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Schalamun M, Hinterdobler W, Schinnerl J, Brecker L, Schmoll M. The transcription factor STE12 influences growth on several carbon sources and production of dehydroacetic acid (DHAA) in Trichoderma reesei. Sci Rep 2024; 14:9625. [PMID: 38671155 PMCID: PMC11053031 DOI: 10.1038/s41598-024-59511-8] [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: 01/07/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
The filamentous ascomycete Trichoderma reesei, known for its prolific cellulolytic enzyme production, recently also gained attention for its secondary metabolite synthesis. Both processes are intricately influenced by environmental factors like carbon source availability and light exposure. Here, we explore the role of the transcription factor STE12 in regulating metabolic pathways in T. reesei in terms of gene regulation, carbon source utilization and biosynthesis of secondary metabolites. We show that STE12 is involved in regulating cellulase gene expression and growth on carbon sources associated with iron homeostasis. STE12 impacts gene regulation in a light dependent manner on cellulose with modulation of several CAZyme encoding genes as well as genes involved in secondary metabolism. STE12 selectively influences the biosynthesis of the sorbicillinoid trichodimerol, while not affecting the biosynthesis of bisorbibutenolide, which was recently shown to be regulated by the MAPkinase pathway upstream of STE12 in the signaling cascade. We further report on the biosynthesis of dehydroacetic acid (DHAA) in T. reesei, a compound known for its antimicrobial properties, which is subject to regulation by STE12. We conclude, that STE12 exerts functions beyond development and hence contributes to balance the energy distribution between substrate consumption, reproduction and defense.
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Affiliation(s)
- Miriam Schalamun
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Konrad Lorenz Strasse 24, 3430, Tulln, Austria
| | - Wolfgang Hinterdobler
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Konrad Lorenz Strasse 24, 3430, Tulln, Austria
- MyPilz GmbH, Wienerbergstrasse 55/13-15, 1120, Vienna, Austria
| | - Johann Schinnerl
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Lothar Brecker
- Department of Organic Chemistry, University of Vienna, Währinger Strasse 38, 1090, Vienna, Austria
| | - Monika Schmoll
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Konrad Lorenz Strasse 24, 3430, Tulln, Austria.
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
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Park ZM, Sporer AJ, Kraft K, Lum KK, Blackman E, Belnap E, Yellman CM, Rose MD. Kar4, the yeast homolog of METTL14, is required for mRNA m6A methylation and meiosis. PLoS Genet 2023; 19:e1010896. [PMID: 37603553 PMCID: PMC10470960 DOI: 10.1371/journal.pgen.1010896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 08/31/2023] [Accepted: 08/03/2023] [Indexed: 08/23/2023] Open
Abstract
KAR4, the yeast homolog of the mammalian mRNA N6A-methyltransferase complex component METTL14, is required for two disparate developmental programs in Saccharomyces cerevisiae: mating and meiosis. To understand KAR4's role in yeast mating and meiosis, we used a genetic screen to isolate 25 function-specific mutant alleles, which map to non-overlapping surfaces on a predicted structure of the Kar4 protein (Kar4p). Most of the mating-specific alleles (Mat-) abolish Kar4p's interaction with the transcription factor Ste12p, indicating that Kar4p's mating function is through Ste12p. In yeast, the mRNA methyltransferase complex was previously defined as comprising Ime4p (Kar4p's paralog and the homolog of mammalian METTL3), Mum2p (homolog of mammalian WTAP), and Slz1p (MIS), but not Kar4p. During meiosis, Kar4p interacts with Ime4p, Mum2p, and Slz1p. Moreover, cells lacking Kar4p have highly reduced levels of mRNA methylation during meiosis indicating that Kar4p is a key member of the methyltransferase complex, as it is in humans. Analysis of kar4Δ/Δ and 7 meiosis-specific alleles (Mei-) revealed that Kar4p is required early in meiosis, before initiation of S-phase and meiotic recombination. High copy expression of the meiotic transcriptional activator IME1 rescued the defect of these Mei- alleles. Surprisingly, Kar4p was also found to be required at a second step for the completion of meiosis and sporulation. Over-expression of IME1 in kar4Δ/Δ permits pre-meiotic S-phase, but most cells remained arrested with a monopolar spindle. Analysis of the function-specific mutants revealed that roughly half became blocked after premeiotic DNA synthesis and did not sporulate (Spo-). Loss of Kar4p's Spo function was suppressed by overexpression of RIM4, a meiotic translational regulator. Overexpression of IME1 and RIM4 together allowed sporulation of kar4Δ/Δ cells. Taken together, these data suggest that Kar4p regulates meiosis at multiple steps, presumably reflecting requirements for methylation in different stages of meiotic gene expression.
