1
|
Kalli S, Vallieres C, Violet J, Sanders JW, Chapman J, Vincken JP, Avery SV, Araya-Cloutier C. Cellular Responses and Targets in Food Spoilage Yeasts Exposed to Antifungal Prenylated Isoflavonoids. Microbiol Spectr 2023; 11:e0132723. [PMID: 37428107 PMCID: PMC10433819 DOI: 10.1128/spectrum.01327-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/17/2023] [Indexed: 07/11/2023] Open
Abstract
Prenylated isoflavonoids are phytochemicals with promising antifungal properties. Recently, it was shown that glabridin and wighteone disrupted the plasma membrane (PM) of the food spoilage yeast Zygosaccharomyces parabailii in distinct ways, which led us to investigate further their modes of action (MoA). Transcriptomic profiling with Z. parabailii showed that genes encoding transmembrane ATPase transporters, including Yor1, and genes homologous to the pleiotropic drug resistance (PDR) subfamily in Saccharomyces cerevisiae were upregulated in response to both compounds. Gene functions involved in fatty acid and lipid metabolism, proteostasis, and DNA replication processes were overrepresented among genes upregulated by glabridin and/or wighteone. Chemogenomic analysis using the genome-wide deletant collection for S. cerevisiae further suggested an important role for PM lipids and PM proteins. Deletants of gene functions involved in biosynthesis of very-long-chain fatty acids (constituents of PM sphingolipids) and ergosterol were hypersensitive to both compounds. Using lipid biosynthesis inhibitors, we corroborated roles for sphingolipids and ergosterol in prenylated isoflavonoid action. The PM ABC transporter Yor1 and Lem3-dependent flippases conferred sensitivity and resistance, respectively, to the compounds, suggesting an important role for PM phospholipid asymmetry in their MoAs. Impaired tryptophan availability, likely linked to perturbation of the PM tryptophan permease Tat2, was evident in response to glabridin. Finally, substantial evidence highlighted a role of the endoplasmic reticulum (ER) in cellular responses to wighteone, including gene functions associated with ER membrane stress or with phospholipid biosynthesis, the primary lipid of the ER membrane. IMPORTANCE Preservatives, such as sorbic acid and benzoic acid, inhibit the growth of undesirable yeast and molds in foods. Unfortunately, preservative tolerance and resistance in food spoilage yeast, such as Zygosaccharomyces parabailii, is a growing challenge in the food industry, which can compromise food safety and increase food waste. Prenylated isoflavonoids are the main defense phytochemicals in the Fabaceae family. Glabridin and wighteone belong to this group of compounds and have shown potent antifungal activity against food spoilage yeasts. The present study demonstrated the mode of action of these compounds against food spoilage yeasts by using advanced molecular tools. Overall, the cellular actions of these two prenylated isoflavonoids share similarities (at the level of the plasma membrane) but also differences. Tryptophan import was specifically affected by glabridin, whereas endoplasmic reticulum membrane stress was specifically induced by wighteone. Understanding the mode of action of these novel antifungal agents is essential for their application in food preservation.
Collapse
Affiliation(s)
- Sylvia Kalli
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Cindy Vallieres
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Joseph Violet
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | | | - John Chapman
- Unilever Foods Innovation Centre, Wageningen, the Netherlands
| | - Jean-Paul Vincken
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Simon V. Avery
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Carla Araya-Cloutier
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, the Netherlands
| |
Collapse
|
2
|
Laidlaw KME, Calder G, MacDonald C. Recycling of cell surface membrane proteins from yeast endosomes is regulated by ubiquitinated Ist1. J Cell Biol 2022; 221:213481. [PMID: 36125415 PMCID: PMC9491851 DOI: 10.1083/jcb.202109137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 07/28/2022] [Accepted: 08/23/2022] [Indexed: 11/22/2022] Open
Abstract
Upon internalization, many surface membrane proteins are recycled back to the plasma membrane. Although these endosomal trafficking pathways control surface protein activity, the precise regulatory features and division of labor between interconnected pathways are poorly defined. In yeast, we show recycling back to the surface occurs through distinct pathways. In addition to retrograde recycling pathways via the late Golgi, used by synaptobrevins and driven by cargo ubiquitination, we find nutrient transporter recycling bypasses the Golgi in a pathway driven by cargo deubiquitination. Nutrient transporters rapidly internalize to, and recycle from, endosomes marked by the ESCRT-III associated factor Ist1. This compartment serves as both “early” and “recycling” endosome. We show Ist1 is ubiquitinated and that this is required for proper endosomal recruitment and cargo recycling to the surface. Additionally, the essential ATPase Cdc48 and its adaptor Npl4 are required for recycling, potentially through regulation of ubiquitinated Ist1. This collectively suggests mechanistic features of recycling from endosomes to the plasma membrane are conserved.
