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Bickers SC, Benlekbir S, Rubinstein JL, Kanelis V. Structure of a dimeric full-length ABC transporter. Nat Commun 2024; 15:9946. [PMID: 39550367 PMCID: PMC11569179 DOI: 10.1038/s41467-024-54147-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Accepted: 10/25/2024] [Indexed: 11/18/2024] Open
Abstract
Activities of ATP binding cassette (ABC) proteins are regulated by multiple mechanisms, including protein interactions, phosphorylation, proteolytic processing, and/or oligomerization of the ABC protein itself. Here we present the structure of yeast cadmium factor 1 (Ycf1p) in its mature form following cleavage by Pep4p protease. Ycf1p, a C subfamily ABC protein (ABCC), is homologue of human multidrug resistance protein 1. Remarkably, a portion of cleaved Ycf1p forms a well-ordered dimer, alongside monomeric particles also present in solution. While numerous other ABC proteins have been proposed to dimerize, no high-resolution structures have been reported. Both phosphorylation of the regulatory (R) region and ATPase activity are lower in the Ycf1p dimer compared to the monomer, indicating that dimerization affects Ycf1p function. The interface between Ycf1p protomers features protein-protein interactions and contains bound lipids, suggesting that lipids stabilize the dimer. The Ycf1p dimer structure may inform the dimerization interfaces of other ABCC dimers.
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Affiliation(s)
- Sarah C Bickers
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Samir Benlekbir
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
| | - Voula Kanelis
- Department of Chemistry, University of Toronto, Toronto, ON, Canada.
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada.
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
- Research Institute, The Hospital for Sick Children, Toronto, ON, Canada.
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2
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Zbieralski K, Staszewski J, Konczak J, Lazarewicz N, Nowicka-Kazmierczak M, Wawrzycka D, Maciaszczyk-Dziubinska E. Multilevel Regulation of Membrane Proteins in Response to Metal and Metalloid Stress: A Lesson from Yeast. Int J Mol Sci 2024; 25:4450. [PMID: 38674035 PMCID: PMC11050377 DOI: 10.3390/ijms25084450] [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: 03/07/2024] [Revised: 04/06/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
In the face of flourishing industrialization and global trade, heavy metal and metalloid contamination of the environment is a growing concern throughout the world. The widespread presence of highly toxic compounds of arsenic, antimony, and cadmium in nature poses a particular threat to human health. Prolonged exposure to these toxins has been associated with severe human diseases, including cancer, diabetes, and neurodegenerative disorders. These toxins are known to induce analogous cellular stresses, such as DNA damage, disturbance of redox homeostasis, and proteotoxicity. To overcome these threats and improve or devise treatment methods, it is crucial to understand the mechanisms of cellular detoxification in metal and metalloid stress. Membrane proteins are key cellular components involved in the uptake, vacuolar/lysosomal sequestration, and efflux of these compounds; thus, deciphering the multilevel regulation of these proteins is of the utmost importance. In this review, we summarize data on the mechanisms of arsenic, antimony, and cadmium detoxification in the context of membrane proteome. We used yeast Saccharomyces cerevisiae as a eukaryotic model to elucidate the complex mechanisms of the production, regulation, and degradation of selected membrane transporters under metal(loid)-induced stress conditions. Additionally, we present data on orthologues membrane proteins involved in metal(loid)-associated diseases in humans.
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Affiliation(s)
| | | | | | | | | | | | - Ewa Maciaszczyk-Dziubinska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland; (K.Z.); (J.S.); (J.K.); (N.L.); (M.N.-K.); (D.W.)
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3
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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: 1.0] [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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Yeast Double Transporter Gene Deletion Library for Identification of Xenobiotic Carriers in Low or High Throughput. mBio 2021; 12:e0322121. [PMID: 34903049 PMCID: PMC8669479 DOI: 10.1128/mbio.03221-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The routes of uptake and efflux should be considered when developing new drugs so that they can effectively address their intracellular targets. As a general rule, drugs appear to enter cells via protein carriers that normally carry nutrients or metabolites. A previously developed pipeline that searched for drug transporters using Saccharomyces cerevisiae mutants carrying single-gene deletions identified import routes for most compounds tested. However, due to the redundancy of transporter functions, we propose that this methodology can be improved by utilizing double mutant strains in both low- and high-throughput screens. We constructed a library of over 14,000 strains harboring double deletions of genes encoding 122 nonessential plasma membrane transporters and performed low- and high-throughput screens identifying possible drug import routes for 23 compounds. In addition, the high-throughput assay enabled the identification of putative efflux routes for 21 compounds. Focusing on azole antifungals, we were able to identify the involvement of the myo-inositol transporter, Itr1p, in the uptake of these molecules and to confirm the role of Pdr5p in their export.
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Bickers SC, Benlekbir S, Rubinstein JL, Kanelis V. Structure of Ycf1p reveals the transmembrane domain TMD0 and the regulatory region of ABCC transporters. Proc Natl Acad Sci U S A 2021; 118:e2025853118. [PMID: 34021087 PMCID: PMC8166025 DOI: 10.1073/pnas.2025853118] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
ATP binding cassette (ABC) proteins typically function in active transport of solutes across membranes. The ABC core structure is composed of two transmembrane domains (TMD1 and TMD2) and two cytosolic nucleotide binding domains (NBD1 and NBD2). Some members of the C-subfamily of ABC (ABCC) proteins, including human multidrug resistance proteins (MRPs), also possess an N-terminal transmembrane domain (TMD0) that contains five transmembrane α-helices and is connected to the ABC core by the L0 linker. While TMD0 was resolved in SUR1, the atypical ABCC protein that is part of the hetero-octameric ATP-sensitive K+ channel, little is known about the structure of TMD0 in monomeric ABC transporters. Here, we present the structure of yeast cadmium factor 1 protein (Ycf1p), a homolog of human MRP1, determined by electron cryo-microscopy (cryo-EM). A comparison of Ycf1p, SUR1, and a structure of MRP1 that showed TMD0 at low resolution demonstrates that TMD0 can adopt different orientations relative to the ABC core, including a ∼145° rotation between Ycf1p and SUR1. The cryo-EM map also reveals that segments of the regulatory (R) region, which links NBD1 to TMD2 and was poorly resolved in earlier ABCC structures, interacts with the L0 linker, NBD1, and TMD2. These interactions, combined with fluorescence quenching experiments of isolated NBD1 with and without the R region, suggest how posttranslational modifications of the R region modulate ABC protein activity. Mapping known mutations from MRP2 and MRP6 onto the Ycf1p structure explains how mutations involving TMD0 and the R region of these proteins lead to disease.
