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Mathematical model of GAL regulon dynamics in Saccharomyces cerevisiae. J Theor Biol 2011; 293:219-35. [PMID: 22024631 DOI: 10.1016/j.jtbi.2011.10.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/24/2011] [Accepted: 10/11/2011] [Indexed: 11/21/2022]
Abstract
Genetic switches are prevalent in nature and provide cells with a strategy to adapt to changing environments. The GAL switch is an intriguing example which is not understood in all detail. The GAL switch allows organisms to metabolize galactose, and controls whether the machinery responsible for the galactose metabolism is turned on or off. Currently, it is not known exactly how the galactose signal is sensed by the transcriptional machinery. Here we utilize quantitative tools to understand the S. cerevisiae cell response to galactose challenge, and to analyze the plausible molecular mechanisms underlying its operation. We work at a population level to develop a dynamic model based on the interplay of the key regulatory proteins Gal4p, Gal80p, and Gal3p. To our knowledge, the model presented here is the first to reproduce qualitatively the bistable network behavior found experimentally. Given the current understanding of the GAL circuit induction (Wightman et al., 2008; Jiang et al., 2009), we propose that the most likely in vivo mechanism leading to the transcriptional activation of the GAL genes is the physical interaction between galactose-activated Gal3p and Gal80p, with the complex Gal3p-Gal80p remaining bound at the GAL promoters. Our mathematical model is in agreement with the flow cytometry profiles of wild type, gal3Δ and gal80Δ mutant strains from Acar et al. (2005), and involves a fraction of actively transcribing cells with the same qualitative features as in the data set collected by Acar et al. (2010). Furthermore, the computational modeling provides an explanation for the contradictory results obtained by independent laboratories when tackling experimentally the issue of binary versus graded response to galactose induction.
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Ferdous A, O’Neal M, Nalley K, Sikder D, Kodadek T, Johnston SA. Phosphorylation of the Gal4 DNA-binding domain is essential for activator mono-ubiquitylation and efficient promoter occupancy. MOLECULAR BIOSYSTEMS 2008; 4:1116-25. [PMID: 18931787 PMCID: PMC4451857 DOI: 10.1039/b809291e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent analysis of a Gal4 mutant (Gap71) carrying three point mutations (S22D, K23Q and K25F) in its DNA-binding domain (DBD), has demonstrated that it cannot occupy GAL promoters efficiently in cells and that it is not mono-ubiquitylated, suggesting a functional link between this modification and stable DNA binding in cells. The mechanistic underpinning of this phenotype is that this protein is hypersensitive to a newly discovered activity of the proteasomal ATPases--their ability to actively dissociate transcription factor-DNA complexes after direct interaction with the activation domain. In this paper, we examine the roles of each of the three point mutations contained in Gap71 individually. These experiments have revealed that serine 22 is a site of phosphorylation in the Gal4 DBD and that lysine 23 is essential for S22 phosphorylation, possibly acting as part of the kinase recognition site. Mutation of either residue blocks Gal4 DBD phosphorylation, its subsequent ubiquitylation and compromises the ability of the activator to bind promoter DNA in vivo. These data represent the first report of an essential phosphorylation event that is critical for the activity of this paradigmatic transcription factor.
