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Bernard A, Rossignol T, Park YK. Biotechnological approaches for producing natural pigments in yeasts. Trends Biotechnol 2024:S0167-7799(24)00175-6. [PMID: 39019677 DOI: 10.1016/j.tibtech.2024.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/13/2024] [Accepted: 06/25/2024] [Indexed: 07/19/2024]
Abstract
Pigments are widely used in the food, cosmetic, textile, pharmaceutical, and materials industries. Demand for natural pigments has been increasing due to concerns regarding potential health problems and environmental pollution from synthetic pigments. Microbial production of natural pigments is a promising alternative to chemical synthesis or extraction from natural sources. Here, we discuss yeasts as promising chassis for producing natural pigments with their advantageous traits such as genetic amenability, safety, rapid growth, metabolic diversity, and tolerance. Metabolic engineering strategies and optimizing strategies in downstream process to enhance production of natural pigments are thoroughly reviewed. We discuss the challenges, including expanding the range of natural pigments and improving their feasibility of industrial scale-up, as well as the potential strategies for future development.
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Affiliation(s)
- Armand Bernard
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Tristan Rossignol
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Young-Kyoung Park
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
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2
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Hénault M, Marsit S, Charron G, Landry CR. The genomic landscape of transposable elements in yeast hybrids is shaped by structural variation and genotype-specific modulation of transposition rate. eLife 2024; 12:RP89277. [PMID: 38411604 PMCID: PMC10911583 DOI: 10.7554/elife.89277] [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] [Indexed: 02/28/2024] Open
Abstract
Transposable elements (TEs) are major contributors to structural genomic variation by creating interspersed duplications of themselves. In return, structural variants (SVs) can affect the genomic distribution of TE copies and shape their load. One long-standing hypothesis states that hybridization could trigger TE mobilization and thus increase TE load in hybrids. We previously tested this hypothesis (Hénault et al., 2020) by performing a large-scale evolution experiment by mutation accumulation (MA) on multiple hybrid genotypes within and between wild populations of the yeasts Saccharomyces paradoxus and Saccharomyces cerevisiae. Using aggregate measures of TE load with short-read sequencing, we found no evidence for TE load increase in hybrid MA lines. Here, we resolve the genomes of the hybrid MA lines with long-read phasing and assembly to precisely characterize the role of SVs in shaping the TE landscape. Highly contiguous phased assemblies of 127 MA lines revealed that SV types like polyploidy, aneuploidy, and loss of heterozygosity have large impacts on the TE load. We characterized 18 de novo TE insertions, indicating that transposition only has a minor role in shaping the TE landscape in MA lines. Because the scarcity of TE mobilization in MA lines provided insufficient resolution to confidently dissect transposition rate variation in hybrids, we adapted an in vivo assay to measure transposition rates in various S. paradoxus hybrid backgrounds. We found that transposition rates are not increased by hybridization, but are modulated by many genotype-specific factors including initial TE load, TE sequence variants, and mitochondrial DNA inheritance. Our results show the multiple scales at which TE load is shaped in hybrid genomes, being highly impacted by SV dynamics and finely modulated by genotype-specific variation in transposition rates.
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Affiliation(s)
- Mathieu Hénault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
| | - Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
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3
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Kaplan K, Levkovich SA, DeRowe Y, Gazit E, Laor Bar-Yosef D. Mind your marker: the effect of common auxotrophic markers on complex traits in yeast. FEBS J 2024. [PMID: 38383986 DOI: 10.1111/febs.17095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 01/02/2024] [Accepted: 02/05/2024] [Indexed: 02/23/2024]
Abstract
Yeast cells are extensively used as a key model organism owing to their highly conserved genome, metabolic pathways, and cell biology processes. To assist in genetic engineering and analysis, laboratory yeast strains typically harbor auxotrophic selection markers. When uncompensated, auxotrophic markers cause significant phenotypic bias compared to prototrophic strains and have different combinatorial influences on the metabolic network. Here, we used BY4741, a laboratory strain commonly used as a "wild type" strain in yeast studies, to generate a set of revertant strains, containing all possible combinations of four common auxotrophic markers (leu2∆, ura3∆, his3∆1, met15∆). We examined the effect of the auxotrophic combinations on complex phenotypes such as resistance to rapamycin, acetic acid, and ethanol. Among the markers, we found that leucine auxotrophy most significantly affected the phenotype. We analyzed the phenotypic bias caused by auxotrophy at the genomic level using a prototrophic version of a genome-wide deletion library and a decreased mRNA perturbation (DAmP) library. Prototrophy was found to suppress rapamycin sensitivity in many mutants previously annotated for the phenotype, raising a possible need for reevaluation of the findings in a native metabolic context. These results reveal a significant phenotypic bias caused by common auxotrophic markers and support the use of prototrophic wild-type strains in yeast research.
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Affiliation(s)
- Keila Kaplan
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Shon A Levkovich
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Yasmin DeRowe
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Ehud Gazit
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
- BLAVATNIK CENTER for Drug Discovery, Tel Aviv University, Israel
| | - Dana Laor Bar-Yosef
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
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4
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Sanyal S, Kouznetsova A, Ström L, Björkegren C. A system for inducible mitochondria-specific protein degradation in vivo. Nat Commun 2024; 15:1454. [PMID: 38365818 PMCID: PMC10873288 DOI: 10.1038/s41467-024-45819-6] [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: 02/24/2023] [Accepted: 02/05/2024] [Indexed: 02/18/2024] Open
Abstract
Targeted protein degradation systems developed for eukaryotes employ cytoplasmic machineries to perform proteolysis. This has prevented mitochondria-specific analysis of proteins that localize to multiple locations, for example, the mitochondria and the nucleus. Here, we present an inducible mitochondria-specific protein degradation system in Saccharomyces cerevisiae based on the Mesoplasma florum Lon (mf-Lon) protease and its corresponding ssrA tag (called PDT). We show that mitochondrially targeted mf-Lon protease efficiently and selectively degrades a PDT-tagged reporter protein localized to the mitochondrial matrix. The degradation can be induced by depleting adenine from the medium, and tuned by altering the promoter strength of the MF-LON gene. We furthermore demonstrate that mf-Lon specifically degrades endogenous, PDT-tagged mitochondrial proteins. Finally, we show that mf-Lon-dependent PDT degradation can also be achieved in human mitochondria. In summary, this system provides an efficient tool to selectively analyze the mitochondrial function of dually localized proteins.