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Affiliation(s)
- Sarah C Bickers
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, ON L5L 1C6, Canada
| | - Samir Benlekbir
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada;
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Voula Kanelis
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada;
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, ON L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
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Kim IS, Choi W, Son J, Lee JH, Lee H, Lee J, Shin SC, Kim HW. Screening and Genetic Network Analysis of Genes Involved in Freezing and Thawing Resistance in DaMDHAR-Expressing Saccharomyces cerevisiae Using Gene Expression Profiling. Genes (Basel) 2021; 12:genes12020219. [PMID: 33546197 PMCID: PMC7913288 DOI: 10.3390/genes12020219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/28/2021] [Accepted: 01/30/2021] [Indexed: 01/24/2023] Open
Abstract
The cryoprotection of cell activity is a key determinant in frozen-dough technology. Although several factors that contribute to freezing tolerance have been reported, the mechanism underlying the manner in which yeast cells respond to freezing and thawing (FT) stress is not well established. Therefore, the present study demonstrated the relationship between DaMDHAR encoding monodehydroascorbate reductase from Antarctic hairgrass Deschampsia antarctica and stress tolerance to repeated FT cycles (FT2) in transgenic yeast Saccharomyces cerevisiae. DaMDHAR-expressing yeast (DM) cells identified by immunoblotting analysis showed high tolerance to FT stress conditions, thereby causing lower damage for yeast cells than wild-type (WT) cells with empty vector alone. To detect FT2 tolerance-associated genes, 3′-quant RNA sequencing was employed using mRNA isolated from DM and WT cells exposed to FT (FT2) conditions. Approximately 332 genes showed ≥2-fold changes in DM cells and were classified into various groups according to their gene expression. The expressions of the changed genes were further confirmed using western blot analysis and biochemical assay. The upregulated expression of 197 genes was associated with pentose phosphate pathway, NADP metabolic process, metal ion homeostasis, sulfate assimilation, β-alanine metabolism, glycerol synthesis, and integral component of mitochondrial and plasma membrane (PM) in DM cells under FT2 stress, whereas the expression of the remaining 135 genes was partially related to protein processing, selenocompound metabolism, cell cycle arrest, oxidative phosphorylation, and α-glucoside transport under the same condition. With regard to transcription factors in DM cells, MSN4 and CIN5 were activated, but MSN2 and MGA1 were not. Regarding antioxidant systems and protein kinases in DM cells under FT stress, CTT1, GTO, GEX1, and YOL024W were upregulated, whereas AIF1, COX2, and TRX3 were not. Gene activation represented by transcription factors and enzymatic antioxidants appears to be associated with FT2-stress tolerance in transgenic yeast cells. RCK1, MET14, and SIP18, but not YPK2, have been known to be involved in the protein kinase-mediated signalling pathway and glycogen synthesis. Moreover, SPI18 and HSP12 encoding hydrophilin in the PM were detected. Therefore, it was concluded that the genetic network via the change of gene expression levels of multiple genes contributing to the stabilization and functionality of the mitochondria and PM, not of a single gene, might be the crucial determinant for FT tolerance in DaMDAHR-expressing transgenic yeast. These findings provide a foundation for elucidating the DaMDHAR-dependent molecular mechanism of the complex functional resistance in the cellular response to FT stress.
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Affiliation(s)
- Il-Sup Kim
- Advanced Bio-Resource Research Center, Kyungpook National University, Daegu 41566, Korea;
| | - Woong Choi
- Korea Polar Research Institute, Incheon 21990, Korea; (W.C.); (J.S.); (J.H.L.); (H.L.); (J.L.); (S.C.S.)
| | - Jonghyeon Son
- Korea Polar Research Institute, Incheon 21990, Korea; (W.C.); (J.S.); (J.H.L.); (H.L.); (J.L.); (S.C.S.)
| | - Jun Hyuck Lee
- Korea Polar Research Institute, Incheon 21990, Korea; (W.C.); (J.S.); (J.H.L.); (H.L.); (J.L.); (S.C.S.)
- Department of Polar Science, University of Science and Technology, Incheon 21990, Korea
| | - Hyoungseok Lee
- Korea Polar Research Institute, Incheon 21990, Korea; (W.C.); (J.S.); (J.H.L.); (H.L.); (J.L.); (S.C.S.)
- Department of Polar Science, University of Science and Technology, Incheon 21990, Korea
| | - Jungeun Lee
- Korea Polar Research Institute, Incheon 21990, Korea; (W.C.); (J.S.); (J.H.L.); (H.L.); (J.L.); (S.C.S.)
- Department of Polar Science, University of Science and Technology, Incheon 21990, Korea
| | - Seung Chul Shin
- Korea Polar Research Institute, Incheon 21990, Korea; (W.C.); (J.S.); (J.H.L.); (H.L.); (J.L.); (S.C.S.)
| | - Han-Woo Kim
- Korea Polar Research Institute, Incheon 21990, Korea; (W.C.); (J.S.); (J.H.L.); (H.L.); (J.L.); (S.C.S.)