Collapse
Affiliation(s)
- Kamilla M E Laidlaw
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Grant Calder
- Imaging and Cytometry Laboratory, Bioscience Technology Facility, Department of Biology, University of York, York, UK
| | - Chris MacDonald
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| |
Collapse
|
3
|
Mahendrarajan V, Bari VK. A critical role of farnesol in the modulation of Amphotericin B and Aureobasidin A antifungal drug susceptibility. Mycology 2022; 13:305-317. [DOI: 10.1080/21501203.2022.2138599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Venkatramanan Mahendrarajan
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda, India
| | - Vinay Kumar Bari
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda, India
| |
Collapse
|
4
|
Bergin SA, Zhao F, Ryan AP, Müller CA, Nieduszynski CA, Zhai B, Rolling T, Hohl TM, Morio F, Scully J, Wolfe KH, Butler G. Systematic Analysis of Copy Number Variations in the Pathogenic Yeast Candida parapsilosis Identifies a Gene Amplification in RTA3 That is Associated with Drug Resistance. mBio 2022; 13:e0177722. [PMID: 36121151 PMCID: PMC9600344 DOI: 10.1128/mbio.01777-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/31/2022] [Indexed: 01/12/2023] Open
Abstract
We analyzed the genomes of 170 C. parapsilosis isolates and identified multiple copy number variations (CNVs). We identified two genes, RTA3 (CPAR2_104610) and ARR3 (CPAR2_601050), each of which was the target of multiple independent amplification events. Phylogenetic analysis shows that most of these amplifications originated only once. For ARR3, which encodes a putative arsenate transporter, 8 distinct CNVs were identified, ranging in size from 2.3 kb to 10.5 kb with 3 to 23 copies. For RTA3, 16 distinct CNVs were identified, ranging in size from 0.3 kb to 4.5 kb with 2 to ~50 copies. One unusual amplification resulted in a DUP-TRP/INV-DUP structure similar to some human CNVs. RTA3 encodes a putative phosphatidylcholine (PC) floppase which is known to regulate the inward translocation of PC in Candida albicans. We found that an increased copy number of RTA3 correlated with resistance to miltefosine, an alkylphosphocholine drug that affects PC metabolism. Additionally, we conducted an adaptive laboratory evolution experiment in which two C. parapsilosis isolates were cultured in increasing concentrations of miltefosine. Two genes, CPAR2_303950 and CPAR2_102700, coding for putative PC flippases homologous to S. cerevisiae DNF1 gained homozygous protein-disrupting mutations in the evolved strains. Overall, our results show that C. parapsilosis can gain resistance to miltefosine, a drug that has recently been granted orphan drug designation approval by the United States Food and Drug Administration for the treatment of invasive candidiasis, through both CNVs or loss-of-function alleles in one of the flippase genes. IMPORTANCE Copy number variations (CNVs) are an important source of genomic diversity that have been associated with drug resistance. We identify two unusual CNVs in the human fungal pathogen Candida parapsilosis. Both target a single gene (RTA3 or ARR3), and they have occurred multiple times in multiple isolates. The copy number of RTA3, a putative floppase that controls the inward translocation of lipids in the cell membrane, correlates with resistance to miltefosine, a derivative of phosphatidylcholine (PC) that was originally developed as an anticancer drug. In 2021, miltefosine was designated an orphan drug by the United States Food and Drug Administration for the treatment of invasive candidiasis. Importantly, we find that resistance to miltefosine is also caused by mutations in flippases, which control the outward movement of lipids, and that many C. parapsilosis isolates are prone to easily acquiring an increased resistance to miltefosine.
Collapse
Affiliation(s)
- Sean A. Bergin
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Fang Zhao
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Adam P. Ryan
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Carolin A. Müller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Conrad A. Nieduszynski
- Earlham Institute, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Bing Zhai
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Thierry Rolling
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tobias M. Hohl
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Florent Morio
- Nantes Université, CHU de Nantes, Cibles et Médicaments des Infections et de l'Immunité, IICiMed, Nantes, France
| | - Jillian Scully
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Kenneth H. Wolfe
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| |
Collapse
|
5
|
Vu BG, Moye-Rowley WS. Nonidentical function of Upc2A binding sites in the Candida glabrata CDR1 promoter. Genetics 2022; 222:iyac135. [PMID: 36063046 PMCID: PMC9526049 DOI: 10.1093/genetics/iyac135] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/15/2022] [Indexed: 01/04/2023] Open
Abstract
Increased expression of the Candida glabrata CDR1 gene, encoding an ATP-binding cassette membrane transporter, is routinely observed in fluconazole-resistant isolates of this pathogenic yeast. CDR1 transcription has been well-documented to be due to activity of the Zn2Cys6 zinc cluster-containing transcription factor Pdr1. Gain-of-function mutations in the gene encoding this factor are the most commonly observed cause of fluconazole hyper-resistance in clinical isolates. We have recently found that the sterol-responsive transcription factor Upc2A also acts to control CDR1 transcription, providing a direct link between ergosterol biosynthesis and expression of Pdr1 target genes. While this earlier work implicated Upc2A as an activator of CDR1 transcription, our further analyses revealed the presence of a second Upc2A binding site that negatively regulated CDR1 expression. This Upc2A binding site designated a sterol-responsive element (SRE) was found to have significant lower affinity for Upc2A DNA-binding than the previously described SRE. This new SRE was designated SRE2 while the original, positively acting site was named SRE1. A mutant version of SRE2 prevented in vitro DNA-binding by recombinant Upc2A and, when introduced into the CDR1 promoter, caused decreased fluconazole susceptibility and increased CDR1 expression. This negative effect caused by loss of SRE2 was shown to be Pdr1 independent, consistent with the presence of at least one additional activator of CDR1 transcription. The ability of Upc2A to exert either positive or negative effects on gene expression resembles behavior of mammalian nuclear receptor proteins and reveals an unexpectedly complex nature for SRE effects on gene regulation.
Collapse
Affiliation(s)
- Bao Gia Vu
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - William Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| |
Collapse
|
6
|
Song L, Xue X, Wang S, Li J, Jin K, Xia Y. MaAts, an Alkylsulfatase, Contributes to Fungal Tolerances against UV-B Irradiation and Heat-Shock in Metarhizium acridum. J Fungi (Basel) 2022; 8:jof8030270. [PMID: 35330272 PMCID: PMC8951457 DOI: 10.3390/jof8030270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 11/30/2022] Open
Abstract
Sulfatases are commonly divided into three classes: type I, type II, and type III sulfatases. The type III sulfatase, alkylsulfatase, could hydrolyze the primary alkyl sulfates, such as sodium dodecyl sulfate (SDS) and sodium octyl sulfate. Thus, it has the potential application of SDS biodegradation. However, the roles of alkylsulfatase in biological control fungus remain unclear. In this study, an alkylsulfatase gene MaAts was identified from Metarhizium acridum. The deletion strain (ΔMaAts) and the complemented strain (CP) were constructed to reveal their functions in M. acridum. The activity of alkylsulfatase in ΔMaAts was dramatically reduced compared to the wild-type (WT) strain. The loss of MaAts delayed conidial germination, conidiation, and significantly declined the fungal tolerances to UV-B irradiation and heat-shock, while the fungal conidial yield and virulence were unaffected in M. acridum. The transcription levels of stress resistance-related genes were significantly changed after MaAts inactivation. Furthermore, digital gene expression profiling showed that 512 differential expression genes (DEGs), including 177 up-regulated genes and 335 down-regulated genes in ΔMaAts, were identified. Of these DEGs, some genes were involved in melanin synthesis, cell wall integrity, and tolerances to various stresses. These results indicate that MaAts and the DEGs involved in fungal stress tolerances may be candidate genes to be adopted to improve the stress tolerances of mycopesticides.
