Repressor structure and the mechanism of positive control

How eukaryotic transcriptional activators work

A specific protein, bound to DNA, can activate transcription of a wide array of genes in many eukaryotes. Further analysis suggests a general outline for how eukaryotic transcriptional activators function and are controlled.

Functional domains required for tat-induced transcriptional activation of the HIV-1 long terminal repeat

The transcriptional regulation of the human immunodeficiency virus (HIV) type I involves the interaction of both viral and cellular proteins. The viral protein tat is important in increasing the amount of viral steady-state mRNA and may also play a role in regulating the translational efficiency of viral mRNA. To identify distinct functional domains of tat, oligonucleotide-directed mutagenesis of the tat gene was performed. Point mutations of cysteine residues in three of the four Cys-X-X-Cys sequences in the tat protein resulted in a marked decrease in transcriptional activation of the HIV long terminal repeat. Point mutations which altered the basic C-domain of the protein also resulted in decreases in transcriptional activity, as did a series of mutations that repositioned either the N or C termini of the protein. Conservative mutations of other amino acids in the cysteine-rich or basic regions and in a series of proline residues in the N terminus of the molecule resulted in minimal changes in tat activation. These results suggest that several domains of tat protein are involved in transcriptional activation with the cysteine-rich domain being required for complete activity of the tat protein.

Cooperativity and hierarchical levels of functional organization in the SV40 enhancer

We have investigated the cell-specific activity of the GT-IIC, GT-I, Sph-II, Sph-I, and octamer motifs of the SV40 enhancer in four cell lines (HeLa cells, MPC11 plasmocytoma B cells, and non-differentiated and retinoic acid-differentiated F9 embryonal carcinoma cells). Our present results reveal the existence of three classes of motifs that interact with cell-specific enhancer factors but that have no enhancer activity of their own: those (class A) that generate enhancer activity following oligomerization of tandem repeats of the motif; those (class B) that cannot enhance transcription when oligomerized as a tandem repeat but whose association with a second motif results in transcription activation after oligomerization; and those (class C) that exhibit enhancer activity when a single copy of the motif is oligomerized. Three levels of functional organization of enhancers can also be defined. The possible implications for enhancer functions are discussed.

Differential protein binding in lymphocytes to a sequence in the enhancer of the mouse retrovirus SL3-3

An electrophoretic mobility shift assay was used to characterize interactions of nuclear proteins with a DNA segment in the enhancer element of the leukemogenic murine retrovirus SL3-3. Mutation of a DNA sequence of the 5'-TGTGG-3' type decreased transcription in vivo specifically in T-lymphocyte cell lines. Extracts of nuclei from different T-lymphocyte cell lines or cells from lymphoid organs resulted in much higher amounts of complexes in vitro with this DNA sequence than did extracts from other cell lines or organs tested. Differences were also found in the sets of complexes obtained with extracts from the different types of cells. The DNA sequence specificities of the different SL3-3 enhancer factor 1 (SEF1) protein complexes were found to be distinct from those of several other previously identified DNA motifs of the TGTGG type because of differences in several nucleotides critical for binding and because these other DNA motifs could not compete with the identified DNA sequence for binding of SEF1. Limited treatment with several different proteases cleaved the SEF1 proteins such that their DNA-binding domain(s) remained and created complexes with decreased and nondistinguishable electrophoretic mobility shifts and with new properties. These results indicate that the SEF1 proteins have a structure with a flexible and relatively vulnerable hinge region linking a DNA-binding domain(s) to a more variable domain(s) with other functions. We suggest that the binding of SEF1 is an essential factor for the T-cell tropism of SL3-3 and the ability of this virus to cause T-cell lymphomas.

Amino acid sequence template useful for alpha-helix-turn-alpha-helix prediction

Necessary stereochemical requirements for an amino acid sequence segment to fold into an alpha-helix-turn-alpha-helix supersecondary structure are presented in sequence template form. The usefulness of the template is illustrated by alpha-helix-turn-alpha-helix predictions consistent with experimental data from the large T antigens of two polyoma viruses, simian virus 40 (segment 143-165) and mouse polyoma virus (segment 297-319), and the yeast transcription activator GCN4 (segment 256-278).