- Department of Polar Science, University of Science and Technology, Incheon 21990, Korea
- Correspondence:
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Li J, Vázquez-García I, Persson K, González A, Yue JX, Barré B, Hall MN, Long A, Warringer J, Mustonen V, Liti G. Shared Molecular Targets Confer Resistance over Short and Long Evolutionary Timescales. Mol Biol Evol 2019; 36:691-708. [PMID: 30657986 DOI: 10.1093/molbev/msz006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Pre-existing and de novo genetic variants can both drive adaptation to environmental changes, but their relative contributions and interplay remain poorly understood. Here we investigated the evolutionary dynamics in drug-treated yeast populations with different levels of pre-existing variation by experimental evolution coupled with time-resolved sequencing and phenotyping. We found a doubling of pre-existing variation alone boosts the adaptation by 64.1% and 51.5% in hydroxyurea and rapamycin, respectively. The causative pre-existing and de novo variants were selected on shared targets: RNR4 in hydroxyurea and TOR1, TOR2 in rapamycin. Interestingly, the pre-existing and de novo TOR variants map to different functional domains and act via distinct mechanisms. The pre-existing TOR variants from two domesticated strains exhibited opposite rapamycin resistance effects, reflecting lineage-specific functional divergence. This study provides a dynamic view on how pre-existing and de novo variants interactively drive adaptation and deepens our understanding of clonally evolving populations.
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Affiliation(s)
- Jing Li
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
| | - Ignacio Vázquez-García
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom.,Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Statistics, Columbia University, New York, NY
| | - Karl Persson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | | | - Jia-Xing Yue
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
| | - Benjamin Barré
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
| | | | - Anthony Long
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Gianni Liti
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
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Sousa CA, Hanselaer S, Soares EV. ABCC subfamily vacuolar transporters are involved in Pb (lead) detoxification in Saccharomyces cerevisiae. Appl Biochem Biotechnol 2014; 175:65-74. [PMID: 25240850 DOI: 10.1007/s12010-014-1252-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 09/10/2014] [Indexed: 01/12/2023]
Abstract
The present work has as objective to contribute for the elucidation of the mechanism associated with Pb detoxification, using the yeast Saccharomyces cerevisiae as a model organism. The deletion of GTT1 or GTT2 genes, coding for functional glutathione transferases (GST) enzymes in S. cerevisiae, caused an increased susceptibility to high Pb concentrations (500-1000 μmol L(-1)). These results suggest that the formation of glutathione-Pb conjugate (GS-Pb), dependent of GSTs, is important in Pb detoxification. The involvement of ATP-binding cassette (ABC) vacuolar transporters, belonging to class C subfamily (ABCC) in vacuolar compartmentalization of Pb, was evaluated. For this purpose, mutant strains disrupted in YCF1, VMR1, YBT1 or BPT 1 genes were used. All mutants tested, without vacuolar ABCC transporters, presented an increased sensitivity to 500-1000 μmol L(-1) Pb comparative to wild-type strain. Taken together, the obtained results suggest that Pb detoxification, by vacuolar compartmentalization, can occur as a result of the concerted action of GSTs and vacuolar ABCC transporters. Pb is conjugated with glutathione, catalysed by glutathione transferases and followed to the transport of GS-Pb conjugate to the vacuole by ABCC transporters.
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Affiliation(s)
- Cátia A Sousa
- Bioengineering Laboratory-CIETI, Chemical Engineering Department, ISEP-School of Engineering of Polytechnic Institute of Porto, Rua Dr António Bernardino de Almeida, 431, 4200-072, Porto, Portugal
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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: 0.6] [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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10
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Yeast ABC proteins involved in multidrug resistance. Cell Mol Biol Lett 2013; 19:1-22. [PMID: 24297686 PMCID: PMC6275743 DOI: 10.2478/s11658-013-0111-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 11/27/2013] [Indexed: 01/03/2023] Open
Abstract
Pleiotropic drug resistance is a complex phenomenon that involves many proteins that together create a network. One of the common mechanisms of multidrug resistance in eukaryotic cells is the active efflux of a broad range of xenobiotics through ATP-binding cassette (ABC) transporters. Saccharomyces cerevisiae is often used as a model to study such activity because of the functional and structural similarities of its ABC transporters to mammalian ones. Numerous ABC transporters are found in humans and some are associated with the resistance of tumors to chemotherapeutics. Efflux pump modulators that change the activity of ABC proteins are the most promising candidate drugs to overcome such resistance. These modulators can be chemically synthesized or isolated from natural sources (e.g., plant alkaloids) and might also be used in the treatment of fungal infections. There are several generations of synthetic modulators that differ in specificity, toxicity and effectiveness, and are often used for other clinical effects.
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11
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Mapping the functional yeast ABC transporter interactome. Nat Chem Biol 2013; 9:565-72. [PMID: 23831759 PMCID: PMC3835492 DOI: 10.1038/nchembio.1293] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 06/11/2013] [Indexed: 12/17/2022]
Abstract
ABC transporters are a ubiquitous class of integral membrane proteins of immense clinical interest because of their strong association with human disease and pharmacology. To improve our understanding of these proteins, we used Membrane Yeast Two-Hybrid (MYTH) technology to map the protein interactome of all non-mitochondrial ABC transporters in the model organism Saccharomy cescerevisiae, and combined this data with previously reported yeast ABC transporter interactions in the BioGRID database to generate a comprehensive, integrated interactome. We show that ABC transporters physically associate with proteins involved in a surprisingly diverse range of functions. We specifically examine the importance of the physical interactions of ABC transporters in both the regulation of one another and in the modulation of proteins involved in zinc homeostasis. The interaction network presented here will be a powerful resource for increasing our fundamental understanding of the cellular role and regulation of ABC transporters.