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Affiliation(s)
- Swastika Sanyal
- Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83, Huddinge, Sweden.
| | - Anna Kouznetsova
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77, Stockholm, Sweden
| | - Lena Ström
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77, Stockholm, Sweden
| | - Camilla Björkegren
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77, Stockholm, Sweden.
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5
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Graber JH, Hoskinson D, Liu H, Kaczmarek Michaels K, Benson PS, Maki NJ, Wilson CL, McGrath C, Puleo F, Pearson E, Kuehner JN, Moore C. Mutations in yeast Pcf11, a conserved protein essential for mRNA 3' end processing and transcription termination, elicit the Environmental Stress Response. Genetics 2024; 226:iyad199. [PMID: 37967370 PMCID: PMC10847720 DOI: 10.1093/genetics/iyad199] [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: 07/11/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/17/2023] Open
Abstract
The Pcf11 protein is an essential subunit of the large complex that cleaves and polyadenylates eukaryotic mRNA precursor. It has also been functionally linked to gene-looping, termination of RNA Polymerase II (Pol II) transcripts, and mRNA export. We have examined a poorly characterized but conserved domain (amino acids 142-225) of the Saccharomyces cerevisiae Pcf11 and found that while it is not needed for mRNA 3' end processing or termination downstream of the poly(A) sites of protein-coding genes, its presence improves the interaction with Pol II and the use of transcription terminators near gene promoters. Analysis of genome-wide Pol II occupancy in cells with Pcf11 missing this region, as well as Pcf11 mutated in the Pol II CTD Interacting Domain, indicates that systematic changes in mRNA expression are mediated primarily at the level of transcription. Global expression analysis also shows that a general stress response, involving both activation and suppression of specific gene sets known to be regulated in response to a wide variety of stresses, is induced in the two pcf11 mutants, even though cells are grown in optimal conditions. The mutants also cause an unbalanced expression of cell wall-related genes that does not activate the Cell Wall Integrity pathway but is associated with strong caffeine sensitivity. Based on these findings, we propose that Pcf11 can modulate the expression level of specific functional groups of genes in ways that do not involve its well-characterized role in mRNA 3' end processing.
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Affiliation(s)
- Joel H Graber
- Mount Desert Island Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Derick Hoskinson
- Department of Development, Molecular, and Chemical Biology and School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Huiyun Liu
- Department of Development, Molecular, and Chemical Biology and School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Katarzyna Kaczmarek Michaels
- Department of Development, Molecular, and Chemical Biology and School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Peter S Benson
- Mount Desert Island Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Nathaniel J Maki
- Mount Desert Island Biological Laboratory, Bar Harbor, ME 04609, USA
| | | | - Caleb McGrath
- Department of Biology, Emmanuel College, Boston, MA 02115, USA
| | - Franco Puleo
- Department of Development, Molecular, and Chemical Biology and School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Erika Pearson
- Department of Development, Molecular, and Chemical Biology and School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Jason N Kuehner
- Department of Biology, Emmanuel College, Boston, MA 02115, USA
| | - Claire Moore
- Department of Development, Molecular, and Chemical Biology and School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA 02111, USA
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6
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Cong H, Li C, Wang Y, Zhang Y, Ma D, Li L, Jiang J. The Mechanism of Transcription Factor Swi6 in Regulating Growth and Pathogenicity of Ceratocystis fimbriata: Insights from Non-Targeted Metabolomics. Microorganisms 2023; 11:2666. [PMID: 38004677 PMCID: PMC10673406 DOI: 10.3390/microorganisms11112666] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/22/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Ceratocystis fimbriata (C. fimbriata) is a notorious pathogenic fungus that causes sweet potato black rot disease. The APSES transcription factor Swi6 in fungi is located downstream of the cell wall integrity (CWI)-mitogen-activated protein kinase (MAPK) signaling pathway and has been identified to be involved in cell wall integrity and virulence in several filamentous pathogenic fungi. However, the specific mechanisms by which Swi6 regulates the growth and pathogenicity of plant pathogenic fungi remain elusive. In this study, the SWI6 deletion mutants and complemented strains of C. fimbriata were generated. Deletion of Swi6 in C. fimbriata resulted in aberrant growth patterns. Pathogenicity assays on sweet potato storage roots revealed a significant decrease in virulence in the mutant. Non-targeted metabolomic analysis using LC-MS identified a total of 692 potential differentially accumulated metabolites (PDAMs) in the ∆Cfswi6 mutant compared to the wild type, and the results of KEGG enrichment analysis demonstrated significant enrichment of PDAMs within various metabolic pathways, including amino acid metabolism, lipid metabolism, nucleotide metabolism, GPI-anchored protein synthesis, and ABC transporter metabolism. These metabolic pathways were believed to play a crucial role in mediating the growth and pathogenicity of C. fimbriata through the regulation of CWI. Firstly, the deletion of the SWI6 gene led to abnormal amino acid and lipid metabolism, potentially exacerbating energy storage imbalance. Secondly, significant enrichment of metabolites related to GPI-anchored protein biosynthesis implied compromised cell wall integrity. Lastly, disruption of ABC transport protein metabolism may hinder intracellular transmembrane transport. Importantly, this study represents the first investigation into the potential regulatory mechanisms of SWI6 in plant filamentous pathogenic fungi from a metabolic perspective. The findings provide novel insights into the role of SWI6 in the growth and virulence of C. fimbriata, highlighting its potential as a target for controlling this pathogen.
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Affiliation(s)
- Hao Cong
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (H.C.); (C.L.); (Y.W.); (Y.Z.)
| | - Changgen Li
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (H.C.); (C.L.); (Y.W.); (Y.Z.)
| | - Yiming Wang
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (H.C.); (C.L.); (Y.W.); (Y.Z.)
| | - Yongjing Zhang
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (H.C.); (C.L.); (Y.W.); (Y.Z.)
| | - Daifu Ma
- Chinese Academy of Agricultural Sciences Sweet Potato Research Institute, Xuzhou 221131, China;
| | - Lianwei Li
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (H.C.); (C.L.); (Y.W.); (Y.Z.)
| | - Jihong Jiang
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (H.C.); (C.L.); (Y.W.); (Y.Z.)