Interactions between Escherichia coli RNA polymerase and lambda repressor. Mutations in PRM affect repression of PR

The rightward operator, OR, of bacteriophage lambda is part of a complex regulatory region that includes PRM, the promoter for repressor synthesis by a prophage, the rightward early promoter PR, and three repressor-binding sites, OR1, OR2 and OR3. By binding to OR2, repressor blocks transcription from PR and simultaneously stimulates the formation of open complexes between RNA polymerase and PRM. In this letter, we describe a test of the hypothesis that the interaction between RNA polymerase bound at PRM and repressor bound at OR2 increases the apparent affinity of repressor for OR. One implication of this hypothesis is that the amount of repressor required for repression of PR should be inversely correlated with PRM promoter strength. This is indeed the case. The amount of repressor required for 50% repression of PR is decreased by prmup-1, an "up" mutation of PRM, and is increased by prm- mutations. An unexpected finding is that in addition to their effect on the apparent affinity of repressor for OR, mutations in the -35 region of PRM alter the shape of repressor-titration curves. We propose that these mutations alter the interaction between RNA polymerase bound at PRM and repressor bound at OR2 in such a way that cooperativity in the binding of repressor to OR1 and OR2 is also disrupted.

Cell division inhibition gene dicB is regulated by a locus similar to lambdoid bacteriophage immunity loci

A mutation (dicA1) of a repressor gene located in the terminus region of the Escherichia coli chromosome has previously been shown to lead to temperature-dependent inhibition of division, and to be complemented by plasmids carrying either dicA or an adjacent gene dicC. In this study, operon fusions in the region coding for the division inhibition gene dicB have been used to show that temperature sensitivity does not result from high temperature inactivation of the dicA repressor. Sequence comparisons indicate that dicA and dicC are similar to genes c2 and cro respectively of bacteriophage P22, and carry similarly organized tandem operators, indicating a common evolutionary origin for dicAC and P22 immC. Nevertheless, the consensus half-operator sequence of dicAC, TGTTA-GYYA, differs significantly from that of P22 immC (ATT-TAAGAN). An analysis of the in vivo control of promoters dicAp, dicBp and dicCp placed upstream of malQ shows that the dicAC system is functionally similar to that of an immunity region, with the possible exception of an absence of pairwise cooperative binding. Our results also indicate that the dicA1 mutation causes a switch to permanent control by dicC at all temperatures.

Differential protein binding in lymphocytes to a sequence in the enhancer of the mouse retrovirus SL3-3

An electrophoretic mobility shift assay was used to characterize interactions of nuclear proteins with a DNA segment in the enhancer element of the leukemogenic murine retrovirus SL3-3. Mutation of a DNA sequence of the 5'-TGTGG-3' type decreased transcription in vivo specifically in T-lymphocyte cell lines. Extracts of nuclei from different T-lymphocyte cell lines or cells from lymphoid organs resulted in much higher amounts of complexes in vitro with this DNA sequence than did extracts from other cell lines or organs tested. Differences were also found in the sets of complexes obtained with extracts from the different types of cells. The DNA sequence specificities of the different SL3-3 enhancer factor 1 (SEF1) protein complexes were found to be distinct from those of several other previously identified DNA motifs of the TGTGG type because of differences in several nucleotides critical for binding and because these other DNA motifs could not compete with the identified DNA sequence for binding of SEF1. Limited treatment with several different proteases cleaved the SEF1 proteins such that their DNA-binding domain(s) remained and created complexes with decreased and nondistinguishable electrophoretic mobility shifts and with new properties. These results indicate that the SEF1 proteins have a structure with a flexible and relatively vulnerable hinge region linking a DNA-binding domain(s) to a more variable domain(s) with other functions. We suggest that the binding of SEF1 is an essential factor for the T-cell tropism of SL3-3 and the ability of this virus to cause T-cell lymphomas.

