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M Ptashne

Publications and source records attributed to M Ptashne.

At least 91 records · Page 5Linked to original sources
PubMed1987

The carboxy-terminal 30 amino acids of GAL4 are recognized by GAL80.

In wild-type yeast the action of the transcriptional activator GAL4 is inhibited by GAL80, and galactose relieves this inhibition. We show that deletion mutants of GAL4 lacking 30 amino acids of the carboxyl terminus activate transcription constitutively, whereas other deletion mutants bearing the carboxy-terminal 30 amino acids are inhibited by GAL80. Moreover, GAL4 fragments bearing these 30 amino acids, when expressed from a strong promoter on multicopy plasmids, free the endogenous GAL4 from inhibition by GAL80. These and other results suggest that GAL80 recognizes the carboxy-terminal 30 amino acids of GAL4, forming a complex that, though bound to DNA, does not activate transcription.

Amino Acid Sequence↗
PubMed1987

Deletion analysis of GAL4 defines two transcriptional activating segments.

We describe the activities of a wide array of deletion mutants of GAL4, a yeast transcriptional activator. We identify two short regions of GAL4, each of which activates transcription when fused to the DNA-binding region of the molecule. Very large portions of GAL4 are not required for gene activation.

Base Sequence↗
PubMed1987

Mutants of the catabolite activator protein of Escherichia coli that are specifically deficient in the gene-activation function.

In the presence of cyclic AMP, the catabolite activator protein (CAP) of Escherichia coli binds DNA and stimulates transcription at a number of promoters. We have examined a model of CAP bound at the gal promoter and, using directed mutagenesis, have isolated CAP mutants that are analogous to the lambda repressor positive control (pc) mutants. These CAP mutants bind DNA but are defective in stimulating transcription at the gal P1 promoter. These mutants are also altered in positive control at the lac and malT promoters, where CAP binds to sites further upstream from the transcription start site.

Binding Sites↗
PubMed1986

How lambda repressor and lambda Cro distinguish between OR1 and OR3.

Although lambda repressor and lambda Cro bind to the same six operators on the phage chromosome, the fine specificities of the two proteins differ: repressor binds more tightly to OR1 than to OR3, and vice versa for Cro. In this paper, we change base pairs in the operators and amino acids in the proteins to analyze the basis for these preferences. We find that these preferences are determined by residues 5 and 6 of the recognition helices of the two proteins and by the amino-terminal arm, in the case of repressor. We also find that the most important base pairs in the operator which enable repressor and Cro to discriminate between OR1 and OR3 are position 3 (for Cro) and positions 5 and 8 (for repressor). These and previous results show how repressor and Cro recognize and distinguish between two related operator sequences.

Amino Acid Sequence↗
PubMed1986

Homologous interactions of lambda repressor and lambda Cro with the lambda operator.

Lambda repressor and lambda Cro bind to the same six sites on the phage chromosome but with different relative affinities. Nucleotides at certain positions in the operator are conserved in all sites, as are amino acids at certain positions in the recognition alpha-helices of repressor and Cro. Here we focus on one of the conserved amino acids, a serine found at position 2 of each recognition helix. We show that, contrary to a previous model, both serines contact the same conserved position in the operator, position 4. We suggest a simplified view of how repressor and Cro recognized similar operator sites but distinguish differently among them.

Amino Acid Sequence↗
PubMed1986

Cooperative binding of lambda repressors to sites separated by integral turns of the DNA helix.

Lambda repressors bind cooperatively to adjacent pairs of operator sites. Here we show that repressors bind cooperatively to pairs of operator sites whose centers have been separated by five or six turns of the helix. No cooperativity is observed when the centers of these sites are on opposite sides of the DNA helix. Cooperativity depends upon the same part of the protein (the carboxyl domain) that mediates cooperativity when the sites are adjacent. As the repressors bind, the DNA between the sites becomes alternately sensitive and resistant to DNAase I cleavage at half turn intervals. We suggest that when repressors bind cooperatively to separated sites, the DNA forms a loop, thus allowing the two repressors to touch.

Base Sequence↗
PubMed1986

Separation of DNA binding from the transcription-activating function of a eukaryotic regulatory protein.

The yeast GAL4 protein (881 amino acids) binds to specific DNA sites upstream of target genes and activates transcription. Derivatives of this protein bearing as few as 74 amino terminal residues bind to these sites but fail to activate transcription. When appropriately positioned in front of a gene these derivatives act as repressors. These and related findings support the idea that GAL4 activates transcription by touching other DNA-bound proteins.

Amino Acid Sequence↗
PubMed1986

Activation of transcription by the bacteriophage 434 repressor.