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7
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Pavão G, Sfalcin I, Bonatto D. Biocontainment Techniques and Applications for Yeast Biotechnology. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9040341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Biocontainment techniques for genetically modified yeasts (GMYs) are pivotal due to the importance of these organisms for biotechnological processes and also due to the design of new yeast strains by using synthetic biology tools and technologies. Due to the large genetic modifications that many yeast strains display, it is highly desirable to avoid the leakage of GMY cells into natural environments and, consequently, the spread of synthetic genes and circuits by horizontal or vertical gene transfer mechanisms within the microorganisms. Moreover, it is also desirable to avoid patented yeast gene technologies spreading outside the production facility. In this review, the different biocontainment technologies currently available for GMYs were evaluated. Interestingly, uniplex-type biocontainment approaches (UTBAs), which rely on nutrient auxotrophies induced by gene mutation or deletion or the expression of the simple kill switches apparatus, are still the major biocontainment approaches in use with GMY. While bacteria such as Escherichia coli account for advanced biocontainment technologies based on synthetic biology and multiplex-type biocontainment approaches (MTBAs), GMYs are distant from this scenario due to many reasons. Thus, a comparison of different UTBAs and MTBAs applied for GMY and genetically engineered microorganisms (GEMs) was made, indicating the major advances of biocontainment techniques for GMYs.
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8
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Hoffmann SA, Diggans J, Densmore D, Dai J, Knight T, Leproust E, Boeke JD, Wheeler N, Cai Y. Safety by design: Biosafety and biosecurity in the age of synthetic genomics. iScience 2023; 26:106165. [PMID: 36895643 PMCID: PMC9988571 DOI: 10.1016/j.isci.2023.106165] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Technologies to profoundly engineer biology are becoming increasingly affordable, powerful, and accessible to a widening group of actors. While offering tremendous potential to fuel biological research and the bioeconomy, this development also increases the risk of inadvertent or deliberate creation and dissemination of pathogens. Effective regulatory and technological frameworks need to be developed and deployed to manage these emerging biosafety and biosecurity risks. Here, we review digital and biological approaches of a range of technology readiness levels suited to address these challenges. Digital sequence screening technologies already are used to control access to synthetic DNA of concern. We examine the current state of the art of sequence screening, challenges and future directions, and environmental surveillance for the presence of engineered organisms. As biosafety layer on the organism level, we discuss genetic biocontainment systems that can be used to created host organisms with an intrinsic barrier against unchecked environmental proliferation.
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Affiliation(s)
- Stefan A Hoffmann
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - James Diggans
- Twist Bioscience, 681 Gateway Boulevard, South San Francisco, CA 9408, USA
| | - Douglas Densmore
- Department of Electrical and Computer Engineering, Boston University, 610 Commonwealth Avenue, Boston, MA 02215, USA
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Tom Knight
- Ginkgo Bioworks, 27 Drydock Avenue, Boston, MA 02210, USA
| | - Emily Leproust
- Twist Bioscience, 681 Gateway Boulevard, South San Francisco, CA 9408, USA
| | - Jef D Boeke
- Institute for Systems Genetics, and Department of Biochemistry & Molecular Pharmacology, NYU Langone Health, 435 East 30th Street, New York, NY 10016, USA.,Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Nicole Wheeler
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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9
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De Novo Purine Nucleotide Biosynthesis Pathway Is Required for Development and Pathogenicity in Magnaporthe oryzae. J Fungi (Basel) 2022; 8:jof8090915. [PMID: 36135640 PMCID: PMC9502316 DOI: 10.3390/jof8090915] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 12/04/2022] Open
Abstract
Purine nucleotides are indispensable compounds for many organisms and participate in basic vital activities such as heredity, development, and growth. Blocking of purine nucleotide biosynthesis may inhibit proliferation and development and is commonly used in cancer therapy. However, the function of the purine nucleotide biosynthesis pathway in the pathogenic fungus Magnaporthe oryzae is not clear. In this study, we focused on the de novo purine biosynthesis (DNPB) pathway and characterized MoAde8, a phosphoribosylglycinamide formyltransferase, catalyzing the third step of the DNPB pathway in M. oryzae. MoAde8 was knocked out, and the mutant (∆Moade8) exhibited purine auxotroph, defects in aerial hyphal growth, conidiation, and pathogenicity, and was more sensitive to hyperosmotic stress and oxidative stress. Moreover, ∆Moade8 caused decreased activity of MoTor kinase due to blocked purine nucleotide synthesis. The autophagy level was also impaired in ∆Moade8. Additionally, MoAde5, 7, 6, and 12, which are involved in de novo purine nucleotide biosynthesis, were also analyzed, and the mutants showed defects similar to the defects of ∆Moade8. In summary, de novo purine nucleotide biosynthesis is essential for conidiation, development, and pathogenicity in M. oryzae.
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10
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Hayashi S, Matsui M, Ikeda A, Yoshihisa T. Six identical tRNATrpCCA genes express a similar amount of mature tRNATrpCCA but unequally contribute to yeast cell growth. Biosci Biotechnol Biochem 2022; 86:1398-1404. [PMID: 35948278 DOI: 10.1093/bbb/zbac134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/28/2022] [Indexed: 11/14/2022]
Abstract
Saccharomyces cerevisiae has six synonymous tRNATrpCCA genes encoding the identical sequence, including their intronic region. They are supposed to express tRNATrpCCA in the same quality and quantity. Here, we generated single to quintuple deletion strains with all the possible combinations of the synonymous tRNATrpCCA genes to analyze whether those individual genes equally contribute cell viability and tRNA production. The quintuple deletion strains that only harbor tW(CCA)J, tW(CCA)M, or tW(CCA)P were viable but almost lethal while the other quintuple deletions showed moderately impaired growth. Theses growth differences were not obvious among the quadruple deletion strains, which expressed almost one third of mature tRNATrpCCA in the wild type. Therefore, no dosage compensation operates for tRNATrpCCA amount, and growth variations among the quintuple deletion strains may not simply reflect differences in tRNATrpCCA shortage. Yeast may retain the redundancy of tRNATrpCCA genes for a noncanonical function(s) beyond supply of the tRNA to translation.
