1
|
Martinez KP, Gasmi N, Jeronimo C, Klimova N, Robert F, Turcotte B. Yeast zinc cluster transcription factors involved in the switch from fermentation to respiration show interdependency for DNA binding revealing a novel type of DNA recognition. Nucleic Acids Res 2024; 52:2242-2259. [PMID: 38109318 PMCID: PMC10954478 DOI: 10.1093/nar/gkad1185] [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: 03/27/2023] [Revised: 11/22/2023] [Accepted: 11/29/2023] [Indexed: 12/20/2023] Open
Abstract
In budding yeast, fermentation is the most important pathway for energy production. Under low-glucose conditions, ethanol is used for synthesis of this sugar requiring a shift to respiration. This process is controlled by the transcriptional regulators Cat8, Sip4, Rds2 and Ert1. We characterized Gsm1 (glucose starvation modulator 1), a paralog of Rds2 and Ert1. Genome-wide analysis showed that Gsm1 has a DNA binding profile highly similar to Rds2. Binding of Gsm1 and Rds2 is interdependent at the gluconeogenic gene FBP1. However, Rds2 is required for Gsm1 to bind at other promoters but not the reverse. Gsm1 and Rds2 also bind to DNA independently of each other. Western blot analysis revealed that Rds2 controls expression of Gsm1. In addition, we showed that the DNA binding domains of Gsm1 and Rds2 bind cooperatively in vitro to the FBP1 promoter. In contrast, at the HAP4 gene, Ert1 cooperates with Rds2 for DNA binding. Mutational analysis suggests that Gsm1/Rds2 and Ert1/Rds2 bind to short common DNA stretches, revealing a novel mode of binding for this class of factors. Two-point mutations in a HAP4 site convert it to a Gsm1 binding site. Thus, Rds2 controls binding of Gsm1 at many promoters by two different mechanisms: regulation of Gsm1 levels and increased DNA binding by formation of heterodimers.
Collapse
Affiliation(s)
- Karla Páez Martinez
- Department of Medicine, McGill University Health Centre, 1001 Boul. Décarie, Room E02.7212, Montréal, QC H4A 3J1, Canada
| | - Najla Gasmi
- Department of Biochemistry, McGill University, 1001 Boul. Décarie, Room E02.7212, Montréal, QC H4A 3J1, Canada
| | - Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Natalia Klimova
- Department of Medicine, McGill University Health Centre, 1001 Boul. Décarie, Room E02.7212, Montréal, QC H4A 3J1, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
- Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, QC H3T 1J4, Canada
| | - Bernard Turcotte
- Department of Medicine, McGill University Health Centre, 1001 Boul. Décarie, Room E02.7212, Montréal, QC H4A 3J1, Canada
- Department of Biochemistry, McGill University, 1001 Boul. Décarie, Room E02.7212, Montréal, QC H4A 3J1, Canada
- Department of Microbiology and Immunology, McGill University, 1001 Boul. Décarie, Room E02.7212, Montréal, QC H4A 3J1, Canada
| |
Collapse
|
2
|
Buechel ER, Pinkett HW. Activity of the pleiotropic drug resistance transcription factors Pdr1p and Pdr3p is modulated by binding site flanking sequences. FEBS Lett 2024; 598:169-186. [PMID: 37873734 PMCID: PMC10843404 DOI: 10.1002/1873-3468.14762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/25/2023]
Abstract
The transcription factors Pdr1p and Pdr3p regulate pleiotropic drug resistance (PDR) in Saccharomyces cerevisiae via the PDR responsive elements (PDREs) to modulate gene expression. However, the exact mechanisms underlying the differences in their regulons remain unclear. Employing genomic occupancy profiling (CUT&RUN), binding assays, and transcription studies, we characterized the differences in sequence specificity between transcription factors. Findings reveal distinct preferences for core PDRE sequences and the flanking sequences for both proteins. While flanking sequences moderately alter DNA binding affinity, they significantly impact Pdr1/3p transcriptional activity. Notably, both proteins demonstrated the ability to bind half sites, showing potential enhancement of transcription from adjacent PDREs. This insight sheds light on ways Pdr1/3p can differentially regulate PDR.