Collapse
Affiliation(s)
- Lei Song
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 401331, China; (L.S.); (X.X.); (S.W.); (J.L.)
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing 401331, China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing 401331, China
| | - Xiaoning Xue
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 401331, China; (L.S.); (X.X.); (S.W.); (J.L.)
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing 401331, China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing 401331, China
| | - Shuqin Wang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 401331, China; (L.S.); (X.X.); (S.W.); (J.L.)
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing 401331, China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing 401331, China
| | - Juan Li
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 401331, China; (L.S.); (X.X.); (S.W.); (J.L.)
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing 401331, China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing 401331, China
| | - Kai Jin
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 401331, China; (L.S.); (X.X.); (S.W.); (J.L.)
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing 401331, China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing 401331, China
- Correspondence: (K.J.); (Y.X.); Tel.: +86-23-65120990 (Y.X.)
| | - Yuxian Xia
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 401331, China; (L.S.); (X.X.); (S.W.); (J.L.)
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing 401331, China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing 401331, China
- Correspondence: (K.J.); (Y.X.); Tel.: +86-23-65120990 (Y.X.)
| |
Collapse
|
7
|
Amoiradaki K, Bunting KR, Paine KM, Ayre JE, Hogg K, Laidlaw KME, MacDonald C. The Rpd3-Complex Regulates Expression of Multiple Cell Surface Recycling Factors in Yeast. Int J Mol Sci 2021; 22:12477. [PMID: 34830359 PMCID: PMC8617818 DOI: 10.3390/ijms222212477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022] Open
Abstract
Intracellular trafficking pathways control residency and bioactivity of integral membrane proteins at the cell surface. Upon internalisation, surface cargo proteins can be delivered back to the plasma membrane via endosomal recycling pathways. Recycling is thought to be controlled at the metabolic and transcriptional level, but such mechanisms are not fully understood. In yeast, recycling of surface proteins can be triggered by cargo deubiquitination and a series of molecular factors have been implicated in this trafficking. In this study, we follow up on the observation that many subunits of the Rpd3 lysine deacetylase complex are required for recycling. We validate ten Rpd3-complex subunits in recycling using two distinct assays and developed tools to quantify both. Fluorescently labelled Rpd3 localises to the nucleus and complements recycling defects, which we hypothesised were mediated by modulated expression of Rpd3 target gene(s). Bioinformatics implicated 32 candidates that function downstream of Rpd3, which were over-expressed and assessed for capacity to suppress recycling defects of rpd3∆ cells. This effort yielded three hits: Sit4, Dit1 and Ldb7, which were validated with a lipid dye recycling assay. Additionally, the essential phosphatidylinositol-4-kinase Pik1 was shown to have a role in recycling. We propose recycling is governed by Rpd3 at the transcriptional level via multiple downstream target genes.
Collapse
Affiliation(s)
- Konstantina Amoiradaki
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK; (K.A.); (K.R.B.); (K.M.P.); (J.E.A.); (K.M.E.L.)
| | - Kate R. Bunting
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK; (K.A.); (K.R.B.); (K.M.P.); (J.E.A.); (K.M.E.L.)
| | - Katherine M. Paine
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK; (K.A.); (K.R.B.); (K.M.P.); (J.E.A.); (K.M.E.L.)
| | - Josephine E. Ayre
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK; (K.A.); (K.R.B.); (K.M.P.); (J.E.A.); (K.M.E.L.)
| | - Karen Hogg
- Imaging and Cytometry Laboratory, Bioscience Technology Facility, University of York, York YO10 5DD, UK;
| | - Kamilla M. E. Laidlaw
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK; (K.A.); (K.R.B.); (K.M.P.); (J.E.A.); (K.M.E.L.)
| | - Chris MacDonald
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK; (K.A.); (K.R.B.); (K.M.P.); (J.E.A.); (K.M.E.L.)
| |
Collapse
|
8
|
Kumari S, Kumar M, Gaur NA, Prasad R. Multiple roles of ABC transporters in yeast. Fungal Genet Biol 2021; 150:103550. [PMID: 33675986 DOI: 10.1016/j.fgb.2021.103550] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 01/29/2021] [Accepted: 02/25/2021] [Indexed: 12/20/2022]
Abstract
The ATP binding cassette (ABC) transporters, first discovered as high-affinity nutrient importers in bacteria, rose to prominence when their ability to confer multidrug resistance (MDR) to cancer cells was realized. The most characterized human permeability glycoprotein (P-gp) is a dominant exporter of anti-cancer drugs and its overexpression is directly linked to MDR. The overexpression of drug efflux pumps belonging to the ABC superfamily is also a frequent cause of resistance to antifungals. Fungi has a battery of ABC proteins, but in variable numbers and at different subcellular locations. These proteins perform many critical functions, from serving as gatekeepers for xenobiotic cleansing to translocating various structurally unrelated cargoes, including lipids, fatty acids, ions, peptides, sterols, metabolites and toxins. Their emerging additional roles in cellular physiology and virulence call for attention to analyze and re-examine their divergent functions in yeast. In brief, this review traces the history of ABC transporters in yeast and discusses their typical physiological functions that go beyond their well-known role as antifungal drug efflux pumps.
Collapse
Affiliation(s)
- Sonam Kumari
- Yeast Biofuel Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Mohit Kumar
- Yeast Biofuel Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; Amity Institute of Integrative Science and Health, Amity Institute of Biotechnology, Amity University Gurgaon, 122413 Haryana, India
| | - Naseem A Gaur
- Yeast Biofuel Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India.
| | - Rajendra Prasad
- Amity Institute of Integrative Science and Health, Amity Institute of Biotechnology, Amity University Gurgaon, 122413 Haryana, India.
| |
Collapse
|
9
|
Abstract
G-protein-coupled receptors (GPCRs) are the largest family of transmembrane receptors in fungi. These receptors have an important role in the transduction of extracellular signals into intracellular sites in response to diverse stimuli. They enable fungi to coordinate cell function and metabolism, thereby promoting their survival and propagation, and sense certain fundamentally conserved elements, such as nutrients, pheromones, and stress, for adaptation to their niches, environmental stresses, and host environment, causing disease and pathogen virulence. This chapter highlights the role of GPCRs in fungi in coordinating cell function and metabolism. Fungal cells sense the molecular interactions between extracellular signals. Their respective sensory systems are described here in detail.
