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Marešová A, Oravcová M, Rodríguez-López M, Hradilová M, Zemlianski V, Häsler R, Hernández P, Bähler J, Převorovský M. Critical importance of DNA binding for CSL protein functions in fission yeast. J Cell Sci 2024; 137:jcs261568. [PMID: 38482739 DOI: 10.1242/jcs.261568] [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: 08/22/2023] [Accepted: 03/07/2024] [Indexed: 05/01/2024] Open
Abstract
CSL proteins [named after the homologs CBF1 (RBP-Jκ in mice), Suppressor of Hairless and LAG-1] are conserved transcription factors found in animals and fungi. In the fission yeast Schizosaccharomyces pombe, they regulate various cellular processes, including cell cycle progression, lipid metabolism and cell adhesion. CSL proteins bind to DNA through their N-terminal Rel-like domain and central β-trefoil domain. Here, we investigated the importance of DNA binding for CSL protein functions in fission yeast. We created CSL protein mutants with disrupted DNA binding and found that the vast majority of CSL protein functions depend on intact DNA binding. Specifically, DNA binding is crucial for the regulation of cell adhesion, lipid metabolism, cell cycle progression, long non-coding RNA expression and genome integrity maintenance. Interestingly, perturbed lipid metabolism leads to chromatin structure changes, potentially linking lipid metabolism to the diverse phenotypes associated with CSL protein functions. Our study highlights the critical role of DNA binding for CSL protein functions in fission yeast.
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Affiliation(s)
- Anna Marešová
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - Martina Oravcová
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - María Rodríguez-López
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Miluše Hradilová
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czechia
| | - Viacheslav Zemlianski
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - Robert Häsler
- Center for Inflammatory Skin Diseases, Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Rosalind-Franklin-Straße 9, 24105 Kiel, Germany
| | - Pablo Hernández
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jürg Bähler
- Institute of Healthy Ageing and Department of Genetics, Evolution and Environment , University College London, Gower Street, London WC1E 6BT, UK
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
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Zhang YG, Zhang T, Lin L. Identification of Flo11-like Adhesin in Schizosaccharomyces pombe and the Mechanism of Small-Molecule Compounds Mediating Biofilm Formation in Yeasts. Microorganisms 2024; 12:358. [PMID: 38399762 PMCID: PMC10893080 DOI: 10.3390/microorganisms12020358] [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: 12/31/2023] [Revised: 02/04/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Fungal infection is initiated by the adhesion of pathogens to biotic and abiotic surfaces, with various manifestations including biofilm formation and invasive growth, etc. A previous report, though devoid of functional data, speculated that the Schizosaccharomyces pombe glycoprotein SPBPJ4664.02 could be the homology of Saccharomyces cerevisiae Flo11. Here, our studies with S. pombe substantiated the previously proposed speculation by (1) the deletion of SPBPJ4664.02 attenuated biofilm formation and invasive growth in S. pombe; (2) the S. pombe's lack of SPBPJ4664.02 could be complemented by expressing S. cerevisiae flo11. Furthermore, indole-3-acetic acid (IAA) and dodecanol were examined in S. pombe for their respective effects on biofilm formation. IAA and dodecanol at high concentrations could inhibit biofilm formation, whereas opposing effects were observed with low concentrations of these molecules. Mechanism studies with the SPBPJ4664.02Δ and SPBPJ4664.02Δ/flo11OE versus the wild type have demonstrated that IAA or dodecanol might exert regulatory effects downstream of SPBPJ4664.02 in the signaling pathway for biofilm formation. Moreover, our research extrapolated to Candida albicans has pinpointed that IAA inhibited biofilm formation at high concentrations, consistent with the transcriptional downregulation of the biofilm-related genes. Dodecanol suppressed C. albicans biofilm formation at all the concentrations tested, in accord with the downregulation of biofilm-related transcripts.
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Affiliation(s)
- Yu-Gang Zhang
- Medical School, Key Laboratory of Developmental Genes and Human Diseases (MOE), School of Life Science and Technology, Southeast University, Nanjing 210096, China;
| | - Tong Zhang
- Department of Bioengineering, Medical School, Southeast University, Nanjing 210009, China;
| | - Lan Lin
- Medical School, Key Laboratory of Developmental Genes and Human Diseases (MOE), School of Life Science and Technology, Southeast University, Nanjing 210096, China;
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Kang WH, Park YD, Lim JY, Park HM. LAMMER Kinase Governs the Expression and Cellular Localization of Gas2, a Key Regulator of Flocculation in Schizosaccharomyces pombe. J Microbiol 2024; 62:21-31. [PMID: 38180730 DOI: 10.1007/s12275-023-00097-7] [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: 07/26/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 01/06/2024]
Abstract
It was reported that LAMMER kinase in Schizosaccharomyces pombe plays an important role in cation-dependent and galactose-specific flocculation. Analogous to other flocculating yeasts, when cell wall extracts of the Δlkh1 strain were treated to the wild-type strain, it displayed flocculation. Gas2, a 1,3-β-glucanosyl transferase, was isolated from the EDTA-extracted cell-surface proteins in the Δlkh1 strain. While disruption of the gas2+ gene was not lethal and reduced the flocculation activity of the ∆lkh1 strain, the expression of a secreted form of Gas2, in which the GPI anchor addition sequences had been removed, conferred the ability to flocculate upon the WT strain. The Gas2-mediated flocculation was strongly inhibited by galactose but not by glucose. Immunostaining analysis showed that the cell surface localization of Gas2 was crucial for the flocculation of fission yeast. In addition, we identified the regulation of mbx2+ expression by Lkh1 using RT-qPCR. Taken together, we found that Lkh1 induces asexual flocculation by regulating not only the localization of Gas2 but also the transcription of gas2+ through Mbx2.
