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Kumawat R, Tomar RS. Dissecting the role of mitogen-activated protein kinase Hog1 in yeast flocculation. FEBS J 2024; 291:3080-3103. [PMID: 38648231 DOI: 10.1111/febs.17137] [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: 09/20/2023] [Revised: 01/25/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024]
Abstract
Living organisms are frequently exposed to multiple biotic and abiotic stress forms during their lifetime. Organisms cope with stress conditions by regulating their gene expression programs. In response to different environmental stress conditions, yeast cells activate different tolerance mechanisms, many of which share common signaling pathways. Flocculation is one of the key mechanisms underlying yeast survival under unfavorable environmental conditions, and the Tup1-Cyc8 corepressor complex is a major regulator of this process. Additionally, yeast cells can utilize different mitogen-activated protein kinase (MAPK) pathways to modulate gene expression during stress conditions. Here, we show that the high osmolarity glycerol (HOG) MAPK pathway is involved in the regulation of yeast flocculation. We observed that the HOG MAPK pathway was constitutively activated in flocculating cells, and found that the interaction between phosphorylated Hog1 and the FLO genes promoter region increased significantly upon sodium chloride exposure. We found that treatment of cells with cantharidin decreased Hog1 phosphorylation, causing a sharp reduction in the expression of FLO genes and the flocculation phenotype. Similarly, deletion of HOG1 in yeast cells reduced flocculation. Altogether, our results suggest a role for HOG MAPK signaling in the regulation of FLO genes and yeast flocculation.
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Affiliation(s)
- Ramesh Kumawat
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, India
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2
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Wei S, Li M, Lang X, Robertson NR, Park SY, Cutler SR, Wheeldon I. Repurposing plant hormone receptors as chemically-inducible genetic switches for dynamic regulation in yeast. Metab Eng 2024; 83:102-109. [PMID: 38554744 DOI: 10.1016/j.ymben.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/28/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
Precise control of gene expression is critical for optimizing cellular metabolism and improving the production of valuable biochemicals. However, hard-wired approaches to pathway engineering, such as optimizing promoters, can take time and effort. Moreover, limited tools exist for controlling gene regulation in non-conventional hosts. Here, we develop a two-channel chemically-regulated gene expression system for the multi-stress tolerant yeast Kluyveromyces marxianus and use it to tune ethyl acetate production, a native metabolite produced at high titers in this yeast. To achieve this, we repurposed the plant hormone sensing modules (PYR1ABA/HAB1 and PYR1*MANDI/HAB1*) for high dynamic-range gene activation and repression controlled by either abscisic acid (ABA) or mandipropamid (mandi). To redirect metabolic flux towards ethyl acetate biosynthesis, we simultaneously repress pyruvate dehydrogenase (PDA1) and activate pyruvate decarboxylase (PDC1) to enhance ethyl acetate titers. Thus, we have developed new tools for chemically tuning gene expression in K. marxianus and S. cerevisiae that should be deployable across many non-conventional eukaryotic hosts.
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Affiliation(s)
- Shuang Wei
- Biochemistry and Molecular Biology, University of California, Riverside, Riverside, CA, USA
| | - Mengwan Li
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Xuye Lang
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Nicholas R Robertson
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Sang-Youl Park
- Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Sean R Cutler
- Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA; Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA; Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA; Center for Industrial Biotechnology, University of California, Riverside, Riverside, CA, USA.
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3
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Lee B, Hokamp K, Alhussain MM, Bamagoos AA, Fleming AB. The influence of flocculation upon global gene transcription in a yeast CYC8 mutant. Microb Genom 2024; 10:001216. [PMID: 38529898 PMCID: PMC10995634 DOI: 10.1099/mgen.0.001216] [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: 12/05/2023] [Accepted: 02/29/2024] [Indexed: 03/27/2024] Open
Abstract
The transcriptome from a Saccharomyces cerevisiae tup1 deletion mutant was one of the first comprehensive yeast transcriptomes published. Subsequent transcriptomes from tup1 and cyc8 mutants firmly established the Tup1-Cyc8 complex as predominantly acting as a repressor of gene transcription. However, transcriptomes from tup1/cyc8 gene deletion or conditional mutants would all have been influenced by the striking flocculation phenotypes that these mutants display. In this study, we have separated the impact of flocculation from the transcriptome in a cyc8 conditional mutant to reveal those genes (i) subject solely to Cyc8p-dependent regulation, (ii) regulated by flocculation only and (iii) regulated by Cyc8p and further influenced by flocculation. We reveal a more accurate list of Cyc8p-regulated genes that includes newly identified Cyc8p-regulated genes that were masked by the flocculation phenotype and excludes genes which were indirectly influenced by flocculation and not regulated by Cyc8p. Furthermore, we show evidence that flocculation exerts a complex and potentially dynamic influence upon global gene transcription. These data should be of interest to future studies into the mechanism of action of the Tup1-Cyc8 complex and to studies involved in understanding the development of flocculation and its impact upon cell function.
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Affiliation(s)
- Brenda Lee
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Karsten Hokamp
- Department of Genetics, School of Genetics and Microbiology, Smurfit Institute, Trinity College Dublin, Dublin, Ireland
| | - Mohamed M. Alhussain
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Atif A. Bamagoos
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Alastair B. Fleming
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
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4
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Lee B, Church M, Hokamp K, Alhussain MM, Bamagoos AA, Fleming AB. Systematic analysis of tup1 and cyc8 mutants reveals distinct roles for TUP1 and CYC8 and offers new insight into the regulation of gene transcription by the yeast Tup1-Cyc8 complex. PLoS Genet 2023; 19:e1010876. [PMID: 37566621 PMCID: PMC10446238 DOI: 10.1371/journal.pgen.1010876] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/23/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
The Tup1-Cyc8 complex in Saccharomyces cerevisiae was one of the first global co-repressors of gene transcription discovered. However, despite years of study, a full understanding of the contribution of Tup1p and Cyc8p to complex function is lacking. We examined TUP1 and CYC8 single and double deletion mutants and show that CYC8 represses more genes than TUP1, and that there are genes subject to (i) unique repression by TUP1 or CYC8, (ii) redundant repression by TUP1 and CYC8, and (iii) there are genes at which de-repression in a cyc8 mutant is dependent upon TUP1, and vice-versa. We also reveal that Tup1p and Cyc8p can make distinct contributions to commonly repressed genes most likely via specific interactions with different histone deacetylases. Furthermore, we show that Tup1p and Cyc8p can be found independently of each other to negatively regulate gene transcription and can persist at active genes to negatively regulate on-going transcription. Together, these data suggest that Tup1p and Cyc8p can associate with active and inactive genes to mediate distinct negative and positive regulatory roles when functioning within, and possibly out with the complex.
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Affiliation(s)
- Brenda Lee
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Michael Church
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Karsten Hokamp
- Department of Genetics, School of Genetics and Microbiology, Smurfit Institute, Trinity College Dublin, Dublin, Ireland
| | - Mohamed M. Alhussain
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Atif A. Bamagoos
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Alastair B. Fleming
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
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Huang Z, Lou J, Gao Y, Noman M, Li D, Song F. FonTup1 functions in growth, conidiogenesis and pathogenicity of Fusarium oxysporum f. sp. niveum through modulating the expression of the tricarboxylic acid cycle genes. Microbiol Res 2023; 272:127389. [PMID: 37099956 DOI: 10.1016/j.micres.2023.127389] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 04/28/2023]
Abstract
The Tup1-Cyc8 complex is a highly conserved transcriptional corepressor that regulates intricate genetic network associated with various biological processes in fungi. Here, we report the role and mechanism of FonTup1 in regulating physiological processes and pathogenicity in watermelon Fusarium wilt fungus, Fusarium oxysporum f. sp. niveum (Fon). FonTup1 deletion impairs mycelial growth, asexual reproduction, and macroconidia morphology, but not macroconidial germination in Fon. The ΔFontup1 mutant exhibits altered tolerance to cell wall perturbing agent (congo red) and osmotic stressors (sorbitol or NaCl), but unchanged sensitivity to paraquat. The deletion of FonTup1 significantly decreases the pathogenicity of Fon toward watermelon plants through attenuating the ability to colonize and grow within the host. Transcriptome analysis revealed that FonTup1 regulates primary metabolic pathways, including the tricarboxylic acid (TCA) cycle, via altering the expression of corresponding genes. Downregulation of three malate dehydrogenase genes, FonMDH1-3, occurs in ΔFontup1, and disruption of FonMDH2 causes significant abnormalities in mycelial growth, conidiation, and virulence of Fon. These findings demonstrate that FonTup1, as a global transcriptional corepressor, plays crucial roles in different biological processes and pathogenicity of Fon through regulating various primary metabolic processes, including the TCA cycle. This study highlights the importance and molecular mechanism of the Tup1-Cyc8 complex in multiple basic biological processes and pathogenicity of phytopathogenic fungi.
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Affiliation(s)
- Ziling Huang
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Crop Diseases and Insect Pests of Ministry of Agriculture and Rural Affairs, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jiajun Lou
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Crop Diseases and Insect Pests of Ministry of Agriculture and Rural Affairs, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yizhou Gao
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Crop Diseases and Insect Pests of Ministry of Agriculture and Rural Affairs, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Muhammad Noman
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Crop Diseases and Insect Pests of Ministry of Agriculture and Rural Affairs, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Dayong Li
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Crop Diseases and Insect Pests of Ministry of Agriculture and Rural Affairs, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Fengming Song
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Crop Diseases and Insect Pests of Ministry of Agriculture and Rural Affairs, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
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6
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Functional characterization and comparative analysis of gene repression-mediating domains interacting with yeast pleiotropic corepressors Sin3, Cyc8 and Tup1. Curr Genet 2023; 69:127-139. [PMID: 36854981 PMCID: PMC10163088 DOI: 10.1007/s00294-023-01262-6] [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: 01/13/2023] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 03/02/2023]
Abstract
Transcriptional corepressors Sin3, Cyc8 and Tup1 are important for downregulation of gene expression by recruiting various histone deacetylases once they gain access to defined genomic locations by interaction with pathway-specific repressor proteins. In this work we systematically investigated whether 17 yeast repressor proteins (Cti6, Dal80, Fkh1, Gal80, Mig1, Mot3, Nrg1, Opi1, Rdr1, Rox1, Sko1, Ume6, Ure2, Xbp1, Yhp1, Yox1 and Whi5) representing several unrelated regulatory pathways are able to bind to Sin3, Cyc8 and Tup1. Our results show that paired amphipathic helices 1 and 2 (PAH1 and PAH2) of Sin3 are functionally redundant for some regulatory pathways. WD40 domains of Tup1 proved to be sufficient for interaction with repressor proteins. Using length variants of selected repressors, we mapped corepressor interaction domains (CIDs) in vitro and assayed gene repression in vivo. Systematic comparison of CID minimal sequences allowed us to define several related positional patterns of hydrophobic amino acids some of which could be confirmed as functionally supported by site-directed mutagenesis. Although structural predictions indicated that certain CIDs may be α-helical, most repression domains appear to be randomly structured and must be considered as intrinsically disordered regions (IDR) adopting a defined conformation only by interaction with a corepressor.