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Affiliation(s)
- Sachiko Hayashi
- Graduate School of Science, University of Hyogo, Ako-gun, Japan
| | | | | | - Tohru Yoshihisa
- Graduate School of Science, University of Hyogo, Ako-gun, Japan.,Faculty of Science, University of Hyogo
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11
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Aron O, Otieno FJ, Tijjani I, Yang Z, Xu H, Weng S, Guo J, Lu S, Wang Z, Tang W. De novo purine nucleotide biosynthesis mediated by MoAde4 is required for conidiation, host colonization and pathogenicity in Magnaporthe oryzae. Appl Microbiol Biotechnol 2022; 106:5587-5602. [PMID: 35918446 DOI: 10.1007/s00253-022-12100-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 11/02/2022]
Abstract
Amidophosphoribosyltransferase catalyzes the conversion of 5-phosphoribosyl-1-pyrophosphate into 5-phosphoribosyl-1-amine in the de novo purine biosynthetic pathway. Herein, we identified and characterized the functions of MoAde4, an orthologue of yeast Ade4 in Magnaporthe oryzae. MoAde4 is a 537-amino acid protein containing GATase_6 and pribosyltran domains. MoADE4 transcripts were highly expressed during the conidiation, early-infection, and late-infection stages of the fungus. Disruption of the MoADE4 gene resulted in ΔMoade4 exhibiting adenine, adenosine, and hypoxanthine auxotrophy on minimal medium. Conidia quantification assays showed that sporulation was significantly reduced in the ΔMoade4 mutant. The conidia of ΔMoade4 could still form appressoria but mostly failed to penetrate the rice cuticle. Pathogenicity tests showed that ΔMoade4 was completely nonpathogenic on rice and barley leaves, which was attributed to restricted infectious hyphal growth within the primary cells. The ΔMoade4 mutant was defective in the induction of strong host immunity. Exogenous adenine partially rescued conidiation, infectious hyphal growth, and the pathogenicity defects of the ΔMoade4 mutant on barley and rice leaves. Taken together, our results demonstrated that purine nucleotide biosynthesis orchestrated by MoAde4 is required for fungal development and pathogenicity in M. oryzae. These findings therefore act as a suitable target for antifungal development against recalcitrant plant fungal pathogens. KEY POINTS: • MoAde4 is crucial for de novo purine nucleotide biosynthesis. • MoAde4 is pivotal for conidiogenesis and appressorium development of M. oryzae. • MoAde4 is involoved in the pathogenicity of M. oryzae.
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Affiliation(s)
- Osakina Aron
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Frankine Jagero Otieno
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ibrahim Tijjani
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zifeng Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huxiao Xu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuning Weng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiayuan Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Songmao Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
| | - Wei Tang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou, 350013, China.
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12
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Chappleboim A, Joseph-Strauss D, Gershon O, Friedman N. Transcription feedback dynamics in the wake of cytoplasmic mRNA degradation shutdown. Nucleic Acids Res 2022; 50:5864-5880. [PMID: 35640599 PMCID: PMC9177992 DOI: 10.1093/nar/gkac411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/02/2022] [Accepted: 05/09/2022] [Indexed: 01/02/2023] Open
Abstract
In the last decade, multiple studies demonstrated that cells maintain a balance of mRNA production and degradation, but the mechanisms by which cells implement this balance remain unknown. Here, we monitored cells' total and recently-transcribed mRNA profiles immediately following an acute depletion of Xrn1-the main 5'-3' mRNA exonuclease-which was previously implicated in balancing mRNA levels. We captured the detailed dynamics of the adaptation to rapid degradation of Xrn1 and observed a significant accumulation of mRNA, followed by a delayed global reduction in transcription and a gradual return to baseline mRNA levels. We found that this transcriptional response is not unique to Xrn1 depletion; rather, it is induced earlier when upstream factors in the 5'-3' degradation pathway are perturbed. Our data suggest that the mRNA feedback mechanism monitors the accumulation of inputs to the 5'-3' exonucleolytic pathway rather than its outputs.
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Affiliation(s)
- Alon Chappleboim
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Daphna Joseph-Strauss
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Omer Gershon
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nir Friedman
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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13
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Different life strategies in genetic backgrounds of the Saccharomyces cerevisiae yeast cells. Fungal Biol 2022; 126:498-510. [DOI: 10.1016/j.funbio.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 11/18/2022]
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14
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Qin H, Yu Z, Zhu Z, Lin Y, Xia J, Jia Y. The integrated analyses of metabolomics and transcriptomics in gill of GIFT tilapia in response to long term salinity challenge. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2021.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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15
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Kokina A, Tanilas K, Ozolina Z, Pleiko K, Shvirksts K, Vamza I, Liepins J. Purine Auxotrophic Starvation Evokes Phenotype Similar to Stationary Phase Cells in Budding Yeast. J Fungi (Basel) 2021; 8:29. [PMID: 35049969 PMCID: PMC8780165 DOI: 10.3390/jof8010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/20/2021] [Accepted: 12/24/2021] [Indexed: 11/25/2022] Open
Abstract
Purine auxotrophy is an abundant trait among eukaryotic parasites and a typical marker for many budding yeast strains. Supplementation with an additional purine source (such as adenine) is necessary to cultivate these strains. If not supplied in adequate amounts, purine starvation sets in. We explored purine starvation effects in a model organism, a budding yeast Saccharomyces cerevisiae ade8 knockout, at the level of cellular morphology, central carbon metabolism, and global transcriptome. We observed that purine-starved cells stopped their cycle in G1/G0 state and accumulated trehalose, and the intracellular concentration of AXP decreased, but adenylate charge remained stable. Cells became tolerant to severe environmental stresses. Intracellular RNA concentration decreased, and massive downregulation of ribosomal biosynthesis genes occurred. We proved that the expression of new proteins during purine starvation is critical for cells to attain stress tolerance phenotype Msn2/4p targets are upregulated in purine-starved cells when compared to cells cultivated in purine-rich media. The overall transcriptomic response to purine starvation resembles that of stationary phase cells. Our results demonstrate that the induction of a strong stress resistance phenotype in budding yeast can be caused not only by natural starvation, but also starvation for metabolic intermediates, such as purines.
