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Creamer DR, Beynon RJ, Hubbard SJ, Ashe MP, Grant CM. Isoform-specific sequestration of protein kinase A fine-tunes intracellular signaling during heat stress. Cell Rep 2024; 43:114360. [PMID: 38865242 DOI: 10.1016/j.celrep.2024.114360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/24/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
Protein kinase A (PKA) is a conserved kinase crucial for fundamental biological processes linked to growth, development, and metabolism. The PKA catalytic subunit is expressed as multiple isoforms in diverse eukaryotes; however, their contribution to ensuring signaling specificity in response to environmental cues remains poorly defined. Catalytic subunit activity is classically moderated via interaction with an inhibitory regulatory subunit. Here, a quantitative mass spectrometry approach is used to examine heat-stress-induced changes in the binding of yeast Tpk1-3 catalytic subunits to the Bcy1 regulatory subunit. We show that Tpk3 is not regulated by Bcy1 binding but, instead, is deactivated upon heat stress via reversible sequestration into cytoplasmic granules. These "Tpk3 granules" are enriched for multiple PKA substrates involved in various metabolic processes, with the Hsp42 sequestrase required for their formation. Hence, regulated sequestration of Tpk3 provides a mechanism to control isoform-specific kinase signaling activity during stress conditions.
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Affiliation(s)
- Declan R Creamer
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Simon J Hubbard
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Mark P Ashe
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Chris M Grant
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.
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2
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Komath SS. To each its own: Mechanisms of cross-talk between GPI biosynthesis and cAMP-protein kinase A signaling in Candida albicans versus Saccharomyces cerevisiae. J Biol Chem 2024:107444. [PMID: 38838772 DOI: 10.1016/j.jbc.2024.107444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024] Open
Abstract
C. albicans is an opportunistic fungal pathogen that can switch between yeast and hyphal morphologies depending on the environmental cues it receives. The switch to hyphal form is crucial for the establishment of invasive infections. The hyphal form is also characterized by the cell surface expression of hyphae-specific proteins, many of which are GPI-anchored and important determinants of its virulence. The coordination between hyphal morphogenesis and the expression of GPI-anchored proteins is made possible by an interesting cross-talk between GPI biosynthesis and the cAMP-PKA signaling cascade in the fungus; a parallel interaction is not found in its human host. On the other hand, in the non-pathogenic yeast, S. cerevisiae, GPI biosynthesis is shut down when filamentation is activated and vice versa. This too is achieved by a cross-talk between GPI biosynthesis and cAMP-PKA signaling. How are diametrically opposite effects obtained from the cross-talk between two reasonably well-conserved pathways present ubiquitously across eukarya? This Review attempts to provide a model to explain these differences. In order to do so, it first provides an overview of the two pathways for the interested reader, highlighting the similarities and differences that are observed in C. albicans versus the well-studied S. cerevisiae model, before going on to explain how the different mechanisms of regulation are effected. While commonalities enable the development of generalized theories it is hoped that a more nuanced approach, that takes into consideration species-specific differences, will enable organism-specific understanding of these processes and contribute to the development of targeted therapies.
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3
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Galello F, Bermúdez-Moretti M, Martínez MCO, Rossi S, Portela P. The cAMP-PKA signalling crosstalks with CWI and HOG-MAPK pathways in yeast cell response to osmotic and thermal stress. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:90-105. [PMID: 38495453 PMCID: PMC10941952 DOI: 10.15698/mic2024.03.818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/19/2024]
Abstract
The yeast Saccharomyces cerevisiae is widely used in food and non-food industries. During industrial fermentation yeast strains are exposed to fluctuations in oxygen concentration, osmotic pressure, pH, ethanol concentration, nutrient availability and temperature. Fermentation performance depends on the ability of the yeast strains to adapt to these changes. Suboptimal conditions trigger responses to the external stimuli to allow homeostasis to be maintained. Stress-specific signalling pathways are activated to coordinate changes in transcription, translation, protein function, and metabolic fluxes while a transient arrest of growth and cell cycle progression occur. cAMP-PKA, HOG-MAPK and CWI signalling pathways are turned on during stress response. Comprehension of the mechanisms involved in the responses and in the adaptation to these stresses during fermentation is key to improving this industrial process. The scope of this review is to outline the advancement of knowledge about the cAMP-PKA signalling and the crosstalk of this pathway with the CWI and HOG-MAPK cascades in response to the environmental challenges heat and hyperosmotic stress.
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Affiliation(s)
- Fiorella Galello
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
| | - Mariana Bermúdez-Moretti
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
| | - María Clara Ortolá Martínez
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
| | - Silvia Rossi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
| | - Paula Portela
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
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4
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Wagner ER, Nightingale NM, Jen A, Overmyer KA, McGee M, Coon JJ, Gasch AP. PKA regulatory subunit Bcy1 couples growth, lipid metabolism, and fermentation during anaerobic xylose growth in Saccharomyces cerevisiae. PLoS Genet 2023; 19:e1010593. [PMID: 37410771 DOI: 10.1371/journal.pgen.1010593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 06/22/2023] [Indexed: 07/08/2023] Open
Abstract
Organisms have evolved elaborate physiological pathways that regulate growth, proliferation, metabolism, and stress response. These pathways must be properly coordinated to elicit the appropriate response to an ever-changing environment. While individual pathways have been well studied in a variety of model systems, there remains much to uncover about how pathways are integrated to produce systemic changes in a cell, especially in dynamic conditions. We previously showed that deletion of Protein Kinase A (PKA) regulatory subunit BCY1 can decouple growth and metabolism in Saccharomyces cerevisiae engineered for anaerobic xylose fermentation, allowing for robust fermentation in the absence of division. This provides an opportunity to understand how PKA signaling normally coordinates these processes. Here, we integrated transcriptomic, lipidomic, and phospho-proteomic responses upon a glucose to xylose shift across a series of strains with different genetic mutations promoting either coupled or decoupled xylose-dependent growth and metabolism. Together, results suggested that defects in lipid homeostasis limit growth in the bcy1Δ strain despite robust metabolism. To further understand this mechanism, we performed adaptive laboratory evolutions to re-evolve coupled growth and metabolism in the bcy1Δ parental strain. The evolved strain harbored mutations in PKA subunit TPK1 and lipid regulator OPI1, among other genes, and evolved changes in lipid profiles and gene expression. Deletion of the evolved opi1 gene partially reverted the strain's phenotype to the bcy1Δ parent, with reduced growth and robust xylose fermentation. We suggest several models for how cells coordinate growth, metabolism, and other responses in budding yeast and how restructuring these processes enables anaerobic xylose utilization.
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Affiliation(s)
- Ellen R Wagner
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Nicole M Nightingale
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Annie Jen
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Katherine A Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
- National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, United States of America
| | - Mick McGee
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Joshua J Coon
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
- National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, United States of America
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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5
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Kim C, Kim JG, Kim KY. Anti- Candida Potential of Sclareol in Inhibiting Growth, Biofilm Formation, and Yeast-Hyphal Transition. J Fungi (Basel) 2023; 9:jof9010098. [PMID: 36675919 PMCID: PMC9862543 DOI: 10.3390/jof9010098] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/06/2023] [Accepted: 01/08/2023] [Indexed: 01/13/2023] Open
Abstract
Even though Candida albicans commonly colonizes on most mucosal surfaces including the vaginal and gastrointestinal tract, it can cause candidiasis as an opportunistic infectious fungus. The emergence of resistant Candida strains and the toxicity of anti-fungal agents have encouraged the development of new classes of potential anti-fungal agents. Sclareol, a labdane-type diterpene, showed anti-Candida activity with a minimum inhibitory concentration of 50 μg/mL in 24 h based on a microdilution anti-fungal susceptibility test. Cell membrane permeability with propidium iodide staining and mitochondrial membrane potential with JC-1 staining were increased in C. albicans by treatment of sclareol. Sclareol also suppressed the hyphal formation of C. albicans in both liquid and solid media, and reduced biofilm formation. Taken together, sclareol induces an apoptosis-like cell death against Candida spp. and suppressed biofilm and hyphal formation in C. albicans. Sclareol is of high interest as a novel anti-fungal agent and anti-virulence factor.
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Affiliation(s)
- Chaerim Kim
- Department of Life Science, Gachon University, Seongnam 13120, Gyeonggi-do, Republic of Korea
| | - Jae-Goo Kim
- Graduate School of Biotechnology, Kyung Hee University, Yingin 17104, Gyeonggi-do, Republic of Korea
| | - Ki-Young Kim
- Graduate School of Biotechnology, Kyung Hee University, Yingin 17104, Gyeonggi-do, Republic of Korea
- College of Life Science, Kyung Hee University, Yongin 17104, Gyeonggi-do, Republic of Korea
- Correspondence: ; Tel.: +82-312012633
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6
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Phosphorylation of Jhd2 by the Ras-cAMP-PKA(Tpk2) pathway regulates histone modifications and autophagy. Nat Commun 2022; 13:5675. [PMID: 36167807 PMCID: PMC9515143 DOI: 10.1038/s41467-022-33423-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/16/2022] [Indexed: 11/12/2022] Open
Abstract
Cells need to coordinate gene expression with their metabolic states to maintain cell homeostasis and growth. How cells transduce nutrient availability to appropriate gene expression remains poorly understood. Here we show that glycolysis regulates histone modifications and gene expression by activating protein kinase A (PKA) via the Ras-cyclic AMP pathway. The catalytic subunit of PKA, Tpk2 antagonizes Jhd2-catalyzed H3K4 demethylation by phosphorylating Jhd2 at Ser321 and Ser340 in response to glucose availability. Tpk2-catalyzed Jhd2 phosphorylation impairs its nuclear localization, reduces its binding to chromatin, and promotes its polyubiquitination and degradation by the proteasome. Tpk2-catalyzed Jhd2 phosphorylation also maintains H3K14 acetylation by preventing the binding of histone deacetylase Rpd3 to chromatin. By phosphorylating Jhd2, Tpk2 regulates gene expression, maintains normal chronological life span and promotes autophagy. These results provide a direct connection between metabolism and histone modifications and shed lights on how cells rewire their biological responses to nutrient signals. How cells transduce nutrient availability to appropriate gene expression remains poorly understood. Here the authors show that the nutrient sensor, protein kinase A modulates histone modifications and gene transcription by phosphorylating histone demethylase.
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7
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Yeast Protein Kinase A Isoforms: A Means of Encoding Specificity in the Response to Diverse Stress Conditions? Biomolecules 2022; 12:biom12070958. [PMID: 35883514 PMCID: PMC9313097 DOI: 10.3390/biom12070958] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 02/07/2023] Open
Abstract
Eukaryotic cells have developed a complex circuitry of signalling molecules which monitor changes in their intra- and extracellular environments. One of the most widely studied signalling pathways is the highly conserved cyclic AMP (cAMP)/protein kinase A (PKA) pathway, which is a major glucose sensing circuit in the yeast Saccharomyces cerevisiae. PKA activity regulates diverse targets in yeast, positively activating the processes that are associated with rapid cell growth (e.g., fermentative metabolism, ribosome biogenesis and cell division) and negatively regulating the processes that are associated with slow growth, such as respiratory growth, carbohydrate storage and entry into stationary phase. As in higher eukaryotes, yeast has evolved complexity at the level of the PKA catalytic subunit, and Saccharomyces cerevisiae expresses three isoforms, denoted Tpk1-3. Despite evidence for isoform differences in multiple biological processes, the molecular basis of PKA signalling specificity remains poorly defined, and many studies continue to assume redundancy with regards to PKA-mediated regulation. PKA has canonically been shown to play a key role in fine-tuning the cellular response to diverse stressors; however, recent studies have now begun to interrogate the requirement for individual PKA catalytic isoforms in coordinating distinct steps in stress response pathways. In this review, we discuss the known non-redundant functions of the Tpk catalytic subunits and the evolving picture of how these isoforms establish specificity in the response to different stress conditions.
