The Saccharomyces cerevisiae SPT13/GAL11 gene has both positive and negative regulatory roles in transcription

Possible Role for Allelic Variation in Yeast MED15 in Ecological Adaptation

The propensity for Saccharomyces cerevisiae yeast to ferment sugars into ethanol and CO₂ has long been useful in the production of a wide range of food and drink. In the production of alcoholic beverages, the yeast strain selected for fermentation is crucial because not all strains are equally proficient in tolerating fermentation stresses. One potential mechanism by which domesticated yeast may have adapted to fermentation stresses is through changes in the expression of stress response genes. MED15 is a general transcriptional regulator and RNA Pol II Mediator complex subunit which modulates the expression of many metabolic and stress response genes. In this study, we explore the role of MED15 in alcoholic fermentation. In addition, we ask whether MED15 alleles from wine, sake or palm wine yeast improve fermentation activity and grape juice fermentation stress responses. And last, we investigate to what extent any differences in activity are due to allelic differences in the lengths of three polyglutamine tracts in MED15. We find that strains lacking MED15 are deficient in fermentation and fermentation stress responses and that MED15 alleles from alcoholic beverage yeast strains can improve both the fermentation capacity and the response to ethanol stresses when transplanted into a standard laboratory strain. Finally, we find that polyglutamine tract length in the Med15 protein is one determinant in the efficiency of the alcoholic fermentation process. These data lead to a working model in which polyglutamine tract length and other types of variability within transcriptional hubs like the Mediator subunit, Med15, may contribute to a reservoir of transcriptional profiles that may provide a fitness benefit in the face of environmental fluctuations.

MED15 prion-like domain forms a coiled-coil responsible for its amyloid conversion and propagation

A disordered to β-sheet transition was thought to drive the functional switch of Q/N-rich prions, similar to pathogenic amyloids. However, recent evidence indicates a critical role for coiled-coil (CC) regions within yeast prion domains in amyloid formation. We show that many human prion-like domains (PrLDs) contain CC regions that overlap with polyQ tracts. Most of the proteins bearing these domains are transcriptional coactivators, including the Mediator complex subunit 15 (MED15) involved in bridging enhancers and promoters. We demonstrate that the human MED15-PrLD forms homodimers in solution sustained by CC interactions and that it is this CC fold that mediates the transition towards a β-sheet amyloid state, its chemical or genetic disruption abolishing aggregation. As in functional yeast prions, a GFP globular domain adjacent to MED15-PrLD retains its structural integrity in the amyloid state. Expression of MED15-PrLD in human cells promotes the formation of cytoplasmic and perinuclear inclusions, kidnapping endogenous full-length MED15 to these aggregates in a prion-like manner. The prion-like properties of MED15 are conserved, suggesting novel mechanisms for the function and malfunction of this transcription coactivator.

The maize premature senesence2 encodes for PHYTOCHROME-DEPENDENT LATE-FLOWERING and its expression modulation improves agronomic traits under abiotic stresses

Among the various abiotic stresses, water and nitrogen are major stress factors that limit crop productivity worldwide. Since leaf nutrients remobilization during leaf senescence might impact response to abiotic stress in crops, we undertook a forward screen of the Mutator-active approach to identify premature senescence loci in maize. A mutant line isolated from a cross between a Pioneer Brand elite line and a public Mutator-active material, designated premature senescence2 (pre2), expressed leaf senescence during flower initiation. The Pre2 gene encodes PHYTOCHROME-DEPENDENT LATE-FLOWERING (PHL) protein, a nuclear receptor coactivator. The pre2-1 mutant allele was not a null mutation but produced a functional wild-type transcript along with multiple mRNA species of varying lengths resulting from the alternate splicing of the Pre2 gene. The PHL accelerates flowering by suppressing the inhibitory effect of phyB on flowering in Arabidopsis (Endo et al., 2013). The ZmPRE2 polypeptide is highly conserved in plant species and has two identifiable motifs namely SPT20 and MED15. The Spt20 domain, which is a part of the SAGA (Spt-Ada-Gcn5 acetyltransferase) complex, is involved in histone deacetylation and MED15 proteins have nuclear functions in mediating DNA Pol II transcription. The differential spliced mature transcripts in both the pre2 alleles, as a result of transposon interference, were producing truncated proteins that lacked polyglutamine (Q) tract near the C-terminus and might be causative of the premature senescence phenotype in maize. Endogenous gene suppression of ZmPre2 by RNAi improves maize agronomic performance under both water stress and suboptimal nitrogen conditions. The homozygous T-DNA knockout of the pre2 homolog in Arabidopsis (At1G72390; the same insertional allele used by Endo et al., 2013) results in higher biomass, delayed maturity, enhanced tolerance to drought, and improved nitrogen utilization efficiency. The Arabidopsis mutant also showed hypersensitive response to 1 µM ABA (abscisic acid) concentration. These results indicate that the PHL protein plays a direct or indirect role in ABA-dependent drought and N signaling pathways.

Med15: Glutamine-Rich Mediator Subunit with Potential for Plasticity

The Mediator complex is required for basal activity of the RNA polymerase (Pol) II transcriptional apparatus and for responsiveness to some activator proteins. Med15, situated in the Mediator tail, plays a role in transmitting regulatory information from distant DNA-bound transcription factors to the transcriptional apparatus poised at promoters. Yeast Med15 and its orthologs share an unusual, glutamine-rich amino acid composition. Here, we discuss this sequence feature and the tendency of polyglutamine tracts to vary in length among strains of Saccharomyces cerevisiae, and we propose that different polyglutamine tract lengths may be adaptive within certain domestication habitats.

Role of Saccharomyces cerevisiae Rap1 protein in Ty1 and Ty1-mediated transcription

Binding sites for the transcription factor Rap1 are widespread in the yeast genome. With respect to many, but not all, genes, Rap1p has an apparent activation function. Whether Rap1 is itself a transcriptional activator, or whether it is in some way required for activation by additional factors, is not clear. We have identified a previously unrecognized Rap1p binding site in the internal regulatory region of Ty1 elements. We demonstrate that this site is capable of binding Rap1 in vitro and that, in vivo, Rap1p plays an important regulatory role in Ty1 and Ty1-mediated adjacent gene expression. Our data suggest that in Ty1 elements, maximal levels of RAP1-mediated activation depend on the formation of a complex with Mcm1, an independent DNA-binding protein that functions in transcription as well as in DNA replication, and with a third factor, IBF, previously identified as a binding activity with a site situated between the Rap1p and Mcm1p binding sites in this region of Ty1 elements.

