deamination of amino acids is thought to neutralize the acidic microenvironment of phagosomes, a presumed requisite for survival and initiation of hyphal growth. Here, in contrast to an existing model, we show that mitochondrial-localized NAD+-dependent glutamate dehydrogenase (GDH2) catalyzing the deamination of glutamate to α-ketoglutarate, and not the cytosolic urea amidolyase (DUR1,2), accounts for the observed alkalization of media when amino acids are the sole sources of carbon and nitrogen. C. albicans strains lacking GDH2 (gdh2-/-) are viable and do not extrude ammonia on amino acid-based media. Environmental alkalization does not occur under conditions of high glucose (2%), a finding attributable to glucose-repression of GDH2 expression and mitochondrial function. Consistently, inhibition of oxidative phosphorylation or mitochondrial translation by antimycin A or chloramphenicol, respectively, prevents alkalization. GDH2 expression and mitochondrial function are derepressed as glucose levels are lowered from 2% (~110 mM) to 0.2% (~11 mM), or when glycerol is used as primary carbon source. Using time-lapse microscopy, we document that gdh2-/- cells survive, filament and escape from primary murine macrophages at rates indistinguishable from wildtype. In intact hosts, such as in fly and murine models of systemic candidiasis, gdh2-/- mutants are as virulent as wildtype. Thus, although Gdh2 has a critical role in central nitrogen metabolism, Gdh2-catalyzed deamination of glutamate is surprisingly dispensable for escape from macrophages and virulence. Consistently, using the pH-sensitive dye (pHrodo), we observed no significant difference between wildtype and gdh2-/- mutants in phagosomal pH modulation. Following engulfment of fungal cells, the phagosomal compartment is rapidly acidified and hyphal growth initiates and sustained under consistently acidic conditions within phagosomes. Together, our results demonstrate that amino acid-dependent alkalization is not essential for hyphal growth, survival in macrophages and hosts. An accurate understanding of the microenvironment within macrophage phagosomes and the metabolic events underlying the survival of phagocytized C. albicans cells and their escape are critical to understanding the host-pathogen interactions that ultimately determine the pathogenic outcome. Candida albicans is a commensal component of the human microflora and the most common fungal pathogen. The incidence of candidiasis is low in healthy populations. Consequently, environmental factors, such as interactions with innate immune cells, play critical roles. Macrophages provide the first line of defense and rapidly internalize C. albicans cells within specialized intracellular compartments called phagosomes. The microenvironment within phagosomes is dynamic and ill defined, but has a low pH, and contains potent hydrolytic enzymes and oxidative stressors. Despite the inhospitable conditions, phagocytized C. albicans cells catabolize amino acids to obtain energy to survive and grow. Here, we have critically examined amino acid catabolism and ammonia extrusion in C. albicans, the latter is thought to neutralize the phagosomal pH and induce the switch of morphologies from round “yeast-like” to elongated hyphal cells that can pierce the phagosomal membrane leading to escape from macrophages. We report that Gdh2, which catalyzes the deamination of glutamate to α-ketoglutarate, is responsible for the observed environmental alkalization when C. albicans catabolize amino acids in vitro. However, the phagosomes formed as macrophages engulf wildtype or gdh2-/- cells rapidly become acidified, indicating that Gdh2 has no apparent role in modulating phagosomal pH. Strikingly, and similar to wildtype cells, gdh2-/- cells initiate and sustain hyphal growth enabling them to escape from macrophages. Also, Gdh2 is dispensable for virulent growth in systemic models of infection. These results provide new insights into host-pathogen interactions that determine the pathogenic outcome of C. albicans infections.
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Milhomem Cruz-Leite VR, Salem-Izacc SM, Novaes E, Neves BJ, de Almeida Brito W, O'Hara Souza Silva L, Paccez JD, Parente-Rocha JA, Pereira M, Maria de Almeida Soares C, Borges CL. Nitrogen Catabolite Repression in members of Paracoccidioides complex. Microb Pathog 2020; 149:104281. [PMID: 32585293 DOI: 10.1016/j.micpath.2020.104281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/24/2020] [Accepted: 05/25/2020] [Indexed: 01/15/2023]
Abstract
Paracoccidioides complex is a genus that comprises pathogenic fungi which are responsible by systemic disease Paracoccidioidomycosis. In host tissues, pathogenic fungi need to acquire nutrients in order to survive, making the uptake of nitrogen essential for their establishment and dissemination. Nitrogen utilization is employed by the alleviation of Nitrogen Catabolite Repression (NCR) which ensures the use of non-preferential or alternative nitrogen sources when preferential sources are not available. NCR is controlled by GATA transcription factors which act through GATA binding sites on promoter regions in NCR-sensitive genes. This process is responsible for encoding proteins involved with the scavenge, uptake and catabolism of a wide variety of non-preferential nitrogen sources. In this work, we predict the existence of AreA GATA transcription factor and feature the zinc finger domain by three-dimensional structure in Paracoccidioides. Furthermore, we demonstrate the putative genes involved with NCR response by means of in silico analysis. The gene expression profile under NCR conditions was evaluated. Demonstrating that P. lutzii supported transcriptional regulation and alleviated NCR in non-preferential nitrogen-dependent medium. The elucidation of NCR in members of Paracoccidioides complex will provide new knowledge about survival, dissemination and virulence for these pathogens with regard to nitrogen-scavenging strategies in the interactions of host-pathogens.
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Affiliation(s)
| | - Silvia Maria Salem-Izacc
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.
| | - Evandro Novaes
- Escola de Agronomia, Setor de Melhoramento de Plantas, Universidade Federal de Goiás, Campus II Samambaia, Rodovia Goiânia a Nova Veneza, Goiás, Brazil.
| | - Bruno Junior Neves
- Centro Universitário de Anápolis - UniEVANGÉLICA, Anápolis, Goiás, Brazil.
| | - Wesley de Almeida Brito
- Centro Universitário de Anápolis - UniEVANGÉLICA, Anápolis, Goiás, Brazil; Universidade Estadual de Goiás - UEG - CCET, Anápolis, Goiás, Brazil.
| | - Lana O'Hara Souza Silva
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.
| | - Juliano Domiraci Paccez
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.
| | - Juliana Alves Parente-Rocha
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.
| | - Maristela Pereira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.
| | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.
| | - Clayton Luiz Borges
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.
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Role of Amino Acid Metabolism in the Virulence of Human Pathogenic Fungi. CURRENT CLINICAL MICROBIOLOGY REPORTS 2019. [DOI: 10.1007/s40588-019-00124-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Silao FGS, Ward M, Ryman K, Wallström A, Brindefalk B, Udekwu K, Ljungdahl PO. Mitochondrial proline catabolism activates Ras1/cAMP/PKA-induced filamentation in Candida albicans. PLoS Genet 2019; 15:e1007976. [PMID: 30742618 PMCID: PMC6386415 DOI: 10.1371/journal.pgen.1007976] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/22/2019] [Accepted: 01/21/2019] [Indexed: 11/18/2022] Open
Abstract
Amino acids are among the earliest identified inducers of yeast-to-hyphal transitions in Candida albicans, an opportunistic fungal pathogen of humans. Here, we show that the morphogenic amino acids arginine, ornithine and proline are internalized and metabolized in mitochondria via a PUT1- and PUT2-dependent pathway that results in enhanced ATP production. Elevated ATP levels correlate with Ras1/cAMP/PKA pathway activation and Efg1-induced gene expression. The magnitude of amino acid-induced filamentation is linked to glucose availability; high levels of glucose repress mitochondrial function thereby dampening filamentation. Furthermore, arginine-induced morphogenesis occurs more rapidly and independently of Dur1,2-catalyzed urea degradation, indicating that mitochondrial-generated ATP, not CO2, is the primary morphogenic signal derived from arginine metabolism. The important role of the SPS-sensor of extracellular amino acids in morphogenesis is the consequence of induced amino acid permease gene expression, i.e., SPS-sensor activation enhances the capacity of cells to take up morphogenic amino acids, a requisite for their catabolism. C. albicans cells engulfed by murine macrophages filament, resulting in macrophage lysis. Phagocytosed put1-/- and put2-/- cells do not filament and exhibit reduced viability, consistent with a critical role of mitochondrial proline metabolism in virulence.