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Genetic suppressors of Δgrx3 Δgrx4, lacking redundant multidomain monothiol yeast glutaredoxins, rescue growth and iron homeostasis. Biosci Rep 2022; 42:231328. [PMID: 35593209 PMCID: PMC9202360 DOI: 10.1042/bsr20212665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 11/26/2022] Open
Abstract
Saccharomyces cerevisiae Grx3 and Grx4 are multidomain monothiol glutaredoxins that are redundant with each other. They can be efficiently complemented by heterologous expression of their mammalian ortholog, PICOT, which has been linked to tumor development and embryogenesis. PICOT is now believed to act as a chaperone distributing Fe-S clusters, although the first link to iron metabolism was observed with its yeast counterparts. Like PICOT, yeast Grx3 and Grx4 reside in the cytosol and nucleus where they form unusual Fe-S clusters coordinated by two glutaredoxins with CGFS motifs and two molecules of glutathione. Depletion or deletion of Grx3/Grx4 leads to functional impairment of virtually all cellular iron-dependent processes and loss of cell viability, thus making these genes the most upstream components of the iron utilization system. Nevertheless, the Δgrx3/4 double mutant in the BY4741 genetic background is viable and exhibits slow but stable growth under hypoxic conditions. Upon exposure to air, growth of the double deletion strain ceases, and suppressor mutants appear. Adopting a high copy-number library screen approach, we discovered novel genetic interactions: overexpression of ESL1, ESL2, SOK1, SFP1 or BDF2 partially rescues growth and iron utilization defects of Δgrx3/4. This genetic escape from the requirement for Grx3/Grx4 has not been previously described. Our study shows that even a far-upstream component of the iron regulatory machinery (Grx3/4) can be bypassed, and cellular networks involving RIM101 pH sensing, cAMP signaling, mTOR nutritional signaling, or bromodomain acetylation, may confer the bypassing activities.
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9
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Cañonero L, Pautasso C, Galello F, Sigaut L, Pietrasanta L, Arroyo J, Bermúdez-Moretti M, Portela P, Rossi S. Heat stress regulates the expression of TPK1 gene at transcriptional and post-transcriptional levels in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119209. [PMID: 34999138 DOI: 10.1016/j.bbamcr.2021.119209] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/16/2021] [Accepted: 12/28/2021] [Indexed: 12/11/2022]
Abstract
In Saccharomyces cerevisiae cAMP regulates different cellular processes through PKA. The specificity of the response of the cAMP-PKA pathway is highly regulated. Here we address the mechanism through which the cAMP-PKA pathway mediates its response to heat shock and thermal adaptation in yeast. PKA holoenzyme is composed of a regulatory subunit dimer (Bcy1) and two catalytic subunits (Tpk1, Tpk2, or Tpk3). PKA subunits are differentially expressed under certain growth conditions. Here we demonstrate the increased abundance and half-life of TPK1 mRNA and the assembly of this mRNA in cytoplasmic foci during heat shock at 37 °C. The resistance of the foci to cycloheximide-induced disassembly along with the polysome profiling analysis suggest that TPK1 mRNA is impaired for entry into translation. TPK1 expression was also evaluated during a recurrent heat shock and thermal adaptation. Tpk1 protein level is significantly increased during the recovery periods. The crosstalk of cAMP-PKA pathway and CWI signalling was also studied. Wsc3 sensor and some components of the CWI pathway are necessary for the TPK1 expression upon heat shock. The assembly in foci upon thermal stress depends on Wsc3. Tpk1 expression is lower in a wsc3∆ mutant than in WT strain during thermal adaptation and thus the PKA levels are also lower. An increase in Tpk1 abundance in the PKA holoenzyme in response to heat shock is presented, suggesting that a recurrent stress enhanced the fitness for the coming favourable conditions. Therefore, the regulation of TPK1 expression by thermal stress contributes to the specificity of cAMP-PKA signalling.
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Affiliation(s)
- Luciana Cañonero
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica, Buenos Aires, Argentina; CONICET Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Constanza Pautasso
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica, Buenos Aires, Argentina; CONICET Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Fiorella Galello
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica, Buenos Aires, Argentina; CONICET Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Lorena Sigaut
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Física, Buenos Aires, Argentina; CONICET Universidad de Buenos Aires, Instituto de Física de Buenos Aires (IFIBA), Buenos Aires, Argentina
| | - Lia Pietrasanta
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Física, Buenos Aires, Argentina; CONICET Universidad de Buenos Aires, Instituto de Física de Buenos Aires (IFIBA), Buenos Aires, Argentina
| | - Javier Arroyo
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, Madrid, Spain
| | - Mariana Bermúdez-Moretti
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica, Buenos Aires, Argentina; CONICET Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Paula Portela
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica, Buenos Aires, Argentina; CONICET Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Silvia Rossi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica, Buenos Aires, Argentina; CONICET Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina.
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10
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Multi-Omics Analysis of Multiple Glucose-Sensing Receptor Systems in Yeast. Biomolecules 2022; 12:biom12020175. [PMID: 35204676 PMCID: PMC8961648 DOI: 10.3390/biom12020175] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 12/13/2022] Open
Abstract
The yeast Saccharomyces cerevisiae has long been used to produce alcohol from glucose and other sugars. While much is known about glucose metabolism, relatively little is known about the receptors and signaling pathways that indicate glucose availability. Here, we compare the two glucose receptor systems in S. cerevisiae. The first is a heterodimer of transporter-like proteins (transceptors), while the second is a seven-transmembrane receptor coupled to a large G protein (Gpa2) that acts in coordination with two small G proteins (Ras1 and Ras2). Through comprehensive measurements of glucose-dependent transcription and metabolism, we demonstrate that the two receptor systems have distinct roles in glucose signaling: the G-protein-coupled receptor directs carbohydrate and energy metabolism, while the transceptors regulate ancillary processes such as ribosome, amino acids, cofactor and vitamin metabolism. The large G-protein transmits the signal from its cognate receptor, while the small G-protein Ras2 (but not Ras1) integrates responses from both receptor pathways. Collectively, our analysis reveals the molecular basis for glucose detection and the earliest events of glucose-dependent signal transduction in yeast.
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11
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Brink DP, Borgström C, Persson VC, Ofuji Osiro K, Gorwa-Grauslund MF. D-Xylose Sensing in Saccharomyces cerevisiae: Insights from D-Glucose Signaling and Native D-Xylose Utilizers. Int J Mol Sci 2021; 22:12410. [PMID: 34830296 PMCID: PMC8625115 DOI: 10.3390/ijms222212410] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022] Open
Abstract
Extension of the substrate range is among one of the metabolic engineering goals for microorganisms used in biotechnological processes because it enables the use of a wide range of raw materials as substrates. One of the most prominent examples is the engineering of baker's yeast Saccharomyces cerevisiae for the utilization of d-xylose, a five-carbon sugar found in high abundance in lignocellulosic biomass and a key substrate to achieve good process economy in chemical production from renewable and non-edible plant feedstocks. Despite many excellent engineering strategies that have allowed recombinant S. cerevisiae to ferment d-xylose to ethanol at high yields, the consumption rate of d-xylose is still significantly lower than that of its preferred sugar d-glucose. In mixed d-glucose/d-xylose cultivations, d-xylose is only utilized after d-glucose depletion, which leads to prolonged process times and added costs. Due to this limitation, the response on d-xylose in the native sugar signaling pathways has emerged as a promising next-level engineering target. Here we review the current status of the knowledge of the response of S. cerevisiae signaling pathways to d-xylose. To do this, we first summarize the response of the native sensing and signaling pathways in S. cerevisiae to d-glucose (the preferred sugar of the yeast). Using the d-glucose case as a point of reference, we then proceed to discuss the known signaling response to d-xylose in S. cerevisiae and current attempts of improving the response by signaling engineering using native targets and synthetic (non-native) regulatory circuits.
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Affiliation(s)
- Daniel P. Brink
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
| | - Celina Borgström
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
- BioZone Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College St., Toronto, ON M5S 3E5, Canada
| | - Viktor C. Persson
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
| | - Karen Ofuji Osiro
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy, Brasília 70770-901, DF, Brazil
| | - Marie F. Gorwa-Grauslund
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
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12
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Kang S, Seo H, Lee MG, Yun CW. Regulation of Copper Metabolism by Nitrogen Utilization in Saccharomyces cerevisiae. J Fungi (Basel) 2021; 7:jof7090756. [PMID: 34575794 PMCID: PMC8469692 DOI: 10.3390/jof7090756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/03/2021] [Accepted: 09/10/2021] [Indexed: 11/17/2022] Open
Abstract
To understand the relationship between carbon or nitrogen utilization and iron homeostasis, we performed an iron uptake assay with several deletion mutants with partial defects in carbon or nitrogen metabolism. Among them, some deletion mutants defective in carbon metabolism partially and the MEP2 deletion mutant showed lower iron uptake activity than the wild type. Mep2 is known as a high-affinity ammonia transporter in Saccharomyces cerevisiae. Interestingly, we found that nitrogen starvation resulted in lower iron uptake activity than that of wild-type cells without downregulation of the genes involved in the high-affinity iron uptake system FET3/FTR1. However, the gene expression of FRE1 and CTR1 was downregulated by nitrogen starvation. The protein level of Ctr1 was also decreased by nitrogen starvation, and addition of copper to the nitrogen starvation medium partially restored iron uptake activity. However, the expression of MAC1, which is a copper-responsive transcriptional activator, was not downregulated by nitrogen starvation at the transcriptional level but was highly downregulated at the translational level. Mac1 was downregulated dramatically under nitrogen starvation, and treatment with MG132, which is an inhibitor of proteasome-dependent protein degradation, partially attenuated the downregulation of Mac1. Taken together, these results suggest that nitrogen starvation downregulates the high-affinity iron uptake system by degrading Mac1 in a proteasome-dependent manner and eventually downregulates copper metabolism.
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Affiliation(s)
| | | | | | - Cheol-Won Yun
- Correspondence: ; Tel.: +82-2-3290-3456; Fax: +82-2-927-9028
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13
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Urita A, Ishibashi Y, Kawaguchi R, Yanase Y, Tani M. Crosstalk between protein kinase A and the HOG pathway under impaired biosynthesis of complex sphingolipids in budding yeast. FEBS J 2021; 289:766-786. [PMID: 34492172 DOI: 10.1111/febs.16188] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/03/2021] [Accepted: 09/06/2021] [Indexed: 11/28/2022]
Abstract
Complex sphingolipids are important components of the lipid bilayer of budding yeast Saccharomyces cerevisiae, and a defect of the biosynthesis causes widespread cellular dysfunction. In this study, we found that mutations causing upregulation of the cAMP/protein kinase A (PKA) pathway cause hypersensitivity to the defect of complex sphingolipid biosynthesis caused by repression of AUR1 encoding inositol phosphorylceramide synthase, whereas loss of PKA confers resistance to the defect. Loss of PDE2 encoding cAMP phosphodiesterase or PKA did not affect the reduction in complex sphingolipid levels and ceramide accumulation caused by AUR1 repression, suggesting that the change in sensitivity to the AUR1 repression due to the mutation of the cAMP/PKA pathway is not caused by exacerbation or suppression of the abnormal metabolism of sphingolipids. We also identified PBS2 encoding MAPKK in the high-osmolarity glycerol (HOG) pathway as a multicopy suppressor gene that rescues the hypersensitivity to AUR1 repression caused by deletion of IRA2, which causes hyperactivation of the cAMP/PKA pathway. Since the HOG pathway has been identified as one of the rescue systems against the growth defect caused by the impaired biosynthesis of complex sphingolipids, it was assumed that PKA affects activation of the HOG pathway under AUR1-repressive conditions. Under AUR1-repressive conditions, hyperactivation of PKA suppressed the phosphorylation of Hog1, MAPK in the HOG pathway, and transcriptional activation downstream of the HOG pathway. These findings suggested that PKA is possibly involved in the avoidance of excessive activation of the HOG pathway under impaired biosynthesis of complex sphingolipids.
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Affiliation(s)
- Atsuya Urita
- Department of Chemistry, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Yohei Ishibashi
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Ryotaro Kawaguchi
- Department of Chemistry, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Yukimi Yanase
- Department of Chemistry, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Motohiro Tani
- Department of Chemistry, Faculty of Sciences, Kyushu University, Fukuoka, Japan
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14
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Sellers-Moya Á, Nuévalos M, Molina M, Martín H. Clotrimazole-Induced Oxidative Stress Triggers Novel Yeast Pkc1-Independent Cell Wall Integrity MAPK Pathway Circuitry. J Fungi (Basel) 2021; 7:jof7080647. [PMID: 34436186 PMCID: PMC8399625 DOI: 10.3390/jof7080647] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 01/13/2023] Open
Abstract
Azoles are one of the most widely used drugs to treat fungal infections. To further understand the fungal response to azoles, we analyzed the MAPK circuitry of the model yeast Saccharomyces cerevisiae that operates under treatment with these antifungals. Imidazoles, and particularly clotrimazole, trigger deeper changes in MAPK phosphorylation than triazoles, involving a reduction in signaling through the mating pathway and the activation of the MAPKs Hog1 and Slt2 from the High-Osmolarity Glycerol (HOG) and the Cell Wall Integrity (CWI) pathways, respectively. Clotrimazole treatment leads to actin aggregation, mitochondrial alteration, and oxidative stress, which is essential not only for the activation of both MAPKs, but also for the appearance of a low-mobility form of Slt2 caused by additional phosphorylation to that occurring at the conserved TEY activation motif. Clotrimazole-induced ROS production and Slt2 phosphorylation are linked to Tpk3-mediated PKA activity. Resistance to clotrimazole depends on HOG and CWI-pathway-mediated stress responses. However, Pkc1 and other proteins acting upstream in the pathway are not critical for the activation of the Slt2 MAPK module, suggesting a novel rewiring of signaling through the CWI pathway. We further show that the strong impact of azole treatment on MAPK signaling is conserved in other yeast species.