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7
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Mao YS, Chen JW, Wang ZH, Xu MY, Gao XD. Roles of the transcriptional regulators Fts1, YlNrg1, YlTup1, and YlSsn6 in the repression of the yeast-to-filament transition in the dimorphic yeast Yarrowia lipolytica. Mol Microbiol 2023; 119:126-142. [PMID: 36537557 DOI: 10.1111/mmi.15017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/04/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
In dimorphic fungi, the yeast-to-filament transition critical for cell survival under nutrient starvation is controlled by both activators and repressors. However, very few filamentation repressors are known. Here we report that, in the dimorphic yeast Yarrowia lipolytica, the conserved transcription factor YlNrg1 plays a minor role whereas Fts1, a newly identified Zn(II)2 Cys6 zinc cluster transcription factor, plays a key role in filamentation repression. FTS1 deletion caused hyperfilamentation whereas Fts1 overexpression drastically reduced filamentation. The expression of FTS1 is downregulated substantially during the yeast-to-filament transition. Transcriptome sequencing revealed that Fts1 represses 401 genes, including the filamentation-activating transcription factor genes MHY1, YlAZF1, and YlWOR4 and key cell wall protein genes. Tup1-Ssn6, a general transcriptional corepressor, is involved in the repression of many cellular functions in fungi. We show that both YlTup1 and YlSsn6 strongly repress filamentation in Y. lipolytica. YlTup1 and YlSsn6 together repress 1383 genes, including a large number of transcription factor and cell wall protein genes, which overlap substantially with Fts1-repressed genes. Fts1 interacts with both YlTup1 and YlSsn6, and LexA-Fts1 fusion represses a lexAop-promoter-lacZ reporter in a Tup1-Ssn6-dependent manner. Our findings suggest that Fts1 functions as a transcriptional repressor, directing the repression of target genes through the Tup1-Ssn6 corepressor.
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Affiliation(s)
- Yi-Sheng Mao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jia-Wen Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhen-Hua Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Meng-Yang Xu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiang-Dong Gao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
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8
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Tup1 is critical for transcriptional repression in Quiescence in S. cerevisiae. PLoS Genet 2022; 18:e1010559. [PMID: 36542663 DOI: 10.1371/journal.pgen.1010559] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/05/2023] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Upon glucose starvation, S. cerevisiae shows a dramatic alteration in transcription, resulting in wide-scale repression of most genes and activation of some others. This coincides with an arrest of cellular proliferation. A subset of such cells enters quiescence, a reversible non-dividing state. Here, we demonstrate that the conserved transcriptional corepressor Tup1 is critical for transcriptional repression after glucose depletion. We show that Tup1-Ssn6 binds new targets upon glucose depletion, where it remains as the cells enter the G0 phase of the cell cycle. In addition, we show that Tup1 represses a variety of glucose metabolism and transport genes. We explored how Tup1 mediated repression is accomplished and demonstrated that Tup1 coordinates with the Rpd3L complex to deacetylate H3K23. We found that Tup1 coordinates with Isw2 to affect nucleosome positions at glucose transporter HXT family genes during G0. Finally, microscopy revealed that a quarter of cells with a Tup1 deletion contain multiple DAPI puncta. Taken together, these findings demonstrate the role of Tup1 in transcriptional reprogramming in response to environmental cues leading to the quiescent state.
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Ma QZ, Wu HY, Xie SP, Zhao BS, Yin XM, Ding SL, Guo YS, Xu C, Zang R, Geng YH, Zhang M. BsTup1 is required for growth, conidiogenesis, stress response and pathogenicity of Bipolaris sorokiniana. Int J Biol Macromol 2022; 220:721-732. [PMID: 35981683 DOI: 10.1016/j.ijbiomac.2022.07.250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/05/2022]
Abstract
Tup1, a conserved transcriptional repressor, plays a critical role in the growth and development of fungi. Here, we identified a BsTup1 gene from the plant pathogenic fungus Bipolaris sorokiniana. The expression of BsTup1 showed a more than three-fold increase during the conidial stage compared with mycelium stage. Deletion of BsTup1 led to decrease hyphal growth and defect in conidia formation. A significant difference was detected in osmotic, oxidative, or cell wall stress responses between the WT and ΔBsTup1 strains. Pathogenicity assays showed that virulence of the ΔBsTup1 mutant was dramatically decreased on wheat and barely leaves. Moreover, it was observed that hyphal tips of the mutants could not form appressorium-like structures on the inner epidermis of onion and barley coleoptile. Yeast two-hybrid assays indicated that BsTup1 could interact with the BsSsn6. RNAseq revealed significant transcriptional changes in the ΔBsTup1 mutant with 2369 genes down-regulated and 2962 genes up-regulated. In these genes, we found that a subset of genes involved in fungal growth, sporulation, cell wall integrity, osmotic stress, oxidation stress, and pathogenicity, which were misregulated in the ΔBsTup1 mutant. These data revealed that BsTup1 has multiple functions in fungal growth, development, stress response and pathogenesis in B. sorokiniana.
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Affiliation(s)
- Qing-Zhou Ma
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Hai-Yan Wu
- Analytical Instrument Center, Henan Agricultural University, Zhengzhou 450002, China
| | - Shun-Pei Xie
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Bing-Sen Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Xin-Ming Yin
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Sheng-Li Ding
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Ya-Shuang Guo
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Chao Xu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Rui Zang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Yue-Hua Geng
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China.
| | - Meng Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China.
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Tup1 Paralog CgTUP11 Is a Stronger Repressor of Transcription than CgTUP1 in Candida glabrata. mSphere 2022; 7:e0076521. [PMID: 35341317 PMCID: PMC9044973 DOI: 10.1128/msphere.00765-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
TUP1 is a well-characterized repressor of transcription in Saccharomyces cerevisiae and Candida albicans and is observed as a single-copy gene. We observe that most species that experienced a whole-genome duplication outside of the Saccharomyces genus have two copies of TUP1 in the Saccharomycotina yeast clade. We focused on Candida glabrata and demonstrated that the uncharacterized TUP1 homolog, C. glabrata TUP11 (CgTUP11), is most like the S. cerevisiae TUP1 (ScTUP1) gene through phenotypic assays and transcriptome sequencing (RNA-seq). Whereas CgTUP1 plays a role in gene repression, it is much less repressive in standard growth media. Through RNA-seq and reverse transcription-quantitative PCR (RT-qPCR), we observed that genes associated with pathogenicity (YPS2, YPS4, and HBN1) are upregulated upon deletion of either paralog, and loss of both paralogs is synergistic. Loss of the corepressor CgCYC8 mimics the loss of both paralogs, but not to the same extent as the Cgtup1Δ Cgtup11Δ mutant for these pathogenesis-related genes. In contrast, genes involved in energy metabolism (CgHXT2, CgADY2, and CgFBP1) exhibit similar behavior (dependence on both paralogs), but deletion of CgCYC8 is very similar to the Cgtup1Δ Cgtup11Δ mutant. Finally, some genes (CgMFG1 and CgRIE1) appear to only be dependent on CgTUP11 and CgCYC8 and not CgTUP1. These data indicate separable and overlapping roles for the two TUP1 paralogs and that other genes may function as the CgCyc8 corepressor. Through a comparison by RNA-seq of Sctup1Δ, it was found that TUP1 homologs regulate similar genes in the two species. This work highlights that studies focused only on Saccharomyces may miss important biological processes because of paralog loss after genome duplication. IMPORTANCE Due to a whole-genome duplication, many yeast species related to C. glabrata have two copies of the well-characterized TUP1 gene, unlike most Saccharomyces species. This work identifies roles for the paralogs in C. glabrata, highlights the importance of the uncharacterized paralog, called TUP11, and suggests that the two paralogs have both overlapping and unique functions. The TUP1 paralogs likely influence pathogenicity based on tup mutants upregulating genes that are associated with pathogenicity.
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11
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Ma X, Jiang Y, Ma L, Luo S, Du H, Li X, Xing F. Corepressors SsnF and RcoA Regulate Development and Aflatoxin B1 Biosynthesis in Aspergillus flavus NRRL 3357. Toxins (Basel) 2022; 14:toxins14030174. [PMID: 35324671 PMCID: PMC8954095 DOI: 10.3390/toxins14030174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 02/04/2023] Open
Abstract
Aspergillus flavus is a saprophytic fungus that can be found across the entire world. It can produce aflatoxin B1 (AFB1), which threatens human health. CreA, as the central factor in carbon catabolite repression (CCR), regulates carbon catabolism and AFB1 biosynthesis in A. flavus. Additionally, SsnF-RcoA are recognized as the corepressors of CreA in CCR. In this study, ssnF and rcoA not only regulated the expressions of CCR factors and hydrolase genes, but also positively affected mycelia growth, conidia production, sclerotia formation, and osmotic stress response in A. flavus. More importantly, SsnF and RcoA were identified as positive regulators for AFB1 biosynthesis, as they modulate the AF cluster genes and the relevant regulators at a transcriptional level. Additionally, the interactions of SsnF-CreA and RcoA-CreA were strong and moderate, respectively. However, the interaction of SsnF and RcoA was weak. The interaction models of CreA-SsnF, CreA-RcoA, and SsnF-RcoA were also simulated with a docking analysis. All things considered, SsnF and RcoA are not just the critical regulators of the CCR pathway, but the global regulators involving in morphological development and AFB1 biosynthesis in A. flavus.
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Affiliation(s)
| | | | | | | | | | - Xu Li
- Correspondence: (X.L.); (F.X.)
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12
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Hu Y, Li M, Liu Z, Song X, Qu Y, Qin Y. Carbon catabolite repression involves physical interaction of the transcription factor CRE1/CreA and the Tup1-Cyc8 complex in Penicillium oxalicum and Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:244. [PMID: 34952627 PMCID: PMC8710005 DOI: 10.1186/s13068-021-02092-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 12/04/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Cellulolytic enzyme production in filamentous fungi requires a release from carbon catabolite repression (CCR). The protein CRE1/CreA (CRE = catabolite responsive element) is a key transcription factor (TF) that is involved in CCR and represses cellulolytic gene expression. CRE1/CreA represents the functional equivalent of Mig1p, an important Saccharomyces cerevisiae TF in CCR that exerts its repressive effect by recruiting a corepressor complex Tup1p-Cyc8p. Although it is known from S. cerevisiae that CRE1/CreA might repress gene expression via interacting with the corepressor complex Tup1-Cyc8, this mechanism is unconfirmed in other filamentous fungi, since the physical interaction has not yet been verified in these organisms. The precise mechanism on how CRE1/CreA achieves transcriptional repression after DNA binding remains unknown. RESULTS The results from tandem affinity purification and bimolecular fluorescence complementation revealed a direct physical interaction between the TF CRE1/CreA and the complex Tup1-Cyc8 in the nucleus of cellulolytic fungus Trichoderma reesei and Penicillium oxalicum. Both fungi have the ability to secrete a complex arsenal of enzymes to synergistically degrade lignocellulosic materials. In P. oxalicum, the protein PoCyc8, a subunit of complex Tup1-Cyc8, interacts directly with TF PoCreA and histone H3 lysine 36 (H3K36) methyltransferase PoSet2 in the nucleus. The di-methylation level of H3K36 in the promoter of prominent cellulolytic genes (cellobiohydrolase-encoding gene Pocbh1/cel7A and endoglucanase-encoding gene Poegl1/cel7B) is positively correlated with the expression levels of TF PoCreA. Since the methylation of H3K36 was also demonstrated to be a repression marker of cellulolytic gene expression, it appears feasible that the cellulolytic genes are repressed via PoCreA-Tup1-Cyc8-Set2-mediated transcriptional repression. CONCLUSION This study verifies the long-standing conjecture that the TF CRE1/CreA represses gene expression by interacting with the corepressor complex Tup1-Cyc8 in filamentous fungi. A reasonable explanation is proposed that PoCreA represses gene expression by recruiting complex PoTup1-Cyc8. Histone methyltransferase Set2, which methylates H3K36, is also involved in the regulatory network by interacting with PoCyc8. The findings contribute to the understanding of CCR mechanism in filamentous fungi and could aid in biotechnologically relevant enzyme production.
