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Alkhadrawi AM, Xue H, Ahmad N, Akram M, Wang Y, Li C. Molecular study on the role of vacuolar transporters in glycyrrhetinic acid production in engineered Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183890. [PMID: 35181296 DOI: 10.1016/j.bbamem.2022.183890] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 02/06/2022] [Accepted: 02/09/2022] [Indexed: 12/25/2022]
Abstract
Glycyrrhetinic acid (GA) is one of the major bioactive components of the leguminous plant, Glycyrrhiza spp. (Chinese licorice). Owing to GA's complicated chemical structure, its production by chemical synthesis is challenging and requires other efficient strategies such as microbial synthesis. Earlier investigations employed numerous approaches to improve GA yield by refining the synthetic pathway and improving the metabolic flux. Nevertheless, the metabolic role of transporters in GA biosynthesis in microbial cell factories has not been studied so far. In this study, we investigated the role of yeast ATP binding cassette (ABC) vacuolar transporters in GA production. Molecular docking of GA and its precursors, β-Amyrin and 11-oxo-β-amyrin, was performed with five vacuolar ABC transporters (Bpt1p, Vmr1p, Ybt1p, Ycf1p and Nft1p). Based on docking scores, two top scoring transporters were selected (Bpt1p and Vmr1p) to investigate transporters' functions on GA production via overexpression and knockout experiments in one GA-producing yeast strain (GA166). Results revealed that GA and its precursors exhibited the highest predicted binding affinity towards BPT1 (ΔG = -10.9, -10.6, -10.9 kcal/mol for GA, β-amyrin and 11-oxo-β-amyrin, respectively). Experimental results showed that the overexpression of BPT1 and VMR1 restored the intracellular as well as extracellular GA production level under limited nutritional conditions, whereas knockout of BPT1 resulted in a total loss of GA production. These results suggest that the activity of BPT1 is required for GA production in engineered Saccharomyces cerevisiae.
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Affiliation(s)
- Adham M Alkhadrawi
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, PR China
| | - Haijie Xue
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, PR China
| | - Nadeem Ahmad
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, PR China; Department of Pharmacy, COMSATS University Islamabad, Abbottabad campus, Abbottabad 22060, Pakistan
| | - Muhammad Akram
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, PR China; Department of Life Sciences, School of Science, University of Management and Technology, Lahore, 54770, Pakistan
| | - Ying Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, PR China.
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, PR China; Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, PR China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.
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2
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Vishwakarma P, Meena NK, Prasad R, Lynn AM, Banerjee A. ABC-finder: A containerized web server for the identification and topology prediction of ABC proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183640. [PMID: 33957109 DOI: 10.1016/j.bbamem.2021.183640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/09/2021] [Accepted: 04/27/2021] [Indexed: 12/15/2022]
Abstract
In view of the multiple clinical and physiological implications of ABC transporter proteins, there is a considerable interest among researchers to characterize them functionally. However, such characterizations are based on the premise that ABC proteins are accurately identified in the proteome of an organism, and their topology is correctly predicted. With this objective, we have developed ABC-finder, i.e., a Docker-based package for the identification of ABC proteins in all organisms, and visualization of the topology of ABC proteins using a web browser. ABC-finder is built and deployed in a Linux container, making it scalable for many concurrent users on our servers and enabling users to download and run it locally. Overall, ABC-finder is a convenient, portable, and platform-independent tool for the identification and topology prediction of ABC proteins. ABC-finder is accessible at http://abc-finder.osdd.jnu.ac.in.
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Affiliation(s)
- Poonam Vishwakarma
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Naveen Kumar Meena
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rajendra Prasad
- Amity Institute of Biotechnology and Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurugram, India.
| | - Andrew M Lynn
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
| | - Atanu Banerjee
- Amity Institute of Biotechnology and Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurugram, India.
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Khunweeraphong N, Kuchler K. Multidrug Resistance in Mammals and Fungi-From MDR to PDR: A Rocky Road from Atomic Structures to Transport Mechanisms. Int J Mol Sci 2021; 22:4806. [PMID: 33946618 PMCID: PMC8124828 DOI: 10.3390/ijms22094806] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/19/2022] Open
Abstract
Multidrug resistance (MDR) can be a serious complication for the treatment of cancer as well as for microbial and parasitic infections. Dysregulated overexpression of several members of the ATP-binding cassette transporter families have been intimately linked to MDR phenomena. Three paradigm ABC transporter members, ABCB1 (P-gp), ABCC1 (MRP1) and ABCG2 (BCRP) appear to act as brothers in arms in promoting or causing MDR in a variety of therapeutic cancer settings. However, their molecular mechanisms of action, the basis for their broad and overlapping substrate selectivity, remains ill-posed. The rapidly increasing numbers of high-resolution atomic structures from X-ray crystallography or cryo-EM of mammalian ABC multidrug transporters initiated a new era towards a better understanding of structure-function relationships, and for the dynamics and mechanisms driving their transport cycles. In addition, the atomic structures offered new evolutionary perspectives in cases where transport systems have been structurally conserved from bacteria to humans, including the pleiotropic drug resistance (PDR) family in fungal pathogens for which high resolution structures are as yet unavailable. In this review, we will focus the discussion on comparative mechanisms of mammalian ABCG and fungal PDR transporters, owing to their close evolutionary relationships. In fact, the atomic structures of ABCG2 offer excellent models for a better understanding of fungal PDR transporters. Based on comparative structural models of ABCG transporters and fungal PDRs, we propose closely related or even conserved catalytic cycles, thus offering new therapeutic perspectives for preventing MDR in infectious disease settings.