Collapse
Affiliation(s)
- Evan R. Buechel
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Heather W. Pinkett
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| |
Collapse
|
3
|
Buechel ER, Pinkett HW. Unraveling the Half and Full Site Sequence Specificity of the Saccharomyces cerevisiae Pdr1p and Pdr3p Transcription Factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.553033. [PMID: 37609128 PMCID: PMC10441396 DOI: 10.1101/2023.08.11.553033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The transcription factors Pdr1p and Pdr3p regulate pleotropic drug resistance (PDR) in Saccharomyces cerevisiae , via the PDR responsive elements (PDREs) to modulate gene expression. However, the exact mechanisms underlying the differences in their regulons remain unclear. Employing genomic occupancy profiling (CUT&RUN), binding assays, and transcription studies, we characterized the differences in sequence specificity between transcription factors. Findings reveal distinct preferences for core PDRE sequences and the flanking sequences for both proteins. While flanking sequences moderately alter DNA binding affinity, they significantly impact Pdr1/3p transcriptional activity. Notably, both proteins demonstrated the ability to bind half sites, showing potential enhancement of transcription from adjacent PDREs. This insight sheds light on ways Pdr1/3 can differentially regulate PDR.
Collapse
|
4
|
Garg A, Goldgur Y, Sanchez AM, Schwer B, Shuman S. Structure of Fission Yeast Transcription Factor Pho7 Bound to pho1 Promoter DNA and Effect of Pho7 Mutations on DNA Binding and Phosphate Homeostasis. Mol Cell Biol 2019; 39:e00132-19. [PMID: 31010807 PMCID: PMC6580706 DOI: 10.1128/mcb.00132-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/11/2019] [Accepted: 04/15/2019] [Indexed: 11/20/2022] Open
Abstract
Pho7 is the Schizosaccharomyces pombe fission yeast Zn2Cys6 transcriptional factor that drives a response to phosphate starvation in which phosphate acquisition genes are upregulated. Here we report a crystal structure at 1.6-Å resolution of the Pho7 DNA-binding domain (DBD) bound at its target site 2 in the pho1 promoter (5'-TCGGAAATTAAAAA). Comparison to the previously reported structure of Pho7 DBD in complex with its binding site in the tgp1 promoter (5'-TCGGACATTCAAAT) reveals shared determinants of target site specificity as well as variations in the protein-DNA interface that accommodate different promoter DNA sequences. Mutagenesis of Pho7 amino acids at the DNA interface identified nucleobase contacts at the periphery of the footprint that are essential for the induction of pho1 expression in response to phosphate starvation and for Pho7 binding to site 1 in the pho1 promoter.
Collapse
Affiliation(s)
- Angad Garg
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York, USA
| | - Yehuda Goldgur
- Structural Biology Program, Sloan-Kettering Institute, New York, New York, USA
| | - Ana M Sanchez
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York, USA
| | - Beate Schwer
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York, USA
| |
Collapse
|
5
|
Garg A, Goldgur Y, Schwer B, Shuman S. Distinctive structural basis for DNA recognition by the fission yeast Zn2Cys6 transcription factor Pho7 and its role in phosphate homeostasis. Nucleic Acids Res 2019; 46:11262-11273. [PMID: 30212894 PMCID: PMC6265462 DOI: 10.1093/nar/gky827] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/05/2018] [Indexed: 01/11/2023] Open
Abstract
Pho7, a member of the Zn2Cys6 family of fungal transcription factors, is the key transcriptional activator underlying fission yeast phosphate homeostasis, a physiological response to phosphate starvation in which the pho1, pho84 and tgp1 genes are upregulated. Here, we delineated a minimized 61-amino-acid Pho7 DNA-binding domain (DBD) and determined the 1.7 Å crystal structure of the DBD at its target site in the tgp1 promoter. Two distinctive features of the Pho7 DBD are: it binds DNA as a monomer, unlike most other fungal zinc-cluster factors that bind as homodimers; and it makes extensive interactions with its asymmetric target sequence over a 14-bp footprint that entails hydrogen bonding to 13 individual bases within, and remote from, the CGG triplet typically recognized by other Zn2Cys6 DBDs. Base pair substitutions at Pho7 sites in the tgp1 and pho1 promoters highlight the importance of the 5′-CGG triplet for Pho7 binding in vitro and Pho7-dependent gene expression in vivo. We identify several DBD amino acids at which alanine substitution effaced or attenuated the pho1 phosphate starvation response and concordantly reduced Pho7 binding to a pho1 promoter site.