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Affiliation(s)
- Yueyan Hu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
- Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
- NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-Based Medicine, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
| | - Mengxue Li
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
| | - Zhongjiao Liu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
| | - Xin Song
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
- Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
| | - Yinbo Qu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
- Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
| | - Yuqi Qin
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
- Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
- NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-Based Medicine, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
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Lettow J, Aref R, Schüller HJ. Transcriptional repressor Gal80 recruits corepressor complex Cyc8-Tup1 to structural genes of the Saccharomyces cerevisiae GAL regulon. Curr Genet 2021; 68:115-124. [PMID: 34622331 PMCID: PMC8801411 DOI: 10.1007/s00294-021-01215-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/14/2021] [Accepted: 09/26/2021] [Indexed: 11/30/2022]
Abstract
Under non-inducing conditions (absence of galactose), yeast structural genes of the GAL regulon are repressed by Gal80, preventing interaction of Gal4 bound to UASGAL promoter motifs with general factors of the transcriptional machinery. In this work, we show that Gal80 is also able to interact with histone deacetylase-recruiting corepressor proteins Cyc8 and Tup1, indicating an additional mechanism of gene repression. This is supported by our demonstration that a lexA–Gal80 fusion efficiently mediates repression of a reporter gene with an upstream lexA operator sequence. Corepressor interaction and in vivo gene repression could be mapped to a Gal80 minimal domain of 65 amino acids (aa 81-145). Site-directed mutagenesis of selected residues within this domain showed that a cluster of aromatic-hydrophobic amino acids (YLFV, aa 118-121) is important, although not solely responsible, for gene repression. Using chromatin immunoprecipitation, Cyc8 and Tup1 were shown to be present at the GAL1 promoter in a wild-type strain but not in a gal80 mutant strain under non-inducing (derepressing) growth conditions. Expression of a GAL1–lacZ fusion was elevated in a tup1 mutant (but not in a cyc8 mutant) grown in derepressing medium, indicating that Tup1 may be mainly responsible for this second mechanism of Gal80-dependent gene repression.
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Affiliation(s)
- Julia Lettow
- Center for Functional Genomics of Microbes, Abteilung Molekulare Genetik und Infektionsbiologie, Felix-Hausdorff-Str. 8, 17487, Greifswald, Germany
| | - Rasha Aref
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Shoubra El-Khaymah, Cairo, 11241, Egypt
| | - Hans-Joachim Schüller
- Center for Functional Genomics of Microbes, Abteilung Molekulare Genetik und Infektionsbiologie, Felix-Hausdorff-Str. 8, 17487, Greifswald, Germany.
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14
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Parnell EJ, Parnell TJ, Stillman DJ. Genetic analysis argues for a coactivator function for the Saccharomyces cerevisiae Tup1 corepressor. Genetics 2021; 219:6329640. [PMID: 34849878 DOI: 10.1093/genetics/iyab120] [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: 06/23/2021] [Accepted: 07/20/2021] [Indexed: 11/14/2022] Open
Abstract
The Tup1-Cyc8 corepressor complex of Saccharomyces cerevisiae is recruited to promoters by DNA-binding proteins to repress transcription of genes, including the a-specific mating-type genes. We report here a tup1(S649F) mutant that displays mating irregularities and an α-predominant growth defect. RNA-Seq and ChIP-Seq were used to analyze gene expression and Tup1 occupancy changes in mutant vs wild type in both a and α cells. Increased Tup1(S649F) occupancy tended to occur upstream of upregulated genes, whereas locations with decreased occupancy usually did not show changes in gene expression, suggesting this mutant not only loses corepressor function but also behaves as a coactivator. Based upon studies demonstrating a dual role of Tup1 in both repression and activation, we postulate that the coactivator function of Tup1(S649F) results from diminished interaction with repressor proteins, including α2. We also found that large changes in mating-type-specific gene expression between a and α or between mutant and wild type were not easily explained by the range of Tup1 occupancy levels within their promoters, as predicted by the classic model of a-specific gene repression by Tup1. Most surprisingly, we observed Tup1 occupancy upstream of the a-specific gene MFA2 and the α-specific gene MF(ALPHA)1 in cells in which each gene was expressed rather than repressed. These results, combined with the identification of additional mating-related genes upregulated in the tup1(S649F) α strain, illustrate that the role of Tup1 in distinguishing mating types in yeast appears to be both more comprehensive and more nuanced than previously appreciated.
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Affiliation(s)
- Emily J Parnell
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
| | - Timothy J Parnell
- Bioinformatics Shared Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - David J Stillman
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
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15
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Azizoglu A, Brent R, Rudolf F. A precisely adjustable, variation-suppressed eukaryotic transcriptional controller to enable genetic discovery. eLife 2021; 10:69549. [PMID: 34342575 PMCID: PMC8421071 DOI: 10.7554/elife.69549] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/02/2021] [Indexed: 11/13/2022] Open
Abstract
Conditional expression of genes and observation of phenotype remain central to biological discovery. Current methods enable either on/off or imprecisely controlled graded gene expression. We developed a 'well-tempered' controller, WTC846, for precisely adjustable, graded, growth condition independent expression of genes in Saccharomyces cerevisiae. Controlled genes are expressed from a strong semisynthetic promoter repressed by the prokaryotic TetR, which also represses its own synthesis; with basal expression abolished by a second, 'zeroing' repressor. The autorepression loop lowers cell-to-cell variation while enabling precise adjustment of protein expression by a chemical inducer. WTC846 allelic strains in which the controller replaced the native promoters recapitulated known null phenotypes (CDC42, TPI1), exhibited novel overexpression phenotypes (IPL1), showed protein dosage-dependent growth rates and morphological phenotypes (CDC28, TOR2, PMA1 and the hitherto uncharacterized PBR1), and enabled cell cycle synchronization (CDC20). WTC846 defines an 'expression clamp' allowing protein dosage to be adjusted by the experimenter across the range of cellular protein abundances, with limited variation around the setpoint.
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Affiliation(s)
| | - Roger Brent
- Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
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16
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Wang L, Zhang W, Cao Y, Zheng F, Zhao G, Lv X, Meng X, Liu W. Interdependent recruitment of CYC8/TUP1 and the transcriptional activator XYR1 at target promoters is required for induced cellulase gene expression in Trichoderma reesei. PLoS Genet 2021; 17:e1009351. [PMID: 33606681 PMCID: PMC7894907 DOI: 10.1371/journal.pgen.1009351] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/12/2021] [Indexed: 11/19/2022] Open
Abstract
Cellulase production in filamentous fungus Trichoderma reesei is highly responsive to various environmental cues involving multiple positive and negative regulators. XYR1 (Xylanase regulator 1) has been identified as the key transcriptional activator of cellulase gene expression in T. reesei. However, the precise mechanism by which XYR1 achieves transcriptional activation of cellulase genes is still not fully understood. Here, we identified the TrCYC8/TUP1 complex as a novel coactivator for XYR1 in T. reesei. CYC8/TUP1 is the first identified transcriptional corepressor complex mediating repression of diverse genes in Saccharomyces cerevisiae. Knockdown of Trcyc8 or Trtup1 resulted in markedly impaired cellulase gene expression in T. reesei. We found that TrCYC8/TUP1 was recruited to cellulase gene promoters upon cellulose induction and this recruitment is dependent on XYR1. We further observed that repressed Trtup1 or Trcyc8 expression caused a strong defect in XYR1 occupancy and loss of histone H4 at cellulase gene promoters. The defects in XYR1 binding and transcriptional activation of target genes in Trtup1 or Trcyc8 repressed cells could not be overcome by XYR1 overexpression. Our results reveal a novel coactivator function for TrCYC8/TUP1 at the level of activator binding, and suggest a mechanism in which interdependent recruitment of XYR1 and TrCYC8/TUP1 to cellulase gene promoters represents an important regulatory circuit in ensuring the induced cellulase gene expression. These findings thus contribute to unveiling the intricate regulatory mechanism underlying XYR1-mediated cellulase gene activation and also provide an important clue that will help further improve cellulase production by T. reesei.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, People’s Republic of China
| | - Weixin Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, People’s Republic of China
| | - Yanli Cao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, People’s Republic of China
| | - Fanglin Zheng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, People’s Republic of China
| | - Guolei Zhao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, People’s Republic of China
| | - Xinxing Lv
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, People’s Republic of China
| | - Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, People’s Republic of China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, People’s Republic of China
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17
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Hsp104-dependent ability to assimilate mannitol and sorbitol conferred by a truncated Cyc8 with a C-terminal polyglutamine in Saccharomyces cerevisiae. PLoS One 2020; 15:e0242054. [PMID: 33175887 PMCID: PMC7657529 DOI: 10.1371/journal.pone.0242054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/27/2020] [Indexed: 12/26/2022] Open
Abstract
Tup1-Cyc8 (also known as Tup1-Ssn6) is a general transcriptional corepressor. D-Mannitol (mannitol) and D-sorbitol (sorbitol) are the major polyols in nature. Budding yeast Saccharomyces cerevisiae is unable to assimilate mannitol or sorbitol, but acquires the ability to assimilate mannitol due to a spontaneous mutation in TUP1 or CYC8. In this study, we found that spontaneous mutation of TUP1 or CYC8 also permitted assimilation of sorbitol. Some spontaneous nonsense mutations of CYC8 produced a truncated Cyc8 with a C-terminal polyglutamine. The effects were guanidine hydrochloride-sensitive and were dependent on Hsp104, but were complemented by introduction of CYC8, ruling out involvement of a prion. Assimilation of mannitol and sorbitol conferred by other mutations of TUP1 or CYC8 was guanidine hydrochloride-tolerant. It is physiologically reasonable that S. cerevisiae carries this mechanism to acquire the ability to assimilate major polyols in nature.