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Abstract
All fungal genomes harbour numerous ABC (ATP-binding cassette) proteins located in various cellular compartments such as the plasma membrane, vacuoles, peroxisomes and mitochondria. Most of them have initially been discovered through their ability to confer resistance to a multitude of drugs, a phenomenon called PDR (pleiotropic drug resistance) or MDR (multidrug resistance). Studying the mechanisms underlying PDR/MDR in yeast is of importance in two ways: first, ABC proteins can confer drug resistance on pathogenic fungi such as Candida spp., Aspergillus spp. or Cryptococcus neoformans; secondly, the well-established genetic, biochemical and cell biological tractability of Saccharomyces cerevisiae makes it an ideal tool to study basic mechanisms of drug transport by ABC proteins. In the past, knowledge from yeast has complemented work on human ABC transporters involved in anticancer drug resistance or genetic diseases. Interestingly, increasing evidence available from yeast and other organisms suggests that ABC proteins play a physiological role in membrane homoeostasis and lipid distribution, although this is being intensely debated in the literature.
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Wysocki R, Tamás MJ. How Saccharomyces cerevisiae copes with toxic metals and metalloids. FEMS Microbiol Rev 2011; 34:925-51. [PMID: 20374295 DOI: 10.1111/j.1574-6976.2010.00217.x] [Citation(s) in RCA: 213] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Toxic metals and metalloids are widespread in nature and can locally reach fairly high concentrations. To ensure cellular protection and survival in such environments, all organisms possess systems to evade toxicity and acquire tolerance. This review provides an overview of the molecular mechanisms that contribute to metal toxicity, detoxification and tolerance acquisition in budding yeast Saccharomyces cerevisiae. We mainly focus on the metals/metalloids arsenic, cadmium, antimony, mercury, chromium and selenium, and emphasize recent findings on sensing and signalling mechanisms and on the regulation of tolerance and detoxification systems that safeguard cellular and genetic integrity.
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Affiliation(s)
- Robert Wysocki
- Institute of Genetics and Microbiology, University of Wroclaw, Wroclaw, Poland
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14
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Wawrzycka D, Sobczak I, Bartosz G, Bocer T, Ułaszewski S, Goffeau A. Vmr 1p is a novel vacuolar multidrug resistance ABC transporter in Saccharomyces cerevisiae. FEMS Yeast Res 2010; 10:828-38. [PMID: 20846144 DOI: 10.1111/j.1567-1364.2010.00673.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The Saccharomyces cerevisiae Yhl035p/Vmr1p is an ABC transporter of the MRP subfamily that is conserved in all post Whole Genome Duplication species. The deletion of the YHL035 gene caused growth sensitivity to several amphiphilic drugs such as cycloheximide, 2,4-dichlorophenoxyacetic acid, 2,4-dinitrophenol as well as to cadmium and other toxic metals. Vmr1p-GFP was located in the vacuolar membrane. The ATP-dependent transport of a DNP-S-glutathione conjugate was reduced in a vesicular fraction from the VMR1 deletant. The energy-dependent efflux of rhodamine 6G was increased by VMR1 deletion. Growth sensitivity to cadmium of the VMR1-deleted strain was more pronounced in glycerol/ethanol than in glucose-grown cells. The VMR1 promoter had higher activity when grown in glycerol/ethanol compared with glucose. In glucose, the VMR1 promoter was activated by the deletion of the glucose-dependent repressor ADR1.
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Affiliation(s)
- Donata Wawrzycka
- Genetics and Microbiology Institute, Wrocław University, Wrocław, Poland
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15
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Pickin KA, Ezenwajiaku N, Overcash H, Sethi M, Knecht MR, Paumi CM. Suppression of Ycf1p function by Cka1p-dependent phosphorylation is attenuated in response to salt stress. FEMS Yeast Res 2010; 10:839-57. [PMID: 20812950 DOI: 10.1111/j.1567-1364.2010.00677.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The yeast vacuolar membrane protein Ycf1p and its mammalian counterpart, MRP1, belong to the ABCC subfamily of ATP-binding cassette transporters. Genetic evidence suggests that the yeast casein kinase 2α, Cka1p, negatively regulates Ycf1p function via phosphorylation of Ser251 within the N-terminus. In this study, we provide strong evidence that Cka1p regulates Ycf1p function via phosphorylation of Ser251. We show that the CK2 holoenzyme interacts with Ycf1p. However, genetic analysis suggests that only Cka1p is required for Ser251 phosphorylation, as the deletion of CKA1 significantly reduces Ser251 phosphorylation in vivo. Furthermore, purified recombinant Cka1p phosphorylates a Ycf1p-derived peptide containing Ser251. We also demonstrate that Ycf1p function is induced in response to high salt stress. Induction of the Ycf1p function strongly correlates with reduced phosphorylation of Ser251. Importantly, Cka1p activity in vivo is similarly reduced in response to salt stress, consistent with our finding that Cka1p directly phosphorylates Ser251 of Ycf1p. We provide genetic and biochemical evidence that strongly suggests that the induction of Ycf1p function is the result of decreased phosphorylation of Ser251. In conclusion, our work demonstrates a novel biochemical role for Cka1p regulation of Ycf1p function in the cellular response of yeast to salt stress.
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Affiliation(s)
- Kerry A Pickin
- Department of Toxicology, University of Kentucky, Lexington, KY 40536, USA
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16
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ABC transporters in Saccharomyces cerevisiae and their interactors: new technology advances the biology of the ABCC (MRP) subfamily. Microbiol Mol Biol Rev 2010; 73:577-93. [PMID: 19946134 DOI: 10.1128/mmbr.00020-09] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Members of the ATP-binding cassette (ABC) transporter superfamily exist in bacteria, fungi, plants, and animals and play key roles in the efflux of xenobiotic compounds, physiological substrates, and toxic intracellular metabolites. Based on sequence relatedness, mammalian ABC proteins have been divided into seven subfamilies, ABC subfamily A (ABCA) to ABCG. This review focuses on recent advances in our understanding of ABC transporters in the model organism Saccharomyces cerevisiae. We propose a revised unified nomenclature for the six yeast ABC subfamilies to reflect the current mammalian designations ABCA to ABCG. In addition, we specifically review the well-studied yeast ABCC subfamily (formerly designated the MRP/CFTR subfamily), which includes six members (Ycf1p, Bpt1p, Ybt1p/Bat1p, Nft1p, Vmr1p, and Yor1p). We focus on Ycf1p, the best-characterized yeast ABCC transporter. Ycf1p is located in the vacuolar membrane in yeast and functions in a manner analogous to that of the human multidrug resistance-related protein (MRP1, also called ABCC1), mediating the transport of glutathione-conjugated toxic compounds. We review what is known about Ycf1p substrates, trafficking, processing, posttranslational modifications, regulation, and interactors. Finally, we discuss a powerful new yeast two-hybrid technology called integrated membrane yeast two-hybrid (iMYTH) technology, which was designed to identify interactors of membrane proteins. iMYTH technology has successfully identified novel interactors of Ycf1p and promises to be an invaluable tool in future efforts to comprehensively define the yeast ABC interactome.