Collapse
Affiliation(s)
- Angad Garg
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Yehuda Goldgur
- Structural Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| |
Collapse
|
6
|
Defining the DNA Binding Site Recognized by the Fission Yeast Zn 2Cys 6 Transcription Factor Pho7 and Its Role in Phosphate Homeostasis. mBio 2017; 8:mBio.01218-17. [PMID: 28811350 PMCID: PMC5559640 DOI: 10.1128/mbio.01218-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fission yeast phosphate homeostasis entails transcriptional induction of genes encoding phosphate-mobilizing proteins under conditions of phosphate starvation. Transcription factor Pho7, a member of the Zn2Cys6 family of fungal transcription regulators, is the central player in the starvation response. The DNA binding sites in the promoters of phosphate-responsive genes have not been defined, nor have any structure-function relationships been established for the Pho7 protein. Here we narrow this knowledge gap by (i) delineating an autonomous DNA-binding domain (DBD) within Pho7 that includes the Zn2Cys6 module, (ii) deploying recombinant Pho7 DBD in DNase I footprinting and electrophoretic mobility shift assays (EMSAs) to map the Pho7 recognition sites in the promoters of the phosphate-regulated pho1 and tgp1 genes to a 12-nucleotide sequence motif [5′-TCG(G/C)(A/T)xxTTxAA], (iii) independently identifying the same motif as a Pho7 recognition element via in silico analysis of available genome-wide ChIP-seq data, (iv) affirming that mutations in the two Pho7 recognition sites in the pho1 promoter efface pho1 expression in vivo, and (v) establishing that the zinc-binding cysteines and a pair of conserved arginines in the DBD are essential for Pho7 activity in vivo. Fungi respond to phosphate starvation by inducing the transcription of a set of phosphate acquisition genes that comprise a phosphate regulon. Pho7, a member of the Zn2Cys6 family of fungal transcription regulators, is the central player in the phosphate starvation response in fission yeast. The present study identifies a 12-nucleotide Pho7 DNA binding motif [5′-TCG(G/C)(A/T)xxTTxAA] in the promoters of phosphate-regulated genes, pinpoints DNA and protein features important for Pho7 binding to DNA, and correlates them with Pho7-dependent gene expression in vivo. The results highlight distinctive properties of Pho7 vis-a-vis other fungal zinc binuclear cluster transcription factors as well as the divergent cast of transcription factors deployed for phosphate homeostasis in fission yeast versus budding yeast.