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Affiliation(s)
| | | | - María Molina
- Correspondence: (M.M.); (H.M.); Tel.: +34-91-3941888 (M.M. & H.M.)
| | - Humberto Martín
- Correspondence: (M.M.); (H.M.); Tel.: +34-91-3941888 (M.M. & H.M.)
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15
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Palermo GCDL, Coutouné N, Bueno JGR, Maciel LF, Dos Santos LV. Exploring metal ion metabolisms to improve xylose fermentation in Saccharomyces cerevisiae. Microb Biotechnol 2021; 14:2101-2115. [PMID: 34313008 PMCID: PMC8449651 DOI: 10.1111/1751-7915.13887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/25/2021] [Indexed: 01/22/2023] Open
Abstract
The development of high‐performance xylose‐fermenting yeast is essential to achieve feasible conversion of biomass‐derived sugars in lignocellulose‐based biorefineries. However, engineered C5‐strains of Saccharomyces cerevisiae still present low xylose consumption rates under anaerobic conditions. Here, we explore alternative metabolisms involved in metal homeostasis, which positively affect C5 fermentation and analyse the non‐obvious regulatory network connection of both metabolisms using time‐course transcriptome analysis. Our results indicated the vacuolar Fe2+/Mn2+ transporter CCC1, and the protein involved in heavy metal ion homeostasis BSD2, as promising new targets for rational metabolic engineering strategies, enhancing xylose consumption in nine and 2.3‐fold compared with control. Notably, intracellular metal concentration levels were affected differently by mutations and the results were compared with positive controls isu1Δ, a Fe‐S cluster scaffold protein, and ssk2Δ, a component of HOG pathway. Temporal expression profiles indicate a metabolic remodelling in response to xylose, demonstrating changes in the main sugar sensing signalling pathways.
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Affiliation(s)
- Gisele Cristina de Lima Palermo
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-100, Brazil.,Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Natalia Coutouné
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-100, Brazil.,Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - João Gabriel Ribeiro Bueno
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-100, Brazil.,Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Lucas Ferreira Maciel
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-100, Brazil
| | - Leandro Vieira Dos Santos
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-100, Brazil.,Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
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16
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Alqahtani FM, Handy ST, Sutton CL, Farone MB. Combining Genome-Wide Gene Expression Analysis (RNA-seq) and a Gene Editing Platform (CRISPR-Cas9) to Uncover the Selectively Pro-oxidant Activity of Aurone Compounds Against Candida albicans. Front Microbiol 2021; 12:708267. [PMID: 34335543 PMCID: PMC8319688 DOI: 10.3389/fmicb.2021.708267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/23/2021] [Indexed: 11/13/2022] Open
Abstract
Candida albicans is the major fungal cause of healthcare-associated bloodstream infections worldwide with a 40% mortality rate. The scarcity of antifungal treatments due to the eukaryotic origin of fungal cells has challenged the development of selectively antifungal drugs. In an attempt to identify novel antifungal agents, aurones SH1009 and SH9051, as synthetically bioactive compounds, have been recently documented as anti-Candida agents. Since the molecular mechanisms behind the inhibitory activities of these aurones in C. albicans are unclear, this study aimed to determine the comprehensive cellular processes affected by these aurones and their molecular targets. Genome-wide transcriptional analysis of SH1009- and SH9051-treated C. albicans revealed uniquely repressed expression in different metabolic pathways, particularly trehalose and sulfur amino acid metabolic processes for SH1009 and SH9051, respectively. In contrast, the most commonly enriched process for both aurones was the up-regulation of RNA processing and ribosomal cleavages as an indicator of high oxidative stress, suggesting that a common aspect in the chemical structure of both aurones led to pro-oxidative properties. Additionally, uniquely induced responses (iron ion homeostasis for SH1009 and arginine biosynthesis for SH9051) garnered attention on key roles for the aurone functional groups. Deletion of the transcription factor for the trehalose biosynthesis pathway, Tye7p, resulted in an SH1009-resistant mutant, which also exhibited low trehalose content, validating the primary molecular target of SH1009. Aurone SH9051 uniquely simulated an exogenous supply of methionine or cysteine, leading to sulfur amino acid catabolism as evidenced by quantifying an overproduction of sulfite. Phenyl aurone, the common structure of aurones, contributed proportionally in the pro-oxidative activity through ferric ion reduction effects leading to high ROS levels. Our results determined selective and novel molecular mechanisms for aurone SH1009 and also elucidated the diverse cellular effects of different aurones based on functional groups.
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Affiliation(s)
- Fatmah M Alqahtani
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, United States
| | - Scott T Handy
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, TN, United States
| | - Caleb L Sutton
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, United States
| | - Mary B Farone
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, United States
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17
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Zhang M, Gao ZC, Chi Z, Liu GL, Hu Z, Chi ZM. cAMP-PKA and HOG1 signaling pathways regulate liamocin production by different ways via the transcriptional activator Msn2 in Aureobasidium melanogenum. Enzyme Microb Technol 2020; 143:109705. [PMID: 33375973 DOI: 10.1016/j.enzmictec.2020.109705] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/13/2022]
Abstract
Liamocins, as the secondary metabolites synthesized and secreted by Aureobasidium spp., consist of a single mannitol or a single arabitol head group partially O-acylated with three 3,5-dihydroxydecanoic ester groups or directly esterified with three or four 3,5-dihydroxydecanoic ester tails. Very recently, the whole synthetic pathway of liamocins in A. melanogenum 6-1-2 has been elucidated. It was found that the promoter sequences of all the genes related to liamocin synthesis in A. melanogenum 6-1-2 had stress regulatory elements with core sequences of AGGGG or CCCCT. Therefore, expression of all the genes would be regulated by the Msn2. In this study, it was found that removal of the single one MSN2 gene in A. melanogenum 6-1-2 made the mutant decrease yield of extracellular liamocin by 92.28 %, while complementation of the MSN2 gene in the mutant rendered liamocin synthesis to be restored. When A. melanogenum 6-1-2 was cultured in the liamocin fermentation medium with high glucose and low nitrogen, the Msn2 was localized in the nucleus and positively regulated the expression of the genes related to liamocin biosynthesis. Furthermore, when the key BCY1 gene encoding regulatory subunit of the cAMP-PKA signaling pathway in A. melanogenum 6-1-2 was knocked out, the amount of extracellular liamocins synthesized by the mutant was decreased by 96.73 % and the Msn2 was localized in the cytoplasm. Similarly, when the key HOG1 gene in the HOG1 signaling pathway was deleted, liamocin biosynthesis in the knockout strain was decreased by 98.09 %. However, it was found that the Hog1 may be one part of the general transcription complex to regulate the transcription of the MSN2 gene, leading to the reduced Msn2 and liamocin synthesis in the mutant. In addition, the key TOR1 gene and SNF1 gene in the TOR1 signaling pathway and the SNF1 signaling pathway were not involved in the regulation of the Msn2 activity and liamocin synthesis. It was concluded that the transcriptional activator Msn2, the HOG1 signaling pathway and the cAMP-PKA signaling pathway were involved in the regulation of liamocin biosynthesis and production.
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Affiliation(s)
- Mei Zhang
- College of Marine Life Science, Ocean University of China, Yushan Road, No. 5, Qingdao, China
| | - Zhi-Chao Gao
- College of Marine Life Science, Ocean University of China, Yushan Road, No. 5, Qingdao, China
| | - Zhe Chi
- College of Marine Life Science, Ocean University of China, Yushan Road, No. 5, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266003, Qingdao, China
| | - Guang-Lei Liu
- College of Marine Life Science, Ocean University of China, Yushan Road, No. 5, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266003, Qingdao, China
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, 515063, China
| | - Zhen-Ming Chi
- College of Marine Life Science, Ocean University of China, Yushan Road, No. 5, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266003, Qingdao, China.
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18
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cAMP-PKA signal transduction specificity in Saccharomyces cerevisiae. Curr Genet 2020; 66:1093-1099. [PMID: 32935175 DOI: 10.1007/s00294-020-01107-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 08/23/2020] [Accepted: 09/01/2020] [Indexed: 01/02/2023]
Abstract
Living cells have developed a set of complex signaling responses, which allow them to withstand different environmental challenges. Signaling pathways enable the cell to monitor external and internal states and to articulate the appropriate physiological responses. Cellular signal transmission requires the dynamic formation of spatiotemporal controlled molecular interactions. One of the most important signaling circuits in Saccharomyces cerevisiae is the one controlled by cAMP-Protein Kinase A (PKA). In budding yeast, extracellular glucose and a plethora of signals related with growth and stress conditions regulate the intracellular cAMP levels that modulate PKA activity which in turn regulates a broad range of cellular processes. The cAMP-PKA signaling output requires a controlled specificity of the PKA responses. In this review we discuss the molecular mechanisms that are involved in the establishment of the specificity in the cAMP-PKA signaling pathway in S.cerevisiae.
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19
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Reca S, Galello F, Ojeda L, Pautasso C, Cañonero L, Moreno S, Portela P, Rossi S. Chromatin remodeling and transcription of the TPK1 subunit of PKA during stress in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194599. [DOI: 10.1016/j.bbagrm.2020.194599] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/22/2020] [Accepted: 06/22/2020] [Indexed: 01/10/2023]
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20
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Molecular Elucidation of Riboflavin Production and Regulation in Candida albicans, toward a Novel Antifungal Drug Target. mSphere 2020; 5:5/4/e00714-20. [PMID: 32759338 PMCID: PMC7407072 DOI: 10.1128/msphere.00714-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Candida albicans is an important fungal pathogen causing common superficial infections as well as invasive diseases with an extremely high morbidity and mortality. Antifungal therapies are limited in efficiency and availability. In this research, we describe the regulation of riboflavin production in C. albicans. Since riboflavin biosynthesis is essential to this organism, we can appreciate that targeting it would be a promising new strategy to combat these fungal infections. We provide evidence that one particular enzyme in the production process, CaRib1, would be most promising as an antifungal drug target, as it plays a central role in regulation and proves to be essential in a mouse model of systemic infection. Candida albicans is a major cause of fungal infections, both superficial and invasive. The economic costs as well as consequences for patient welfare are substantial. Only a few treatment options are available due to the high resemblance between fungal targets and host molecules, as both are eukaryotes. Riboflavin is a yellow pigment, also termed vitamin B2. Unlike animals, fungi can synthesize this essential component themselves, thereby leading us to appreciate that targeting riboflavin production is a promising novel strategy against fungal infections. Here, we report that the GTP cyclohydrolase encoded by C. albicansRIB1 (CaRIB1) is essential and rate-limiting for production of riboflavin in the fungal pathogen. We confirm the high potential of CaRib1 as an antifungal drug target, as its deletion completely impairs in vivo infectibility by C. albicans in model systems. Furthermore, the stimulating effect of iron deprivation and PKA activation on riboflavin production seems to involve CaRib1 and the upstream transcription factor CaSef1. Gathering insights in the synthesis mechanism of riboflavin in pathogenic fungi, like C. albicans, will allow us to design a novel strategy and specifically target this process to combat fungal infections. IMPORTANCECandida albicans is an important fungal pathogen causing common superficial infections as well as invasive diseases with an extremely high morbidity and mortality. Antifungal therapies are limited in efficiency and availability. In this research, we describe the regulation of riboflavin production in C. albicans. Since riboflavin biosynthesis is essential to this organism, we can appreciate that targeting it would be a promising new strategy to combat these fungal infections. We provide evidence that one particular enzyme in the production process, CaRib1, would be most promising as an antifungal drug target, as it plays a central role in regulation and proves to be essential in a mouse model of systemic infection.
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21
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Schrank S, Barrington N, Stutzmann GE. Calcium-Handling Defects and Neurodegenerative Disease. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a035212. [PMID: 31427373 DOI: 10.1101/cshperspect.a035212] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Calcium signaling is critical to neuronal function and regulates highly diverse processes such as gene transcription, energy production, protein handling, and synaptic structure and function. Because there are many common underlying calcium-mediated pathological features observed across several neurological conditions, it has been proposed that neurodegenerative diseases have an upstream underlying calcium basis in their pathogenesis. With certain diseases such as Alzheimer's, Parkinson's, and Huntington's, specific sources of calcium dysregulation originating from distinct neuronal compartments or channels have been shown to have defined roles in initiating or sustaining disease mechanisms. Herein, we will review the major hallmarks of these diseases, and how they relate to calcium dysregulation. We will then discuss neuronal calcium handling throughout the neuron, with special emphasis on channels involved in neurodegeneration.
