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Jordan EN, Shirali Hossein Zade R, Pillay S, van Lent P, Abeel T, Kayser O. Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol. NPJ Syst Biol Appl 2024; 10:63. [PMID: 38821949 PMCID: PMC11143246 DOI: 10.1038/s41540-024-00382-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 05/13/2024] [Indexed: 06/02/2024] Open
Abstract
Yeast metabolism can be engineered to produce xenobiotic compounds, such as cannabinoids, the principal isoprenoids of the plant Cannabis sativa, through heterologous metabolic pathways. However, yeast cell factories continue to have low cannabinoid production. This study employed an integrated omics approach to investigate the physiological effects of cannabidiol on S. cerevisiae CENPK2-1C yeast cultures. We treated the experimental group with 0.5 mM CBD and monitored CENPK2-1C cultures. We observed a latent-stationary phase post-diauxic shift in the experimental group and harvested samples in the inflection point of this growth phase for transcriptomic and metabolomic analysis. We compared the transcriptomes of the CBD-treated yeast and the positive control, identifying eight significantly overexpressed genes with a log fold change of at least 1.5 and a significant adjusted p-value. Three notable genes were PDR5 (an ABC-steroid and cation transporter), CIS1, and YGR035C. These genes are all regulated by pleiotropic drug resistance linked promoters. Knockout and rescue of PDR5 showed that it is a causal factor in the post-diauxic shift phenotype. Metabolomic analysis revealed 48 significant spectra associated with CBD-fed cell pellets, 20 of which were identifiable as non-CBD compounds, including fatty acids, glycerophospholipids, and phosphate-salvage indicators. Our results suggest that mitochondrial regulation and lipidomic remodeling play a role in yeast's response to CBD, which are employed in tandem with pleiotropic drug resistance (PDR). We conclude that bioengineers should account for off-target product C-flux, energy use from ABC-transport, and post-stationary phase cell growth when developing cannabinoid-biosynthetic yeast strains.
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Affiliation(s)
- Erin Noel Jordan
- Technical Biochemistry, TU Dortmund University, Emil-Figge-Straße 66, 44227, Dortmund, Germany.
| | - Ramin Shirali Hossein Zade
- Delft Bioinformatics Lab, Delft University of Technology Van Mourik, Broekmanweg 6, 2628 XE, Delft, The Netherlands
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Stephanie Pillay
- Delft Bioinformatics Lab, Delft University of Technology Van Mourik, Broekmanweg 6, 2628 XE, Delft, The Netherlands
| | - Paul van Lent
- Delft Bioinformatics Lab, Delft University of Technology Van Mourik, Broekmanweg 6, 2628 XE, Delft, The Netherlands
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology Van Mourik, Broekmanweg 6, 2628 XE, Delft, The Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Oliver Kayser
- Technical Biochemistry, TU Dortmund University, Emil-Figge-Straße 66, 44227, Dortmund, Germany.
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Geck RC, Moresi NG, Anderson LM, Brewer R, Renz TR, Taylor MB, Dunham MJ. Experimental evolution of S. cerevisiae for caffeine tolerance alters multidrug resistance and TOR signaling pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.28.591555. [PMID: 38746122 PMCID: PMC11092465 DOI: 10.1101/2024.04.28.591555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Caffeine is a natural compound that inhibits the major cellular signaling regulator TOR, leading to widespread effects including growth inhibition. S. cerevisiae yeast can adapt to tolerate high concentrations of caffeine in coffee and cacao fermentations and in experimental systems. While many factors affecting caffeine tolerance and TOR signaling have been identified, further characterization of their interactions and regulation remain to be studied. We used experimental evolution of S. cerevisiae to study the genetic contributions to caffeine tolerance in yeast, through a collaboration between high school students evolving yeast populations coupled with further research exploration in university labs. We identified multiple evolved yeast populations with mutations in PDR1 and PDR5, which contribute to multidrug resistance, and showed that gain-of-function mutations in multidrug resistance family transcription factors PDR1, PDR3, and YRR1 differentially contribute to caffeine tolerance. We also identified loss-of-function mutations in TOR effectors SIT4, SKY1, and TIP41, and show that these mutations contribute to caffeine tolerance. These findings support the importance of both the multidrug resistance family and TOR signaling in caffeine tolerance, and can inform future exploration of networks affected by caffeine and other TOR inhibitors in model systems and industrial applications.
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Affiliation(s)
- Renee C Geck
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Naomi G Moresi
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Leah M Anderson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | | | | | - M Bryce Taylor
- Program in Biology, Loras College, Dubuque, IA 52001, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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3
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Nogami R, Nagata M, Imada R, Kai K, Kawaguchi T, Tani S. Cycloheximide in the nanomolar range inhibits seed germination of Orobanche minor. JOURNAL OF PESTICIDE SCIENCE 2024; 49:22-30. [PMID: 38450089 PMCID: PMC10912901 DOI: 10.1584/jpestics.d23-038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/29/2023] [Indexed: 03/08/2024]
Abstract
From the 992 samples of culture extracts of microorganisms isolated from soil in Japan, we found that the extract of Streptomyces sp. no. 226 inhibited Orobanche minor seed germination without significantly affecting the seed germination of Trifolium pratense and the growth of Aspergillus oryzae and Escherichia coli. Using ESI-MS, 1H-NMR, and 13C-NMR, we identified the active compound as cycloheximide. Cycloheximide had half-maximum inhibitory concentrations of 2.6 ng/mL for the inhibition of seed germination of O. minor and 2.5 µg/mL for that of the conidial germination of A. oryzae. Since cycloheximide is known to inhibit translation by interacting with ribosomal protein L28 (RPL28) in yeast, we investigated whether RPL protein of O. minor plays a critical role in the inhibition of O. minor seed germination. Our data suggested that O. minor RPL27A was not sensitive to cycloheximide by comparing it to the strain expressing S. cerevisiae RPL28. These findings suggest the presence of an unidentified mechanism by which cycloheximide hinders O. minor seed germination.
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Affiliation(s)
- Ryosuke Nogami
- Graduate School of Agriculture, Osaka Metropolitan University
| | - Mari Nagata
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Risa Imada
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Kenji Kai
- Graduate School of Agriculture, Osaka Metropolitan University
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Takashi Kawaguchi
- Graduate School of Agriculture, Osaka Metropolitan University
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Shuji Tani
- Graduate School of Agriculture, Osaka Metropolitan University
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
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4
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Buechel ER, Pinkett HW. Activity of the pleiotropic drug resistance transcription factors Pdr1p and Pdr3p is modulated by binding site flanking sequences. FEBS Lett 2024; 598:169-186. [PMID: 37873734 PMCID: PMC10843404 DOI: 10.1002/1873-3468.14762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/25/2023]
Abstract
The transcription factors Pdr1p and Pdr3p regulate pleiotropic drug resistance (PDR) in Saccharomyces cerevisiae via the PDR responsive elements (PDREs) to modulate gene expression. However, the exact mechanisms underlying the differences in their regulons remain unclear. Employing genomic occupancy profiling (CUT&RUN), binding assays, and transcription studies, we characterized the differences in sequence specificity between transcription factors. Findings reveal distinct preferences for core PDRE sequences and the flanking sequences for both proteins. While flanking sequences moderately alter DNA binding affinity, they significantly impact Pdr1/3p transcriptional activity. Notably, both proteins demonstrated the ability to bind half sites, showing potential enhancement of transcription from adjacent PDREs. This insight sheds light on ways Pdr1/3p can differentially regulate PDR.
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Affiliation(s)
- Evan R. Buechel
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Heather W. Pinkett
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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5
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Buechel ER, Pinkett HW. Unraveling the Half and Full Site Sequence Specificity of the Saccharomyces cerevisiae Pdr1p and Pdr3p Transcription Factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.553033. [PMID: 37609128 PMCID: PMC10441396 DOI: 10.1101/2023.08.11.553033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The transcription factors Pdr1p and Pdr3p regulate pleotropic drug resistance (PDR) in Saccharomyces cerevisiae , via the PDR responsive elements (PDREs) to modulate gene expression. However, the exact mechanisms underlying the differences in their regulons remain unclear. Employing genomic occupancy profiling (CUT&RUN), binding assays, and transcription studies, we characterized the differences in sequence specificity between transcription factors. Findings reveal distinct preferences for core PDRE sequences and the flanking sequences for both proteins. While flanking sequences moderately alter DNA binding affinity, they significantly impact Pdr1/3p transcriptional activity. Notably, both proteins demonstrated the ability to bind half sites, showing potential enhancement of transcription from adjacent PDREs. This insight sheds light on ways Pdr1/3 can differentially regulate PDR.
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6
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Banerjee A, Rahman H, Prasad R, Golin J. How Fungal Multidrug Transporters Mediate Hyperresistance Through DNA Amplification and Mutation. Mol Microbiol 2022; 118:3-15. [PMID: 35611562 DOI: 10.1111/mmi.14947] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/18/2022] [Accepted: 05/21/2022] [Indexed: 11/30/2022]
Abstract
A significant portion of clinically observed antifungal resistance is mediated by ATP-binding cassette (ABC) and major facilitator superfamily (MFS) transport pumps that reside in the plasma membrane. We review the mechanisms responsible for this phenomenon. Hyperresistance is often brought about by several kinds of DNA amplification or by gain-of-function mutations in a variety of transcription factors. Both of these result in overexpression of ABC and MFS transporters. Recently, however, several additional modes of resistance have been observed. These include mutations in non-conserved nucleotides leading to altered mRNA stability and a mutation in yeast transporter Pdr5, which improves cooperativity between drug-binding sites.