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Affiliation(s)
- Anwarul Ferdous
- Departments of Internal Medicine, Molecular Biology and Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-8573
| | - Melissa O’Neal
- Departments of Internal Medicine, Molecular Biology and Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-8573
| | - Kip Nalley
- Departments of Internal Medicine, Molecular Biology and Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-8573
| | - Devanjan Sikder
- Departments of Internal Medicine, Molecular Biology and Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-8573
| | - Thomas Kodadek
- Departments of Internal Medicine, Molecular Biology and Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-8573
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Sellick CA, Campbell RN, Reece RJ. Galactose metabolism in yeast-structure and regulation of the leloir pathway enzymes and the genes encoding them. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008; 269:111-50. [PMID: 18779058 DOI: 10.1016/s1937-6448(08)01003-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The enzymes of the Leloir pathway catalyze the conversion of galactose to a more metabolically useful version, glucose-6-phosphate. This pathway is required as galactose itself cannot be used for glycolysis directly. In most organisms, including the yeast Saccharomyces cerevisiae, five enzymes are required to catalyze this conversion: a galactose mutarotase, a galactokinase, a galactose-1-phosphate uridyltransferase, a UDP-galactose-4-epimerase, and a phosphoglucomutase. In yeast, the genes encoding these enzymes are tightly controlled at the level of transcription and are only transcribed under specific sets of conditions. In the presence of glucose, the genes encoding the Leloir pathway enzymes (often called the GAL genes) are repressed through the action of a transcriptional repressor Mig1p. In the presence of galactose, but in the absence of glucose, the concerted actions of three other proteins Gal4p, Gal80p, and Gal3p, and two small molecules (galactose and ATP) enable the rapid and high-level activation of the GAL genes. The precise molecular mechanism of the GAL genetic switch is controversial. Recent work on solving the three-dimensional structures of the various GAL enzymes proteins and the GAL transcriptional switch proteins affords a unique opportunity to delve into the precise, and potentially unambiguous, molecular mechanism of a highly exploited transcriptional circuit. Understanding the details of the transcriptional and metabolic events that occur in this pathway can be used as a paradigm for understanding the integration of metabolism and transcriptional control more generally, and will assist our understanding of fundamental biochemical processes and how these might be exploited.
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Leverentz MK, Reece RJ. Phosphorylation of Zn(II)2Cys6 proteins: a cause or effect of transcriptional activation? Biochem Soc Trans 2007; 34:794-7. [PMID: 17052200 DOI: 10.1042/bst0340794] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Many Zn(II)2Cys6 transcriptional regulators exhibit changes in phosphorylation that are coincident with their roles in transcriptional activation. It is, however, unclear whether these changes occur as a cause of, or as a result of, transcriptional activation. In this paper, we explore the relationship between these two events and collate data available on the phosphorylation state of those transcriptional regulators where the relationship has not been clearly identified.
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Affiliation(s)
- M K Leverentz
- Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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5
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Smidtas S, Schächter V, Képès F. The adaptive filter of the yeast galactose pathway. J Theor Biol 2006; 242:372-81. [DOI: 10.1016/j.jtbi.2006.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2005] [Revised: 02/20/2006] [Accepted: 03/10/2006] [Indexed: 11/16/2022]
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6
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Sellick CA, Reece RJ. Eukaryotic transcription factors as direct nutrient sensors. Trends Biochem Sci 2005; 30:405-12. [PMID: 15950477 DOI: 10.1016/j.tibs.2005.05.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2005] [Revised: 05/03/2005] [Accepted: 05/24/2005] [Indexed: 11/23/2022]
Abstract
The recognition of changes in environmental conditions, and the ability to adapt to these changes, is essential for the viability of cells. There are numerous well-characterized systems by which the presence or absence of an individual metabolite can be recognized by a cell. The recognition of a metabolite is, however, just one step of a process that often results in changes in the expression of sets of genes required to respond to that metabolite. The signalling pathway between metabolite recognition and transcriptional control is often complex. However, recent evidence from yeast suggests that complex signalling pathways might be circumvented via the direct interaction between individual metabolites and regulators of RNA polymerase II transcription.
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Affiliation(s)
- Christopher A Sellick
- The University of Manchester, Faculty of Life Sciences, The Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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7
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Erkine AM. Activation domains of gene-specific transcription factors: are histones among their targets? Biochem Cell Biol 2004; 82:453-9. [PMID: 15284898 DOI: 10.1139/o04-036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Activation domains of promoter-specific transcription factors are critical entities involved in recruitment of multiple protein complexes to gene promoters. The activation domains often retain functionality when transferred between very diverse eukaryotic phyla, yet the amino acid sequences of activation domains do not bear any specific consensus or secondary structure. Activation domains function in the context of chromatin structure and are critical for chromatin remodeling, which is associated with transcription initiation. The mechanisms of direct and indirect recruitment of chromatin-remodeling and histone-modifying complexes, including mechanisms involving direct interactions between activation domains and histones, are discussed.Key words: activation domain, transcription, chromatin, nucleosome.