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Affiliation(s)
- Agnese Kokina
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
| | - Kristel Tanilas
- Center of Food and Fermentation Technologies, Akadeemia Tee 15A, 12618 Tallinn, Estonia;
| | - Zane Ozolina
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
| | - Karlis Pleiko
- Faculty of Medicine, University of Latvia, Jelgavas 3, LV-1004 Riga, Latvia;
- Laboratory of Precision and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Karlis Shvirksts
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
| | - Ilze Vamza
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
| | - Janis Liepins
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
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16
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Johnson MS, Gopalakrishnan S, Goyal J, Dillingham ME, Bakerlee CW, Humphrey PT, Jagdish T, Jerison ER, Kosheleva K, Lawrence KR, Min J, Moulana A, Phillips AM, Piper JC, Purkanti R, Rego-Costa A, McDonald MJ, Nguyen Ba AN, Desai MM. Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations. eLife 2021; 10:e63910. [PMID: 33464204 PMCID: PMC7815316 DOI: 10.7554/elife.63910] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 12/12/2020] [Indexed: 01/25/2023] Open
Abstract
Laboratory experimental evolution provides a window into the details of the evolutionary process. To investigate the consequences of long-term adaptation, we evolved 205 Saccharomyces cerevisiae populations (124 haploid and 81 diploid) for ~10,000,000 generations in three environments. We measured the dynamics of fitness changes over time, finding repeatable patterns of declining adaptability. Sequencing revealed that this phenotypic adaptation is coupled with a steady accumulation of mutations, widespread genetic parallelism, and historical contingency. In contrast to long-term evolution in E. coli, we do not observe long-term coexistence or populations with highly elevated mutation rates. We find that evolution in diploid populations involves both fixation of heterozygous mutations and frequent loss-of-heterozygosity events. Together, these results help distinguish aspects of evolutionary dynamics that are likely to be general features of adaptation across many systems from those that are specific to individual organisms and environmental conditions.
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Affiliation(s)
- Milo S Johnson
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Quantitative Biology Initiative, Harvard UniversityCambridgeUnited States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard UniversityCambridgeUnited States
| | - Shreyas Gopalakrishnan
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Quantitative Biology Initiative, Harvard UniversityCambridgeUnited States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard UniversityCambridgeUnited States
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Juhee Goyal
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- John A Paulson School of Engineering and Applied Sciences, Harvard UniversityCambridgeUnited States
| | - Megan E Dillingham
- Quantitative Biology Initiative, Harvard UniversityCambridgeUnited States
- Graduate Program in Systems, Synthetic, and Quantitative Biology, Harvard UniversityCambridgeUnited States
| | - Christopher W Bakerlee
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Quantitative Biology Initiative, Harvard UniversityCambridgeUnited States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard UniversityCambridgeUnited States
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Parris T Humphrey
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Quantitative Biology Initiative, Harvard UniversityCambridgeUnited States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard UniversityCambridgeUnited States
| | - Tanush Jagdish
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Quantitative Biology Initiative, Harvard UniversityCambridgeUnited States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard UniversityCambridgeUnited States
- Graduate Program in Systems, Synthetic, and Quantitative Biology, Harvard UniversityCambridgeUnited States
| | - Elizabeth R Jerison
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Department of Physics, Harvard UniversityCambridgeUnited States
- Department of Applied Physics, Stanford UniversityStanfordUnited States
| | - Katya Kosheleva
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Department of Physics, Harvard UniversityCambridgeUnited States
| | - Katherine R Lawrence
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Quantitative Biology Initiative, Harvard UniversityCambridgeUnited States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard UniversityCambridgeUnited States
- Department of Physics, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Jiseon Min
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Quantitative Biology Initiative, Harvard UniversityCambridgeUnited States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard UniversityCambridgeUnited States
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
- John A Paulson School of Engineering and Applied Sciences, Harvard UniversityCambridgeUnited States
| | - Alief Moulana
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Angela M Phillips
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Julia C Piper
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- AeroLabs, Aeronaut Brewing CoSomervilleUnited States
| | - Ramya Purkanti
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- The Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Artur Rego-Costa
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Michael J McDonald
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- School of Biological Sciences, Monash UniversityVictoria, MonashAustralia
| | - Alex N Nguyen Ba
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Quantitative Biology Initiative, Harvard UniversityCambridgeUnited States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard UniversityCambridgeUnited States
- Department of Physics, Harvard UniversityCambridgeUnited States
- Department of Cell and Systems Biology, University of TorontoTorontoCanada
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Quantitative Biology Initiative, Harvard UniversityCambridgeUnited States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard UniversityCambridgeUnited States
- Department of Physics, Harvard UniversityCambridgeUnited States
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17
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Molecular signatures of aneuploidy-driven adaptive evolution. Nat Commun 2020; 11:588. [PMID: 32001709 PMCID: PMC6992709 DOI: 10.1038/s41467-019-13669-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 11/15/2019] [Indexed: 02/06/2023] Open
Abstract
Alteration of normal ploidy (aneuploidy) can have a number of opposing effects, such as unbalancing protein abundances and inhibiting cell growth but also accelerating genetic diversification and rapid adaptation. The interplay of these detrimental and beneficial effects remains puzzling. Here, to understand how cells develop tolerance to aneuploidy, we subject disomic (i.e. with an extra chromosome copy) strains of yeast to long-term experimental evolution under strong selection, by forcing disomy maintenance and daily population dilution. We characterize mutations, karyotype alterations and gene expression changes, and dissect the associated molecular strategies. Cells with different extra chromosomes accumulated mutations at distinct rates and displayed diverse adaptive events. They tended to evolve towards normal ploidy through chromosomal DNA loss and gene expression changes. We identify genes with recurrent mutations and altered expression in multiple lines, revealing a variant that improves growth under genotoxic stresses. These findings support rapid evolvability of disomic strains that can be used to characterize fitness effects of mutations under different stress conditions. Aneuploidy (abnormal chromosome number) can enable rapid adaptation to stress conditions, but it also entails fitness costs from gene imbalance. Here, the authors experimentally evolve yeast while forcing maintenance of aneuploidy to identify the mechanisms that promote tolerance of aneuploidy.
