A protein involved in minichromosome maintenance in yeast binds a transcriptional enhancer conserved in eukaryotes

The phenotype of the minichromosome maintenance mutant mcm3 is characteristic of mutants defective in DNA replication

MCM3 is an essential gene involved in the maintenance of minichromosomes in yeast cells. It encodes a protein of 971 amino acids that shows striking homology to the Mcm2 protein. We have mapped the mcm3-1 mutation of the left arm of chromosome V approximately 3 kb centromere proximal of anp1. The mcm3-1 mutant was found to be thermosensitive for growth. Under permissive growth conditions, it was defective in minichromosome maintenance in an autonomously replicating sequence-specific manner and showed an increase in chromosome loss and recombination. Under nonpermissive conditions, mcm3-1 exhibited a cell cycle arrest phenotype, arresting at the large-bud stage with an undivided nucleus that had a DNA content of nearly 2n. These phenotypes are consistent with incomplete replication of the genome of the mcm3-1 mutant, possibly as a result of limited replication initiation at selective autonomously replicating sequences leading to cell cycle arrest before mitosis. The phenotype exhibited by the mcm3 mutant is very similar to that of mcm2, suggesting that the Mcm2 and Mcm3 protein may play interacting roles in DNA replication.

The PRE and PQ box are functionally distinct yeast pheromone response elements

Saccharomyces cerevisiae mating pheromones function by binding to cell surface receptors and activating signal transduction processes which regulate gene expression. In this report, we have analyzed the minimum sequence requirements for conferring both a and alpha mating pheromone inducibilities onto a heterologous promoter. Here we show that the repetitive pheromone response element (PRE) which binds to STE12 protein is sufficient to confer pheromone responsiveness only when present in multiple copies. Moreover, by itself, it is preferentially responsive to alpha factor in a cells. In contrast, a single copy of the PQ box of the STE3 upstream activation sequence (UAS) is sufficient to confer a-factor responsiveness in alpha cells. The PQ box binds both MCM1 and MAT alpha 1 in a cooperative manner, and neither the P nor Q site alone is sufficient to confer a-factor responsiveness. In a cells, however, even multiple copies of the PQ box fail to confer alpha-factor responsiveness. Therefore, the PRE and the PQ box are functionally distinct pheromone-responsive elements with opposite cell type specificities. Moreover, these results indicate that the MCM1 protein functions in a signal transduction pathway in a manner analogous to that of its mammalian homolog, the serum response factor, which regulates the expression of the c-fos proto-oncogene in mammals.

In vitro regulation of a SIN3-dependent DNA-binding activity by stimulatory and inhibitory factors

The yeast SIN3 gene (also known as SDII, is a known negative regulator of the yeast HO gene. A DNA-binding activity, called SDP1, which binds to the HO promoter, is absent in extracts prepared from sin3 mutants and has been proposed to function as a repressor. We show that SIN3 does not encode SDP1 and that SDP1 DNA-binding activity is modulated in vitro by two factors, an inhibitory factor, I-SDP1, and a stimulatory factor, S-SDP1. I-SDP1 acts as an in vitro inhibitor of the SDP1 DNA-binding activity. Restoration of the DNA-binding activity is achieved by inclusion of a stimulatory factor, S-SDP1, which copurifies with the SIN3 protein. SDP1 DNA-binding activity was restored by treating a protein fraction containing SDP1 and I-SDP1 with the dissociating agent formamide.

A sensitive method for the determination of protein-DNA binding specificities

We describe a sensitive and rapid method for determination of the sequence specificity of DNA binding proteins. The method allows recovery of specific sites using the small amounts of protein present in crude cell extracts or produced by cell-free translation reactions. Extract proteins are incubated with a pool of random sequence oligonucleotides, complexes purified by immunoprecipitation, and bound DNA amplified by the Polymerase Chain Reaction (PCR). This DNA is then used in further rounds of binding, immunoprecipitation, and amplification, until specific binding is detectable. With the transcription factor SRF as a model system, we demonstrate that authentic high affinity binding sites are recovered, and show that epitope tagging can be used to allow recovery of sites when specific antibodies are unavailable. We also show that specific sites bound by the Fos protein, which binds DNA with high affinity only when complexed with other polypeptides, are easily recovered by this technique.