Collapse
Affiliation(s)
- Abd El-Latif Hesham
- Department of Genetics Faculty of Agriculture, Beni-Suef University, Beni-Suef, Egypt
| | | | | | | | - Vijai Kumar Gupta
- AgroBioSciences and Chemical & Biochemical Sciences Department, University Mohammed VI Polytechnic (UM6P), Benguerir, Morocco
| |
Collapse
|
10
|
Claus S, Jezierska S, Van Bogaert INA. Protein‐facilitated transport of hydrophobic molecules across the yeast plasma membrane. FEBS Lett 2019; 593:1508-1527. [DOI: 10.1002/1873-3468.13469] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 05/31/2019] [Accepted: 06/03/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Silke Claus
- Biochemical and Microbial Technology Universiteit Gent Belgium
| | | | - Inge N. A. Van Bogaert
- Lab. of Industrial Microbiology and Biocatalysis Faculty of Bioscience Engineering Ghent University Belgium
| |
Collapse
|
11
|
Construction and Use of a Recyclable Marker To Examine the Role of Major Facilitator Superfamily Protein Members in Candida glabrata Drug Resistance Phenotypes. mSphere 2018; 3:mSphere00099-18. [PMID: 29600281 PMCID: PMC5874441 DOI: 10.1128/msphere.00099-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 02/27/2018] [Indexed: 11/27/2022] Open
Abstract
Export of drugs is a problem for chemotherapy of infectious organisms. A class of membrane proteins called the major facilitator superfamily contains a large number of proteins that often elevate drug resistance when overproduced but do not impact this phenotype when the gene is removed. We wondered if this absence of a phenotype for a disruption allele might be due to the redundancy of this group of membrane proteins. We describe the production of an easy-to-use recyclable marker cassette that will allow construction of strains lacking multiple members of the MFS family of transporter proteins. Candida glabrata is the second most common species causing candidiasis. C. glabrata can also readily acquire resistance to azole drugs, complicating its treatment. Here we add to the collection of disruption markers to aid in genetic analysis of this yeast. This new construct is marked with a nourseothricin resistance cassette that produces an estrogen-activated form of Cre recombinase in a methionine-regulated manner. This allows eviction and reuse of this cassette in a facile manner. Using this new disruption marker, we have constructed a series of strains lacking different members of the major facilitator superfamily (MFS) of membrane transporter proteins. The presence of 15 MFS proteins that may contribute to drug resistance in C. glabrata placed a premium on development of a marker that could easily be reused to construct multiple gene-disrupted strains. Employing this recyclable marker, we found that loss of the MFS transporter-encoding gene FLR1 caused a dramatic increase in diamide resistance (as seen before), and deletion of two other MFS-encoding genes did not influence this phenotype. Interestingly, loss of FLR1 led to an increase in levels of oxidized glutathione, suggesting a possible molecular explanation for this enhanced oxidant sensitivity. We also found that while overproduction of the transcription factor Yap1 could suppress the fluconazole sensitivity caused by loss of the important ATP-binding cassette transporter protein Cdr1, this required the presence of FLR1. IMPORTANCE Export of drugs is a problem for chemotherapy of infectious organisms. A class of membrane proteins called the major facilitator superfamily contains a large number of proteins that often elevate drug resistance when overproduced but do not impact this phenotype when the gene is removed. We wondered if this absence of a phenotype for a disruption allele might be due to the redundancy of this group of membrane proteins. We describe the production of an easy-to-use recyclable marker cassette that will allow construction of strains lacking multiple members of the MFS family of transporter proteins.
Collapse
|
12
|
Sarmiento‐Villamil JL, García‐Pedrajas NE, Baeza‐Montañez L, García‐Pedrajas MD. The APSES transcription factor Vst1 is a key regulator of development in microsclerotium- and resting mycelium-producing Verticillium species. MOLECULAR PLANT PATHOLOGY 2018; 19:59-76. [PMID: 27696683 PMCID: PMC6638171 DOI: 10.1111/mpp.12496] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 09/28/2016] [Accepted: 09/28/2016] [Indexed: 05/12/2023]
Abstract
Plant pathogens of the genus Verticillium pose a threat to many important crops worldwide. They are soil-borne fungi which invade the plant systemically, causing wilt symptoms. We functionally characterized the APSES family transcription factor Vst1 in two Verticillium species, V. dahliae and V. nonalfalfae, which produce microsclerotia and melanized hyphae as resistant structures, respectively. We found that, in V. dahliae Δvst1 strains, microsclerotium biogenesis stalled after an initial swelling of hyphal cells and cultures were never pigmented. In V. nonalfalfae Δvst1, melanized hyphae were also absent. These results suggest that Vst1 controls melanin biosynthesis independent of its role in morphogenesis. The absence of vst1 also had a great impact on sporulation in both species, affecting the generation of the characteristic verticillate conidiophore structure and sporulation rates in liquid medium. In contrast with these key roles in development, Vst1 activity was dispensable for virulence. We performed a microarray analysis comparing global transcription patterns of wild-type and Δvst1 in V. dahliae. G-protein/cyclic adenosine monophosphate (G-protein/cAMP) signalling and mitogen-activated protein kinase (MAPK) cascades are known to regulate fungal morphogenesis and virulence. The microarray analysis revealed a negative interaction of Vst1 with G-protein/cAMP signalling and a positive interaction with MAPK signalling. This analysis also identified Rho signalling as a potential regulator of morphogenesis in V. dahliae, positively interacting with Vst1. Furthermore, it exposed the association of secondary metabolism and development in this species, identifying Vst1 as a potential co-regulator of both processes. Characterization of the putative Vst1 targets identified in this study will aid in the dissection of specific aspects of development.