Collapse
|
7
|
Böhm L, Muralidhara P, Pérez JC. ACandida albicansregulator of disseminated infection operates primarily as a repressor and governs cell surface remodeling. Mol Microbiol 2016; 100:328-44. [DOI: 10.1111/mmi.13320] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2015] [Indexed: 11/26/2022]
Affiliation(s)
- Lena Böhm
- Interdisciplinary Center for Clinical Research, University Hospital Würzburg; Würzburg Germany
- Institute for Molecular Infection Biology, University of Würzburg; Würzburg Germany
| | | | - J. Christian Pérez
- Interdisciplinary Center for Clinical Research, University Hospital Würzburg; Würzburg Germany
- Institute for Molecular Infection Biology, University of Würzburg; Würzburg Germany
| |
Collapse
|
8
|
Silvestrini L, Rossi B, Gallmetzer A, Mathieu M, Scazzocchio C, Berardi E, Strauss J. Interaction of Yna1 and Yna2 Is Required for Nuclear Accumulation and Transcriptional Activation of the Nitrate Assimilation Pathway in the Yeast Hansenula polymorpha. PLoS One 2015; 10:e0135416. [PMID: 26335797 PMCID: PMC4559421 DOI: 10.1371/journal.pone.0135416] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 07/21/2015] [Indexed: 12/11/2022] Open
Abstract
A few yeasts, including Hansenula polymorpha are able to assimilate nitrate and use it as nitrogen source. The genes necessary for nitrate assimilation are organised in this organism as a cluster comprising those encoding nitrate reductase (YNR1), nitrite reductase (YNI1), a high affinity transporter (YNT1), as well as the two pathway specific Zn(II)2Cys2 transcriptional activators (YNA1, YNA2). Yna1p and Yna2p mediate induction of the system and here we show that their functions are interdependent. Yna1p activates YNA2 as well as its own (YNA1) transcription thus forming a nitrate-dependent autoactivation loop. Using a split-YFP approach we demonstrate here that Yna1p and Yna2p form a heterodimer independently of the inducer and despite both Yna1p and Yna2p can occupy the target promoter as mono- or homodimer individually, these proteins are transcriptionally incompetent. Subsequently, the transcription factors target genes containing a conserved DNA motif (termed nitrate-UAS) determined in this work by in vitro and in vivo protein-DNA interaction studies. These events lead to a rearrangement of the chromatin landscape on the target promoters and are associated with the onset of transcription of these target genes. In contrast to other fungi and plants, in which nuclear accumulation of the pathway-specific transcription factors only occur in the presence of nitrate, Yna1p and Yna2p are constitutively nuclear in H. polymorpha. Yna2p is needed for this nuclear accumulation and Yna1p is incapable of strictly positioning in the nucleus without Yna2p. In vivo DNA footprinting and ChIP analyses revealed that the permanently nuclear Yna1p/Yna2p heterodimer only binds to the nitrate-UAS when the inducer is present. The nitrate-dependent up-regulation of one partner protein in the heterodimeric complex is functionally similar to the nitrate-dependent activation of nuclear accumulation in other systems.
Collapse
Affiliation(s)
- Lucia Silvestrini
- Fungal Genetics and Genomics Unit, Division of Microbial Genetics and Pathogen Interactions, BOKU-University of Natural Resources and Life Sciences Vienna, University and Research Center Tulln, Konrad Lorenz Strasse 24, 3430, Tulln/Donau, Austria
- Laboratorio di Genetica Microbica, DiSA, Universitá Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Beatrice Rossi
- Laboratorio di Genetica Microbica, DiSA, Universitá Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Universitè Paris-Sud, Orsay, France
| | - Andreas Gallmetzer
- Fungal Genetics and Genomics Unit, Division of Microbial Genetics and Pathogen Interactions, BOKU-University of Natural Resources and Life Sciences Vienna, University and Research Center Tulln, Konrad Lorenz Strasse 24, 3430, Tulln/Donau, Austria
| | - Martine Mathieu
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Universitè Paris-Sud, Orsay, France
| | - Claudio Scazzocchio
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Universitè Paris-Sud, Orsay, France
- Department of Microbiology, Imperial College, London, United Kingdom
| | - Enrico Berardi
- Laboratorio di Genetica Microbica, DiSA, Universitá Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Joseph Strauss
- Fungal Genetics and Genomics Unit, Division of Microbial Genetics and Pathogen Interactions, BOKU-University of Natural Resources and Life Sciences Vienna, University and Research Center Tulln, Konrad Lorenz Strasse 24, 3430, Tulln/Donau, Austria
- Health and Environment Department, Austrian Institute of Technology GmbH (AIT), University and Research Center Tulln, Konrad Lorenz Strasse 24, 3430, Tulln/Donau, Austria
- * E-mail:
| |
Collapse
|
9
|
Gressler M, Hortschansky P, Geib E, Brock M. A new high-performance heterologous fungal expression system based on regulatory elements from the Aspergillus terreus terrein gene cluster. Front Microbiol 2015; 6:184. [PMID: 25852654 PMCID: PMC4360782 DOI: 10.3389/fmicb.2015.00184] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/19/2015] [Indexed: 11/13/2022] Open
Abstract
Recently, the Aspergillus terreus terrein gene cluster was identified and selected for development of a new heterologous expression system. The cluster encodes the specific transcription factor TerR that is indispensable for terrein cluster induction. To identify TerR binding sites, different recombinant versions of the TerR DNA-binding domain were analyzed for specific motif recognition. The high affinity consensus motif TCGGHHWYHCGGH was identified from genes required for terrein production and binding site mutations confirmed their essential contribution to gene expression in A. terreus. A combination of TerR with its terA target promoter was tested as recombinant expression system in the heterologous host Aspergillus niger. TerR mediated target promoter activation was directly dependent on its transcription level. Therefore, terR was expressed under control of the regulatable amylase promoter PamyB and the resulting activation of the terA target promoter was compared with activation levels obtained from direct expression of reporters from the strong gpdA control promoter. Here, the coupled system outcompeted the direct expression system. When the coupled system was used for heterologous polyketide synthase expression high metabolite levels were produced. Additionally, expression of the Aspergillus nidulans polyketide synthase gene orsA revealed lecanoric acid rather than orsellinic acid as major polyketide synthase product. Domain swapping experiments assigned this depside formation from orsellinic acid to the OrsA thioesterase domain. These experiments confirm the suitability of the expression system especially for high-level metabolite production in heterologous hosts.