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18
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Diverse roles of Tup1p and Cyc8p transcription regulators in the development of distinct types of yeast populations. Curr Genet 2018; 65:147-151. [PMID: 30191307 DOI: 10.1007/s00294-018-0883-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 08/31/2018] [Accepted: 08/31/2018] [Indexed: 02/03/2023]
Abstract
Yeasts create multicellular structures of varying complexity, such as more complex colonies and biofilms and less complex flocs, each of which develops via different mechanisms. Colony biofilms originate from one or more cells that, through growth and division, develop a complicated three-dimensional structure consisting of aerial parts, agar-embedded invasive parts and a central cavity, filled with extracellular matrix. In contrast, flocs arise relatively quickly by aggregation of planktonic cells growing in liquid cultures after they reach the appropriate growth phase and/or exhaust nutrients such as glucose. Creation of both types of structures is dependent on the presence of flocculins: Flo11p in the former case and Flo1p in the latter. We recently showed that formation of both types of structures by wild Saccharomyces cerevisiae strain BR-F is regulated via transcription regulators Tup1p and Cyc8p, but in a divergent manner. Biofilm formation is regulated by Cyc8p and Tup1p antagonistically: Cyc8p functions as a repressor of FLO11 gene expression and biofilm formation, whereas Tup1p counteracts the Cyc8p repressor function and positively regulates biofilm formation and Flo11p expression. In addition, Tup1p stabilizes Flo11p probably by repressing a gene coding for a cell wall or extracellular protease that is involved in Flo11p degradation. In contrast, formation of BR-F flocs is co-repressed by the Cyc8p-Tup1p complex. These findings point to different mechanisms involved in yeast multicellularity.
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19
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Nguyen PV, Hlaváček O, Maršíková J, Váchová L, Palková Z. Cyc8p and Tup1p transcription regulators antagonistically regulate Flo11p expression and complexity of yeast colony biofilms. PLoS Genet 2018; 14:e1007495. [PMID: 29965985 PMCID: PMC6044549 DOI: 10.1371/journal.pgen.1007495] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/13/2018] [Accepted: 06/16/2018] [Indexed: 12/26/2022] Open
Abstract
Yeast biofilms are complex multicellular structures, in which the cells are well protected against drugs and other treatments and thus highly resistant to antifungal therapies. Colony biofilms represent an ideal system for studying molecular mechanisms and regulations involved in development and internal organization of biofilm structure as well as those that are involved in fungal domestication. We have identified here antagonistic functional interactions between transcriptional regulators Cyc8p and Tup1p that modulate the life-style of natural S. cerevisiae strains between biofilm and domesticated mode. Herein, strains with different levels of Cyc8p and Tup1p regulators were constructed, analyzed for processes involved in colony biofilm development and used in the identification of modes of regulation of Flo11p, a key adhesin in biofilm formation. Our data show that Tup1p and Cyc8p regulate biofilm formation in the opposite manner, being positive and negative regulators of colony complexity, cell-cell interaction and adhesion to surfaces. Notably, in-depth analysis of regulation of expression of Flo11p adhesin revealed that Cyc8p itself is the key repressor of FLO11 expression, whereas Tup1p counteracts Cyc8p's repressive function and, in addition, counters Flo11p degradation by an extracellular protease. Interestingly, the opposing actions of Tup1p and Cyc8p concern processes crucial to the biofilm mode of yeast multicellularity, whereas other multicellular processes such as cell flocculation are co-repressed by both regulators. This study provides insight into the mechanisms regulating complexity of the biofilm lifestyle of yeast grown on semisolid surfaces.
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Affiliation(s)
- Phu Van Nguyen
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Otakar Hlaváček
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Jana Maršíková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Libuše Váchová
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Zdena Palková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
- * E-mail:
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20
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Orikasa Y, Mikumo D, Ohwada T. A 2-Deoxyglucose-Resistant Mutant of Saccharomyces cerevisiae Shows Enhanced Maltose Fermentative Ability by the Activation of MAL Genes. Foods 2018; 7:foods7040052. [PMID: 29614773 PMCID: PMC5920417 DOI: 10.3390/foods7040052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 03/24/2018] [Accepted: 03/29/2018] [Indexed: 11/16/2022] Open
Abstract
Saccharomyces cerevisiae MCD4 is a 2-deoxyglucose (2-DOG)-resistant mutant derived from the wild-type strain, AK46, wherein the 2-DOG resistance improves the maltose fermentative ability. In the MAL gene cluster, mutations were detected in MAL11 and MAL31, which encode maltose permeases, and in MAL13 and MAL33, which encode transcriptional activators. In maltose medium, the expression of MAL11 and MAL31 in MCD4 was 2.1 and 4.2 times significantly higher than that in AK46, respectively. Besides, the expression of MAL13 and MAL33 also tended to be higher than that of AK46. Although no mutations were found in MAL12 and MAL32 (which encode α-glucosidases), their expression was significantly higher (4.9 and 4.4 times, respectively) than that in AK46. Since the expression of major catabolite repression-related genes did not show significant differences between MCD4 and AK46, these results showed that the higher maltose fermentative ability of MCD4 is due to the activation of MAL genes encoding two maltose permeases and two α-glucosidases.
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Affiliation(s)
- Yoshitake Orikasa
- Department of Life and Food Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan.
- The United Graduate School of Agricultural Science, Iwate University, Morioka, Iwate 020-8550, Japan.
| | - Dai Mikumo
- The United Graduate School of Agricultural Science, Iwate University, Morioka, Iwate 020-8550, Japan.
- Research Center, Nippon Beet Sugar Manufacturing Co., Inada-cho, Obihiro, Hokkaido 080-0831, Japan.
| | - Takuji Ohwada
- Department of Life and Food Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan.
- The United Graduate School of Agricultural Science, Iwate University, Morioka, Iwate 020-8550, Japan.
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Alkafeef SS, Yu C, Huang L, Liu H. Wor1 establishes opaque cell fate through inhibition of the general co-repressor Tup1 in Candida albicans. PLoS Genet 2018; 14:e1007176. [PMID: 29337983 PMCID: PMC5786334 DOI: 10.1371/journal.pgen.1007176] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/26/2018] [Accepted: 12/29/2017] [Indexed: 12/17/2022] Open
Abstract
The pathogenic fungus Candida albicans can undergo phenotypic switching between two heritable states: white and opaque. This phenotypic plasticity facilitates its colonization in distinct host niches. The master regulator WOR1 is exclusively expressed in opaque phase cells. Positive feedback regulation by Wor1 on the WOR1 promoter is essential for opaque formation, however the underlying mechanism of how Wor1 functions is not clear. Here, we use tandem affinity purification coupled with mass spectrometry to identify Wor1-interacting proteins. Tup1 and its associated complex proteins are found as the major factors associated with Wor1. Tup1 occupies the same regions of the WOR1 promoter as Wor1 preferentially in opaque cells. Loss of Tup1 is sufficient to induce the opaque phase, even in the absence of Wor1. This is the first such report of a bypass of Wor1 in opaque formation. These genetic analyses suggest that Tup1 is a key repressor of the opaque state, and Wor1 functions via alleviating Tup1 repression at the WOR1 promoter. Opaque cells convert to white en masse at 37°C. We show that this conversion occurs only in the presence of glycolytic carbon sources. The opaque state is stabilized when cells are cultured on non-glycolytic carbon sources, even in a MTLa/α background. We further show that temperature and carbon source affect opaque stability by altering the levels of Wor1 and Tup1 at the WOR1 promoter. We propose that Wor1 and Tup1 form the core regulatory circuit controlling the opaque transcriptional program. This model provides molecular insights on how C. albicans adapts to different host signals to undergo phenotypic switching for colonization in distinct host niches.
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Affiliation(s)
- Selma S. Alkafeef
- Department of Biological Chemistry, University of California, Irvine, California, United States of America
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, California, United States of America
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, California, United States of America
| | - Haoping Liu
- Department of Biological Chemistry, University of California, Irvine, California, United States of America
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22
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Lin X, Yu AQ, Zhang CY, Pi L, Bai XW, Xiao DG. Functional analysis of the global repressor Tup1 for maltose metabolism in Saccharomyces cerevisiae: different roles of the functional domains. Microb Cell Fact 2017; 16:194. [PMID: 29121937 PMCID: PMC5679332 DOI: 10.1186/s12934-017-0806-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/31/2017] [Indexed: 11/15/2022] Open
Abstract
Background Tup1 is a general transcriptional repressor of diverse gene families coordinately controlled by glucose repression, mating type, and other mechanisms in Saccharomyces cerevisiae. Several functional domains of Tup1 have been identified, each of which has differing effects on transcriptional repression. In this study, we aim to investigate the role of Tup1 and its domains in maltose metabolism of industrial baker’s yeast. To this end, a battery of in-frame truncations in the TUP1 gene coding region were performed in the industrial baker’s yeasts with different genetic background, and the maltose metabolism, leavening ability, MAL gene expression levels, and growth characteristics were investigated. Results The results suggest that the TUP1 gene is essential to maltose metabolism in industrial baker’s yeast. Importantly, different domains of Tup1 play different roles in glucose repression and maltose metabolism of industrial baker’s yeast cells. The Ssn6 interaction, N-terminal repression and C-terminal repression domains might play roles in the regulation of MAL transcription by Tup1 for maltose metabolism of baker’s yeast. The WD region lacking the first repeat could influence the regulation of maltose metabolism directly, rather than indirectly through glucose repression. Conclusions These findings lay a foundation for the optimization of industrial baker’s yeast strains for accelerated maltose metabolism and facilitate future research on glucose repression in other sugar metabolism. Electronic supplementary material The online version of this article (10.1186/s12934-017-0806-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xue Lin
- Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.,College of Food Science and Technology, Hainan University, Haikou, 570228, China
| | - Ai-Qun Yu
- Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Cui-Ying Zhang
- Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| | - Li Pi
- Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Xiao-Wen Bai
- Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Dong-Guang Xiao
- Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
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Tartas A, Zarkadas C, Palaiomylitou M, Gounalaki N, Tzamarias D, Vlassi M. Ssn6-Tup1 global transcriptional co-repressor: Role of the N-terminal glutamine-rich region of Ssn6. PLoS One 2017; 12:e0186363. [PMID: 29053708 PMCID: PMC5650148 DOI: 10.1371/journal.pone.0186363] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/29/2017] [Indexed: 11/19/2022] Open
Abstract
The Ssn6-Tup1 complex is a general transcriptional co-repressor formed by the interaction of Ssn6, a tetratricopeptide repeat (TPR) protein, with the Tup1 repressor. We have previously shown that the N-terminal domain of Ssn6 comprising TPRs 1 to 3 is necessary and sufficient for this interaction and that TPR1 plays critical role. In a subsequent study, we provided evidence that in the absence of Tup1, TPR1 is susceptible to proteolysis and that conformational change(s) accompany the Ssn6-Tup1 complex formation. In this study, we address the question whether the N-terminal non-TPR, glutamine-rich tail of Ssn6 (NTpolyQ), plays any role in the Ssn6/Tup1 association. Our biochemical and yeast-two-hybrid data show that truncation/deletion of the NTpolyQ domain of Ssn6 results in its self association and prevents Tup1 interaction. These results combined with in silico modeling data imply a major role of the NTpolyQ tail of Ssn6 in regulating its interaction with Tup1.