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17
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Paumi CM, Chuk M, Chevelev I, Stagljar I, Michaelis S. Negative regulation of the yeast ABC transporter Ycf1p by phosphorylation within its N-terminal extension. J Biol Chem 2008; 283:27079-88. [PMID: 18667437 DOI: 10.1074/jbc.m802569200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The yeast vacuolar membrane protein Ycf1p and its mammalian counterpart, MRP1, belong to the ABCC subfamily of ATP-binding cassette (ABC) transporters that rid cells of toxic endogenous and xenobiotic compounds. Like most members of the ABCC subfamily, Ycf1p contains an N-terminal extension in addition to its ABC "core" domain and transports substrates in the form of glutathione conjugates. Ycf1p is subject to complex regulation to ensure its optimal function. Previous studies showed that Ycf1p activity is stimulated by a guanine nucleotide exchange factor, Tus1p, and is positively regulated by phosphorylation in its ABC core domain at residues Ser-908 and Thr-911. Here we provide evidence that phosphorylation of Ser-251 in the Ycf1p N-terminal extension negatively regulates activity. Mutant Ycf1p-S251A exhibits increased resistance to cadmium in vivo and increased Ycf1p-dependent transport of [(3)H]estradiol-beta-17-glucuronide in vitro as compared with wild-type Ycf1p. Activity is restored to the wild-type level for Ycf1-S251E. To identify kinase(s) that negatively regulate Ycf1p function, we conducted an integrated membrane yeast two-hybrid (iMYTH) screen and identified two kinase genes, CKA1 and HAL5, deletion of which increases Ycf1p function. Genetic evidence suggests that Cka1p may regulate Ycf1p function through phosphorylation of Ser-251 either directly or indirectly. Overall, this study provides compelling evidence that negative, as well as positive, regulation of Ycf1p is mediated by phosphorylation.
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Affiliation(s)
- Christian M Paumi
- Department of Cell Biology, The Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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18
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Wei W, McCusker JH, Hyman RW, Jones T, Ning Y, Cao Z, Gu Z, Bruno D, Miranda M, Nguyen M, Wilhelmy J, Komp C, Tamse R, Wang X, Jia P, Luedi P, Oefner PJ, David L, Dietrich FS, Li Y, Davis RW, Steinmetz LM. Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. Proc Natl Acad Sci U S A 2007; 104:12825-30. [PMID: 17652520 PMCID: PMC1933262 DOI: 10.1073/pnas.0701291104] [Citation(s) in RCA: 206] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We sequenced the genome of Saccharomyces cerevisiae strain YJM789, which was derived from a yeast isolated from the lung of an AIDS patient with pneumonia. The strain is used for studies of fungal infections and quantitative genetics because of its extensive phenotypic differences to the laboratory reference strain, including growth at high temperature and deadly virulence in mouse models. Here we show that the approximately 12-Mb genome of YJM789 contains approximately 60,000 SNPs and approximately 6,000 indels with respect to the reference S288c genome, leading to protein polymorphisms with a few known cases of phenotypic changes. Several ORFs are found to be unique to YJM789, some of which might have been acquired through horizontal transfer. Localized regions of high polymorphism density are scattered over the genome, in some cases spanning multiple ORFs and in others concentrated within single genes. The sequence of YJM789 contains clues to pathogenicity and spurs the development of more powerful approaches to dissecting the genetic basis of complex hereditary traits.
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Affiliation(s)
- Wu Wei
- *Bioinformatics Center, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
- Shanghai Center for Bioinformation Technology, Shanghai 200235, People's Republic of China
| | - John H. McCusker
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Richard W. Hyman
- Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304
| | - Ted Jones
- Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304
| | - Ye Ning
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Zhiwei Cao
- Shanghai Center for Bioinformation Technology, Shanghai 200235, People's Republic of China
| | - Zhenglong Gu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853; and
| | - Dan Bruno
- Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304
| | - Molly Miranda
- Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304
| | - Michelle Nguyen
- Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304
| | - Julie Wilhelmy
- Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304
| | - Caridad Komp
- Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304
| | - Raquel Tamse
- Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304
| | - Xiaojing Wang
- *Bioinformatics Center, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
- Shanghai Center for Bioinformation Technology, Shanghai 200235, People's Republic of China
| | - Peilin Jia
- *Bioinformatics Center, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
- Shanghai Center for Bioinformation Technology, Shanghai 200235, People's Republic of China
| | - Philippe Luedi
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Peter J. Oefner
- Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304
| | - Lior David
- Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304
| | - Fred S. Dietrich
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Yixue Li
- *Bioinformatics Center, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
- Shanghai Center for Bioinformation Technology, Shanghai 200235, People's Republic of China
| | - Ronald W. Davis
- Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304
| | - Lars M. Steinmetz
- Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- **To whom correspondence should be addressed. E-mail:
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19
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Paumi CM, Menendez J, Arnoldo A, Engels K, Iyer KR, Thaminy S, Georgiev O, Barral Y, Michaelis S, Stagljar I. Mapping protein-protein interactions for the yeast ABC transporter Ycf1p by integrated split-ubiquitin membrane yeast two-hybrid analysis. Mol Cell 2007; 26:15-25. [PMID: 17434123 DOI: 10.1016/j.molcel.2007.03.011] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Revised: 01/19/2007] [Accepted: 03/09/2007] [Indexed: 11/28/2022]
Abstract
The ATP binding cassette (ABC) transporters are important in human health and disease and represent the largest family of transmembrane proteins; however, their highly hydrophobic nature complicates the use of standard biochemical approaches to identify interacting proteins. Here, we report the development of a modified version of the split-ubiquitin membrane yeast two-hybrid (MYTH) technology using genomically integrated "bait" constructs, hence the designation iMYTH. We used iMYTH in a library-screening format and identified six potential interacting partners of the yeast ABC transporter Ycf1p. Strains deleted for several of these genes result in arsenite sensitivity similar to a Deltaycf1 strain. Transport assays show that one of these, Tus1p, a guanine nucleotide exchange factor (GEF) for the small GTPase Rho1p, is a Rho1p-dependent-positive regulator of Ycf1p. Our study provides proof of principle that iMYTH is an ideal methodology to identify physiological interactors and regulators of ABC transporters and other yeast transmembrane proteins.