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Affiliation(s)
| | - Karl Kuchler
- Center for Medical Biochemistry, Max Perutz Labs Vienna, Campus Vienna Biocenter, Medical University of Vienna, Dr. Bohr-Gasse 9/2, A-1030 Vienna, Austria;
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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.
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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.
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Víglaš J, Olejníková P. An update on ABC transporters of filamentous fungi - from physiological substrates to xenobiotics. Microbiol Res 2021; 246:126684. [PMID: 33529790 DOI: 10.1016/j.micres.2020.126684] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/13/2020] [Accepted: 12/18/2020] [Indexed: 02/02/2023]
Abstract
The superfamily of ATP-binding cassette (ABC) transporters is a large family of proteins with a wide substrate repertoire and range of functions. The main role of these proteins is in the transportation of different molecules across biological membranes. Due to the broad range of substrates, ABC transporters can transport not only natural metabolites but also various xenobiotics, including antifungal compounds, which makes some ABC transporters key players in antifungal resistance. Alternatively, ABC proteins without transport function seem to be essential for fungal cell viability. In this work, we review the individual subfamilies of ABC transporters in filamentous fungi regarding physiological substrates, clinical and agricultural significance. Subfamilies are defined using well-studied transporters in yeast, which may help to clarify their role in filamentous fungi.
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Affiliation(s)
- Ján Víglaš
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 81237, Bratislava, Slovakia.
| | - Petra Olejníková
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 81237, Bratislava, Slovakia.
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Grechko V, Podolsky D, Cheshchevik V. Identification new potential multidrug resistance proteins of Saccharomyces cerevisiae. J Microbiol Methods 2020; 176:106029. [DOI: 10.1016/j.mimet.2020.106029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/28/2020] [Accepted: 08/06/2020] [Indexed: 10/23/2022]
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Miletić Vukajlović J, Drakulić D, Pejić S, Ilić TV, Stefanović A, Petković M, Schiller J. Increased plasma phosphatidylcholine/lysophosphatidylcholine ratios in patients with Parkinson's disease. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8595. [PMID: 31519070 DOI: 10.1002/rcm.8595] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/03/2019] [Accepted: 09/08/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE Changes in lipid composition might be associated with the onset and progression of various neurodegenerative diseases. Herein, we investigated the changes in the plasma phosphatidylcholine (PC)/lysophosphatidylcholine (LPC) ratios in patients with Parkinson's disease (PD) in comparison with healthy subjects and their correlation with clinico-pathological features. METHODS The study included 10 controls and 25 patients with PD. All patients were assigned to groups based on clinico-pathological characteristics (gender, age at examination, duration of disease and Hoehn and Yahr (H&Y) stage). The analysis of the PC/LPC intensity ratios in plasma lipid extracts was performed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. RESULTS PD patients exhibited an increased PC/LPC intensity ratio in comparison with the control group of healthy subjects. Furthermore, the investigated ratio was shown to be correlated with clinico-pathological parameters, in particular with H&Y stage and disease duration. The PC/LPC intensity ratio in plasma samples of PD patients was found to be elevated in all examined H&Y stages and throughout the disease duration. CONCLUSIONS To our knowledge, this is the first study examining the PC/LPC ratios in plasma of patients with PD and illustrating their correlation with clinico-pathological features. Although the presented results may be considered as preliminary due to the limited number of participants, the observed alterations of PC/LPC ratios in plasma might be a first step in the characterization of plasma lipid changes in PD patients and an indicator of lipid reconfiguration.
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Affiliation(s)
- Jadranka Miletić Vukajlović
- Department of Physical Chemistry, VINČA Institute of Nuclear Sciences - University of Belgrade, Belgrade, Republic of Serbia
| | - Dunja Drakulić
- Department of Molecular Biology and Endocrinology, VINČA Institute of Nuclear Sciences - University of Belgrade, Belgrade, Republic of Serbia
| | - Snežana Pejić
- Department of Molecular Biology and Endocrinology, VINČA Institute of Nuclear Sciences - University of Belgrade, Belgrade, Republic of Serbia
| | - Tihomir V Ilić
- Medical Faculty of Medical Military Academy, Clinic of Neurology, University of Defense, Belgrade, Republic of Serbia
| | - Aleksandra Stefanović
- Department of Medical Biochemistry, Faculty of Pharmacy - University of Belgrade, Belgrade, Republic of Serbia
| | - Marijana Petković
- Madeira Chemistry Research Centre, University of Madeira, Funchal, Portugal
- Department of Atomic Physics, VINČA Institute of Nuclear Sciences - University of Belgrade, Belgrade, Republic of Serbia
| | - Jürgen Schiller
- Institute of Medical Physics and Biophysics, Medical Department, University of Leipzig, Leipzig, Germany
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8
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Domingo G, Villa F, Vannini C, Garuglieri E, Onelli E, Bracale M, Cappitelli F. Label-Free Proteomic Approach to Study the Non-lethal Effects of Silver Nanoparticles on a Gut Bacterium. Front Microbiol 2019; 10:2709. [PMID: 31866956 PMCID: PMC6906586 DOI: 10.3389/fmicb.2019.02709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 11/08/2019] [Indexed: 01/14/2023] Open
Abstract
Among all the food-related nanoparticles consumed every day, silver nanoparticles (AgNPs) have become one of the most commonly utilized because of their antimicrobial properties. Despite their common use, the effects of sublethal concentrations of AgNPs, especially on gut biofilms, have been poorly investigated. To address this issue, we investigated in vitro the proteomic response of a monospecies Escherichia coli gut biofilm to chronic and acute exposures in sublethal concentrations of AgNPs. We used a new gel- and label-free proteomic approach based on shotgun nanoflow liquid chromatography-tandem mass spectrometry. This approach allows a quantification of the whole proteome at a dynamic range that is higher than the traditional proteomic investigation. To assess all different possible exposure scenarios, we compared the biofilm proteome of four treatments: (i) untreated cells for the control treatment, (ii) cells treated with 1 μg/ml AgNPs for 24 h for the acute treatment, (iii) cells grown with 1 μg/ml AgNPs for 96 h for the chronic treatment, and (iv) cells grown in the presence of 1 μg/ml AgNPs for 72 h and then further treated for 24 h with 10 μg/ml AgNPs for the chronic + acute treatment. Among the 1,917 proteins identified, 212 were significantly differentially expressed proteins. Several pathways were altered including biofilm formation, bacterial adhesion, stress response to reactive oxygen species, and glucose utilization.