The phenotype of the minichromosome maintenance mutant mcm3 is characteristic of mutants defective in DNA replication

MCM3 is an essential gene involved in the maintenance of minichromosomes in yeast cells. It encodes a protein of 971 amino acids that shows striking homology to the Mcm2 protein. We have mapped the mcm3-1 mutation of the left arm of chromosome V approximately 3 kb centromere proximal of anp1. The mcm3-1 mutant was found to be thermosensitive for growth. Under permissive growth conditions, it was defective in minichromosome maintenance in an autonomously replicating sequence-specific manner and showed an increase in chromosome loss and recombination. Under nonpermissive conditions, mcm3-1 exhibited a cell cycle arrest phenotype, arresting at the large-bud stage with an undivided nucleus that had a DNA content of nearly 2n. These phenotypes are consistent with incomplete replication of the genome of the mcm3-1 mutant, possibly as a result of limited replication initiation at selective autonomously replicating sequences leading to cell cycle arrest before mitosis. The phenotype exhibited by the mcm3 mutant is very similar to that of mcm2, suggesting that the Mcm2 and Mcm3 protein may play interacting roles in DNA replication.

DNA sequences required for yeast actin gene transcription do not include conserved CCAAT motifs

Sequences required for Saccharomyces cerevisiae actin gene transcription were mapped and compared to the regulatory region of the actin gene from a thermophilic fungus, Thermomyces lanuginosus. Two CCAAT motifs conserved in position in these two species could be mutated without affecting promoter activity, regardless of whether the yeast were grown in fermentable or non-fermentable carbon sources. Two TATA-like sequences and an upstream activation sequence (UAS) composed of multiple elements were identified. The contribution of sequence motifs within these elements to UAS activity varied depending on the carbon source. The Thermomyces gene contains sequences highly homologous to this UAS, but in the opposite orientation.

Mutations that define the optimal half-site for binding yeast GCN4 activator protein and identify an ATF/CREB-like repressor that recognizes similar DNA sites

The yeast GCN4 transcriptional activator protein binds as a dimer to a dyad-symmetric sequence, indicative of a protein-DNA complex in which two protein monomers interact with adjacent half-sites. However, the optimal GCN4 recognition site, ATGA(C/G)TCAT, is inherently asymmetric because it contains an odd number of base pairs and because mutation of the central C.G base pair strongly reduces specific DNA binding. From this asymmetry, we suggested previously that GCN4 interacts with nonequivalent and possibly overlapping half-sites (ATGAC and ATGAG) that have different affinities. Here, we examine the nature of GCN4 half-sites by creating symmetrical derivatives of the optimal GCN4 binding sequence that delete or insert a single base pair at the center of the site. In vitro, GCN4 bound efficiently to the sequence ATGACGTCAT, whereas it failed to bind to ATGAGCTCAT or ATGATCAT. These observations strongly suggest that (i) GCN4 specifically recognizes the central base pair, (ii) the optimal half-site for GCN4 binding is ATGAC, not ATGAG, and (iii) GCN4 is a surprisingly flexible protein that can accommodate the insertion of a single base pair in the center of its compact binding site. The ATGACGTCAT sequence strongly resembles sites bound by the yeast and mammalian ATF/CREB family of proteins, suggesting that GCN4 and the ATF/CREB proteins recognize similar half-sites but have different spacing requirements. Unexpectedly, in the context of the his3 promoter, the ATGACGTCAT derivative reduced transcription below the basal level in a GCN4-independent manner, presumably reflecting DNA binding by a distinct ATF/CREB-like repressor protein. In other promoter contexts, however, the same site acted as a weak upstream activating sequence.