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Affiliation(s)
- Zachory M. Park
- Department of Biology, Georgetown University, Washington DC, United States of America
| | - Abigail J. Sporer
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Katherine Kraft
- Department of Biology, Georgetown University, Washington DC, United States of America
| | - Krystal K. Lum
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Edith Blackman
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Ethan Belnap
- Department of Biology, Georgetown University, Washington DC, United States of America
| | | | - Mark D. Rose
- Department of Biology, Georgetown University, Washington DC, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
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Park ZM, Sporer A, Kraft K, Lum K, Blackman E, Belnap E, Yellman C, Rose MD. Kar4, the Yeast Homolog of METTL14, is Required for mRNA m 6 A Methylation and Meiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.29.526094. [PMID: 36747717 PMCID: PMC9900893 DOI: 10.1101/2023.01.29.526094] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
KAR4 , the yeast homolog of the mammalian mRNA N 6 A-methyltransferase complex component METTL14 , is required for two disparate developmental programs in Saccharomyces cerevisiae : mating and meiosis. To understand KAR4 's role in yeast mating and meiosis, we used a genetic screen to isolate 25 function-specific mutant alleles, which map to non-overlapping surfaces on a predicted structure of the Kar4 protein (Kar4p). Most of the mating-specific alleles (Mat - ) abolish Kar4p's interaction with the transcription factor Ste12p, indicating that Kar4p's mating function is through Ste12p. In yeast, the mRNA methyltransferase complex was previously defined as comprising Ime4p (Kar4p's paralog and the homolog of mammalian METTL3), Mum2p (homolog of mammalian WTAP), and Slz1p (MIS), but not Kar4p. During meiosis, Kar4p interacts with Ime4p, Mum2p, and Slz1p. Moreover, cells lacking Kar4p have highly reduced levels of mRNA methylation during meiosis indicating that Kar4p is a key member of the methyltransferase complex, as it is in humans. Analysis of kar4 Δ/Δ and 7 meiosis-specific alleles (Mei - ) revealed that Kar4p is required early in meiosis, before initiation of S-phase and meiotic recombination. High copy expression of the meiotic transcriptional activator IME1 rescued the defect of these Mei- alleles. Surprisingly, Kar4p was also found to be required at a second step for the completion of meiosis and sporulation. Over-expression of IME1 in kar4 Δ/Δ permits pre-meiotic S-phase, but most cells remained arrested with a monopolar spindle. Analysis of the function-specific mutants revealed that roughly half became blocked after premeiotic DNA synthesis and did not sporulate (Spo - ). Loss of Kar4p's Spo function was suppressed by overexpression of RIM4 , a meiotic translational regulator. Overexpression of IME1 and RIM4 together allowed sporulation of kar4 Δ/Δ cells. Taken together, these data suggest that Kar4p regulates meiosis at multiple steps, presumably reflecting requirements for methylation in different stages of meiotic gene expression. Author Summary In yeast, KAR4 is required for mating and meiosis. A genetic screen for function-specific mutations identified 25 alleles that map to different surfaces on a predicted structure of the Kar4 protein (Kar4p). The mating-specific alleles interfere with Kar4p's ability to interact with the transcription factor Ste12p, its known partner in mating. The meiosis-specific alleles revealed an independent function: Kar4p is required for entry into meiosis and initiation of S-phase. During meiosis, Kar4p interacts with all components of the mRNA methyltransferase complex and kar4 Δ/Δ mutants have greatly reduced levels of mRNA methylation. Thus, Kar4p is a member of the yeast methyltransferase complex. Overexpression of the meiotic transcriptional activator IME1 rescued the meiotic entry defect but did not lead to sporulation, implying that Kar4p has more than one meiotic function. Suppression by Ime1p overexpression led to arrest after premeiotic DNA synthesis, but before sporulation. Loss of Kar4's sporulation function can be suppressed by overexpression of a translation regulator, Rim4p. Overexpression of both IME1 and RIM4 allowed sporulation in kar4 Δ/Δ cells.