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Affiliation(s)
- Atanu Banerjee
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, India
| | - Hadiar Rahman
- Laboratory of Cell Biology, Center for Cancer Research, NCI, NIH, Bethesda, MD
| | - Rajendra Prasad
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, India.,Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurugram, India
| | - John Golin
- Department of Biology, Stern College, Yeshiva University, New York, NY
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7
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James JE, Lamping E, Santhanam J, Cannon RD. PDR Transporter ABC1 Is Involved in the Innate Azole Resistance of the Human Fungal Pathogen Fusarium keratoplasticum. Front Microbiol 2021; 12:673206. [PMID: 34149660 PMCID: PMC8211738 DOI: 10.3389/fmicb.2021.673206] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/22/2021] [Indexed: 12/30/2022] Open
Abstract
Fusarium keratoplasticum is arguably the most common Fusarium solani species complex (FSSC) species associated with human infections. Invasive fusariosis is a life-threatening fungal infection that is difficult to treat with conventional azole antifungals. Azole drug resistance is often caused by the increased expression of pleiotropic drug resistance (PDR) ATP-binding cassette (ABC) transporters of the ABCG sub-family. Most investigations of Fusarium ABC transporters associated with azole antifungal drug resistance are limited to plant pathogens. Through the manual curation of the entire ABCG protein family of four FSSC species including the fully annotated genome of the plant pathogen Nectria haematococca we identified PDR transporters ABC1 and ABC2 as the efflux pump candidates most likely to be associated with the innate azole resistance phenotype of Fusarium keratoplasticum. An initial investigation of the transcriptional response of logarithmic phase F. keratoplasticum cells to 16 mg/L voriconazole confirmed strong upregulation (372-fold) of ABC1 while ABC2 mRNA levels were unaffected by voriconazole exposure over a 4 h time-period. Overexpression of F. keratoplasticum ABC1 and ABC2 in the genetically modified Saccharomyces cerevisiae host ADΔΔ caused up to ∼1,024-fold increased resistance to a number of xenobiotics, including azole antifungals. Although ABC1 and ABC2 were only moderately (20% and 10%, respectively) expressed compared to the Candida albicans multidrug efflux pump CDR1, overexpression of F. keratoplasticum ABC1 caused even higher resistance levels to certain xenobiotics (e.g., rhodamine 6G and nigericin) than CDR1. Our investigations suggest an important role for ABC1 orthologues in the innate azole resistance phenotype of FSSC species.
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Affiliation(s)
- Jasper Elvin James
- Biomedical Science Programme, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.,Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
| | - Erwin Lamping
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
| | - Jacinta Santhanam
- Biomedical Science Programme, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Richard David Cannon
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
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8
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Ueda Y, Tahara YO, Miyata M, Ogita A, Yamaguchi Y, Tanaka T, Fujita KI. Involvement of a Multidrug Efflux Pump and Alterations in Cell Surface Structure in the Synergistic Antifungal Activity of Nagilactone E and Anethole against Budding Yeast Saccharomyces cerevisiae. Antibiotics (Basel) 2021; 10:antibiotics10050537. [PMID: 34066540 PMCID: PMC8148520 DOI: 10.3390/antibiotics10050537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/02/2021] [Accepted: 05/03/2021] [Indexed: 11/16/2022] Open
Abstract
Nagilactone E, an antifungal agent derived from the root bark of Podocarpus nagi, inhibits 1,3-β glucan synthesis; however, its inhibitory activity is weak. Anethole, the principal component of anise oil, enhances the antifungal activity of nagilactone E. We aimed to determine the combinatorial effect and underlying mechanisms of action of nagilactone E and anethole against the budding yeast Saccharomyces cerevisiae. Analyses using gene-deficient strains showed that the multidrug efflux pump PDR5 is associated with nagilactone E resistance; its transcription was gradually restricted in cells treated with the drug combination for a prolonged duration but not in nagilactone-E-treated cells. Green-fluorescent-protein-tagged Pdr5p was intensively expressed and localized on the plasma membrane of nagilactone-E-treated cells but not in drug-combination-treated cells. Quick-freeze deep-etch electron microscopy revealed the smoothening of intertwined fiber structures on the cell surface of drug-combination-treated cells and spheroplasts, indicating a decline in cell wall components and loss of cell wall strength. Anethole enhanced the antifungal activity of nagilactone E by enabling its retention within cells, thereby accelerating cell wall damage. The combination of nagilactone E and anethole can be employed in clinical settings as an antifungal, as well as a food preservative to restrict food spoilage.
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Affiliation(s)
- Yuki Ueda
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (Y.U.); (Y.O.T.); (M.M.); (A.O.); (Y.Y.); (T.T.)
| | - Yuhei O. Tahara
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (Y.U.); (Y.O.T.); (M.M.); (A.O.); (Y.Y.); (T.T.)
| | - Makoto Miyata
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (Y.U.); (Y.O.T.); (M.M.); (A.O.); (Y.Y.); (T.T.)
| | - Akira Ogita
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (Y.U.); (Y.O.T.); (M.M.); (A.O.); (Y.Y.); (T.T.)
- Research Center for Urban Health and Sports, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Yoshihiro Yamaguchi
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (Y.U.); (Y.O.T.); (M.M.); (A.O.); (Y.Y.); (T.T.)
| | - Toshio Tanaka
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (Y.U.); (Y.O.T.); (M.M.); (A.O.); (Y.Y.); (T.T.)
| | - Ken-ichi Fujita
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (Y.U.); (Y.O.T.); (M.M.); (A.O.); (Y.Y.); (T.T.)
- Correspondence: ; Tel.: +81-6-6605-2580
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9
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Swagatika S, Tomar RS. ABC transporter Pdr5 is required for cantharidin resistance in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2021; 553:141-147. [PMID: 33770579 DOI: 10.1016/j.bbrc.2021.03.074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 03/15/2021] [Indexed: 01/22/2023]
Abstract
Cantharidin is a potent anti-cancer drug and is known to exert its cytotoxic effects in several cancer cell lines. Although we have ample knowledge about its mode of action, we still know a little about cantharidin associated drug resistance mechanisms which dictates the efficacy and cytotoxic potential of this drug. In this direction, in the present study we employed Sacharomyces cerevisiae as a model organism and screened mutants of pleiotropic drug resistance network of genes for their susceptibility to cantharidin. We show that growth of pdr1Δ and pdr1Δpdr3Δ was severely reduced in presence of cantharidin whereas that of pdr3Δ remain unaffected when compared to wildtype. Loss of one of the PDR1 target genes PDR5, encoding an ABC membrane efflux pump, rendered the cells hypersensitive whereas overexpression of it conferred resistance. Additionally, cantharidin induced the upregulation of both PDR1 and PDR5 genes. Interestingly, pdr1Δpdr5Δ double deletion mutants were hypersensitive to cantharidin showing a synergistic effect in its cellular detoxification. Furthermore, transcriptional activation of PDR5 post cantharidin treatment was majorly dependent on the presence of Pdr1 and less significantly of Pdr3 transcription factors. Altogether our findings suggest that Pdr1 acts to increase cantharidin resistance by elevating the level of Pdr5 which serves as a major detoxification safeguard under CAN stress.
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Affiliation(s)
- Swati Swagatika
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, 462066, MP, India
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, 462066, MP, India.
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10
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Balarezo-Cisneros LN, Parker S, Fraczek MG, Timouma S, Wang P, O’Keefe RT, Millar CB, Delneri D. Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and in trans effects on the protein regulatory network. PLoS Genet 2021; 17:e1008761. [PMID: 33493158 PMCID: PMC7886133 DOI: 10.1371/journal.pgen.1008761] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 02/16/2021] [Accepted: 12/19/2020] [Indexed: 12/19/2022] Open
Abstract
Non-coding RNAs (ncRNAs), including the more recently identified Stable Unannotated Transcripts (SUTs) and Cryptic Unstable Transcripts (CUTs), are increasingly being shown to play pivotal roles in the transcriptional and post-transcriptional regulation of genes in eukaryotes. Here, we carried out a large-scale screening of ncRNAs in Saccharomyces cerevisiae, and provide evidence for SUT and CUT function. Phenotypic data on 372 ncRNA deletion strains in 23 different growth conditions were collected, identifying ncRNAs responsible for significant cellular fitness changes. Transcriptome profiles were assembled for 18 haploid ncRNA deletion mutants and 2 essential ncRNA heterozygous deletants. Guided by the resulting RNA-seq data we analysed the genome-wide dysregulation of protein coding genes and non-coding transcripts. Novel functional ncRNAs, SUT125, SUT126, SUT035 and SUT532 that act in trans by modulating transcription factors were identified. Furthermore, we described the impact of SUTs and CUTs in modulating coding gene expression in response to different environmental conditions, regulating important biological process such as respiration (SUT125, SUT126, SUT035, SUT432), steroid biosynthesis (CUT494, SUT053, SUT468) or rRNA processing (SUT075 and snR30). Overall, these data capture and integrate the regulatory and phenotypic network of ncRNAs and protein-coding genes, providing genome-wide evidence of the impact of ncRNAs on cellular homeostasis. A quarter of the yeast genome comprises non-coding RNA molecules (ncRNAs), which do not translate into proteins but are involved in the regulation of gene expression. ncRNAs can affect nearby genes by physically interfering with their transcription (cis mode of action), or they interact with DNA, proteins or other RNAs to regulate the expression of distant genes (trans mode of action). Examples of cis-acting ncRNAs have been broadly described, however, genome-wide studies to identify functional trans-acting ncRNAs involved in global gene regulation are still lacking. Here, we used a ncRNA yeast deletion collection to score ncRNA impact on cellular function in different environmental conditions. A group of 20 ncRNA deletion mutants with broad fitness diversity were selected to investigate the ncRNA effect on the protein and ncRNA expression network. We showed a high correlation between altered phenotypes and global transcriptional changes, in an environmental dependent manner. We confirmed the trans acting regulation of ncRNAs in the genome and their role in altering the expression of transcription factors. These findings support the notion of the involvement of ncRNAs in fine tuning cellular expression via regulation of transcription factors, as an advantageous RNA-mediated mechanism that can be fast and cost-effective for the cells.