Binding of yeast a1 and alpha 2 as a heterodimer to the operator DNA of a haploid-specific gene

The mating-type locus (MAT) encodes several DNA-binding proteins, which determine the three cell types of Saccharomyces cerevisiae: the a and alpha haploid cell types, and the a/alpha diploid cell type. One of the products of MAT, alpha 2, functions in two cell types. In alpha cells, alpha 2 represses the a-specific genes by binding to the operator as a dimer. In a/alpha diploid cells, alpha 2 acts with a1, a product of the other MAT allele, to repress a different set of genes, the haploid-specific genes. Until now, the nature of the interaction between a1 and alpha 2 was not known, although it had been suggested that alpha 2 may form a heterodimer with a1. I show, by using proteins synthesized in vitro, that a1 and alpha 2 bind the operator of a haploid-specific gene as a heterodimer. The ability of alpha 2 to form both homodimers and heterodimers with a1, each with a different DNA-binding specificity, explains the dual regulatory functions of alpha 2. This is the first example of regulation by heterodimerization among homeobox-containing proteins, a class that includes proteins responsible for the specification of segment identity in Drosophila, mammals and other eukaryotes.

Mutations that define the optimal half-site for binding yeast GCN4 activator protein and identify an ATF/CREB-like repressor that recognizes similar DNA sites

The yeast GCN4 transcriptional activator protein binds as a dimer to a dyad-symmetric sequence, indicative of a protein-DNA complex in which two protein monomers interact with adjacent half-sites. However, the optimal GCN4 recognition site, ATGA(C/G)TCAT, is inherently asymmetric because it contains an odd number of base pairs and because mutation of the central C.G base pair strongly reduces specific DNA binding. From this asymmetry, we suggested previously that GCN4 interacts with nonequivalent and possibly overlapping half-sites (ATGAC and ATGAG) that have different affinities. Here, we examine the nature of GCN4 half-sites by creating symmetrical derivatives of the optimal GCN4 binding sequence that delete or insert a single base pair at the center of the site. In vitro, GCN4 bound efficiently to the sequence ATGACGTCAT, whereas it failed to bind to ATGAGCTCAT or ATGATCAT. These observations strongly suggest that (i) GCN4 specifically recognizes the central base pair, (ii) the optimal half-site for GCN4 binding is ATGAC, not ATGAG, and (iii) GCN4 is a surprisingly flexible protein that can accommodate the insertion of a single base pair in the center of its compact binding site. The ATGACGTCAT sequence strongly resembles sites bound by the yeast and mammalian ATF/CREB family of proteins, suggesting that GCN4 and the ATF/CREB proteins recognize similar half-sites but have different spacing requirements. Unexpectedly, in the context of the his3 promoter, the ATGACGTCAT derivative reduced transcription below the basal level in a GCN4-independent manner, presumably reflecting DNA binding by a distinct ATF/CREB-like repressor protein. In other promoter contexts, however, the same site acted as a weak upstream activating sequence.

The specificities of Sex combs reduced and Antennapedia are defined by a distinct portion of each protein that includes the homeodomain

The sequence requirements for distinguishing the functional specificities of two homeodomain proteins, Antennapedia and Sex combs reduced, involved in the specification of segmental identities in Drosophila, have been determined. A series of deletions and hybrid proteins was generated and assayed for their function in vivo after heat shock-induced ectopic expression during development. A distinct portion of each protein, including the residues within and adjacent to both ends of the homeodomain, has been found to almost entirely determine its functional specificity as measured by diagnostic cuticular transformations of embryonic and adult head structures. The remaining sequences contribute to the potency with which the proteins act in different cells and are to a limited extent functionally transferable from one protein to the other.