Bacteriophage 434 encodes a repressor that, like bacteriophage lambda repressor, both activates and represses transcription. As in the lambda chromosome, a region of the 434 chromosome, called the right operator, contains three repressor binding sites (OR1, OR2, and OR3) that mediate these effects on two adjacent promoters. We now show that a part of the 434 repressor, the amino-terminal domain, activates leftward transcription when bound to OR2. We show that 434 repressor bound to OR2 closely approaches (touches) RNA polymerase bound to the leftward promoter. Model building based on ethylation interference and other experiments suggests that in three cases, those involving lambda repressor, 434 repressor, and bacteriophage P22 repressor, and in spite of differences in detailed arrangements, transcription is activated by a contact between the repressor and the same part of RNA polymerase.

Coliphages↗
PubMed1986

Site-directed mutagenesis of an invariant amino acid residue at the variable-diversity segments junction of an antibody.

Structural analysis of 21 murine A/J antibodies specific for the hapten p-azobenzenearsonate (Ars), and bearing the major cross reactive idiotype (IdCRI), has revealed an invariant amino acid residue, serine, encoded by the variable-diversity gene segments junction of the heavy chain. To test whether this serine residue is essential for Ars binding, we changed it either to alanine or to threonine by oligonucleotide-directed mutagenesis of a heavy chain gene. Genes containing the mutations were separately introduced into mouse hybridoma cells producing the homologous light chain, and the resulting proteins were tested for antigen binding and idiotypic expression. Whereas the serine to threonine mutant retains full antigen binding activity, the serine to alanine mutant does not bind either to Ars-bovine serum albumin-Sepharose or to the Ars-tyrosine hapten. Both mutants show the same reactivity as wild type towards a series of anti-idiotypic antibodies. These results suggest that a hydroxyl group at the variable-diversity gene segments junction of A/J anti-Ars antibodies is essential for antigen binding.

Amino Acid Sequence↗
PubMed1985

A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor.

We describe a new protein that binds to DNA and activates gene transcription in yeast. This protein, LexA-GAL4, is a hybrid of LexA, an Escherichia coli repressor protein, and GAL4, a Saccharomyces cerevisiae transcriptional activator. The hybrid protein, synthesized in yeast, activates transcription of a gene if and only if a lexA operator is present near the transcription start site. Thus, the DNA binding function of GAL4 can be replaced with that of a prokaryotic repressor without loss of the transcriptional activation function. These results suggest that DNA-bound LexA-GAL4 and DNA-bound GAL4 activate transcription by contacting other proteins.

Bacterial Proteins↗
PubMed1985

Specific DNA binding of GAL4, a positive regulatory protein of yeast.

We show by the following series of experiments that the yeast positive regulatory protein GAL4 binds to four sites in the upstream activating sequence UASG to activate transcription of the adjacent GAL1 and GAL10 genes. GAL4 protein expressed in E. coli protected guanine residues in UASG from methylation by dimethyl sulfate. The same set of protections was seen in vivo in yeast and depended on the GAL4+ allele. This protection pattern is consistent with the idea that GAL4 protein binds to four related 17 bp sequences, each of which displays approximate 2-fold rotational symmetry. A single near-consensus synthetic 17 bp oligonucleotide, installed in front of the yeast GAL1 or CYC1 transcription units, conferred a high level of galactose inducibility upon these genes. Further experiments suggest that one mechanism of glucose repression is inhibition of the binding of GAL4 protein to DNA.

Base Sequence↗
PubMed1985

NH2-terminal arm of phage lambda repressor contributes energy and specificity to repressor binding and determines the effects of operator mutations.

Several lines of evidence indicate that the phage lambda repressor recognizes its operator by using, in part, an alpha helix (the "recognition helix"), which it inserts into the major groove of DNA. In addition to its recognition helix, lambda repressor has an "arm," consisting of the first six amino acids, that wraps around the DNA helix. We constructed plasmids that, in Escherichia coli, direct the expression of derivatives of lambda repressor that lack the NH2-terminal one, three, six, or seven amino acids. We studied these modified proteins in vivo and in vitro, and from our results we argue that the arm: contributes a large portion of the binding energy; helps to determine sequence specificity of binding and, in particular, the relative affinities for two wild-type binding sites; determines entirely repressor's response to one operator mutation (a "back-side" mutation); magnifies repressor's response to other operator mutations ("front-side" mutations); and increases the sensitivity of repressor binding to salt concentration and temperature.

Amino Acid Sequence↗
PubMed1984

Substituting an alpha-helix switches the sequence-specific DNA interactions of a repressor.