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Affiliation(s)
- Laura Natalia Balarezo-Cisneros
- Manchester Institute of Biotechnology, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Steven Parker
- Manchester Institute of Biotechnology, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Marcin G. Fraczek
- Manchester Institute of Biotechnology, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Soukaina Timouma
- Manchester Institute of Biotechnology, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Ping Wang
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Raymond T. O’Keefe
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Catherine B. Millar
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- * E-mail: (CM); (DD)
| | - Daniela Delneri
- Manchester Institute of Biotechnology, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- * E-mail: (CM); (DD)
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11
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Buechel ER, Pinkett HW. Transcription factors and ABC transporters: from pleiotropic drug resistance to cellular signaling in yeast. FEBS Lett 2020; 594:3943-3964. [PMID: 33089887 DOI: 10.1002/1873-3468.13964] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/07/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022]
Abstract
Budding yeast Saccharomyces cerevisiae survives in microenvironments utilizing networks of regulators and ATP-binding cassette (ABC) transporters to circumvent toxins and a variety of drugs. Our understanding of transcriptional regulation of ABC transporters in yeast is mainly derived from the study of multidrug resistance protein networks. Over the past two decades, this research has not only expanded the role of transcriptional regulators in pleiotropic drug resistance (PDR) but evolved to include the role that regulators play in cellular signaling and environmental adaptation. Inspection of the gene networks of the transcriptional regulators and characterization of the ABC transporters has clarified that they also contribute to environmental adaptation by controlling plasma membrane composition, toxic-metal sequestration, and oxidative stress adaptation. Additionally, ABC transporters and their regulators appear to be involved in cellular signaling for adaptation of S. cerevisiae populations to nutrient availability. In this review, we summarize the current understanding of the S. cerevisiae transcriptional regulatory networks and highlight recent work in other notable fungal organisms, underlining the expansion of the study of these gene networks across the kingdom fungi.
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Affiliation(s)
- Evan R Buechel
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Heather W Pinkett
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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12
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Evolutionary engineering and molecular characterization of a caffeine-resistant Saccharomyces cerevisiae strain. World J Microbiol Biotechnol 2019; 35:183. [PMID: 31728740 DOI: 10.1007/s11274-019-2762-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 11/05/2019] [Indexed: 12/30/2022]
Abstract
Caffeine is a naturally occurring alkaloid, where its major consumption occurs with beverages such as coffee, soft drinks and tea. Despite a variety of reports on the effects of caffeine on diverse organisms including yeast, the complex molecular basis of caffeine resistance and response has yet to be understood. In this study, a caffeine-hyperresistant and genetically stable Saccharomyces cerevisiae mutant was obtained for the first time by evolutionary engineering, using batch selection in the presence of gradually increased caffeine stress levels and without any mutagenesis of the initial population prior to selection. The selected mutant could resist up to 50 mM caffeine, a level, to our knowledge, that has not been reported for S. cerevisiae so far. The mutant was also resistant to the cell wall-damaging agent lyticase, and it showed cross-resistance against various compounds such as rapamycin, antimycin, coniferyl aldehyde and cycloheximide. Comparative transcriptomic analysis results revealed that the genes involved in the energy conservation and production pathways, and pleiotropic drug resistance were overexpressed. Whole genome re-sequencing identified single nucleotide polymorphisms in only three genes of the caffeine-hyperresistant mutant; PDR1, PDR5 and RIM8, which may play a potential role in caffeine-hyperresistance.
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13
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Pinneh EC, Mina JG, Stark MJR, Lindell SD, Luemmen P, Knight MR, Steel PG, Denny PW. The identification of small molecule inhibitors of the plant inositol phosphorylceramide synthase which demonstrate herbicidal activity. Sci Rep 2019; 9:8083. [PMID: 31147620 PMCID: PMC6542793 DOI: 10.1038/s41598-019-44544-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 05/17/2019] [Indexed: 12/16/2022] Open
Abstract
Resistance to 157 different herbicides and 88% of known sites of action has been observed, with many weeds resistant to two or more modes. Coupled with tighter environmental regulation, this demonstrates the need to identify new modes of action and novel herbicides. The plant sphingolipid biosynthetic enzyme, inositol phosphorylceramide synthase (IPCS), has been identified as a novel, putative herbicide target. The non-mammalian nature of this enzyme offers the potential of discovering plant specific inhibitory compounds with minimal impact on animals and humans, perhaps leading to the development of new non-toxic herbicides. The best characterised and most highly expressed isoform of the enzyme in the model-dicot Arabidopsis, AtIPCS2, was formatted into a yeast-based assay which was then utilized to screen a proprietary library of over 11,000 compounds provided by Bayer AG. Hits from this screen were validated in a secondary in vitro enzyme assay. These studies led to the identification of a potent inhibitor that showed selectivity for AtIPCS2 over the yeast orthologue, and activity against Arabidopsis seedlings. This work highlighted the use of a yeast-based screening assay to discover herbicidal compounds and the status of the plant IPCS as a novel herbicidal target.
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Affiliation(s)
- Elizabeth C Pinneh
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
- Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - John G Mina
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Michael J R Stark
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Stephen D Lindell
- Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Peter Luemmen
- Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Marc R Knight
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Patrick G Steel
- Department of Chemistry, Durham University, Durham, DH1 3LE, UK.
| | - Paul W Denny
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK.
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14
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J B, Das A. An edible fungi Pleurotus ostreatus inhibits adipogenesis via suppressing expression of PPAR γ and C/EBP α in 3T3-L1 cells: In vitro validation of gene knock out of RNAs in PPAR γ using CRISPR spcas9. Biomed Pharmacother 2019; 116:109030. [PMID: 31152927 DOI: 10.1016/j.biopha.2019.109030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/21/2019] [Accepted: 05/21/2019] [Indexed: 10/26/2022] Open
Abstract
OBJECTIVE Obesity is now well recognized as a disorder, one that is essentially preventable through changes in lifestyle. Obesity is also a main concern associated with expanded morbidity and mortality from many noncommunicable illnesses (NCDs). The study aimed to determine the antiobesity effect of Pleurotus ostreatus (PO) and its bioactive anthraquinone (AQ). The overall promoter genes CEBPα (CCAAT enhancer binding protein α) and PPARγ (Peroxisome proliferator activated receptor γ) in controlling the homeostasis of glucose was analysed using 3T3-L1 cell line. Finally, an insilico study was carried out using CRISPR software to identify the RNA's involved in adipogenesis especially of the control gene PPARγ. MATERIALS AND METHODS Preliminary screening of the edible fungi and their bio actives led to the marvellous discovery of side effect free agonists for treating obesity (adipogenesis). An edible fungi Pleurotus ostreatus (PO) were analysed in a screening platform with different series of tests for adipocyte differentiation, triglyceride analysis, lipolysis determination, glucose uptake assay, cytotoxicity assay and lipase activity followed by specific gene expression analysis. The gene knockout mechanism was also elucidated by CRISPR spcas 9 tool. RESULTS The antiadipogenic (antiobesity) activity of DMSO extract of PO were found to stimulate the insulin dependent uptake of glucose. The extract also decreased the levels of triglycerides and glycerol accumulation in differentiated adipocyte cells. The binding FABP4 (Fatty acid binding protein) and transport protein FATP1 (Fatty acid transport protein) along with the fat breaking LPL (lipoprotein lipase) was found to be inhibited after the PO treatment at varying concentration (0-300 μg/ml). CRISPR spcas9 genome editing software was used as an insilico approach in validating the efficiency of mouse embryonic and human adipogenic cell line (3T3-L1). These tool analysed and found 4 RNAs gene knock out possibilities in PPARγ and their efficiency for further treating obesity. CONCLUSION These novel finding contribute to the confirmation that edible fungi PO and it's bioactive AQ is an adequate supplement for constraining the lipid and triglycerides in differentiated mature adipocytes by reversing the fat deposition. Thereby, forbidding the enzymes linked with fat absorption. Besides, the CRISPR tool identified gene knock out possibilities of control gene PPARγ, will pave a way in further research for treating obesity.
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Affiliation(s)
- Bindhu J
- Molecular Diagnostics and Bacterial Pathogenomics Research Laboratory, Department of Biotechnology, Bannari Amman Institute of Technology, Sathyamangalam, 638401, India
| | - Arunava Das
- Molecular Diagnostics and Bacterial Pathogenomics Research Laboratory, Department of Biotechnology, Bannari Amman Institute of Technology, Sathyamangalam, 638401, India.
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15
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Amini S, Jacobsen A, Ivanova O, Lijnzaad P, Heringa J, Holstege FCP, Feenstra KA, Kemmeren P. The ability of transcription factors to differentially regulate gene expression is a crucial component of the mechanism underlying inversion, a frequently observed genetic interaction pattern. PLoS Comput Biol 2019; 15:e1007061. [PMID: 31083661 PMCID: PMC6532943 DOI: 10.1371/journal.pcbi.1007061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 05/23/2019] [Accepted: 04/30/2019] [Indexed: 12/21/2022] Open
Abstract
Genetic interactions, a phenomenon whereby combinations of mutations lead to unexpected effects, reflect how cellular processes are wired and play an important role in complex genetic diseases. Understanding the molecular basis of genetic interactions is crucial for deciphering pathway organization as well as understanding the relationship between genetic variation and disease. Several hypothetical molecular mechanisms have been linked to different genetic interaction types. However, differences in genetic interaction patterns and their underlying mechanisms have not yet been compared systematically between different functional gene classes. Here, differences in the occurrence and types of genetic interactions are compared for two classes, gene-specific transcription factors (GSTFs) and signaling genes (kinases and phosphatases). Genome-wide gene expression data for 63 single and double deletion mutants in baker's yeast reveals that the two most common genetic interaction patterns are buffering and inversion. Buffering is typically associated with redundancy and is well understood. In inversion, genes show opposite behavior in the double mutant compared to the corresponding single mutants. The underlying mechanism is poorly understood. Although both classes show buffering and inversion patterns, the prevalence of inversion is much stronger in GSTFs. To decipher potential mechanisms, a Petri Net modeling approach was employed, where genes are represented as nodes and relationships between genes as edges. This allowed over 9 million possible three and four node models to be exhaustively enumerated. The models show that a quantitative difference in interaction strength is a strict requirement for obtaining inversion. In addition, this difference is frequently accompanied with a second gene that shows buffering. Taken together, these results provide a mechanistic explanation for inversion. Furthermore, the ability of transcription factors to differentially regulate expression of their targets provides a likely explanation why inversion is more prevalent for GSTFs compared to kinases and phosphatases.