The 9aaTAD Transactivation Domains: From Gal4 to p53

The family of the Nine amino acid Transactivation Domain, 9aaTAD family, comprises currently over 40 members. The 9aaTAD domains are universally recognized by the transcriptional machinery from yeast to man. We had identified the 9aaTAD domains in the p53, Msn2, Pdr1 and B42 activators by our prediction algorithm. In this study, their competence to activate transcription as small peptides was proven. Not surprisingly, we elicited immense 9aaTAD divergence in hundreds of identified orthologs and numerous examples of the 9aaTAD species' convergence. We found unforeseen similarity of the mammalian p53 with yeast Gal4 9aaTAD domains. Furthermore, we identified artificial 9aaTAD domains generated accidentally by others. From an evolutionary perspective, the observed easiness to generate 9aaTAD transactivation domains indicates the natural advantage for spontaneous generation of transcription factors from DNA binding precursors.

Relationships Between RNA Polymerase II Activity and Spt Elongation Factors to Spt- Phenotype and Growth in Saccharomyces cerevisiae

The interplay between adjacent transcription units can result in transcription-dependent alterations in chromatin structure or recruitment of factors that determine transcription outcomes, including the generation of intragenic or other cryptic transcripts derived from cryptic promoters. Mutations in a number of genes in Saccharomyces cerevisiae confer both cryptic intragenic transcription and the Suppressor of Ty (Spt^-) phenotype for the lys2-128∂ allele of the LYS2 gene. Mutants that suppress lys2-128∂ allow transcription from a normally inactive Ty1 ∂ promoter, conferring a LYS⁺ phenotype. The arrangement of transcription units at lys2-128∂ is reminiscent of genes containing cryptic promoters within their open reading frames. We set out to examine the relationship between RNA Polymerase II (Pol II) activity, functions of Spt elongation factors, and cryptic transcription because of the previous observation that increased-activity Pol II alleles confer an Spt^- phenotype. We identify both cooperating and antagonistic genetic interactions between Pol II alleles and alleles of elongation factors SPT4, SPT5, and SPT6. We find that cryptic transcription at FLO8 and STE11 is distinct from that at lys2-128∂, though all show sensitivity to reduction in Pol II activity, especially the expression of lys2-128∂ found in Spt^- mutants. We determine that the lys2-128∂ Spt^- phenotypes for spt6-1004 and increased activity rpo21/rpb1 alleles each require transcription from the LYS2 promoter. Furthermore, we identify the Ty1 transcription start site (TSS) within the ∂ element as the position of Spt^- transcription in tested Spt^- mutants.

Shared structural features of the 9aaTAD family in complex with CBP

Analysis of E2A, MLL, FOXO3 and p53 structural data defines fundamental requirements and sheds light on the ambiguous 9aaTAD domain.

Linking DNA replication to heterochromatin silencing and epigenetic inheritance

Chromatin is organized into distinct functional domains. During mitotic cell division, both genetic information encoded in DNA sequence and epigenetic information embedded in chromatin structure must be faithfully duplicated. The inheritance of epigenetic states is critical in maintaining the genome integrity and gene expression state. In this review, we will discuss recent progress on how proteins known to be involved in DNA replication and DNA replication-coupled nucleosome assembly impact on the inheritance and maintenance of heterochromatin, a tightly compact chromatin structure that silences gene transcription. As heterochromatin is important in regulating gene expression and maintaining genome stability, understanding how heterochromatin states are inherited during S phase of the cell cycle is of fundamental importance.

Origins and activity of the Mediator complex

The Mediator is a large, multisubunit RNA polymerase II transcriptional regulator that was first identified in Saccharomyces cerevisiae as a factor required for responsiveness of Pol II and the general initiation factors to DNA binding transactivators. Since its discovery in yeast, Mediator has been shown to be an integral and highly evolutionarily conserved component of the Pol II transcriptional machinery with critical roles in multiple stages of transcription, from regulation of assembly of the Pol II initiation complex to regulation of Pol II elongation. Here we provide a brief overview of the evolutionary origins of Mediator, its subunit composition, and its remarkably diverse collection of activities in Pol II transcription.

The Saccharomyces cerevisiae ESU1 gene, which is responsible for enhancement of termination suppression, corresponds to the 3'-terminal half of GAL11

A DNA fragment enhancing efficiency of [PSI+]-dependent termination suppressor, sup111, was isolated from a genomic library of Saccharomyces cerevisiae and its function was attributed to an ORF of 1272 bp. This ORF, designated ESU1 (enhancer of termination suppression), corresponded to the 3'-terminal portion of GAL11. Contrasting to ESU1, GAL11 lowered the suppression efficiency of [PSI+] sup111. ESU1 possesses a TATA-like sequence of its own and three ATG codons following it within a distance of about 70 bp and all in the same reading frame as GAL11. A 52.7 kDa protein corresponding in size to the predicted Esu1 protein is detected by western blot analysis using anti-Gal11 antiserum. We therefore conclude that ESU1 is the gene that encodes a polypeptide corresponding to the C-terminal 424 amino acids of Gal11. It was further found that ESU1 increases the level of GAL11 mRNA and probably also of its own mRNA. Moreover, ESU1 increased the cellular level of mRNA transcribed from the leu2-1(UAA) mutant gene, while GAL11 did not. Based on these findings, we propose the following scheme for the events taking place in the [PSI+] sup111 cell that is transformed with an ESU1-bearing plasmid: (a) ESU1 stimulates transcription of leu2-1; (b) leu2-1 mRNA is not effectively degraded because of the possession of sup111, which belongs to the upf group; (c) [PSI+] causes increased mis-termination due to depletion of eRF3; (d) functional Leu2 product is made using leu2-1 mRNA; and (d) suppression of leu2-1 is eventually accomplished.