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Affiliation(s)
- Christian M Paumi
- Department of Cell Biology, The Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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20
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Deeley RG, Westlake C, Cole SPC. Transmembrane transport of endo- and xenobiotics by mammalian ATP-binding cassette multidrug resistance proteins. Physiol Rev 2006; 86:849-99. [PMID: 16816140 DOI: 10.1152/physrev.00035.2005] [Citation(s) in RCA: 552] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Multidrug Resistance Proteins (MRPs), together with the cystic fibrosis conductance regulator (CFTR/ABCC7) and the sulfonylurea receptors (SUR1/ABCC8 and SUR2/ABCC9) comprise the 13 members of the human "C" branch of the ATP binding cassette (ABC) superfamily. All C branch proteins share conserved structural features in their nucleotide binding domains (NBDs) that distinguish them from other ABC proteins. The MRPs can be further divided into two subfamilies "long" (MRP1, -2, -3, -6, and -7) and "short" (MRP4, -5, -8, -9, and -10). The short MRPs have a typical ABC transporter structure with two polytropic membrane spanning domains (MSDs) and two NBDs, while the long MRPs have an additional NH2-terminal MSD. In vitro, the MRPs can collectively confer resistance to natural product drugs and their conjugated metabolites, platinum compounds, folate antimetabolites, nucleoside and nucleotide analogs, arsenical and antimonial oxyanions, peptide-based agents, and, under certain circumstances, alkylating agents. The MRPs are also primary active transporters of other structurally diverse compounds, including glutathione, glucuronide, and sulfate conjugates of a large number of xeno- and endobiotics. In vivo, several MRPs are major contributors to the distribution and elimination of a wide range of both anticancer and non-anticancer drugs and metabolites. In this review, we describe what is known of the structure of the MRPs and the mechanisms by which they recognize and transport their diverse substrates. We also summarize knowledge of their possible physiological functions and evidence that they may be involved in the clinical drug resistance of various forms of cancer.
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Affiliation(s)
- Roger G Deeley
- Division of Cancer Biology and Genetics, Cancer Research Institute and Department of Biochemistry, Queen's University Kingdom, Ontario, Canada.
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21
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Frelet A, Klein M. Insight in eukaryotic ABC transporter function by mutation analysis. FEBS Lett 2006; 580:1064-84. [PMID: 16442101 DOI: 10.1016/j.febslet.2006.01.024] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Revised: 01/10/2006] [Accepted: 01/10/2006] [Indexed: 11/21/2022]
Abstract
With regard to structure-function relations of ATP-binding cassette (ABC) transporters several intriguing questions are in the spotlight of active research: Why do functional ABC transporters possess two ATP binding and hydrolysis domains together with two ABC signatures and to what extent are the individual nucleotide-binding domains independent or interacting? Where is the substrate-binding site and how is ATP hydrolysis functionally coupled to the transport process itself? Although much progress has been made in the elucidation of the three-dimensional structures of ABC transporters in the last years by several crystallographic studies including novel models for the nucleotide hydrolysis and translocation catalysis, site-directed mutagenesis as well as the identification of natural mutations is still a major tool to evaluate effects of individual amino acids on the overall function of ABC transporters. Apart from alterations in characteristic sequence such as Walker A, Walker B and the ABC signature other parts of ABC proteins were subject to detailed mutagenesis studies including the substrate-binding site or the regulatory domain of CFTR. In this review, we will give a detailed overview of the mutation analysis reported for selected ABC transporters of the ABCB and ABCC subfamilies, namely HsCFTR/ABCC7, HsSUR/ABCC8,9, HsMRP1/ABCC1, HsMRP2/ABCC2, ScYCF1 and P-glycoprotein (Pgp)/MDR1/ABCB1 and their effects on the function of each protein.
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Affiliation(s)
- Annie Frelet
- Zurich Basel Plant Science Center, University of Zurich, Plant Biology, Zollikerstrasse 107, CH-8008 Zurich, Switzerland
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22
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Jungwirth H, Kuchler K. Yeast ABC transporters-- a tale of sex, stress, drugs and aging. FEBS Lett 2005; 580:1131-8. [PMID: 16406363 DOI: 10.1016/j.febslet.2005.12.050] [Citation(s) in RCA: 165] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 12/13/2005] [Accepted: 12/14/2005] [Indexed: 12/31/2022]
Abstract
Yeast ATP-binding cassette (ABC) proteins are implicated in many biological phenomena, often acting at crossroads of vital cellular processes. Their functions encompass peptide pheromone secretion, regulation of mitochondrial function, vacuolar detoxification, as well as pleiotropic drug resistance and stress adaptation. Because yeast harbors several homologues of mammalian ABC proteins with medical importance, understanding their molecular mechanisms, substrate interaction and three-dimensional structure of yeast ABC proteins might help identifying new approaches aimed at combating drug resistance or other ABC-mediated diseases. This review provides a comprehensive discussion on the functions of the ABC protein family in the yeast Saccharomyces cerevisiae.