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Affiliation(s)
- Alexandre M Erkine
- Division of Basic Biomedical Sciences, University of South Dakota School of Medicine, Vermillion 57069, USA.
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8
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Bhatnagar D, Ehrlich KC, Cleveland TE. Molecular genetic analysis and regulation of aflatoxin biosynthesis. Appl Microbiol Biotechnol 2003; 61:83-93. [PMID: 12655449 DOI: 10.1007/s00253-002-1199-x] [Citation(s) in RCA: 139] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2002] [Revised: 11/04/2002] [Accepted: 11/08/2002] [Indexed: 11/25/2022]
Abstract
Aflatoxins, produced by some Aspergillus species, are toxic and extremely carcinogenic furanocoumarins. Recent investigations of the molecular mechanism of AFB biosynthesis showed that the genes required for biosynthesis are in a 70 kb gene cluster. They encode a DNA-binding protein functioning in aflatoxin pathway gene regulation, and other enzymes such as cytochrome p450-type monooxygenases, dehydrogenases, methyltransferases, and polyketide and fatty acid synthases. Information gained from these studies has led to a better understanding of aflatoxin biosynthesis by these fungi. The characterization of genes involved in aflatoxin formation affords the opportunity to examine the mechanism of molecular regulation of the aflatoxin biosynthetic pathway, particularly during the interaction between aflatoxin-producing fungi and plants.
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Affiliation(s)
- D Bhatnagar
- Southern Regional Research Center, ARS, USDA, New Orleans, LA 70124, USA.
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9
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Sharma D, Ohri S, Dixit A. The -148 to -124 region of c-jun interacts with a positive regulatory factor in rat liver and enhances transcription. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:181-9. [PMID: 12605669 DOI: 10.1046/j.1432-1033.2003.03369.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The c-jun gene encodes the protein Jun, a component of the essential transcription factor, AP1. Jun/AP-1 occupies a central position in signal transduction pathways as it is responsible for the induction of a number of genes in response to growth promoters. However, the exact mechanisms leading to an enhanced expression of the c-jun gene itself during proliferation, differentiation, cell growth and development are not fully understood. Cell culture studies have given some insight in the mechanisms involved in the up-regulation of c-jun expression by UV irradiation and phorbol esters. However, it is well known that transformed cells do not accurately reflect the biology of a normal cell. We now report the identification of a positive regulatory factor from normal rat liver that activates transcription from the c-jun promoter by binding to the -148 to -124 region of c-jun. Preincubation of fractionated rat liver nuclear extract with an oligonucleotide encompassing this region of the gene significantly reduced transcription from cloned c-jun promoter. In vitro transfection studies using green fluorescent protein as a reporter gene under the control of the c-jun promoter with (-148 to +53) and without (-123 to +53) this region further confirmed its role in transcription. A DNA-binding protein factor, interacting with this region of c-jun was identified from rat liver by using electrophoretic mobility shift assays. This factor binds to its recognition sequence only in the phosphorylated form and exhibits high affinity and specificity. UV cross-linking studies, South-Western analysis and affinity purification collectively indicated the factor to be approximately 40 kDa and to bind to its recognition sequence as a dimer.
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Affiliation(s)
- Dipali Sharma
- Gene Regulation Laboratory, Center for Biotechnology, Jawaharlal Nehru University, New Delhi-110067, India
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Chang C, Gonzalez F, Rothermel B, Sun L, Johnston SA, Kodadek T. The Gal4 activation domain binds Sug2 protein, a proteasome component, in vivo and in vitro. J Biol Chem 2001; 276:30956-63. [PMID: 11418596 DOI: 10.1074/jbc.m102254200] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
An in vivo protein interaction assay was used to search a yeast cDNA library for proteins that bind to the acidic activation domain (AD) of the yeast Gal4 protein. Sug2 protein, a component of the 19 S regulatory particle of the 26 S proteasome, was one of seven proteins identified in this screen. In vitro binding assays confirm a direct interaction between these proteins. SUG2 and SUG1, another 19 S component, were originally discovered as a mutation able to suppress the phenotype of a Gal4 truncation mutant (Gal4(D)p) lacking much of its AD. Sug1p has previously been shown to bind the Gal4 AD in vitro. Taken together, these genetic and biochemical data suggest a biologically significant interaction between the Gal4 protein and the 19 S regulatory particle of the proteasome. Indeed, it is demonstrated here that the Gal4 AD interacts specifically with immunopurified 19 S complex. The proteasome regulatory particle has been shown recently to play a direct role in RNA polymerase II transcription and the activator-19 S interaction could be important in recruiting this large complex to transcriptionally active GAL genes.