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Affiliation(s)
- Guido Domingo
- Department of Biotechnology and Life Sciences, Università degli Studi dell'Insubria, Varese, Italy
| | - Federica Villa
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
| | - Candida Vannini
- Department of Biotechnology and Life Sciences, Università degli Studi dell'Insubria, Varese, Italy
| | - Elisa Garuglieri
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
| | - Elisabetta Onelli
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Marcella Bracale
- Department of Biotechnology and Life Sciences, Università degli Studi dell'Insubria, Varese, Italy
| | - Francesca Cappitelli
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
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Moreno A, Banerjee A, Prasad R, Falson P. PDR-like ABC systems in pathogenic fungi. Res Microbiol 2019; 170:417-425. [PMID: 31562919 DOI: 10.1016/j.resmic.2019.09.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/12/2019] [Accepted: 09/16/2019] [Indexed: 01/23/2023]
Abstract
ABC transporters of the Pleiotropic Drug Resistance (PDR) family are the main actors of antifungal resistance in pathogenic fungi. While their involvement in clinical resistant strains has been proven, their transport mechanism remains unclear. Notably, one hallmark of PDR transporters is their asymmetry, with one canonical nucleotide-binding site capable of ATP hydrolysis while the other site is not. Recent publications reviewed here show that the so-called "deviant" site is of crucial importance for drug transport and is a step towards alleviating the mystery around the existence of non-catalytic binding sites.
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Affiliation(s)
- Alexis Moreno
- Drug Resistance & Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS-Lyon 1 University Research Lab n° 5086, Institut de Biologie et Chimie des Protéines, Lyon, France.
| | - Atanu Banerjee
- Amity Institute of Biotechnology and Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon, India.
| | - Rajendra Prasad
- Amity Institute of Biotechnology and Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon, India.
| | - Pierre Falson
- Drug Resistance & Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS-Lyon 1 University Research Lab n° 5086, Institut de Biologie et Chimie des Protéines, Lyon, France.
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10
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Rizzo J, Stanchev LD, da Silva VK, Nimrichter L, Pomorski TG, Rodrigues ML. Role of lipid transporters in fungal physiology and pathogenicity. Comput Struct Biotechnol J 2019; 17:1278-1289. [PMID: 31921394 PMCID: PMC6944739 DOI: 10.1016/j.csbj.2019.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/20/2019] [Accepted: 09/02/2019] [Indexed: 02/08/2023] Open
Abstract
The fungal cell wall and membrane are the most common targets of antifungal agents, but the potential of membrane lipid organization in regulating drug-target interactions has yet to be investigated. Energy-dependent lipid transporters have been recently associated with virulence and drug resistance in many pathogenic fungi. To illustrate this view, we discuss (i) the structural and biological aspects of ATP-driven lipid transporters, comprising P-type ATPases and ATP-binding cassette transporters, (ii) the role of these transporters in fungal physiology and virulence, and (iii) the potential of lipid transporters as targets for the development of novel antifungals. These recent observations indicate that the lipid-trafficking machinery in fungi is a promising target for studies on physiology, pathogenesis and drug development.
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Affiliation(s)
- Juliana Rizzo
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Lyubomir Dimitrov Stanchev
- Department of Molecular Biochemistry, Ruhr University Bochum, Faculty of Chemistry and Biochemistry, 44780 Bochum, Germany
- Department of Plant Biology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C,Denmark
| | - Vanessa K.A. da Silva
- Programa de Pós-Graduação em Biologia Parasitária do Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Leonardo Nimrichter
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry, Ruhr University Bochum, Faculty of Chemistry and Biochemistry, 44780 Bochum, Germany
- Department of Plant Biology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C,Denmark
| | - Marcio L. Rodrigues
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
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Nam O, Park JM, Lee H, Jin E. De novo transcriptome profile of coccolithophorid alga Emiliania huxleyi CCMP371 at different calcium concentrations with proteome analysis. PLoS One 2019; 14:e0221938. [PMID: 31465514 PMCID: PMC6715215 DOI: 10.1371/journal.pone.0221938] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 08/19/2019] [Indexed: 12/16/2022] Open
Abstract
The haptophyte alga Emiliania huxleyi is the most abundant coccolithophore in the modern ocean and produces elaborate calcite crystals, called coccolith, in a separate intracellular compartment known as the coccolith vesicle. Despite the importance of biomineralization in coccolithophores, the molecular mechanism underlying it remains unclear. Understanding this precise machinery at the molecular level will provide the knowledge needed to enable further manipulation of biomineralization. In our previous study, altering the calcium concentration modified the calcifying ability of E. huxleyi CCMP371. Therefore in this study, we tested E. huxleyi cells acclimated to three different calcium concentrations (0, 0.1, and 10 mM). To understand the whole transcript profile at different calcium concentrations, RNA-sequencing was performed and used for de novo assembly and annotation. The differentially expressed genes (DEGs) among the three different calcium concentrations were analyzed. The functional classification by gene ontology (GO) revealed that 'intrinsic component of membrane' was the most enriched of the GO terms at the ambient calcium concentration (10 mM) compared with the limited calcium concentrations (0 and 0.1 mM). Moreover, the DEGs in those comparisons were enriched mainly in 'secondary metabolites biosynthesis, transport and catabolism' and 'signal transduction mechanisms' in the KOG clusters and 'processing in endoplasmic reticulum', and 'ABC transporters' in the KEGG pathways. Furthermore, metabolic pathways involved in protein synthesis were enriched among the differentially expressed proteins. The results of this study provide a molecular profile for understanding the expression of transcripts and proteins in E. huxleyi at different calcium concentrations, which will help to identify the detailed mechanism of its calcification.