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Affiliation(s)
- Won-Hwa Kang
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
- Y-Biologics Co. Ltd., Daejeon, 34013, Republic of Korea
| | - Yoon-Dong Park
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Joo-Yeon Lim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
- Department of Microbiology and Immunology, Indiana University School of Medicine-Terre Haute, Terre Haute, IN, 47809, USA
| | - Hee-Moon Park
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea.
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Park K, Lim JY, Kim JH, Lee J, Shin S, Park HM. LAMMER Kinase Modulates Cell Cycle by Phosphorylating the MBF Repressor, Yox1, in Schizosaccharomyces pombe. MYCOBIOLOGY 2023; 51:372-378. [PMID: 37929004 PMCID: PMC10621261 DOI: 10.1080/12298093.2023.2262806] [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: 07/23/2023] [Accepted: 09/11/2023] [Indexed: 11/07/2023]
Abstract
Lkh1, a LAMMER kinase homolog in the fission yeast Schizosaccharomyces pombe, acts as a negative regulator of filamentous growth and flocculation. It is also involved in the response to oxidative stress. The lkh1-deletion mutant displays slower cell growth, shorter cell size, and abnormal DNA content compared to the wild type. These phenotypes suggest that Lkh1 controls cell size and cell cycle progression. When we performed microarray analysis using the lkh1-deletion mutant, we found that only four of the up-regulated genes in the lkh1-deletion were associated with the cell cycle. Interestingly, all of these genes are regulated by the Mlu1 cell cycle box binding factor (MBF), which is a transcription complex responsible for regulating the expression of cell cycle genes during the G1/S phase. Transcription analyses of the MBF-dependent cell-cycle genes, including negative feedback regulators, confirmed the up-regulation of these genes by the deletion of lkh1. Pull-down assay confirmed the interaction between Lkh1 and Yox1, which is a negative feedback regulator of MBF. This result supports the involvement of LAMMER kinase in cell cycle regulation by modulating MBF activity. In vitro kinase assay and NetPhosK 2.0 analysis with the Yox1T40,41A mutant allele revealed that T40 and T41 residues are the phosphorylation sites mediated by Lkh1. These sites affect the G1/S cell cycle progression of fission yeast by modulating the activity of the MBF complex.
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Affiliation(s)
- Kibum Park
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Joo-Yeon Lim
- Department of Microbiology and Immunology, Indiana University School of Medicine-Terre Haute, Terre Haute, IN, USA
| | - Je-Hoon Kim
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Jieun Lee
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Songju Shin
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Hee-Moon Park
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
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Chatfield-Reed K, Marno Jones K, Shah F, Chua G. Genetic-interaction screens uncover novel biological roles and regulators of transcription factors in fission yeast. G3 GENES|GENOMES|GENETICS 2022; 12:6655692. [PMID: 35924983 PMCID: PMC9434175 DOI: 10.1093/g3journal/jkac194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 12/05/2022]
Abstract
In Schizosaccharomyces pombe, systematic analyses of single transcription factor deletion or overexpression strains have made substantial advances in determining the biological roles and target genes of transcription factors, yet these characteristics are still relatively unknown for over a quarter of them. Moreover, the comprehensive list of proteins that regulate transcription factors remains incomplete. To further characterize Schizosaccharomyces pombe transcription factors, we performed synthetic sick/lethality and synthetic dosage lethality screens by synthetic genetic array. Examination of 2,672 transcription factor double deletion strains revealed a sick/lethality interaction frequency of 1.72%. Phenotypic analysis of these sick/lethality strains revealed potential cell cycle roles for several poorly characterized transcription factors, including SPBC56F2.05, SPCC320.03, and SPAC3C7.04. In addition, we examined synthetic dosage lethality interactions between 14 transcription factors and a miniarray of 279 deletion strains, observing a synthetic dosage lethality frequency of 4.99%, which consisted of known and novel transcription factor regulators. The miniarray contained deletions of genes that encode primarily posttranslational-modifying enzymes to identify putative upstream regulators of the transcription factor query strains. We discovered that ubiquitin ligase Ubr1 and its E2/E3-interacting protein, Mub1, degrade the glucose-responsive transcriptional repressor Scr1. Loss of ubr1+ or mub1+ increased Scr1 protein expression, which resulted in enhanced repression of flocculation through Scr1. The synthetic dosage lethality screen also captured interactions between Scr1 and 2 of its known repressors, Sds23 and Amk2, each affecting flocculation through Scr1 by influencing its nuclear localization. Our study demonstrates that sick/lethality and synthetic dosage lethality screens can be effective in uncovering novel functions and regulators of Schizosaccharomyces pombe transcription factors.
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Affiliation(s)
- Kate Chatfield-Reed
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
| | - Kurtis Marno Jones
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
| | - Farah Shah
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
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Sanchez AM, Garg A, Shuman S, Schwer B. Inositol pyrophosphates impact phosphate homeostasis via modulation of RNA 3' processing and transcription termination. Nucleic Acids Res 2019; 47:8452-8469. [PMID: 31276588 PMCID: PMC6895273 DOI: 10.1093/nar/gkz567] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/10/2019] [Accepted: 07/03/2019] [Indexed: 12/24/2022] Open
Abstract
Fission yeast phosphate acquisition genes pho1, pho84, and tgp1 are repressed in phosphate-rich medium by transcription of upstream lncRNAs. Here, we show that phosphate homeostasis is subject to metabolite control by inositol pyrophosphates (IPPs), exerted through the 3'-processing/termination machinery and the Pol2 CTD code. Increasing IP8 (via Asp1 IPP pyrophosphatase mutation) de-represses the PHO regulon and leads to precocious termination of prt lncRNA synthesis. pho1 de-repression by IP8 depends on cleavage-polyadenylation factor (CPF) subunits, termination factor Rhn1, and the Thr4 letter of the CTD code. pho1 de-repression by mutation of the Ser7 CTD letter depends on IP8. Simultaneous inactivation of the Asp1 and Aps1 IPP pyrophosphatases is lethal, but this lethality is suppressed by mutations of CPF subunits Ppn1, Swd22, Ssu72, and Ctf1 and CTD mutation T4A. Failure to synthesize IP8 (via Asp1 IPP kinase mutation) results in pho1 hyper-repression. Synthetic lethality of asp1Δ with Ppn1, Swd22, and Ssu72 mutations argues that IP8 plays an important role in essential 3'-processing/termination events, albeit in a manner genetically redundant to CPF. Transcriptional profiling delineates an IPP-responsive regulon composed of genes overexpressed when IP8 levels are increased. Our results establish a novel role for IPPs in cell physiology.