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Affiliation(s)
- Saman Amini
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Annika Jacobsen
- Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Olga Ivanova
- Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Philip Lijnzaad
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jaap Heringa
- Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - K. Anton Feenstra
- Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands
- * E-mail:
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16
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Dhar R, Missarova AM, Lehner B, Carey LB. Single cell functional genomics reveals the importance of mitochondria in cell-to-cell phenotypic variation. eLife 2019; 8:38904. [PMID: 30638445 PMCID: PMC6366901 DOI: 10.7554/elife.38904] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 01/13/2019] [Indexed: 12/12/2022] Open
Abstract
Mutations frequently have outcomes that differ across individuals, even when these individuals are genetically identical and share a common environment. Moreover, individual microbial and mammalian cells can vary substantially in their proliferation rates, stress tolerance, and drug resistance, with important implications for the treatment of infections and cancer. To investigate the causes of cell-to-cell variation in proliferation, we used a high-throughput automated microscopy assay to quantify the impact of deleting >1500 genes in yeast. Mutations affecting mitochondria were particularly variable in their outcome. In both mutant and wild-type cells mitochondrial membrane potential - but not amount - varied substantially across individual cells and predicted cell-to-cell variation in proliferation, mutation outcome, stress tolerance, and resistance to a clinically used anti-fungal drug. These results suggest an important role for cell-to-cell variation in the state of an organelle in single cell phenotypic variation.
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Affiliation(s)
- Riddhiman Dhar
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain.,Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
| | - Alsu M Missarova
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Lucas B Carey
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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17
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Sayyed K, Le Vée M, Chamieh H, Fardel O, Abdel-Razzak Z. Cigarette smoke condensate alters Saccharomyces cerevisiae efflux transporter mRNA and activity and increases caffeine toxicity. Toxicology 2018; 409:129-136. [DOI: 10.1016/j.tox.2018.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/07/2018] [Accepted: 08/12/2018] [Indexed: 01/06/2023]
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18
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Yamawaki C, Oyama M, Yamaguchi Y, Ogita A, Tanaka T, Fujita KI. Curcumin potentiates the fungicidal effect of dodecanol by inhibiting drug efflux in wild-type budding yeast. Lett Appl Microbiol 2018; 68:17-23. [PMID: 30276838 DOI: 10.1111/lam.13083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 09/18/2018] [Accepted: 09/27/2018] [Indexed: 12/01/2022]
Abstract
Drug resistance commonly occurs when treating immunocompromised patients who have fungal infections. Curcumin, is a compound isolated from Curcuma longa, has been reported to inhibit drug efflux in several human cell lines and nonpathogenic budding yeast Saccharomyces cerevisiae cells that overexpresses the ATP-binding cassette (ABC) transporters S. cerevisiae Pdr5p and pathogenic Candida albicans Cdr1p and Cdr2p. The aim of this study was to examine the effects of curcumin on multidrug resistance in a wild-type strain of the budding yeast with an intrinsic expression system of multidrug efflux-related genes. The antifungal activity of dodecanol alone was temporary against S. cerevisiae; however, restoration of cell viability was completely inhibited when the cells were co-treated with dodecanol and curcumin. Furthermore, restriction of rhodamine 6G (R6G) efflux from the cells and intracellular accumulation of R6G were observed with curcumin treatment. Reverse transcription-polymerase chain reaction analysis revealed that curcumin reduced the dodecanol-induced overexpression of the ABC transporter-related genes PDR1, PDR3 and PDR5 to their control levels in untreated cells. Curcumin can directly restrict the glucose-induced drug efflux and inhibits the expression of the ABC transporter gene PDR5, and can thereby inhibit the efflux of dodecanol from S. cerevisiae cells. Curcumin is effective in potentiating the efficacy of antifungal drugs via its effects on ABC transporters. SIGNIFICANCE AND IMPACT OF THE STUDY: Drug resistance is common in immunocompromised patients with fungal infections. Curcumin, isolated from Curcuma longa, inhibits drug efflux in nonpathogenic budding yeast Saccharomyces cerevisiae cells overexpressing ABC transporters S. cerevisiae Pdr5p and pathogenic Candida albicans Cdr1p and Cdr2p. We examined the effects of curcumin on multidrug resistance in a wild-type strain of the budding yeast with an intrinsic expression system of multidrug efflux-related genes. Curcumin directly inhibited drug efflux and also suppressed the PDR5 expression, thereby enhancing the antifungal effects. Thus, curcumin potentially promotes the efficacy of antifungals via its effects on ABC transporters in wild-type fungal strains.
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Affiliation(s)
- C Yamawaki
- Graduate School of Science, Osaka City University, Osaka, Japan
| | - M Oyama
- Graduate School of Science, Osaka City University, Osaka, Japan
| | - Y Yamaguchi
- Graduate School of Science, Osaka City University, Osaka, Japan.,Advanced Research Institute for Natural Science and Technology, Osaka City University, Osaka, Japan
| | - A Ogita
- Graduate School of Science, Osaka City University, Osaka, Japan.,Research Center for Urban Health and Sports, Osaka City University, Osaka, Japan
| | - T Tanaka
- Graduate School of Science, Osaka City University, Osaka, Japan
| | - K-I Fujita
- Graduate School of Science, Osaka City University, Osaka, Japan
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19
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Zhu X, Cai J, Zhou F, Wu Z, Li D, Li Y, Xie Z, Zhou Y, Liang Y. Genome-wide screening of budding yeast with honokiol to associate mitochondrial function with lipid metabolism. Traffic 2018; 19:867-878. [PMID: 30120820 DOI: 10.1111/tra.12611] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 08/11/2018] [Accepted: 08/13/2018] [Indexed: 12/24/2022]
Abstract
Honokiol (HNK), an important medicinal component of Magnolia officinalis, is reported to possess pharmacological activities against a variety of diseases. However, the molecular mechanisms of HNK medicinal functions are not fully clear. To systematically study the mechanisms of HNK action, we screened a yeast mutant library based on the conserved nature of its genes among eukaryotes. We identified genes associated with increased resistance or sensitivity to HNK after mutation. After functional classification of these genes, we found that most HNK-resistant strains in the largest functional category were petites with mutations in mitochondrial genes, indicating that mitochondria were related to HNK resistance. Additional analysis showed that resistance of petite mutants to HNK was associated with upregulation of the ATP-binding cassette transporter Pdr5, which pumps out HNK. We also found that several HNK-sensitive mitochondria mutants were not petites, and had larger lipid droplets (LDs). Furthermore, HNK treatment on wild-type yeast cells seemed to disrupt mitochondrial morphology, induced triacylglycerol synthesis, and generated supersized LDs surrounded by mitochondria and endoplasmic reticulum (ER). These changes are also applied to atp7Δ mutant if no carbon resource was available. These results suggested that HNK treatment partly impaired normal mitochondrial function to form larger LDs by altering lipid metabolism.
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Affiliation(s)
- Xiaolong Zhu
- College of Life Sciences, Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, China
| | - Juan Cai
- College of Life Sciences, Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Fan Zhou
- College of Life Sciences, Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Zulin Wu
- College of Life Sciences, Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Dan Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Technology, Shanghai Jiao Tong University, Shanghai, China
| | - Youbin Li
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Zhiping Xie
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Technology, Shanghai Jiao Tong University, Shanghai, China
| | - Yiting Zhou
- Department of Biochemistry and Molecular Biology, Dr. Li Dak Sam & Yap Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yongheng Liang
- College of Life Sciences, Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
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20
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Khakhina S, Simonicova L, Moye-Rowley WS. Positive autoregulation and repression of transactivation are key regulatory features of the Candida glabrata Pdr1 transcription factor. Mol Microbiol 2018; 107:747-764. [PMID: 29363861 DOI: 10.1111/mmi.13913] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 01/15/2018] [Accepted: 01/19/2018] [Indexed: 12/23/2022]
Abstract
Resistance to azole drugs, the major clinical antifungal compounds, is most commonly due to gain-of-function (GOF) substitution mutations in a gene called PDR1 in the fungal pathogen Candida glabrata. PDR1 encodes a zinc cluster-containing transcription factor. GOF forms of Pdr1 drive high level expression of downstream target gene expression with accompanying azole resistance. PDR1 has two homologous genes in Saccharomyces cerevisiae, called ScPDR1 and ScPDR3. This study provides evidence that the PDR1 gene in C. glabrata represents a blend of the properties found in the two S. cerevisiae genes. We demonstrated that GOF Pdr1 derivatives are overproduced at the protein level and less stable than the wild-type protein. Overproduction of wild-type Pdr1 increased target gene expression but to a lesser extent than GOF derivatives. Site-directed mutagenesis of Pdr1 binding sites in the PDR1 promoter provided clear demonstration that autoregulation of PDR1 is required for its normal function. An internal deletion mutant of Pdr1 lacking its central regulatory domain behaved as a hyperactive transcription factor that was lethal unless conditionally expressed. A full understanding of the regulation of Pdr1 will provide a new avenue of interfering with azole resistance in C. glabrata.