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18
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Sosa Y, Deniskin R, Frame IJ, Steiginga MS, Bandyopadhyay D, Graybill TL, Kallal LA, Ouellette MT, Pope AJ, Widdowson KL, Young RJ, Akabas MH. Identification via a Parallel Hit Progression Strategy of Improved Small Molecule Inhibitors of the Malaria Purine Uptake Transporter that Inhibit Plasmodium falciparum Parasite Proliferation. ACS Infect Dis 2019; 5:1738-1753. [PMID: 31373203 DOI: 10.1021/acsinfecdis.9b00168] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Emerging resistance to current antimalarial medicines underscores the importance of identifying new drug targets and novel compounds. Malaria parasites are purine auxotrophic and import purines via the Plasmodium falciparum equilibrative nucleoside transporter type 1 (PfENT1). We previously showed that PfENT1 inhibitors block parasite proliferation in culture. Our goal was to identify additional, possibly more optimal chemical starting points for a drug discovery campaign. We performed a high throughput screen (HTS) of GlaxoSmithKline's 1.8 million compound library with a yeast-based assay to identify PfENT1 inhibitors. We used a parallel progression strategy for hit validation and expansion, with an emphasis on chemical properties in addition to potency. In one arm, the most active hits were tested for human cell toxicity; 201 had minimal toxicity. The second arm, hit expansion, used a scaffold-based substructure search with the HTS hits as templates to identify over 2000 compounds; 123 compounds had activity. Of these 324 compounds, 175 compounds inhibited proliferation of P. falciparum parasite strain 3D7 with IC50 values between 0.8 and ∼180 μM. One hundred forty-two compounds inhibited PfENT1 knockout (pfent1Δ) parasite growth, indicating they also hit secondary targets. Thirty-two hits inhibited growth of 3D7 but not pfent1Δ parasites. Thus, PfENT1 inhibition was sufficient to block parasite proliferation. Therefore, PfENT1 may be a viable target for antimalarial drug development. Six compounds with novel chemical scaffolds were extensively characterized in yeast-, parasite-, and human-erythrocyte-based assays. The inhibitors showed similar potencies against drug sensitive and resistant P. falciparum strains. They represent attractive starting points for development of novel antimalarial drugs.
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Affiliation(s)
| | | | | | - Matthew S. Steiginga
- Platform Technology & Science and Discovery Partners in Academia, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Deepak Bandyopadhyay
- Platform Technology & Science and Discovery Partners in Academia, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Todd L. Graybill
- Platform Technology & Science and Discovery Partners in Academia, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Lorena A. Kallal
- Platform Technology & Science and Discovery Partners in Academia, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Michael T. Ouellette
- Platform Technology & Science and Discovery Partners in Academia, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Andrew J. Pope
- Platform Technology & Science and Discovery Partners in Academia, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Katherine L. Widdowson
- Platform Technology & Science and Discovery Partners in Academia, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Robert J. Young
- Platform Technology & Science and Discovery Partners in Academia, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
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19
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Kokina A, Ozolina Z, Liepins J. Purine auxotrophy: Possible applications beyond genetic marker. Yeast 2019; 36:649-656. [PMID: 31334866 DOI: 10.1002/yea.3434] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/12/2019] [Accepted: 07/16/2019] [Indexed: 01/09/2023] Open
Abstract
Exploring new drug candidates or drug targets against many illnesses is necessary as "traditional" treatments lose their effectivity. Cancer and sicknesses caused by protozoan parasites are among these diseases. Cell purine metabolism is an important drug target. Theoretically, inhibiting purine metabolism could stop the proliferation of unwanted cells. Purine metabolism is similar across all eukaryotes. However, some medically important organisms or cell lines rely on their host purine metabolism. Protozoans causing malaria, leishmaniasis, or toxoplasmosis are purine auxotrophs. Some cancer forms have also lost the ability to synthesize purines de novo. Budding yeast can serve as an effective model for eukaryotic purine metabolism, and thus, purine auxotrophic strains could be an important tool. In this review, we present the common principles of purine metabolism in eukaryotes, effects of purine starvation in eukaryotic cells, and purine-starved Saccharomyces cerevisiae as a model for purine depletion-elicited metabolic states with applications in evolution studies and pharmacology. Purine auxotrophic yeast strains behave differently when growing in media with sufficient supplementation with adenine or in media depleted of adenine (starvation). In the latter, they undergo cell cycle arrest at G1/G0 and become stress resistant. Importantly, similar effects have also been observed among parasitic protozoans or cancer cells. We consider that studies on metabolic changes caused by purine auxotrophy could reveal new options for parasite or cancer therapy. Further, knowledge on phenotypic changes will improve the use of auxotrophic strains in high-throughput screening for primary drug candidates.
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Affiliation(s)
- Agnese Kokina
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Zane Ozolina
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Janis Liepins
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
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20
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Liu M, Hilty C. Metabolic Measurements of Nonpermeating Compounds in Live Cells Using Hyperpolarized NMR. Anal Chem 2018; 90:1217-1222. [PMID: 29227628 PMCID: PMC6200330 DOI: 10.1021/acs.analchem.7b03901] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hyperpolarization by dissolution dynamic nuclear polarization (D-DNP) has emerged as a technique for enhancing NMR signals by several orders of magnitude, thereby facilitating the characterization of metabolic pathways both in vivo and in vitro. Following the introduction of an externally hyperpolarized compound, real-time NMR enables the measurement of metabolic flux in the corresponding pathway. Spin relaxation however limits the maximum experimental time and prevents the use of this method with compounds exhibiting slow membrane transport rates. Here, we demonstrate that on-line electroporation can serve as a method for membrane permeabilization for use with D-DNP in cell cultures. An electroporation apparatus hyphenated with stopped-flow sample injection permits the introduction of the hyperpolarized metabolite within 3 s after the electrical pulse. In yeast cells that do not readily take up pyruvate, the addition of the electroporation pulse to the D-DNP experiment increases the signals of the downstream metabolic products CO2 and HCO3-, which otherwise are near the detection limit, by 8.2- and 8.6-fold. Modeling of the time dependence of these signals then permits the determination of the respective kinetic rate constants. The observed conversion rate from pyruvate to CO2 normalized for cell density was found to increase by a factor of 12 due to the alleviation of the membrane transport limitation. The use of electroporation therefore extends the applicability of D-DNP to in vitro studies with a wider range of metabolites and at the same time reduces the influence of membrane transport on the observed conversion rates.