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Affiliation(s)
- Ana M Sanchez
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Angad Garg
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
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7
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Su Y, Chen J, Huang Y. Disruption of ppr3, ppr4, ppr6 or ppr10 induces flocculation and filamentous growth in Schizosaccharomyces pombe. FEMS Microbiol Lett 2019; 365:5033677. [PMID: 29878109 DOI: 10.1093/femsle/fny141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 06/05/2018] [Indexed: 11/14/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are major players in mitochondrial and chloroplast RNA metabolism, which is essential for normal organellar function. The fission yeast Schizosaccharomyces pombe has 10 PPR proteins. We have previously reported that loss of ppr3, ppr4, ppr6 or ppr10 perturbs iron homeostasis leading to accumulation of reactive oxygen species and apoptotic cell death. In the present study, we show that loss of ppr3, ppr4, ppr6 or ppr10 can cause non-sexual flocculation and filamentous growth of cells. Furthermore, expression of a number of genes encoding cell-surface flocculins and cell wall-remodeling enzymes are induced in these ppr-deletion mutants. We also show that Δppr10 cells, and, to a lesser extent, Δppr4 and Δppr6 cells, exhibited increased tolerance to H2O2 toxicity compared with the wild-type strain. Finally, we found that overexpression of genes involved in iron uptake and/or iron homeostasis could cause the flocculation of wild-type cells. Our findings suggest that an elevated level of intracellular iron in the mutant caused by loss of ppr3, ppr4, ppr6 or ppr10 may result in flocculation and filamentous growth in S. pombe.
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Affiliation(s)
- Yang Su
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jie Chen
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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Katz ME. Nutrient sensing-the key to fungal p53-like transcription factors? Fungal Genet Biol 2018; 124:8-16. [PMID: 30579885 DOI: 10.1016/j.fgb.2018.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/12/2018] [Accepted: 12/18/2018] [Indexed: 02/02/2023]
Abstract
The mammalian tumour suppressor protein, p53, plays an important role in cell cycle control, DNA repair and apoptotic cell death. Transcription factors belonging to the "p53-like" superfamily are found exclusively in the Amorphea branch of eukaryotes, which includes animals, fungi and slime molds. Many members of the p53-like superfamily (proteins containing p53, Rel/Dorsal, T-box, STAT, Runt, Ndt80, and the CSL DNA-binding domains) are involved in development. Two families of p53-like proteins (Ndt80 and CSL) are widespread in fungi as well as animals. The Basidiomycetes and the Ascomycetes have undergone reciprocal loss of the Ndt80 and CSL classes of transcription factors, with the CSL class preserved in only one branch of Ascomycetes and the Ndt80 class found in only one branch of Basidiomycetes. Recent studies have greatly expanded the known functions of fungal Ndt80-like proteins and shown that they play important roles in sexual reproduction, cell death, N-acetylglucosamine sensing and catabolism, secondary metabolism, and production of extracellular hydrolases such as proteases, chitinases and cellulases. In the opportunistic pathogen, Candida albicans, Ndt80-like proteins are essential for hyphal growth and virulence and also play a role in antifungal resistance. These recent studies have confirmed that nutrient sensing is a common feature of fungal Ndt80-like proteins and is also found in fungal CSL-like transcription factors, which in animals is the mediator of Notch signalling. Thus, nutrient sensing may represent the ancestral role of the p53-like superfamily.
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Affiliation(s)
- Margaret E Katz
- Molecular and Cellular Biology, University of New England, Armidale, NSW 2351, Australia.
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Zach R, Tvarůžková J, Schätz M, Ťupa O, Grallert B, Převorovský M. Mitotic defects in fission yeast lipid metabolism 'cut' mutants are suppressed by ammonium chloride. FEMS Yeast Res 2018; 18:5040229. [PMID: 29931271 PMCID: PMC6037054 DOI: 10.1093/femsyr/foy064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/15/2018] [Indexed: 01/01/2023] Open
Abstract
Fission yeast 'cut' mutants show defects in temporal coordination of nuclear division with cytokinesis, resulting in aberrant mitosis and lethality. Among other causes, the 'cut' phenotype can be triggered by genetic or chemical perturbation of lipid metabolism, supposedly resulting in shortage of membrane phospholipids and insufficient nuclear envelope expansion during anaphase. Interestingly, penetrance of the 'cut' phenotype in mutants of the transcription factor cbf11 and acetyl-coenzyme A carboxylase cut6, both related to lipid metabolism, is highly dependent on growth media, although the specific nutrient(s) affecting 'cut' occurrence is not known. In this study, we set out to identify the growth media component(s) responsible for 'cut' phenotype suppression in Δcbf11 and cut6-621 cells. We show that mitotic defects occur rapidly in Δcbf11 cells upon shift from the minimal EMM medium ('cut' suppressing) to the complex YES medium ('cut' promoting). By growing cells in YES medium supplemented with individual EMM components, we identified ammonium chloride, an efficiently utilized nitrogen source, as a specific and potent suppressor of the 'cut' phenotype in both Δcbf11 and cut6-621. Furthermore, we found that ammonium chloride boosts lipid droplet formation in wild-type cells. Our findings suggest a possible involvement of nutrient-responsive signaling in 'cut' suppression.
