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Query: UNIPROT:P06889 (Mol)
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Two proteins that bind to yeast ARS DNA have been purified using conventional and oligonucleotide affinity chromatography. One protein has been purified to homogeneity and has a mass of 135 kDa. Competitive binding studies and DNase I footprinting show that the protein binds to a sequence about 80 base pairs away from the core consensus in the region known as domain B. This region has previously been shown to be required for efficient replication of plasmids carrying ARS1 elements. To investigate further whether the protein might have a function related to the ability of ARSs to act as replicators, binding to another ARS was tested. The protein binds to the functional ARS adjacent to the silent mating type locus HMR, called the HMR-E ARS, about 60 base pairs from the core consensus sequence. Surprisingly, there is little homology between the binding site at the HMR-E ARS and the binding site at ARS1. The 135-kDa protein is probably the same as ABF-I (SBF I) (Shore, D., Stillman, D. J. Brand, A. H., and Nasmyth, K. A. (1987) EMBO J. 6, 461-467; Buchman, A. R., Kimmerly, W. J., Rine, J., and Kornberg, R. D. (1988) Mol. Cell. Biol. 8, 210-225). A second DNA-binding protein was separated from ABF-I during later stages of the purification. This protein, which we designate ABF-III, also binds specifically to the ARS1 sequence, as shown by DNase I footprinting, at a site adjacent to the ABF-I recognition site. Purification of these two ARS binding proteins should aid in our understanding of the complex mechanisms that regulate eukaryotic DNA replication.
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PMID:Purification and characterization of proteins that bind to yeast ARSs. 305 6

General regulatory factor I (GRFI) is a yeast protein that binds in vitro to specific DNA sequences at diverse genetic elements. A strategy was pursued to test whether GRFI functions in vivo at the sequences bound by the factor in vitro. Matches to a consensus sequence for GRFI binding were found in a variety of locations: upstream activating sequences (UASs), silencers, telomeres, and transcribed regions. All occurrences of the consensus sequence bound both crude and purified GRFI in vitro. All binding sites for GRFI, regardless of origin, provided UAS function in test plasmids. Also, GRFI binding sites specifically stimulated transcription in a yeast in vitro system, indicating that GRFI can function as a positive transcription factor. The stimulatory effect of GRFI binding sites at UASs for the PYK1 and ENO1 genes is significantly enhanced by flanking DNA elements. By contrast, regulatory sequences that flank the GRFI binding site at HMR E convert this region to a transcriptional silencer.
Mol Cell Biol 1988 Dec
PMID:Connections between transcriptional activators, silencers, and telomeres as revealed by functional analysis of a yeast DNA-binding protein. 307 72

We have isolated and sequenced a cDNA clone encompassing the entire protein coding region of the Xenopus laevis estrogen receptor (xER). The Xenopus ER, the first steroid hormone receptor to be sequenced from a cold-blooded organism, exhibits two regions of striking amino acid homology with the human and avian ERs. In the putative DNA binding region, the amino acid sequence of the xER differs from those of the human and avian ERs at only one of 83 amino acids. The putative hormone binding region contains 44 and 46 amino acid blocks in which the sequence is identical in the Xenopus and human ERs. Blot hybridizations of Xenopus liver RNA suggest that the xER is encoded by four mRNAs with lengths of approximately 9, 6.5, 2.8, and 2.5 kilobases. In contrast, hybridization of human RNA to a human ER cDNA clone reveals only a single major ER RNA, approximately 6.7 kilobases in length.
Mol Endocrinol 1987 May
PMID:The Xenopus laevis estrogen receptor: sequence homology with human and avian receptors and identification of multiple estrogen receptor messenger ribonucleic acids. 327 94