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Affiliation(s)
- Mengxiao Liu
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, TX 77843, USA
| | - Christian Hilty
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, TX 77843, USA
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21
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Brink DP, Borgström C, Tueros FG, Gorwa-Grauslund MF. Real-time monitoring of the sugar sensing in Saccharomyces cerevisiae indicates endogenous mechanisms for xylose signaling. Microb Cell Fact 2016; 15:183. [PMID: 27776527 PMCID: PMC5078928 DOI: 10.1186/s12934-016-0580-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 10/14/2016] [Indexed: 12/03/2022] Open
Abstract
Background The sugar sensing and carbon catabolite repression in Baker’s yeast Saccharomyces cerevisiae is governed by three major signaling pathways that connect carbon source recognition with transcriptional regulation. Here we present a screening method based on a non-invasive in vivo reporter system for real-time, single-cell screening of the sugar signaling state in S. cerevisiae in response to changing carbon conditions, with a main focus on the response to glucose and xylose. Results The artificial reporter system was constructed by coupling a green fluorescent protein gene (yEGFP3) downstream of endogenous yeast promoters from the Snf3p/Rgt2p, SNF1/Mig1p and cAMP/PKA signaling pathways: HXT1p/2p/4p; SUC2p, CAT8p; TPS1p/2p and TEF4p respectively. A panel of eight biosensors strains was generated by single copy chromosomal integration of the different constructs in a W303-derived strain. The signaling biosensors were validated for their functionality with flow cytometry by comparing the fluorescence intensity (FI) response in the presence of high or nearly depleted glucose to the known induction/repression conditions of the eight different promoters. The FI signal correlated with the known patterns of the selected promoters while maintaining a non-invasive property on the cellular phenotype, as was demonstrated in terms of growth, metabolites and enzyme activity. Conclusions Once verified, the sensors were used to evaluate the signaling response to varying conditions of extracellular glucose, glycerol and xylose by screening in 96-well microtiter plates. We show that these yeast strains, which do not harbor any recombinant pathways for xylose utilization, are lacking a signaling response for extracellular xylose. However, for the HXT2p/4p sensors, a shift in the flow cytometry population dynamics indicated that internalized xylose does affect the signaling. These results suggest that the previously observed effects of this pentose on the S. cerevisiae physiology and gene regulation can be attributed to xylose and not only to a lack of glucose. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0580-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel P Brink
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 22100, Lund, Sweden.
| | - Celina Borgström
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 22100, Lund, Sweden
| | - Felipe G Tueros
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 22100, Lund, Sweden
| | - Marie F Gorwa-Grauslund
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 22100, Lund, Sweden
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22
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Mülleder M, Campbell K, Matsarskaia O, Eckerstorfer F, Ralser M. Saccharomyces cerevisiae single-copy plasmids for auxotrophy compensation, multiple marker selection, and for designing metabolically cooperating communities. F1000Res 2016; 5:2351. [PMID: 27830062 PMCID: PMC5081161 DOI: 10.12688/f1000research.9606.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/16/2016] [Indexed: 01/23/2023] Open
Abstract
Auxotrophic markers are useful tools in cloning and genome editing, enable a large spectrum of genetic techniques, as well as facilitate the study of metabolite exchange interactions in microbial communities. If unused background auxotrophies are left uncomplemented however, yeast cells need to be grown in nutrient supplemented or rich growth media compositions, which precludes the analysis of biosynthetic metabolism, and which leads to a profound impact on physiology and gene expression. Here we present a series of 23 centromeric plasmids designed to restore prototrophy in typical Saccharomyces cerevisiae laboratory strains. The 23 single-copy plasmids complement for deficiencies in HIS3, LEU2, URA3, MET17 or LYS2 genes and in their combinations, to match the auxotrophic background of the popular functional-genomic yeast libraries that are based on the S288c strain. The plasmids are further suitable for designing self-establishing metabolically cooperating (SeMeCo) communities, and possess a uniform multiple cloning site to exploit multiple parallel selection markers in protein expression experiments.
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Affiliation(s)
- Michael Mülleder
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,Mill Hill Laboratory, The Francis Crick Institute, London, UK
| | - Kate Campbell
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,Chalmers University of Technology, Gothenburg, Sweden
| | - Olga Matsarskaia
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Florian Eckerstorfer
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,Mill Hill Laboratory, The Francis Crick Institute, London, UK
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23
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Bruder S, Reifenrath M, Thomik T, Boles E, Herzog K. Parallelised online biomass monitoring in shake flasks enables efficient strain and carbon source dependent growth characterisation of Saccharomyces cerevisiae. Microb Cell Fact 2016; 15:127. [PMID: 27455954 PMCID: PMC4960845 DOI: 10.1186/s12934-016-0526-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 07/18/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Baker's yeast, Saccharomyces cerevisiae, as one of the most often used workhorses in biotechnology has been developed into a huge family of application optimised strains in the last decades. Increasing numbers of strains render their characterisation highly challenging, even with the simple methods of growth-based analytics. Here we present a new sensor system for the automated, non-invasive and parallelisable monitoring of biomass in continuously shaken shake flask cultures, called CGQ ("cell growth quantifier"). The CGQ implements a dynamic approach of backscattered light measurement, allowing for efficient and accurate growth-based strain characterisation, as exemplarily demonstrated for the four most commonly used laboratory and industrial yeast strains, BY4741, W303-1A, CEN.PK2-1C and Ethanol Red. RESULTS Growth experiments revealed distinct carbon source utilisation differences between the investigated S. cerevisiae strains. Phenomena such as diauxic shifts, morphological changes and oxygen limitations were clearly observable in the growth curves. A strictly monotonic non-linear correlation of OD600 and the CGQ's backscattered light intensities was found, with strain-to-strain as well as growth-phase related differences. The CGQ measurements showed high resolution, sensitivity and smoothness even below an OD600 of 0.2 and were furthermore characterised by low background noise and signal drift in combination with high reproducibility. CONCLUSIONS With the CGQ, shake flask fermentations can be automatically monitored regarding biomass and growth rates with high resolution and parallelisation. This makes the CGQ a valuable tool for growth-based strain characterisation and development. The exceptionally high resolution allows for the identification of distinct metabolic differences and shifts as well as for morphologic changes. Applications that will benefit from that kind of automatized biomass monitoring include, amongst many others, the characterization of deregulated native or integrated heterologous pathways, the fast detection of co-fermentation as well as the realisation of rational and growth-data driven evolutionary engineering approaches.