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Affiliation(s)
- Róbert Zach
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jarmila Tvarůžková
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Schätz
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Computing and Control Engineering, University of Chemistry and Technology, Prague, Czech Republic
| | - Ondřej Ťupa
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Computing and Control Engineering, University of Chemistry and Technology, Prague, Czech Republic
| | - Beáta Grallert
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
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Burr R, Ribbens D, Raychaudhuri S, Stewart EV, Ho J, Espenshade PJ. Dsc E3 ligase localization to the Golgi requires the ATPase Cdc48 and cofactor Ufd1 for activation of sterol regulatory element-binding protein in fission yeast. J Biol Chem 2017; 292:16333-16350. [PMID: 28821619 DOI: 10.1074/jbc.m117.802025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/08/2017] [Indexed: 11/06/2022] Open
Abstract
Sterol regulatory element-binding proteins (SREBPs) in the fission yeast Schizosaccharomyces pombe regulate lipid homeostasis and the hypoxic response under conditions of low sterol or oxygen availability. SREBPs are cleaved in the Golgi through the combined action of the Dsc E3 ligase complex, the rhomboid protease Rbd2, and the essential ATPases associated with diverse cellular activities (AAA+) ATPase Cdc48. The soluble SREBP N-terminal transcription factor domain is then released into the cytosol to enter the nucleus and regulate gene expression. Previously, we reported that Cdc48 binding to Rbd2 is required for Rbd2-mediated SREBP cleavage. Here, using affinity chromatography and mass spectrometry experiments, we identified Cdc48-binding proteins in S. pombe, generating a list of many previously unknown potential Cdc48-binding partners. We show that the established Cdc48 cofactor Ufd1 is required for SREBP cleavage but does not interact with the Cdc48-Rbd2 complex. Cdc48-Ufd1 is instead required at a step prior to Rbd2 function, during Golgi localization of the Dsc E3 ligase complex. Together, these findings demonstrate that two distinct Cdc48 complexes, Cdc48-Ufd1 and Cdc48-Rbd2, are required for SREBP activation and low-oxygen adaptation in S. pombe.
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Affiliation(s)
- Risa Burr
- From the Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Diedre Ribbens
- From the Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Sumana Raychaudhuri
- From the Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Emerson V Stewart
- From the Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Jason Ho
- From the Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Peter J Espenshade
- From the Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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11
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Su Y, Yang Y, Huang Y. Loss of ppr3, ppr4, ppr6, or ppr10 perturbs iron homeostasis and leads to apoptotic cell death in Schizosaccharomyces pombe. FEBS J 2017; 284:324-337. [PMID: 27886462 DOI: 10.1111/febs.13978] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/19/2016] [Accepted: 11/23/2016] [Indexed: 12/31/2022]
Abstract
Pentatricopeptide repeat (PPR) proteins characterized by tandem arrays of a degenerate 35-amino-acid repeat belong to a large family of RNA-binding proteins that are involved in post-transcriptional control of organelle gene expression. PPR proteins are ubiquitous in eukaryotes, and particularly prevalent in higher plants. Schizosaccharomyces pombe has 10 PPR proteins. Among them, ppr3, ppr4, ppr6, and ppr10 participate in mitochondrial post-transcriptional processes and are required for mitochondrial electron transport chain (ETC) function. In the present work, we showed that deletion of ppr3, ppr4, ppr6, or ppr10 led to apoptotic cell death, as revealed by DAPI and Annexin V-FITC staining. These mutants also exhibited elevated levels of reactive oxygen species (ROS). RNA sequencing (RNA-seq) and quantitative RT-PCR analyses revealed that deletion of ppr10 affected critical biological processes. In particular, a core set of genes involved in iron uptake and/or iron homeostasis was elevated in the Δppr10 mutant, suggesting an elevated level of intracellular iron in the mutant. Consistent with this notion, Δppr3, Δppr4, Δppr6, and Δppr10 mutants exhibited increased sensitivity to iron. Furthermore, the iron chelator, bathophenanthroline disulfonic acid, but not the calcium chelator EGTA, nearly restored the viabilities of Δppr3, Δppr4, Δppr6, and Δppr10 mutants, and reduced ROS levels in the mutants. These results show for the first time that deletion of a ppr gene leads to perturbation of iron homeostasis. Our results also suggest that disrupted iron homeostasis in Δppr3, Δppr4, Δppr6, and Δppr10 mutants may lead to an increase in the level of ROS and induction of apoptotic cell death in S. pombe. DATABASE The RNA-seq data have been deposited in the National Center for Biotechnology Information (NCBI) BioProject database (accession number SRP091623) and Gene Expression Omnibus (GEO) database (accession number GSE90144).
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Affiliation(s)
- Yang Su
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, China
| | - Yanmei Yang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, China
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, China
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Copley RR. The Unicellular Ancestry of Groucho-Mediated Repression and the Origins of Metazoan Transcription Factors. Genome Biol Evol 2016; 8:1859-67. [PMID: 27189982 PMCID: PMC4943189 DOI: 10.1093/gbe/evw118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Groucho is a co-repressor that interacts with many transcription factors playing a crucial role in animal development. The evolutionary origins of Groucho are not clear. It is generally regarded as being a distinct animal-specific protein, although with similarities to the yeast Tup-like proteins. Here, it is shown that Groucho has true orthologs in unicellular relatives of animals. Based on their phylogenetic distribution, and an analysis of ligand-binding residues, these genes are unlikely to be orthologs of the fungal Tup-like genes. By identifying conserved candidate Groucho interaction motifs (GIMs) in nonmetazoan transcription factors, it is demonstrated that the details of molecular interactions between Groucho and transcription factors are likely to have been established prior to the origin of animals, but that the association of GIMs with many transcription factor types can be regarded as a metazoan innovation.