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Affiliation(s)
- Sean Schrank
- Center for Neurodegenerative Disease and Therapeutics, Rosalind Franklin University, North Chicago, Illinois 60064.,School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, Illinois 60064
| | - Nikki Barrington
- Center for Neurodegenerative Disease and Therapeutics, Rosalind Franklin University, North Chicago, Illinois 60064.,School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, Illinois 60064.,Chicago Medical School, Rosalind Franklin University, North Chicago, Illinois 60064
| | - Grace E Stutzmann
- Center for Neurodegenerative Disease and Therapeutics, Rosalind Franklin University, North Chicago, Illinois 60064.,School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, Illinois 60064.,Chicago Medical School, Rosalind Franklin University, North Chicago, Illinois 60064
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22
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Osiro KO, Borgström C, Brink DP, Fjölnisdóttir BL, Gorwa-Grauslund MF. Exploring the xylose paradox in Saccharomyces cerevisiae through in vivo sugar signalomics of targeted deletants. Microb Cell Fact 2019; 18:88. [PMID: 31122246 PMCID: PMC6532234 DOI: 10.1186/s12934-019-1141-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 05/17/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There have been many successful strategies to implement xylose metabolism in Saccharomyces cerevisiae, but no effort has so far enabled xylose utilization at rates comparable to that of glucose (the preferred sugar of this yeast). Many studies have pointed towards the engineered yeast not sensing that xylose is a fermentable carbon source despite growing and fermenting on it, which is paradoxical. We have previously used fluorescent biosensor strains to in vivo monitor the sugar signalome in yeast engineered with xylose reductase and xylitol dehydrogenase (XR/XDH) and have established that S. cerevisiae senses high concentrations of xylose with the same signal as low concentration of glucose, which may explain the poor utilization. RESULTS In the present study, we evaluated the effects of three deletions (ira2∆, isu1∆ and hog1∆) that have recently been shown to display epistatic effects on a xylose isomerase (XI) strain. Through aerobic and anaerobic characterization, we showed that the proposed effects in XI strains were for the most part also applicable in the XR/XDH background. The ira2∆isu1∆ double deletion led to strains with the highest specific xylose consumption- and ethanol production rates but also the lowest biomass titre. The signalling response revealed that ira2∆isu1∆ changed the low glucose-signal in the background strain to a simultaneous signalling of high and low glucose, suggesting that engineering of the signalome can improve xylose utilization. CONCLUSIONS The study was able to correlate the previously proposed beneficial effects of ira2∆, isu1∆ and hog1∆ on S. cerevisiae xylose uptake, with a change in the sugar signalome. This is in line with our previous hypothesis that the key to resolve the xylose paradox lies in the sugar sensing and signalling networks. These results indicate that the future engineering targets for improved xylose utilization should probably be sought not in the metabolic networks, but in the signalling ones.
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Affiliation(s)
- Karen O Osiro
- Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Celina Borgström
- Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Daniel P Brink
- Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
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23
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Daghino S, Di Vietro L, Petiti L, Martino E, Dallabona C, Lodi T, Perotto S. Yeast expression of mammalian Onzin and fungal FCR1 suggests ancestral functions of PLAC8 proteins in mitochondrial metabolism and DNA repair. Sci Rep 2019; 9:6629. [PMID: 31036870 PMCID: PMC6488628 DOI: 10.1038/s41598-019-43136-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/11/2019] [Indexed: 01/07/2023] Open
Abstract
The cysteine-rich PLAC8 domain of unknown function occurs in proteins found in most Eukaryotes. PLAC8-proteins play important yet diverse roles in different organisms, such as control of cell proliferation in animals and plants or heavy metal resistance in plants and fungi. Mammalian Onzin can be either pro-proliferative or pro-apoptotic, depending on the cell type, whereas fungal FCR1 confers cadmium tolerance. Despite their different role in different organisms, we hypothesized common ancestral functions linked to the PLAC8 domain. To address this hypothesis, and to investigate the molecular function of the PLAC8 domain, murine Onzin and fungal FCR1 were expressed in the PLAC8-free yeast Saccharomyces cerevisiae. The two PLAC8-proteins localized in the nucleus and induced almost identical phenotypes and transcriptional changes when exposed to cadmium stress. Like FCR1, Onzin also reduced DNA damage and increased cadmium tolerance by a DUN1-dependent pathway. Both proteins activated transcription of ancient mitochondrial pathways such as leucine and Fe-S cluster biosynthesis, known to regulate cell proliferation and DNA repair in yeast. These results strongly suggest a common ancestral function of PLAC8 proteins and open new perspectives to understand the role of the PLAC8 domain in the cellular biology of Eukaryotes.
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Affiliation(s)
- Stefania Daghino
- Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, 10125, Torino, Italy
| | - Luigi Di Vietro
- Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, 10125, Torino, Italy.,Department of Biochemistry and Biotechnology, Bayer SAS, centre de recherche "la Dargoire" 14, impasse Pierre Baizet CS 99163, 69263, Lyon, CEDEX 09, France
| | - Luca Petiti
- Italian Institute for Genomic Medicine, via Nizza 52, 10126, Torino, Italy
| | - Elena Martino
- Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, 10125, Torino, Italy
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Viale delle Scienze 11/A, 43124, Parma, Italy
| | - Tiziana Lodi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Viale delle Scienze 11/A, 43124, Parma, Italy
| | - Silvia Perotto
- Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, 10125, Torino, Italy.
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24
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Bouchez C, Devin A. Mitochondrial Biogenesis and Mitochondrial Reactive Oxygen Species (ROS): A Complex Relationship Regulated by the cAMP/PKA Signaling Pathway. Cells 2019; 8:cells8040287. [PMID: 30934711 PMCID: PMC6523352 DOI: 10.3390/cells8040287] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/15/2019] [Accepted: 03/20/2019] [Indexed: 12/23/2022] Open
Abstract
Mitochondrial biogenesis is a complex process. It requires the contribution of both the nuclear and the mitochondrial genomes and therefore cross talk between the nucleus and mitochondria. Cellular energy demand can vary by great length and it is now well known that one way to adjust adenosine triphosphate (ATP) synthesis to energy demand is through modulation of mitochondrial content in eukaryotes. The knowledge of actors and signals regulating mitochondrial biogenesis is thus of high importance. Here, we review the regulation of mitochondrial biogenesis both in yeast and in mammalian cells through mitochondrial reactive oxygen species.
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Affiliation(s)
- Cyrielle Bouchez
- Université Bordeaux, IBGC, UMR 5095, 33077 Bordeaux cedex, France.
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, 1, rue Camille Saint Saëns, 33077 Bordeaux Cedex, France.
| | - Anne Devin
- Université Bordeaux, IBGC, UMR 5095, 33077 Bordeaux cedex, France.
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, 1, rue Camille Saint Saëns, 33077 Bordeaux Cedex, France.
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Abstract
Filamentous growth is a fungal morphogenetic response that is critical for virulence in some fungal species. Many aspects of filamentous growth remain poorly understood. We have identified an aspect of filamentous growth in the budding yeast Saccharomyces cerevisiae and the human pathogen Candida albicans where cells behave collectively to invade surfaces in aggregates. These responses may reflect an extension of normal filamentous growth, as they share the same signaling pathways and effector processes. Aggregate responses may involve cooperation among individual cells, because aggregation was stimulated by cell adhesion molecules, secreted enzymes, and diffusible molecules that promote quorum sensing. Our study may provide insights into the genetic basis of collective cellular responses in fungi. The study may have ramifications in fungal pathogenesis, in situations where collective responses occur to promote virulence. Many fungal species, including pathogens, undergo a morphogenetic response called filamentous growth, where cells differentiate into a specialized cell type to promote nutrient foraging and surface colonization. Despite the fact that filamentous growth is required for virulence in some plant and animal pathogens, certain aspects of this behavior remain poorly understood. By examining filamentous growth in the budding yeast Saccharomyces cerevisiae and the opportunistic pathogen Candida albicans, we identify responses where cells undergo filamentous growth in groups of cells or aggregates. In S. cerevisiae, aggregate invasive growth was regulated by signaling pathways that control normal filamentous growth. These pathways promoted aggregation in part by fostering aspects of microbial cooperation. For example, aggregate invasive growth required cellular contacts mediated by the flocculin Flo11p, which was produced at higher levels in aggregates than cells undergoing regular invasive growth. Aggregate invasive growth was also stimulated by secreted enzymes, like invertase, which produce metabolites that are shared among cells. Aggregate invasive growth was also induced by alcohols that promote density-dependent filamentous growth in yeast. Aggregate invasive growth also required highly polarized cell morphologies, which may affect the packing or organization of cells. A directed selection experiment for aggregating phenotypes uncovered roles for the fMAPK and RAS pathways, which indicates that these pathways play a general role in regulating aggregate-based responses in yeast. Our study extends the range of responses controlled by filamentation regulatory pathways and has implications in understanding aspects of fungal biology that may be relevant to fungal pathogenesis. IMPORTANCE Filamentous growth is a fungal morphogenetic response that is critical for virulence in some fungal species. Many aspects of filamentous growth remain poorly understood. We have identified an aspect of filamentous growth in the budding yeast Saccharomyces cerevisiae and the human pathogen Candida albicans where cells behave collectively to invade surfaces in aggregates. These responses may reflect an extension of normal filamentous growth, as they share the same signaling pathways and effector processes. Aggregate responses may involve cooperation among individual cells, because aggregation was stimulated by cell adhesion molecules, secreted enzymes, and diffusible molecules that promote quorum sensing. Our study may provide insights into the genetic basis of collective cellular responses in fungi. The study may have ramifications in fungal pathogenesis, in situations where collective responses occur to promote virulence.
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Myers KS, Riley NM, MacGilvray ME, Sato TK, McGee M, Heilberger J, Coon JJ, Gasch AP. Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast. PLoS Genet 2019; 15:e1008037. [PMID: 30856163 PMCID: PMC6428351 DOI: 10.1371/journal.pgen.1008037] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 03/21/2019] [Accepted: 02/20/2019] [Indexed: 01/08/2023] Open
Abstract
Microbes can be metabolically engineered to produce biofuels and biochemicals, but rerouting metabolic flux toward products is a major hurdle without a systems-level understanding of how cellular flux is controlled. To understand flux rerouting, we investigated a panel of Saccharomyces cerevisiae strains with progressive improvements in anaerobic fermentation of xylose, a sugar abundant in sustainable plant biomass used for biofuel production. We combined comparative transcriptomics, proteomics, and phosphoproteomics with network analysis to understand the physiology of improved anaerobic xylose fermentation. Our results show that upstream regulatory changes produce a suite of physiological effects that collectively impact the phenotype. Evolved strains show an unusual co-activation of Protein Kinase A (PKA) and Snf1, thus combining responses seen during feast on glucose and famine on non-preferred sugars. Surprisingly, these regulatory changes were required to mount the hypoxic response when cells were grown on xylose, revealing a previously unknown connection between sugar source and anaerobic response. Network analysis identified several downstream transcription factors that play a significant, but on their own minor, role in anaerobic xylose fermentation, consistent with the combinatorial effects of small-impact changes. We also discovered that different routes of PKA activation produce distinct phenotypes: deletion of the RAS/PKA inhibitor IRA2 promotes xylose growth and metabolism, whereas deletion of PKA inhibitor BCY1 decouples growth from metabolism to enable robust fermentation without division. Comparing phosphoproteomic changes across ira2Δ and bcy1Δ strains implicated regulatory changes linked to xylose-dependent growth versus metabolism. Together, our results present a picture of the metabolic logic behind anaerobic xylose flux and suggest that widespread cellular remodeling, rather than individual metabolic changes, is an important goal for metabolic engineering.