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Affiliation(s)
- Stefan Bruder
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Mara Reifenrath
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Thomas Thomik
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Eckhard Boles
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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Alam MT, Zelezniak A, Mülleder M, Shliaha P, Schwarz R, Capuano F, Vowinckel J, Radmanesfahar E, Krüger A, Calvani E, Michel S, Börno S, Christen S, Patil KR, Timmermann B, Lilley KS, Ralser M. The metabolic background is a global player in Saccharomyces gene expression epistasis. Nat Microbiol 2016; 1:15030. [PMID: 27572163 PMCID: PMC5131842 DOI: 10.1038/nmicrobiol.2015.30] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 12/17/2015] [Indexed: 01/20/2023]
Abstract
The regulation of gene expression in response to nutrient availability is fundamental to the genotype-phenotype relationship. The metabolic-genetic make-up of the cell, as reflected in auxotrophy, is hence likely to be a determinant of gene expression. Here, we address the importance of the metabolic-genetic background by monitoring transcriptome, proteome and metabolome in a repertoire of 16 Saccharomyces cerevisiae laboratory backgrounds, combinatorially perturbed in histidine, leucine, methionine and uracil biosynthesis. The metabolic background affected up to 85% of the coding genome. Suggesting widespread confounding, these transcriptional changes show, on average, 83% overlap between unrelated auxotrophs and 35% with previously published transcriptomes generated for non-metabolic gene knockouts. Background-dependent gene expression correlated with metabolic flux and acted, predominantly through masking or suppression, on 88% of transcriptional interactions epistatically. As a consequence, the deletion of the same metabolic gene in a different background could provoke an entirely different transcriptional response. Propagating to the proteome and scaling up at the metabolome, metabolic background dependencies reveal the prevalence of metabolism-dependent epistasis at all regulatory levels. Urging a fundamental change of the prevailing laboratory practice of using auxotrophs and nutrient supplemented media, these results reveal epistatic intertwining of metabolism with gene expression on the genomic scale.
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Affiliation(s)
- Mohammad Tauqeer Alam
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Aleksej Zelezniak
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
- The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, United Kingdom
| | - Michael Mülleder
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Pavel Shliaha
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Roland Schwarz
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Floriana Capuano
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Elahe Radmanesfahar
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Antje Krüger
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin, Germany
| | - Enrica Calvani
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Steve Michel
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin, Germany
| | - Stefan Börno
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin, Germany
| | - Stefan Christen
- Department of Molecular Systems Biology, Eidgenoessische Technische Hochschule, Zurich, Switzerland
| | | | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin, Germany
| | - Kathryn S Lilley
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
- The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, United Kingdom
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25
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Targeting the Plasmodium vivax equilibrative nucleoside transporter 1 (PvENT1) for antimalarial drug development. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2015; 6:1-11. [PMID: 26862473 PMCID: PMC4706624 DOI: 10.1016/j.ijpddr.2015.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/18/2015] [Accepted: 11/25/2015] [Indexed: 11/26/2022]
Abstract
Infection with Plasmodium falciparum and vivax cause most cases of malaria. Emerging resistance to current antimalarial medications makes new drug development imperative. Ideally a new antimalarial drug should treat both falciparum and vivax malaria. Because malaria parasites are purine auxotrophic, they rely on purines imported from the host erythrocyte via Equilibrative Nucleoside Transporters (ENTs). Thus, the purine import transporters represent a potential target for antimalarial drug development. For falciparum parasites the primary purine transporter is the P. falciparum Equilibrative Nucleoside Transporter Type 1 (PfENT1). Recently we identified potent PfENT1 inhibitors with nanomolar IC50 values using a robust, yeast-based high throughput screening assay. In the current work we characterized the Plasmodium vivax ENT1 (PvENT1) homologue and its sensitivity to the PfENT1 inhibitors. We expressed a yeast codon-optimized PvENT1 gene in Saccharomyces cerevisiae. PvENT1-expressing yeast imported both purines ([3H]adenosine) and pyrimidines ([3H]uridine), whereas wild type (fui1Δ) yeast did not. Based on radiolabel substrate uptake inhibition experiments, inosine had the lowest IC50 (3.8 μM), compared to guanosine (14.9 μM) and adenosine (142 μM). For pyrimidines, thymidine had an IC50 of 183 μM (vs. cytidine and uridine; mM range). IC50 values were higher for nucleobases compared to the corresponding nucleosides; hypoxanthine had a 25-fold higher IC50 than inosine. The archetypal human ENT1 inhibitor 4-nitrobenzylthioinosine (NBMPR) had no effect on PvENT1, whereas dipyridamole inhibited PvENT1, albeit with a 40 μM IC50, a 1000-fold less sensitive than human ENT1 (hENT1). The PfENT1 inhibitors blocked transport activity of PvENT1 and the five known naturally occurring non-synonymous single nucleotide polymorphisms (SNPs) with similar IC50 values. Thus, the PfENT1 inhibitors also target PvENT1. This implies that development of novel antimalarial drugs that target both falciparum and vivax ENT1 may be feasible. PvENT1 can be functionally expressed in Saccharomyces cerevisiae. PvENT1 transports purine and pyrimidine nucleosides and nucleobases but does not transport nucleotides. PvENT1 is inhibited by recently described PfENT1 inhibitors with similar potency. Identified PvENT1 non-synonymous SNPs do not change PfENT1 inhibitor potency. Plasmodium ENTs may be feasible target for development of novel antimalarial drugs.
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Key Words
- ACT, Artemisinin-based Combination Therapies
- CQ, chloroquine
- Drug development
- EC50, concentration causing 50% of maximal effect
- ENT, equilibrative nucleoside transporter
- EV, empty vector
- HTS, high throughput screen
- IC50, concentration causing 50% inhibition
- Malaria
- NBMPR, 4-nitrobenzylthioinosine
- Nucleoside/nucleobase transport
- Parasite
- PfENT1, P. falciparum ENT type 1
- Plasmodium vivax
- Purines
- PvENT1, P. vivax ENT type 1
- SDM, synthetic defined media
- SNP, single nucleotide polymorphism
- Single-nucleotide polymorphism (SNP)
- Transporter
- WHO, World Health Organization
- WT, wild type
- hENT1, human ENT type 1
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