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Affiliation(s)
- Athanassios Tartas
- Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Ag. Paraskevi Attikis, Athens, Greece
| | - Christoforos Zarkadas
- Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Ag. Paraskevi Attikis, Athens, Greece
| | - Maria Palaiomylitou
- Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Ag. Paraskevi Attikis, Athens, Greece
| | - Niki Gounalaki
- Institute of Molecular Biology & Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
| | - Dimitris Tzamarias
- Biology Department, University of Crete, Heraklion, Crete, Greece
- * E-mail: (MV); (DT)
| | - Metaxia Vlassi
- Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Ag. Paraskevi Attikis, Athens, Greece
- * E-mail: (MV); (DT)
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Metabolic Adaptation to Nutrients Involves Coregulation of Gene Expression by the RNA Helicase Dbp2 and the Cyc8 Corepressor in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2017; 7:2235-2247. [PMID: 28500049 PMCID: PMC5499131 DOI: 10.1534/g3.117.041814] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cells fine-tune their metabolic programs according to nutrient availability in order to maintain homeostasis. This is achieved largely through integrating signaling pathways and the gene expression program, allowing cells to adapt to nutritional change. Dbp2, a member of the DEAD-box RNA helicase family in Saccharomyces cerevisiae, has been proposed to integrate gene expression with cellular metabolism. Prior work from our laboratory has reported the necessity of DBP2 in proper gene expression, particularly for genes involved in glucose-dependent regulation. Here, by comparing differentially expressed genes in dbp2∆ to those of 700 other deletion strains from other studies, we find that CYC8 and TUP1, which form a complex and inhibit transcription of numerous genes, corepress a common set of genes with DBP2. Gene ontology (GO) annotations reveal that these corepressed genes are related to cellular metabolism, including respiration, gluconeogenesis, and alternative carbon-source utilization genes. Consistent with a direct role in metabolic gene regulation, loss of either DBP2 or CYC8 results in increased cellular respiration rates. Furthermore, we find that corepressed genes have a propensity to be associated with overlapping long noncoding RNAs and that upregulation of these genes in the absence of DBP2 correlates with decreased binding of Cyc8 to these gene promoters. Taken together, this suggests that Dbp2 integrates nutrient availability with energy homeostasis by maintaining repression of glucose-repressed, Cyc8-targeted genes across the genome.
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Masuda R, Iguchi N, Tukuta K, Nagoshi T, Kemuriyama K, Muraguchi H. The Coprinopsis cinerea Tup1 homologue Cag1 is required for gill formation during fruiting body morphogenesis. Biol Open 2016; 5:1844-1852. [PMID: 27815245 PMCID: PMC5200907 DOI: 10.1242/bio.021246] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The pileus (cap) of the fruiting body in homobasidiomycete fungi bears the hymenium, a layer of cells that includes the basidia where nuclear fusion, meiosis and sporulation occur. Coprinopsis cinerea is a model system for studying fruiting body development. The hymenium of C. cinerea forms at the surface of the gills in the pileus. In a previous study, we identified a mutation called cap-growthless1-1 (cag1-1) that blocks gill formation, which yields primordia that never mature. In this study, we found that the cag1 gene encodes a homologue of Saccharomyces cerevisiae Tup1. The C. cinerea genome contains another Tup1 homologue gene called Cc.tupA. Reciprocal tagging of Cag1 and Cc.TupA with green and red fluorescent proteins revealed that the relative ratios of the amounts of the two Tup1 paralogues varied among tissues. Compared with Cc.TupA, Cag1 was preferentially expressed in the gill trama tissue cells, suggesting that the function of Cag1 is required for gill trama tissue differentiation and maintenance. Yeast two-hybrid analysis and co-localisation of Cag1 and Cc.TupA suggested that Cag1 interacts with Cc.TupA in the nuclei of certain cells. Summary: Cag1, a Tup1 homologue in Coprinopsis cinerea, is required for gill formation in fruiting body development and is highly expressed in the central region of gills.
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Affiliation(s)
- Ryo Masuda
- Department of Biotechnology, Faculty of Bioresource Sciences, Akita Prefectural University, Akita 010-0195, Japan
| | - Naoki Iguchi
- Department of Biotechnology, Faculty of Bioresource Sciences, Akita Prefectural University, Akita 010-0195, Japan
| | - Kooki Tukuta
- Department of Biotechnology, Faculty of Bioresource Sciences, Akita Prefectural University, Akita 010-0195, Japan
| | - Takahiro Nagoshi
- Department of Biotechnology, Faculty of Bioresource Sciences, Akita Prefectural University, Akita 010-0195, Japan
| | - Kazuki Kemuriyama
- Department of Biotechnology, Faculty of Bioresource Sciences, Akita Prefectural University, Akita 010-0195, Japan
| | - Hajime Muraguchi
- Department of Biotechnology, Faculty of Bioresource Sciences, Akita Prefectural University, Akita 010-0195, Japan
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Vega M, Riera A, Fernández-Cid A, Herrero P, Moreno F. Hexokinase 2 Is an Intracellular Glucose Sensor of Yeast Cells That Maintains the Structure and Activity of Mig1 Protein Repressor Complex. J Biol Chem 2016; 291:7267-85. [PMID: 26865637 DOI: 10.1074/jbc.m115.711408] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 11/06/2022] Open
Abstract
Hexokinase 2 (Hxk2) fromSaccharomyces cerevisiaeis a bi-functional enzyme, being both a catalyst in the cytosol and an important regulator of the glucose repression signal in the nucleus. Despite considerable recent progress, little is known about the regulatory mechanism that controls nuclear Hxk2 association with theSUC2promoter chromatin and how this association is necessary forSUC2gene repression. Our data indicate that in theSUC2promoter context, Hxk2 functions through a variety of structurally unrelated factors, mainly the DNA-binding Mig1 and Mig2 repressors and the regulatory Snf1 and Reg1 factors. Hxk2 sustains the repressor complex architecture maintaining transcriptional repression at theSUC2gene. Using chromatin immunoprecipitation assays, we discovered that the Hxk2 in its open configuration, at low glucose conditions, leaves the repressor complex that induces its dissociation and promotesSUC2gene expression. In high glucose conditions, Hxk2 adopts a close conformation that promotes Hxk2 binding to the Mig1 protein and the reassembly of theSUC2repressor complex. Additional findings highlight the possibility that Hxk2 constitutes an intracellular glucose sensor that operates by changing its conformation in response to cytoplasmic glucose levels that regulate its interaction with Mig1 and thus its recruitment to the repressor complex of theSUC2promoter. Thus, our data indicate that Hxk2 is more intimately involved in gene regulation than previously thought.
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Affiliation(s)
- Montserrat Vega
- From the Department of Biochemistry and Molecular Biology, University of Oviedo, 33006-Oviedo, Spain
| | - Alberto Riera
- From the Department of Biochemistry and Molecular Biology, University of Oviedo, 33006-Oviedo, Spain
| | - Alejandra Fernández-Cid
- From the Department of Biochemistry and Molecular Biology, University of Oviedo, 33006-Oviedo, Spain
| | - Pilar Herrero
- From the Department of Biochemistry and Molecular Biology, University of Oviedo, 33006-Oviedo, Spain
| | - Fernando Moreno
- From the Department of Biochemistry and Molecular Biology, University of Oviedo, 33006-Oviedo, Spain
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Sugar and Glycerol Transport in Saccharomyces cerevisiae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:125-168. [PMID: 26721273 DOI: 10.1007/978-3-319-25304-6_6] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In Saccharomyces cerevisiae the process of transport of sugar substrates into the cell comprises a complex network of transporters and interacting regulatory mechanisms. Members of the large family of hexose (HXT) transporters display uptake efficiencies consistent with their environmental expression and play physiological roles in addition to feeding the glycolytic pathway. Multiple glucose-inducing and glucose-independent mechanisms serve to regulate expression of the sugar transporters in yeast assuring that expression levels and transporter activity are coordinated with cellular metabolism and energy needs. The expression of sugar transport activity is modulated by other nutritional and environmental factors that may override glucose-generated signals. Transporter expression and activity is regulated transcriptionally, post-transcriptionally and post-translationally. Recent studies have expanded upon this suite of regulatory mechanisms to include transcriptional expression fine tuning mediated by antisense RNA and prion-based regulation of transcription. Much remains to be learned about cell biology from the continued analysis of this dynamic process of substrate acquisition.
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KAEA (SUDPRO), a member of the ubiquitous KEOPS/EKC protein complex, regulates the arginine catabolic pathway and the expression of several other genes in Aspergillus nidulans. Gene 2015. [DOI: 10.1016/j.gene.2015.07.066] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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29
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Tanaka N, Mukai Y. Yeast Cyc8p and Tup1p proteins function as coactivators for transcription of Stp1/2p-dependent amino acid transporter genes. Biochem Biophys Res Commun 2015; 468:32-8. [DOI: 10.1016/j.bbrc.2015.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 11/01/2015] [Indexed: 10/22/2022]
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30
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Hickey CM, Hochstrasser M. STUbL-mediated degradation of the transcription factor MATα2 requires degradation elements that coincide with corepressor binding sites. Mol Biol Cell 2015; 26:3401-12. [PMID: 26246605 PMCID: PMC4591686 DOI: 10.1091/mbc.e15-06-0436] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 07/30/2015] [Indexed: 11/16/2022] Open
Abstract
The yeast cell type regulator MATα (α2) is degraded through two ubiquitylation pathways, one of which has been minimally characterized. We identify two regions in α2 important for this pathway and show that these regions overlap specific binding sites for α2 corepressors, suggesting that α2 degradation is coordinated with its functional status. The yeast transcription factor MATα2 (α2) is a short-lived protein known to be ubiquitylated by two distinct pathways, one involving the ubiquitin-conjugating enzymes (E2s) Ubc6 and Ubc7 and the ubiquitin ligase (E3) Doa10 and the other operating with the E2 Ubc4 and the heterodimeric E3 Slx5/Slx8. Although Slx5/Slx8 is a small ubiquitin-like modifier (SUMO)-targeted ubiquitin ligase (STUbL), it does not require SUMO to target α2 but instead directly recognizes α2. Little is known about the α2 determinants required for its Ubc4- and STUbL-mediated degradation or how these determinants substitute for SUMO in recognition by the STUbL pathway. We describe two distinct degradation elements within α2, both of which are necessary for α2 recognition specifically by the Ubc4 pathway. Slx5/Slx8 can directly ubiquitylate a C-terminal fragment of α2, and mutating one of the degradation elements impairs this ubiquitylation. Surprisingly, both degradation elements identified here overlap specific interaction sites for α2 corepressors: the Mcm1 interaction site in the central α2 linker and the Ssn6 (Cyc8) binding site in the α2 homeodomain. We propose that competitive binding to α2 by the ubiquitylation machinery and α2 cofactors is balanced so that α2 can function in transcription repression yet be short lived enough to allow cell-type switching.
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Affiliation(s)
- Christopher M Hickey
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
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31
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Ng CH, Akhter A, Yurko N, Burgener JM, Rosonina E, Manley JL. Sumoylation controls the timing of Tup1-mediated transcriptional deactivation. Nat Commun 2015; 6:6610. [PMID: 25766875 PMCID: PMC4360881 DOI: 10.1038/ncomms7610] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 02/11/2015] [Indexed: 02/08/2023] Open
Abstract
The small ubiquitin-like modifier (SUMO) is implicated in various cellular activities, including transcriptional regulation. We previously showed that the yeast activator Gcn4 becomes sumoylated during activation, facilitating its eventual promoter eviction and transcriptional shut off. Here we show that the corepressor Tup1 is sumoylated, at two specific lysines, under various stress conditions. Mutation of these sites has no effect on Tup1 recruitment or RNAP II promoter occupancy immediately following induction. However, Tup1 levels subsequently decrease, while RNAP II and transcription increase in Tup1 mutant cells. Consistent with this, a Tup1 mutant displaying increased sumoylation led to reduced transcription. We also show that coordinated sumoylation of Gcn4 and Tup1 enhances Gcn4 promoter eviction, and that multiple Tup1-interacting proteins become sumoylated after stress. Together, our studies provide evidence that coordinated sumoylation of Gcn4, Tup1, and likely other factors, dampens activated transcription by stabilizing Tup1 binding and stimulating Gcn4 and RNAP II removal.