Collapse
Affiliation(s)
- Jorge L. Sarmiento‐Villamil
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’ ‐ Universidad de Málaga ‐ Consejo Superior de Investigaciones Científicas (IHSM‐UMA‐CSIC), Estación Experimental ‘La Mayora’, 29750 Algarrobo‐CostaMálagaSpain
| | - Nicolás E. García‐Pedrajas
- Department of Computing and Numerical Analysis, C2 Building 3rd FloorCampus Universitario de RabanalesCórdoba14071Spain
| | - Lourdes Baeza‐Montañez
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’ ‐ Universidad de Málaga ‐ Consejo Superior de Investigaciones Científicas (IHSM‐UMA‐CSIC), Estación Experimental ‘La Mayora’, 29750 Algarrobo‐CostaMálagaSpain
| | - María D. García‐Pedrajas
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’ ‐ Universidad de Málaga ‐ Consejo Superior de Investigaciones Científicas (IHSM‐UMA‐CSIC), Estación Experimental ‘La Mayora’, 29750 Algarrobo‐CostaMálagaSpain
| |
Collapse
|
13
|
Srivastava A, Sircaik S, Husain F, Thomas E, Ror S, Rastogi S, Alim D, Bapat P, Andes DR, Nobile CJ, Panwar SL. Distinct roles of the 7-transmembrane receptor protein Rta3 in regulating the asymmetric distribution of phosphatidylcholine across the plasma membrane and biofilm formation in Candida albicans. Cell Microbiol 2017; 19. [PMID: 28745020 DOI: 10.1111/cmi.12767] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 07/10/2017] [Accepted: 07/14/2017] [Indexed: 12/17/2022]
Abstract
Fungal pathogens such as Candida albicans exhibit several survival mechanisms to evade attack by antifungals and colonise host tissues. Rta3, a member of the Rta1-like family of lipid-translocating exporters has a 7-transmembrane domain topology, similar to the G-protein-coupled receptors and is unique to the fungal kingdom. Our findings point towards a role for the plasma membrane localised Rta3 in providing tolerance to miltefosine, an analogue of alkylphosphocholine, by maintaining mitochondrial energetics. Concurrent with miltefosine susceptibility, the rta3Δ/Δ strain displays increased inward translocation (flip) of fluorophore-labelled phosphatidylcholine (PC) across the plasma membrane attributed to enhanced PC-specific flippase activity. We also assign a novel role to Rta3 in the Bcr1-regulated pathway for in vivo biofilm development. Transcriptome analysis reveals that Rta3 regulates expression of Bcr1 target genes involved in cell surface properties, adhesion, and hyphal growth. We show that rta3Δ/Δ mutant is biofilm-defective in a rat venous catheter model of infection and that BCR1 overexpression rescues this defect, indicating that Bcr1 functions downstream of Rta3 to mediate biofilm formation in C. albicans. The identification of this novel Rta3-dependent regulatory network that governs biofilm formation and PC asymmetry across the plasma membrane will provide important insights into C. albicans pathogenesis.
Collapse
Affiliation(s)
- Archita Srivastava
- Yeast Molecular Genetics Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shabnam Sircaik
- Yeast Molecular Genetics Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Farha Husain
- Yeast Molecular Genetics Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Edwina Thomas
- Yeast Molecular Genetics Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shivani Ror
- Yeast Molecular Genetics Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sumit Rastogi
- Yeast Molecular Genetics Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Darakshan Alim
- Yeast Molecular Genetics Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Priyanka Bapat
- Department of Molecular and Cell Biology, University of California, Merced, California, USA.,Quantitative and System Biology Graduate Program, University of California, Merced, California, USA
| | - David R Andes
- Department of Medicine, Section of Infectious Diseases, University of Wisconsin, Madison, Wisconsin, USA
| | - Clarissa J Nobile
- Department of Molecular and Cell Biology, University of California, Merced, California, USA
| | - Sneh L Panwar
- Yeast Molecular Genetics Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
14
|
TOR Complex 2-Regulated Protein Kinase Fpk1 Stimulates Endocytosis via Inhibition of Ark1/Prk1-Related Protein Kinase Akl1 in Saccharomyces cerevisiae. Mol Cell Biol 2017; 37:MCB.00627-16. [PMID: 28069741 PMCID: PMC5359421 DOI: 10.1128/mcb.00627-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/03/2017] [Indexed: 12/23/2022] Open
Abstract
Depending on the stress, plasma membrane alterations activate or inhibit yeast target of rapamycin (TOR) complex 2, which, in turn, upregulates or downregulates the activity of its essential downstream effector, protein kinase Ypk1. Through phosphorylation of multiple substrates, Ypk1 controls many processes that restore homeostasis. One such substrate is protein kinase Fpk1, which is negatively regulated by Ypk1. Fpk1 phosphorylates and stimulates flippases that translocate aminoglycerophospholipids from the outer to the inner leaflet of the plasma membrane. Fpk1 has additional roles, but other substrates were uncharacterized. We show that Fpk1 phosphorylates and inhibits protein kinase Akl1, related to protein kinases Ark1 and Prk1, which modulate the dynamics of actin patch-mediated endocytosis. Akl1 has two Fpk1 phosphorylation sites (Ark1 and Prk1 have none) and is hypophosphorylated when Fpk1 is absent. Conversely, under conditions that inactivate TORC2-Ypk1 signaling, which alleviates Fpk1 inhibition, Akl1 is hyperphosphorylated. Monitoring phosphorylation of known Akl1 substrates (Sla1 and Ent2) confirmed that Akl1 is hyperactive when not phosphorylated by Fpk1. Fpk1-mediated negative regulation of Akl1 enhances endocytosis, because an Akl1 mutant immune to Fpk1 phosphorylation causes faster dissociation of Sla1 from actin patches, confers elevated resistance to doxorubicin (a toxic compound whose entry requires endocytosis), and impedes Lucifer yellow uptake (a marker of fluid phase endocytosis). Thus, TORC2-Ypk1, by regulating Fpk1-mediated phosphorylation of Akl1, adjusts the rate of endocytosis.