Collapse
Affiliation(s)
- Markus Gressler
- Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute Jena, Germany
| | - Peter Hortschansky
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute Jena, Germany
| | - Elena Geib
- Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute Jena, Germany
| | - Matthias Brock
- Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute Jena, Germany ; Institute for Microbiology, Friedrich Schiller University Jena, Germany
| |
Collapse
|
10
|
How duplicated transcription regulators can diversify to govern the expression of nonoverlapping sets of genes. Genes Dev 2014; 28:1272-7. [PMID: 24874988 PMCID: PMC4066398 DOI: 10.1101/gad.242271.114] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The duplication of transcription regulators can elicit major regulatory network rearrangements over evolutionary timescales. However, few examples of duplications resulting in gene network expansions are understood in molecular detail. Here we show that four Candida albicans transcription regulators that arose by successive duplications have differentiated from one another by acquiring different intrinsic DNA-binding specificities, different preferences for half-site spacing, and different associations with cofactors. The combination of these three mechanisms resulted in each of the four regulators controlling a distinct set of target genes, which likely contributed to the adaption of this fungus to its human host. Our results illustrate how successive duplications and diversification of an ancestral transcription regulator can underlie major changes in an organism's regulatory circuitry.
Collapse
|
11
|
Mutations in the basic loop of the Zn binuclear cluster of the UaY transcriptional activator suppress mutations in the dimerisation domain. Fungal Genet Biol 2012; 49:731-43. [DOI: 10.1016/j.fgb.2012.06.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 06/06/2012] [Accepted: 06/08/2012] [Indexed: 11/19/2022]
|
12
|
Petrovska I, Kumamoto CA. Functional importance of the DNA binding activity of Candida albicans Czf1p. PLoS One 2012; 7:e39624. [PMID: 22761849 PMCID: PMC3384613 DOI: 10.1371/journal.pone.0039624] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 05/29/2012] [Indexed: 01/07/2023] Open
Abstract
The human opportunistic pathogen Candida albicans undergoes a reversible morphological transition between the yeast and hyphal states in response to a variety of signals. One such environmental trigger is growth within a semisolid matrix such as agar medium. This growth condition is of interest because it may mimic the growth of C. albicans in contact with host tissue during infection. During growth within a semisolid matrix, hyphal growth is positively regulated by the transcriptional regulator Czf1p and negatively by a second key transcriptional regulator, Efg1p. Genetic studies indicate that Czf1p, a member of the zinc-cluster family of transcriptional regulators, exerts its function by opposing the inhibitory influence of Efg1p on matrix-induced filamentous growth. We examined the importance of the two known activities of Czf1p, DNA-binding and interaction with Efg1p. We found that the two activities were separable by mutation allowing us to demonstrate that the DNA-binding activity of Czf1p was essential for its role as a positive regulator of morphogenesis. Surprisingly, however, interactions with Efg1p appeared to be largely dispensable. Our studies provide the first evidence of a key role for the DNA-binding activity of Czf1p in the morphological yeast-to-hyphal transition triggered by matrix-embedded growth.