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Affiliation(s)
- Kevin S. Myers
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Nicholas M. Riley
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Matthew E. MacGilvray
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Trey K. Sato
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Mick McGee
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Justin Heilberger
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, United States of America
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Audrey P. Gasch
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, United States of America
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Glucose Signaling Is Connected to Chromosome Segregation Through Protein Kinase A Phosphorylation of the Dam1 Kinetochore Subunit in Saccharomyces cerevisiae. Genetics 2018; 211:531-547. [PMID: 30546002 DOI: 10.1534/genetics.118.301727] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/10/2018] [Indexed: 11/18/2022] Open
Abstract
The Dam1 complex is an essential component of the outer kinetochore that mediates attachments between spindle microtubules and chromosomes. Dam1p, a subunit of the Dam1 complex, binds to microtubules and is regulated by Aurora B/Ipl1p phosphorylation. We find that overexpression of cAMP-dependent protein kinase (PKA) catalytic subunits (i.e., TPK1, TPK2, TPK3) is lethal in DAM1 mutants and increases the rate of chromosome loss in wild-type cells. Replacing an evolutionarily conserved PKA site (S31) in Dam1p with a nonphosphorylatable alanine suppressed the high-copy PKA dosage lethality in dam1-1 Consistent with Dam1p as a target of PKA, we find that in vitro PKA can directly phosphorylate S31 in Dam1p and we observed phosphorylation of S31 in Dam1p purified from asynchronously growing yeast cells. Cells carrying high-copy TPK2 or a Dam1p phospho-mimetic S31D mutant displayed a reduction in Dam1p localization at the kinetochore, suggesting that PKA phosphorylation plays a role in assembly and/or stability of the Dam1 complex. Furthermore, we observed spindle defects associated with S31 phosphorylation. Finally, we find that phosphorylation of Dam1p on S31 is reduced when glucose is limiting as well as during α-factor arrest, conditions that inhibit PKA activity. These observations suggest that the PKA site of Dam1p participates in regulating kinetochore activity. While PKA is a well-established effector of glucose signaling, our work shows for the first time that glucose-dependent PKA activity has an important function in chromosome segregation.
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de Assis LJ, Manfiolli A, Mattos E, Fabri JHTM, Malavazi I, Jacobsen ID, Brock M, Cramer RA, Thammahong A, Hagiwara D, Ries LNA, Goldman GH. Protein Kinase A and High-Osmolarity Glycerol Response Pathways Cooperatively Control Cell Wall Carbohydrate Mobilization in Aspergillus fumigatus. mBio 2018; 9:e01952-18. [PMID: 30538182 PMCID: PMC6299480 DOI: 10.1128/mbio.01952-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/06/2018] [Indexed: 02/07/2023] Open
Abstract
Aspergillus fumigatus mitogen-activated protein kinases (MAPKs) are involved in maintaining the normal morphology of the cell wall and providing resistance against cell wall-damaging agents. Upon cell wall stress, cell wall-related sugars need to be synthesized from carbohydrate storage compounds. Here we show that this process is dependent on cAMP-dependent protein kinase A (PKA) activity and regulated by the high-osmolarity glycerol response (HOG) MAPKs SakA and MpkC. These protein kinases are necessary for normal accumulation/degradation of trehalose and glycogen, and the lack of these genes reduces glucose uptake and glycogen synthesis. Alterations in glycogen synthesis were observed for the sakA and mpkC deletion mutants, which also displayed alterations in carbohydrate exposure on the cell wall. Carbohydrate mobilization is controlled by SakA interaction with PkaC1 and PkaR, suggesting a putative mechanism where the PkaR regulatory subunit leaves the complex and releases the SakA-PkaC1 complex for activation of enzymes involved in carbohydrate mobilization. This work reveals the communication between the HOG and PKA pathways for carbohydrate mobilization for cell wall construction.IMPORTANCEAspergillus fumigatus is an opportunistic human pathogen causing allergic reactions or systemic infections such as invasive pulmonary aspergillosis, especially in immunocompromised patients. The fungal cell wall is the main component responsible for recognition by the immune system, due to the specific composition of polysaccharide carbohydrates exposed on the surface of the fungal cell wall called pathogen-associated molecular patterns (PAMPs). Key enzymes in the fungal cell wall biosynthesis are a good target for fungal drug development. This report elucidates the cooperation between the HOG and PKA pathways in the mobilization of carbohydrates for fungal cell wall biosynthesis. We suggest that the reduced mobilization of simple sugars causes defects in the structure of the fungal cell wall. In summary, we propose that SakA is important for PKA activity, therefore regulating the availability and mobilization of monosaccharides for fungal cell wall biosynthesis during cell wall damage and the osmotic stress response.
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Affiliation(s)
- Leandro José de Assis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Adriana Manfiolli
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Eliciane Mattos
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - João H T Marilhano Fabri
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Paulo, Brazil
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Paulo, Brazil
| | - Ilse D Jacobsen
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
| | - Matthias Brock
- Fungal Genetics and Biology Group, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Robert A Cramer
- Geisel School of Medicine at Dartmouth, Department of Microbiology and Immunology, Hanover, New Hampshire, USA
| | - Arsa Thammahong
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Daisuke Hagiwara
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | | | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
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29
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Li S, Giardina DM, Siegal ML. Control of nongenetic heterogeneity in growth rate and stress tolerance of Saccharomyces cerevisiae by cyclic AMP-regulated transcription factors. PLoS Genet 2018; 14:e1007744. [PMID: 30388117 PMCID: PMC6241136 DOI: 10.1371/journal.pgen.1007744] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 11/14/2018] [Accepted: 10/05/2018] [Indexed: 01/01/2023] Open
Abstract
Genetically identical cells exhibit extensive phenotypic variation even under constant and benign conditions. This so-called nongenetic heterogeneity has important clinical implications: within tumors and microbial infections, cells show nongenetic heterogeneity in growth rate and in susceptibility to drugs or stress. The budding yeast, Saccharomyces cerevisiae, shows a similar form of nongenetic heterogeneity in which growth rate correlates positively with susceptibility to acute heat stress at the single-cell level. Using genetic and chemical perturbations, combined with high-throughput single-cell assays of yeast growth and gene expression, we show here that heterogeneity in intracellular cyclic AMP (cAMP) levels acting through the conserved Ras/cAMP/protein kinase A (PKA) pathway and its target transcription factors, Msn2 and Msn4, underlies this nongenetic heterogeneity. Lower levels of cAMP correspond to slower growth, as shown by direct comparison of cAMP concentration in subpopulations enriched for slower vs. faster growing cells. Concordantly, an endogenous reporter of this pathway’s activity correlates with growth in individual cells. The paralogs Msn2 and Msn4 differ in their roles in nongenetic heterogeneity in a way that demonstrates slow growth and stress tolerance are not inevitably linked. Heterogeneity in growth rate requires each, whereas only Msn2 is required for heterogeneity in expression of Tsl1, a subunit of trehalose synthase that contributes to acute-stress tolerance. Perturbing nongenetic heterogeneity by mutating genes in this pathway, or by culturing wild-type cells with the cell-permeable cAMP analog 8-bromo-cAMP or the PKA inhibitor H89, significantly impacts survival of acute heat stress. Perturbations that increase intracellular cAMP levels reduce the slower-growing subpopulation and increase susceptibility to acute heat stress, whereas PKA inhibition slows growth and decreases susceptibility to acute heat stress. Loss of Msn2 reduces, but does not completely eliminate, the correlation in individual cells between growth rate and acute-stress survival, suggesting a major role for the Msn2 pathway in nongenetic heterogeneity but also a residual benefit of slow growth. Our results shed light on the genetic control of nongenetic heterogeneity and suggest a possible means of defeating bet-hedging pathogens or tumor cells by making them more uniformly susceptible to treatment. Nongenetic heterogeneity exists when a trait differs among individuals that have identical genotypes and environments. A clonal population can maximize its long-term success in an uncertain environment by diversifying its phenotypes via nongenetic heterogeneity: the currently unfavored ones may become the favored ones when conditions change. Nongenetic heterogeneity has clinical relevance. For example, populations of tumor cells or infectious microbes show cell-to-cell differences in growth and in drug or stress tolerance. This heterogeneity hampers efficient treatment and can potentiate harmful evolution of a tumor or pathogen. We show that in budding yeast, heterogeneity in intracellular cyclic AMP levels acting through the conserved Ras/cAMP/protein kinase A (PKA) pathway and its target transcription factors, Msn2 and Msn4, underlies the nongenetic heterogeneity of both single-cell growth rate and acute heat-stress tolerance. Perturbations of this pathway significantly affect population survival upon acute heat stress. These results illuminate a mechanism of nongenetic heterogeneity and suggest the potential value of antitumor or antifungal treatment strategies that target nongenetic heterogeneity to render the tumor or pathogen population more uniformly susceptible to a second drug that aims to kill.
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Affiliation(s)
- Shuang Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Daniella M. Giardina
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Mark L. Siegal
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- * E-mail:
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30
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Martins TS, Costa V, Pereira C. Signaling pathways governing iron homeostasis in budding yeast. Mol Microbiol 2018; 109:422-432. [DOI: 10.1111/mmi.14009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Telma S. Martins
- I3S-Instituto de Investigação e Inovação em Saúde; Universidade do Porto; Porto Portugal
- IBMC-Instituto de Biologia Molecular e Celular; Universidade do Porto; Porto Portugal
| | - Vítor Costa
- I3S-Instituto de Investigação e Inovação em Saúde; Universidade do Porto; Porto Portugal
- IBMC-Instituto de Biologia Molecular e Celular; Universidade do Porto; Porto Portugal
- Departamento de Biologia Molecular; Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto; Porto Portugal
| | - Clara Pereira
- I3S-Instituto de Investigação e Inovação em Saúde; Universidade do Porto; Porto Portugal
- IBMC-Instituto de Biologia Molecular e Celular; Universidade do Porto; Porto Portugal
- Departamento de Biologia Molecular; Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto; Porto Portugal
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31
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The Gcn2-eIF2α pathway connects iron and amino acid homeostasis in Saccharomyces cerevisiae. Biochem J 2018; 475:1523-1534. [PMID: 29626156 DOI: 10.1042/bcj20170871] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 04/01/2018] [Accepted: 04/03/2018] [Indexed: 01/02/2023]
Abstract
In eukaryotic cells, amino acid biosynthesis is feedback-inhibited by amino acids through inhibition of the conserved protein kinase Gcn2. This decreases phosphorylation of initiation factor eIF2α, resulting in general activation of translation but inhibition of translation of mRNA for transcription factor (TF) Gcn4 in yeast or ATF4 in mammals. These TFs are positive regulators of amino acid biosynthetic genes. As several enzymes of amino acid biosynthesis contain iron-sulfur clusters (ISCs) and iron excess is toxic, iron and amino acid homeostasis should be co-ordinated. Working with the yeast Saccharomyces cerevisiae, we found that amino acid supplementation down-regulates expression of genes for iron uptake and decreases intracellular iron content. This cross-regulation requires Aft1, the major TF activated by iron scarcity, as well as Gcn2 and phosphorylatable eIF2α but not Gcn4. A mutant with constitutive activity of Gcn2 (GCN2c ) shows less repression of iron transport genes by amino acids and increased nuclear localization of Aft1 in an iron-poor medium, and increases iron content in this medium. As Aft1 is activated by depletion of mitochondrial ISCs, it is plausible that the Gcn2-eIF2α pathway inhibits the formation of these complexes. Accordingly, the GCN2c mutant has strongly reduced activity of succinate dehydrogenase, an iron-sulfur mitochondrial enzyme, and is unable to grow in media with very low iron or with galactose instead of glucose, conditions where formation of ISCs is specially needed. This mechanism adjusts the uptake of iron to the needs of amino acid biosynthesis and expands the list of Gcn4-independent activities of the Gcn2-eIF2α regulatory system.
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Martins TS, Pereira C, Canadell D, Vilaça R, Teixeira V, Moradas-Ferreira P, de Nadal E, Posas F, Costa V. The Hog1p kinase regulates Aft1p transcription factor to control iron accumulation. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:61-70. [DOI: 10.1016/j.bbalip.2017.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/15/2017] [Accepted: 10/09/2017] [Indexed: 12/22/2022]
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33
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Isom DG, Page SC, Collins LB, Kapolka NJ, Taghon GJ, Dohlman HG. Coordinated regulation of intracellular pH by two glucose-sensing pathways in yeast. J Biol Chem 2017; 293:2318-2329. [PMID: 29284676 DOI: 10.1074/jbc.ra117.000422] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 12/22/2017] [Indexed: 12/19/2022] Open
Abstract
The yeast Saccharomyces cerevisiae employs multiple pathways to coordinate sugar availability and metabolism. Glucose and other sugars are detected by a G protein-coupled receptor, Gpr1, as well as a pair of transporter-like proteins, Rgt2 and Snf3. When glucose is limiting, however, an ATP-driven proton pump (Pma1) is inactivated, leading to a marked decrease in cytoplasmic pH. Here we determine the relative contribution of the two sugar-sensing pathways to pH regulation. Whereas cytoplasmic pH is strongly dependent on glucose abundance and is regulated by both glucose-sensing pathways, ATP is largely unaffected and therefore cannot account for the changes in Pma1 activity. These data suggest that the pH is a second messenger of the glucose-sensing pathways. We show further that different sugars differ in their ability to control cellular acidification, in the manner of inverse agonists. We conclude that the sugar-sensing pathways act via Pma1 to invoke coordinated changes in cellular pH and metabolism. More broadly, our findings support the emerging view that cellular systems have evolved the use of pH signals as a means of adapting to environmental stresses such as those caused by hypoxia, ischemia, and diabetes.