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Affiliation(s)
- Fitz Gerald S. Silao
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Meliza Ward
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Kicki Ryman
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Axel Wallström
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Björn Brindefalk
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Klas Udekwu
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Per O. Ljungdahl
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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Dal81 Regulates Expression of Arginine Metabolism Genes in Candida parapsilosis. mSphere 2018; 3:3/2/e00028-18. [PMID: 29564399 PMCID: PMC5853489 DOI: 10.1128/msphere.00028-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 02/08/2018] [Indexed: 01/26/2023] Open
Abstract
Fungi can use a wide variety of nitrogen sources. In the absence of preferred sources such as ammonium, glutamate, and glutamine, secondary sources, including most other amino acids, are used. Expression of the nitrogen utilization pathways is very strongly controlled at the transcriptional level. Here, we investigated the regulation of nitrogen utilization in the pathogenic yeast Candida parapsilosis. We found that the functions of many regulators are conserved with respect to Saccharomyces cerevisiae and other fungi. For example, the core GATA activators GAT1 and GLN3 have a conserved role in nitrogen catabolite repression (NCR). There is one ortholog of GZF3 and DAL80, which represses expression of genes in preferred nitrogen sources. The regulators PUT3 and UGA3 are required for metabolism of proline and γ-aminobutyric acid (GABA), respectively. However, the role of the Dal81 transcription factor is distinctly different. In S. cerevisiae, Dal81 is a positive regulator of acquisition of nitrogen from GABA, allantoin, urea, and leucine, and it is required for maximal induction of expression of the relevant pathway genes. In C. parapsilosis, induction of GABA genes is independent of Dal81, and deleting DAL81 has no effect on acquisition of nitrogen from GABA or allantoin. Instead, Dal81 represses arginine synthesis during growth under preferred nitrogen conditions. IMPORTANCE Utilization of nitrogen by fungi is controlled by nitrogen catabolite repression (NCR). Expression of many genes is switched off during growth on nonpreferred nitrogen sources. Gene expression is regulated through a combination of activation and repression. Nitrogen regulation has been studied best in the model yeast Saccharomyces cerevisiae. We found that although many nitrogen regulators have a conserved function in Saccharomyces species, some do not. The Dal81 transcriptional regulator has distinctly different functions in S. cerevisiae and C. parapsilosis. In the former, it regulates utilization of nitrogen from GABA and allantoin, whereas in the latter, it regulates expression of arginine synthesis genes. Our findings make an important contribution to our understanding of nitrogen regulation in a human-pathogenic fungus.
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Ries LNA, Beattie S, Cramer RA, Goldman GH. Overview of carbon and nitrogen catabolite metabolism in the virulence of human pathogenic fungi. Mol Microbiol 2017; 107:277-297. [PMID: 29197127 DOI: 10.1111/mmi.13887] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/20/2017] [Accepted: 11/23/2017] [Indexed: 12/12/2022]
Abstract
It is estimated that fungal infections, caused most commonly by Candida albicans, Aspergillus fumigatus and Cryptococcus neoformans, result in more deaths annually than malaria or tuberculosis. It has long been hypothesized the fungal metabolism plays a critical role in virulence though specific nutrient sources utilized by human pathogenic fungi in vivo has remained enigmatic. However, the metabolic utilisation of preferred carbon and nitrogen sources, encountered in a host niche-dependent manner, is known as carbon catabolite and nitrogen catabolite repression (CCR, NCR), and has been shown to be important for virulence. Several sensory and uptake systems exist, including carbon and nitrogen source-specific sensors and transporters, that allow scavenging of preferred nutrient sources. Subsequent metabolic utilisation is governed by transcription factors, whose functions and essentiality differ between fungal species. Furthermore, additional factors exist that contribute to the implementation of CCR and NCR. The role of the CCR and NCR-related factors in virulence varies greatly between fungal species and a substantial gap in knowledge exists regarding specific pathways. Further elucidation of carbon and nitrogen metabolism mechanisms is therefore required in a fungal species- and animal model-specific manner in order to screen for targets that are potential candidates for anti-fungal drug development.
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Affiliation(s)
- Laure Nicolas Annick Ries
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, Ribeirão Preto, São Paulo, 3900, CEP 14049-900, Brazil
| | - Sarah Beattie
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, 74 College Street Remsen 213, Hanover, NH 03755, USA
| | - Robert A Cramer
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, 74 College Street Remsen 213, Hanover, NH 03755, USA
| | - Gustavo H Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café s/n°, Ribeirão Preto, São Paulo, CEP 14040903, Brazil
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12
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Abstract
All organisms can respond to the availability of nutrients by regulating their metabolism, growth, and cell division. Central to the regulation of growth in response to nutrient availability is the target of rapamycin (TOR) signaling that is composed of two structurally distinct complexes: TOR complex 1 (TORC1) and TOR complex 2 (TORC2). The TOR genes were first identified in yeast as target of rapamycin, a natural product of a soil bacterium, which proved beneficial as an immunosuppressive and anticancer drug and is currently being tested for a handful of other pathological conditions including diabetes, neurodegeneration, and age-related diseases. Studies of the TOR pathway unraveled a complex growth-regulating network. TOR regulates nutrient uptake, transcription, protein synthesis and degradation, as well as metabolic pathways, in a coordinated manner that ensures that cells grow or cease growth in response to nutrient availability. The identification of specific signals and mechanisms that stimulate TOR signaling is an active and exciting field of research that has already identified nitrogen and amino acids as key regulators of TORC1 activity. The signals, as well as the cellular functions of TORC2, are far less well understood. Additional open questions in the field concern the relationships between TORC1 and TORC2, as well as the links with other nutrient-responsive pathways. Here I review the main features of TORC1 and TORC2, with a particular focus on yeasts as model organisms.