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Affiliation(s)
- C Chang
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8573, USA
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Des Etages SA, Saxena D, Huang HL, Falvey DA, Barber D, Brandriss MC. Conformational changes play a role in regulating the activity of the proline utilization pathway-specific regulator in Saccharomyces cerevisiae. Mol Microbiol 2001; 40:890-9. [PMID: 11401696 DOI: 10.1046/j.1365-2958.2001.02432.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In Saccharomyces cerevisiae, the ability to use proline as a nitrogen source requires the Put3p transcriptional regulator, which turns on the expression of the proline utilization genes, PUT1 and PUT2, in the presence of the inducer proline and in the absence of preferred nitrogen sources. Changes in target gene expression occur through an alteration in activity of the DNA-bound Put3p, a member of the Zn(II)2Cys6 binuclear cluster family of proteins. Here, we report that the 'on' conformation can be mimicked in the absence of proline by the insertion of an epitope tag in several different places in the protein, as well as by specific amino acid changes that suppress a put3 mutation leading to non-inducibility of the pathway. In addition, the presence of proline causes a conformational change in the Put3 protein detected by increased sensitivity to thrombin or V8 protease. These findings suggest that Put3p shifts from an inactive to an activate state via conformational changes.
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Affiliation(s)
- S A Des Etages
- Department of Microbiology and Molecular Genetics, Room MSB F-607, UMDNJ - New Jersey Medical School, 185 S. Orange Ave., Newark, NJ 07103, USA
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Bash R, Lohr D. Yeast chromatin structure and regulation of GAL gene expression. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2000; 65:197-259. [PMID: 11008489 DOI: 10.1016/s0079-6603(00)65006-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Yeast genomic DNA is covered by nucleosome cores spaced by short, discrete length linkers. The short linkers, reinforced by novel histone properties, create a number of unique and dynamic nucleosome structural features in vivo: permanent unpeeling of DNA from the ends of the core, an inability to bind even full 147 bp core DNA lengths, and facility to undergo a conformational transition that resembles the changes found in active chromatin. These features probably explain how yeast can maintain most of its genome in a transcribable state and avoid large-scale packaging away of inactive genes. The GAL genes provide a closely regulated system in which to study gene-specific chromatin structure. GAL structural genes are inactive without galactose but are highly transcribed in its presence; the expression patterns of the regulatory genes can account for many of the features of GAL structural gene control. In the inactive state, GAL genes demonstrate a characteristic promoter chromosomal organization; the major upstream activation sequence (UASG) elements lie in open, hypersensitive regions, whereas the TATA and transcription start sites are in nucleosomes. This organization helps implement gene regulation in this state and may benefit the organism. Induction of GAL expression triggers Gal4p-dependent upstream nucleosome disruption. Disruption is transient and can readily be reversed by a Gal80p-dependent nucleosome deposition process. Both are sensitive to the metabolic state of the cell. Induction triggers different kinds of nucleosome changes on the coding sequences, perhaps reflecting the differing roles of nucleosomes on coding versus promoter regions. GAL gene activation is a complex process involving multiple Gal4p activities, numerous positive and negative cofactors, and the histone tails. DNA bending and chromosomal architecture of the promoter regions may also play a role in GAL regulation. Regulator-mediated competition between nucleosomes and the TATA binding protein complex for the TATA region is probably a central aspect of GAL regulation and a focal point for the numerous factors and processes that contribute to it.