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Affiliation(s)
- Daniel G Isom
- From the Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599-7365, .,the Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida 33136, and
| | - Stephani C Page
- From the Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599-7365
| | - Leonard B Collins
- the Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina 27599-7432
| | - Nicholas J Kapolka
- the Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida 33136, and
| | - Geoffrey J Taghon
- the Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida 33136, and
| | - Henrik G Dohlman
- From the Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599-7365,
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34
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Pentland DR, Piper-Brown E, Mühlschlegel FA, Gourlay CW. Ras signalling in pathogenic yeasts. MICROBIAL CELL 2017; 5:63-73. [PMID: 29417055 PMCID: PMC5798406 DOI: 10.15698/mic2018.02.612] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The small GTPase Ras acts as a master regulator of growth, stress response and cell death in eukaryotic cells. The control of Ras activity is fundamental, as highlighted by the oncogenic properties of constitutive forms of Ras proteins. Ras also plays a crucial role in the pathogenicity of fungal pathogens where it has been found to regulate a number of adaptions required for virulence. The importance of Ras in fungal disease raises the possibility that it may provide a useful target for the development of new treatments at a time when resistance to available antifungals is increasing. New findings suggest that important regulatory sequences found within fungal Ras proteins that are not conserved may prove useful in the development of new antifungals. Here we review the roles of Ras protein function and signalling in the major human yeast pathogens Candida albicans and Cryptococcus neoformans and discuss the potential for targeting Ras as a novel approach to anti-fungal therapy.
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Affiliation(s)
- Daniel R Pentland
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom, CT2 7NJ
| | - Elliot Piper-Brown
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom, CT2 7NJ
| | - Fritz A Mühlschlegel
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom, CT2 7NJ.,Laboratoire national de santé, 1, Rue Louis Rech, L-3555 Dudelange, Luxembourg
| | - Campbell W Gourlay
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom, CT2 7NJ
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35
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Selvaraj P, Shen Q, Yang F, Naqvi NI. Cpk2, a Catalytic Subunit of Cyclic AMP-PKA, Regulates Growth and Pathogenesis in Rice Blast. Front Microbiol 2017; 8:2289. [PMID: 29209297 PMCID: PMC5702331 DOI: 10.3389/fmicb.2017.02289] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/06/2017] [Indexed: 12/11/2022] Open
Abstract
The cAMP-Protein Kinase A signaling, anchored on CpkA, is necessary for appressorium development and host penetration, but indispensable for infectious growth in Magnaporthe oryzae. In this study, we identified and characterized the gene encoding the second catalytic subunit, CPK2, whose expression was found to be lower compared to CPKA at various stages of pathogenic growth in M. oryzae. Deletion of CPK2 caused no alterations in vegetative growth, conidiation, appressorium formation, or pathogenicity. Surprisingly, the cpkAΔcpk2Δ double deletion strain displayed significant reduction in growth rate and conidiation compared to the single deletion mutants. Interestingly, loss of CPKA and CPK2 resulted in morphogenetic defects in germ tubes (with curled/wavy and serpentine growth pattern) on hydrophobic surfaces, and a complete failure to produce appressoria therein, thus suggesting an important role for CPK2-mediated cAMP-PKA in surface sensing and response pathway. CPKA promoter-driven expression of CPK2 partially suppressed the defects in host penetration and pathogenicity in the cpkAΔ. Such ectopic CPK2 expressing strain successfully penetrated the rice leaves, but was unable to produce proper secondary invasive hyphae, thus underscoring the importance of CpkA in growth and differentiation in planta. The Cpk2-GFP localized to the nuclei and cytoplasmic vesicles in conidia and germ tubes. The Cpk2-GFP colocalized with CpkA-mCherry on vesicles in the cytosol, but such overlap was not evident in the nuclei. Our studies indicate that CpkA and Cpk2 share overlapping functions, but also play distinct roles during pathogenesis-associated signaling and morphogenesis in the rice blast fungus.
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Affiliation(s)
- Poonguzhali Selvaraj
- Temasek Life Sciences Laboratory and Department of Biological Sciences, 1 Research Link, National University of Singapore, Singapore, Singapore
| | - Qing Shen
- Temasek Life Sciences Laboratory and Department of Biological Sciences, 1 Research Link, National University of Singapore, Singapore, Singapore
| | - Fan Yang
- Temasek Life Sciences Laboratory and Department of Biological Sciences, 1 Research Link, National University of Singapore, Singapore, Singapore
| | - Naweed I Naqvi
- Temasek Life Sciences Laboratory and Department of Biological Sciences, 1 Research Link, National University of Singapore, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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36
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Barraza CE, Solari CA, Marcovich I, Kershaw C, Galello F, Rossi S, Ashe MP, Portela P. The role of PKA in the translational response to heat stress in Saccharomyces cerevisiae. PLoS One 2017; 12:e0185416. [PMID: 29045428 PMCID: PMC5646765 DOI: 10.1371/journal.pone.0185416] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 09/12/2017] [Indexed: 11/18/2022] Open
Abstract
Cellular responses to stress stem from a variety of different mechanisms, including translation arrest and relocation of the translationally repressed mRNAs to ribonucleoprotein particles like stress granules (SGs) and processing bodies (PBs). Here, we examine the role of PKA in the S. cerevisiae heat shock response. Under mild heat stress Tpk3 aggregates and promotes aggregation of eIF4G, Pab1 and eIF4E, whereas severe heat stress leads to the formation of PBs and SGs that contain both Tpk2 and Tpk3 and a larger 48S translation initiation complex. Deletion of TPK2 or TPK3 impacts upon the translational response to heat stress of several mRNAs including CYC1, HSP42, HSP30 and ENO2. TPK2 deletion leads to a robust translational arrest, an increase in SGs/PBs aggregation and translational hypersensitivity to heat stress, whereas TPK3 deletion represses SGs/PBs formation, translational arrest and response for the analyzed mRNAs. Therefore, this work provides evidence indicating that Tpk2 and Tpk3 have opposing roles in translational adaptation during heat stress, and highlight how the same signaling pathway can be regulated to generate strikingly distinct physiological outputs.
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Affiliation(s)
- Carla E Barraza
- Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
| | - Clara A Solari
- Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
| | - Irina Marcovich
- Instituto de Investigaciones en Ingenieria Genetica y Biologia Molecular "Dr. Hector N. Torres", Buenos Aires, Argentina
| | - Christopher Kershaw
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Fiorella Galello
- Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
| | - Silvia Rossi
- Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
| | - Mark P Ashe
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Paula Portela
- Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina
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González B, Mas A, Beltran G, Cullen PJ, Torija MJ. Role of Mitochondrial Retrograde Pathway in Regulating Ethanol-Inducible Filamentous Growth in Yeast. Front Physiol 2017; 8:148. [PMID: 28424625 PMCID: PMC5372830 DOI: 10.3389/fphys.2017.00148] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/24/2017] [Indexed: 12/17/2022] Open
Abstract
In yeast, ethanol is produced as a by-product of fermentation through glycolysis. Ethanol also stimulates a developmental foraging response called filamentous growth and is thought to act as a quorum-sensing molecule. Ethanol-inducible filamentous growth was examined in a small collection of wine/European strains, which validated ethanol as an inducer of filamentous growth. Wine strains also showed variability in their filamentation responses, which illustrates the striking phenotypic differences that can occur among individuals. Ethanol-inducible filamentous growth in Σ1278b strains was independent of several of the major filamentation regulatory pathways [including fMAPK, RAS-cAMP, Snf1, Rpd3(L), and Rim101] but required the mitochondrial retrograde (RTG) pathway, an inter-organellar signaling pathway that controls the nuclear response to defects in mitochondrial function. The RTG pathway regulated ethanol-dependent filamentous growth by maintaining flux through the TCA cycle. The ethanol-dependent invasive growth response required the polarisome and transcriptional induction of the cell adhesion molecule Flo11p. Our results validate established stimuli that trigger filamentous growth and show how stimuli can trigger highly specific responses among individuals. Our results also connect an inter-organellar pathway to a quorum sensing response in fungi.
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Affiliation(s)
- Beatriz González
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i VirgiliTarragona, Spain
| | - Albert Mas
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i VirgiliTarragona, Spain
| | - Gemma Beltran
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i VirgiliTarragona, Spain
| | - Paul J Cullen
- Department of Biological Sciences, University at BuffaloBuffalo, NY, USA
| | - María Jesús Torija
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i VirgiliTarragona, Spain
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Hu G, Caza M, Bakkeren E, Kretschmer M, Bairwa G, Reiner E, Kronstad J. A P4-ATPase subunit of the Cdc50 family plays a role in iron acquisition and virulence in Cryptococcus neoformans. Cell Microbiol 2017; 19. [PMID: 28061020 DOI: 10.1111/cmi.12718] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/01/2016] [Accepted: 01/03/2017] [Indexed: 12/29/2022]
Abstract
The pathogenic fungus Cryptococcus neoformans delivers virulence factors such as capsule polysaccharide to the cell surface to cause disease in vertebrate hosts. In this study, we screened for mutants sensitive to the secretion inhibitor brefeldin A to identify secretory pathway components that contribute to virulence. We identified an ortholog of the cell division control protein 50 (Cdc50) family of the noncatalytic subunit of type IV P-type ATPases (flippases) that establish phospholipid asymmetry in membranes and function in vesicle-mediated trafficking. We found that a cdc50 mutant in C. neoformans was defective for survival in macrophages, attenuated for virulence in mice and impaired in iron acquisition. The mutant also showed increased sensitivity to drugs associated with phospholipid metabolism (cinnamycin and miltefosine), the antifungal drug fluconazole and curcumin, an iron chelator that accumulates in the endoplasmic reticulum. Cdc50 is expected to function with catalytic subunits of flippases, and we previously documented the involvement of the flippase aminophospholipid translocases (Apt1) in virulence factor delivery. A comparison of phenotypes with mutants defective in genes encoding candidate flippases (designated APT1, APT2, APT3, and APT4) revealed similarities primarily between cdc50 and apt1 suggesting a potential functional interaction. Overall, these results highlight the importance of membrane composition and homeostasis for the ability of C. neoformans to cause disease.
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Affiliation(s)
- Guanggan Hu
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Mélissa Caza
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Erik Bakkeren
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.,Institute of Microbiology, Zurich, Switzerland
| | - Matthias Kretschmer
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Gaurav Bairwa
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Ethan Reiner
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - James Kronstad
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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Pang CNI, Lai YW, Campbell LT, Chen SCA, Carter DA, Wilkins MR. Transcriptome and network analyses in Saccharomyces cerevisiae reveal that amphotericin B and lactoferrin synergy disrupt metal homeostasis and stress response. Sci Rep 2017; 7:40232. [PMID: 28079179 PMCID: PMC5228129 DOI: 10.1038/srep40232] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 12/02/2016] [Indexed: 12/16/2022] Open
Abstract
Invasive fungal infections are difficult to treat. The few available antifungal drugs have problems with toxicity or efficacy, and resistance is increasing. To overcome these challenges, existing therapies may be enhanced by synergistic combination with another agent. Previously, we found amphotericin B (AMB) and the iron chelator, lactoferrin (LF), were synergistic against a range of different fungal pathogens. This study investigates the mechanism of AMB-LF synergy, using RNA-seq and network analyses. AMB treatment resulted in increased expression of genes involved in iron homeostasis and ATP synthesis. Unexpectedly, AMB-LF treatment did not lead to increased expression of iron and zinc homeostasis genes. However, genes involved in adaptive response to zinc deficiency and oxidative stress had decreased expression. The clustering of co-expressed genes and network analysis revealed that many iron and zinc homeostasis genes are targets of transcription factors Aft1p and Zap1p. The aft1Δ and zap1Δ mutants were hypersensitive to AMB and H2O2, suggesting they are key regulators of the drug response. Mechanistically, AMB-LF synergy could involve AMB affecting the integrity of the cell wall and membrane, permitting LF to disrupt intracellular processes. We suggest that Zap1p- and Aft1p-binding molecules could be combined with existing antifungals to serve as synergistic treatments.