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Affiliation(s)
- Zachory M. Park
- Department of Biology, Georgetown University, Washington DC, 20057, USA
| | - Abigail Sporer
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Katherine Kraft
- Department of Biology, Georgetown University, Washington DC, 20057, USA
| | - Krystal Lum
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Edith Blackman
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Ethan Belnap
- Department of Biology, Georgetown University, Washington DC, 20057, USA
| | | | - Mark D. Rose
- Department of Biology, Georgetown University, Washington DC, 20057, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
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Sharmeen N, Law C, Wu C. Polarization and cell-fate decision facilitated by the adaptor Ste50p in Saccharomyces cerevisiae. PLoS One 2022; 17:e0278614. [PMID: 36538537 PMCID: PMC9767377 DOI: 10.1371/journal.pone.0278614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022] Open
Abstract
In response to pheromone, many proteins localize on the plasma membrane of yeast cell to reform it into a polarized shmoo structure. The adaptor protein Ste50p, known as a pheromone signal enhancer critical for shmoo polarization, has never been explored systematically for its localization and function in the polarization process. Time-lapse single-cell imaging and quantitation shown here characterizes Ste50p involvement in the establishment of cell polarity. We found that Ste50p patches on the cell cortex mark the point of shmoo initiation, these patches could move, and remain associated with the growing shmoo tip in a pheromone concentration time-dependent manner until shmoo maturation. A Ste50p mutant impaired in patch localization suffers a delay in polarization. By quantitative analysis we show that polarization correlates with the rising levels of Ste50p, enabling rapid cell responses to pheromone that correspond to a critical level of Ste50p at the initial G1 phase. We exploited the quantitative differences in the pattern of Ste50p expression to correlate with the cell-cell phenotypic heterogeneity, showing Ste50p involvement in the cellular differentiation choice. Taken together, these findings present Ste50p to be part of the early shmoo development phase, suggesting that Ste50p may be involved with the polarisome in the initiation of polarization, and plays a role in regulating the polarized growth of shmoo during pheromone response.
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Affiliation(s)
- Nusrat Sharmeen
- Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, Quebec, Canada
- * E-mail:
| | - Chris Law
- Centre for Microscopy and Cellular Imaging, Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Cunle Wu
- Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, Quebec, Canada
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
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Pomeroy AE, Peña MI, Houser JR, Dixit G, Dohlman HG, Elston TC, Errede B. A predictive model of gene expression reveals the role of network motifs in the mating response of yeast. Sci Signal 2021; 14:14/670/eabb5235. [PMID: 33593998 DOI: 10.1126/scisignal.abb5235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Cells use signaling pathways to receive and process information about their environment. These nonlinear systems rely on feedback and feedforward regulation to respond appropriately to changing environmental conditions. Mathematical models describing signaling pathways often lack predictive power because they are not trained on data that encompass the diverse time scales on which these regulatory mechanisms operate. We addressed this limitation by measuring transcriptional changes induced by the mating response in Saccharomyces cerevisiae exposed to different dynamic patterns of pheromone. We found that pheromone-induced transcription persisted after pheromone removal and showed long-term adaptation upon sustained pheromone exposure. We developed a model of the regulatory network that captured both characteristics of the mating response. We fit this model to experimental data with an evolutionary algorithm and used the parameterized model to predict scenarios for which it was not trained, including different temporal stimulus profiles and genetic perturbations to pathway components. Our model allowed us to establish the role of four architectural elements of the network in regulating gene expression. These network motifs are incoherent feedforward, positive feedback, negative feedback, and repressor binding. Experimental and computational perturbations to these network motifs established a specific role for each in coordinating the mating response to persistent and dynamic stimulation.
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Affiliation(s)
- Amy E Pomeroy
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Matthew I Peña
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - John R Houser
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gauri Dixit
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Henrik G Dohlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Timothy C Elston
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. .,Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Beverly Errede
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Engineering a Model Cell for Rational Tuning of GPCR Signaling. Cell 2019; 177:782-796.e27. [PMID: 30955892 PMCID: PMC6476273 DOI: 10.1016/j.cell.2019.02.023] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/20/2018] [Accepted: 02/13/2019] [Indexed: 12/18/2022]
Abstract
G protein-coupled receptor (GPCR) signaling is the primary method eukaryotes use to respond to specific cues in their environment. However, the relationship between stimulus and response for each GPCR is difficult to predict due to diversity in natural signal transduction architecture and expression. Using genome engineering in yeast, we constructed an insulated, modular GPCR signal transduction system to study how the response to stimuli can be predictably tuned using synthetic tools. We delineated the contributions of a minimal set of key components via computational and experimental refactoring, identifying simple design principles for rationally tuning the dose response. Using five different GPCRs, we demonstrate how this enables cells and consortia to be engineered to respond to desired concentrations of peptides, metabolites, and hormones relevant to human health. This work enables rational tuning of cell sensing while providing a framework to guide reprogramming of GPCR-based signaling in other systems.