Two DNA-binding factors from Saccharomyces cerevisiae have been characterized, GRFI (general regulatory factor I) and ABFI (ARS-binding factor I), that recognize specific sequences within diverse genetic elements. GRFI bound to sequences at the negative regulatory elements (silencers) of the silent mating type loci HML E and HMR E and to the upstream activating sequence (UAS) required for transcription of the MAT alpha genes. A putative conserved UAS located at genes involved in translation (RPG box) was also recognized by GRFI. In addition, GRFI bound with high affinity to sequences with the (C1-3A)-repeat region at yeast telomeres. Binding sites for GRFI with the highest affinity appeared to be of the form 5'-(A/G)(A/C)ACCCANNCA(T/C)(T/C)-3', where N is any nucleotide. ABFI-binding sites were located next to autonomously replicating sequences (ARSs) at controlling elements of the silent mating type loci HMR E, HMR I, and HML I and were associated with ARS1, ARS2, and the 2 micron plasmid ARS. Two tandem ABFI binding sites were found between the HIS3 and DED1 genes, several kilobase pairs from any ARS, indicating that ABFI-binding sites are not restricted to ARSs. The sequences recognized by ABFI showed partial dyad-symmetry and appeared to be variations of the consensus 5'-TATCATTNNNNACGA-3'. GRFI and ABFI were both abundant DNA-binding factors and did not appear to be encoded by the SIR genes, whose products are required for repression of the silent mating type loci. Together, these results indicate that both GRFI and ABFI play multiple roles within the cell.
Mol Cell Biol 1988 Jan
PMID:Two DNA-binding factors recognize specific sequences at silencers, upstream activating sequences, autonomously replicating sequences, and telomeres in Saccharomyces cerevisiae. 327 67

Mutations in the ARD1 gene prevent yeast cells from displaying G1-specific growth arrest in response to nitrogen deprivation and cause MATa haploids (but not MAT alpha haploids) to be mating defective. Analysis of cell type-specific gene expression by examination of RNA transcripts and measurement of beta-galactosidase activity from yeast gene-lacZ fusions demonstrated that the mating defect of MATa ard1 mutants was due to an inability to express genes required by MATa cells for the mating process. The lack of mating-specific gene expression in MATa cells was found to be due solely to derepression of the normally silent alpha information at the HML locus. The cryptic a information at the HMR locus was only very slightly derepressed in ard1 mutants, to a level insufficient to affect the mating efficiency of MAT alpha cells. The preferential elevation of expression from HML over HMR was also observed in ard1 mutants which contained the alternate arrangement of a information at HML and alpha information at HMR. Hence, the effect of the ard1 mutation was position specific (rather than information specific). Although the phenotype of ard1 mutants resembled that of cells with mutations in the SIR1 gene, both genetic and biochemical findings indicated that ARD1 control of HML expression was independent of the regulation imposed by SIR1 and the other SIR genes. These results suggest that the ARD1 gene encodes a protein product that acts, directly or indirectly, at the HML locus to repress its expression and, by analogy, may control expression of other genes involved in monitoring nutritional conditions.
Mol Cell Biol 1987 Oct
PMID:The yeast ARD1 gene product is required for repression of cryptic mating-type information at the HML locus. 331 86

In Saccharomyces cerevisiae, two cis-acting regulatory sites called E and I flank the silent mating-type gene, HMRa, and mediate SIR-dependent transcriptional repression of the a1-a2 promoters. It has been shown previously that the E and I sites have plasmid replicator (ARS) activity. We show in this report that the ARS activity of the E and I sites is governed by the SIR genotype of the cell. In wild-type cells, a plasmid carrying the E site from HMRa (HMR E) in the vector YIp5 exhibited very high mitotic stability at a copy number of approximately 25 per cell. However, in sir2, sir3, or sir4 mutants, plasmids with HMR E had the low mitotic stability characteristic of plasmids containing ARS1, a SIR-independent replicator. Elevated mitotic stability of plasmids that carry HMR E is due to a segregation mechanism provided by SIR and HMR E. In sir2 and sir4 mutants, the plasmid copy number was significantly lowered, suggesting that these gene products also participate in the replication of plasmids carrying HMR E. The phenotype of point mutations introduced at an 11-base-pair ARS consensus sequence present at HMR E indicated that this sequence is functional but not absolutely required for autonomous replication of the plasmid and that it is not required for SIR-dependent mitotic stabilization. A plasmid carrying both a centromere and HMR E exhibited reduced mitotic stability in wild-type cells. This destabilization appeared to be due to antagonism between the segregation functions provided by the centromere and by HMR E.
Mol Cell Biol 1987 Dec
PMID:Replication and segregation of plasmids containing cis-acting regulatory sites of silent mating-type genes in Saccharomyces cerevisiae are controlled by the SIR genes. 332 22

A macromolecule with high affinity for the ecdysteroid analogue ponasterone A was isolated from nuclei of larvae of the blowfly Calliphora vicina. The ecdysteroid-binding molecule revealed characteristics of the moulting hormone receptor. It was sensitive towards protease but not towards nucleases. The nuclear protein had a limited binding capacity (0.2 pmol ponasterone A/mg protein), showed hormone analogue specificity and high affinity for ecdysteroids. Enzyme activities were present in the nuclear extract that metabolized ecdysteroids and thereby interfered with the binding assay. After their removal by DEAE-cellulose chromatography the ecdysteroid receptor preparation was stable at 20 degrees C for hours. This allowed a reliable determination of dissociation constants at equilibrium conditions. The hormone receptor complex had a KD of 1 nM, 30 nM, and 2000 nM with ponasterone A, 20-hydroxyecdysone, and ecdysone, respectively. The apparent molecular mass of the ecdysteroid receptor was 105,000 as determined by gel filtration.
Mol Cell Endocrinol 1988 Jun
PMID:Ecdysteroid receptors of the blowfly Calliphora vicina: partial purification and characterization of ecdysteroid binding. 340 63