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Affiliation(s)
- Richard R Copley
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 181 chemin du Lazaret, 06230 Villefranche-sur-mer, France
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13
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Binding Sites in the EFG1 Promoter for Transcription Factors in a Proposed Regulatory Network: A Functional Analysis in the White and Opaque Phases of Candida albicans. G3-GENES GENOMES GENETICS 2016; 6:1725-37. [PMID: 27172219 PMCID: PMC4889668 DOI: 10.1534/g3.116.029785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In Candida albicans the transcription factor Efg1, which is differentially expressed in the white phase of the white-opaque transition, is essential for expression of the white phenotype. It is one of six transcription factors included in a proposed interactive transcription network regulating white-opaque switching and maintenance of the alternative phenotypes. Ten sites were identified in the EFG1 promoter that differentially bind one or more of the network transcription factors in the white and/or opaque phase. To explore the functionality of these binding sites in the differential expression of EFG1, we generated targeted deletions of each of the 10 binding sites, combinatorial deletions, and regional deletions using a Renillareniformis luciferase reporter system. Individually targeted deletion of only four of the 10 sites had minor effects consistent with differential expression of EFG1, and only in the opaque phase. Alternative explanations are considered.
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14
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Chatfield-Reed K, Vachon L, Kwon EJG, Chua G. Conserved and Diverged Functions of the Calcineurin-Activated Prz1 Transcription Factor in Fission Yeast. Genetics 2016; 202:1365-75. [PMID: 26896331 PMCID: PMC4905549 DOI: 10.1534/genetics.115.184218] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/10/2016] [Indexed: 11/23/2022] Open
Abstract
Gene regulation in response to intracellular calcium is mediated by the calcineurin-activated transcription factor Prz1 in the fission yeast Schizosaccharomyces pombe Genome-wide studies of the Crz1 and CrzA fungal orthologs have uncovered numerous target genes involved in conserved and species-specific cellular processes. In contrast, very few target genes of Prz1 have been published. This article identifies an extensive list of genes using transcriptome and ChIP-chip analyses under inducing conditions of Prz1, including CaCl2 and tunicamycin treatment, as well as a ∆pmr1 genetic background. We identified 165 upregulated putative target genes of Prz1 in which the majority contained a calcium-dependent response element in their promoters, similar to that of the Saccharomyces cerevisiae ortholog Crz1 These genes were functionally enriched for Crz1-conserved processes such as cell-wall biosynthesis. Overexpression of prz1(+)increased resistance to the cell-wall degradation enzyme zymolyase, likely from upregulation of theO-mannosyltransferase encoding gene omh1(+) Loss of omh1(+)abrogates this phenotype. We uncovered a novel inhibitory role in flocculation for Prz1. Loss of prz1(+)resulted in constitutive flocculation and upregulation of genes encoding the flocculins Gsf2 and Pfl3, as well as the transcription factor Cbf12. The constitutive flocculation of the ∆prz1 strain was abrogated by the loss of gsf2(+) or cbf12(+) This study reveals that Prz1 functions as a positive and negative transcriptional regulator of genes involved in cell-wall biosynthesis and flocculation, respectively. Moreover, comparison of target genes between Crz1/CrzA and Prz1 indicate some conservation in DNA-binding specificity, but also substantial rewiring of the calcineurin-mediated transcriptional regulatory network.
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Affiliation(s)
- Kate Chatfield-Reed
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Lianne Vachon
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Eun-Joo Gina Kwon
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Gordon Chua
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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15
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Quesnel DM, Oldenburg TBP, Larter SR, Gieg LM, Chua G. Biostimulation of Oil Sands Process-Affected Water with Phosphate Yields Removal of Sulfur-Containing Organics and Detoxification. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:13012-13020. [PMID: 26448451 DOI: 10.1021/acs.est.5b01391] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The ability to mitigate toxicity of oil sands process-affected water (OSPW) for return into the environment is an important issue for effective tailings management in Alberta, Canada. OSPW toxicity has been linked to classical naphthenic acids (NAs), but the toxic contribution of other acid-extractable organics (AEOs) remains unknown. Here, we examine the potential for in situ bioremediation of OSPW AEOs by indigenous algae. Phosphate biostimulation was performed in OSPW to promote the growth of indigenous photosynthetic microorganisms and subsequent toxicity and chemical changes were determined. After 12 weeks, the AEO fraction of phosphate-biostimulated OSPW was significantly less toxic to the fission yeast Schizosaccharomyces pombe than unstimulated OSPW. Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) analysis of the AEO fraction in phosphate-biostimulated OSPW showed decreased levels of SO3 class compounds, including a subset that may represent linear arylsulfonates. A screen with S. pombe transcription factor mutant strains for growth sensitivity to the AEO fraction or sodium dodecylbenzenesulfonate revealed a mode of toxic action consistent with oxidative stress and detrimental effects on cellular membranes. These findings demonstrate a potential algal-based in situ bioremediation strategy for OSPW AEOs and uncover a link between toxicity and AEOs other than classical NAs.