It has been suggested that many DNA-binding proteins use an alpha-helix for specific sequence recognition. We have used amino acid sequence homologies to identify the presumptive DNA-recognition helices in two related proteins whose structures are unknown--the repressor and cro protein of bacteriophage 434. The 434 repressor and cro protein each bind to three similar sites in the rightward phage 434 operator, OR, and they make different contacts in each binding site, as revealed by the chemical probe dimethyl sulfate. We substituted the putative recognition alpha-helix of 434 repressor with the putative recognition alpha-helix of 434 cro protein to create a hybrid protein named repressor*. The specific DNA contacts made by repressor* are like those of 434 cro protein.

Base Sequence↗
PubMed1984

Amino terminus of the yeast GAL4 gene product is sufficient for nuclear localization.

We have studied the intracellular compartmentalization in yeast of Escherichia coli beta-galactosidase bearing heterologous amino acid sequences at its amino terminus. Chimeras containing as few as 74 NH2-terminal amino acids of GAL4, a yeast positive regulatory protein, at the amino terminus accumulate in the cell nucleus. This and other results are consistent with the proposal that the GAL4 gene product mediates positive control by binding to DNA and that the information for nuclear localization resides in its amino terminus. The amino acid sequence of the GAL4 amino terminus does not agree with the previously proposed consensus sequences responsible for nuclear localization. The beta-galactosidase activity in cells bearing the non-nuclear chimeric proteins is 10-fold greater than in cells bearing chimeric proteins that specifically concentrate in the nucleus.

Base Sequence↗
PubMed1984

Synthesis in Escherichia coli of human adenovirus type 12 transforming proteins encoded by early region 1A 13S mRNA and 12S mRNA.

Human adenovirus (Ad)-encoded early region 1A (E1A) tumor (T) antigens have been implicated in the positive regulation of viral early genes, the positive and negative regulation of some cellular genes, and cell immortalization and transformation. To further study the Ad E1A T antigens and to facilitate their purification, we have cloned cDNA copies of the Ad12 E1A 13S mRNA and 12S mRNA downstream of a hybrid Escherichia coli trp-lac (tac) promoter. Up to 8% of the protein synthesized in E. coli cells transformed by each of the two different Ad12 E1A cDNA constructs were immunoprecipitated as a Mr 47,000 protein by antibody to a synthetic peptide encoded in the Ad12 E1A DNA sequence. Both proteins produced in E. coli appear to be authentic and complete Ad12 E1A T antigens because they possess (i) the Ad12 E1A NH2-terminal amino acid sequence predicted from the DNA sequence; (ii) the Ad12 E1A COOH-terminal sequence, as shown by immunoprecipitation with anti-peptide antibody; and (iii) a molecular weight and an acidic isoelectric point similar to that of the E1A T antigens synthesized in Ad12-infected and transformed mammalian cells. The T antigens were purified to near homogeneity in yields of 100-200 micrograms per g wet weight of transformed E. coli cells.

Adenoviruses, Human↗
PubMed1984

Cocrystals of the DNA-binding domain of phage 434 repressor and a synthetic phage 434 operator.

The amino-terminal domain of the phage 434 repressor forms cocrystals with a synthetic phage 434 operator. The cocrystals diffract to at least 4 A, and x-ray crystallographic analysis of them is in progress. An analysis of the packing in the cocrystals shows that complexes consisting of dimers of amino-terminal domain bound specifically to operators are stacked end to end in longer protein-DNA rods parallel to the unit cell body diagonals. The DNA in the complexes has 10.5 base pairs per turn and a rise per base of 3.26 A--values consistent with B-form DNA--indicating that DNA is neither unwound nor overwound by bound repressor. The packing analysis suggests an approach that might facilitate the cocrystallization of other DNA-binding proteins with the DNA they recognize.

Base Composition↗
PubMed1984

Use of lacZ fusions to delimit regulatory elements of the inducible divergent GAL1-GAL10 promoter in Saccharomyces cerevisiae.

We present the DNA sequence of a 914-base pair fragment from Saccharomyces cerevisiae that contains the GAL1-GAL10 divergent promoter, 140 base pairs of GAL10 coding sequence, and 87 base pairs of GAL1 coding sequence. From this fragment, we constructed four pairs of GAL1-lacZ and GAL10-lacZ fusions on various types of yeast plasmid vectors. On each type of vector, the fused genes were induced by galactose and repressed by glucose. The response of a GAL1-lacZ fusion to gal4 and gal80 regulatory mutations was similar to the response of intact chromosomal GAL1 and GAL10 genes. A set of deletions that removed various portions of the GAL10 regulatory sequences from a GAL10-CYC1-lacZ fusion was constructed in vitro. These deletions defined a relatively guanine-cytosine-rich region of 45 base pairs that contained sequences necessary for full-strength galactose induction and an adjacent guanine-cytosine rich 55 base pairs that contained sequences sufficient for weak induction.

Alleles↗