Collapse
Affiliation(s)
- Ivana Petrovska
- Graduate Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Carol A. Kumamoto
- Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Boston, Massachusetts, United States of America
| |
Collapse
|
13
|
Metabolic control of transcription: paradigms and lessons from Saccharomyces cerevisiae. Biochem J 2008; 414:177-87. [PMID: 18687061 DOI: 10.1042/bj20080923] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The comparatively simple eukaryote Saccharomyces cerevisiae is composed of some 6000 individual genes. Specific sets of these genes can be transcribed co-ordinately in response to particular metabolic signals. The resultant integrated response to nutrient challenge allows the organism to survive and flourish in a variety of environmental conditions while minimal energy is expended upon the production of unnecessary proteins. The Zn(II)2Cys6 family of transcriptional regulators is composed of some 46 members in S. cerevisiae and many of these have been implicated in mediating transcriptional responses to specific nutrients. Gal4p, the archetypical member of this family, is responsible for the expression of the GAL genes when galactose is utilized as a carbon source. The regulation of Gal4p activity has been studied for many years, but we are still uncovering both nuances and fundamental control mechanisms that impinge on its function. In the present review, we describe the latest developments in the regulation of GAL gene expression and compare the mechanisms employed here with the molecular control of other Zn(II)2Cys6 transcriptional regulators. This reveals a wide array of protein-protein, protein-DNA and protein-nutrient interactions that are employed by this family of regulators.
Collapse
|
14
|
Hong M, Fitzgerald MX, Harper S, Luo C, Speicher DW, Marmorstein R. Structural basis for dimerization in DNA recognition by Gal4. Structure 2008; 16:1019-26. [PMID: 18611375 PMCID: PMC2515386 DOI: 10.1016/j.str.2008.03.015] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Revised: 03/28/2008] [Accepted: 03/28/2008] [Indexed: 01/07/2023]
Abstract
Gal4 is a Zn2Cys6 binuclear cluster containing transcription factor that binds DNA as a homodimer and can activate transcription by interacting with the mutant Gal11P protein. Although structures have been reported of the Gal4 dimerization domain and the binuclear cluster domain bound to DNA as a dimer, the structure of the "complete" Gal4 dimer bound to DNA has not previously been described. Here we report the structure of a complete Gal4 dimer bound to DNA and additional biochemical studies to address the molecular basis for Gal4 dimerization in DNA binding. We find that Gal4 dimerization on DNA is mediated by an intertwined helical bundle that deviates significantly from the solution NMR structure of the free dimerization domain. Associated biochemical studies show that the dimerization domain of Gal4 is important for DNA binding and protein thermostability. We also map the interaction surface of the Gal4 dimerization domain with Gal11P.
Collapse
Affiliation(s)
- Manqing Hong
- The Wistar Institute, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | | | | | | |
Collapse
|
15
|
Bellizzi JJ, Sorger PK, Harrison SC. Crystal structure of the yeast inner kinetochore subunit Cep3p. Structure 2007; 15:1422-30. [PMID: 17997968 PMCID: PMC2288795 DOI: 10.1016/j.str.2007.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Revised: 09/07/2007] [Accepted: 09/10/2007] [Indexed: 01/07/2023]
Abstract
In budding yeast, the four-protein CBF3 complex (Skp1p-Ctf13p-Cep3p-Ndc10p) initiates kinetochore assembly by binding to the CDEIII locus of centromeric DNA. A Cep3p dimer recruits a Skp1p-Ctf13p heterodimer and contacts two sites on CDEIII. We report here the crystal structure, determined at 2.8 A resolution by multiple isomorphous replacement with anomalous scattering, of a truncated Cep3p (Cep3p [47-608]), comprising all but an N-terminal, Zn(2)Cys(6)-cluster, DNA-binding module. Cep3p has a well-ordered structure throughout essentially all of its polypeptide chain, unlike most yeast transcription factors, including those with Zn(2)Cys(6) clusters, such as Gal4p. This difference may reflect an underlying functional distinction: whereas any particular transcription factor must adapt to a variety of upstream activating sites, Cep3p scaffolds kinetochore assembly on centromeres uniformly configured on all 16 yeast chromosomes. We have, using the structure of Cep3p (47-608) and the known structures of Zn(2)Cys(6)-cluster domains, modeled the interaction of Cep3p with CDEIII.