Binding of the cyclic AMP receptor protein of Escherichia coli to RNA polymerase

Fluorescence polarization studies were used to study the interaction of a fluorescein-labelled conjugate of the Escherichia coli cyclic AMP receptor protein (F-CRP) and RNA polymerase. Under conditions of physiological ionic strength, F-CRP binds to RNA polymerase holoenzyme in a cyclic AMP-dependent manner; the dissociation constant was about 3 microM in the presence of cyclic AMP and about 100 microM in its absence. Binding to core RNA polymerase under the same conditions was weak (Kdiss. approx. 80-100 microM) and independent of cyclic AMP. Competition experiments established that native CRP and F-CRP compete for the same binding site on RNA polymerase holoenzyme and that the native protein binds about 3 times more strongly than does F-CRP. Analytical ultracentrifuge studies showed that CRP binds predominantly to the monomeric rather than the dimeric form of RNA polymerase.

Three binding sites for AraC protein are required for autoregulation of araC in Escherichia coli

Three binding sites for AraC protein were shown to be required for the autoregulation of araC: araI1, araO1, and araO2. Selective inactivation of AraC-binding sites on the DNA demonstrated that araO1 and araO2 are required in vivo to produce repression of araC in the presence of arabinose, whereas araI1 and araO2 are required in its absence. We found that the low-affinity site araO2 is essential for araC autoregulation; araO1 and araI1 provide high-affinity AraC-binding sites, which allow cooperative binding at araO2. Profound effects on the araBAD promoter and the araC promoter are produced by ligand-induced changes in AraC occupancy of functional sites on the DNA. We suggest that AraC exerts its multiplicity of controls through two alternative states of cooperative interactions with DNA and we illustrate this with a model. This model presents our interpretations of activation and repression of the araBAD operon and the autoregulation of the araC gene.

The abundance and in vitro DNA binding of three cellular proteins interacting with the adenovirus EIIa early promoter are not modified by the EIa gene products

Specific protein binding on the EIa-inducible adenovirus EIIa early (EIIaE) promoter was analyzed by the sensitive electrophoretic band-shift assay and by protection against DNase I digestion. Three factors were identified, and precise mapping of the cognate-binding sites revealed their correspondence to promoter elements essential for constitutive EIIaE transcription. One binds to the major upstream element located between -82 and -64 (with respect to the major EIIaE cap site), another appears to interact with sequences on either side of this region, and the last one binds to an element located further upstream. Comparison of the binding activities of the factors present in extracts from cells infected with wild-type adenovirus (adenovirus type 5) or with the EIa deletion mutant dl312 did not reveal striking differences. Not only were the general binding patterns indistinguishable, but the concentration of each of the identified factors as well as their affinity for the cognate-binding sites were unchanged. Our results suggest that the EIa-mediated activation of the EIIaE transcription complexes involves appropriate interactions between transcription factors, rather than their increased binding to DNA.

Metal-dependent binding of a factor in vivo to the metal-responsive elements of the metallothionein 1 gene promoter

Using the technique of genomic footprinting, we demonstrate cadmium-inducible protection from dimethyl sulfate (DMS) modification of guanine residues in vivo in five metal-responsive elements (MREs) in the promoter of the rat metallothionein 1 (MT-1) gene. We also identify a site of extreme DMS hyperreactivity which, like the MRE protection, occurs only after metal ion induction. With this hyperreactive site as an indicator, we can measure the kinetics of induction and deinduction. Changes in the intracellular metal ion concentrations are reflected in alterations in the reactivity with DMS of guanine residues in the MT-1 gene promoter. Lastly, for both control and metal-induced cells, we observe DMS protection and enhancement of a binding site (located 5' of the distal MRE) which is a consensus sequence for the Sp1 transcription factor. Transfection experiments with deletion mutations of a fusion gene construct indicate both that a sequence region which includes this GC box regulates the basal level of expression of the MT-1 gene and that increasing the number of MREs in the promoter increases the induced level of transcription. Our genomic footprinting and transfection data together suggest that (i) a transcription factor, possibly Sp1, plays an important role in regulating the basal level of expression of the MT-1 gene and (ii) metal induction involves the metal-dependent binding to a sequence-specific binding factor which responds to changes in intracellular metal ion levels.