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Preferences in a trait decision determined by transcription factor variants. Proc Natl Acad Sci U S A 2018; 115:E7997-E8006. [PMID: 30068600 DOI: 10.1073/pnas.1805882115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Few mechanisms are known that explain how transcription factors can adjust phenotypic outputs to accommodate differing environments. In Saccharomyces cerevisiae, the decision to mate or invade relies on environmental cues that converge on a shared transcription factor, Ste12. Specificity toward invasion occurs via Ste12 binding cooperatively with the cofactor Tec1. Here, we determine the range of phenotypic outputs (mating vs. invasion) of thousands of DNA-binding domain variants in Ste12 to understand how preference for invasion may arise. We find that single amino acid changes in the DNA-binding domain can shift the preference of yeast toward either mating or invasion. These mutations define two distinct regions of this domain, suggesting alternative modes of DNA binding for each trait. We characterize the DNA-binding specificity of wild-type Ste12 to identify a strong preference for spacing and orientation of both homodimeric and heterodimeric sites. Ste12 mutants that promote hyperinvasion in a Tec1-independent manner fail to bind cooperative sites with Tec1 and bind to unusual dimeric Ste12 sites composed of one near-perfect and one highly degenerate site. We propose a model in which Ste12 alone may have evolved to activate invasion genes, which could explain how preference for invasion arose in the many fungal pathogens that lack Tec1.
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Aymoz D, Solé C, Pierre JJ, Schmitt M, de Nadal E, Posas F, Pelet S. Timing of gene expression in a cell-fate decision system. Mol Syst Biol 2018; 14:e8024. [PMID: 29695607 PMCID: PMC5916086 DOI: 10.15252/msb.20178024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During development, morphogens provide extracellular cues allowing cells to select a specific fate by inducing complex transcriptional programs. The mating pathway in budding yeast offers simplified settings to understand this process. Pheromone secreted by the mating partner triggers the activity of a MAPK pathway, which results in the expression of hundreds of genes. Using a dynamic expression reporter, we quantified the kinetics of gene expression in single cells upon exogenous pheromone stimulation and in the physiological context of mating. In both conditions, we observed striking differences in the timing of induction of mating‐responsive promoters. Biochemical analyses and generation of synthetic promoter variants demonstrated how the interplay between transcription factor binding and nucleosomes contributes to determine the kinetics of transcription in a simplified cell‐fate decision system.
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Affiliation(s)
- Delphine Aymoz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Carme Solé
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jean-Jerrold Pierre
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Marta Schmitt
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Eulàlia de Nadal
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesc Posas
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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Mapping the fine structure of a eukaryotic promoter input-output function. Nat Genet 2013; 45:1207-15. [PMID: 23955598 DOI: 10.1038/ng.2729] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Accepted: 07/22/2013] [Indexed: 12/16/2022]
Abstract
The precise tuning of gene expression levels is essential for the optimal performance of transcriptional regulatory networks. We created 209 variants of the Saccharomyces cerevisiae PHO5 promoter to quantify how different binding sites for the transcription factor Pho4 affect its output. We found that transcription-factor binding affinities determined in vitro could quantitatively predict the output of a complex yeast promoter. Promoter output was precisely tunable by subtle changes in binding-site affinity of less than 3 kcal mol(-1), which are accessible by modifying 1-2 bases. Our results provide insights into how transcription-factor binding sites regulate gene expression, their possible evolution and how they can be used to precisely tune gene expression. More generally, we show that in vitro binding-energy landscapes of transcription factors can precisely predict the output of a native yeast promoter, indicating that quantitative models of transcriptional regulatory networks are feasible.
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Abstract
Centromeres are specialized chromosomal loci that are essential for proper chromosome segregation. Recent data show that a certain level of active transcription, regulated by transcription factors Cbf1 and Ste12, makes a direct contribution to centromere function in Saccharomyces cerevisiae. Here, we discuss the requirement and function of transcription at centromeres.