An interactive gene network for securin-separase, condensin, cohesin, Dis1/Mtc1 and histones constructed by mass transformation

The small genome of fission yeast Schizosaccharomyces pombe contains 4824 predicted genes and gene disruption suggests that approximately 850 are essential for viability. To obtain information on interactions among genes required for chromosome segregation, an approach called Strategy B was taken using mass transformation of the 1015 temperature-sensitive (ts) mutants that were made by random mutagenesis and transformed by plasmids carrying the genes for securin, separase, condensin, cohesin, kinetochore microtubule-binding proteins Dis1/Mtc1 or histones. Mutant strains whose phenotypes were either suppressed or inhibited by plasmids were selected. Each plasmid interacted positively or negatively with the average 14 strains. Identification of the mutant gene products by cloning revealed many hitherto unknown interactions. The interactive networks of segregation therefore may consist of genes with a variety of functions. For example, separase/Cut1 interacts with Cdc48/p97/VCP, which stabilizes securin and separase. Surprisingly, S. pombe cdc48 mutants displayed the mitotic phenotype highly similar to separase/cut1 mutants. This approach also provides a novel way of mutant isolation, resulting in two histone H2B strains and a cohesion mutant with a new phenotype.

Gal11 is a general activator of basal transcription, whose activity is regulated by the general repressor Sin4 in yeast

Mutations in SIN4, which encodes a global transcriptional regulator in Saccharomyces cerevisiae, have been suggested to lead to an increase in basal transcription of various genes by causing an alteration in chromatin structure. We reported previously that this activation of basal transcription occurs via a mechanism that differs from activator-mediated transcriptional enhancement. This finding prompted us to seek general activators of basal transcription by screening for extragenic suppressors of a sin4 mutation using PHO5, which is activated by the transcriptional activator Pho4, as a reporter gene. One of the mutations found, the semi-dominant ABE1-1, is described here. The ABE1-1 mutation reduced the enhanced basal transcription of PHO5 caused by the sin4 mutation, but did not impair Pho4-mediated activation of PHO5. The ABE1-1 mutation also suppressed the aggregation phenotype and the rough colony morphology of the sin4 mutant cells, while it exacerbated temperature sensitive growth and telomere shortening, suggesting that Abe1p is involved in the basal transcription not only of PHO5 but also of other diversely regulated genes. SWI1, which encodes a component of the Swi-Snf complex that has chromatin remodeling activity, was identified as a gene-dosage suppressor of the ABE1-1 mutation. ABE1-1 was found to be allelic to GAL11. These observations suggest that Gal11 acts as a general activator for the basal transcription of various genes, possibly by relieving torsional stress in chromatin, and that its function is repressed by the Sin4 protein.

Restoration of silencing in Saccharomyces cerevisiae by tethering of a novel Sir2-interacting protein, Esc8

We previously described two classes of SIR2 mutations specifically defective in either telomeric/HM silencing (class I) or rDNA silencing (class II) in S. cerevisiae. Here we report the identification of genes whose protein products, when either overexpressed or directly tethered to the locus in question, can establish silencing in SIR2 class I mutants. Elevated dosage of SCS2, previously implicated as a regulator of both inositol biosynthesis and telomeric silencing, suppressed the dominant-negative effect of a SIR2-143 mutation. In a genetic screen for proteins that restore silencing when tethered to a telomere, we isolated ESC2 and an uncharacterized gene, (YOL017w), which we call ESC8. Both Esc2p and Esc8p interact with Sir2p in two-hybrid assays, and the Esc8p-Sir2 interaction is detected in vitro. Interestingly, Esc8p has a single close homolog in yeast, the ISW1-complex factor Ioc3p, and has also been copurified with Isw1p, raising the possibility that Esc8p is a component of an Isw1p-containing nucleosome remodeling complex. Whereas esc2 and esc8 deletion mutants alone have only marginal silencing defects, cells lacking Isw1p show a strong silencing defect at HMR but not at telomeres. Finally, we show that Esc8p interacts with the Gal11 protein, a component of the RNA pol II mediator complex.

Transcriptional coactivator complexes

The last two decades have witnessed a tremendous expansion in our knowledge of the mechanisms employed by eukaryotic cells to control gene activity. A critical insight to transcriptional control mechanisms was provided by the discovery of coactivators, a diverse array of cellular factors that connect sequence-specific DNA binding activators to the general transcriptional machinery, or that help activators and the transcriptional apparatus to navigate through the constraints of chromatin. A number of coactivators have been isolated as large multifunctional complexes, and biochemical, genetic, molecular, and cellular strategies have all contributed to uncovering many of their components, activities, and modes of action. Coactivator functions can be broadly divide into two classes: (a) adaptors that direct activator recruitment of the transcriptional apparatus, (b) chromatin-remodeling or -modifying enzymes. Strikingly, several distinct coactivator complexes nonetheless share many subunits and appear to be assembled in a modular fashion. Such structural and functional modularity could provide the cell with building blocks from which to construct a versatile array of coactivator complexes according to its needs. The extent of functional interplay between these different activities in gene-specific transcriptional regulation is only now becoming apparent, and will remain an active area of research for years to come.

Med9/Cse2 and Gal11 modules are required for transcriptional repression of distinct group of genes

The yeast Mediator is composed of two subcomplexes, Rgr1 and Srb4, known to be required for diverse aspects of transcriptional regulation; however, their structural and functional organizations have not yet been deciphered in detail. Biochemical analyses designed to determine the subunit composition of the Rgr1 subcomplex revealed that the regulator-interacting subcomplex has a modular structure and is composed of the Gal11, Med9/Cse2, and Med10/Nut2 modules. Genome-wide gene expression and Northern analyses performed in the presence or absence of the various Mediator modules revealed a distinct requirement for the Gal11, Med9/Cse2, and Med10/Nut2 modules in transcriptional repression as well as activation. GST pull-down analysis revealed that the transcriptional repressor Tup1 binds to distinct but overlapping regions of the Gal11 module that were shown previously to be transcriptional activator binding sites. These data suggest that competition between transcriptional activators and repressors for a common binding site in the Mediator and distinct conformational changes in the Mediator induced by repressor binding may underlie the mechanism of transcriptional repression in eukaryotes.