Purification and cloning of a DNA binding protein from yeast that binds to both silencer and activator elements

A DNA binding protein (RAP1, previously called SBF-E) has been shown to bind to putative regulatory sites at both yeast mating-type silencers, yet is not the product of genetically identified regulators of the silent loci. Here, we report the purification of RAP1 by DNA affinity chromatography, and the isolation of its gene from a lambda gt11 genomic library using antibodies raised against the protein. Disruption of the chromosomal copy of this gene is lethal. We show that RAP1 protein also binds in vitro to the upstream activation site (UAS) of MAT alpha and ribosomal protein genes. In addition, we show that two different UAS-associated RAP1 binding sites can substitute in vivo for a silencer binding site. Our results suggest that RAP1 may be a transcriptional regulator that can play a role in either repression or activation of transcription, depending upon the context of its binding site.

Arabinose-induced binding of AraC protein to araI2 activates the araBAD operon promoter

The state of Escherichia coli araI DNA occupancy by AraC protein has been found to change from a two-turn to a four-turn occupancy upon the addition of the inducer arabinose. The araI site is separable into two contiguous regions, araI1 and araI2. araI1 binds both ligand-bound and ligand-free AraC protein, whereas araI2 binds AraC protein in the presence of arabinose only. A mutation in araI and a known mutation in araC led to the loss of araI2 binding, while binding to araI1 was unaffected. Both mutants failed to activate the promoter of the araBAD operon. We propose that araI2 occupancy by AraC protein leads to RNA polymerase recognition of the araBAD promoter and that araI1 acts as a switch mechanism allowing both the repressor and the activator forms of AraC protein to regulate the araBAD promoter.

The nucleotide sequence of the sigma factor gene ntrA (rpoN) of Azotobacter vinelandii: analysis of conserved sequences in NtrA proteins

The nucleotide sequence of the Azotobacter vinelandii ntrA gene has been determined. It encodes a 56916 Dalton acidic polypeptide (AvNtrA) with substantial homology to NtrA from Klebsiella pneumoniae (KpNtrA) and Rhizobium meliloti (RmNtrA). NtrA has been shown to act as a novel RNA polymerase sigma factor but the predicted sequence of AvNtrA substantiates our previous analysis of KpNtrA in showing no substantial homology to other known sigma factors. Alignment of the predicted amino acid sequences of AvNtrA, KpNtrA and RmNtrA identified three regions; two showing greater than 50% homology and an intervening sequence of less than 10% homology. The predicted protein contains a short sequence near the centre with homology to a conserved region in other sigma factors. The C-terminal region contains a region of homology to the beta' subunit of RNA polymerase (RpoC) and two highly conserved regions one of which is significantly homologous to known DNA-binding motifs. In A. vinelandii, ntrA is followed by another open reading frame (ORF) which is highly homologous to a comparable ORF downstream of ntrA in K. pneumoniae and R. meliloti.

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.

Mutants of GAL4 protein altered in an activation function

Activating region I of GAL4 has been defined as a region 48 amino acids long which, when attached to GAL4's DNA-binding domain, activates transcription in yeast. Here we describe mutants bearing changes in and around this highly acidic activating region. We find mutations that increase the activation function invariably increase the acidity of the region and some but not all of the mutations that decrease the activation function decrease the acidity of the region.