Yeast Gal11 protein mediates the transcriptional activation signal of two different transacting factors, Gal4 and general regulatory factor I/repressor/activator site binding protein 1/translation upstream factor

GAL11 was first identified as a gene required for full expression of some of the galactose-inducible genes in the yeast Saccharomyces cerevisiae. A null mutation within the GAL11 locus causes defects in mating, growth on nonfermentable carbon sources, and sporulation of gal11 homozygotes. The mating defect was observed only in MAT alpha gal11 strains. Northern hybridization analysis revealed that a gal11 mutation impaired transcription of alpha-specific genes (MF alpha 1 and STE3) but not of an a-specific gene (STE2). Furthermore, this mutation reduced expression of the MAT alpha locus, suggesting that a deficiency in MAT alpha 1 protein is responsible for the reduced expression of alpha-specific genes. Since general regulatory factor I (GRFI)/repressor/activator site binding protein 1 (RAP1)/translation upstream factor (TUF) is believed to be an activator of MAT alpha expression, we examined whether PYK1, which is known to be regulated by GRFI/RAP1/TUF, is also affected by the gal11 mutation. It was determined that the level of PYK1 message was significantly lowered by the mutation. The requirement for functional GAL11 in transcriptional activation was bypassed when either the upstream activating sequence of galactose-inducible genes or of PYK1 was placed very close to the TATA box, suggesting that one of the Gal11 protein functions is to mediate the activation signal of Gal4 and GRFI/RAP1/TUF, when the respective binding site is situated at the naturally occurring distance from the TATA box.

Yeast alpha 2 repressor positions nucleosomes in TRP1/ARS1 chromatin

The yeast alpha 2 repressor suppresses expression of a-mating-type-specific genes in haploid alpha and diploid a/alpha cell types. We inserted the alpha 2-binding site into the multicopy TRP1/ARS1 yeast plasmid and examined the effects of alpha 2 on the chromatin structure of the derivative plasmids in alpha cells, and a/alpha cells. Whereas no effect on nucleosome position was observed in a cells, nucleosomes were precisely and stably positioned over sequences flanking the alpha 2 operator in alpha and a/alpha cells. In addition, when the alpha 2 operator was located upstream of the TRP1 gene, an extended array of positioned nucleosomes was formed in alpha cells and a/alpha cells, with formation of a nucleosome not present in a cells, and TRP1 mRNA production was substantially reduced. These data indicate that alpha 2 causes a positioning of nucleosomes over sequences proximal to its operator in TRP1/ARS1 chromatin and suggest that changes in chromatin structure may be related to alpha 2 repression of cell-type-specific genes.

In vivo degradation of a transcriptional regulator: the yeast alpha 2 repressor

Metabolic instability is characteristic of regulatory proteins whose in vivo concentrations must vary as a function of time. The cell type-specific alpha 2 repressor of the yeast S. cerevisiae is shown here to have a half-life of only approximately 5 min. Each of the two structural domains of alpha 2 carries a sequence that can independently target a normally long-lived protein for rapid destruction. Moreover, these two degradation signals are shown to operate via distinct mechanisms. Mutants deficient in the degradation of alpha 2 have been isolated and found to have a number of additional defects, indicating that the pathways responsible for alpha 2 turnover include components with multiple functions. Finally, we demonstrate that a short-lived subunit of an oligomeric protein can be degraded in vivo without destabilizing other, long-lived subunits of the same protein. This subunit-specific degradation makes possible a novel type of posttranslational remodeling in which a heteromeric protein could be functionally modified by selective, degradation-mediated replacement of its subunits.

Identification of a Saccharomyces cerevisiae DNA-binding protein involved in transcriptional regulation

A DNA-binding protein has been identified from extracts of the budding yeast Saccharomyces cerevisiae which binds to sites present in the promoter regions of a number of yeast genes transcribed by RNA polymerase II, including SIN3 (also known as SDI1), SWI5, CDC9, and TOP1. This protein also binds to a site present in the enhancer for the 35S rRNA gene, which is transcribed by RNA polymerase I, and appears to be identical to the previously described REB1 protein (B. E. Morrow, S. P. Johnson, and J. R. Warner, J. Biol. Chem. 264:9061-9068, 1989). When oligonucleotides containing a REB1-binding site are placed between the CYC1 upstream activating sequence and TATA box, transcription by RNA polymerase II in vivo is substantially reduced, suggesting that REB1 acts as a repressor of RNA polymerase II transcription. The in vitro levels of the REB1 DNA-binding activity are reduced in extracts prepared from strains bearing a mutation in the SIN3 gene. A greater reduction in REB1 activity is observed if the sin3 mutant strain is grown in media containing galactose as a carbon source.