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Affiliation(s)
- Chi Nam Ignatius Pang
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Kensington, New South Wales, Australia
| | - Yu-Wen Lai
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Leona T Campbell
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Sharon C-A Chen
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Sydney Medical School, University of Sydney, Westmead, NSW, Australia
| | - Dee A Carter
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Kensington, New South Wales, Australia
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General Amino Acid Control and 14-3-3 Proteins Bmh1/2 Are Required for Nitrogen Catabolite Repression-Sensitive Regulation of Gln3 and Gat1 Localization. Genetics 2016; 205:633-655. [PMID: 28007891 DOI: 10.1534/genetics.116.195800] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 12/21/2016] [Indexed: 01/08/2023] Open
Abstract
Nitrogen catabolite repression (NCR), the ability of Saccharomyces cerevisiae to use good nitrogen sources in preference to poor ones, derives from nitrogen-responsive regulation of the GATA family transcription activators Gln3 and Gat1 In nitrogen-replete conditions, the GATA factors are cytoplasmic and NCR-sensitive transcription minimal. When only poor nitrogen sources are available, Gln3 is nuclear, dramatically increasing GATA factor-mediated transcription. This regulation was originally attributed to mechanistic Tor protein kinase complex 1 (mTorC1)-mediated control of Gln3 However, we recently showed that two regulatory systems act cumulatively to maintain cytoplasmic Gln3 sequestration, only one of which is mTorC1. Present experiments demonstrate that the other previously elusive component is uncharged transfer RNA-activated, Gcn2 protein kinase-mediated general amino acid control (GAAC). Gcn2 and Gcn4 are required for NCR-sensitive nuclear Gln3-Myc13 localization, and from epistasis experiments Gcn2 appears to function upstream of Ure2 Bmh1/2 are also required for nuclear Gln3-Myc13 localization and appear to function downstream of Ure2 Overall, Gln3 phosphorylation levels decrease upon loss of Gcn2, Gcn4, or Bmh1/2 Our results add a new dimension to nitrogen-responsive GATA-factor regulation and demonstrate the cumulative participation of the mTorC1 and GAAC pathways, which respond oppositely to nitrogen availability, in the nitrogen-responsive control of catabolic gene expression in yeast.
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41
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Papp L, Sipiczki M, Miklós I. Expression pattern and phenotypic characterization of the mutant strain reveals target genes and processes regulated by pka1 in the dimorphic fission yeast Schizosaccharomyces japonicus. Curr Genet 2016; 63:487-497. [PMID: 27678009 DOI: 10.1007/s00294-016-0651-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 09/10/2016] [Accepted: 09/13/2016] [Indexed: 12/01/2022]
Abstract
The cAMP cascade plays an important role in several biological processes. Thus, study of its molecular details can contribute to a better understanding of these processes, treatment of diseases, or even finding antifungal drug targets. To gain further information about the PKA pathway, and its evolutionarily conserved and species-specific features, the central regulator pka1 gene, which encodes the cAMP-dependent protein kinase catalytic subunit, was studied in the less known haplontic, dimorphic fission yeast Schizosaccharomyces japonicus. Namely, this species belongs to a highly divergent phylogenetic branch of fungi. Furthermore, S. japonicus had only a single copy pka1 gene in contrast to the budding yeasts. Therefore, the pka1 deleted mutant was created, whose RNA sequencing and phenotypic studies revealed that the Pka1 regulated at least 373 genes, among them further kinases, phosphatases and transcriptional regulators. It regulated elongation of hyphae, cell size, aging and stress response. Furthermore, half of the pka1 target genes seemed to be conserved in Schizosaccharomyces pombe and S. japonicus. However, there were oppositely regulated genes in the two closely related species. The target genes suggest that this single gene must be able to fulfill all the functions of TPK1-3 of Saccharomyces cerevisiae. Thus, our results shed light on certain similarities and differences of the PKA pathway of S. japonicus compared to the budding yeasts and confirmed the multifunctionality of the pka1 gene, but further experiments are needed to prove its involvement in the metabolic processes and transport.
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Affiliation(s)
- László Papp
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Matthias Sipiczki
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Ida Miklós
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.
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Toxoplasma gondii Cyclic AMP-Dependent Protein Kinase Subunit 3 Is Involved in the Switch from Tachyzoite to Bradyzoite Development. mBio 2016; 7:mBio.00755-16. [PMID: 27247232 PMCID: PMC4895117 DOI: 10.1128/mbio.00755-16] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Toxoplasma gondii is an obligate intracellular apicomplexan parasite that infects warm-blooded vertebrates, including humans. Asexual reproduction in T. gondii allows it to switch between the rapidly replicating tachyzoite and quiescent bradyzoite life cycle stages. A transient cyclic AMP (cAMP) pulse promotes bradyzoite differentiation, whereas a prolonged elevation of cAMP inhibits this process. We investigated the mechanism(s) by which differential modulation of cAMP exerts a bidirectional effect on parasite differentiation. There are three protein kinase A (PKA) catalytic subunits (TgPKAc1 to -3) expressed in T. gondii. Unlike TgPKAc1 and TgPKAc2, which are conserved in the phylum Apicomplexa, TgPKAc3 appears evolutionarily divergent and specific to coccidian parasites. TgPKAc1 and TgPKAc2 are distributed in the cytomembranes, whereas TgPKAc3 resides in the cytosol. TgPKAc3 was genetically ablated in a type II cyst-forming strain of T. gondii (PruΔku80Δhxgprt) and in a type I strain (RHΔku80Δhxgprt), which typically does not form cysts. The Δpkac3 mutant exhibited slower growth than the parental and complemented strains, which correlated with a higher basal rate of tachyzoite-to-bradyzoite differentiation. 3-Isobutyl-1-methylxanthine (IBMX) treatment, which elevates cAMP levels, maintained wild-type parasites as tachyzoites under bradyzoite induction culture conditions (pH 8.2/low CO2), whereas the Δpkac3 mutant failed to respond to the treatment. This suggests that TgPKAc3 is the factor responsible for the cAMP-dependent tachyzoite maintenance. In addition, the Δpkac3 mutant had a defect in the production of brain cysts in vivo, suggesting that a substrate of TgPKAc3 is probably involved in the persistence of this parasite in the intermediate host animals. Toxoplasma gondii is one of the most prevalent eukaryotic parasites in mammals, including humans. Parasites can switch from rapidly replicating tachyzoites responsible for acute infection to slowly replicating bradyzoites that persist as a latent infection. Previous studies have demonstrated that T. gondii cAMP signaling can induce or suppress bradyzoite differentiation, depending on the strength and duration of cAMP signal. Here, we report that TgPKAc3 is responsible for cAMP-dependent tachyzoite maintenance while suppressing differentiation into bradyzoites, revealing one mechanism underlying how this parasite transduces cAMP signals during differentiation.
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Guo L, Breakspear A, Zhao G, Gao L, Kistler HC, Xu JR, Ma LJ. Conservation and divergence of the cyclic adenosine monophosphate-protein kinase A (cAMP-PKA) pathway in two plant-pathogenic fungi: Fusarium graminearum and F. verticillioides. MOLECULAR PLANT PATHOLOGY 2016; 17:196-209. [PMID: 25907134 PMCID: PMC4736682 DOI: 10.1111/mpp.12272] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The cyclic adenosine monophosphate-protein kinase A (cAMP-PKA) pathway is a central signalling cascade that transmits extracellular stimuli and governs cell responses through the second messenger cAMP. The importance of cAMP signalling in fungal biology has been well documented and the key conserved components, adenylate cyclase (AC) and the catalytic subunit of PKA (CPKA), have been functionally characterized. However, other genes involved in this signalling pathway and their regulation are not well understood in filamentous fungi. Here, we performed a comparative transcriptomics analysis of AC and CPKA mutants in two closely related fungi: Fusarium graminearum (Fg) and F. verticillioides (Fv). Combining available Fg transcriptomics and phenomics data, we reconstructed the Fg cAMP signalling pathway. We developed a computational program that combines sequence conservation and patterns of orthologous gene expression to facilitate global transcriptomics comparisons between different organisms. We observed highly correlated expression patterns for most orthologues (80%) between Fg and Fv. We also identified a subset of 482 (6%) diverged orthologues, whose expression under all conditions was at least 50% higher in one genome than in the other. This enabled us to dissect the conserved and unique portions of the cAMP-PKA pathway. Although the conserved portions controlled essential functions, such as metabolism, the cell cycle, chromatin remodelling and the oxidative stress response, the diverged portions had species-specific roles, such as the production and detoxification of secondary metabolites unique to each species. The evolution of the cAMP-PKA signalling pathway seems to have contributed directly to fungal divergence and niche adaptation.
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Affiliation(s)
- Li Guo
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Andrew Breakspear
- USDA-ARS, Cereal Disease Laboratory, University of Minnesota, St Paul, MN, 55108, USA
| | - Guoyi Zhao
- Department of Electrical & Computer Engineering, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Lixin Gao
- Department of Electrical & Computer Engineering, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - H Corby Kistler
- USDA-ARS, Cereal Disease Laboratory, University of Minnesota, St Paul, MN, 55108, USA
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA
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Montalvo-Arredondo J, Jiménez-Benítez Á, Colón-González M, González-Flores J, Flores-Villegas M, González A, Riego-Ruiz L. Functional roles of a predicted branched chain aminotransferase encoded by the LkBAT1 gene of the yeast Lachancea kluyveri. Fungal Genet Biol 2015; 85:71-82. [PMID: 26563416 DOI: 10.1016/j.fgb.2015.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 11/06/2015] [Accepted: 11/07/2015] [Indexed: 02/07/2023]
Abstract
Branched chain amino acid aminotransferases (BCATs) catalyze the last step of the biosynthesis and the first step of the catabolism of branched chain amino acids. In Saccharomyces cerevisiae, BCATs are encoded by the ScBAT1 and ScBAT2 paralogous genes. Analysis of Lachancea kluyveri genome sequence, allowed the identification of the LkBAT1 locus, which could presumably encode a BCAT. A second unlinked locus (LkBAT1bis), exhibiting sequence similarity to LkBAT1 was also identified. To determine the function of these putative BCATs, L. kluyveri mutant strains lacking LkBAT1, LkBAT1bis or both genes were generated and tested for VIL metabolism. LkBat1 displayed branched chain aminotransferase activity and is required for VIL biosynthesis and catabolism. However, Lkbat1Δ mutant is a valine and isoleucine auxotroph and a leucine bradytroph indicating that L. kluyveri harbors an alternative enzyme(s) involved in leucine biosynthesis. Additionally, heterologous reciprocal gene complementation between S. cerevisiae and L. kluyveri orthologous LkBAT1, ScBAT1 and ScBAT2 genes, confirmed that the mitochondrial LkBat1 functions as BCAT in S. cerevisiae, restoring wild type phenotype to the ScBAT1 null mutant. Conversely, LkBAT1bis did not display a role in BCAAs metabolism. However, when ethanol was used as carbon source, deletion of LkBAT1bis in an Lkbat1Δ null strain resulted in an extended 'lag' growth phase, pointing to a potential function of LkBAT1 and LkBAT1bis in the aerobic metabolism of L. kluyveri. These results confirm the BCAT function of LkBAT1 in L. kluyveri, and further support the proposition that the BCAT function in ancestral-type yeasts has been distributed in the two paralogous genes present in S. cerevisiae.
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Affiliation(s)
- Javier Montalvo-Arredondo
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, no. 2055, Col. Lomas 4 Sección, San Luis Potosí, San Luis Potosí 78216, Mexico.
| | - Ángel Jiménez-Benítez
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, no. 2055, Col. Lomas 4 Sección, San Luis Potosí, San Luis Potosí 78216, Mexico.
| | - Maritrini Colón-González
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México D.F. 04510, Mexico.
| | - James González-Flores
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México D.F. 04510, Mexico.
| | - Mirelle Flores-Villegas
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México D.F. 04510, Mexico.
| | - Alicia González
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México D.F. 04510, Mexico.
| | - Lina Riego-Ruiz
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, no. 2055, Col. Lomas 4 Sección, San Luis Potosí, San Luis Potosí 78216, Mexico.
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Choi J, Jung WH, Kronstad JW. The cAMP/protein kinase A signaling pathway in pathogenic basidiomycete fungi: Connections with iron homeostasis. J Microbiol 2015; 53:579-87. [PMID: 26231374 DOI: 10.1007/s12275-015-5247-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 07/03/2015] [Accepted: 07/03/2015] [Indexed: 12/26/2022]
Abstract
A number of pathogenic species of basidiomycete fungi are either life-threatening pathogens of humans or major economic pests for crop production. Sensing the host is a key aspect of pathogen proliferation during disease, and signal transduction pathways are critically important for detecting environmental conditions and facilitating adaptation. This review focuses on the contributions of the cAMP/protein kinase A (PKA) signaling pathway in Cryptococcus neoformans, a species that causes meningitis in humans, and Ustilago maydis, a model phytopathogen that causes a smut disease on maize. Environmental sensing by the cAMP/PKA pathway regulates the production of key virulence traits in C. neoformans including the polysaccharide capsule and melanin. For U. maydis, the pathway controls the dimorphic transition from budding growth to the filamentous cell type required for proliferation in plant tissue. We discuss recent advances in identifying new components of the cAMP/PKA pathway in these pathogens and highlight an emerging theme that pathway signaling influences iron acquisition.