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13
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Böttcher B, Pöllath C, Staib P, Hube B, Brunke S. Candida species Rewired Hyphae Developmental Programs for Chlamydospore Formation. Front Microbiol 2016; 7:1697. [PMID: 27833594 PMCID: PMC5081361 DOI: 10.3389/fmicb.2016.01697] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/12/2016] [Indexed: 01/14/2023] Open
Abstract
Chlamydospore formation is a characteristic of many fungal species, among them the closely related human-pathogenic dimorphic yeasts Candida albicans and C. dubliniensis. Whereas function and regulation of filamentation are well-studied in these species, the basis of chlamydospore formation is mostly unknown. Here, we investigate the contribution of environmental and genetic factors and identified central proteins involved in species-specific regulation of chlamydosporulation. We show that specific nutrient levels strongly impact chlamydospore initiation, with starvation favoring sporulation and elevated levels of saccharides or peptone inhibiting it. Thresholds for these nutritional effects differ between C. albicans and C. dubliniensis, which explain species-specific chlamydospore formation on certain diagnostic media. A C. albicans nrg1Δ mutant phenocopied C. dubliniensis, putting Nrg1 regulation at the basis of species-specific chlamydospore formation under various conditions. By screening a series of potential chlamydospore regulators, we identified the TOR and cAMP pathways as crucial for sporulation. As rapamycin treatment blocked chlamydosporulation, a low basal Tor1 activity seems to be essential. In addition, TOR effector pathways play an important role, and loss of the NCR (nitrogen catabolite repression) gene regulators Gat1 and Gln3 reduced chlamydospore formation. A severe reduction was seen for a C. albicans gcn4Δ deletion strain, implicating a link between regulation of amino acid biosynthesis and chlamydospore development. On the other hand, deletion of the GTPase gene RAS1 and the adenylyl cyclase gene CYR1 caused a defect in chlamydospore formation that was mostly rescued by cAMP supplementation. Thus, cAMP-signaling is a second major pathway to control chlamydospore production. Finally, we confirmed light exposure to have a repressive effect on chlamydosporulation. However, permanent illumination only reduced, but not abolished chlamydospore production of C. albicans whereas C. dubliniensis sporulation was unaffected. In summary, we describe novel environmental factors which determine chlamydosporulation and propose a first model for the regulatory network of chlamydospore formation by different Candida species.
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Affiliation(s)
- Bettina Böttcher
- Department of Microbial Pathogenicity Mechanisms, Hans-Knöll-Institute Jena, Germany
| | - Christine Pöllath
- Department of Microbial Pathogenicity Mechanisms, Hans-Knöll-InstituteJena, Germany; Institute for Medical Microbiology, Jena University HospitalJena, Germany; Center for Sepsis Control and Care, Jena University HospitalJena, Germany
| | - Peter Staib
- Department of Research and Development, Kneipp GmbH Würzburg, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Hans-Knöll-InstituteJena, Germany; Center for Sepsis Control and Care, Jena University HospitalJena, Germany; Friedrich Schiller University JenaJena, Germany
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Hans-Knöll-Institute Jena, Germany
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14
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Pérez-delos Santos FJ, Riego-Ruiz L. Gln3 is a main regulator of nitrogen assimilation in Candida glabrata. Microbiology (Reading) 2016; 162:1490-1499. [DOI: 10.1099/mic.0.000312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Francisco J. Pérez-delos Santos
- Laboratory of Functional and Comparative Genomics, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), A. C., San Luis Potosí, México
| | - Lina Riego-Ruiz
- Laboratory of Functional and Comparative Genomics, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), A. C., San Luis Potosí, México
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15
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Mycelial development preceding basidioma formation in Moniliophthora perniciosa is associated to chitin, sugar and nutrient metabolism alterations involving autophagy. Fungal Genet Biol 2016; 86:33-46. [DOI: 10.1016/j.fgb.2015.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 12/02/2015] [Accepted: 12/12/2015] [Indexed: 02/07/2023]
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16
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Chowdhury T, Köhler JR. Ribosomal protein S6 phosphorylation is controlled by TOR and modulated by PKA in Candida albicans. Mol Microbiol 2015; 98:384-402. [PMID: 26173379 DOI: 10.1111/mmi.13130] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2015] [Indexed: 12/25/2022]
Abstract
TOR and PKA signaling pathways control eukaryotic cell growth and proliferation. TOR activity in model fungi, such as Saccharomyces cerevisiae, responds principally to nutrients, e.g., nitrogen and phosphate sources, which are incorporated into the growing cell mass; PKA signaling responds to the availability of the cells' major energy source, glucose. In the fungal commensal and pathogen, Candida albicans, little is known of how these pathways interact. Here, the signal from phosphorylated ribosomal protein S6 (P-S6) was defined as a surrogate marker for TOR-dependent anabolic activity in C. albicans. Nutritional, pharmacologic and genetic modulation of TOR activity elicited corresponding changes in P-S6 levels. The P-S6 signal corresponded to translational activity of a GFP reporter protein. Contributions of four PKA pathway components to anabolic activation were then examined. In high glucose concentrations, only Tpk2 was required to upregulate P-S6 to physiologic levels, whereas all four tested components were required to downregulate P-S6 in low glucose. TOR was epistatic to PKA components with respect to P-S6. In many host niches inhabited by C. albicans, glucose is scarce, with protein being available as a nitrogen source. We speculate that PKA may modulate TOR-dependent cell growth to a rate sustainable by available energy sources, when monomers of anabolic processes, such as amino acids, are abundant.
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Affiliation(s)
- Tahmeena Chowdhury
- Division of Infectious Diseases, Boston Children's Hospital/Harvard Medical School, Boston, MA, 02115, USA
| | - Julia R Köhler
- Division of Infectious Diseases, Boston Children's Hospital/Harvard Medical School, Boston, MA, 02115, USA
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17
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TORC1 Regulates Developmental Responses to Nitrogen Stress via Regulation of the GATA Transcription Factor Gaf1. mBio 2015; 6:e00959. [PMID: 26152587 PMCID: PMC4488950 DOI: 10.1128/mbio.00959-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The TOR (target of rapamycin [sirolimus]) is a universally conserved kinase that couples nutrient availability to cell growth. TOR complex 1 (TORC1) in Schizosaccharomyces pombe positively regulates growth in response to nitrogen availability while suppressing cellular responses to nitrogen stress. Here we report the identification of the GATA transcription factor Gaf1 as a positive regulator of the nitrogen stress-induced gene isp7+, via three canonical GATA motifs. We show that under nitrogen-rich conditions, TORC1 positively regulates the phosphorylation and cytoplasmic retention of Gaf1 via the PP2A-like phosphatase Ppe1. Under nitrogen stress conditions when TORC1 is inactivated, Gaf1 becomes dephosphorylated and enters the nucleus. Gaf1 was recently shown to negatively regulate the transcription induction of ste11+, a major regulator of sexual development. Our findings support a model of a two-faceted role of Gaf1 during nitrogen stress. Gaf1 positively regulates genes that are induced early in the response to nitrogen stress, while inhibiting later responses, such as sexual development. Taking these results together, we identify Gaf1 as a novel target for TORC1 signaling and a step-like mechanism to modulate the nitrogen stress response. TOR complex 1 (TORC1) is an evolutionary conserved protein complex that positively regulates growth and proliferation, while inhibiting starvation responses. In fission yeast, the activity of TORC1 is downregulated in response to nitrogen starvation, and cells reprogram their transcriptional profile and prepare for sexual development. We identify Gaf1, a GATA-like transcription factor that regulates transcription and sexual development in response to starvation, as a downstream target for TORC1 signaling. Under nitrogen-rich conditions, TORC1 positively regulates the phosphorylation and cytoplasmic retention of Gaf1 via the PP2A-like phosphatase Ppe1. Under nitrogen stress conditions when TORC1 is inactivated, Gaf1 becomes dephosphorylated and enters the nucleus. Budding yeast TORC1 regulates GATA transcription factors via the phosphatase Sit4, a structural homologue of Ppe1. Thus, the TORC1-GATA transcription module appears to be conserved in evolution and may also be found in higher eukaryotes.