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Affiliation(s)
- Dean M Quesnel
- Department of Biological Sciences, and ‡PRG, Department of Geosciences, University of Calgary , 2500 University Drive NW, Calgary, Alberta Canada T2N 1N4
| | - Thomas B P Oldenburg
- Department of Biological Sciences, and ‡PRG, Department of Geosciences, University of Calgary , 2500 University Drive NW, Calgary, Alberta Canada T2N 1N4
| | - Stephen R Larter
- Department of Biological Sciences, and ‡PRG, Department of Geosciences, University of Calgary , 2500 University Drive NW, Calgary, Alberta Canada T2N 1N4
| | - Lisa M Gieg
- Department of Biological Sciences, and ‡PRG, Department of Geosciences, University of Calgary , 2500 University Drive NW, Calgary, Alberta Canada T2N 1N4
| | - Gordon Chua
- Department of Biological Sciences, and ‡PRG, Department of Geosciences, University of Calgary , 2500 University Drive NW, Calgary, Alberta Canada T2N 1N4
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16
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Převorovský M, Oravcová M, Tvarůžková J, Zach R, Folk P, Půta F, Bähler J. Fission Yeast CSL Transcription Factors: Mapping Their Target Genes and Biological Roles. PLoS One 2015; 10:e0137820. [PMID: 26366556 PMCID: PMC4569565 DOI: 10.1371/journal.pone.0137820] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 08/24/2015] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Cbf11 and Cbf12, the fission yeast CSL transcription factors, have been implicated in the regulation of cell-cycle progression, but no specific roles have been described and their target genes have been only partially mapped. METHODOLOGY/PRINCIPAL FINDINGS Using a combination of transcriptome profiling under various conditions and genome-wide analysis of CSL-DNA interactions, we identify genes regulated directly and indirectly by CSL proteins in fission yeast. We show that the expression of stress-response genes and genes that are expressed periodically during the cell cycle is deregulated upon genetic manipulation of cbf11 and/or cbf12. Accordingly, the coordination of mitosis and cytokinesis is perturbed in cells with genetically manipulated CSL protein levels, together with other specific defects in cell-cycle progression. Cbf11 activity is nutrient-dependent and Δcbf11-associated defects are mitigated by inactivation of the protein kinase A (Pka1) and stress-activated MAP kinase (Sty1p38) pathways. Furthermore, Cbf11 directly regulates a set of lipid metabolism genes and Δcbf11 cells feature a stark decrease in the number of storage lipid droplets. CONCLUSIONS/SIGNIFICANCE Our results provide a framework for a more detailed understanding of the role of CSL proteins in the regulation of cell-cycle progression in fission yeast.
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Affiliation(s)
- Martin Převorovský
- Research Department of Genetics, Evolution & Environment and UCL Cancer Institute, University College London, London, United Kingdom
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Martina Oravcová
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Jarmila Tvarůžková
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Róbert Zach
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Petr Folk
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - František Půta
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Jürg Bähler
- Research Department of Genetics, Evolution & Environment and UCL Cancer Institute, University College London, London, United Kingdom
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17
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The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe. Genetics 2015; 201:737-44. [PMID: 26265703 DOI: 10.1534/genetics.115.177329] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 07/30/2015] [Indexed: 02/07/2023] Open
Abstract
The rate at which new mutations arise in the genome is a key factor in the evolution and adaptation of species. Here we describe the rate and spectrum of spontaneous mutations for the fission yeast Schizosaccharomyces pombe, a key model organism with many similarities to higher eukaryotes. We undertook an ∼1700-generation mutation accumulation (MA) experiment with a haploid S. pombe, generating 422 single-base substitutions and 119 insertion-deletion mutations (indels) across the 96 replicates. This equates to a base-substitution mutation rate of 2.00 × 10(-10) mutations per site per generation, similar to that reported for the distantly related budding yeast Saccharomyces cerevisiae. However, these two yeast species differ dramatically in their spectrum of base substitutions, the types of indels (S. pombe is more prone to insertions), and the pattern of selection required to counteract a strong AT-biased mutation rate. Overall, our results indicate that GC-biased gene conversion does not play a major role in shaping the nucleotide composition of the S. pombe genome and suggest that the mechanisms of DNA maintenance may have diverged significantly between fission and budding yeasts. Unexpectedly, CpG sites appear to be excessively liable to mutation in both species despite the likely absence of DNA methylation.
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18
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Matsuda A, Chikashige Y, Ding DQ, Ohtsuki C, Mori C, Asakawa H, Kimura H, Haraguchi T, Hiraoka Y. Highly condensed chromatins are formed adjacent to subtelomeric and decondensed silent chromatin in fission yeast. Nat Commun 2015; 6:7753. [PMID: 26205977 PMCID: PMC4525289 DOI: 10.1038/ncomms8753] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 06/08/2015] [Indexed: 11/09/2022] Open
Abstract
It is generally believed that silent chromatin is condensed and transcriptionally active chromatin is decondensed. However, little is known about the relationship between the condensation levels and gene expression. Here we report the condensation levels of interphase chromatin in the fission yeast Schizosaccharomyces pombe examined by super-resolution fluorescence microscopy. Unexpectedly, silent chromatin is less condensed than the euchromatin. Furthermore, the telomeric silent regions are flanked by highly condensed chromatin bodies, or 'knobs'. Knob regions span ∼50 kb of sequence devoid of methylated histones. Knob condensation is independent of HP1 homologue Swi6 and other gene silencing factors. Disruption of methylation at lysine 36 of histone H3 (H3K36) eliminates knob formation and gene repression at the subtelomeric and adjacent knob regions. Thus, epigenetic marks at H3K36 play crucial roles in the formation of a unique chromatin structure and in gene regulation at those regions in S. pombe.