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Affiliation(s)
- Chong Han Ng
- 1] Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, 1117 Fairchild Center, New York, New York 10027, USA [2] Faculty of Information Science &Technology, Multimedia University, Jalan Ayer Keroh Lama, 75450 Bukit Beruang, Melaka, Malaysia
| | - Akhi Akhter
- Department of Biology, York University, Toronto, Ontario, Canada M3J 1P3
| | - Nathan Yurko
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, 1117 Fairchild Center, New York, New York 10027, USA
| | - Justin M Burgener
- Department of Biology, York University, Toronto, Ontario, Canada M3J 1P3
| | - Emanuel Rosonina
- Department of Biology, York University, Toronto, Ontario, Canada M3J 1P3
| | - James L Manley
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, 1117 Fairchild Center, New York, New York 10027, USA
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32
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Lee JE, Oh JH, Ku M, Kim J, Lee JS, Kang SO. Ssn6 has dual roles in Candida albicans filament development through the interaction with Rpd31. FEBS Lett 2015; 589:513-20. [PMID: 25601565 DOI: 10.1016/j.febslet.2015.01.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/09/2015] [Accepted: 01/09/2015] [Indexed: 11/30/2022]
Abstract
Ssn6 is a crucial regulator of morphological transition and virulence in the fungal pathogen Candida albicans. Ssn6 has previously been reported to act in complex with the transcriptional repressor Tup1. Here, we report that Ssn6 also interacts with the histone deacetylase Rpd31, independently of Tup1. The ssn6/rpd31 double mutant strain formed elongated filaments, but failed to form filament extension, and this coincided with the down-regulation of the filament extension gene UME6. Occupancy patterns of Ssn6 and Rpd31 differed at the promoters of UME6 and the metabolic gene INO1. These findings indicate that, in C. albicans, Ssn6 has dual roles in filament development, depending on the interaction with Rpd31.
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Affiliation(s)
- Ji-Eun Lee
- Laboratory of Biophysics, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Jang-Hyun Oh
- Laboratory of Biophysics, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - MyungHee Ku
- Laboratory of Biophysics, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Jueun Kim
- Department of Molecular Biosciences, College of Biomedical Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do 200-701, Republic of Korea
| | - Jung-Shin Lee
- Department of Molecular Biosciences, College of Biomedical Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do 200-701, Republic of Korea.
| | - Sa-Ouk Kang
- Laboratory of Biophysics, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea.
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33
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Acquisition of the ability to assimilate mannitol by Saccharomyces cerevisiae through dysfunction of the general corepressor Tup1-Cyc8. Appl Environ Microbiol 2014; 81:9-16. [PMID: 25304510 DOI: 10.1128/aem.02906-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Saccharomyces cerevisiae normally cannot assimilate mannitol, a promising brown macroalgal carbon source for bioethanol production. The molecular basis of this inability remains unknown. We found that cells capable of assimilating mannitol arose spontaneously from wild-type S. cerevisiae during prolonged culture in mannitol-containing medium. Based on microarray data, complementation analysis, and cell growth data, we demonstrated that acquisition of mannitol-assimilating ability was due to spontaneous mutations in the genes encoding Tup1 or Cyc8, which constitute a general corepressor complex that regulates many kinds of genes. We also showed that an S. cerevisiae strain carrying a mutant allele of CYC8 exhibited superior salt tolerance relative to other ethanologenic microorganisms; this characteristic would be highly beneficial for the production of bioethanol from marine biomass. Thus, we succeeded in conferring the ability to assimilate mannitol on S. cerevisiae through dysfunction of Tup1-Cyc8, facilitating production of ethanol from mannitol.
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34
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Fleming AB, Beggs S, Church M, Tsukihashi Y, Pennings S. The yeast Cyc8-Tup1 complex cooperates with Hda1p and Rpd3p histone deacetylases to robustly repress transcription of the subtelomeric FLO1 gene. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1242-55. [PMID: 25106892 PMCID: PMC4316177 DOI: 10.1016/j.bbagrm.2014.07.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/28/2014] [Accepted: 07/29/2014] [Indexed: 12/02/2022]
Abstract
We demonstrate that the yeast flocculation gene, FLO1, is representative of a distinct subset of subtelomeric genes that are robustly repressed by the Cyc8–Tup1 complex. We have examined Cyc8–Tup1 localisation, histone acetylation and long-range chromatin remodelling within the extensive FLO1 upstream region. We show that Cyc8–Tup1 is localised in a DNase I hypersensitive site within an ordered array of strongly positioned nucleosomes around − 700 base pairs upstream of the transcription start site. In cyc8 deletion mutant strains, Tup1p localisation is absent, with concomitant histone hyperacetylation of adjacent regions at the FLO1 promoter. This is accompanied by extensive histone depletion across the upstream region and gene activation. The yeast histone deacetylases, Hda1p and Rpd3p, occupy the repressed FLO1 promoter region in a Cyc8–Tup1 dependent manner and coordinate histone deacetylation, nucleosome stabilisation and gene repression. Moreover, we show that the ATP-dependent chromatin remodelling complex Swi–Snf occupies the site vacated by Cyc8–Tup1 in a cyc8 mutant. These data suggest that distinctly bound Cyc8–Tup1 cooperates with Hda1p and Rpd3p to establish or maintain an extensive array of strongly positioned, deacetylated nucleosomes over the FLO1 promoter and upstream region which inhibit histone acetylation, block Swi–Snf binding and prevent transcription. Cyc8–Tup1 repression activity is enriched at chromosome subtelomeric regions. The subtelomeric FLO1 gene is subject to chromatin-mediated repression by Cyc8–Tup1. Cyc8–Tup1 promotes long-range nucleosome positioning and histone deacetylation. Hda1p and Rpd3p cooperate with Cyc8–Tup1 to facilitate this repressive chromatin. Swi–Snf directs extensive nucleosome remodelling when Cyc8–Tup1 is absent.
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Affiliation(s)
- Alastair B Fleming
- School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin 2, Ireland; School of Biomedical Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK.
| | - Suzanne Beggs
- School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin 2, Ireland
| | - Michael Church
- School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin 2, Ireland
| | | | - Sari Pennings
- School of Biomedical Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK; Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
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35
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Lin X, Zhang CY, Bai XW, Song HY, Xiao DG. Effects of MIG1, TUP1 and SSN6 deletion on maltose metabolism and leavening ability of baker's yeast in lean dough. Microb Cell Fact 2014; 13:93. [PMID: 24993311 PMCID: PMC4094228 DOI: 10.1186/s12934-014-0093-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 06/18/2014] [Indexed: 11/17/2022] Open
Abstract
Background Glucose repression is a global regulatory system in baker’s yeast. Maltose metabolism in baker’s yeast strains is negatively influenced by glucose, thereby affecting metabolite productivity (leavening ability in lean dough). Even if the general repression system constituted by MIG1, TUP1 and SSN6 factors has already been reported, the functions of these three genes in maltose metabolism remain unclear. In this work, we explored the effects of MIG1 and/or TUP1 and/or SSN6 deletion on the alleviation of glucose-repression to promote maltose metabolism and leavening ability of baker’s yeast. Results Results strongly suggest that the deletion of MIG1 and/or TUP1 and/or SSN6 can exert various effects on glucose repression for maltose metabolism. The deletion of TUP1 was negative for glucose derepression to facilitate the maltose metabolism. By contrast, the deletion of MIG1 and/or SSN6, rather than other double-gene or triple-gene mutations could partly relieve glucose repression, thereby promoting maltose metabolism and the leavening ability of baker’s yeast in lean dough. Conclusions The mutants of industrial baker’s yeast with enhanced maltose metabolism and leavening ability in lean dough were developed by genetic engineering. These baker’s yeast strains had excellent potential industrial applications.
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Affiliation(s)
| | - Cui-Ying Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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36
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Kim JH, Roy A, Jouandot D, Cho KH. The glucose signaling network in yeast. Biochim Biophys Acta Gen Subj 2013; 1830:5204-10. [PMID: 23911748 DOI: 10.1016/j.bbagen.2013.07.025] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 07/24/2013] [Accepted: 07/26/2013] [Indexed: 01/26/2023]
Abstract
BACKGROUND Most cells possess a sophisticated mechanism for sensing glucose and responding to it appropriately. Glucose sensing and signaling in the budding yeast Saccharomyces cerevisiae represent an important paradigm for understanding how extracellular signals lead to changes in the gene expression program in eukaryotes. SCOPE OF REVIEW This review focuses on the yeast glucose sensing and signaling pathways that operate in a highly regulated and cooperative manner to bring about glucose-induction of HXT gene expression. MAJOR CONCLUSIONS The yeast cells possess a family of glucose transporters (HXTs), with different kinetic properties. They employ three major glucose signaling pathways-Rgt2/Snf3, AMPK, and cAMP-PKA-to express only those transporters best suited for the amounts of glucose available. We discuss the current understanding of how these pathways are integrated into a regulatory network to ensure efficient uptake and utilization of glucose. GENERAL SIGNIFICANCE Elucidating the role of multiple glucose signals and pathways involved in glucose uptake and metabolism in yeast may reveal the molecular basis of glucose homeostasis in humans, especially under pathological conditions, such as hyperglycemia in diabetics and the elevated rate of glycolysis observed in many solid tumors.
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Affiliation(s)
- Jeong-Ho Kim
- Department of Biochemistry and Molecular Medicine, The George Washington University Medical Center, 2300 Eye Street, Washington, DC 20037, USA.
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37
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Roy A, Shin YJ, Cho KH, Kim JH. Mth1 regulates the interaction between the Rgt1 repressor and the Ssn6-Tup1 corepressor complex by modulating PKA-dependent phosphorylation of Rgt1. Mol Biol Cell 2013; 24:1493-503. [PMID: 23468525 PMCID: PMC3639059 DOI: 10.1091/mbc.e13-01-0047] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The yeast glucose transporter gene (HXT) repressor Rgt1 recruits the general corepressor complex Ssn6-Tup1 to bring about repression. The glucose-responsive transcription factor Mth1 is a transcriptional corepressor that mediates the interaction of Rgt1 with Ssn6-Tup1 by blocking the PKA-dependent phosphorylation of Rgt1. Glucose uptake, the first, rate-limiting step of its utilization, is facilitated by glucose transporters. Expression of several glucose transporter (HXT) genes in yeast is repressed by the Rgt1 repressor, which recruits the glucose-responsive transcription factor Mth1 and the general corepressor complex Ssn6-Tup1 in the absence of glucose; however, it is derepressed when Mth1 is inactivated by glucose. Here we show that Ssn6-Tup1 interferes with the DNA-binding ability of Rgt1 in the absence of Mth1 and that the Rgt1 function abrogated by Ssn6 overexpression is restored by co-overexpression of Mth1. Thus Mth1 likely regulates Rgt1 function not by modulating its DNA-binding activity directly but by functionally antagonizing Ssn6-Tup1. Mth1 does so by acting as a scaffold-like protein to recruit Ssn6-Tup1 to Rgt1. Supporting evidence shows that Mth1 blocks the protein kinase A–dependent phosphorylation of Rgt1 that impairs the ability of Rgt1 to interact with Ssn6-Tup1. Of note, Rgt1 can bind DNA in the absence of Ssn6-Tup1 but does not inhibit transcription, suggesting that dissociation of Rgt1 from Ssn6-Tup1, but not from DNA, is necessary and sufficient for the expression of its target genes. Taken together, these findings show that Mth1 is a transcriptional corepressor that facilitates the recruitment of Ssn6-Tup1 by Rgt1.