The abundance and in vitro DNA binding of three cellular proteins interacting with the adenovirus EIIa early promoter are not modified by the EIa gene products

Specific protein binding on the EIa-inducible adenovirus EIIa early (EIIaE) promoter was analyzed by the sensitive electrophoretic band-shift assay and by protection against DNase I digestion. Three factors were identified, and precise mapping of the cognate-binding sites revealed their correspondence to promoter elements essential for constitutive EIIaE transcription. One binds to the major upstream element located between -82 and -64 (with respect to the major EIIaE cap site), another appears to interact with sequences on either side of this region, and the last one binds to an element located further upstream. Comparison of the binding activities of the factors present in extracts from cells infected with wild-type adenovirus (adenovirus type 5) or with the EIa deletion mutant dl312 did not reveal striking differences. Not only were the general binding patterns indistinguishable, but the concentration of each of the identified factors as well as their affinity for the cognate-binding sites were unchanged. Our results suggest that the EIa-mediated activation of the EIIaE transcription complexes involves appropriate interactions between transcription factors, rather than their increased binding to DNA.

Metal-dependent binding of a factor in vivo to the metal-responsive elements of the metallothionein 1 gene promoter

Using the technique of genomic footprinting, we demonstrate cadmium-inducible protection from dimethyl sulfate (DMS) modification of guanine residues in vivo in five metal-responsive elements (MREs) in the promoter of the rat metallothionein 1 (MT-1) gene. We also identify a site of extreme DMS hyperreactivity which, like the MRE protection, occurs only after metal ion induction. With this hyperreactive site as an indicator, we can measure the kinetics of induction and deinduction. Changes in the intracellular metal ion concentrations are reflected in alterations in the reactivity with DMS of guanine residues in the MT-1 gene promoter. Lastly, for both control and metal-induced cells, we observe DMS protection and enhancement of a binding site (located 5' of the distal MRE) which is a consensus sequence for the Sp1 transcription factor. Transfection experiments with deletion mutations of a fusion gene construct indicate both that a sequence region which includes this GC box regulates the basal level of expression of the MT-1 gene and that increasing the number of MREs in the promoter increases the induced level of transcription. Our genomic footprinting and transfection data together suggest that (i) a transcription factor, possibly Sp1, plays an important role in regulating the basal level of expression of the MT-1 gene and (ii) metal induction involves the metal-dependent binding to a sequence-specific binding factor which responds to changes in intracellular metal ion levels.

Distinguishing between mechanisms of eukaryotic transcriptional activation with bacteriophage T7 RNA polymerase

To distinguish between mechanisms of eukaryotic transcriptional activation, we tested whether yeast upstream promoter elements can stimulate transcription by a heterologous transcription machinery, bacteriophage T7 RNA polymerase. The gal enhancer-like element recognized by GAL4 protein or the ded1 poly(dA-dT) element was placed upstream of the T7 promoter and his3 structural gene, and T7 RNA polymerase was produced in yeast cells. Under conditions where the gal element would normally be either activating or nonactivating, his3 transcription by T7 RNA polymerase was not stimulated above the level observed in the absence of any upstream element. In contrast, the ded1 poly(dA-dT) element stimulated transcription 7-fold, similar to the enhancement observed on the native ded1 promoter. Activation by the ded1 element thus may involve effects on the chromatin template that facilitate entry of the transcription machinery, whereas activation by the gal element may involve specific contacts between GAL4 and the transcriptional machinery.

Structure and evolution of prokaryotic and eukaryotic RNA polymerases: a model

A comparative overview of the subunit taxonomy and sequences of eukaryotic and prokaryotic RNA polymerases indicates the presence of a core structure conserved between both sets of enzymes. The differentiation between prokaryotic and eukaryotic polymerases is ascribed to domains and subunits peripheral to the largely conserved central structure. Possible subunit and domain functions are outlined. The core's flexible shape is largely determined by the elongated architecture of the two largest subunits, which can be oriented along the DNA axis with their bulkier amino-terminal head regions looking towards the 3' end of the gene to be transcribed and their more slender carboxyl-terminal domains at the tail end of the enzyme. The two largest prokaryotic subunits appear originally derived from a single gene.