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Affiliation(s)
- Onyou Nam
- Department of Life Science, Hanyang University, Seoul, Republic of Korea
| | - Jong-Moon Park
- Gachon Institute of Pharmaceutical Sciences, Gachon College of Pharmacy, Gachon University, Incheon, Republic of Korea
| | - Hookeun Lee
- Gachon Institute of Pharmaceutical Sciences, Gachon College of Pharmacy, Gachon University, Incheon, Republic of Korea
| | - EonSeon Jin
- Department of Life Science, Hanyang University, Seoul, Republic of Korea
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Wasi M, Khandelwal NK, Moorhouse AJ, Nair R, Vishwakarma P, Bravo Ruiz G, Ross ZK, Lorenz A, Rudramurthy SM, Chakrabarti A, Lynn AM, Mondal AK, Gow NAR, Prasad R. ABC Transporter Genes Show Upregulated Expression in Drug-Resistant Clinical Isolates of Candida auris: A Genome-Wide Characterization of ATP-Binding Cassette (ABC) Transporter Genes. Front Microbiol 2019; 10:1445. [PMID: 31379756 PMCID: PMC6647914 DOI: 10.3389/fmicb.2019.01445] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 06/07/2019] [Indexed: 01/08/2023] Open
Abstract
ATP-binding cassette (ABC) superfamily members have a key role as nutrient importers and exporters in bacteria. However, their role as drug exporters in eukaryotes brought this superfamily member to even greater prominence. The capacity of ABC transporters to efflux a broad spectrum of xenobiotics represents one of the major mechanisms of clinical multidrug resistance in pathogenic fungi including Candida species. Candida auris, a newly emerged multidrug-resistant fungal pathogen of humans, has been responsible for multiple outbreaks of drug-resistant infections in hospitals around the globe. Our study has analyzed the entire complement of ABC superfamily transporters to assess whether these play a major role in drug resistance mechanisms of C. auris. Our bioinformatics analyses identified 28 putative ABC proteins encoded in the genome of the C. auris type-strain CBS 10913T; 20 of which contain transmembrane domains (TMDs). Quantitative real-time PCR confirmed the expression of all 20 TMD transporters, underlining their potential in contributing to the C. auris drug-resistant phenotype. Changes in transcript levels after short-term exposure of drugs and in drug-resistant C. auris isolates suggested their importance in the drug resistance phenotype of this pathogen. CAUR_02725 orthologous to CDR1, a major multidrug exporter in other yeasts, showed consistently higher expression in multidrug-resistant strains of C. auris. Homologs of other ABC transporter genes, such as CDR4, CDR6, and SNQ2, also displayed raised expression in a sub-set of clinical isolates. Together, our analysis supports the involvement of these transporters in multidrug resistance in C. auris.
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Affiliation(s)
- Mohd Wasi
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | | | - Remya Nair
- Amity Institute of Biotechnology and Integrative Sciences and Health, Amity University Gurugram, Gurgaon, India
| | - Poonam Vishwakarma
- School of Computational and Integrative Science, Jawaharlal Nehru University, New Delhi, India
| | - Gustavo Bravo Ruiz
- The Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Zoe K. Ross
- MRC Centre for Medical Mycology, University of Aberdeen, Aberdeen, United Kingdom
- The Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Alexander Lorenz
- The Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Shivaprakash M. Rudramurthy
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Andrew M. Lynn
- School of Computational and Integrative Science, Jawaharlal Nehru University, New Delhi, India
| | - Alok K. Mondal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Neil A. R. Gow
- MRC Centre for Medical Mycology, University of Aberdeen, Aberdeen, United Kingdom
- The Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
- School of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Rajendra Prasad
- Amity Institute of Biotechnology and Integrative Sciences and Health, Amity University Gurugram, Gurgaon, India
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Vacuolar Sequestration of Azoles, a Novel Strategy of Azole Antifungal Resistance Conserved across Pathogenic and Nonpathogenic Yeast. Antimicrob Agents Chemother 2019; 63:AAC.01347-18. [PMID: 30642932 DOI: 10.1128/aac.01347-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/29/2018] [Indexed: 11/20/2022] Open
Abstract
Target alteration and overproduction and drug efflux through overexpression of multidrug transporters localized in the plasma membrane represent the conventional mechanisms of azole antifungal resistance. Here, we identify a novel conserved mechanism of azole resistance not only in the budding yeast Saccharomyces cerevisiae but also in the pathogenic yeast Candida albicans We observed that the vacuolar-membrane-localized, multidrug resistance protein (MRP) subfamily, ATP-binding cassette (ABC) transporter of S. cerevisiae, Ybt1, could import azoles into vacuoles. Interestingly, the Ybt1 homologue in C. albicans, Mlt1p, could also fulfill this function. Evidence that the process is energy dependent comes from the finding that a Mlt1p mutant version made by converting a critical lysine residue in the Walker A motif of nucleotide-binding domain 1 (required for ATP hydrolysis) to alanine (K710A) was not able to transport azoles. Additionally, we have shown that, as for other eukaryotic MRP subfamily members, deletion of the conserved phenylalanine amino acid at position 765 (F765Δ) results in mislocalization of the Mlt1 protein; this mislocalized protein was devoid of the azole-resistant attribute. This finding suggests that the presence of this protein on vacuolar membranes is an important factor in azole resistance. Further, we report the importance of conserved residues, because conversion of two serines (positions 973 and 976, in the regulatory domain and in the casein kinase I [CKI] consensus sequence, respectively) to alanine severely affected the drug resistance. Hence, the present study reveals vacuolar sequestration of azoles by the ABC transporter Ybt1 and its homologue Mlt1 as an alternative strategy to circumvent drug toxicity among pathogenic and nonpathogenic yeasts.