The Gal4 activation domain binds Sug2 protein, a proteasome component, in vivo and in vitro

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.

Chromatin and transcription in Saccharomyces cerevisiae

A central problem in eukaryotic transcription is how proteins gain access to DNA packaged in nucleosomes. Research on the interplay between chromatin and transcription has progressed with the use of yeast genetics as a useful tool to characterize factors involved in this process. These factors have both positive and negative effects on the stability of nucleosomes, thereby controlling the role of chromatin in transcription in vivo. The negative effectors include the structural components of chromatin, the histones and non-histone chromatin associated proteins, as well as regulatory components like chromatin assembly factors and histone deacetylase complexes. The positive factors are involved in remodeling chromatin and several multiprotein complexes have been described: Swi/Snf, Srb/mediator and SAGA. The components of each of these complexes, as well as the functional relationships between them are covered by this review.

Sac3, an Snf1-like serine/threonine kinase that positively and negatively regulates the responses of Chlamydomonas to sulfur limitation

The Sac3 gene product of Chlamydomonas positively and negatively regulates the responses of the cell to sulfur limitation. In wild-type cells, arylsulfatase activity is detected only during sulfur limitation. The sac3 mutant expresses arylsulfatase activity even when grown in nutrient-replete medium, which suggests that the Sac3 protein has a negative effect on the induction of arylsulfatase activity. In contrast to its effect on arylsulfatase activity, Sac3 positively regulates the high-affinity sulfate transport system-the sac3 mutant is unable to fully induce high-affinity sulfate transport during sulfur limitation. We have complemented the sac3 mutant and cloned a cDNA copy of the Sac3 gene. The deduced amino acid sequence of the Sac3 gene product is similar to the catalytic domain of the yeast Snf1 family of serine/threonine kinases and is therefore classified as a Snf1-related kinase (SnRK). Specifically, Sac3 falls within the SnRK2 subfamily of kinases from vascular plants. In addition to the 11 subdomains common to Snf1-like serine/threonine kinases, Sac3 and the plant kinases have two additional subdomains and a highly acidic C-terminal region. The role of Sac3 in the signal transduction system that regulates the responses of Chlamydomonas to sulfur limitation is discussed.

Specific components of the SAGA complex are required for Gcn4- and Gcr1-mediated activation of the his4-912delta promoter in Saccharomyces cerevisiae

Mutations selected as suppressors of Ty or solo delta insertion mutations in Saccharomyces cerevisiae have identified several genes, SPT3, SPT7, SPT8, and SPT20, that encode components of the SAGA complex. However, the mechanism by which SAGA activates transcription of specific RNA polymerase II-dependent genes is unknown. We have conducted a fine-structure mutagenesis of one widely used SAGA-dependent promoter, the delta element of his4-912delta, to identify sequence elements important for its promoter activity. Our analysis has characterized three delta regions necessary for full promoter activity and accurate start site selection: an upstream activating sequence, a TATA region, and an initiator region. In addition, we have shown that factors present at the adjacent UASHIS4 (Gcn4, Bas1, and Pho2) also activate the delta promoter in his4-912delta. Our results suggest a model in which the delta promoter in his4-912delta is primarily activated by two factors: Gcr1 acting at the UASdelta and Gcn4 acting at the UASHIS4. Finally, we tested whether activation by either of these factors is dependent on components of the SAGA complex. Our results demonstrate that Spt3 and Spt20 are required for full delta promoter activity, but that Gcn5, another member of SAGA, is not required. Spt3 appears to be partially required for activation of his4-912delta by both Gcr1 and Gcn4. Thus, our work suggests that SAGA exerts a large effect on delta promoter activity through a combination of smaller effects on multiple factors.

Genetics of transcriptional regulation in yeast: connections to the RNA polymerase II CTD

Transcriptional regulation is important in all eukaryotic organisms for cell growth, development, and responses to environmental change. Saccharomyces cerevisiae, or bakers' yeast, has provided a powerful system for genetic analysis of transcriptional regulation, and findings from the study of this model system have proven broadly applicable to higher organisms. Transcriptional regulation requires the interactions of regulatory proteins with various components of the transcription machinery. Recently, genetic analysis of a diverse set of transcriptional regulatory responses has converged with studies of the function of the RNA polymerase II carboxy-terminal domain (CTD) to reveal regulatory roles for proteins associated with the CTD. These proteins, designated Srb/mediator proteins, are broadly involved in both positive and negative regulatory responses in vivo. This review focuses on the connections between genetic analysis of transcriptional regulation and the functions of the Srb/mediator proteins associated with the RNA polymerase II CTD.

Yeast Gal11 and transcription factor IIE function through a common pathway in transcriptional regulation

The global transcription regulator Gal11, a component of RNA polymerase II holoenzyme, is required for full expression of many genes in yeast. We previously reported that Gal11 binds the small (Tfa2) and large (Tfa1) subunits of the general transcription factor (TF) IIE through Gal11 functional domains A and B, respectively. Here we demonstrate that the C-terminal basic region in Tfa2 is responsible for binding to domain A, whereas both the N-terminal hydrophobic and internal glutamic acid-rich regions in Tfa1 are responsible for binding to domain B. Yeast cells bearing a C-terminal deletion encompassing the Gal11-interacting region in each of the two TFIIE subunits, being viable, exhibited no obvious phenotype. In contrast, combination of the two deletions (TFIIE-DeltaC) showed phenotypes similar to those of gal11 null mutations. The levels of mRNA from TATA-containing genes, but not from TATA-less genes, decreased in TFIIE-DeltaC to an extent comparable to that in the gal11 null mutant. Combination of TFIIE-DeltaC with a gal11 null mutation did not result in an enhanced effect, suggesting that both TFIIE and Gal11 act in a common regulatory pathway. In a reconstituted cell-free system, Gal11 protein stimulated basal transcription in the presence of wild-type TFIIE. Such a stimulation was not seen in the presence of TFIIE-DeltaC.