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Affiliation(s)
- R Bash
- Department of Chemistry and Biochemistry, Arizona State University, Tempe 85287, USA
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Su K, Roos MD, Yang X, Han I, Paterson AJ, Kudlow JE. An N-terminal region of Sp1 targets its proteasome-dependent degradation in vitro. J Biol Chem 1999; 274:15194-202. [PMID: 10329728 DOI: 10.1074/jbc.274.21.15194] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The transcription factor Sp1 is important for the expression of many cellular genes. Previously, it was shown that reduced O-glycosylation of Sp1 is associated with increased proteasome susceptibility. Sp1 undergoes proteasome-dependent degradation in cells stressed with glucose deprivation and adenylate cyclase activation, and this process is blocked in cells treated with glucosamine. In this study, using a reconstituted in vitro system, we identified the principal structural determinant in Sp1 that targets Sp1 for proteasome-dependent degradation. We found by using deletion analysis that the N-terminal 54 amino acids of Sp1 is required for Sp1 degradation. This element can act as an independent processing signal by directing degradation of an unrelated protein. Recognition of this Sp1 element by the proteasome-dependent system is saturable, and ubiquitination of this element is not required for recognition. Time course experiments revealed that Sp1 degradation is a two-step process. First, a discrete endoproteolytic cleavage occurs downstream of the target region immediately C-terminal to Leu56. The Sp1 sequence C-terminal to the cleavage site is subsequently degraded, whereas the N-terminal peptide remains intact. The identification of this Sp1 degradation-targeting signal will facilitate the identification of the critical proteins involved in the control of Sp1 proteasome-dependent degradation and the role of OGlcNAc in this process.
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Affiliation(s)
- K Su
- Departments of Medicine and Cell Biology, Division of Endocrinology and Metabolism, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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Zenke FT, Kapp L, Breunig KD. Regulated phosphorylation of the Gal4p inhibitor Gal80p of Kluyveromyces lactis revealed by mutational analysis. Biol Chem 1999; 380:419-30. [PMID: 10355628 DOI: 10.1515/bc.1999.056] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The yeast Gal80 protein inhibits the transcription activation function of Gal4p by physically interacting with the activation domain (Gal4-AD). Gal80p interaction with Gal1p or Gal3p is required to relieve Gal4p inhibition in response to galactose. Gal80p orthologs of Saccharomyces cerevisiae and Kluyveromyces lactis, ScGal80p and KIGal80p, can also inhibit the heterologous Gal4p variants; however, heterologous Gal3p/Gal1p only regulate ScGal80p but not KIGal80p. To compare KIGal80p and ScGal80p, point mutations known to affect ScGal80p function were introduced at corresponding positions in KIGal80p, and Gal4p regulation in vivo and KIGal80p-binding to Gst-Gal1p and Gst-Gal4-AD in vitro were analysed. The in vitro binding properties of the KIGal80p mutants were similar to those of ScGal80p, but two out of four mutants differed in Gal4p regulation. E. g. KIGAL80s-0(G302R) but not ScGAL80s-0 (G301R) alleviates Gal4p inhibition. Possibly, this difference is related to a role of phosphorylation in the regulation of Gal80p function in K. lactis. Wild-type and mutant forms of KIGal80p are shown to be subject to carbon source regulated phosphorylation whereas no evidence for ScGal80p phosphorylation exists. (Hyper-)phosphorylation of KIGal80p is strongly reduced in galactose-containing medium. This reduction requires KIGal1p but no interaction with KIGal4p. The inhibition deficient KIGal80s-0p (G302R) variant is under-phosphorylated. We thus propose that phosphorylation of Gal80p in Kluyveromyces lactis contributes to the regulation of Gal4p mediated transcription.