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Wasi M, Khandelwal NK, Vishwakarma P, Lynn AM, Mondal AK, Prasad R. Inventory of ABC proteins and their putative role in salt and drug tolerance in Debaryomyces hansenii. Gene 2018; 676:227-242. [DOI: 10.1016/j.gene.2018.07.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/27/2018] [Accepted: 07/11/2018] [Indexed: 10/28/2022]
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15
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Dube G, Kadoo N, Prashant R. Exploring the biological roles of Dothideomycetes ABC proteins: Leads from their phylogenetic relationships with functionally-characterized Ascomycetes homologs. PLoS One 2018; 13:e0197447. [PMID: 30071023 PMCID: PMC6071951 DOI: 10.1371/journal.pone.0197447] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 05/02/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The ATP-binding cassette (ABC) superfamily is one of the largest, ubiquitous and diverse protein families in nature. Categorized into nine subfamilies, its members are important to most organisms including fungi, where they play varied roles in fundamental cellular processes, plant pathogenesis or fungicide tolerance. However, these proteins are not yet well-understood in the class Dothideomycetes, which includes several phytopathogens that infect a wide range of food crops including wheat, barley and maize and cause major economic losses. RESULTS We analyzed the genomes of 14 Dothideomycetes fungi (Test set) and seven well-known Ascomycetes fungi (Model set- that possessed gene expression/ functional analysis data about the ABC genes) and predicted 578 and 338 ABC proteins from each set respectively. These proteins were classified into subfamilies A to I, which revealed the distribution of the subfamily members across the Dothideomycetes and Ascomycetes genomes. Phylogenetic analysis of Dothideomycetes ABC proteins indicated evolutionary relationships among the subfamilies within this class. Further, phylogenetic relationships among the ABC proteins from the Model and the Test fungi within each subfamily were analyzed, which aided in classifying these proteins into subgroups. We compiled and curated functional and gene expression information from the previous literature for 118 ABC genes and mapped them on the phylogenetic trees, which suggested possible roles in pathogenesis and/or fungicide tolerance for the newly identified Dothideomycetes ABC proteins. CONCLUSIONS The present analysis is one of the firsts to extensively analyze ABC proteins from Dothideomycetes fungi. Their phylogenetic analysis and annotating the clades with functional information indicated a subset of Dothideomycetes ABC genes that could be considered for experimental validation for their roles in plant pathogenesis and/or fungicide tolerance.
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Affiliation(s)
- Gaurav Dube
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
| | - Narendra Kadoo
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Ramya Prashant
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
- MIT School of Bioengineering Sciences & Research, MIT-Art, Design and Technology University, Pune, India
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16
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Kovalchuk A, Lee YH, Asiegbu FO. Diversity and evolution of ABC proteins in basidiomycetes. Mycologia 2017; 105:1456-70. [DOI: 10.3852/13-001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Andriy Kovalchuk
- Department of Forest Sciences, P.O. Box 27, Latokartanonkaari 7, 00014 University of Helsinki, Helsinki, Finland
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University Seoul 151-921, Korea
| | - Fred O. Asiegbu
- Department of Forest Sciences, P.O. Box 27, Latokartanonkaari 7, 00014 University of Helsinki, Helsinki, Finland
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Pomorski TG, Menon AK. Lipid somersaults: Uncovering the mechanisms of protein-mediated lipid flipping. Prog Lipid Res 2016; 64:69-84. [PMID: 27528189 DOI: 10.1016/j.plipres.2016.08.003] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 08/10/2016] [Indexed: 12/22/2022]
Abstract
Membrane lipids diffuse rapidly in the plane of the membrane but their ability to flip spontaneously across a membrane bilayer is hampered by a significant energy barrier. Thus spontaneous flip-flop of polar lipids across membranes is very slow, even though it must occur rapidly to support diverse aspects of cellular life. Here we discuss the mechanisms by which rapid flip-flop occurs, and what role lipid flipping plays in membrane homeostasis and cell growth. We focus on conceptual aspects, highlighting mechanistic insights from biochemical and in silico experiments, and the recent, ground-breaking identification of a number of lipid scramblases.
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Affiliation(s)
- Thomas Günther Pomorski
- Faculty of Chemistry and Biochemistry, Molecular Biochemistry, Ruhr University Bochum, Universitätstrasse 150, D-44780 Bochum, Germany; Centre for Membrane Pumps in Cells and Disease-PUMPKIN, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark.
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA.