The activity of a series of folic acid analogues as substrates for partially purified mouse liver folylpolyglutamate synthetase was determined and the effects of substituents on the binding to, and catalytic processes of, this enzyme were inferred. A 4-amino group improved substrate activity primarily by decreasing the apparent Km while N10-methyl substitution substantially diminished utilization as a substrate, again, by effects on Km. Isosteric replacement of N-10 altered substrate activity. A free alpha-carboxyl group in the amino acid side chain was required for catalysis as was the presence of the side chain amide carbonyl group. Modification of the amino acid side chain length profoundly affected activity. Several observations were made that may be relevant to chemotherapy with folate antimetabolites: 1) 7-hydroxymethotrexate was a substrate for this enzyme; 2) substrate activity and substrate inhibition were observed with CB 3717, a potent inhibitor of thymidylate synthase; 3) potent classical dihydrofolate reductase inhibitors were identified that were either not substrates for mouse liver folylpolyglutamate synthetase (e.g., 4-amino-4-deoxy-N10-methylpteroyl-L-alpha-aminoadipate) or were much better substrates than methotrexate for this enzyme (e.g., aminopterin); and 4) leucovorin and methotrexate appeared to be substrates for the same synthetase, but leucovorin saturated the reaction at much lower concentrations. These results have implications for the design of folylpolyglutamate synthetase inhibitors and for the selection of dihydrofolate reductase inhibitors that are either not polyglutamated or are efficiently polyglutamated in vivo.
Mol Pharmacol 1985 Jan
PMID:Structural features of 4-amino antifolates required for substrate activity with mammalian folylpolyglutamate synthetase. 383 5

Homothallic switching of the mating type genes of Saccharomyces cerevisiae occurs by a gene conversion event, replacing sequences at the expressed MAT locus with a DNA segment copied from one of two unexpressed loci, HML or HMR. The transposed Ya or Y alpha sequences are flanked by homologous regions that are believed to be essential for switching. We examined the transposition of a mating type gene (hmr alpha 1-delta 6) which contains a 150-base-pair deletion spanning the site where the HO endonuclease generates a double-stranded break in MAT that initiates the gene conversion event. Despite the fact that the ends of the cut MAT region no longer share homology with the donor hmr alpha 1-delta 6, switching of MATa or MAT alpha to mat alpha 1-delta 6 was efficient. However, there was a marked increase in the number of aberrant events, especially the formation of haploid-inviable fusions between MAT and the hmr alpha 1-delta 6 donor locus.
Mol Cell Biol 1985 Aug
PMID:Homothallic switching of Saccharomyces cerevisiae mating type genes by using a donor containing a large internal deletion. 391 86

There are three loci in the yeast Saccharomyces, each containing one of two possible genetic elements that can determine cell type. At one of these loci, MAT, this information is expressed to establish the mating type of the cell. At the other two loci, HML and HMR, this same information is phenotypically and transcriptionally silent, even though a large amount of identical sequence flanks MAT, HML and HMR coding regions. Transcriptional repression of HML and HMR requires the trans active gene products of four loci, designated variously as MAR or SIR, that are unlinked to each other or to MAT, HML or HMR. We have examined the phenotypic expression of a cloned, plasmid-borne copy of HML and of various deletion and insertion derivatives of this plasmid following their reintroduction into Mar+/Sir+ yeast strains. From these data, we have identified two sites flanking the locus, both of which are required for MAR/SIR repression of the locus. In addition, we demonstrate that each of these sites promotes autonomous replication in yeast. Abraham et al. (1984) have presented evidence demonstrating that a similar regulatory structure exists at the other silent locus, HMR. From an analysis of the sequences of these four regulatory sites, we have identified several specific sequences that may be involved in mediating repression of these loci and in promoting replication in yeast. These results are discussed in the context of potential models for the mechanism of regulation of the silent mating type loci.
J Mol Biol 1984 Oct 05
PMID:Identification of sites required for repression of a silent mating type locus in yeast. 609 45


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