The yeast HRS1 gene is involved in positive and negative regulation of transcription and shows genetic characteristics similar to SIN4 and GAL11

We provide genetic evidence that HRS1/PGD1, a yeast gene previously identified as a suppressor of the hyper-recombination phenotype of hpr1, has positive and negative roles in transcriptional regulation. We have analyzed three differently regulated promoters, GAL1, PHO5 and HSP26, by beta-galactosidase assays of lacZ-fused promoters and by Northern analysis of the endogenous genes. Transcription of these promoters was derepressed in hrs1delta mutants under conditions in which it is normally repressed in wild type. Under induced conditions it was either strongly reduced or significantly enhanced depending on the promoter system analyzed. Constitutive transcription was not affected, as determined in ADH1 and TEF2. In addition, Hrs1p was required for mating-factor expression, telomere-linked DNA silencing and DNA supercoiling of plasmids. Furthermore, hrs1delta suppressed Ty-insertion mutations and conferred a Gal- phenotype. Many of these phenotypes also result from mutations in GAL11, SIN4 or RGR1, which encode proteins of the RNA polII mediator. We also show that gal11delta and sin4delta partially suppress the hyper-rec phenotype of hpr1 mutants, although to a lesser extent than hrs1delta. Our results provide new evidence for the connection between hpr1delta-induced deletions and transcription. We discuss the possibility that Hrs1p might be a component of the RNA polII transcription machinery.

Core promoter elements are essential as selective determinants for function of the yeast transcription factor GAL11

The GAL11 gene product, which copurifies with RNA polymerase II holoenzyme, is necessary for full expression of many, but not all, genes in yeast. Here we shows that the GAL11 dependence of a gene for expression is determined by the core promoter structure. In the GAL80 gene, a gal11 null mutation caused reduction of TATA-dependent transcription, but exerted no effect on initiator-mediated transcription. GAL11 stimulated TATA-dependent transcription, but did not affect the TATA-independent transcription in HIS4. GAL11 was also required for transcription mediated by a canonical TATA sequence but not by a nonconsensus TATA sequence of HIS3. These results suggest that GAL11 is specifically involved in the transcription machinery formed on the TATA element.

Suppressors of defective silencing in yeast: effects on transcriptional repression at the HMR locus, cell growth and telomere structure

To identify factors that affect transcriptional silencing at the HMR mating-type locus in yeast, we characterized a set of extragenic suppressor mutations that restore metastable repression in cells containing both a mutant silencer-binding protein (rap1s) and a mutated silencer element (hmr delta A). A total of 57 suppressors comprising 21 different complementation groups was identified. This report describes a detailed genetic analysis of these suppressors of defective silencing (sds) mutants. The sds mutants fall into several distinct categories based on secondary phenotypes, such as their ability to suppress the rap1s telomere lengthening phenotype, general effects on telomere length, temperature-dependent growth defects, and the ability to bypass the requirement for cis regulatory elements at the HMR-E silencer. One particular mutant, sds4-1, strongly suppresses the rap1s silencing defect, restores telomeres to nearly wild-type length, and displays a severe growth defect at all temperatures. SDS4 mutations also suppress the silencing defect caused by mutations in the RAP1-interacting factor RIF1. We cloned the SDS4 gene and show that it is identical to GAL11(SPT13), which encodes a component of a protein complex that mediates transcriptional activation. Possible mechanism(s) of suppression by sds4 and the other sds mutations is discussed.

Contact with a component of the polymerase II holoenzyme suffices for gene activation

In yeast strains bearing the point mutation called GAL11P (for potentiator), certain GAL4 derivatives lacking any classical activating region work as strong activators. The P mutation confers upon GAL11, a component of the RNA polymerase II holoenzyme, the ability to interact with a portion of the dimerization region of GAL4. The region of GAL11 affected by the P mutation is evidently functionally inert in ordinary cells, suggesting that this mutation is of no functional significance beyond creating an artificial target for the GAL4 dimerization fragment. From these observations and further analyses of GAL11, we propose that a single activator-holoenzyme contact can trigger gene activation simply by recruiting the latter to DNA.

The essential transcription factor, Mcm1, is a downstream target of Sln1, a yeast "two-component" regulator

In a search for mutants exhibiting altered activity of the yeast transcription factor, Mcm1, we have identified the SLN1 gene, whose product is highly related to bacterial two-component sensor-regulator proteins. sln1 alleles identified in our screen increased Mcm1p-mediated transcriptional activation, while deletion of the SLN1 locus severely reduced Mcm1p activity. Our data establish that Mcm1p is a downstream target of the Sln1 signaling pathway. Yeast Sln1p was recently shown to be involved in osmoregulation and to depend on the Hog1 MAP kinase (Maeda, T., Wurgler-Murphy, S., and Saito, H. (1994) Nature 369, 242-245). We show that SLN1-mediated regulation of Mcm1p activity is independent of the Hog1 MAP kinase, and suggest that the role of SLN1 is not restricted to osmoregulation.

Genetic interactions between SIN3 mutations and the Saccharomyces cerevisiae transcriptional activators encoded by MCM1, STE12, and SWI1

SIN3 was first identified by a mutation which suppresses the effects of an swi5 mutation on expression of the HO gene in Saccharomyces cerevisiae. We now show that a sin3 mutation also partially suppresses the effects of swi1 on HO transcription, and partially suppresses the growth defect and inositol requirement observed in swi1 mutants. This suggests that SIN3 and SWI1 may play opposite regulatory roles in controlling expression of many yeast genes. Yeast SIN3 has been shown to function as a negative transcriptional regulator of a number of yeast genes. However, expression of the yeast STE6 gene is reduced in a sin3 mutant strain. This suggests that SIN3 functions as a positive regulator for STE6 transcription, although this apparent activation function could be indirect. In order to understand how SIN3 functions in STE6 regulation, we have performed a genetic analysis. It has been previously demonstrated that MCM1 and STE12 are transcriptional activators of a-specific genes such as STE6, and we now show that SWI1 is also required for STE6 expression. Our data suggest that STE12 and SWI1 function in different pathways of activation, and that STE12 is epistatic to SIN3 and SWI1. We show that the activities of the Mcm1p and Ste12p activators are modestly reduced in a sin3 mutant strain, and that phosphorylation of the Ste12p activator is decreased in a sin3 mutant. Thus, it is possible that the decreased transcription of STE6 in sin3 mutants is due to the combined effect of the diminished activities of Mcm1p and Ste12p.