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18
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Castelhano Santos N, Pereira MO, Lourenço A. Pathogenicity phenomena in three model systems: from network mining to emerging system-level properties. Brief Bioinform 2013; 16:169-82. [PMID: 24106130 DOI: 10.1093/bib/bbt071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Understanding the interconnections of microbial pathogenicity phenomena, such as biofilm formation, quorum sensing and antimicrobial resistance, is a tremendous open challenge for biomedical research. Progress made by wet-lab researchers and bioinformaticians in understanding the underlying regulatory phenomena has been significant, with converging evidence from multiple high-throughput technologies. Notably, network reconstructions are already of considerable size and quality, tackling both intracellular regulation and signal mediation in microbial infection. Therefore, it stands to reason that in silico investigations would play a more active part in this research. Drug target identification and drug repurposing could take much advantage of the ability to simulate pathogen regulatory systems, host-pathogen interactions and pathogen cross-talking. Here, we review the bioinformatics resources and tools available for the study of the gram-negative bacterium Pseudomonas aeruginosa, the gram-positive bacterium Staphylococcus aureus and the fungal species Candida albicans. The choice of these three microorganisms fits the rationale of the review converging into pathogens of great clinical importance, which thrive in biofilm consortia and manifest growing antimicrobial resistance.
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19
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Lee IR, Morrow CA, Fraser JA. Nitrogen regulation of virulence in clinically prevalent fungal pathogens. FEMS Microbiol Lett 2013; 345:77-84. [PMID: 23701678 DOI: 10.1111/1574-6968.12181] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 05/17/2013] [Accepted: 05/18/2013] [Indexed: 11/25/2022] Open
Abstract
The habitats of fungal pathogens range from environmental to commensal, and the nutrient content of these different niches varies considerably. Upon infection of humans, nutrient availability changes significantly depending on the site and pathophysiology of infection. Nonetheless, a common feature enabling successful establishment in these niches is the ability to metabolise available nutrients including sources of nitrogen, carbon and essential metals such as iron. In particular, nitrogen source utilisation influences specific morphological transitions, sexual and asexual sporulation and virulence factor production. All these physiological changes confer selective advantages to facilitate fungal survival, proliferation and colonisation. The three most well-studied components of the nitrogen regulatory circuit that commonly impact fungal pathogenesis are the ammonium permeases (the nitrogen availability sensor candidate), ureases (a nitrogen-scavenging enzyme) and GATA transcription factors (global regulators of nitrogen catabolism). In certain species, the ammonium permease induces a morphological switch from yeast to invasive filamentous growth forms or infectious spores, while in others, urease is a bona fide virulence factor. In all species studied thus far, transcription of the ammonium permease and urease-encoding genes is modulated by GATA factors. Fungal pathogens therefore integrate the expression of different virulence-associated phenotypes into the regulatory network controlling nitrogen catabolism.
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Affiliation(s)
- I Russel Lee
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, Australia
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20
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Diverse Hap43-independent functions of the Candida albicans CCAAT-binding complex. EUKARYOTIC CELL 2013; 12:804-15. [PMID: 23543673 DOI: 10.1128/ec.00014-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The CCAAT motif is ubiquitous in promoters of eukaryotic genomes. The CCAAT-binding complex (CBC) is conserved across a wide range of organisms, specifically recognizes the CCAAT motif, and modulates transcription directly or in cooperation with other transcription factors. In Candida albicans, CBC is known to interact with the repressor Hap43 to negatively regulate iron utilization genes in response to iron deprivation. However, the extent of additional functions of CBC is unclear. In this study, we explored new roles of CBC in C. albicans and found that CBC pleiotropically regulates many virulence traits in vitro, including negative control of genes responsible for ribosome biogenesis and translation and positive regulation of low-nitrogen-induced filamentation. In addition, C. albicans CBC is involved in utilization of host proteins as nitrogen sources and in repression of cellular flocculation and adhesin gene expression. Moreover, our epistasis analyses suggest that CBC acts as a downstream effector of Rhb1-TOR signaling and controls low-nitrogen-induced filamentation via the Mep2-Ras1-protein kinase A (PKA)/mitogen-activated protein kinase (MAPK) pathway. Importantly, the phenotypes identified here are all independent of Hap43. Finally, deletion of genes encoding CBC components slightly attenuated C. albicans virulence in both zebrafish and murine models of infection. Our results thus highlight new roles of C. albicans CBC in regulating multiple virulence traits in response to environmental perturbations and, finally, suggest potential targets for antifungal therapies as well as extending our understanding of the pathogenesis of other fungal pathogens.
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21
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Tsai PW, Chen YT, Hsu PC, Lan CY. Study of Candida albicans and its interactions with the host: A mini review. Biomedicine (Taipei) 2013. [DOI: 10.1016/j.biomed.2012.12.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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22
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Lu Y, Su C, Liu H. A GATA transcription factor recruits Hda1 in response to reduced Tor1 signaling to establish a hyphal chromatin state in Candida albicans. PLoS Pathog 2012; 8:e1002663. [PMID: 22536157 PMCID: PMC3334898 DOI: 10.1371/journal.ppat.1002663] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 03/08/2012] [Indexed: 01/15/2023] Open
Abstract
Candida albicans is an important opportunistic fungal pathogen of immunocompromised individuals. One critical virulence attribute is its morphogenetic plasticity. Hyphal development requires two temporally linked changes in promoter chromatin, which is sequentially regulated by temporarily clearing the transcription inhibitor Nrg1 upon activation of the cAMP/PKA pathway and promoter recruitment of the histone deacetylase Hda1 under reduced Tor1 signaling. Molecular mechanisms for the temporal connection and the link to Tor1 signaling are not clear. Here, through a forward genetic screen, we report the identification of the GATA family transcription factor Brg1 as the factor that recruits Hda1 to promoters of hypha-specific genes during hyphal elongation. BRG1 expression requires both the removal of Nrg1 and a sub-growth inhibitory level of rapamycin; therefore, it is a sensitive readout of Tor1 signaling. Interestingly, promoters of hypha-specific genes are not accessible to Brg1 in yeast cells. Furthermore, ectopic expression of Brg1 cannot induce hyphae, but can sustain hyphal development. Nucleosome mapping of a hypha-specific promoter shows that Nrg1 binding sites are in nucleosome free regions in yeast cells, whereas Brg1 binding sites are occupied by nucleosomes. Nucleosome disassembly during hyphal initiation exposes the binding sites for both regulators. During hyphal elongation, Brg1-mediated Hda1 recruitment causes nucleosome repositioning and occlusion of Nrg1 binding sites. We suggest that nucleosome repositioning is the underlying mechanism for the yeast-hyphal transition. The hypha-specific regulator Ume6 is a key downstream target of Brg1 and functions after Brg1 as a built-in positive feedback regulator of the hyphal transcriptional program to sustain hyphal development. With the levels of Nrg1 and Brg1 dynamically and sensitively controlled by the two major cellular growth pathways, temporal changes in nucleosome positioning during the yeast-to-hypha transition provide a mechanism for signal integration and cell fate specification. This mechanism is likely used broadly in development. Candida is part of the gut microflora in healthy individuals, but can disseminate and cause systemic disease when the host's immune system is suppressed. Its ability to grow as yeast and hyphae in response to environmental cues is a major virulence attribute. Hyphal development requires temporary clearing of the transcription inhibitor Nrg1 upon activation of cAMP/PKA for initiation and promoter recruitment of the histone deacetylase Hda1 under reduced Tor1 signaling for maintenance. Here, we show that, during hyphal initiation when Nrg1 is gone, expression of the GATA family transcription factor Brg1 is activated under reduced Tor1 signaling. Accumulated Brg1 recruits Hda1 to hyphal promoters to reposition nucleosomes, leading to obstruction of Nrg1 binding sites and sustained hyphal development. The nucleosome repositioning during the yeast-hyphal transition provides a mechanism for temporal integration of extracellular signals and cell-fate specification. The hypha-specific transcription factor Ume6 functions after Brg1 in this succession of feed-forward regulation of hyphal development. Since misregulation of either Nrg1 or Ume6 causes altered virulence, and Brg1 regulates both Nrg1 accessibility and Ume6 transcription, our findings should provide a better understanding of how Candida controls its morphological program in different host niches to exist as a commensal and a pathogen.