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18
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Yeast ABC transporters in lipid trafficking. Fungal Genet Biol 2016; 93:25-34. [DOI: 10.1016/j.fgb.2016.05.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 05/28/2016] [Accepted: 05/31/2016] [Indexed: 12/31/2022]
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19
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Pleiotropic effects of the vacuolar ABC transporter MLT1 of Candida albicans on cell function and virulence. Biochem J 2016; 473:1537-52. [PMID: 27026051 PMCID: PMC4888455 DOI: 10.1042/bcj20160024] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/29/2016] [Indexed: 01/14/2023]
Abstract
Among the several mechanisms that contribute to MDR (multidrug resistance), the overexpression of drug-efflux pumps belonging to the ABC (ATP-binding cassette) superfamily is the most frequent cause of resistance to antifungal agents. The multidrug transporter proteins Cdr1p and Cdr2p of the ABCG subfamily are major players in the development of MDR in Candida albicans. Because several genes coding for ABC proteins exist in the genome of C. albicans, but only Cdr1p and Cdr2p have established roles in MDR, it is implicit that the other members of the ABC family also have alternative physiological roles. The present study focuses on an ABC transporter of C. albicans, Mlt1p, which is localized in the vacuolar membrane and specifically transports PC (phosphatidylcholine) into the vacuolar lumen. Transcriptional profiling of the mlt1∆/∆ mutant revealed a down-regulation of the genes involved in endocytosis, oxidoreductase activity, virulence and hyphal development. High-throughput MS-based lipidome analysis revealed that the Mlt1p levels affect lipid homoeostasis and thus lead to a plethora of physiological perturbations. These include a delay in endocytosis, inefficient sequestering of reactive oxygen species (ROS), defects in hyphal development and attenuated virulence. The present study is an emerging example where new and unconventional roles of an ABC transporter are being identified.
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20
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Kovalchuk A, Kohler A, Martin F, Asiegbu FO. Diversity and evolution of ABC proteins in mycorrhiza-forming fungi. BMC Evol Biol 2015; 15:249. [PMID: 26707138 PMCID: PMC4692070 DOI: 10.1186/s12862-015-0526-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 10/28/2015] [Indexed: 11/22/2022] Open
Abstract
Background Transporter proteins are predicted to have an important role in the mycorrhizal symbiosis, due to the fact that this type of an interaction between plants and fungi requires a continuous nutrient and signalling exchange. ABC transporters are one of the large groups of transporter proteins found both in plants and in fungi. The crucial role of plant ABC transporters in the formation of the mycorrhizal symbiosis has been demonstrated recently. Some of the fungal ABC transporter-encoding genes are also induced during the mycorrhiza formation. However, no experimental evidences of the direct involvement of fungal ABC transporters in this process are available so far. To facilitate the identification of fungal ABC proteins with a potential role in the establishment of the mycorrhizal symbiosis, we have performed an inventory of the ABC protein-encoding genes in the genomes of 25 species of mycorrhiza-forming fungi. Results We have identified, manually annotated and curated more than 1300 gene models of putative ABC protein-encoding genes. Out of those, more than 1000 models are predicted to encode functional proteins, whereas about 300 models represent gene fragments or putative pseudogenes. We have also performed the phylogenetic analysis of the identified sequences. The sets of ABC proteins in the mycorrhiza-forming species were compared to the related saprotrophic or plant-pathogenic fungal species. Our results demonstrate the high diversity of ABC genes in the genomes of mycorrhiza-forming fungi. Via comparison of transcriptomics data from different species, we have identified candidate groups of ABC transporters that might have a role in the process of the mycorrhiza formation. Conclusions Results of our inventory will facilitate the identification of fungal transporters with a role in the mycorrhiza formation. We also provide the first data on ABC protein-coding genes for the phylum Glomeromycota and for orders Pezizales, Atheliales, Cantharellales and Sebacinales, contributing to the better knowledge of the diversity of this protein family within the fungal kingdom. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0526-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andriy Kovalchuk
- Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland.
| | - Annegret Kohler
- UMR 1136, INRA/Université de Lorraine, Interactions Arbres/Microorganismes, INRA, Institut National de la Recherche Agronomique, Centre INRA de Nancy, 54280, Champenoux, France.
| | - Francis Martin
- UMR 1136, INRA/Université de Lorraine, Interactions Arbres/Microorganismes, INRA, Institut National de la Recherche Agronomique, Centre INRA de Nancy, 54280, Champenoux, France.
| | - Fred O Asiegbu
- Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland.
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21
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Farmer K, Smith CA, Hayley S, Smith J. Major Alterations of Phosphatidylcholine and Lysophosphotidylcholine Lipids in the Substantia Nigra Using an Early Stage Model of Parkinson's Disease. Int J Mol Sci 2015; 16:18865-77. [PMID: 26274953 PMCID: PMC4581276 DOI: 10.3390/ijms160818865] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 08/06/2015] [Accepted: 08/06/2015] [Indexed: 01/14/2023] Open
Abstract
Parkinson’s disease (PD) is a progressive neurodegenerative disease affecting the nigrostriatal pathway, where patients do not manifest motor symptoms until >50% of neurons are lost. Thus, it is of great importance to determine early neuronal changes that may contribute to disease progression. Recent attention has focused on lipids and their role in pro- and anti-apoptotic processes. However, information regarding the lipid alterations in animal models of PD is lacking. In this study, we utilized high performance liquid chromatography electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS) and novel HPLC solvent methodology to profile phosphatidylcholines and sphingolipids within the substantia nigra. The ipsilateral substantia nigra pars compacta was collected from rats 21 days after an infusion of 6-hydroxydopamine (6-OHDA), or vehicle into the anterior dorsal striatum. We identified 115 lipid species from their mass/charge ratio using the LMAPS Lipid MS Predict Database. Of these, 19 lipid species (from phosphatidylcholine and lysophosphotidylcholine lipid classes) were significantly altered by 6-OHDA, with most being down-regulated. The two lipid species that were up-regulated were LPC (16:0) and LPC (18:1), which are important for neuroinflammatory signalling. These findings provide a first step in the characterization of lipid changes in early stages of PD-like pathology and could provide novel targets for early interventions in PD.