Positive and negative transcriptional regulation by the yeast GAL11 protein depends on the structure of the promoter and a combination of cis elements

GAL11 was first identified as a gene required for full expression of some galactose-inducible genes that are activated by GAL4, and it was subsequently shown to be necessary for full expression of another set of genes activated by RAP1/GRF1/TUF. Genetic analysis suggests that GAL11 functions as a coactivator, mediating the interaction of sequence-specific activators with basal transcription factors. To test this hypothesis, we first tried to identify functional domains by deletion analysis and found that the 866-910 region is indispensable for function. Using reporters bearing various upstream activating sequences (UAS) and different core promoter structures, we show that the involvement of GAL11 in transcriptional activation varies with the target promoter and the particular combination of cis elements. Gel electrophoresis in the presence of chloroquine shows that GAL11 affects the chromatin structure of a circular plasmid. Based on these findings, the role of GAL11 in regulation of transcription, including an alteration in chromatin structure, is discussed.

Yeast GAL11 protein stimulates basal transcription in a gene-specific manner by a mechanism distinct from that by DNA-bound activators

The GAL11 gene encodes an auxiliary transcription factor required for full expression of many, if not all, genes of the yeast Saccharomyces cerevisiae. We have recently shown that GAL11-encoded protein (Gal11p) enhances basal transcription from the CYC1 promoter in a cell-free transcription system [(1993) Proc. Natl. Acad. Sci. USA 90, 8382-8386]. Here we indicate that Gal11p stimulates basal transcription in a gene-specific manner in vitro. We further suggest that the mechanism underlying the transcriptional stimulation by Gal11p is distinct from that by DNA-bound activators, since Gal11p stimulated transcription in a reaction system where activators were unable to enhance transcription due to the lack of intermediary factors.

The Saccharomyces cerevisiae SGE1 gene product: a novel drug-resistance protein within the major facilitator superfamily

Several pleiotropic drug sensitivities have been described in yeast. Some involve the loss of putative drug efflux pumps analogous to mammalian P-glycoproteins, others are caused by defects in sterol synthesis resulting in higher plasma membrane permeability. We have constructed a Saccharomyces cerevisiae strain that exhibits a strong crystal violet-sensitive phenotype. By selecting cells of the supersensitive strain for normal sensitivity after transformation with a wild-type yeast genomic library, a complementing 10-kb DNA fragment was isolated, a 3.4-kb subfragment of which was sufficient for complementation. DNA sequence analysis revealed that the complementing fragment comprised the recently sequenced SGE1 gene, a partial multicopy suppressor of gal11 mutations. The supersensitive strain was found to be a sge1 null mutant. Overexpression of SGE1 on a high-copy-number plasmid increased the resistance of the supersensitive strain. Disruption of SGE1 in a wild-type strain increased the sensitivity of the strain. These features of the SGE1 phenotype, as well as sequence homologies of SGE1 at the amino acid level, confirm that the Sge1 protein is a member of the drug-resistance protein family within the major facilitator superfamily (MFS).

The Saccharomyces cerevisiae SPT8 gene encodes a very acidic protein that is functionally related to SPT3 and TATA-binding protein

Mutations in the Saccharomyces cerevisiae SPT8 gene were previously isolated as suppressors of retrotransposon insertion mutations in the 5' regions of the HIS4 and LYS2 genes. Mutations in SPT8 confer phenotypes similar to those caused by particular mutations in SPT15, which encodes the TATA-binding protein (TBP). These phenotypes are also similar to those caused by mutations in the SPT3 gene, which encodes a protein that directly interacts with TBP. We have now cloned and sequenced the SPT8 gene and have shown that it encodes a predicted protein of 602 amino acids with an extremely acidic amino terminus. In addition, the predicted SPT8 amino acid sequence contains one copy of a sequence motif found in multiple copies in a number of other eukaryotic proteins, including the beta subunit of heterotrimeric G proteins. To investigate further the relationship between SPT8, SPT3 and TBP, we have analyzed the effect of an spt8 null mutation in combination with different spt3 and spt15 mutations. This genetic analysis has shown that an spt8 deletion mutation is suppressed by particular spt3 alleles. Taken together with previous results, these data suggest that the SPT8 protein is required, directly or indirectly, for TBP function at particular promoters and that the role of SPT8 may be to promote a functional interaction between SPT3 and TBP.

A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II

A mediator was isolated from yeast that enabled a response to the activator proteins GAL4-VP16 and GCN4 in a transcription system reconstituted with essentially homogeneous basal factors and RNA polymerase II. The mediator comprised some 20 polypeptides, including the three subunits of TFIIF and other polypeptides cross-reactive with antisera against GAL11, SUG1, SRB2, SRB4, SRB5, and SRB6 proteins. Mediator not only enabled activated transcription but also conferred 8-fold greater activity in basal transcription and 12-fold greater efficiency of phosphorylation of RNA polymerase II by the TFIIH-associated C-terminal repeat domain (CTD) kinase, indicative of mediator-CTD interaction. A holoenzyme form of RNA polymerase II was independently isolated that supported a response to activator proteins with purified basal factors. The holoenzyme proved to consist of mediator associated with core 12-subunit RNA polymerase II.

The yeast co-activator GAL11 positively influences transcription of the phosphoglycerate kinase gene, but only when RAP1 is bound to its upstream activation sequence

Transcription of the yeast phosphoglycerate kinase gene (PGK) is activated by an array of nuclear factors including the multifunctional protein RAP1. We have demonstrated that the transcriptional co-activator GAL11, which was identified as an auxiliary factor to GAL4 and which is believed to interact with the zinc finger of the trans-activator, positively influences the level of PGK transcription on both fermentable and non-fermentable carbon sources. This positive effect is only observed when the RAP1 site in the upstream activation sequence (UAS) is present, implying that GAL11 acts through RAP1. Expression of the RAP1 gene is not reduced in the gal11 background, and in vivo footprinting shows that GAL11 does not influence RAP1 DNA-binding activity. Therefore the effect of GAL11 on PGK transcription must be mediated at the PGK UAS, presumably as part of the activation complex. It has been proposed that RAP1 may act as a facilitator of GCR1 binding at the PGK UAS and therefore it is conceivable that the target for GAL11 may in fact be GCR1. A further implication of this study is that GAL11 can interact with proteins such as RAP1 or GCR1 that are apparently structurally dissimilar from GAL4 and other zinc finger DNA-binding proteins.