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Affiliation(s)
- Atsushi Matsuda
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2, Iwaoka, Iwaoka-cho, Kobe 651-2492, Japan
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Yuji Chikashige
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2, Iwaoka, Iwaoka-cho, Kobe 651-2492, Japan
| | - Da-Qiao Ding
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2, Iwaoka, Iwaoka-cho, Kobe 651-2492, Japan
| | - Chizuru Ohtsuki
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Chie Mori
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2, Iwaoka, Iwaoka-cho, Kobe 651-2492, Japan
| | - Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Hiroshi Kimura
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B, Nagatsuda, Yokohama 226-8501, Japan
| | - Tokuko Haraguchi
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2, Iwaoka, Iwaoka-cho, Kobe 651-2492, Japan
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Yasushi Hiraoka
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2, Iwaoka, Iwaoka-cho, Kobe 651-2492, Japan
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
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19
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Jeffares DC, Rallis C, Rieux A, Speed D, Převorovský M, Mourier T, Marsellach FX, Iqbal Z, Lau W, Cheng TM, Pracana R, Mülleder M, Lawson JL, Chessel A, Bala S, Hellenthal G, O’Fallon B, Keane T, Simpson JT, Bischof L, Tomiczek B, Bitton DA, Sideri T, Codlin S, Hellberg JE, van Trigt L, Jeffery L, Li JJ, Atkinson S, Thodberg M, Febrer M, McLay K, Drou N, Brown W, Hayles J, Carazo Salas RE, Ralser M, Maniatis N, Balding DJ, Balloux F, Durbin R, Bähler J. The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nat Genet 2015; 47:235-41. [PMID: 25665008 PMCID: PMC4645456 DOI: 10.1038/ng.3215] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 01/14/2015] [Indexed: 12/14/2022]
Abstract
Natural variation within species reveals aspects of genome evolution and function. The fission yeast Schizosaccharomyces pombe is an important model for eukaryotic biology, but researchers typically use one standard laboratory strain. To extend the usefulness of this model, we surveyed the genomic and phenotypic variation in 161 natural isolates. We sequenced the genomes of all strains, finding moderate genetic diversity (π = 3 × 10(-3) substitutions/site) and weak global population structure. We estimate that dispersal of S. pombe began during human antiquity (∼340 BCE), and ancestors of these strains reached the Americas at ∼1623 CE. We quantified 74 traits, finding substantial heritable phenotypic diversity. We conducted 223 genome-wide association studies, with 89 traits showing at least one association. The most significant variant for each trait explained 22% of the phenotypic variance on average, with indels having larger effects than SNPs. This analysis represents a rich resource to examine genotype-phenotype relationships in a tractable model.
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Affiliation(s)
- Daniel C. Jeffares
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Charalampos Rallis
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Adrien Rieux
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Doug Speed
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Martin Převorovský
- Department of Cell Biology, Charles University in Prague, Prague, Czech Republic
| | - Tobias Mourier
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Winston Lau
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Tammy M.K. Cheng
- Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Rodrigo Pracana
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Michael Mülleder
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jonathan L.D. Lawson
- Department of Genetics, University of Cambridge, Cambridge, UK
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Anatole Chessel
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Sendu Bala
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Garrett Hellenthal
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | | | | | | | - Leanne Bischof
- CSIRO Mathematics, Informatics and Statistics, North Ryde, Australia; The Genome Analysis Centre, Norwich, UK
| | - Bartlomiej Tomiczek
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Danny A. Bitton
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Theodora Sideri
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Sandra Codlin
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | | | - Laurent van Trigt
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Linda Jeffery
- Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Juan-Juan Li
- Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Sophie Atkinson
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Malte Thodberg
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Melanie Febrer
- CSIRO Mathematics, Informatics and Statistics, North Ryde, Australia; The Genome Analysis Centre, Norwich, UK
| | - Kirsten McLay
- CSIRO Mathematics, Informatics and Statistics, North Ryde, Australia; The Genome Analysis Centre, Norwich, UK
| | - Nizar Drou
- CSIRO Mathematics, Informatics and Statistics, North Ryde, Australia; The Genome Analysis Centre, Norwich, UK
| | - William Brown
- Centre for Genetics and Genomics, The University of Nottingham, Nottingham, UK
| | - Jacqueline Hayles
- Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Rafael E. Carazo Salas
- Department of Genetics, University of Cambridge, Cambridge, UK
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Division of Physiology and Metabolism, MRC National Institute for Medical Research, London, UK
| | - Nikolas Maniatis
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - David J. Balding
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Francois Balloux
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | | | - Jürg Bähler
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
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20
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The NuA4 complex promotes translesion synthesis (TLS)-mediated DNA damage tolerance. Genetics 2015; 199:1065-76. [PMID: 25701288 DOI: 10.1534/genetics.115.174490] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 02/13/2015] [Indexed: 01/01/2023] Open
Abstract
Lesions in DNA can block replication fork progression, leading to its collapse and gross chromosomal rearrangements. To circumvent such outcomes, the DNA damage tolerance (DDT) pathway becomes engaged, allowing the replisome to bypass a lesion and complete S phase. Chromatin remodeling complexes have been implicated in the DDT pathways, and here we identify the NuA4 remodeler, which is a histone acetyltransferase, to function on the translesion synthesis (TLS) branch of DDT. Genetic analyses in Saccharomyces cerevisiae showed synergistic sensitivity to MMS when NuA4 alleles, esa1-L254P and yng2Δ, were combined with the error-free bypass mutant ubc13Δ. The loss of viability was less pronounced when NuA4 complex mutants were disrupted in combination with error-prone/TLS factors, such as rev3Δ, suggesting an epistatic relationship between NuA4 and error-prone bypass. Consistent with cellular viability measurements, replication profiles after exposure to MMS indicated that small regions of unreplicated DNA or damage were present to a greater extent in esa1-L254P/ubc13Δ mutants, which persist beyond the completion of bulk replication compared to esa1-L254P/rev3Δ. The critical role of NuA4 in error-prone bypass is functional even after the bulk of replication is complete. Underscoring this observation, when Yng2 expression is restricted specifically to G2/M of the cell cycle, viability and TLS-dependent mutagenesis rates were restored. Lastly, disruption of HTZ1, which is a target of NuA4, also resulted in mutagenic rates of reversion on level with esa1-L254P and yng2Δ mutants, indicating that the histone variant H2A.Z functions in vivo on the TLS branch of DDT.
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21
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Systematic genetic analysis of transcription factors to map the fission yeast transcription-regulatory network. Biochem Soc Trans 2013; 41:1696-700. [DOI: 10.1042/bst20130224] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mapping transcriptional-regulatory networks requires the identification of target genes, binding specificities and signalling pathways of transcription factors. However, the characterization of each transcription factor sufficiently for deciphering such networks remains laborious. The recent availability of overexpression and deletion strains for almost all of the transcription factor genes in the fission yeast Schizosaccharomyces pombe provides a valuable resource to better investigate transcription factors using systematic genetics. In the present paper, I review and discuss the utility of these strain collections combined with transcriptome profiling and genome-wide chromatin immunoprecipitation to identify the target genes of transcription factors.