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Affiliation(s)
- Kyle Farmer
- Carleton University Department of Neuroscience, 1125 Colonel By Drive, Life Sciences Research Building, Ottawa, ON K1S 5B6, Canada.
| | - Catherine A Smith
- Carleton University Department of Neuroscience, 1125 Colonel By Drive, Life Sciences Research Building, Ottawa, ON K1S 5B6, Canada.
| | - Shawn Hayley
- Carleton University Department of Neuroscience, 1125 Colonel By Drive, Life Sciences Research Building, Ottawa, ON K1S 5B6, Canada.
| | - Jeffrey Smith
- Carleton University Department of Chemistry and Institute of Biochemistry, 1125 Colonel By Drive, Steacie Building, Ottawa, ON K1S 5B6, Canada.
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22
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Zhang C, Hicks GR, Raikhel NV. Molecular Composition of Plant Vacuoles: Important but Less Understood Regulations and Roles of Tonoplast Lipids. PLANTS 2015; 4:320-33. [PMID: 27135331 PMCID: PMC4844321 DOI: 10.3390/plants4020320] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/21/2015] [Accepted: 06/03/2015] [Indexed: 11/16/2022]
Abstract
The vacuole is an essential organelle for plant growth and development. It is the location for the storage of nutrients; such as sugars and proteins; and other metabolic products. Understanding the mechanisms of vacuolar trafficking and molecule transport across the vacuolar membrane is of great importance in understanding basic plant development and cell biology and for crop quality improvement. Proteins play important roles in vacuolar trafficking; such proteins include Rab GTPase signaling proteins; cargo recognition receptors; and SNAREs (Soluble NSF Attachment Protein Receptors) that are involved in membrane fusion. Some vacuole membrane proteins also serve as the transporters or channels for transport across the tonoplast. Less understood but critical are the roles of lipids in vacuolar trafficking. In this review, we will first summarize molecular composition of plant vacuoles and we will then discuss our latest understanding on the role of lipids in plant vacuolar trafficking and a surprising connection to ribosome function through the study of ribosomal mutants.
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Affiliation(s)
- Chunhua Zhang
- Center for Plant Cell Biology & Department of Botany and Plant Sciences, University of California, 900 University Ave., Riverside, CA 92521, USA.
| | - Glenn R Hicks
- Center for Plant Cell Biology & Department of Botany and Plant Sciences, University of California, 900 University Ave., Riverside, CA 92521, USA.
| | - Natasha V Raikhel
- Center for Plant Cell Biology & Department of Botany and Plant Sciences, University of California, 900 University Ave., Riverside, CA 92521, USA.
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23
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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.
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24
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Sasser TL, Fratti RA. Class C ABC transporters and Saccharomyces cerevisiae vacuole fusion. CELLULAR LOGISTICS 2014; 4:e943588. [PMID: 25610719 DOI: 10.4161/21592780.2014.943588] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 06/18/2014] [Indexed: 01/05/2023]
Abstract
Membrane fusion is carried out by core machinery that is conserved throughout eukaryotes. This is comprised of Rab GTPases and their effectors, and SNARE proteins, which together are sufficient to drive the fusion of reconstituted proteoliposomes. However, an outer layer of factors that are specific to individual trafficking pathways in vivo regulates the spatial and temporal occurrence of fusion. The homotypic fusion of Saccharomyces cerevisiae vacuolar lysosomes utilizes a growing set of factors to regulate the fusion machinery that include members of the ATP binding cassette (ABC) transporter family. Yeast vacuoles have five class C ABC transporters that are known to transport a variety of toxins into the vacuole lumen as part of detoxifying the cell. We have found that ABCC transporters can also regulate vacuole fusion through novel mechanisms. For instance Ybt1 serves as negative regulator of fusion through its effects on vacuolar Ca2+ homeostasis. Additional studies showed that Ycf1 acts as a positive regulator by affecting the efficient recruitment of the SNARE Vam7. Finally, we discuss the potential interface between the translocation of lipids across the membrane bilayer, also known as lipid flipping, and the efficiency of fusion.