Molecular and genetic analysis of the SNF7 gene in Saccharomyces cerevisiae

Mutations in the SNF7 gene of Saccharomyces cerevisiae prevent full derepression of the SUC2 (invertase) gene in response to glucose limitation. We report the molecular cloning of the SNF7 gene by complementation. Sequence analysis predicts that the gene product is a 27-kDa acidic protein. Disruption of the chromosomal locus causes a fewfold decrease in invertase derepression, a growth defect on raffinose, temperature-sensitive growth on glucose, and a sporulation defect in homozygous diploids. Genetic analysis of the interactions of the snf7 null mutation with ssn6 and spt6/ssn20 suppressor mutations distinguished SNF7 from the SNF2, SNF5 and SNF6 genes. The snf7 mutation also behaved differently from mutations in SNF1 and SNF4 in that snf7 ssn6 double mutants displayed a synthetic phenotype of severe temperature sensitivity for growth. We also mapped SNF7 to the right arm of chromosome XII near the centromere.

Isolation and characterization of SGE1: a yeast gene that partially suppresses the gal11 mutation in multiple copies

Recessive mutations of GAL11 in Saccharomyces cerevisiae cause pleiotropic defects that include weak fermentation of galactose, alpha-specific sterility and slow growth on nonfermentable carbon sources. Recent experiments suggest that Gal11P functions as a "co-activator" that links transcriptional activators, such as Gal4p and Grf1p/Rap1p/Tuf1p, with the basic transcription machinery. In the present experiments we isolated a gene, SGE1, that suppresses gal11 for growth on ethidium bromide/galactose agar when the gene was present in two or more copies. The other gal11 phenotypes were not suppressed by SGE1 in the multiple-copy state. Multiple copies of SGE1 increased expression of galactose-inducible genes in gal11 yeast, presumably at the level of transcription. When SGE1 was disrupted in wild-type yeast, the expression of galactose-inducible genes decreased to 50-60% of the wild-type level, presumably due to effect on transcription. Complete DNA sequence analysis revealed that SGE1 encodes a predicted protein of 543 amino acids. SGE1-specific mRNA of 1.8 kilonucleotides was detected by Northern analysis along the direction of the open reading frame. The gene mapped near RAD56, at the right end of chromosome 16.

Characterization of the MKS1 gene, a new negative regulator of the Ras-cyclic AMP pathway in Saccharomyces cerevisiae

In order to isolate genes that function downstream of the Ras-cAMP pathway in Saccharomyces cerevisiae, a YEp13-based genomic library was screened for clones that inhibit growth of cells with diminished A-kinase activity. One such gene, MKS1, was found to encode a hydrophilic 52 kDa protein that shares weak homology with the yeast SPT2/SIN1 gene product. Three lines of evidence suggest that the MKS1 gene product is a negative regulator downstream of the Ras-cAMP pathway: (i) overexpression of MKS1 inhibits growth of cyr1 disruptant cells on YPD medium containing a low concentration of cAMP; (ii) overexpression of MKS1 does not affect TPK1 expression; and (iii) the temperature-sensitive cyr1-230 mutation is partially suppressed by mks1 disruption. The mks1 mutant shows similar phenotypes to gal11/spt13, i.e., it cannot grow on YPGal containing ethidium bromide at 25 degrees C, or on YPGly or SGal at 37 degrees C. The mks1 gal11 double mutant shows more marked phenotypic changes than the single mutants. These results suggest that MKS1 is involved in transcriptional regulation of several genes by cAMP.

Molecular and genetic characterization of SPT4, a gene important for transcription initiation in Saccharomyces cerevisiae

Mutations in the SPT4 gene of Saccharomyces cerevisiae were isolated as suppressors of delta insertion mutations that interfere with adjacent gene transcription. Recent genetic evidence indicates that the SPT4 protein functions with two other proteins, SPT5 and SPT6, in some aspect of transcription initiation. In this work we have characterized the SPT4 gene and we demonstrate that spt4 mutations, like spt5 and spt6 mutations, cause changes in transcription. Using the cloned SPT4 gene, spt4 null mutations were constructed; in contrast to spt5 and spt6 null mutants, which are inviable, spt4 null mutants are viable and have an Spt- phenotype. The DNA sequence of the SPT4 gene predicts a protein product of 102 amino acids that contains four cysteine residues positioned similarly to those of zinc binding proteins. Mutational analysis suggests that at least some of these cysteines are essential for SPT4 function. Genetic mapping showed that SPT4 is a previously unidentified gene that maps to chromosome VII, between ADE6 and CLY8.

Insertional mutations in mammals and mammalian cells

The retroposon sequences, their mechanisms of transposition and the occurrence of insertional mutation in the mammalian genome are reviewed. Insertional mutations fall into two broad categories: those due to the disruption of a gene following the physical integration of a foreign DNA sequence result in loss of gene product and would be expected to be associated with a recessive mutation. A second class of insertional mutation is well documented in which upon integration the promoter/enhancer activities inherent in the retroposon genome exert their influence on neighboring genes. This promoter/enhancer activity of integrated retroposons may have effects over relatively long distances and thus limit the possibilities of establishing an association between retroposon integration and mutation. It is emphasized that a systematic search for insertional mutations in the mammalian genome involves an extensive two-dimensional array of possible retroposon sequences and mutant alleles. Present results represent only a small portion of the total array. Future studies promise to be fruitful in efforts to isolate genes through insertional tagging, to characterize the mechanisms of retroposon transposition, as well as to study the stability of the mammalian genome.