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Affiliation(s)
- Svetlana Khakhina
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Lucia Simonicova
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - W Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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21
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Zhu X, Zou S, Li Y, Liang Y. Transcriptomic analysis of Saccharomyces cerevisiae upon honokiol treatment. Res Microbiol 2017; 168:626-635. [DOI: 10.1016/j.resmic.2017.04.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/05/2017] [Accepted: 04/20/2017] [Indexed: 01/15/2023]
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22
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Tuning the Sensitivity of the PDR5 Promoter-Based Detection of Diclofenac in Yeast Biosensors. SENSORS 2017; 17:s17071506. [PMID: 28672842 PMCID: PMC5539612 DOI: 10.3390/s17071506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 02/05/2023]
Abstract
The commonly used drug diclofenac is an important environmental anthropogenic pollutant. Currently, detection of diclofenac is mainly based on chemical and physical methods. Here we describe a yeast biosensor that drives the diclofenac-dependent expression of a recombinant fluorescent protein from the authentic promoter of the PDR5 gene. This key component of the pleiotropic drug response encodes a multidrug transporter that is involved in cellular detoxification. We analyse the effects on diclofenac sensitivity of artificial PDR5 promoter derivatives in wild-type and various yeast mutant strains. This approach enabled us to generate sensor strains with elevated drug sensitivity.
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23
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Fujita KI, Ishikura T, Jono Y, Yamaguchi Y, Ogita A, Kubo I, Tanaka T. Anethole potentiates dodecanol's fungicidal activity by reducing PDR5 expression in budding yeast. Biochim Biophys Acta Gen Subj 2016; 1861:477-484. [PMID: 27632201 DOI: 10.1016/j.bbagen.2016.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 08/31/2016] [Accepted: 09/09/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND trans-Anethole (anethole), a major component of anise oil, has a broad antimicrobial spectrum and a weaker antimicrobial potency than other available antibiotics. When combined with polygodial, nagilactone E, and n-dodecanol, anethole has been shown to exhibit synergistic antifungal activity against a budding yeast, Saccharomyces cerevisiae, and a human opportunistic pathogenic yeast, Candida albicans. However, the mechanism underlying this synergistic effect of anethole has not been characterized. METHODS We studied this mechanism using dodecanol-treated S. cerevisiae cells and focusing on genes related to multidrug efflux. RESULTS Although dodecanol transiently reduced the number of colony forming units, this recovered to levels similar to those of untreated cells with continued incubation beyond 24h. Reverse transcription polymerase chain reaction analysis revealed overexpression of an ATP-binding cassette (ABC) transporter gene, PDR5, in addition to a slight increase in PDR11, PDR12, and PDR15 transcriptions in dodecanol-treated cells. In the presence of anethole, these effects were attenuated and the fungicidal activity of dodecanol was extended. Dodecanol showed longer lasting fungicidal activity against a Δpdr5. In addition, Δpdr3 and Δlge1, lack transcription factors of PDR5 and PDR3, were partly and completely susceptible to dodecanol, respectively. Furthermore, combination of anethole with fluconazole was also found to exhibit synergy on C. albicans. CONCLUSIONS These results indicated that although anethole reduced the transcription of several transporters, PDR5 expression was particularly relevant to dodecanol efflux. GENERAL SIGNIFICANCE Anethole is expected to be a promising candidate drug for the inhibition of efflux by reducing the transcription of several ABC transporters.
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Affiliation(s)
- Ken-Ichi Fujita
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan.
| | - Takayuki Ishikura
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan
| | - Yui Jono
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan
| | - Yoshihiro Yamaguchi
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan; Advanced Research Institute for Natural Science and Technology, Osaka City University, Sumiyoshi-ku, Osaka, Japan
| | - Akira Ogita
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan; Research Center for Urban Health and Sports, Osaka City University, Sumiyoshi-ku,Osaka, Japan
| | - Isao Kubo
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Toshio Tanaka
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan
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24
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Coorey NVC, Matthews JH, Bellows DS, Atkinson PH. Pleiotropic drug-resistance attenuated genomic library improves elucidation of drug mechanisms. MOLECULAR BIOSYSTEMS 2016; 11:3129-36. [PMID: 26381459 DOI: 10.1039/c5mb00406c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Identifying Saccharomyces cerevisiae genome-wide gene deletion mutants that confer hypersensitivity to a xenobiotic aids the elucidation of its mechanism of action (MoA). However, the biological activities of many xenobiotics are masked by the pleiotropic drug resistance (PDR) network which effluxes xenobiotics that are PDR substrates. The PDR network in S. cerevisiae is almost entirely under the control of two functionally homologous transcription factors Pdr1p and Pdr3p. Herein we report the construction of a PDR-attenuated haploid non-essential DMA (PA-DMA), lacking PDR1 and PDR3, which permits the MoA elucidation of xenobiotics that are PDR substrates at low concentrations. The functionality of four key cellular processes commonly activated in response to xenobiotic stress: oxidative stress response, general stress response, unfolded stress response and calcium signalling pathways were assessed in the absence of PDR1 and PDR3 genes and were found to unaltered, therefore, these key chemogenomic signatures are not lost when using the PA-DMA. Efficacy of the PA-DMA was demonstrated using cycloheximide and latrunculin A at low nanomolar concentrations to attain chemical genetic profiles that were more specific to their known main mechanisms. We also found a two-fold increase in the number of compounds that are bioactive in the pdr1Δpdr3Δ compared to the wild type strain in screening the commercially available LOPAC(1280) library. The PA-DMA should be particularly applicable to mechanism determination of xenobiotics that have limited availability, such as natural products.
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Affiliation(s)
- Namal V C Coorey
- Centre for Biodiscovery, School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Kelburn, Wellington, 6011, New Zealand.
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25
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Nishida-Aoki N, Mori H, Kuroda K, Ueda M. Activation of the mitochondrial signaling pathway in response to organic solvent stress in yeast. Curr Genet 2014; 61:153-64. [DOI: 10.1007/s00294-014-0463-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 11/18/2014] [Accepted: 11/19/2014] [Indexed: 10/24/2022]
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26
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Knorre DA, Markova OV, Smirnova EA, Karavaeva IE, Sokolov SS, Severin FF. Dodecyltriphenylphosphonium inhibits multiple drug resistance in the yeast Saccharomyces cerevisiae. Biochem Biophys Res Commun 2014; 450:1481-4. [PMID: 25019981 DOI: 10.1016/j.bbrc.2014.07.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 07/03/2014] [Indexed: 11/16/2022]
Abstract
Multiple drug resistance pumps are potential drug targets. Here we asked whether the lipophilic cation dodecyltriphenylphosphonium (C12TPP) can interfere with their functioning. First, we found that suppression of ABC transporter gene PDR5 increases the toxicity of C12TPP in yeast. Second, C12TPP appeared to prevent the efflux of rhodamine 6G - a fluorescent substrate of Pdr5p. Moreover, C12TPP increased the cytostatic effects of some other known Pdr5p substrates. The chemical nature of C12TPP suggests that after Pdr5p-driven extrusion the molecules return to the plasma membrane and then into the cytosol, thus effectively competing with other substrates of the pump.
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Affiliation(s)
- Dmitry A Knorre
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Vorobyevy Gory 1, Moscow, Russia; Institute of Mitoengineering, Moscow State University, Vorobyevy Gory 1, Moscow, Russia.
| | - Olga V Markova
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Vorobyevy Gory 1, Moscow, Russia
| | - Ekaterina A Smirnova
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Vorobyevy Gory 1, Moscow, Russia
| | - Iuliia E Karavaeva
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Vorobyevy Gory 1, Moscow, Russia
| | - Svyatoslav S Sokolov
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Vorobyevy Gory 1, Moscow, Russia
| | - Fedor F Severin
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Vorobyevy Gory 1, Moscow, Russia; Institute of Mitoengineering, Moscow State University, Vorobyevy Gory 1, Moscow, Russia
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27
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Kobayashi Y, Mizunuma M, Osada H, Miyakawa T. Identification ofSaccharomyces cerevisiaeRibosomal Protein L3 as a Target of Curvularol, a G1-Specific Inhibitor of Mammalian Cells. Biosci Biotechnol Biochem 2014; 70:2451-9. [PMID: 17031058 DOI: 10.1271/bbb.60186] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The cellular target of curvularol, a G1-specific cell-cycle inhibitor of mammalian cells, was identified by a genetic approach in Saccharomyces cerevisiae. Since the wild-type W303 strain was highly resistant to curvularol, a drug hypersensitive parental strain was constructed in which various genes implicated in general drug resistance had been disrupted. Curvularol resistant mutants were isolated, and strains that exhibited a semi-dominant, curvularol-specific resistance phenotype were selected. All five strains examined were classified into a single genetic complementation group designated YCR1. A mutant gene responsible for curvularol resistance was identified as an allele of the RPL3 gene encoding the ribosomal protein L3. Sequence analysis of the mutant genes revealed that Trp255Cys and Trp255Leu substitutions of Rpl3p are responsible for curvularol resistance. Rpl3p mutants in which Trp255 residue was replaced by other amino acids were constructed. All of these replacements led to varying degrees of increased resistance to curvularol and growth defects.