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Affiliation(s)
- Yang Lu
- Department of Biological Chemistry, University of California, Irvine, California, United States of America
| | - Chang Su
- Department of Biological Chemistry, University of California, Irvine, California, United States of America
| | - Haoping Liu
- Department of Biological Chemistry, University of California, Irvine, California, United States of America
- * E-mail:
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23
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Lee IR, Lim JWC, Ormerod KL, Morrow CA, Fraser JA. Characterization of an Nmr homolog that modulates GATA factor-mediated nitrogen metabolite repression in Cryptococcus neoformans. PLoS One 2012; 7:e32585. [PMID: 22470421 PMCID: PMC3314646 DOI: 10.1371/journal.pone.0032585] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 02/01/2012] [Indexed: 11/18/2022] Open
Abstract
Nitrogen source utilization plays a critical role in fungal development, secondary metabolite production and pathogenesis. In both the Ascomycota and Basidiomycota, GATA transcription factors globally activate the expression of catabolic enzyme-encoding genes required to degrade complex nitrogenous compounds. However, in the presence of preferred nitrogen sources such as ammonium, GATA factor activity is inhibited in some species through interaction with co-repressor Nmr proteins. This regulatory phenomenon, nitrogen metabolite repression, enables preferential utilization of readily assimilated nitrogen sources. In the basidiomycete pathogen Cryptococcus neoformans, the GATA factor Gat1/Are1 has been co-opted into regulating multiple key virulence traits in addition to nitrogen catabolism. Here, we further characterize Gat1/Are1 function and investigate the regulatory role of the predicted Nmr homolog Tar1. While GAT1/ARE1 expression is induced during nitrogen limitation, TAR1 transcription is unaffected by nitrogen availability. Deletion of TAR1 leads to inappropriate derepression of non-preferred nitrogen catabolic pathways in the simultaneous presence of favoured sources. In addition to exhibiting its evolutionary conserved role of inhibiting GATA factor activity under repressing conditions, Tar1 also positively regulates GAT1/ARE1 transcription under non-repressing conditions. The molecular mechanism by which Tar1 modulates nitrogen metabolite repression, however, remains open to speculation. Interaction between Tar1 and Gat1/Are1 was undetectable in a yeast two-hybrid assay, consistent with Tar1 and Gat1/Are1 each lacking the conserved C-terminus regions present in ascomycete Nmr proteins and GATA factors that are known to interact with each other. Importantly, both Tar1 and Gat1/Are1 are suppressors of C. neoformans virulence, reiterating and highlighting the paradigm of nitrogen regulation of pathogenesis.
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Affiliation(s)
- I. Russel Lee
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Jonathan W. C. Lim
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Kate L. Ormerod
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Carl A. Morrow
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - James A. Fraser
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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24
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Horst RJ, Zeh C, Saur A, Sonnewald S, Sonnewald U, Voll LM. The Ustilago maydis Nit2 homolog regulates nitrogen utilization and is required for efficient induction of filamentous growth. EUKARYOTIC CELL 2012; 11:368-80. [PMID: 22247264 PMCID: PMC3294441 DOI: 10.1128/ec.05191-11] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 12/22/2011] [Indexed: 11/20/2022]
Abstract
Nitrogen catabolite repression (NCR) is a regulatory strategy found in microorganisms that restricts the utilization of complex and unfavored nitrogen sources in the presence of favored nitrogen sources. In fungi, this concept has been best studied in yeasts and filamentous ascomycetes, where the GATA transcription factors Gln3p and Gat1p (in yeasts) and Nit2/AreA (in ascomycetes) constitute the main positive regulators of NCR. The reason why functional Nit2 homologs of some phytopathogenic fungi are required for full virulence in their hosts has remained elusive. We have identified the Nit2 homolog in the basidiomycetous phytopathogen Ustilago maydis and show that it is a major, but not the exclusive, positive regulator of nitrogen utilization. By transcriptome analysis of sporidia grown on artificial media devoid of favored nitrogen sources, we show that only a subset of nitrogen-responsive genes are regulated by Nit2, including the Gal4-like transcription factor Ton1 (a target of Nit2). Ustilagic acid biosynthesis is not under the control of Nit2, while nitrogen starvation-induced filamentous growth is largely dependent on functional Nit2. nit2 deletion mutants show the delayed initiation of filamentous growth on maize leaves and exhibit strongly compromised virulence, demonstrating that Nit2 is required to efficiently initiate the pathogenicity program of U. maydis.
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Affiliation(s)
- Robin J Horst
- Division of Biochemistry, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstr. 5, Erlangen, Germany
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25
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Rhb1 regulates the expression of secreted aspartic protease 2 through the TOR signaling pathway in Candida albicans. EUKARYOTIC CELL 2011; 11:168-82. [PMID: 22194462 DOI: 10.1128/ec.05200-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Candida albicans is a major fungal pathogen in humans. In C. albicans, secreted aspartyl protease 2 (Sap2) is the most highly expressed secreted aspartic protease in vitro and is a virulence factor. Recent research links the small GTPase Rhb1 to C. albicans target of rapamycin (TOR) signaling in response to nitrogen availability. The results of this study show that Rhb1 is related to cell growth through the control of SAP2 expression when protein is the major nitrogen source. This process involves various components of the TOR signaling pathway, including Tor1 kinase and its downstream effectors. TOR signaling not only controls SAP2 transcription but also affects Sap2 protein levels, possibly through general amino acid control. DNA microarray analysis identifies other target genes downstream of Rhb1 in addition to SAP2. These findings provide new insight into nutrients, Rhb1-TOR signaling, and expression of C. albicans virulence factor.
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26
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AreA controls nitrogen source utilisation during both growth programs of the dimorphic fungus Penicillium marneffei. Fungal Biol 2011; 116:145-54. [PMID: 22208609 DOI: 10.1016/j.funbio.2011.10.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 10/28/2011] [Accepted: 10/28/2011] [Indexed: 12/17/2022]
Abstract
The opportunistic pathogen Penicillium marneffei displays a temperature-dependent dimorphic switching program with saprophytic hyphal growth at 25 °C and yeast growth at 37 °C. The areA gene of P. marneffei has been isolated and found to be required for the utilisation of nonpreferred nitrogen sources during both growth programs of P. marneffei, albeit to differing degrees. Based on this functional characterisation and high degree of sequence conservation with other fungal GATA factors, P. marneffei areA represents an orthologue of Aspergillus nidulans areA and Neurospora crassa NIT2. Based on this study it is proposed that AreA is likely to contribute to the pathogenicity of P. marneffei by facilitating growth in the host environment and regulating the expression of potential virulence factors such as extracellular proteases.