Collapse
Affiliation(s)
- John J. Bellizzi
- Jack and Eileen Connors Laboratory of Structural Biology Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston MA 02115
| | - Peter K. Sorger
- Department of Systems Biology, Harvard Medical School, Boston MA 02115
| | - Stephen C. Harrison
- Jack and Eileen Connors Laboratory of Structural Biology Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston MA 02115
- Howard Hughes Medical Institute, Harvard Medical School, Boston MA 02115
| |
Collapse
|
16
|
Soontorngun N, Larochelle M, Drouin S, Robert F, Turcotte B. Regulation of gluconeogenesis in Saccharomyces cerevisiae is mediated by activator and repressor functions of Rds2. Mol Cell Biol 2007; 27:7895-905. [PMID: 17875938 PMCID: PMC2169140 DOI: 10.1128/mcb.01055-07] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Saccharomyces cerevisiae, RDS2 encodes a zinc cluster transcription factor with unknown function. Here, we unravel a key function of Rds2 in gluconeogenesis using chromatin immunoprecipitation-chip technology. While we observed that Rds2 binds to only a few promoters in glucose-containing medium, it binds many additional genes when the medium is shifted to ethanol, a nonfermentable carbon source. Interestingly, many of these genes are involved in gluconeogenesis, the tricarboxylic acid cycle, and the glyoxylate cycle. Importantly, we show that Rds2 has a dual function: it directly activates the expression of gluconeogenic structural genes while it represses the expression of negative regulators of this pathway. We also show that the purified DNA binding domain of Rds2 binds in vitro to carbon source response elements found in the promoters of target genes. Finally, we show that upon a shift to ethanol, Rds2 activation is correlated with its hyperphosphorylation by the Snf1 kinase. In summary, we have characterized Rds2 as a novel major regulator of gluconeogenesis.
Collapse
Affiliation(s)
- Nitnipa Soontorngun
- Department of Medicine, Royal Victoria Hospital, McGill University,Montréal, Québec, Canada H3A 1A1
| | | | | | | | | |
Collapse
|
17
|
MacPherson S, Larochelle M, Turcotte B. A fungal family of transcriptional regulators: the zinc cluster proteins. Microbiol Mol Biol Rev 2006; 70:583-604. [PMID: 16959962 PMCID: PMC1594591 DOI: 10.1128/mmbr.00015-06] [Citation(s) in RCA: 439] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The trace element zinc is required for proper functioning of a large number of proteins, including various enzymes. However, most zinc-containing proteins are transcription factors capable of binding DNA and are named zinc finger proteins. They form one of the largest families of transcriptional regulators and are categorized into various classes according to zinc-binding motifs. This review focuses on one class of zinc finger proteins called zinc cluster (or binuclear) proteins. Members of this family are exclusively fungal and possess the well-conserved motif CysX(2)CysX(6)CysX(5-12)CysX(2)CysX(6-8)Cys. The cysteine residues bind to two zinc atoms, which coordinate folding of the domain involved in DNA recognition. The first- and best-studied zinc cluster protein is Gal4p, a transcriptional activator of genes involved in the catabolism of galactose in the budding yeast Saccharomyces cerevisiae. Since the discovery of Gal4p, many other zinc cluster proteins have been characterized; they function in a wide range of processes, including primary and secondary metabolism and meiosis. Other roles include regulation of genes involved in the stress response as well as pleiotropic drug resistance, as demonstrated in budding yeast and in human fungal pathogens. With the number of characterized zinc cluster proteins growing rapidly, it is becoming more and more apparent that they are important regulators of fungal physiology.
Collapse
Affiliation(s)
- Sarah MacPherson
- Department of Microbiology and Immunology, Royal Victoria Hospital, McGill University, Montréal, Québec, Canada H3A 1A
| | | | | |
Collapse
|