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Affiliation(s)
- F T Zenke
- Institut für Mikrobiologie, Heinrich-Heine-Universität Düsseldorf, Germany
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Habib S, Hasnain SE. A 38-kDa host factor interacts with functionally important motifs within the Autographa californica multinucleocapsid nuclear polyhedrosis virus homologous region (hr1) DNA sequence. J Biol Chem 1996; 271:28250-8. [PMID: 8910443 DOI: 10.1074/jbc.271.45.28250] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We recently demonstrated that the Autographa californica multinucleocapsid nuclear polyhedrosis virus homologous region (hr1) enhances transcription from the viral polyhedrin promoter and also functions as a putative origin of replication (ori). Hr1, carrying five 28-base pair core palindrome units, has also been mapped with respect to its enhancer and ori functions (Habib, S., Pandey, S., Chatterji, U., Burma, S., Ahmad, R., Jain, A., and Hasnain, S. E. (1996) DNA Cell Biol. 15, 737-747). A 38-kDa host factor termed hr1-binding protein (hr1-BP) binds with high specificity and affinity (Kd approximately 6.5 x 10(-11) M) to functionally important motifs within hr1. The core palindrome as well as sequences immediately flanking it are required for this interaction. Divalent cations are not essential, and ionic interactions play only a minor role in complex formation. hr1-BP binds through the minor groove of the double helix to multiple sites within hr1, and binding occurs as a function of the number of modules within hr1. Phosphorylation of hr1-BP is important for host factor-hr1 interaction. Hr1-BP differs in several respects from the other host factor, polyhedrin promoter-binding protein, described previously (Burma, S., Mukherjee, B., Jain, A., Habib, S., and Hasnain, S. E. (1994) J. Biol. Chem. 269, 2750-2757). When hr1-BP was sequestered out, in vivo, by a plasmid carrying hr1 alone, the hr1-mediated enhancement of reporter expression was abolished, demonstrating that the binding of hr1-BP may be crucial for the enhancer activity of the dual function hr1 element.
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Affiliation(s)
- S Habib
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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16
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Shao D, Creasy CL, Bergman LW. Interaction of Saccharomyces cerevisiae Pho2 with Pho4 increases the accessibility of the activation domain of Pho4. MOLECULAR & GENERAL GENETICS : MGG 1996; 251:358-64. [PMID: 8676879 DOI: 10.1007/bf02172527] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In Saccharomyces cerevisiae, expression of acid phosphatase, encoded by the PHO5 gene, requires two positive regulatory factors, Pho4 and Pho2 (also called Bas2 or Grf10). Using GAL4-PHO4 fusions, we demonstrate that a functional interaction between these two proteins is necessary for transcriptional activation to occur. This functional interaction between Pho4 and Pho2 is independent of the presence of the negative regulatory factor, Pho80, which also interacts with Pho4. Interestingly, truncations of Pho4 missing amino acids 252-265, which encompass the basic region of the basic helix-loop-helix (bHLH) DNA binding motif, exhibit high transcriptional activation that is independent of the Pho2 molecule. Single amino acid mutations of highly conserved residues within this area all display this Pho2-independent phenotype. A region near the C-terminus of Pho2 appears to be critical for this interaction with Pho4. A model to account for the requirement for Pho2 in Pho4-dependent transcriptional activation is proposed.
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Affiliation(s)
- D Shao
- Department of Microbiology and Immunology, Medical College of Pennsylvania, Philadelphia 19102, USA
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17
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Hasnain SE, Habib S, Jain A, Burma S, Mukherjee B. Host factor with single-stranded DNA-binding activity involved in transcription from baculovirus polyhedrin promoter. Methods Enzymol 1996; 274:20-32. [PMID: 8902793 DOI: 10.1016/s0076-6879(96)74005-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- S E Hasnain
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, New Delhi, India
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18
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Svetlov VV, Cooper TG. Review: compilation and characteristics of dedicated transcription factors in Saccharomyces cerevisiae. Yeast 1995; 11:1439-84. [PMID: 8750235 DOI: 10.1002/yea.320111502] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- V V Svetlov
- Department of Microbiology and Immunology, University of Tennessee, Memphis 36163, USA
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Yao B, Sollitti P, Zhang X, Marmur J. Shared control of maltose induction and catabolite repression of the MAL structural genes in Saccharomyces. MOLECULAR & GENERAL GENETICS : MGG 1994; 243:622-30. [PMID: 8028578 DOI: 10.1007/bf00279571] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Maltose utilization in yeast requires the presence of any one of the five unlinked, homologous MAL loci. Transcription of the two structural genes MALT (permease) and MALS (maltase) is induced by maltose and catabolite-repressed by glucose. MAL6T and MAL6S share a common 5' intergenic sequence; deletion studies within this sequence revealed a bi-directionally functioning upstream activation sequence (UASM) consisting of four 11 bp homologous sites. Activation of these sites by the MALR protein results in the coordinate expression of MAL6T and MAL6S. The basal promoter activates MALS expression to a greater extent than MALT and is located in a region that overlaps UASM. Deletion of several subsites within the UASM has an asymmetric effect on MAL gene expression, having a greater affect on MALT than on MALS. Catabolite repression of MAL6T and MAL6S by glucose is controlled at several levels. Using disruption mutants, the positively acting MAL1R protein was also found to play a role in catabolite repression of MAL6T and MAL6S.