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27
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The Candida albicans GAP gene family encodes permeases involved in general and specific amino acid uptake and sensing. EUKARYOTIC CELL 2011; 10:1219-29. [PMID: 21764911 DOI: 10.1128/ec.05026-11] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Saccharomyces cerevisiae general amino acid permease Gap1 (ScGap1) not only mediates the uptake of most amino acids but also functions as a receptor for the activation of protein kinase A (PKA). Fungal pathogens can colonize different niches in the host, each containing various levels of different amino acids and sugars. The Candida albicans genome contains six genes homologous to the S. cerevisiae GAP1. The expression of these six genes in S. cerevisiae showed that the products of all six C. albicans genes differ in their transport capacities. C. albicans Gap2 (CaGap2) is the true orthologue of ScGap1 as it transports all tested amino acids. The other CaGap proteins have narrower substrate specificities though CaGap1 and CaGap6 transport several structurally unrelated amino acids. CaGap1, CaGap2, and CaGap6 also function as sensors. Upon detecting some amino acids, e.g., methionine, they are involved in a rapid activation of trehalase, a downstream target of PKA. Our data show that CaGAP genes can be functionally expressed in S. cerevisiae and that CaGap permeases communicate to the intracellular signal transduction pathway similarly to ScGap1.
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28
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Chen SCA, Lewis RE, Kontoyiannis DP. Direct effects of non-antifungal agents used in cancer chemotherapy and organ transplantation on the development and virulence of Candida and Aspergillus species. Virulence 2011; 2:280-95. [PMID: 21701255 PMCID: PMC3173675 DOI: 10.4161/viru.2.4.16764] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 06/01/2011] [Accepted: 06/03/2011] [Indexed: 11/19/2022] Open
Abstract
Conventional antineoplastic, novel immunosuppressive agents and antibiotics used in cancer treatment can directly affect the growth, development and virulence of Candida and Aspergillus species. Cytotoxic and cisplatin compounds have anti-Candida activity and may be synergistic with antifungal drugs; they also inhibit Candida and Aspergillus filamentation/conidation and effect increased virulence in vitro. Glucocorticoids enhance Candida adherence to epithelial cells, germination in serum and in vitro secretion of phospholipases and proteases, as well as growth of A. fumigatus. Calcineurin and target of rapamycin inhibitors perturb Candida and Aspergillus morphogenesis, stress responses and survival in serum, reduce azole tolerance in Candida, but yield conflicting in vivo data. Inhibition of candidal heat shock protein 90 and candidal-specific histone deacetylase represent feasible therapeutic approaches for candidiasis. Tyrosine kinase inhibitors inhibit fungal cell entry into epithelial cells and phagocytosis. Quinolone and other antibiotics may augment activity of azole and polyene agents. The correlation of in vitro effects with clinically meaningful in vivo systems is warranted.
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Affiliation(s)
- Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, University of Sydney, Westmead, NSW Australia
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Lee IR, Chow EWL, Morrow CA, Djordjevic JT, Fraser JA. Nitrogen metabolite repression of metabolism and virulence in the human fungal pathogen Cryptococcus neoformans. Genetics 2011; 188:309-23. [PMID: 21441208 PMCID: PMC3122321 DOI: 10.1534/genetics.111.128538] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 03/22/2011] [Indexed: 12/28/2022] Open
Abstract
Proper regulation of metabolism is essential to maximizing fitness of organisms in their chosen environmental niche. Nitrogen metabolite repression is an example of a regulatory mechanism in fungi that enables preferential utilization of easily assimilated nitrogen sources, such as ammonium, to conserve resources. Here we provide genetic, transcriptional, and phenotypic evidence of nitrogen metabolite repression in the human pathogen Cryptococcus neoformans. In addition to loss of transcriptional activation of catabolic enzyme-encoding genes of the uric acid and proline assimilation pathways in the presence of ammonium, nitrogen metabolite repression also regulates the production of the virulence determinants capsule and melanin. Since GATA transcription factors are known to play a key role in nitrogen metabolite repression, bioinformatic analyses of the C. neoformans genome were undertaken and seven predicted GATA-type genes were identified. A screen of these deletion mutants revealed GAT1, encoding the only global transcription factor essential for utilization of a wide range of nitrogen sources, including uric acid, urea, and creatinine-three predominant nitrogen constituents found in the C. neoformans ecological niche. In addition to its evolutionarily conserved role in mediating nitrogen metabolite repression and controlling the expression of catabolic enzyme and permease-encoding genes, Gat1 also negatively regulates virulence traits, including infectious basidiospore production, melanin formation, and growth at high body temperature (39°-40°). Conversely, Gat1 positively regulates capsule production. A murine inhalation model of cryptococcosis revealed that the gat1Δ mutant is slightly more virulent than wild type, indicating that Gat1 plays a complex regulatory role during infection.
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Affiliation(s)
- I. Russel Lee
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072 Australia and
| | - Eve W. L. Chow
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072 Australia and
| | - Carl A. Morrow
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072 Australia and
| | - Julianne T. Djordjevic
- Centre for Infectious Diseases and Microbiology, Westmead Millennium Institute, University of Sydney at Westmead Hospital, NSW 2145 Australia*
| | - James A. Fraser
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072 Australia and
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Morschhäuser J. Nitrogen regulation of morphogenesis and protease secretion in Candida albicans. Int J Med Microbiol 2011; 301:390-4. [PMID: 21555241 DOI: 10.1016/j.ijmm.2011.04.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the pathogenic yeast Candida albicans, nitrogen availability regulates phenotypes that contribute to the virulence of the fungus, including filamentous growth and protease secretion. Under limiting nitrogen conditions, the ammonium permease Mep2 induces the switch from yeast to filamentous growth. Mep2 is a cytoplasmic membrane protein that mediates uptake of the preferred nitrogen source ammonium. It contains a signaling domain in its C-terminal cytoplasmic tail that induces morphogenesis in response to ammonium availability, presumably by activating the cAMP-PKA pathway and the Cph1-dependent MAP kinase pathway. MEP2 expression itself is regulated by the GATA transcription factors Gat1 and Gln3. These central regulators also control expression of the secreted aspartic protease Sap2, which is induced when proteins are the only available nitrogen source. Under these conditions, Gat1 and Gln3 upregulate the expression of STP1, which encodes a proteolytically activated transcription factor that in turn mediates the expression of SAP2 and several oligopeptide transporters required for growth on proteins. In this way, C. albicans integrates the expression of different virulence-associated phenotypes into the regulatory network controlling nitrogen metabolism.
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Affiliation(s)
- Joachim Morschhäuser
- Institut für Molekulare Infektionsbiologie, Universität Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany.
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Abstract
[URE3] is a prion (infectious protein) of the Saccharomyces cerevisiae Ure2p, a regulator of nitrogen catabolism. We show that wild S. paradoxus can be infected with a [URE3] prion, supporting the use of S. cerevisiae as a prion test bed. We find that the Ure2p of Candida albicans and C. glabrata also regulate nitrogen catabolism. Conservation of amino acid sequence within the prion domain of Ure2p has been proposed as evidence that the [URE3] prion helps its host. We show that the C. albicans Ure2p, which does not conserve this sequence, can nonetheless form a [URE3] prion in S. cerevisiae, but the C. glabrata Ure2p, which does have the conserved sequence, cannot form [URE3] as judged by its performance in S. cerevisiae. These results suggest that the sequence is not conserved to preserve prion forming ability.