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Key Words
- ABC, ATP binding cassette
- Bpt1
- Ca2+ homeostasis
- DAG, diacylglycerol
- HOPS, homotypic fusion and vacuole protein sorting complex
- MDR, multidrug resistance
- MSD, membrane spanning domain
- NBD, nucleotide binding domain
- Nft1
- PA, phosphatidic acid
- PC, phosphatidylcholine
- PE, phosphatidylethanolamine
- PI(3, 5)P2, phosphatidylinositol 3, 5-bisphosphate
- PI, phosphatidylinositol
- PI3P
- PI3P, phosphatidylinositol 3-phosphate
- PS, phosphatidylserine
- PX, phox homology
- SNARE
- SNARE, soluble N-ethylmaleimide-sensitive factor attachment protein receptors
- Vam7
- Vmr1
- Ybt1
- Ycf1
- lipid flipping
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Affiliation(s)
- Terry L Sasser
- Department of Biochemistry; University of Illinois at Urbana-Champaign ; Urbana, IL USA
| | - Rutilio A Fratti
- Department of Biochemistry; University of Illinois at Urbana-Champaign ; Urbana, IL USA
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25
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Structure and mechanism of ATP-dependent phospholipid transporters. Biochim Biophys Acta Gen Subj 2014; 1850:461-75. [PMID: 24746984 DOI: 10.1016/j.bbagen.2014.04.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 04/04/2014] [Accepted: 04/07/2014] [Indexed: 01/09/2023]
Abstract
BACKGROUND ATP-binding cassette (ABC) transporters and P4-ATPases are two large and seemingly unrelated families of primary active pumps involved in moving phospholipids from one leaflet of a biological membrane to the other. SCOPE OF REVIEW This review aims to identify common mechanistic features in the way phospholipid flipping is carried out by two evolutionarily unrelated families of transporters. MAJOR CONCLUSIONS Both protein families hydrolyze ATP, although they employ different mechanisms to use it, and have a comparable size with twelve transmembrane segments in the functional unit. Further, despite differences in overall architecture, both appear to operate by an alternating access mechanism and during transport they might allow access of phospholipids to the internal part of the transmembrane domain. The latter feature is obvious for ABC transporters, but phospholipids and other hydrophobic molecules have also been found embedded in P-type ATPase crystal structures. Taken together, in two diverse groups of pumps, nature appears to have evolved quite similar ways of flipping phospholipids. GENERAL SIGNIFICANCE Our understanding of the structural basis for phospholipid flipping is still limited but it seems plausible that a general mechanism for phospholipid flipping exists in nature. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
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26
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Goffa E, Balazfyova Z, Toth Hervay N, Simova Z, Balazova M, Griac P, Gbelska Y. Isolation and functional analysis of theKlPDR16gene. FEMS Yeast Res 2013; 14:337-45. [DOI: 10.1111/1567-1364.12102] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 09/16/2013] [Accepted: 09/24/2013] [Indexed: 12/22/2022] Open
Affiliation(s)
- Eduard Goffa
- Department of Microbiology and Virology; Comenius University in Bratislava; Bratislava Slovak Republic
| | - Zuzana Balazfyova
- Department of Microbiology and Virology; Comenius University in Bratislava; Bratislava Slovak Republic
| | - Nora Toth Hervay
- Department of Microbiology and Virology; Comenius University in Bratislava; Bratislava Slovak Republic
| | - Zuzana Simova
- Institute of Animal Biochemistry and Genetics; Slovak Academy of Sciences; Ivanka pri Dunaji Slovak Republic
| | - Maria Balazova
- Institute of Animal Biochemistry and Genetics; Slovak Academy of Sciences; Ivanka pri Dunaji Slovak Republic
| | - Peter Griac
- Institute of Animal Biochemistry and Genetics; Slovak Academy of Sciences; Ivanka pri Dunaji Slovak Republic
| | - Yvetta Gbelska
- Department of Microbiology and Virology; Comenius University in Bratislava; Bratislava Slovak Republic
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27
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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.
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Affiliation(s)
- Rajendra Prasad
- Membrane Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India,
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28
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Sasser TL, Lawrence G, Karunakaran S, Brown C, Fratti RA. The yeast ATP-binding cassette (ABC) transporter Ycf1p enhances the recruitment of the soluble SNARE Vam7p to vacuoles for efficient membrane fusion. J Biol Chem 2013; 288:18300-10. [PMID: 23658021 DOI: 10.1074/jbc.m112.441089] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The Saccharomyces cerevisiae vacuole contains five ATP-binding cassette class C (ABCC) transporters, including Ycf1p, a family member that was originally characterized as a Cd(2+) transporter. Ycf1p has also been found to physically interact with a wide array of proteins, including factors that regulate vacuole homeostasis. In this study, we examined the role of Ycf1p and other ABCC transporters in the regulation of vacuole homotypic fusion. We found that deletion of YCF1 attenuated in vitro vacuole fusion by up to 40% relative to wild-type vacuoles. Plasmid-expressed wild-type Ycf1p rescued the deletion phenotype; however, Ycf1p containing a mutation of the conserved Lys-669 to Met in the Walker A box of the first nucleotide-binding domain (Ycf1p(K669M)) was unable to complement the fusion defect of ycf1Δ vacuoles. This indicates that the ATPase activity of Ycf1p is required for its function in regulating fusion. In addition, we found that deleting YCF1 caused a striking decrease in vacuolar levels of the soluble SNARE Vam7p, whereas total cellular levels were not altered. The attenuated fusion of ycf1Δ vacuoles was rescued by the addition of recombinant Vam7p to in vitro experiments. Thus, Ycf1p contributes in the recruitment of Vam7p to the vacuole for efficient membrane fusion.
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Affiliation(s)
- Terry L Sasser
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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29
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The yeast vacuolar ABC transporter Ybt1p regulates membrane fusion through Ca2+ transport modulation. Biochem J 2013; 448:365-72. [PMID: 22970809 DOI: 10.1042/bj20120847] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Ybt1p is a class C ABC transporter (ATP-binding cassette transporter) that is localized to the vacuole of Saccharomyces cerevisiae. Although Ybt1p was originally identified as a bile acid transporter, it has also been found to function in other capacities, including the translocation of phosphatidylcholine to the vacuole lumen, and the regulation of Ca2+ homoeostasis. In the present study we found that deletion of YBT1 enhanced in vitro homotypic vacuole fusion by up to 50% relative to wild-type vacuoles. The increased vacuole fusion was not due to aberrant protein sorting of SNAREs (soluble N-ethylmaleimide-sensitive factor-attachment protein receptors) or recruitment of factors from the cytosol such as Ypt7p and the HOPS (homotypic fusion and vacuole protein sorting) tethering complex. In addition, ybt1Δ vacuoles displayed no observable differences in the formation of SNARE complexes, interactions between SNAREs and HOPS, or formation of vertex microdomains. However, the absence of Ybt1p caused significant changes in Ca2+ transport during fusion. One difference was the prolonged Ca2+ influx exhibited by ybt1Δ vacuoles at the start of the fusion reaction. We also observed a striking delay in SNARE-dependent Ca2+ efflux. As vacuole fusion can be inhibited by high Ca2+ concentrations, we suggest that the delayed efflux in ybt1Δ vacuoles leads to the enhanced SNARE function.
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