Collapse
|
15
|
Makuta H, Obara K, Kihara A. Loop 5 region is important for the activity of the long-chain base transporter Rsb1. J Biochem 2017; 161:207-213. [PMID: 28175317 DOI: 10.1093/jb/mvw059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/05/2016] [Indexed: 11/12/2022] Open
Abstract
Intracellular lipid amounts are regulated not only by metabolism but also by efflux. Yeast Rsb1 is the only known transporter/floppase of the sphingolipid components long-chain bases (LCBs). However, even fundamental knowledge about Rsb1, such as important amino acid residues for activity and substrate recognition, still remains unclear. Rsb1 belongs to the Rta1-like family. To date, it has not been determined whether all family members share a common ability to export LCBs. Here, we revealed that within the Rta1-like family, only Rsb1 suppressed the hypersensitivity of the mutant cells lacking LCB 1-phoshate-degrading enzymes, suggesting that LCB-exporting activity is specific to Rsb1. Rsb1 contains a characteristic region (loop 5), which does not exist in other proteins of the Rta1-like family. We found that deletion of this region caused loss of Rsb1 function. Further mutational analysis of loop 5 revealed that the charged amino acid residues E223, D225 and R236 were important for Rsb1 activity. In addition to LCBs, Rsb1 facilitated the export of 1-hexadecanol, but not palmitic acid, which suggests that Rsb1 recognizes the C1 hydroxyl group. Thus, our findings provide an important clue for understanding the molecular mechanism of LCB export.
Collapse
Affiliation(s)
- Hiroshi Makuta
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Keisuke Obara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Akio Kihara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| |
Collapse
|
16
|
Jadhav S, Russo S, Cowart LA, Greenberg ML. Inositol Depletion Induced by Acute Treatment of the Bipolar Disorder Drug Valproate Increases Levels of Phytosphingosine. J Biol Chem 2017; 292:4953-4959. [PMID: 28100786 DOI: 10.1074/jbc.m117.775460] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 01/17/2017] [Indexed: 12/13/2022] Open
Abstract
Bipolar disorder (BD) is a severe psychiatric illness affecting ∼1% of the world population. Valproate (VPA) and lithium, widely used for the treatment of BD, are not universally effective. These drugs have been shown to cause inositol depletion, but translating this observation to a specific therapeutic mechanism has been difficult, hampering the development of more effective therapies. We have shown previously in yeast that chronic VPA treatment induces the unfolded protein response due to increasing ceramide levels. To gain insight into the mechanisms activated during acute VPA treatment, we performed a genome-wide expression study in yeast treated with VPA for 30 min. We observed increased mRNA and protein levels of RSB1, which encodes an exporter of long chain bases dihydrosphingosine (DHS) and phytosphingosine (PHS), and further saw that VPA increased sensitivity of an rsb1Δ mutant to PHS, suggesting that VPA increases long chain base levels. Consistent with this, PHS levels were elevated in wild type and, to a greater extent, in rsb1Δ cells. Expression of ORM genes (negative regulators of PHS synthesis) and of fatty acid elongase genes FEN1 and SUR4 were decreased, and expression of YOR1 (exporter of PHS-1P) and DPL1 (lyase that degrades DHS-1P and PHS-1P) was increased. These effects were more pronounced in medium lacking inositol, and were mirrored by inositol starvation of an ino1Δ mutant. These findings provide a metabolic explanation as to how VPA-mediated inositol depletion causes increased synthesis of PHS and further support the therapeutic relevance of inositol depletion as a bipolar disorder treatment.
Collapse
Affiliation(s)
- Shyamalagauri Jadhav
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Sarah Russo
- the Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, and.,the Ralph H. Johnson Veterans Affairs Medical Center, Charleston, South Carolina 29425
| | - L Ashley Cowart
- the Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, and.,the Ralph H. Johnson Veterans Affairs Medical Center, Charleston, South Carolina 29425
| | - Miriam L Greenberg
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202,
| |
Collapse
|
17
|
Jadhav S, Russo S, Cottier S, Schneiter R, Cowart A, Greenberg ML. Valproate Induces the Unfolded Protein Response by Increasing Ceramide Levels. J Biol Chem 2016; 291:22253-22261. [PMID: 27590340 DOI: 10.1074/jbc.m116.752634] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Indexed: 11/06/2022] Open
Abstract
Bipolar disorder (BD), which is characterized by depression and mania, affects 1-2% of the world population. Current treatments are effective in only 40-60% of cases and cause severe side effects. Valproate (VPA) is one of the most widely used drugs for the treatment of BD, but the therapeutic mechanism of action of this drug is not understood. This knowledge gap has hampered the development of effective treatments. To identify candidate pathways affected by VPA, we performed a genome-wide expression analysis in yeast cells grown in the presence or absence of the drug. VPA caused up-regulation of FEN1 and SUR4, encoding fatty acid elongases that catalyze the synthesis of very long chain fatty acids (C24 to C26) required for ceramide synthesis. Interestingly, fen1Δ and sur4Δ mutants exhibited VPA sensitivity. In agreement with increased fatty acid elongase gene expression, VPA increased levels of phytoceramide, especially those containing C24-C26 fatty acids. Consistent with an increase in ceramide, VPA decreased the expression of amino acid transporters, increased the expression of ER chaperones, and activated the unfolded protein response element (UPRE), suggesting that VPA induces the UPR pathway. These effects were rescued by supplementation of inositol and similarly observed in inositol-starved ino1Δ cells. Starvation of ino1Δ cells increased expression of FEN1 and SUR4, increased ceramide levels, decreased expression of nutrient transporters, and induced the UPR. These findings suggest that VPA-mediated inositol depletion induces the UPR by increasing the de novo synthesis of ceramide.