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Affiliation(s)
- Adhiraj Roy
- Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA
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A framework for mapping, visualisation and automatic model creation of signal-transduction networks. Mol Syst Biol 2012; 8:578. [PMID: 22531118 PMCID: PMC3361003 DOI: 10.1038/msb.2012.12] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
An intuitive formalism for reconstructing cellular networks from empirical data is presented, and used to build a comprehensive yeast MAP kinase network. The accompanying rxncon software tool can convert networks to a range of standard graphical formats and mathematical models. ![]()
Network mapping at the granularity of empirical data that largely avoids combinatorial complexity Automatic visualisation and model generation with the rxncon open source software tool Visualisation in a range of formats, including all three SBGN formats, as well as contingency matrix or regulatory graph Comprehensive and completely references map of the yeast MAP kinase network in the rxncon format
Intracellular signalling systems are highly complex. This complexity makes handling, analysis and visualisation of available knowledge a major challenge in current signalling research. Here, we present a novel framework for mapping signal-transduction networks that avoids the combinatorial explosion by breaking down the network in reaction and contingency information. It provides two new visualisation methods and automatic export to mathematical models. We use this framework to compile the presently most comprehensive map of the yeast MAP kinase network. Our method improves previous strategies by combining (I) more concise mapping adapted to empirical data, (II) individual referencing for each piece of information, (III) visualisation without simplifications or added uncertainty, (IV) automatic visualisation in multiple formats, (V) automatic export to mathematical models and (VI) compatibility with established formats. The framework is supported by an open source software tool that facilitates integration of the three levels of network analysis: definition, visualisation and mathematical modelling. The framework is species independent and we expect that it will have wider impact in signalling research on any system.
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Parnell EJ, Stillman DJ. Shields up: the Tup1-Cyc8 repressor complex blocks coactivator recruitment. Genes Dev 2012; 25:2429-35. [PMID: 22156205 DOI: 10.1101/gad.181768.111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Tup1-Cyc8 complex is responsible for repression of a large and diverse collection of genes in Saccharomyces cerevisiae. The predominant view has been that Tup1-Cyc8 functions as a corepressor, actively associating with regulatory proteins and organizing chromatin to block transcription. A new study by Wong and Struhl in this issue of Genes & Development (pp. 2525-2539) challenges nearly 20 years of models by demonstrating that Tup1-Cyc8 functions primarily as a shield to block DNA-binding proteins from recruiting transcriptional coactivators.
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Affiliation(s)
- Emily J Parnell
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
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Wong KH, Struhl K. The Cyc8-Tup1 complex inhibits transcription primarily by masking the activation domain of the recruiting protein. Genes Dev 2011; 25:2525-39. [PMID: 22156212 PMCID: PMC3243062 DOI: 10.1101/gad.179275.111] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 10/14/2011] [Indexed: 12/22/2022]
Abstract
The yeast Tup1-Cyc8 corepressor complex is recruited to promoters by DNA-binding repressors, but the mechanisms by which it inhibits expression of genes involved in various stress pathways are poorly understood. Conditional and rapid depletion of Tup1 from the nucleus leads to concurrent nucleosome depletion and histone acetylation, recruitment of coactivators (Swi/Snf, SAGA, and Mediator), and increased transcriptional activity. Conversely, coactivator dissociation occurs rapidly upon rerepression by Cyc8-Tup1, although coactivator association and transcription can be blocked even in the absence of nucleosomes. The coactivators are recruited to the sites where Tup1 was located prior to depletion, indicating that the repressor proteins that recruit Tup1 function as activators in its absence. Last, Cyc8-Tup1 can interact with activation domains in vivo. Thus, Cyc8-Tup1 regulates transcription primarily by masking and inhibiting the transcriptional activation domains of the recruiting proteins, not by acting as a corepressor. We suggest that the corepressor function of Cyc8-Tup1 makes only a modest contribution to expression of target genes, specifically to keep expression levels below the nonactivated state.
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Affiliation(s)
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Elías-Villalobos A, Fernández-Álvarez A, Ibeas JI. The general transcriptional repressor Tup1 is required for dimorphism and virulence in a fungal plant pathogen. PLoS Pathog 2011; 7:e1002235. [PMID: 21909277 PMCID: PMC3164652 DOI: 10.1371/journal.ppat.1002235] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 07/08/2011] [Indexed: 01/22/2023] Open
Abstract
A critical step in the life cycle of many fungal pathogens is the transition between yeast-like growth and the formation of filamentous structures, a process known as dimorphism. This morphological shift, typically triggered by multiple environmental signals, is tightly controlled by complex genetic pathways to ensure successful pathogenic development. In animal pathogenic fungi, one of the best known regulators of dimorphism is the general transcriptional repressor, Tup1. However, the role of Tup1 in fungal dimorphism is completely unknown in plant pathogens. Here we show that Tup1 plays a key role in orchestrating the yeast to hypha transition in the maize pathogen Ustilago maydis. Deletion of the tup1 gene causes a drastic reduction in the mating and filamentation capacity of the fungus, in turn leading to a reduced virulence phenotype. In U. maydis, these processes are controlled by the a and b mating-type loci, whose expression depends on the Prf1 transcription factor. Interestingly, Δtup1 strains show a critical reduction in the expression of prf1 and that of Prf1 target genes at both loci. Moreover, we observed that Tup1 appears to regulate Prf1 activity by controlling the expression of the prf1 transcriptional activators, rop1 and hap2. Additionally, we describe a putative novel prf1 repressor, named Pac2, which seems to be an important target of Tup1 in the control of dimorphism and virulence. Furthermore, we show that Tup1 is required for full pathogenic development since tup1 deletion mutants are unable to complete the sexual cycle. Our findings establish Tup1 as a key factor coordinating dimorphism in the phytopathogen U. maydis and support a conserved role for Tup1 in the control of hypha-specific genes among animal and plant fungal pathogens. Fungal plant pathogens cause serious damage to crops with huge social and economic consequences. To cause disease, many such fungi need to change their morphology between a yeast-like, unicellular form and a filamentous state. This change, known as dimorphism, is tightly controlled by complex genetic pathways to ensure successful pathogenic development. In animal pathogens, one of the most important genes controlling dimorphism is Tup1. In plant pathogens, however, the role for this gene is completely unknown. In this work, we describe the role of Tup1 in the dimorphism and virulence of Ustilago maydis, the plant fungal pathogen that causes maize smut disease. We show that mutant U. maydis cells lacking Tup1 are unable to properly change between yeast-like and filamentous forms, thus compromising its virulence. We look at the underlying genetic pathways, and find that Tup1 regulates key genes known to regulate dimorphism. We also show that Tup1 is essential for the production of mature fungal spores, which normally allow the fungus to disperse and infect new plants. Our results show that Tup1 is a key element in the control of both infectious and dispersible fungal forms and supports an evolutionary-conserved role for this gene in the regulation of dimorphism among animal and plant pathogenic fungi.
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Affiliation(s)
- Alberto Elías-Villalobos
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla, Spain
| | - Alfonso Fernández-Álvarez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla, Spain
| | - José I. Ibeas
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla, Spain
- * E-mail:
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Takayama S, Fujii M, Nakagawa Y, Miki K, Ayusawa D. N-terminal short fragment of TUP1 confers resistance to 5-bromodeoxyuridine in the yeast Saccharomyces cerevisiae. Biochem Biophys Res Commun 2011; 411:25-31. [PMID: 21712029 DOI: 10.1016/j.bbrc.2011.06.064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 06/08/2011] [Indexed: 10/18/2022]
Abstract
Small molecules that exhibit biological activity have contributed to the understanding of the molecular mechanisms of various biological phenomena. 5-Bromodeoxyuridine (BrdU) is a thymidine analogue that modulates various biological phenomena such as cellular differentiation and cellular senescence in cultured mammalian cells. Although BrdU is thought to function through changing chromatin structure and gene expression, its precise molecular mechanisms are not understood. To study the molecular mechanism for the action of BrdU, we have employed the yeast Saccharomyces cerevisiae as a model system, and screened multi-copy suppressor genes that confer resistance to BrdU. Our genetic screen has revealed that expression of the N-terminal short fragment of TUP1, and also disruption of HDA1 or HOS1, histone deacetylases that interact with TUP1, conferred resistance to BrdU. These results suggest the implication of the chromatin proteins in the function of BrdU, and would provide novel clues to answer the old question of how BrdU modulates various biological phenomena.
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Affiliation(s)
- Shinichi Takayama
- Graduate School of Nanobioscience, Yokohama City University, Seto 22-2, Kanazawa-Ku, Yokohama, Kanagawa 236 0027, Japan
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Oberoi J, Fairall L, Watson PJ, Yang JC, Czimmerer Z, Kampmann T, Goult BT, Greenwood JA, Gooch JT, Kallenberger BC, Nagy L, Neuhaus D, Schwabe JW. Structural basis for the assembly of the SMRT/NCoR core transcriptional repression machinery. Nat Struct Mol Biol 2011; 18:177-84. [PMID: 21240272 PMCID: PMC3232451 DOI: 10.1038/nsmb.1983] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2009] [Accepted: 11/08/2010] [Indexed: 11/08/2022]
Abstract
Eukaryotic transcriptional repressors function by recruiting large coregulatory complexes that target histone deacetylase enzymes to gene promoters and enhancers. Transcriptional repression complexes, assembled by the corepressor NCoR and its homolog SMRT, are crucial in many processes, including development and metabolic physiology. The core repression complex involves the recruitment of three proteins, HDAC3, GPS2 and TBL1, to a highly conserved repression domain within SMRT and NCoR. We have used structural and functional approaches to gain insight into the architecture and biological role of this complex. We report the crystal structure of the tetrameric oligomerization domain of TBL1, which interacts with both SMRT and GPS2, and the NMR structure of the interface complex between GPS2 and SMRT. These structures, together with computational docking, mutagenesis and functional assays, reveal the assembly mechanism and stoichiometry of the corepressor complex.