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The GATA-type transcriptional activator Gat1 regulates nitrogen uptake and metabolism in the human pathogen Cryptococcus neoformans. Fungal Genet Biol 2010; 48:192-9. [PMID: 20673806 DOI: 10.1016/j.fgb.2010.07.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 07/22/2010] [Accepted: 07/22/2010] [Indexed: 01/02/2023]
Abstract
Nitrogen uptake and metabolism are essential to microbial growth. Gat1 belongs to a conserved family of zinc finger containing transcriptional regulators known as GATA-factors. These factors activate the transcription of Nitrogen Catabolite Repression (NCR) sensitive genes when preferred nitrogen sources are absent or limiting. Cryptococcus neoformans GAT1 is an ortholog to the Aspergillus nidulans AreA and Candida albicans GAT1 genes. In an attempt to define the function of this transcriptional regulator in C. neoformans, we generated null mutants (gat1Δ) of this gene. The gat1 mutant exhibited impaired growth on all amino acids tested as sole nitrogen sources, with the exception of arginine and proline. Furthermore, the gat1 mutant did not display resistance to rapamycin, an immunosuppressant drug that transiently mimics a low-quality nitrogen source. Gat1 is not required for C. neoformans survival during macrophage infection or for virulence in a mouse model of cryptococcosis. Microarray analysis allowed the identification of target genes that are regulated by Gat1 in the presence of proline, a poor and non-repressing nitrogen source. Genes involved in ergosterol biosynthesis, iron uptake, cell wall organization and capsule biosynthesis, in addition to NCR-sensitive genes, are Gat1-regulated in C. neoformans.
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Krastel K, Senadheera DB, Mair R, Downey JS, Goodman SD, Cvitkovitch DG. Characterization of a glutamate transporter operon, glnQHMP, in Streptococcus mutans and its role in acid tolerance. J Bacteriol 2010; 192:984-93. [PMID: 20023025 PMCID: PMC2812961 DOI: 10.1128/jb.01169-09] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2009] [Accepted: 12/07/2009] [Indexed: 12/11/2022] Open
Abstract
Glutamate contributes to the acid tolerance response (ATR) of many Gram-negative and Gram-positive bacteria, but its role in the ATR of the oral bacterium Streptococcus mutans is unknown. This study describes the discovery and characterization of a glutamate transporter operon designated glnQHMP (Smu.1519 to Smu.1522) and investigates its potential role in acid tolerance. Deletion of glnQHMP resulted in a 95% reduction in transport of radiolabeled glutamate compared to the wild-type UA159 strain. The addition of glutamate to metabolizing UA159 cells resulted in an increased production of acidic end products, whereas the glnQHMP mutant produced less lactic acid than UA159, suggesting a link between glutamate metabolism and acid production and possible acid tolerance. To investigate this possibility, we conducted a microarray analysis with glutamate and under pH 5.5 and pH 7.5 conditions which showed that expression of the glnQHMP operon was downregulated by both glutamate and mild acid. We also measured the growth kinetics of UA159 and its glnQHMP-negative derivative at pH 5.5 and found that the mutant doubled at a much slower rate than the parent strain but survived at pH 3.5 significantly better than the wild type. Taken together, these findings support the involvement of the glutamate transporter operon glnQHMP in the acid tolerance response in S. mutans.
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Affiliation(s)
- Kirsten Krastel
- Dental Research Institute, University of Toronto, 124 Edward Street, Toronto, Ontario M5G 1G6, Canada, Division of Diagnostic Sciences and Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089
| | - Dilani B. Senadheera
- Dental Research Institute, University of Toronto, 124 Edward Street, Toronto, Ontario M5G 1G6, Canada, Division of Diagnostic Sciences and Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089
| | - Richard Mair
- Dental Research Institute, University of Toronto, 124 Edward Street, Toronto, Ontario M5G 1G6, Canada, Division of Diagnostic Sciences and Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089
| | - Jennifer S. Downey
- Dental Research Institute, University of Toronto, 124 Edward Street, Toronto, Ontario M5G 1G6, Canada, Division of Diagnostic Sciences and Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089
| | - Steven D. Goodman
- Dental Research Institute, University of Toronto, 124 Edward Street, Toronto, Ontario M5G 1G6, Canada, Division of Diagnostic Sciences and Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089
| | - Dennis G. Cvitkovitch
- Dental Research Institute, University of Toronto, 124 Edward Street, Toronto, Ontario M5G 1G6, Canada, Division of Diagnostic Sciences and Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089
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TOR signaling in invertebrates. Curr Opin Cell Biol 2009; 21:825-36. [DOI: 10.1016/j.ceb.2009.08.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 08/24/2009] [Accepted: 08/26/2009] [Indexed: 01/31/2023]
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Bastidas RJ, Heitman J, Cardenas ME. The protein kinase Tor1 regulates adhesin gene expression in Candida albicans. PLoS Pathog 2009; 5:e1000294. [PMID: 19197361 PMCID: PMC2631134 DOI: 10.1371/journal.ppat.1000294] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 01/09/2009] [Indexed: 01/09/2023] Open
Abstract
Eukaryotic cell growth is coordinated in response to nutrient availability, growth factors, and environmental stimuli, enabling cell–cell interactions that promote survival. The rapamycin-sensitive Tor1 protein kinase, which is conserved from yeasts to humans, participates in a signaling pathway central to cellular nutrient responses. To gain insight into Tor-mediated processes in human fungal pathogens, we have characterized Tor signaling in Candida albicans. Global transcriptional profiling revealed evolutionarily conserved roles for Tor1 in regulating the expression of genes involved in nitrogen starvation responses and ribosome biogenesis. Interestingly, we found that in C. albicans Tor1 plays a novel role in regulating the expression of several cell wall and hyphal specific genes, including adhesins and their transcriptional repressors Nrg1 and Tup1. In accord with this transcriptional profile, rapamycin induced extensive cellular aggregation in an adhesin-dependent fashion. Moreover, adhesin gene induction and cellular aggregation of rapamycin-treated cells were strongly dependent on the transactivators Bcr1 and Efg1. These findings support models in which Tor1 negatively controls cellular adhesion by governing the activities of Bcr1 and Efg1. Taken together, these results provide evidence that Tor1-mediated cellular adhesion might be broadly conserved among eukaryotic organisms. Living organisms have an intrinsic ability to coordinate their growth and proliferation in response to nutrient availability. In organisms ranging from yeasts to humans, the Tor1 signaling pathway responds to nutrient-derived signals and orchestrates cell growth. Accordingly, we find that in the human fungal pathogen Candida albicans, Tor1 signaling also functions to promote growth. We also uncovered a novel role for the Tor1 molecular pathway in promoting hyphal growth of C. albicans on semi-solid surfaces and in controlling cell–cell adherence. Gene expression analysis and genetic manipulations implicate the known cell surface adhesins Als1 and Als3 as mediators of Tor1-regulated cellular adhesion. Further genetic analysis identified the transcriptional regulators Bcr1, Efg1, Nrg1, and Tup1 that together with Tor1 compose a regulatory network governing adhesin gene expression and cellular adhesion. Given that the Tor pathway is the target of several small molecule inhibitors including rapamycin, a versatile pharmacological drug used in medicine, there is considerable interest in Tor signaling pathways and their function. Moreover, given the potent fungicidal activity of rapamycin against C. albicans, novel antifungal therapies remain to be developed, which may also include novel antifungal therapies with less immunosuppressive rapamycin analogs.