Collapse
Affiliation(s)
- Shyamalagauri Jadhav
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Sarah Russo
- the Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, the Ralph H. Johnson Veterans Affairs Medical Center, Charleston, South Carolina 29401, and
| | - Stéphanie Cottier
- the Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Roger Schneiter
- the Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Ashley Cowart
- the Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, the Ralph H. Johnson Veterans Affairs Medical Center, Charleston, South Carolina 29401, and
| | - Miriam L Greenberg
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202,
| |
Collapse
|
18
|
Control of Plasma Membrane Permeability by ABC Transporters. EUKARYOTIC CELL 2015; 14:442-53. [PMID: 25724885 DOI: 10.1128/ec.00021-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 02/19/2015] [Indexed: 12/13/2022]
Abstract
ATP-binding cassette transporters Pdr5 and Yor1 from Saccharomyces cerevisiae control the asymmetric distribution of phospholipids across the plasma membrane as well as serving as ATP-dependent drug efflux pumps. Mutant strains lacking these transporter proteins were found to exhibit very different resistance phenotypes to two inhibitors of sphingolipid biosynthesis that act either late (aureobasidin A [AbA]) or early (myriocin [Myr]) in the pathway leading to production of these important plasma membrane lipids. These pdr5Δ yor1 strains were highly AbA resistant but extremely sensitive to Myr. We provide evidence that these phenotypic changes are likely due to modulation of the plasma membrane flippase complexes, Dnf1/Lem3 and Dnf2/Lem3. Flippases act to move phospholipids from the outer to the inner leaflet of the plasma membrane. Genetic analyses indicate that lem3Δ mutant strains are highly AbA sensitive and Myr resistant. These phenotypes are fully epistatic to those seen in pdr5Δ yor1 strains. Direct analysis of AbA-induced signaling demonstrated that loss of Pdr5 and Yor1 inhibited the AbA-triggered phosphorylation of the AGC kinase Ypk1 and its substrate Orm1. Microarray experiments found that a pdr5Δ yor1 strain induced a Pdr1-dependent induction of the entire Pdr regulon. Our data support the view that Pdr5/Yor1 negatively regulate flippase function and activity of the nuclear Pdr1 transcription factor. Together, these data argue that the interaction of the ABC transporters Pdr5 and Yor1 with the Lem3-dependent flippases regulates permeability of AbA via control of plasma membrane protein function as seen for the high-affinity tryptophan permease Tat2.
Collapse
|
19
|
Identification of genomic binding sites for Candida glabrata Pdr1 transcription factor in wild-type and ρ0 cells. Antimicrob Agents Chemother 2014; 58:6904-12. [PMID: 25199772 DOI: 10.1128/aac.03921-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The fungal pathogen Candida glabrata is an emerging cause of candidiasis in part owing to its robust ability to acquire tolerance to the major clinical antifungal drug fluconazole. Similar to the related species Candida albicans, C. glabrata most typically gains azole tolerance via transcriptional induction of a suite of resistance genes, including a locus encoding an ABCG-type ATP-binding cassette (ABC) transporter that is referred to as CDR1 in Candida species. In C. glabrata, CDR1 expression is controlled primarily by the activity of a transcriptional activator protein called Pdr1. Strains exhibiting reduced azole susceptibility often contain substitution mutations in PDR1 that in turn lead to elevated mRNA levels of target genes with associated azole resistance. Pdr1 activity is also induced upon loss of the mitochondrial genome status and upon challenge by azole drugs. While extensive analyses of the transcriptional effects of Pdr1 have identified a number of genes that are regulated by this factor, we cannot yet separate direct from indirect target genes. Here we used chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-seq) to identify the promoters and associated genes directly regulated by Pdr1. These genes include many that are shared with the yeast Saccharomyces cerevisiae but others that are unique to C. glabrata, including the ABC transporter-encoding locus YBT1, genes involved in DNA repair, and several others. These data provide the outline for understanding the primary response genes involved in production of Pdr1-dependent azole resistance in C. glabrata.
Collapse
|
20
|
Montefusco DJ, Matmati N, Hannun YA. The yeast sphingolipid signaling landscape. Chem Phys Lipids 2014; 177:26-40. [PMID: 24220500 PMCID: PMC4211598 DOI: 10.1016/j.chemphyslip.2013.10.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/18/2013] [Accepted: 10/19/2013] [Indexed: 12/13/2022]
Abstract
Sphingolipids are recognized as signaling mediators in a growing number of pathways, and represent potential targets to address many diseases. The study of sphingolipid signaling in yeast has created a number of breakthroughs in the field, and has the potential to lead future advances. The aim of this article is to provide an inclusive view of two major frontiers in yeast sphingolipid signaling. In the first section, several key studies in the field of sphingolipidomics are consolidated to create a yeast sphingolipidome that ranks nearly all known sphingolipid species by their level in a resting yeast cell. The second section presents an overview of most known phenotypes identified for sphingolipid gene mutants, presented with the intention of illuminating not yet discovered connections outside and inside of the field.
Collapse
Affiliation(s)
- David J Montefusco
- Dept. Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, United States.
| | - Nabil Matmati
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, United States
| | - Yusuf A Hannun
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, United States.
| |
Collapse
|
21
|
Gsell M, Mascher G, Schuiki I, Ploier B, Hrastnik C, Daum G. Transcriptional response to deletion of the phosphatidylserine decarboxylase Psd1p in the yeast Saccharomyces cerevisiae. PLoS One 2013; 8:e77380. [PMID: 24146988 PMCID: PMC3795641 DOI: 10.1371/journal.pone.0077380] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 09/05/2013] [Indexed: 11/18/2022] Open
Abstract
In the yeast, Saccharomyces cerevisiae, the synthesis of the essential phospholipid phosphatidylethanolamine (PE) is accomplished by a network of reactions which comprises four different pathways. The enzyme contributing most to PE formation is the mitochondrial phosphatidylserine decarboxylase 1 (Psd1p) which catalyzes conversion of phosphatidylserine (PS) to PE. To study the genome wide effect of an unbalanced cellular and mitochondrial PE level and in particular the contribution of Psd1p to this depletion we performed a DNA microarray analysis with a ∆psd1 deletion mutant. This approach revealed that 54 yeast genes were significantly up-regulated in the absence of PSD1 compared to wild type. Surprisingly, marked down-regulation of genes was not observed. A number of different cellular processes in different subcellular compartments were affected in a ∆psd1 mutant. Deletion mutants bearing defects in all 54 candidate genes, respectively, were analyzed for their growth phenotype and their phospholipid profile. Only three mutants, namely ∆gpm2, ∆gph1 and ∆rsb1, were affected in one of these parameters. The possible link of these mutations to PE deficiency and PSD1 deletion is discussed.