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Affiliation(s)
- Jasmeen Oberoi
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester. LE1 9HN
- MRC-Laboratory of Molecular Biology, Hills Road, Cambridge. CB2 0QH
| | - Louise Fairall
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester. LE1 9HN
| | - Peter J. Watson
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester. LE1 9HN
| | - Ji-Chun Yang
- MRC-Laboratory of Molecular Biology, Hills Road, Cambridge. CB2 0QH
| | - Zsolt Czimmerer
- Apoptosis and Genomics Research Group of the Hungarian Academy of Sciences, Department of Biochemistry and Molecular Biology, Life Sciences Building, Medical and Health Science Center, University of Debrecen, Debrecen, Egyetem ter 1. H-4032 Hungary
| | - Thorsten Kampmann
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester. LE1 9HN
| | - Benjamin T. Goult
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester. LE1 9HN
| | - Jacquie A. Greenwood
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester. LE1 9HN
| | - John T. Gooch
- MRC-Laboratory of Molecular Biology, Hills Road, Cambridge. CB2 0QH
| | | | - Laszlo Nagy
- Apoptosis and Genomics Research Group of the Hungarian Academy of Sciences, Department of Biochemistry and Molecular Biology, Life Sciences Building, Medical and Health Science Center, University of Debrecen, Debrecen, Egyetem ter 1. H-4032 Hungary
| | - David Neuhaus
- MRC-Laboratory of Molecular Biology, Hills Road, Cambridge. CB2 0QH
| | - John W.R. Schwabe
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester. LE1 9HN
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A role in the regulation of transcription by light for RCO-1 and RCM-1, the Neurospora homologs of the yeast Tup1-Ssn6 repressor. Fungal Genet Biol 2010; 47:939-52. [PMID: 20709620 DOI: 10.1016/j.fgb.2010.08.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 07/29/2010] [Accepted: 08/02/2010] [Indexed: 12/15/2022]
Abstract
The activation of gene transcription by light is transient since light-dependent mRNA accumulation ceases after long exposures to light. This phenomenon, photoadaptation, has been observed in plants and fungi, and allows the perception of changes in light intensities. In the fungus Neurosporacrassa photoadaptation involves the transient binding of the photoresponsive White Collar Complex (WCC) to the promoters of light-regulated genes. We show that RCO-1 and RCM-1, the Neurospora homologs of the components of the yeast Tup1-Ssn6 repressor complex, participate in photoadaptation. Mutation in either rco-1 or rcm-1 result in high and sustained accumulation of mRNAs for con-10 and other light-regulated genes after long exposures to light. The mutation of rco-1 increased the sensitivity to light for con-10 activation and delayed synthesis and/or degradation of con-10 and con-6 mRNAs without altering the amount or the light-dependent phosphorylation of the photoreceptor WC-1. RCO-1 and RCM-1 are located in the Neurospora nuclei were they regulate gene transcription. We show that RCO-1 and RCM-1 participate in the light-transduction pathway of Neurospora and has a role in photoadaptation by repressing gene transcription after long exposures to light.
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45
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Ferreira ME, Berndt KD, Nilsson J, Wright APH. WD40 domain divergence is important for functional differences between the fission yeast Tup11 and Tup12 co-repressor proteins. PLoS One 2010; 5:e11009. [PMID: 20544037 PMCID: PMC2882346 DOI: 10.1371/journal.pone.0011009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 04/28/2010] [Indexed: 11/19/2022] Open
Abstract
We have previously demonstrated that subsets of Ssn6/Tup target genes have distinct requirements for the Schizosaccharomyces pombe homologs of the Tup1/Groucho/TLE co-repressor proteins, Tup11 and Tup12. The very high level of divergence in the histone interacting repression domains of the two proteins suggested that determinants distinguishing Tup11 and Tup12 might be located in this domain. Here we have combined phylogenetic and structural analysis as well as phenotypic characterization, under stress conditions that specifically require Tup12, to identify and characterize the domains involved in Tup12-specific action. The results indicate that divergence in the repression domain is not generally relevant for Tup12-specific function. Instead, we show that the more highly conserved C-terminal WD40 repeat domain of Tup12 is important for Tup12-specific function. Surface amino acid residues specific for the WD40 repeat domain of Tup12 proteins in different fission yeasts are clustered in blade 3 of the propeller-like structure that is characteristic of WD40 repeat domains. The Tup11 and Tup12 proteins in fission yeasts thus provide an excellent model system for studying the functional divergence of WD40 repeat domains.
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Affiliation(s)
- Monica E. Ferreira
- School of Life Sciences, Södertörn University, Huddinge, Sweden
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Kurt D. Berndt
- School of Life Sciences, Södertörn University, Huddinge, Sweden
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Johan Nilsson
- School of Life Sciences, Södertörn University, Huddinge, Sweden
| | - Anthony P. H. Wright
- School of Life Sciences, Södertörn University, Huddinge, Sweden
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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Plakunov VK, Shelemekh OV. Mechanisms of oxygen regulation in microorganisms. Microbiology (Reading) 2009. [DOI: 10.1134/s0026261709050026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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47
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Palaiomylitou M, Tartas A, Vlachakis D, Tzamarias D, Vlassi M. Investigating the structural stability of the Tup1-interaction domain of Ssn6: evidence for a conformational change on the complex. Proteins 2008; 70:72-82. [PMID: 17634984 DOI: 10.1002/prot.21489] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Ssn6, a tetratricopeptide repeat (TPR) containing protein, associates with the Tup1 repressor to form a global transcriptional co-repressor complex, which is conserved across species. The three N-terminal TPR repeats of Ssn6, out of a total of 10, are involved in this particular interaction. Our previously reported 3D-modeling and mutagenesis data suggested that the structural integrity of TPR1 and its correct positioning relatively to TPR2 are crucial for Tup1 binding. In this study, we first investigate the structural stability of the Tup1 binding domain of Ssn6, in pure form, through a combination of CD spectroscopy and limited proteolysis mapping. The obtained data were next combined with molecular dynamics simulations and disorder/order predictions. This combined study revealed that, although competent to fold, in the absence of Tup1, TPR1 is partially unfolded with its helix B being highly dynamic exposing an apolar surface to the solvent. Subsequent CD spectroscopy on this domain complexed with a Tup1 fragment comprising its Ssn6 binding region provided strong evidence for a conformational change consisting of acquisition of alpha-helical structure with simultaneous stabilization of a coiled-coil configuration upon complex formation. We propose that this conformational change occurs largely in the TPR1 of Ssn6 and is in accord with the concept of folding coupled to binding, proposed for other TPR domains. A possible implication of the structural flexibility of Ssn6 TPR1 in Tup1 recognition is discussed and a novel mode of interaction is proposed for this particular TPR-mediated complex.
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Affiliation(s)
- Maria Palaiomylitou
- Institute of Biology, National Centre for Scientific Research Demokritos, 15310 Ag. Paraskevi Attikis, Greece
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48
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Needham PG, Trumbly RJ. In vitro characterization of the Mig1 repressor from Saccharomyces cerevisiae reveals evidence for monomeric and higher molecular weight forms. Yeast 2007; 23:1151-66. [PMID: 17133623 DOI: 10.1002/yea.1429] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The Mig1 DNA-binding protein of Saccharomyces cerevisiae was expressed and purified from yeast and the physical properties were characterized by several methods, including gel filtration, sucrose gradient sedimentation and native gel electrophoresis. Purified Mig1 exists as a monomer with a Stokes' radius of 48 A and a sedimentation coefficient of 3.55 S. Mig1 has an elongated shape with a frictional coefficient of 1.83. The K(d) of purified Mig1 for the SUC2 A site is 2.8 nM and for SUC2 B site 25.8 nM; these values were similar for Mig1 purified from repressed and derepressed cells. Full-length Mig1 expressed in yeast binds more tightly to SUC2 B than bacterially expressed GST-Mig1. Sucrose gradient sedimentation resolved a larger molecular weight form of Mig1 in whole-cell extracts that was not seen in purified samples and may represent a complex with another protein. This complex is found within the nucleus and is seen only in repressed cells. Mig1 exists in multiple phosphorylation states and only less phosphorylated forms of Mig1 are associated with this complex.
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Affiliation(s)
- Patrick G Needham
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine, 3035 Arlington Avenue, Toledo, OH 43614, USA.
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Labbé S, Pelletier B, Mercier A. Iron homeostasis in the fission yeast Schizosaccharomyces pombe. Biometals 2007; 20:523-37. [PMID: 17211681 DOI: 10.1007/s10534-006-9056-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2006] [Accepted: 11/28/2006] [Indexed: 01/22/2023]
Abstract
Schizosaccharomyces pombe has acquisition processes for iron, an essential nutrient. One pathway consists to produce, excrete, and capture siderophore-iron complexes. A second pathway requires enzymatic reduction of ferric iron at the cell surface prior to uptake by a permease-oxidase complex. Genes encoding proteins involved in iron assimilation are transcriptionally regulated as a function of iron availability. Under high iron conditions, the GATA-type regulator Fep1 represses the expression of iron uptake genes. The repressor function of Fep1 requires the presence of the Tup11 or Tup12 transcriptional co-repressor. Under low iron conditions, two regulatory mechanisms occur. First, the iron transport genes are highly induced. Second, there is a transcription factor cascade implicating the heteromeric CCAAT-binding complex that turns off a set of genes encoding iron-utilizing proteins, presumably to avoid a futile expenditure of energy in producing iron-using proteins that lack the necessary cofactor to function. Thus, collectively, these regulatory responses to variations in iron concentrations ensure that iron is present within cells for essential biochemical reactions, yet prevent the accumulation of iron or iron-using proteins to deleterious levels.
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Affiliation(s)
- Simon Labbé
- Département de Biochimie, Faculté de médecine, Université de Sherbrooke, 3001 12e Ave Nord, Sherbrooke, QC, Canada J1H 5N4.
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50
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Fagerström-Billai F, Durand-Dubief M, Ekwall K, Wright APH. Individual subunits of the Ssn6-Tup11/12 corepressor are selectively required for repression of different target genes. Mol Cell Biol 2006; 27:1069-82. [PMID: 17101775 PMCID: PMC1800702 DOI: 10.1128/mcb.01674-06] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Saccharomyces cerevisiae Ssn6 and Tup1 proteins form a corepressor complex that is recruited to target genes by DNA-bound repressor proteins. Repression occurs via several mechanisms, including interaction with hypoacetylated N termini of histones, recruitment of histone deacetylases (HDACs), and interactions with the RNA polymerase II holoenzyme. The distantly related fission yeast, Schizosaccharomyces pombe, has two partially redundant Tup1-like proteins that are dispensable during normal growth. In contrast, we show that Ssn6 is an essential protein in S. pombe, suggesting a function that is independent of Tup11 and Tup12. Consistently, the group of genes that requires Ssn6 for their regulation overlaps but is distinct from the group of genes that depend on Tup11 or Tup12. Global chip-on-chip analysis shows that Ssn6 is almost invariably found in the same genomic locations as Tup11 and/or Tup12. All three corepressor subunits are generally bound to genes that are selectively regulated by Ssn6 or Tup11/12, and thus, the subunit specificity is probably manifested in the context of a corepressor complex containing all three subunits. The corepressor binds to both the intergenic and coding regions of genes, but differential localization of the corepressor within genes does not appear to account for the selective dependence of target genes on the Ssn6 or Tup11/12 subunits. Ssn6, Tup11, and Tup12 are preferentially found at genomic locations at which histones are deacetylated, primarily by the Clr6 class I HDAC. Clr6 is also important for the repression of corepressor target genes. Interestingly, a subset of corepressor target genes, including direct target genes affected by Ssn6 overexpression, is associated with the function of class II (Clr3) and III (Hst4 and Sir2) HDACs.
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