Novel rpoA mutation that interferes with the function of OmpR and EnvZ, positive regulators of the ompF and ompC genes that code for outer-membrane proteins in Escherichia coli K12

The expression of the ompF and ompC genes that code for major outer-membrane proteins of Escherichia coli is positively regulated by the products of the ompR and envZ genes. Recently, we isolated the ompR77 mutation, which suppresses the envZ11 mutation. In this work, a novel mutation that interferes with the suppression of the envZ11 mutation by ompR77 was isolated. The mutation was located in the rpoA gene that codes for the alpha subunit of DNA-dependent RNA polymerase. These results suggest that an interaction between the positive regulators and RNA polymerase is involved in the initiation of transcription of the ompF and ompC genes. In addition, the results suggest that during transcription the RNA polymerase migrates along DNA strands with the alpha subunit facing backward and the beta beta' subunits facing forward.

Bacteriophage P22 Mnt repressor. DNA binding and effects on transcription in vitro

We have examined the binding of Mnt repressor to operator DNA in vitro and have determined how this binding affects the level of transcription from two nearby promoters, Pant and Pmnt. Mnt binds to a region of DNA that overlaps the startpoint of transcription of Pant and the -35 region of Pmnt. Mnt represses transcription in vitro from Pant and enhances transcription from Pmnt. Protection and interference experiments show that Mnt binds to a single, 17 base-pair operator site. The operator sequence and the protein-DNA contacts are symmetric. Mnt makes major groove contacts on both faces of the operator DNA. At pH 7.5, 200 mM-KCl, 22 degrees C, the Mnt tetramer binds operator with high affinity (Kd = 2.2 X 10(-11M) and the protein-DNA complex is quite stable (t1/2 = 48 min). Operator binding shows large dependencies on pH, salt concentration, and temperature.

Fast abortive initiation of uvrA promoter in a supercoiled plasmid studied by stopped-flow techniques

In order to follow the fast kinetics of abortive initiation (lag time from 1 ms to 10 s), we have built a stopped-flow apparatus equipped for fluorescence detection. The small volume used for each assay (35 microliters), and the short dead time (approximately 0.5 ms) are the essential advantages of this apparatus. Supercoiling of DNA affects considerably the initiation of transcription from the uvrA promoter. It decreases the lag time due to the isomerisation process 3-fold. Nevertheless, it does not change significantly the product KBk2, which is indicative of promoter strength and shows that uvrA is an 'association-limited' promoter. The presence of the LexA repressor increases the lag time considerably. At least for small RNA polymerase concentrations this increase is stronger for supercoiled than for linearized DNA.

Glucocorticoid receptor mutants that define a small region sufficient for enhancer activation

Transcriptional enhancement is a general mechanism for regulation of gene expression in which particular proteins bound to specific DNA sequences stimulate the efficiency of initiation from linked promoters. One such protein, the glucocorticoid receptor, mediates enhancement in a glucocorticoid hormone-dependent manner. In this study, a region of the 795-amino acid rat glucocorticoid receptor that is active in transcriptional enhancement was identified. The active region was defined by expressing various receptor deletion mutants in stably and transiently transfected cells and examining the regulated transcription of hormone-responsive genes. Mutant receptors lacking as many as 439 amino-terminal amino acids retained activity, as did those with as many as 270 carboxyl-terminal amino acids deleted. This suggests that the 86-amino acid segment between the most extensive terminal deletions, which also includes sequences required for specific DNA binding in vitro, is sufficient for enhancer activation. In fact, a 150-amino acid receptor fragment that encompasses this segment mediates constitutive enhancement.

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.

A single polypeptide possesses the binding and transcription activities of the adenovirus major late transcription factor