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22
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Farzadfard F, Perli SD, Lu TK. Tunable and multifunctional eukaryotic transcription factors based on CRISPR/Cas. ACS Synth Biol 2013; 2:604-13. [PMID: 23977949 PMCID: PMC3805333 DOI: 10.1021/sb400081r] [Citation(s) in RCA: 270] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Transcriptional regulation is central
to the complex behavior of
natural biological systems and synthetic gene circuits. Platforms
for the scalable, tunable, and simple modulation of transcription
would enable new abilities to study natural systems and implement
artificial capabilities in living cells. Previous approaches to synthetic
transcriptional regulation have relied on engineering DNA-binding
proteins, which necessitate multistep processes for construction and
optimization of function. Here, we show that the CRISPR/Cas system
of Streptococcus pyogenes can be programmed
to direct both activation and repression to natural and artificial
eukaryotic promoters through the simple engineering of guide RNAs
with base-pairing complementarity to target DNA sites. We demonstrate
that the activity of CRISPR-based transcription factors (crisprTFs)
can be tuned by directing multiple crisprTFs to different positions
in natural promoters and by arraying multiple crisprTF-binding sites
in the context of synthetic promoters in yeast and human cells. Furthermore,
externally controllable regulatory modules can be engineered by layering
gRNAs with small molecule-responsive proteins. Additionally, single
nucleotide substitutions within promoters are sufficient to render
them orthogonal with respect to the same gRNA-guided crisprTF. We
envision that CRISPR-based eukaryotic gene regulation will enable
the facile construction of scalable synthetic gene circuits and open
up new approaches for mapping natural gene networks and their effects
on complex cellular phenotypes.
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Affiliation(s)
- Fahim Farzadfard
- Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- MIT Synthetic Biology Center, 500 Technology Square, Cambridge, Massachusetts 02139, United States
- MIT Microbiology
Program, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Samuel D. Perli
- Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- MIT Synthetic Biology Center, 500 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Timothy K. Lu
- Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- MIT Synthetic Biology Center, 500 Technology Square, Cambridge, Massachusetts 02139, United States
- MIT Microbiology
Program, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Biophysics Program, Harvard University, Cambridge, Massachusetts 02139, United States
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23
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Abstract
In Schizosaccharomyces pombe, over 90% of transcription factor genes are nonessential. Moreover, the majority do not exhibit significant growth defects under optimal conditions when deleted, complicating their functional characterization and target gene identification. Here, we systematically overexpressed 99 transcription factor genes with the nmt1 promoter and found that 64 transcription factor genes exhibited reduced fitness when ectopically expressed. Cell cycle defects were also often observed. We further investigated three uncharacterized transcription factor genes (toe1(+)-toe3(+)) that displayed cell elongation when overexpressed. Ectopic expression of toe1(+) resulted in a G1 delay while toe2(+) and toe3(+) overexpression produced an accumulation of septated cells with abnormalities in septum formation and nuclear segregation, respectively. Transcriptome profiling and ChIP-chip analysis of the transcription factor overexpression strains indicated that Toe1 activates target genes of the pyrimidine-salvage pathway, while Toe3 regulates target genes involved in polyamine synthesis. We also found that ectopic expression of the putative target genes SPBC3H7.05c, and dad5(+) and SPAC11D3.06 could recapitulate the cell cycle phenotypes of toe2(+) and toe3(+) overexpression, respectively. Furthermore, single deletions of the putative target genes urg2(+) and SPAC1399.04c, and SPBC3H7.05c, SPACUNK4.15, and rds1(+), could suppress the phenotypes of toe1(+) and toe2(+) overexpression, respectively. This study implicates new transcription factors and metabolism genes in cell cycle regulation and demonstrates the potential of systematic overexpression analysis to elucidate the function and target genes of transcription factors in S. pombe.
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Matsuzawa T, Kageyama Y, Ooishi K, Kawamukai M, Takegawa K. The zinc finger protein Gsf1 regulates Gsf2-dependent flocculation in fission yeast. FEMS Yeast Res 2013; 13:259-66. [PMID: 23311928 DOI: 10.1111/1567-1364.12029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 12/15/2012] [Accepted: 01/01/2013] [Indexed: 11/30/2022] Open
Abstract
Fission yeast flocculates nonsexually by induction of the flocculin encoded by gsf2(+) which is controlled by the positive regulator Mbx2. Here, we report a novel gene designated gsf1(+) found to be a negative regulator of nonsexual flocculation. We identified gsf1(+) as a multicopy suppressor of a sam2 mutation, which caused growth sensitivity to Ca(2+) and also found a nonsense mutation in gsf1(+) in a previously isolated gsf1 mutant. The gsf1(+) gene encodes a 547-aa protein containing a Zn(2)-Cys(6) binuclear cluster-type zinc finger motif. The Gsf1 protein localized in the nucleus, consistent with a role as a transcription factor. Deletion of gsf1(+) resulted in nonsexual flocculation inducible by CaCl2 , which was suppressed by the addition of EDTA or galactose. Both gsf2(+) and mbx2(+) were highly expressed in the gsf1 mutant. gsf1∆ gsf2∆ and gsf1∆ mbx2∆ double mutants did not flocculate, suggesting that gsf1(+) is an upstream regulator. In addition, the gsf1 mutant was sensitive to CaCl2 , KCl, HU, and TBZ, consistent with the possibility that gsf1(+) plays a role in functions unrelated to flocculation. Taken together, these results suggest that nonsexual flocculation in fission yeast is negatively controlled by Gsf1, which controls expression of mbx2(+) and gsf2(+) .
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Affiliation(s)
- Tomohiko Matsuzawa
- Department of Bioscience & Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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