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Affiliation(s)
- Yoshifumi Kobayashi
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter (AdSM), Hiroshima University, Japan
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28
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Li Y, Ehrhardt K, Zhang MQ, Bleris L. Assembly and validation of versatile transcription activator-like effector libraries. Sci Rep 2014; 4:4857. [PMID: 24798576 PMCID: PMC4010924 DOI: 10.1038/srep04857] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/08/2014] [Indexed: 12/11/2022] Open
Abstract
The ability to perturb individual genes in genome-wide experiments has been instrumental in unraveling cellular and disease properties. Here we introduce, describe the assembly, and demonstrate the use of comprehensive and versatile transcription activator-like effector (TALE) libraries. As a proof of principle, we built an 11-mer library that covers all possible combinations of the nucleotides that determine the TALE-DNA binding specificity. We demonstrate the versatility of the methodology by constructing a constraint library, customized to bind to a known p53 motif. To verify the functionality in assays, we applied the 11-mer library in yeast-one-hybrid screens to discover TALEs that activate human SCN9A and miR-34b respectively. Additionally, we performed a genome-wide screen using the complete 11-mer library to confirm known genes that confer cycloheximide resistance in yeast. Considering the highly modular nature of TALEs and the versatility and ease of constructing these libraries we envision broad implications for high-throughput genomic assays.
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Affiliation(s)
- Yi Li
- 1] Bioengineering Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA [2] Center for Systems Biology, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA
| | - Kristina Ehrhardt
- 1] Bioengineering Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA [2] Center for Systems Biology, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA
| | - Michael Q Zhang
- 1] Center for Systems Biology, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA [2] Molecular and Cell Biology Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA
| | - Leonidas Bleris
- 1] Bioengineering Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA [2] Center for Systems Biology, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA [3] Electrical Engineering Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson TX 75080 USA
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29
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Paul S, Moye-Rowley WS. Multidrug resistance in fungi: regulation of transporter-encoding gene expression. Front Physiol 2014; 5:143. [PMID: 24795641 PMCID: PMC3997011 DOI: 10.3389/fphys.2014.00143] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 03/25/2014] [Indexed: 11/24/2022] Open
Abstract
A critical risk to the continued success of antifungal chemotherapy is the acquisition of resistance; a risk exacerbated by the few classes of effective antifungal drugs. Predictably, as the use of these drugs increases in the clinic, more resistant organisms can be isolated from patients. A particularly problematic form of drug resistance that routinely emerges in the major fungal pathogens is known as multidrug resistance. Multidrug resistance refers to the simultaneous acquisition of tolerance to a range of drugs via a limited or even single genetic change. This review will focus on recent progress in understanding pathways of multidrug resistance in fungi including those of most medical relevance. Analyses of multidrug resistance in Saccharomyces cerevisiae have provided the most detailed outline of multidrug resistance in a eukaryotic microorganism. Multidrug resistant isolates of S. cerevisiae typically result from changes in the activity of a pair of related transcription factors that in turn elicit overproduction of several target genes. Chief among these is the ATP-binding cassette (ABC)-encoding gene PDR5. Interestingly, in the medically important Candida species, very similar pathways are involved in acquisition of multidrug resistance. In both C. albicans and C. glabrata, changes in the activity of transcriptional activator proteins elicits overproduction of a protein closely related to S. cerevisiae Pdr5 called Cdr1. The major filamentous fungal pathogen, Aspergillus fumigatus, was previously thought to acquire resistance to azole compounds (the principal antifungal drug class) via alterations in the azole drug target-encoding gene cyp51A. More recent data indicate that pathways in addition to changes in the cyp51A gene are important determinants in A. fumigatus azole resistance. We will discuss findings that suggest azole resistance in A. fumigatus and Candida species may share more mechanistic similarities than previously thought.
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Affiliation(s)
- Sanjoy Paul
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa Iowa City, IA, USA
| | - W Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa Iowa City, IA, USA
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30
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Voth WP, Takahata S, Nishikawa JL, Metcalfe BM, Näär AM, Stillman DJ. A role for FACT in repopulation of nucleosomes at inducible genes. PLoS One 2014; 9:e84092. [PMID: 24392107 PMCID: PMC3879260 DOI: 10.1371/journal.pone.0084092] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 11/15/2013] [Indexed: 01/22/2023] Open
Abstract
Xenobiotic drugs induce Pleiotropic Drug Resistance (PDR) genes via the orthologous Pdr1/Pdr3 transcription activators. We previously identified the Mediator transcription co-activator complex as a key target of Pdr1 orthologs and demonstrated that Pdr1 interacts directly with the Gal11/Med15 subunit of the Mediator complex. Based on an interaction between Pdr1 and the FACT complex, we show that strains with spt16 or pob3 mutations are sensitive to xenobiotic drugs and display diminished PDR gene induction. Although FACT acts during the activation of some genes by assisting in the nucleosomes eviction at promoters, PDR promoters already contain nucleosome-depleted regions (NDRs) before induction. To determine the function of FACT at PDR genes, we examined the kinetics of RNA accumulation and changes in nucleosome occupancy following exposure to a xenobiotic drug in wild type and FACT mutant yeast strains. In the presence of normal FACT, PDR genes are transcribed within 5 minutes of xenobiotic stimulation and transcription returns to basal levels by 30–40 min. Nucleosomes are constitutively depleted in the promoter regions, are lost from the open reading frames during transcription, and the ORFs are wholly repopulated with nucleosomes as transcription ceases. While FACT mutations cause minor delays in activation of PDR genes, much more pronounced and significant defects in nucleosome repopulation in the ORFs are observed in FACT mutants upon transcription termination. FACT therefore has a major role in nucleosome redeposition following cessation of transcription at the PDR genes, the opposite of its better-known function in nucleosome disassembly.
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Affiliation(s)
- Warren P. Voth
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah, United States of America
| | - Shinya Takahata
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah, United States of America
| | - Joy L. Nishikawa
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts, United States of America
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Benjamin M. Metcalfe
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah, United States of America
| | - Anders M. Näär
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts, United States of America
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David J. Stillman
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah, United States of America
- * E-mail:
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31
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Nishida N, Jing D, Kuroda K, Ueda M. Activation of signaling pathways related to cell wall integrity and multidrug resistance by organic solvent in Saccharomyces cerevisiae. Curr Genet 2013; 60:149-62. [DOI: 10.1007/s00294-013-0419-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 12/13/2013] [Accepted: 12/17/2013] [Indexed: 11/29/2022]
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32
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Khazak V, Eyrisch S, Kato J, Tamanoi F, Golemis EA. A two-hybrid approach to identify inhibitors of the RAS-RAF interaction. Enzymes 2013; 33 Pt A:213-48. [PMID: 25033807 DOI: 10.1016/b978-0-12-416749-0.00010-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
MCP compounds were developed with the idea to inhibit RAS/RAF interaction. They were identified by carrying out high-throughput screens of chemical compounds for their ability to inhibit RAS/RAF interaction in the yeast two-hybrid assay. A number of compounds including MCP1, MCP53, and MCP110 were identified as active compounds. Their inhibition of the RAS signaling was demonstrated by examining RAF and MEK activities, phosphorylation of ERK as well as characterizing their effects on events downstream of RAF. Direct evidence for the inhibition of RAS/RAF interaction was obtained by carrying out co-IP experiments. MCP compounds inhibit proliferation of a wide range of human cancer cell lines. Combination studies with other drugs showed that MCP compounds synergize with MAPK pathway inhibitors as well as with microtubule-targeting chemotherapeutics. In particular, a strong synergy with paclitaxel was observed. Efficacy to inhibit tumor formation was demonstrated using mouse xenograft models. Combination of MCP110 and paclitaxel was particularly effective in inhibiting tumor growth in a mouse xenograft model of colorectal carcinoma.
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Affiliation(s)
- Vladimir Khazak
- Program in Biology, Priaxon Inc., Philadelphia, Pennsylvania, USA.
| | | | - Juran Kato
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Fuyuhiko Tamanoi
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Erica A Golemis
- Program in Biology, Priaxon Inc., Philadelphia, Pennsylvania, USA; Program in Developmental Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA.
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33
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Functional analysis of an ATP-binding cassette transporter protein from Aspergillus fumigatus by heterologous expression in Saccharomyces cerevisiae. Fungal Genet Biol 2013; 57:85-91. [PMID: 23796749 DOI: 10.1016/j.fgb.2013.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 06/11/2013] [Accepted: 06/13/2013] [Indexed: 12/24/2022]
Abstract
Aspergillus fumigatus is the major filamentous fungal pathogen in humans. Although A. fumigatus can be treated with many of the available antifungal drugs, including azole compounds, drug resistant isolates are being recovered at an increasing rate. In other fungal pathogens such as the Candida species, ATP-binding cassette (ABC) transporter proteins play important roles in development of clinically-significant azole resistance phenotypes. Central among these ABC transporter proteins are homologues of the Saccharomyces cerevisiae Pdr5 multidrug transporter. In this work, we test the two A. fumigatus genes encoding proteins sharing the highest degree of sequence similarity to S. cerevisiae Pdr5 for their ability to be function in a heterologous pdr5Δ strain of S. cerevisiae. Expression of full-length cDNAs for these two Afu proteins failed to suppress the drug sensitive phenotype of a pdr5Δ strain and no evidence could be obtained for their expression as green fluorescent protein (GFP) fusions. To improve the expression of one of these Afu ABC transporters (XP_755847), we changed the sequence of the cDNA to use codons corresponding to the major tRNA species in S. cerevisiae. This codon-optimized (CO Afu abcA) cDNA was efficiently expressed in pdr5Δ cells and able to be detected as a GFP fusion protein. The CO Afu abcA did not correct the drug sensitivity of the pdr5Δ strain and exhibited a high degree of perinuclear fluorescence suggesting that this fusion protein was localized to the S. cerevisiae ER. Interestingly, when these experiments were repeated at 37 °C, the CO Afu abcA was able to complement the drug sensitive phenotype of pdr5Δ cells and exhibited less intracellular fluorescence. Additionally, we found that the CO Afu abcA was able to reduce resistance to drugs like phytosphingosine that act via causing mislocalization of amino acid permeases in fungi. These data suggest that the Afu abcA protein can carry out two different functions of Pdr5: drug transport and regulation of protein internalization from the plasma membrane.