A simple approach has been developed for the unambiguous identification and purification of sequence-specific DNA-binding proteins solely on the basis of their ability to bind selectively to their target sequences. Four independent methods were used to identify the promoter-specific RNA polymerase II transcription factor MLTF as a 46-kilodalton (kDa) polypeptide. First, a 46-kDa protein was specifically cross-linked by UV irradiation to a body-labeled DNA fragment containing the MLTF binding site. Second, MLTF sedimented through glycerol gradients at a rate corresponding to a protein of native molecular weight 45,000 to 50,000. Third, a 46-kDa protein was specifically retained on a biotin-streptavidin matrix only when the DNA fragment coupled to the matrix contained the MLTF binding site. Finally, proteins from the most highly purified fraction which were eluted and renatured from the 44- to 48-kDa region of a sodium dodecyl sulfate-polyacrylamide gel exhibited both binding and transcription-stimulatory activities. The DNA-binding activity was purified 100,000-fold by chromatography through three conventional columns plus a DNA affinity column. Purified MLTF was characterized with respect to the kinetic and thermodynamic properties of DNA binding. These parameters indicate a high degree of occupancy of MLTF binding sites in vivo.

Cholera toxin transcriptional activator toxR is a transmembrane DNA binding protein

The toxR gene encodes a transcriptional activator controlling cholera toxin, pilus, and outer-membrane protein expression in V. cholerae. Nucleotide sequence and mutational analysis has identified the toxR gene product as a 32,527 dalton protein. Hydropathicity analysis of the derived amino acid sequence of ToxR predicts a transmembrane structure. The properties of hybrid proteins composed of N-terminal fragments of ToxR fused to the periplasmic enzyme alkaline phosphatase provide additional evidence for the transmembrane topology of the ToxR protein. These fusion proteins also allowed the localization of the transcriptional activation and DNA binding domains of the ToxR protein to its cytoplasmically located N-terminal portion. DNA binding assays and a deletion analysis of the cholera toxin promoter support a model for transcriptional activation that involves ToxR binding to a tandemly repeated 7 bp DNA sequence 56 bp upstream of the transcriptional start point.

Structure and function of E. coli promoter DNA

The process of transcription initiation requires both the recognition of a promoter site by RNA polymerase and the melting of a short stretch of DNA. In this review I discuss the properties of promoters that are relevant to sequence recognition and to the ability of the polymerase to act as a melting protein. The regulation of promoter activity is thus dependent on both factors interacting with RNA polymerase and so altering its affinity for promoter sites and also modulations of DNA structure.

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.

A single polypeptide possesses the binding and transcription activities of the adenovirus major late transcription factor

A simple approach has been developed for the unambiguous identification and purification of sequence-specific DNA-binding proteins solely on the basis of their ability to bind selectively to their target sequences. Four independent methods were used to identify the promoter-specific RNA polymerase II transcription factor MLTF as a 46-kilodalton (kDa) polypeptide. First, a 46-kDa protein was specifically cross-linked by UV irradiation to a body-labeled DNA fragment containing the MLTF binding site. Second, MLTF sedimented through glycerol gradients at a rate corresponding to a protein of native molecular weight 45,000 to 50,000. Third, a 46-kDa protein was specifically retained on a biotin-streptavidin matrix only when the DNA fragment coupled to the matrix contained the MLTF binding site. Finally, proteins from the most highly purified fraction which were eluted and renatured from the 44- to 48-kDa region of a sodium dodecyl sulfate-polyacrylamide gel exhibited both binding and transcription-stimulatory activities. The DNA-binding activity was purified 100,000-fold by chromatography through three conventional columns plus a DNA affinity column. Purified MLTF was characterized with respect to the kinetic and thermodynamic properties of DNA binding. These parameters indicate a high degree of occupancy of MLTF binding sites in vivo.

Bending of promoter DNA on binding of heat shock transcription factor

The Drosophila heat-shock transcription factor (HSTF) has been shown to bind to three domains of the heat shock protein 70 gene (hsp 70) control region. The most critical of these for transcriptional activation appears to be the one closest to the TATA-homology region. This domain, spanning sequences from -40 to -95, consists of two contiguous HSTF binding sites (sites 1 and 2) that are occupied in a cooperative manner (see Fig. 1). Recent alkylation interference and protection studies suggest a conformational change occurs in the protein-DNA complex at site 1 upon sequential HSTF binding at site 2 (ref. 5). We report here that HSTF binding to a single site or to both contiguous sites results in the introduction of a specific DNA bend within this domain of the hsp 70 promoter.