Yeast alpha 2 repressor positions nucleosomes in TRP1/ARS1 chromatin

The yeast alpha 2 repressor suppresses expression of a-mating-type-specific genes in haploid alpha and diploid a/alpha cell types. We inserted the alpha 2-binding site into the multicopy TRP1/ARS1 yeast plasmid and examined the effects of alpha 2 on the chromatin structure of the derivative plasmids in alpha cells, and a/alpha cells. Whereas no effect on nucleosome position was observed in a cells, nucleosomes were precisely and stably positioned over sequences flanking the alpha 2 operator in alpha and a/alpha cells. In addition, when the alpha 2 operator was located upstream of the TRP1 gene, an extended array of positioned nucleosomes was formed in alpha cells and a/alpha cells, with formation of a nucleosome not present in a cells, and TRP1 mRNA production was substantially reduced. These data indicate that alpha 2 causes a positioning of nucleosomes over sequences proximal to its operator in TRP1/ARS1 chromatin and suggest that changes in chromatin structure may be related to alpha 2 repression of cell-type-specific genes.

Identification of a Saccharomyces cerevisiae DNA-binding protein involved in transcriptional regulation

A DNA-binding protein has been identified from extracts of the budding yeast Saccharomyces cerevisiae which binds to sites present in the promoter regions of a number of yeast genes transcribed by RNA polymerase II, including SIN3 (also known as SDI1), SWI5, CDC9, and TOP1. This protein also binds to a site present in the enhancer for the 35S rRNA gene, which is transcribed by RNA polymerase I, and appears to be identical to the previously described REB1 protein (B. E. Morrow, S. P. Johnson, and J. R. Warner, J. Biol. Chem. 264:9061-9068, 1989). When oligonucleotides containing a REB1-binding site are placed between the CYC1 upstream activating sequence and TATA box, transcription by RNA polymerase II in vivo is substantially reduced, suggesting that REB1 acts as a repressor of RNA polymerase II transcription. The in vitro levels of the REB1 DNA-binding activity are reduced in extracts prepared from strains bearing a mutation in the SIN3 gene. A greater reduction in REB1 activity is observed if the sin3 mutant strain is grown in media containing galactose as a carbon source.

Nerve growth factor regulates tyrosine hydroxylase gene transcription through a nucleoprotein complex that contains c-Fos

We have studied nerve growth factor (NGF) regulation of the expression of the tyrosine hydroxylase (TH) gene in PC12 cells. The TH gene encodes the initial and rate-limiting enzyme of the catecholamine biosynthetic pathway. We show that the TH gene is transiently transcriptionally induced by a mechanism reliant on new protein synthesis during 1-2 hr of NGF stimulation, a time following the induction of the c-fos gene at 15 min post-NGF treatment. A potential regulatory sequence located within the TH gene promoter, the TH-FSE, shares homology to a known regulatory element, the fat-specific element (FSE), which is found upstream from genes activated during adipocyte differentiation and binds the Fos-Jun transcription factor complex. We show that the TH-FSE DNA sequence elevates the basal level of transcription from the rat TH promoter and is required for NGF inducibility. This DNA element binds authentic Fos-Jun products produced abundance during NGF stimulation and by in vitro translation. We demonstrate further that the TH-FSE can bind proteins present in PC12 nuclear extracts in a sequence-specific manner. The DNA/nucleoprotein complex that forms increases in abundance during NGF stimulation and reaches a maximum level at 4 hr of treatment. Antibody inhibition studies utilizing an anti-Fos antibody indicate that Fos and/or Fos-related antigen(s) associate with the TH-FSE and suggest that the Fos protein family contributes to the regulation of TH in vivo. These results support a model in which NGF-induced immediate early genes, including c-Fos, contribute to the regulation of delayed early genes such as TH and thereby control neuronal differentiation.