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Affiliation(s)
- Robert J Bastidas
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
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Tsao CC, Chen YT, Lan CY. A small G protein Rhb1 and a GTPase-activating protein Tsc2 involved in nitrogen starvation-induced morphogenesis and cell wall integrity of Candida albicans. Fungal Genet Biol 2008; 46:126-36. [PMID: 19095072 DOI: 10.1016/j.fgb.2008.11.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Revised: 11/21/2008] [Accepted: 11/24/2008] [Indexed: 02/02/2023]
Abstract
Rheb is a new member of the small G proteins of the Ras superfamily in eukaryotic organisms and controls various physiological processes. Activity of Rheb is regulated by Tsc2, a GTPase-activating protein (GAP). In this study, we have identified Candida albicans homologs of Rheb (named as Rhb1) and Tsc2. Deletion of the RHB1 gene showed enhanced sensitivity to rapamycin (an inhibitor of TOR kinase), suggesting that Rhb1 is associated with the TOR signaling pathway in C. albicans. Further analysis indicated RHB1 and TSC2 are involved in nitrogen starvation-induced filamentation, likely by controlling the expression of MEP2 whose gene product is an ammonium permease and a sensor for the nitrogen signal. Moreover, we have demonstrated that Rhb1 is also involved in cell wall integrity pathway, by transferring signals through the TOR kinase and the Mkc1 MAP kinase pathway. Together, this study brings new insights into the complex interplay of signaling and regulatory pathways in C. albicans.
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Affiliation(s)
- Chang-Chih Tsao
- Institute of Molecular and Cellular Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan, ROC
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Vidal EA, Gutiérrez RA. A systems view of nitrogen nutrient and metabolite responses in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2008; 11:521-9. [PMID: 18775665 DOI: 10.1016/j.pbi.2008.07.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Revised: 07/11/2008] [Accepted: 07/31/2008] [Indexed: 05/08/2023]
Abstract
Nitrogen (N) is an essential macronutrient available to plants mainly as nitrate in agricultural soils. Besides its role as a nutrient, inorganic and organic N sources play key roles as signals that control genome-wide gene expression in Arabidopsis and other plant species. Genomics approaches have provided us with thousands of genes whose expression is modulated in response to N treatments in Arabidopsis. Recently, systems approaches have been utilized to map the complex molecular network that plants utilize to integrate metabolic, cellular, and developmental processes to successfully adapt to changing N availability. The challenge now is to understand the molecular mechanisms underlying N regulation of gene networks and bridge the gap between N sensing, signaling, and downstream physiological and developmental changes. We discuss recent advances in this direction.
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Affiliation(s)
- Elena A Vidal
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
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Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Bastidas RJ, Reedy JL, Morales-Johansson H, Heitman J, Cardenas ME. Signaling cascades as drug targets in model and pathogenic fungi. CURRENT OPINION IN INVESTIGATIONAL DRUGS (LONDON, ENGLAND : 2000) 2008; 9:856-864. [PMID: 18666033 PMCID: PMC2715221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Microbes evolved to produce natural products that inhibit growth of competing soil microorganisms. In many cases these compounds act on fungi, which are eukaryotes with conserved gene sequences closely related to metazoans, including humans. The calcineurin inhibitors cyclosporin A and FK-506, the Tor inhibitor rapamycin, and the Hsp90 inhibitor geldanamycin, all act via targets conserved from yeast to humans. This allows the use of genetically tractable fungi as models to elucidate how these drugs and their targets function in yeast and human cells. These inhibitors also enable studies aimed at harnessing their intrinsic antimicrobial activities to develop novel antifungal therapies. Extensive studies have revealed a globally conserved role for the Tor protein in regulating growth and proliferation in response to nutrients, and targeting its essential functions results in robust antifungal action. Similarly, a conserved and essential role for calcineurin in fungal virulence has been established and could be targeted by inhibitors for therapeutic uses in a variety of clinical settings. Finally, the discovery that inhibitors of calcineurin or Hsp90 result in dramatic synergism with either azoles or glucan synthase inhibitors (candins) provides another therapeutic vantage point. Taken together, these fungal targets and their inhibitors provide a robust platform from which to develop novel antimicrobial therapies.
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Affiliation(s)
- Robert J Bastidas
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Research Drive, Box 3546, Durham, NC 27710, USA
| | - Jennifer L Reedy
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Research Drive, Box 3546, Durham, NC 27710, USA
| | - Helena Morales-Johansson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Research Drive, Box 3546, Durham, NC 27710, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Research Drive, Box 3546, Durham, NC 27710, USA
- Department of Medicine, Duke University Medical Center, Research Drive, Box 3546, Durham, NC 27710, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Research Drive, Box 3546, Durham, NC 27710, USA
| | - Maria E. Cardenas
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Research Drive, Box 3546, Durham, NC 27710, USA
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Dabas N, Morschhäuser J. A transcription factor regulatory cascade controls secreted aspartic protease expression in Candida albicans. Mol Microbiol 2008; 69:586-602. [PMID: 18547391 DOI: 10.1111/j.1365-2958.2008.06297.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Secreted aspartic proteases (Saps) contribute to the virulence of Candida albicans, a major fungal pathogen of humans. One function of the Saps, which is specifically mediated by the Sap2p isoenzyme, is the degradation of proteins for use as a nitrogen source. The utilization of alternative nitrogen sources in fungi is controlled by GATA transcription factors and we found that C. albicans mutants lacking the GATA transcription factors Gln3p and Gat1p were unable to grow in a medium containing bovine serum albumin (BSA) as the sole nitrogen source. The growth defect was mainly caused by the inability of gln3Deltagat1Delta mutants to express the SAP2 gene, as SAP2 expression from the constitutive ADH1 promoter restored the ability of the mutants to grow on BSA. Expression of STP1, which encodes a transcription factor that is required for SAP2 induction in the presence of proteins, was regulated by Gln3p and Gat1p, and forced expression of STP1 from a tetracycline-inducible promoter bypassed the requirement of the GATA transcription factors for growth of C. albicans on proteins. SAP2 is repressed when preferred nitrogen sources are available and this nitrogen catabolite repression of SAP2 was correlated with downregulation of STP1 in the presence of high concentrations of ammonium, glutamine or urea. Tetracycline-induced STP1 expression abolished nitrogen catabolite repression of SAP2, demonstrating that the control of STP1 expression levels by the GATA transcription factors is a key aspect of both positive and negative regulation of SAP2 expression. Therefore, secreted aspartic protease expression, a long-known virulence attribute of C. albicans, is controlled by a regulatory cascade in which the general regulators Gln3p and Gat1p control the expression of the transcription factor Stp1p, which in turn mediates SAP2 expression.
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Affiliation(s)
- Neelam Dabas
- Institut für Molekulare Infektionsbiologie, Universität Würzburg, Röntgenring 11, D-97070 Würzburg, Germany
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Recent advances in nitrogen regulation: a comparison between Saccharomyces cerevisiae and filamentous fungi. EUKARYOTIC CELL 2008; 7:917-25. [PMID: 18441120 DOI: 10.1128/ec.00076-08] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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