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Affiliation(s)
- B Yao
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
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Giffin W, Torrance H, Saffran H, MacLeod H, Haché R. Repression of mouse mammary tumor virus transcription by a transcription factor complex. Binding of individual components to separated DNA strands. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)42278-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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21
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Burma S, Mukherjee B, Jain A, Habib S, Hasnain S. An unusual 30-kDa protein binding to the polyhedrin gene promoter of Autographa californica nuclear polyhedrosis virus. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)42007-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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22
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How do “Zn2 cys6” proteins distinguish between similar upstream activation sites? Comparison of the DNA-binding specificity of the GAL4 protein in vitro and in vivo. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(19)74522-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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23
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Gal4 protein binding is required but not sufficient for derepression and induction of GAL2 expression. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)41510-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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24
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Vialard JE, Richardson CD. The 1,629-nucleotide open reading frame located downstream of the Autographa californica nuclear polyhedrosis virus polyhedrin gene encodes a nucleocapsid-associated phosphoprotein. J Virol 1993; 67:5859-66. [PMID: 8371345 PMCID: PMC238004 DOI: 10.1128/jvi.67.10.5859-5866.1993] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A 78-kDa protein was produced in bacteria from a clone of the 1,629-nucleotide open reading frame located immediately downstream from the polyhedrin gene of Autographa californica nuclear polyhedrosis virus. The identity of this protein was confirmed by its reactivity with peptide antiserum and amino terminal peptide sequencing after purification from transformed bacteria. The polypeptide was used to produce polyclonal antisera in rabbits. Immunoblot analysis of insect cells infected with the baculovirus indicated that two related proteins with molecular masses of 78 and 83 kDa were synthesized late in infection. Biochemical fractionation studies indicated that both of these proteins were present in purified nucleocapsids from budded and occluded virus preparations. Immunoprecipitation of 32P-labeled proteins and treatment of purified nucleocapsids with alkaline phosphatase demonstrated that the 83-kDa protein was a phosphorylated derivative of the 78-kDa protein. Furthermore, immunoelectron microscopy revealed that the proteins were localized to regions of nucleocapsid assembly within the infected cell and appeared to be associated with the end structures of mature nucleocapsids.
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Affiliation(s)
- J E Vialard
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
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25
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Abstract
Studies of yeast transcription factors have contributed greatly to understanding basic molecular mechanisms of eukaryotic gene regulation, largely due to powerful genetic approaches that are unavailable in other organisms. The broad outlines of these mechanisms are fairly well understood, and there is an increasing number of examples where detailed information is available.
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Affiliation(s)
- K Struhl
- Department of Biological Chemistry, Harvard Medical School, Boston, Massachusetts 02115
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26
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Leuther KK, Salmeron JM, Johnston SA. Genetic evidence that an activation domain of GAL4 does not require acidity and may form a beta sheet. Cell 1993; 72:575-85. [PMID: 8440021 DOI: 10.1016/0092-8674(93)90076-3] [Citation(s) in RCA: 120] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Regulation of gene expression in eukaryotes relies on intricate protein-protein interactions. Transcription of the galactose genes in yeast has been a productive model for this type of interaction. The positive activator in this system, GAL4, has a bifunctional C-terminus. It contains both a prototypic acidic activation domain and a region that binds the negative regulator, GAL80. We have taken advantage of this colocalization of functions to subject the region to a constrained mutagenesis analysis: one function was maintained, while the other one was altered. This analysis and the experiments it suggested have led us to two conclusions: first, the acidic amino acids are not, as commonly thought, required for activation; second, this region is not unstructured or alpha helical, but its function may require a beta sheet.
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Affiliation(s)
- K K Leuther
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas 75235-8573
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