Collapse
Affiliation(s)
- Martina Gsell
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Gerald Mascher
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Irmgard Schuiki
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Birgit Ploier
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Claudia Hrastnik
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Günther Daum
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
- * E-mail:
| |
Collapse
|
22
|
Prasad R, Singh A. Lipids of Candida albicans and their role in multidrug resistance. Curr Genet 2013; 59:243-50. [PMID: 23974286 DOI: 10.1007/s00294-013-0402-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 07/26/2013] [Accepted: 07/30/2013] [Indexed: 12/20/2022]
Abstract
Over the years, lipids of non-pathogenic yeast such as Saccharomyces cerevisiae have been characterized to some details; however, a comparable situation does not exist for the human pathogenic fungi. This review is an attempt to bring in recent advances made in lipid research by employing high throughput lipidomic methods in terms of lipid analysis of pathogenic yeasts. Several pathogenic fungi exhibit multidrug resistance (MDR) which they acquire during the course of a treatment. Among the several causal factors, lipids by far have emerged as one of the critical contributors in the MDR acquisition in human pathogenic Candida. In this article, we have particularly focused on the role of lipids involved in cross talks between different cellular circuits that impact the acquisition of MDR in Candida.
Collapse
Affiliation(s)
- Rajendra Prasad
- Membrane Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India,
| | | |
Collapse
|
23
|
Functional analysis of an ATP-binding cassette transporter protein from Aspergillus fumigatus by heterologous expression in Saccharomyces cerevisiae. Fungal Genet Biol 2013; 57:85-91. [PMID: 23796749 DOI: 10.1016/j.fgb.2013.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 06/11/2013] [Accepted: 06/13/2013] [Indexed: 12/24/2022]
Abstract
Aspergillus fumigatus is the major filamentous fungal pathogen in humans. Although A. fumigatus can be treated with many of the available antifungal drugs, including azole compounds, drug resistant isolates are being recovered at an increasing rate. In other fungal pathogens such as the Candida species, ATP-binding cassette (ABC) transporter proteins play important roles in development of clinically-significant azole resistance phenotypes. Central among these ABC transporter proteins are homologues of the Saccharomyces cerevisiae Pdr5 multidrug transporter. In this work, we test the two A. fumigatus genes encoding proteins sharing the highest degree of sequence similarity to S. cerevisiae Pdr5 for their ability to be function in a heterologous pdr5Δ strain of S. cerevisiae. Expression of full-length cDNAs for these two Afu proteins failed to suppress the drug sensitive phenotype of a pdr5Δ strain and no evidence could be obtained for their expression as green fluorescent protein (GFP) fusions. To improve the expression of one of these Afu ABC transporters (XP_755847), we changed the sequence of the cDNA to use codons corresponding to the major tRNA species in S. cerevisiae. This codon-optimized (CO Afu abcA) cDNA was efficiently expressed in pdr5Δ cells and able to be detected as a GFP fusion protein. The CO Afu abcA did not correct the drug sensitivity of the pdr5Δ strain and exhibited a high degree of perinuclear fluorescence suggesting that this fusion protein was localized to the S. cerevisiae ER. Interestingly, when these experiments were repeated at 37 °C, the CO Afu abcA was able to complement the drug sensitive phenotype of pdr5Δ cells and exhibited less intracellular fluorescence. Additionally, we found that the CO Afu abcA was able to reduce resistance to drugs like phytosphingosine that act via causing mislocalization of amino acid permeases in fungi. These data suggest that the Afu abcA protein can carry out two different functions of Pdr5: drug transport and regulation of protein internalization from the plasma membrane.
Collapse
|
24
|
Kołaczkowska A, Manente M, Kołaczkowski M, Laba J, Ghislain M, Wawrzycka D. The regulatory inputs controlling pleiotropic drug resistance and hypoxic response in yeast converge at the promoter of the aminocholesterol resistance gene RTA1. FEMS Yeast Res 2011; 12:279-92. [DOI: 10.1111/j.1567-1364.2011.00768.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 11/18/2011] [Accepted: 11/21/2011] [Indexed: 11/30/2022] Open
Affiliation(s)
- Anna Kołaczkowska
- Department of Biochemistry, Pharmacology and Toxicology; University of Environmental and Life Sciences; Wroclaw; Poland
| | - Myriam Manente
- Unité de biochimie physiologique; Institut des sciences de la vie; Université catholique de Louvain; Louvain-la-Neuve; Belgium
| | | | - Justyna Laba
- Department of Biochemistry, Pharmacology and Toxicology; University of Environmental and Life Sciences; Wroclaw; Poland
| | - Michel Ghislain
- Unité de biochimie physiologique; Institut des sciences de la vie; Université catholique de Louvain; Louvain-la-Neuve; Belgium
| | - Donata Wawrzycka
- Department of Genetics and Cell Physiology; Institute of Plant Biology; Wroclaw University; Wroclaw; Poland
| |
Collapse
|
25
|
Gulshan K, Moye-Rowley WS. Vacuolar import of phosphatidylcholine requires the ATP-binding cassette transporter Ybt1. Traffic 2011; 12:1257-68. [PMID: 21649806 DOI: 10.1111/j.1600-0854.2011.01228.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
ATP-binding cassette (ABC) transporters are well known for their roles as multidrug resistance determinants but also play important roles in regulation of lipid levels. In the yeast Saccharomyces cerevisiae, the plasma membrane ABC transporter proteins Pdr5 and Yor1 are required for normal rates of transport of phosphatidyethanolamine to the surface of the cell. Loss of these ABC transporters causes a defect in phospholipid asymmetry across the plasma membrane and has been linked with slowed rates of trafficking of other membrane proteins. Four ABC transporter proteins are found on the limiting membrane of the yeast vacuole and loss of one of these vacuolar ABC transporters, Ybt1, caused a major defect in the normal delivery of the phosphatidylcholine (PC) analog NBD-PC (7-nitro-2,1,3-benzoxadiazol-PC) to the lumen of the vacuole. NBD-PC accumulates on cytosolic membranes in an ybt1Δ strain. We demonstrated that Ybt1 is required to import NBD-PC into vacuoles in the presence of ATP in vitro. Loss of Ybt1 prevented vacuolar remodeling of PC analogs. Turnover of Ybt1 was reduced under conditions in which function of this vacuolar remodeling pathway was required. Our data describe a novel vacuolar route for lipid remodeling and reutilization in addition to previously described enzymatic avenues in the cytoplasm.
Collapse
Affiliation(s)
- Kailash Gulshan
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, 6-530 Bowen Science Building, University of Iowa, Iowa City, IA 52246, USA
| | | |
Collapse
|