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Affiliation(s)
- Jaehyuk Choi
- Division of Life Sciences, and Culture Collection and DNA Bank of Mushrooms, Incheon National University, Incheon, 406-772, Republic of Korea
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Pérez-Landero S, Sandoval-Motta S, Martínez-Anaya C, Yang R, Folch-Mallol JL, Martínez LM, Ventura L, Guillén-Navarro K, Aldana-González M, Nieto-Sotelo J. Complex regulation of Hsf1-Skn7 activities by the catalytic subunits of PKA in Saccharomyces cerevisiae: experimental and computational evidences. BMC SYSTEMS BIOLOGY 2015. [PMID: 26209979 PMCID: PMC4515323 DOI: 10.1186/s12918-015-0185-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Background The cAMP-dependent protein kinase regulatory network (PKA-RN) regulates metabolism, memory, learning, development, and response to stress. Previous models of this network considered the catalytic subunits (CS) as a single entity, overlooking their functional individualities. Furthermore, PKA-RN dynamics are often measured through cAMP levels in nutrient-depleted cells shortly after being fed with glucose, dismissing downstream physiological processes. Results Here we show that temperature stress, along with deletion of PKA-RN genes, significantly affected HSE-dependent gene expression and the dynamics of the PKA-RN in cells growing in exponential phase. Our genetic analysis revealed complex regulatory interactions between the CS that influenced the inhibition of Hsf1/Skn7 transcription factors. Accordingly, we found new roles in growth control and stress response for Hsf1/Skn7 when PKA activity was low (cdc25Δ cells). Experimental results were used to propose an interaction scheme for the PKA-RN and to build an extension of a classic synchronous discrete modeling framework. Our computational model reproduced the experimental data and predicted complex interactions between the CS and the existence of a repressor of Hsf1/Skn7 that is activated by the CS. Additional genetic analysis identified Ssa1 and Ssa2 chaperones as such repressors. Further modeling of the new data foresaw a third repressor of Hsf1/Skn7, active only in theabsence of Tpk2. By averaging the network state over all its attractors, a good quantitative agreement between computational and experimental results was obtained, as the averages reflected more accurately the population measurements. Conclusions The assumption of PKA being one molecular entity has hindered the study of a wide range of behaviors. Additionally, the dynamics of HSE-dependent gene expression cannot be simulated accurately by considering the activity of single PKA-RN components (i.e., cAMP, individual CS, Bcy1, etc.). We show that the differential roles of the CS are essential to understand the dynamics of the PKA-RN and its targets. Our systems level approach, which combined experimental results with theoretical modeling, unveils the relevance of the interaction scheme for the CS and offers quantitative predictions for several scenarios (WT vs. mutants in PKA-RN genes and growth at optimal temperature vs. heat shock). Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0185-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sergio Pérez-Landero
- Instituto de Biología, Universidad Nacional Autónoma de México, 04510, México, D.F., Mexico.
| | - Santiago Sandoval-Motta
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico.
| | - Claudia Martínez-Anaya
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico.
| | - Runying Yang
- Present Address: Department of Anesthesiology, Pharmacology & Therapeutics, The University of British Columbia, Vancouver, V6T 1Z4, BC, Canada.
| | - Jorge Luis Folch-Mallol
- Present Address: Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, 62209, Cuernavaca, Mor., Mexico.
| | - Luz María Martínez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico.
| | - Larissa Ventura
- Present Address: Grupo La Florida México, Tlalnepantla, 54170, Edo. de Méx., Mexico.
| | | | - Maximino Aldana-González
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico.
| | - Jorge Nieto-Sotelo
- Instituto de Biología, Universidad Nacional Autónoma de México, 04510, México, D.F., Mexico.
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Wilderman A, Guo Y, Divakaruni AS, Perkins G, Zhang L, Murphy AN, Taylor SS, Insel PA. Proteomic and Metabolic Analyses of S49 Lymphoma Cells Reveal Novel Regulation of Mitochondria by cAMP and Protein Kinase A. J Biol Chem 2015. [PMID: 26203188 DOI: 10.1074/jbc.m115.658153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyclic AMP (cAMP), acting via protein kinase A (PKA), regulates many cellular responses, but the role of mitochondria in such responses is poorly understood. To define such roles, we used quantitative proteomic analysis of mitochondria-enriched fractions and performed functional and morphologic studies of wild-type (WT) and kin(-) (PKA-null) murine S49 lymphoma cells. Basally, 75 proteins significantly differed in abundance between WT and kin(-) S49 cells. WT, but not kin(-), S49 cells incubated with the cAMP analog 8-(4-chlorophenylthio)adenosine cAMP (CPT-cAMP) for 16 h have (a) increased expression of mitochondria-related genes and proteins, including ones in pathways of branched-chain amino acid and fatty acid metabolism and (b) increased maximal capacity of respiration on branched-chain keto acids and fatty acids. CPT-cAMP also regulates the cellular rate of ATP-utilization, as the rates of both ATP-linked respiration and proton efflux are decreased in WT but not kin(-) cells. CPT-cAMP protected WT S49 cells from glucose or glutamine deprivation, In contrast, CPT-cAMP did not protect kin(-) cells or WT cells treated with the PKA inhibitor H89 from glutamine deprivation. Under basal conditions, the mitochondrial structure of WT and kin(-) S49 cells is similar. Treatment with CPT-cAMP produced apoptotic changes (i.e. decreased mitochondrial density and size and loss of cristae) in WT, but not kin(-) cells. Together, these findings show that cAMP acts via PKA to regulate multiple aspects of mitochondrial function and structure. Mitochondrial perturbation thus likely contributes to cAMP/PKA-mediated cellular responses.
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Affiliation(s)
- Andrea Wilderman
- From the Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0626
| | - Yurong Guo
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0654
| | - Ajit S Divakaruni
- From the Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0626
| | - Guy Perkins
- National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, California 92093-0608, and
| | - Lingzhi Zhang
- From the Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0626
| | - Anne N Murphy
- From the Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0626
| | - Susan S Taylor
- From the Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0626, Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0654
| | - Paul A Insel
- From the Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0626, Department of Medicine, University of California San Diego, La Jolla, California 92093
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Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival. mBio 2015; 6:mBio.00427-15. [PMID: 25873380 PMCID: PMC4453552 DOI: 10.1128/mbio.00427-15] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We studied the flocculation mechanism at the molecular level by determining the atomic structures of N-Flo1p and N-Lg-Flo1p in complex with their ligands. We show that they have similar ligand binding mechanisms but distinct carbohydrate specificities and affinities, which are determined by the compactness of the binding site. We characterized the glycans of Flo1p and their role in this binding process and demonstrate that glycan-glycan interactions significantly contribute to the cell-cell adhesion mechanism. Therefore, the extended flocculation mechanism is based on the self-interaction of Flo proteins and this interaction is established in two stages, involving both glycan-glycan and protein-glycan interactions. The crucial role of calcium in both types of interaction was demonstrated: Ca2+ takes part in the binding of the carbohydrate to the protein, and the glycans aggregate only in the presence of Ca2+. These results unify the generally accepted lectin hypothesis with the historically first-proposed “Ca2+-bridge” hypothesis. Additionally, a new role of cell flocculation is demonstrated; i.e., flocculation is linked to cell conjugation and mating, and survival chances consequently increase significantly by spore formation and by introduction of genetic variability. The role of Flo1p in mating was demonstrated by showing that mating efficiency is increased when cells flocculate and by differential transcriptome analysis of flocculating versus nonflocculating cells in a low-shear environment (microgravity). The results show that a multicellular clump (floc) provides a uniquely organized multicellular ultrastructure that provides a suitable microenvironment to induce and perform cell conjugation and mating. Yeast cells can form multicellular clumps under adverse growth conditions that protect cells from harsh environmental stresses. The floc formation is based on the self-interaction of Flo proteins via an N-terminal PA14 lectin domain. We have focused on the flocculation mechanism and its role. We found that carbohydrate specificity and affinity are determined by the accessibility of the binding site of the Flo proteins where the external loops in the ligand-binding domains are involved in glycan recognition specificity. We demonstrated that, in addition to the Flo lectin-glycan interaction, glycan-glycan interactions also contribute significantly to cell-cell recognition and interaction. Additionally, we show that flocculation provides a uniquely organized multicellular ultrastructure that is suitable to induce and accomplish cell mating. Therefore, flocculation is an important mechanism to enhance long-term yeast survival.
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Binder U, Benčina M, Fizil Á, Batta G, Chhillar AK, Marx F. Protein kinase A signaling and calcium ions are major players in PAF mediated toxicity against Aspergillus niger. FEBS Lett 2015; 589:1266-71. [PMID: 25882631 PMCID: PMC4424949 DOI: 10.1016/j.febslet.2015.03.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 03/27/2015] [Accepted: 03/30/2015] [Indexed: 11/16/2022]
Abstract
Aspergillus niger is highly susceptible to the antifungal protein PAF. Ca2+ and cAMP/PKA signalling are interconnected in response to PAF. PAF toxicity requires the activation of the cAMP/PkaA signaling cascade. PAF evokes a sustained increase in the [Ca2+]c resting level. Only a functional PAF protein interferes with the fungal Ca2+ homeostasis. PAF represents a promising molecule to develop new antifungal strategies.
The Penicillium chrysogenum antifungal protein PAF is toxic against potentially pathogenic Ascomycetes. We used the highly sensitive aequorin-expressing model Aspergillus niger to identify a defined change in cytoplasmic free Ca2+ dynamics in response to PAF. This Ca2+ signature depended on an intact positively charged lysine-rich PAF motif. By combining Ca2+ measurements in A. niger mutants with deregulated cAMP/protein kinase A (PKA) signaling, we proved the interconnection of Ca2+ perturbation and cAMP/PKA signaling in the mechanistic function of PAF. A deep understanding of the mode of action of PAF is an invaluable prerequisite for its future application as new antifungal drug.
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Affiliation(s)
- Ulrike Binder
- Biocenter, Division of Molecular Biology, Medical University of Innsbruck, Innrain 80, A-6020 Innsbruck, Austria; Division of Hygiene and Medical Microbiology, Schöpfstrasse 41, Medical University of Innsbruck, A-6020 Innsbruck, Austria
| | - Mojca Benčina
- Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Ádám Fizil
- Department of Organic Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Gyula Batta
- Department of Organic Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Anil K Chhillar
- Biocenter, Division of Molecular Biology, Medical University of Innsbruck, Innrain 80, A-6020 Innsbruck, Austria; Centre for Biotechnology, Maharshi Dayanand University, IN-124001 Rohtak, Haryana, India
| | - Florentine Marx
- Biocenter, Division of Molecular Biology, Medical University of Innsbruck, Innrain 80, A-6020 Innsbruck, Austria.
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Developmental Growth Control Exerted via the Protein A Kinase Tpk2 in Ashbya gossypii. EUKARYOTIC CELL 2015; 14:593-601. [PMID: 25862153 DOI: 10.1128/ec.00045-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/03/2015] [Indexed: 01/18/2023]
Abstract
Sporulation in Ashbya gossypii is induced by nutrient-limited conditions and leads to the formation of haploid spores. Using RNA-seq, we have determined a gene set induced upon sporulation, which bears considerable overlap with that of Saccharomyces cerevisiae but also contains A. gossypii-specific genes. Addition of cyclic AMP (cAMP) to nutrient-limited media blocks sporulation and represses the induction of sporulation specific genes. Deletion of the protein kinase A (PKA) catalytic subunits encoded by TPK1 and TPK2 showed reduced growth in tpk1 but enhanced growth in the tpk2 strain; however, both mutants sporulated well. Sporulation can be blocked by cAMP in tpk1 but not in tpk2 strains. Similarly, TPK2 acts at a second developmental switch promoting the break in spore dormancy. In S. cerevisiae, PKA phosphorylates and inhibits Msn2/4. The transcript profiles of the tpk1 and msn2/4 mutants were very similar to that of the wild type under sporulation conditions. However, deletion of the single A. gossypii MSN2/4 homolog generated a specific sporulation defect. We identified a set of genes involved in spore wall assembly that was downregulated in the msn2/4 mutant, particularly DIT2, suggesting that poor spore viability may be due to lysis of spores. Our results reveal specific functional differences between the two catalytic PKA subunits in A. gossypii and identified Tpk2 as the key A kinase that transduces developmental decisions of growth. Our data also suggest that Msn2/4 is involved only at a late step of sporulation in A. gossypii and is not a major regulator of IME1.
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