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34
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A functional variomics tool for discovering drug-resistance genes and drug targets. Cell Rep 2013; 3:577-85. [PMID: 23416056 DOI: 10.1016/j.celrep.2013.01.019] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/17/2012] [Accepted: 01/16/2013] [Indexed: 01/29/2023] Open
Abstract
Comprehensive discovery of genetic mechanisms of drug resistance and identification of in vivo drug targets represent significant challenges. Here we present a functional variomics technology in the model organism Saccharomyces cerevisiae. This tool analyzes numerous genetic variants and effectively tackles both problems simultaneously. Using this tool, we discovered almost all genes that, due to mutations or modest overexpression, confer resistance to rapamycin, cycloheximide, and amphotericin B. Most significant among the resistance genes were drug targets, including multiple targets of a given drug. With amphotericin B, we discovered the highly conserved membrane protein Pmp3 as a potent resistance factor and a possible target. Widespread application of this tool should allow rapid identification of conserved resistance mechanisms and targets of many more compounds. New genes and alleles that confer resistance to other stresses can also be discovered. Similar tools in other systems, such as human cell lines, will also be useful.
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35
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Balazfyova Z, Hervay NT, Gbelska Y. Gain-of-function mutation in the KlPDR1 gene encoding multidrug resistance regulator in Kluyveromyces lactis. Yeast 2013; 30:71-80. [PMID: 23361926 DOI: 10.1002/yea.2941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 12/28/2012] [Indexed: 11/10/2022] Open
Abstract
KlPdr1p is a single Kluyveromyces lactis homologue of Saccharomyces cerevisiae ScPdr1p/ScPdr3p, the main transcriptional regulators of genes involved in S. cerevisiae multidrug resistance. KlPDR1 deletion leads to a sharp increase in K. lactis drug susceptibility. The presence of putative PDRE and YRE regulatory elements in the KlPDR1 gene promoter suggests an autoregulation of its transcription as well as its control by KlYap1p, the transcription factor involved in oxidative stress response. In this study, one plasmid-borne Klpdr1-1 allele that led to amino acid substitution (L273P) in the KlPdr1p was isolated. Overexpression of the Klpdr1-1 allele from a multicopy plasmid in the K. lactis wild-type and Klpdr1Δ mutant strain increased the tolerance of transformants to oligomycin. The plasmid-borne Klpdr1-1 allele increased the activation of the ScPDR5 promoter and complemented the drug hypersensitivity of the S. cerevisiae pdr1Δ pdr3Δ mutant strain. The results indicate that L273P amino acid substitution is the result of a gain-of-function mutation in the KlPDR1 gene that confers KlPdr1p hyperactivity, as revealed by a high expression of the ABC transporter gene KlPDR5, leading to multidrug resistance and rhodamine 6G efflux out of the cells.
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Affiliation(s)
- Zuzana Balazfyova
- Department of Microbiology and Virology, Comenius University in Bratislava, Slovak Republic
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36
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Prasad R, Goffeau A. Yeast ATP-Binding Cassette Transporters Conferring Multidrug Resistance. Annu Rev Microbiol 2012; 66:39-63. [DOI: 10.1146/annurev-micro-092611-150111] [Citation(s) in RCA: 164] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rajendra Prasad
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India;
| | - Andre Goffeau
- Institut des Sciences de la Vie, Université Catholique de Louvain, Louvain-la-Neuve, 1349 Belgium;
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37
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Mutations in the basic loop of the Zn binuclear cluster of the UaY transcriptional activator suppress mutations in the dimerisation domain. Fungal Genet Biol 2012; 49:731-43. [DOI: 10.1016/j.fgb.2012.06.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 06/06/2012] [Accepted: 06/08/2012] [Indexed: 11/19/2022]
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38
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Kołaczkowska A, Manente M, Kołaczkowski M, Laba J, Ghislain M, Wawrzycka D. The regulatory inputs controlling pleiotropic drug resistance and hypoxic response in yeast converge at the promoter of the aminocholesterol resistance gene RTA1. FEMS Yeast Res 2011; 12:279-92. [DOI: 10.1111/j.1567-1364.2011.00768.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 11/18/2011] [Accepted: 11/21/2011] [Indexed: 11/30/2022] Open
Affiliation(s)
- Anna Kołaczkowska
- Department of Biochemistry, Pharmacology and Toxicology; University of Environmental and Life Sciences; Wroclaw; Poland
| | - Myriam Manente
- Unité de biochimie physiologique; Institut des sciences de la vie; Université catholique de Louvain; Louvain-la-Neuve; Belgium
| | | | - Justyna Laba
- Department of Biochemistry, Pharmacology and Toxicology; University of Environmental and Life Sciences; Wroclaw; Poland
| | - Michel Ghislain
- Unité de biochimie physiologique; Institut des sciences de la vie; Université catholique de Louvain; Louvain-la-Neuve; Belgium
| | - Donata Wawrzycka
- Department of Genetics and Cell Physiology; Institute of Plant Biology; Wroclaw University; Wroclaw; Poland
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39
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Antifungal resistance and new strategies to control fungal infections. Int J Microbiol 2011; 2012:713687. [PMID: 22187560 PMCID: PMC3236459 DOI: 10.1155/2012/713687] [Citation(s) in RCA: 262] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 09/06/2011] [Indexed: 11/28/2022] Open
Abstract
Despite improvement of antifungal therapies over the last 30 years, the phenomenon of antifungal resistance is still of major concern in clinical practice. In the last 10 years the molecular mechanisms underlying this phenomenon were extensively unraveled. In this paper, after a brief overview of currently available antifungals, molecular mechanisms of antifungal resistance will be detailed. It appears that major mechanisms of resistance are essential due to the deregulation of antifungal resistance effector genes. This deregulation is a consequence of point mutations occurring in transcriptional regulators of these effector genes. Resistance can also follow the emergence of point mutations directly in the genes coding antifungal targets. In addition we further describe new strategies currently undertaken to discover alternative therapy targets and antifungals. Identification of new antifungals is essentially achieved by the screening of natural or synthetic chemical compound collections. Discovery of new putative antifungal targets is performed through genome-wide approaches for a better understanding of the human pathogenic fungi biology.
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40
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Gallo-Ebert C, McCourt PC, Donigan M, Villasmil ML, Chen W, Pandya D, Franco J, Romano D, Chadwick SG, Gygax SE, Nickels JT. Arv1 lipid transporter function is conserved between pathogenic and nonpathogenic fungi. Fungal Genet Biol 2011; 49:101-13. [PMID: 22142782 DOI: 10.1016/j.fgb.2011.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 11/10/2011] [Accepted: 11/16/2011] [Indexed: 10/14/2022]
Abstract
The lipid transporter Arv1 regulates sterol trafficking, and glycosylphosphatidylinositol and sphingolipid biosyntheses in Saccharomyces cerevisiae. ScArv1 contains an Arv1 homology domain (AHD) that is conserved at the amino acid level in the pathogenic fungal species, Candida albicans and Candida glabrata. Here we show S. cerevisiae cells lacking Arv1 are highly susceptible to antifungal drugs. In the presence of drug, Scarv1 cells are unable to induce ERG gene expression, have an altered pleiotrophic drug response, and are defective in multi-drug resistance efflux pump expression. All phenotypes are remediated by ectopic expression of CaARV1 or CgARV1. The AHDs of these pathogenic fungi are required for specific drug tolerance, demonstrating conservation of function. In order to understand how Arv1 regulates antifungal susceptibility, we examined sterol trafficking. CaARV1/CgARV1 expression suppressed the sterol trafficking defect of Scarv1 cells. Finally, we show that C. albicansarv1/arv1 cells are avirulent using a BALB/c disseminated mouse model. We suggest that overall cell survival in response to antifungal treatment requires the lipid transporter function of Arv1.
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41
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Differential involvement of mitochondrial dysfunction, cytochrome P450 activity, and active transport in the toxicity of structurally related NSAIDs. Toxicol In Vitro 2011; 26:197-205. [PMID: 22138569 DOI: 10.1016/j.tiv.2011.11.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 11/15/2011] [Accepted: 11/17/2011] [Indexed: 12/23/2022]
Abstract
Non-steroidal anti-inflammatory drugs (NSAIDs) are widely used in the treatment of pain and inflammation. However, this group of drugs is associated with serious adverse drug reactions. Previously, we studied the mechanisms underlying toxicity of the NSAID diclofenac using Saccharomycescerevisiae as model system. We identified the involvement of several mitochondrial proteins, a transporter and cytochrome P450 activity in diclofenac toxicity. In this study, we investigated if these processes are also involved in the toxicity of other NSAIDs. We divided the NSAIDs into three classes based on their toxicity mechanisms. Class I consists of diclofenac, indomethacin and ketoprofen. Mitochondrial respiration and reactive oxygen species (ROS) play a major role in the toxicity of this class. Metabolism by cytochrome P450s further increases their toxicity, while ABC-transporters decrease the toxicity. Mitochondria and oxidative metabolism also contribute to toxicity of class II drugs ibuprofen and naproxen, but another cellular target dominates their toxicity. Interestingly, ibuprofen was the only NSAID that was unable to induce upregulation of the multidrug resistance response. The class III NSAIDs sulindac, ketorolac and zomepirac were relatively non-toxic in yeast. In conclusion, we demonstrate the use of yeast to investigate the mechanisms underlying the toxicity of structurally related drugs.