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Affiliation(s)
- Helmut Jungwirth
- Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University Vienna, Campus Vienna Biocenter, Austria
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23
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Braun BR, van het Hoog M, d'Enfert C, Martchenko M, Dungan J, Kuo A, Inglis DO, Uhl MA, Hogues H, Berriman M, Lorenz M, Levitin A, Oberholzer U, Bachewich C, Harcus D, Marcil A, Dignard D, Iouk T, Zito R, Frangeul L, Tekaia F, Rutherford K, Wang E, Munro CA, Bates S, Gow NA, Hoyer LL, Köhler G, Morschhäuser J, Newport G, Znaidi S, Raymond M, Turcotte B, Sherlock G, Costanzo M, Ihmels J, Berman J, Sanglard D, Agabian N, Mitchell AP, Johnson AD, Whiteway M, Nantel A. A human-curated annotation of the Candida albicans genome. PLoS Genet 2005; 1:36-57. [PMID: 16103911 PMCID: PMC1183520 DOI: 10.1371/journal.pgen.0010001] [Citation(s) in RCA: 242] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2005] [Accepted: 03/14/2005] [Indexed: 11/24/2022] Open
Abstract
Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained sequencing errors (or possibly mutations) that affect their reading frame. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy. We also observed that, compared to other fungi, the protein-coding sequences in the C. albicans genome are especially rich in short sequence repeats. Finally, our improved annotation permitted a detailed analysis of several multigene families, and comparative genomic studies showed that C. albicans has a far greater catabolic range, encoding respiratory Complex 1, several novel oxidoreductases and ketone body degrading enzymes, malonyl-CoA and enoyl-CoA carriers, several novel amino acid degrading enzymes, a variety of secreted catabolic lipases and proteases, and numerous transporters to assimilate the resulting nutrients. The results of these efforts will ensure that the Candida research community has uniform and comprehensive genomic information for medical research as well as for future diagnostic and therapeutic applications.
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Affiliation(s)
- Burkhard R Braun
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Marco van het Hoog
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Christophe d'Enfert
- Unité Postulante Biologie et Pathogénicité Fongiques, INRA USC 2019, Institut Pasteur, Paris, France
| | - Mikhail Martchenko
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Jan Dungan
- Department of Stomatology, University of California, San Francisco, California, United States of America
| | - Alan Kuo
- Department of Stomatology, University of California, San Francisco, California, United States of America
| | - Diane O Inglis
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - M. Andrew Uhl
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Hervé Hogues
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | | | - Michael Lorenz
- Department of Microbiology and Molecular Genetics, Utah-Houston Medical School, Houston, Texas, United States of America
| | - Anastasia Levitin
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Ursula Oberholzer
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Catherine Bachewich
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Doreen Harcus
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Anne Marcil
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Daniel Dignard
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Tatiana Iouk
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Rosa Zito
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Lionel Frangeul
- Plate-Forme Intégration et Analyse Génomique, Institut Pasteur, Paris, France
| | - Fredj Tekaia
- Unité de Génétique Moléculaire des Levures, Institut Pasteur, Paris, France
| | | | - Edwin Wang
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Carol A Munro
- School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Steve Bates
- School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Neil A Gow
- School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Lois L Hoyer
- Department of Veterinary Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Gerwald Köhler
- Department of Stomatology, University of California, San Francisco, California, United States of America
| | - Joachim Morschhäuser
- Institut für Molekulare Infektionsbiologie, Universität Wurzburg, Wurzburg, Germany
| | - George Newport
- Department of Stomatology, University of California, San Francisco, California, United States of America
| | - Sadri Znaidi
- Institut de Recherches Cliniques de Montreal, Montreal, Quebec, Canada
| | - Martine Raymond
- Institut de Recherches Cliniques de Montreal, Montreal, Quebec, Canada
| | - Bernard Turcotte
- Department of Medicine, Royal Victoria Hospital, McGill University, Montreal, Quebec, Canada
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Palo Alto, California, United States of America
| | - Maria Costanzo
- Department of Genetics, Stanford University School of Medicine, Palo Alto, California, United States of America
| | - Jan Ihmels
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Judith Berman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Dominique Sanglard
- Institute of Microbiology, University Hospital Lausanne, Lausanne, Switzerland
| | - Nina Agabian
- Department of Stomatology, University of California, San Francisco, California, United States of America
| | - Aaron P Mitchell
- Department of Microbiology and Institute of Cancer Research, Columbia University, New York, New York, United States of America
| | - Alexander D Johnson
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Malcolm Whiteway
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - André Nantel
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
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24
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Eraso P, Martínez-Burgos M, Falcón-Pérez JM, Portillo F, Mazón MJ. Ycf1-dependent cadmium detoxification by yeast requires phosphorylation of residues Ser908 and Thr911. FEBS Lett 2005; 577:322-6. [PMID: 15556603 DOI: 10.1016/j.febslet.2004.10.030] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2004] [Revised: 10/08/2004] [Accepted: 10/11/2004] [Indexed: 11/24/2022]
Abstract
Yeast cadmium factor (Ycf1), an ATP-binding cassette (ABC) protein of the multidrug resistance protein subfamily, is a vacuolar GS-conjugate transporter required for heavy metal and drug detoxification. There is evidence that phosphorylation may play a critical role in the function of ABC transporters from higher organisms. In this work, the possibility of Ycf1 phosphorylation was examined using site-directed mutagenesis. We demonstrate that Ser908 and Thr911, within the regulatory domain (R domain), are functionally important for Ycf1 transport activity and likely sites for phosphorylation. Mutation of these residues to alanine severely impaired the Ycf1-dependent cadmium detoxification capacity and transport activity, while replacement by acidic residues (mimicking phosphorylation) significantly suppressed the cadmium resistance and transport defects. Both in vitro treatment of Ycf1 with alkaline phosphatase and changes in the electrophoretic mobility of the S908A, T911A and double mutant S908A/T911A proteins supported the conclusion that Ycf1 is a phosphoprotein. The screening of the yeast kinome identified four protein kinases affecting cadmium detoxification, but none of them was involved directly in the phosphorylation of Ycf1. Our data strongly implicate Ycf1 phosphorylation as a key determinant in cadmium resistance in yeast, a significant finding given that very little is known about phosphorylation of ABC transporters in yeast.