SPT4, SPT5 and SPT6 interactions: effects on transcription and viability in Saccharomyces cerevisiae

The SPT4, SPT5 and SPT6 genes of Saccharomyces cerevisiae were identified originally by mutations that suppress delta insertion mutations at HIS4 and LYS2. Subsequent analysis has demonstrated that spt4, spt5 and spt6 mutations confer similar pleiotropic phenotypes. They suppress delta insertion mutations by altering transcription and are believed to be required for normal transcription of several other loci. We have now analyzed interactions between SPT4, SPT5 and SPT6. First, the combination of mutations in any two of these three genes causes lethality in haploids. Second, some recessive mutations in different members of this set fail to complement each other. Third, mutations in all three genes alter transcription in similar ways. Finally, the results of coimmunoprecipitation experiments demonstrate that at least the SPT5 and SPT6 proteins interact physically. Taken together, these genetic and biochemical results indicate that SPT4, SPT5 and SPT6 function together in a transcriptional process that is essential for viability in yeast.

Ssn6-Tup1 is a general repressor of transcription in yeast

The homeodomain protein alpha 2 and the SRF-like protein Mcm1 are required to establish cell type in the yeast Saccharomyces cerevisiae. Together, these regulatory proteins recognize a specific DNA operator, marking a set of genes for transcriptional repression. In this paper, we show that occupancy of the operator by alpha 2-Mcm1 is not sufficient to bring about repression. Rather, repression is effected only when Ssn6 (a TPR protein) and Tup1 (a beta-transducin repeat protein) are also present in the cell. We show that Ssn6 represses transcription when brought to a promoter by a bacterial DNA-binding domain and that Tup1 is required for this repression. Based on these and other results, we propose that Ssn6-Tup1 is a general repressor of transcription in yeast, recruited to target promoters by a variety of sequence-specific DNA-binding proteins.

The Saccharomyces cerevisiae SPT14 gene is essential for normal expression of the yeast transposon, Ty, as well as for expression of the HIS4 gene and several genes in the mating pathway

To investigate the role of the trans-acting transcription factor encoded by the essential SPT14 (SPT = Suppressor of Ty insertion mutations) gene, we have cloned, mapped and sequenced the gene. From the analysis of the effect of spt14 mutations on expression of various genes, we conclude that the SPT14 product has an important role in activation of Ty transcription as well as in the regulation of other genes including HIS4 and several of the a- and alpha-specific mating type genes. Similarities in the phenotypes of spt14 and spt13 mutants (suppression of Ty insertion mutations but not delta insertion mutations), lead to the suggestion that the SPT14 gene and the previously characterized SPT13/GAL11 gene might encode transcriptional regulators with related functions. Our current findings show that in contrast to SPT13/GAL11, which appears negatively to regulate Ty transcription, SPT14 plays a role in the activation of Ty transcription. Thus, despite the similarities in the suppression phenotype exhibited by spt13 and spt14 mutants, SPT13/GAL11 and SPT14 probably differ in their transcriptional roles.

Histone regulatory (hir) mutations suppress delta insertion alleles in Saccharomyces cerevisiae

Changes in histone gene dosage as well as mutations within some histone genes suppress delta insertion mutations in the HIS4 and LYS2 loci of Saccharomyces cerevisiae by altering the site of transcription initiation. We have found that three histone regulatory (hir) mutations, identified by their effects on the regulation of histone gene expression, suppress the same insertion mutations. In addition, we have examined whether any previously identified spt (suppressor of Ty) mutations might suppress the delta insertion alleles because of effects on histone gene regulation. Our results demonstrate that mutations in the histone genes SPT11/HTA1 and SPT12/HTB1 and in three other SPT genes, SPT1, SPT10 and SPT21, confer Hir- phenotypes. The spt1 mutation was found to be an allele of HIR2 while the spt10 and spt21 mutations are not in any of the known HIR genes.

GAL11P: a yeast mutation that potentiates the effect of weak GAL4-derived activators

A mutant yeast in which a weak GAL4-derived activator functions as a strong activator bears a single mis-sense mutation in GAL11 (a.k.a. SPT13). The first 74 amino acids of GAL4, including the zinc-dependent DNA binding region, attached to an acidic activating sequence, are sufficient to respond both to GAL11 and to our mutant GAL11P (potentiator). PPR1, a yeast activator with a similar zinc finger sequence, also responds to GAL11 and to GAL11P, whereas regulators bearing unrelated DNA binding motifs do not. GAL11 itself works as a strong activator when tethered to DNA by fusion to the bacterial LexA protein, and deletion of GAL11 is known to cause a 5- to 10-fold reduction in GAL4 activity. We suggest that a complex of GAL4 and GAL11 constitutes a particularly strong activator; evidence that the putative GAL4-GAL11 complex ordinarily forms preferentially on DNA suggests a biological rationale for GAL11 action.

Transcriptional control by galactose of a yeast gene encoding a protein homologous to mammalian aldo/keto reductases

Expression of the S. cerevisiae gene, GCY, encoding a 35-kDa protein with striking homology to mammalian aldo/keto reductases, is under the control of galactose: the intracellular concentration of the respective mRNA (about 1300 nt in length) varies strongly with the carbon source. It is particularly high when galactose is the sole energy source but is low as soon as glucose is present. Lactate, glycerol and raffinose lead to intermediate expression. Both Northern blot analyses and lacZ fusion data indicate a 20- to 50-fold increase in the steady state concentrations of mRNA and beta Gal activity, respectively, when grown on galactose as compared to glucose. The gene is derepressed after cultivation on glycerol in the wt and in a gal80 mutant background but remains uninducible by galactose in strains carrying either a gal2 or a gal4 mutation, affecting galactose permease and the GAL gene trans-activator, respectively. Analysis of GCY expression in gal regulatory mutants reveals epistasis interactions of the gal4 and the gal80 mutations as expected if GCY is regulated by the Gal control system. Repression of GCY transcription by glucose is observed in all three above gal mutant strains. The results suggest that the gene is both positively controlled by galactose and negatively by glucose. Analysis of a set of upstream deletions identifies a single UAS matching the consensus for GAL gene upstream regulation sites. By contrast to other genes regulated by galactose, disruption mutants of GCY exhibit no obvious phenotype, and in particular do not lose the ability to grow on and adapt to galactose. Enzyme tests with AKR-specific substrates suggest that GCY encodes a carbonyl reductase.