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42
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Hervay NT, Hodurova Z, Balazfyova Z, Gbelska Y. Autoactivated KlPDR1 gene in the control of multidrug resistance in Kluyveromyces lactis. Can J Microbiol 2011; 57:844-9. [PMID: 21950796 DOI: 10.1139/w11-071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The KlPDR1 gene encodes a zinc finger transcription factor that has recently been shown to be involved in the control of multidrug resistance of Kluyveromyces lactis . In this work, we provide evidence that the K. lactis KlPDR1 gene is under positive autoregulation by KlPdr1p, which plays a role in the activation of the main multidrug resistance transporter gene KlPDR5. Electrophoretic mobility shift assays, as well as the use of gusA reporter constructs, enabled us to identify the 5'-tataTCCGGGTAactt-3' sequence motif in the KlPDR1 promoter (in the position -326 to -319 bp) as the PDRE (pleiotropic drug responsive element) for the binding of KlPdr1p. The drug sensitivity of Klpdr1Δ mutant cells was complemented by introducing the plasmid-born KlPDR1 gene. The KlPdr1p activated the expression of the P(KlPDR1)-gusA fusion gene, and the expression of the KlPDR1 gene was induced by fluconazole. The PDRE was also found in the promoter of KlPDR5, a gene encoding the ATP-dependent efflux pump responsible for the drug resistance phenomenon in K. lactis.
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Affiliation(s)
- Nora Toth Hervay
- Comenius University in Bratislava, Department of Microbiology and Virology, Slovak Republic
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43
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Formenti LR, Kielland-Brandt MC. Sensitivity to lovastatin of Saccharomyces cerevisiae strains deleted for pleiotropic drug resistance (PDR) genes. J Mol Microbiol Biotechnol 2011; 20:191-5. [PMID: 21757925 DOI: 10.1159/000329068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The use of statins is well established in human therapy, and model organisms such as Saccharomyces cerevisiae are commonly used in studies of drug action at molecular and cellular levels. The investigation of the resistance mechanisms towards statins may suggest new approaches to improve therapy based on the use of statins. We investigated the susceptibility to lovastatin of S. cerevisiae strains deleted for PDR genes, responsible for exporting hydrophobic and amphiphilic drugs, such as lovastatin. Strains deleted for the genes tested, PDR1, PDR3, PDR5 and SNQ2, exhibited remarkably different phenotypes, with deletion of PDR5 causing the highest sensitivity to lovastatin. The study helped clarifying which pdr mutants to use in studies of physiological actions of statins in yeast.
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Affiliation(s)
- Luca Riccardo Formenti
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Lyngby. lrf @ bio.dtu.dk
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44
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van Leeuwen JS, Orij R, Luttik MAH, Smits GJ, Vermeulen NPE, Vos JC. Subunits Rip1p and Cox9p of the respiratory chain contribute to diclofenac-induced mitochondrial dysfunction. Microbiology (Reading) 2011; 157:685-694. [DOI: 10.1099/mic.0.044578-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The widely used drug diclofenac can cause serious heart, liver and kidney injury, which may be related to its ability to cause mitochondrial dysfunction. Using Saccharomyces cerevisiae as a model system, we studied the mechanisms of diclofenac toxicity and the role of mitochondria therein. We found that diclofenac reduced cell growth and viability and increased levels of reactive oxygen species (ROS). Strains increasingly relying on respiration for their energy production showed enhanced sensitivity to diclofenac. Furthermore, oxygen consumption was inhibited by diclofenac, suggesting that the drug inhibits respiration. To identify the site of respiratory inhibition, we investigated the effects of deletion of respiratory chain subunits on diclofenac toxicity. Whereas deletion of most subunits had no effect, loss of either Rip1p of complex III or Cox9p of complex IV resulted in enhanced resistance to diclofenac. In these deletion strains, diclofenac did not increase ROS formation as severely as in the wild-type. Our data are consistent with a mechanism of toxicity in which diclofenac inhibits respiration by interfering with Rip1p and Cox9p in the respiratory chain, resulting in ROS production that causes cell death.
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Affiliation(s)
- Jolanda S. van Leeuwen
- LACDR, Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Rick Orij
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Marijke A. H. Luttik
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Gertien J. Smits
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Nico P. E. Vermeulen
- LACDR, Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - J. Chris Vos
- LACDR, Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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Miranda MN, Masuda CA, Ferreira-Pereira A, Carvajal E, Ghislain M, Montero-Lomelí M. The serine/threonine protein phosphatase Sit4p activates multidrug resistance in Saccharomyces cerevisiae. FEMS Yeast Res 2010; 10:674-86. [PMID: 20608983 DOI: 10.1111/j.1567-1364.2010.00656.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Multidrug resistance in Saccharomyces cerevisiae is frequently associated with gain-of-function mutations in zinc finger-containing transcription factors Pdr1p and Pdr3p. These regulatory proteins activate the expression of several ATP-binding cassette transporter genes, leading to elevated drug resistance. Here, we report that loss of the type 2A-related serine/threonine protein phosphatase Sit4p renders yeast cells sensitive to cycloheximide, azoles, daunorubicin and rhodamine 6G. This effect is a consequence of the decreased transcriptional levels of mainly PDR3 and its target genes, PDR5, SNQ2 and YOR1, which encode multidrug efflux pumps. The multidrug sensitivity of sit4 mutant cells is suppressed by the PDR1-3 mutant allele, which encodes a hyperactive form of Pdr1p. Sit4p is known to associate with regulatory proteins Sap155p, Sap4p, Sap185p and Sap190p. We found that the sap155 mutant strain is sensitive to azoles, but not to cycloheximide, while the sap155sap4 and sap185sap190 mutant strains are sensitive to both drugs. This finding indicates that the Sit4p-Sap protein complex subtly modulates the expression of drug efflux pumps. Drug resistance conferred by the expression of the Candida albicans CDR1 gene, an ortholog of PDR5 in S. cerevisiae, is also positively modulated by Sit4p. These data uncover a new regulatory pathway that connects multidrug resistance to Sit4p function.
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Affiliation(s)
- Michel N Miranda
- Centro de Ciências da Saúde, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Shahi P, Gulshan K, Näär AM, Moye-Rowley WS. Differential roles of transcriptional mediator subunits in regulation of multidrug resistance gene expression in Saccharomyces cerevisiae. Mol Biol Cell 2010; 21:2469-82. [PMID: 20505076 PMCID: PMC2903675 DOI: 10.1091/mbc.e09-10-0899] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Med12 is a transcriptional Mediator subunit most typically associated with negative control of gene expression. Here Med12 is demonstrated to serve as a positive regulator required for activation of multidrug resistance gene expression in yeast cells lacking their mitochondrial genome. The multiprotein transcriptional Mediator complex provides a key link between RNA polymerase II and upstream transcriptional activator proteins. Previous work has established that the multidrug resistance transcription factors Pdr1 and Pdr3 interact with the Mediator component Med15/Gal11 to drive normal levels of expression of the ATP-binding cassette transporter-encoding gene PDR5 in Saccharomyces cerevisiae. PDR5 transcription is induced upon loss of the mitochondrial genome (ρ0 cells) and here we provide evidence that this ρ0 induction is Med15 independent. A search through other known Mediator components determined that Med12/Srb8, a member of the CDK8 Mediator submodule, is required for ρ0 activation of PDR5 transcription. The CDK8 submodule contains the cyclin C homologue (CycC/Srb11), cyclin-dependent kinase Cdk8/Srb10, and the large Med13/Srb9 protein. Loss of these other proteins did not lead to the same block in PDR5 induction. Chromatin immunoprecipitation analyses demonstrated that Med15 is associated with the PDR5 promoter in both ρ+ and ρ0, whereas Med12 recruitment to this target promoter is highly responsive to loss of the mitochondrial genome. Coimmunoprecipitation experiments revealed that association of Pdr3 with Med12 can only be detected in ρ0 cells. These experiments uncover the unique importance of Med12 in activated transcription of PDR5 seen in ρ0 cells.
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Affiliation(s)
- Puja Shahi
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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Dzugasova V, Borecka S, Batova M, Pilisiova R, Hervayova N, Subik J. Site-directed mutagenesis of Asp853 in Pdr3p transcriptional activator from Saccharomyces cerevisiae. Yeast 2010; 27:277-84. [PMID: 20146400 DOI: 10.1002/yea.1751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The PDR3 gene encodes one of the main transcriptional activators involved in the control of multidrug resistance in the yeast Saccharomyces cerevisiae. Recently, it has been demonstrated that a specific D853Y mutation results in the loss of transactivation activity of Pdr3p and its conversion to multicopy suppressor of multidrug resistance. In this study, the Asp853 in Pdr3p was replaced by eight different amino acids and the function of mutated proteins was analysed. Different levels of complementation of cycloheximide hypersensitivity and expression of autoregulated PDR3 and its PDR5 target in the pdr1Deltapdr3Delta mutant strain, ranging from that of the wild-type to loss-of-function alleles, were observed in pdr3 mutants containing Pro, Glu, Arg, Asn, Ser, Leu, Phe, Ile or Tyr instead of Asp853 in Pdr3p. The introduction of the D853Y mutation into gain-of-function Pdr3p suppressed the transcription of the PDR3 and PDR5 genes and reduced both the rhodamine 6G efflux rate and the drug resistance level in corresponding double mutants. The results indicate that, while Pdr3p can tolerate several substitutions of Asp853, the occurrence of a hydrophobic amino acid at this position has an adverse effect on its function.
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Affiliation(s)
- Vladimira Dzugasova
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Slovak Republic
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Microarray analysis of p-anisaldehyde-induced transcriptome of Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2009; 37:313-22. [DOI: 10.1007/s10295-009-0676-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 11/29/2009] [Indexed: 10/20/2022]
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Zhang M, Hanna M, Li J, Butcher S, Dai H, Xiao W. Creation of a Hyperpermeable Yeast Strain to Genotoxic Agents through Combined Inactivation of PDR and CWP Genes. Toxicol Sci 2009; 113:401-11. [DOI: 10.1093/toxsci/kfp267] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Manente M, Ghislain M. The lipid-translocating exporter family and membrane phospholipid homeostasis in yeast. FEMS Yeast Res 2009; 9:673-87. [DOI: 10.1111/j.1567-1364.2009.00513.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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