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Affiliation(s)
- Pilar Eraso
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Madrid, Spain
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25
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26
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Ernst R, Klemm R, Schmitt L, Kuchler K. Yeast ATP-binding cassette transporters: cellular cleaning pumps. Methods Enzymol 2005; 400:460-84. [PMID: 16399365 DOI: 10.1016/s0076-6879(05)00026-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Numerous ATP-binding cassette (ABC) proteins have been implicated in multidrug resistance, and some are also intimately connected to genetic diseases. For example, mammalian ABC proteins such as P-glycoproteins or multidrug resistance-associated proteins are associated with multidrug resistance phenomena (MDR), thus hampering anticancer therapy. Likewise, homologues in bacteria, fungi, or parasites are tightly associated with multidrug and antibiotic resistance. Several orthologues of mammalian MDR genes operate in the unicellular eukaryote Saccharomyces cerevisiae. Their functions have been linked to stress response, cellular detoxification, and drug resistance. This chapter discusses those yeast ABC transporters implicated in pleiotropic drug resistance and cellular detoxification. We describe strategies for their overexpression, biochemical purification, functional analysis, and a reconstitution in phospholipid vesicles, all of which are instrumental to better understanding their mechanisms of action and perhaps their physiological function.
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Affiliation(s)
- Robert Ernst
- Institute of Biochemistry, Membrane Transport Group, Heinrich-Heine University of Düsseldorf, Germany
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Nagata K, Yamamoto A, Ban N, Tanaka AR, Matsuo M, Kioka N, Inagaki N, Ueda K. Human ABCA3, a product of a responsible gene for abca3 for fatal surfactant deficiency in newborns, exhibits unique ATP hydrolysis activity and generates intracellular multilamellar vesicles. Biochem Biophys Res Commun 2004; 324:262-8. [PMID: 15465012 DOI: 10.1016/j.bbrc.2004.09.043] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2004] [Indexed: 10/26/2022]
Abstract
ABCA3 is highly expressed at the membrane of lamellar bodies in alveolar type II cells, in which pulmonary surfactant is stored. ABCA3 gene mutations cause fatal surfactant deficiency in newborns. We established HEK293 cells stably expressing human ABCA3 and analyzed the function. Exogenously expressed ABCA3 is glycosylated and localized at the intracellular vesicle membrane. ABCA3 is efficiently photoaffinity labeled by 8-azido-[alpha(32)P]ATP, but not by 8-azido-[gamma(32)P]ATP, when the membrane fraction is incubated in the presence of orthovanadate. Photoaffinity labeling of ABCA3 shows unique metal ion-dependence and is largely reduced by membrane pretreatment with 5% methyl-beta-cyclodextrin, which depletes cholesterol. Electron micrographs show that HEK293/hABCA3 cells contain multivesicular, lamellar body-like structures, which do not exist in HEK293 host cells. Some fuzzy components such as lipids accumulate in the vesicles. These results suggest that ABCA3 shows ATPase activity, which is induced by lipids, and may be involved in the biogenesis of lamellar body-like structures.
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Affiliation(s)
- Koh Nagata
- Laboratory of Cellular Biochemistry, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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Sauerborn R, Polancec DS, Zaja R, Smital T. Identification of the multidrug resistance-associated protein (mrp) related gene in red mullet (Mullus barbatus). MARINE ENVIRONMENTAL RESEARCH 2004; 58:199-204. [PMID: 15178032 DOI: 10.1016/j.marenvres.2004.03.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Multixenobiotic resistance mechanism (MXR) in aquatic organisms is mediated by the activity of the P-glycoprotein (Pgp) transporter that binds and actively effluxes different chemicals out of cell. In addition to the Pgp, several other, non-Pgp transport proteins have been recently identified in different human and animal tissues. Given their characteristics and tissue distribution we hypothesized that members of the so-called multidrug resistance-associated protein (MRP) family may be expressed in aquatic organisms. This study attempted to identify MRP related genes in different tissues of several marine and freshwater bivalves (Mytilus galloprovincialis, Dreissena polymorpha, Anodonta cygnea) and fish species (Mullus barbatus, Cyprinus carpio, Salmo trutta). Following an alignment of known MRP1 and MRP2 human sequences, as well as the GenBank available mrp2 sequences from different animals, we determined highly conserved regions and used them to design three pairs of consensus primers. Total RNA was isolated, reverse transcribed to cDNA and the obtained cDNAs were PCR amplified with the corresponding primers. The amplified PCR products were sequenced and their homology compared with Pgp and MRP protein sequences from different species. The expression of MRP related mRNA was clearly identified only in liver tissue isolated from red mullet, with homologies at the protein level ranging from 75% to 76%. Described results clearly pointed at the possibility that at least in the red mullet MXR as a general defense mechanism may be mediated by the activities of at least two different types of transport proteins.
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Affiliation(s)
- Roberta Sauerborn
- Laboratory for Molecular Ecotoxicology, Department for Marine and Environmental Research, Rudjer Boskovic Institute, Bijenicka 54, 10002 Zagreb, Croatia
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29
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Current awareness on yeast. Yeast 2003; 20:1309-16. [PMID: 14664230 DOI: 10.1002/yea.951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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