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Analysis of Cryptococcus neoformans sexual development reveals rewiring of the pheromone-response network by a change in transcription factor identity. Genetics 2012; 191:435-49. [PMID: 22466042 DOI: 10.1534/genetics.112.138958] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The fundamental mechanisms that control eukaryotic development include extensive regulation at the level of transcription. Gene regulatory networks, composed of transcription factors, their binding sites in DNA, and their target genes, are responsible for executing transcriptional programs. While divergence of these control networks drives species-specific gene expression that contributes to biological diversity, little is known about the mechanisms by which these networks evolve. To investigate how network evolution has occurred in fungi, we used a combination of microarray expression profiling, cis-element identification, and transcription-factor characterization during sexual development of the human fungal pathogen Cryptococcus neoformans. We first defined the major gene expression changes that occur over time throughout sexual development. Through subsequent bioinformatic and molecular genetic analyses, we identified and functionally characterized the C. neoformans pheromone-response element (PRE). We then discovered that transcriptional activation via the PRE requires direct binding of the high-mobility transcription factor Mat2, which we conclude functions as the elusive C. neoformans pheromone-response factor. This function of Mat2 distinguishes the mechanism of regulation through the PRE of C. neoformans from all other fungal systems studied to date and reveals species-specific adaptations of a fungal transcription factor that defies predictions on the basis of sequence alone. Overall, our findings reveal that pheromone-response network rewiring has occurred at the level of transcription factor identity, despite the strong conservation of upstream and downstream components, and serve as a model for how selection pressures act differently on signaling vs. gene regulatory components during eukaryotic evolution.
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Cdk8 regulates stability of the transcription factor Phd1 to control pseudohyphal differentiation of Saccharomyces cerevisiae. Mol Cell Biol 2011; 32:664-74. [PMID: 22124158 DOI: 10.1128/mcb.05420-11] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The yeast Saccharomyces differentiates into filamentous pseudohyphae when exposed to a poor source of nitrogen in a process involving a collection of transcription factors regulated by nutrient signaling pathways. Phd1 is important for this process in that it regulates expression of most other transcription factors involved in differentiation and can induce filamentation on its own when overproduced. In this article, we show that Phd1 is an unstable protein whose degradation is initiated through phosphorylation by Cdk8 of the RNA polymerase II mediator subcomplex. Phd1 is stabilized by cdk8 disruption, and the naturally filamenting Σ1278b strain was found to have a sequence polymorphism that eliminates a Cdk8 phosphorylation site, which both stabilizes the protein and contributes to enhanced differentiation. In nitrogen-starved cells, PHD1 expression is upregulated and the Phd1 protein becomes stabilized, which causes its accumulation during differentiation. PHD1 expression is partially dependent upon Ste12, which was also previously shown to be destabilized by Cdk8-dependent phosphorylations, but to a significantly smaller extent than Phd1. These observations demonstrate the central role that Cdk8 plays in initiation of differentiation. Cdk8 activity is inhibited in cells shifted to limiting nutrient conditions, and we argue that this effect drives the initiation of differentiation through stabilization of multiple transcription factors, including Phd1, that cause activation of genes necessary for filamentous response.
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Ohkuni K, Kitagawa K. Endogenous transcription at the centromere facilitates centromere activity in budding yeast. Curr Biol 2011; 21:1695-703. [PMID: 22000103 DOI: 10.1016/j.cub.2011.08.056] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 05/06/2011] [Accepted: 08/23/2011] [Indexed: 11/15/2022]
Abstract
BACKGROUND The centromere (CEN) DNA-kinetochore complex is the specialized chromatin structure that mediates chromosome attachment to the spindle and is required for high-fidelity chromosome segregation. Although kinetochore function is conserved from budding yeast to humans, it was thought that transcription had no role in centromere function in budding yeast, in contrast to other eukaryotes including fission yeast. RESULTS We report here that transcription at the centromere facilitates centromere activity in the budding yeast Saccharomyces cerevisiae. We identified transcripts at CEN DNA and found that Cbf1, which is a transcription factor that binds to CEN DNA, is required for transcription at CEN DNA. Chromosome instability of cbf1Δ cells is suppressed by transcription driven from an artificial promoter. Furthermore, we have identified Ste12, which is a transcription factor, and Dig1, a Ste12 inhibitor, as a novel CEN-associated protein complex by an in vitro kinetochore assembly system. Dig1 represses Ste12-dependent transcription at the centromere. CONCLUSIONS Our studies reveal that transcription at the centromere plays an important role in centromere function in budding yeast.
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Affiliation(s)
- Kentaro Ohkuni
- Center for Childhood Cancer, The Research Institute, Nationwide Children's Hospital, Columbus, OH 43205, USA
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