Overproduction of the yeast STE12 protein leads to constitutive transcriptional induction

Haploid a and alpha cells of the yeast Saccharomyces cerevisiae respond to the pheromones alpha- and a-factor, respectively, by increasing transcription of inducible genes, arresting cell division, and forming cell-surface projections. These responses are dependent on the activity of several genes, including STE12, whose product binds to the pheromone response element located within the regulatory DNA sequences of inducible genes. We assayed the effects of overproducing the STE12 protein in both STE+ cells, as well as ste2, ste7, and ste11 mutant cells. We find that overproduction leads to increased transcription of pheromone-inducible genes and is able to suppress the mating defect of the ste mutants. These results suggest that one effect of pheromone treatment may be to increase the ability of the STE12 protein to activate transcription. In addition, we observed that cells cannot tolerate very high levels of the STE12 protein, and many arrest in G1 with a large size and morphological changes. Thus, constitutively high-level transcription of pheromone-inducible genes causes cells to display some features similar to treatment with pheromone.

Yeast repressor alpha 2 binds to its operator cooperatively with yeast protein Mcm1

To bring about repression of a family fo genes in Saccharomyces cerevisiae called the a-specific genes, two transcriptional regulatory proteins, alpha 2 and GRM (general regulator of matin type), bind cooperatively to an operator found upstream of each a-specific gene. To date, GRM has been defined only biochemically. In this communication we show that the product of a single yeast gene (MCM1) is sufficient to bind cooperatively with alpha 2 to the operator. We also show that antiserum raised against the MCM1 gene product recognizes GRM from yeast cells. These results, in combination with previous observations, provide strong evidence that MCM1 encodes the GRM activity.

Identification, purification, and cloning of a polypeptide (PRTF/GRM) that binds to mating-specific promoter elements in yeast

In yeast the alpha-specific regulators, alpha 1 and alpha 2 have been proposed to be DNA-binding proteins, both of which have to interact with an additional factor called PRTF or GRM, respectively, to exert their biological functions. Although the cis-acting sequence requirements for alpha 1 and alpha 2 are different, their target sequences share a common motif. PRTF or GRM is thought to act via this common DNA sequence; therefore, it has been suggested that they represent the same factor. I purified a protein that binds to this common promoter element by DNA affinity chromatography. The purified protein is able to recruit the alpha-specific activator alpha 1 to its binding sites, suggesting that it is indeed PRTF. Further evidence is presented to show that PRTF and GRM are the same protein and that PRTF plays a role in the activation of a-specific genes. Specific antibodies to the purified protein were obtained. They identify the protein as a component of DNA-protein complexes that formed with cell-type-specific promoter sequences. Using these antibodies, the gene encoding the protein was cloned from a yeast lambda gt11 expression library. The DNA sequence established that the gene encoding PRTF/GRM is identical with a previously described gene, FUN80 (essential factor of unknown function) or MCM1 (minichromosome maintenance). Sequence comparison showed further that PRTF/GRM shares similarities with a repressor from yeast, ARGRI, and the mammalian transcription factor SRF.

A regulatory hierarchy for cell specialization in yeast

The specialized sets of genes that determine different cell types in yeast are controlled by combinations of DNA-binding proteins some of which are present only in certain cell types whereas others are present in all cell types. Final differentiation requires an inductive signal that triggers both gene transcription and cell-cycle arrest. Synthesis of the proteins coded by the 'master regulatory' mating-type locus is regulated so as to generate a heterogeneous mitotic cell population containing a stem-cell lineage.

Yeast repressor alpha 2 binds to its operator cooperatively with yeast protein Mcm1

To bring about repression of a family fo genes in Saccharomyces cerevisiae called the a-specific genes, two transcriptional regulatory proteins, alpha 2 and GRM (general regulator of matin type), bind cooperatively to an operator found upstream of each a-specific gene. To date, GRM has been defined only biochemically. In this communication we show that the product of a single yeast gene (MCM1) is sufficient to bind cooperatively with alpha 2 to the operator. We also show that antiserum raised against the MCM1 gene product recognizes GRM from yeast cells. These results, in combination with previous observations, provide strong evidence that MCM1 encodes the GRM activity.