Functional dissection of a eukaryotic transcriptional activator protein, GCN4 of yeast

Yeast GCN4 protein binds specifically to the promoters of amino acid biosynthetic genes and coordinately induces their transcription. Serially deleted GCN4 and hybrid LexA-GCN4 proteins were assayed for specific DNA binding activity in vitro, and for stimulation of transcription in vivo. The specific DNA binding activity resides in the 60 C-terminal amino acids, a basic region of GCN4. However, certain deletions containing the entire DNA binding region are unable to activate transcription and instead act as repressors in vivo. The activation function appears to critically involve just 19 amino acids that are centrally located in an acidic region of GCN4. In addition to their functional separation, the DNA binding and transcriptional activation regions of the protein can be separated physically by elastase cleavage. The implications of these results for the mechanisms of DNA sequence recognition and transcription activation are discussed.

Sigma factors from E. coli, B. subtilis, phage SP01, and phage T4 are homologous proteins

We show, using dot matrix comparisons and statistical analysis of sequence alignments, that seven sequenced sigma factors, E. coli sigma-70 and sigma-32, B. subtilis sigma-43 and sigma-29, phage SP01 gene products 28 and 34, and phage T4 gene product 55, comprise a homologous family of proteins. Sigma-70, sigma-32, and sigma-43 each have two copies of a sequence similar to the helix-turn-helix DNA binding motif seen in CRP, and lambda repressor and cro proteins. B. subtilis sigma-29, SP01 gp28, and SP01 gp34 have at least one copy similar to this sequence. We propose that a second sequence, conserved in all seven proteins is the core RNA polymerase binding site. A third region, present only in sigma-70 and sigma-43, may also be involved in interaction with core. Available mutational evidence supports our model for sigma factor structure.

Gene regulation by proteins acting nearby and at a distance

Transcription of genes can be controlled by regulatory proteins that bind to sites on the DNA either nearby or at a considerable distance. Recent experiments suggest a unified view of these apparently disparate types of gene regulation.

Expression, purification and operator binding of the transposon Tn1721-encoded Tet repressor

The regulation of expression of the Tn1721-encoded tetracycline-resistance determinant is described at the molecular level. The transcriptional control element consists of overlapping divergent promoters, which are negatively regulated by two operators with nearly identical sequence. The mRNA for the regulatory gene tetR is translated without a ribosome-binding site. This result is confirmed by S1 nuclease mapping and RNA sequencing of the tetR mRNA. The start nucleotide for transcription of this mRNA is the adenosine residue of the sequence 5'-AUG. Determination of the N-terminal amino acid sequence of the purified Tet repressor proves that this AUG is the initiation codon for translation. The Tet repressor protein is further used to map the two tet operators by DNase I footprinting. Tight contacts of the protein to the N-7 positions of two guanosine residues in each operator are determined from methylation protection experiments with dimethylsulfate. The differential regulation and positive control of transcription of the tetR gene that is possible with this arrangement of promoters and operators is discussed.

Analysis of forward mutations induced by N-methyl-N'-nitro-N-nitrosoguanidine in the bacteriophage P22 mnt repressor gene

We describe the isolation and genetic characterization of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG)-induced mutations in the phage P22 mnt repressor gene cloned in plasmid pBR322. Mutations in the mnt repressor gene or its operator on this plasmid, pPY98, confer a tetracycline resistance phenotype, whereas the wild-type plasmid confers tetracycline sensitivity. Cells carrying pPY98 were briefly exposed to MNNG to give 20 to 40% survival and a 50- to 100-fold increase in tetracycline-resistant cells. DNA sequence analysis showed that 29 of 30 MNNG-induced mutations were GC-to-AT transitions and one was an AT-to-GC transition. About 80% of the mutations are in three hotspots. This mutation spectrum is consistent with the proposed mechanism of mutagenic action of MNNG, which involves mispairing of an alkylated base, O6-methylguanine. The mnt gene may be a useful target for determining mutagenic specificity at the nucleotide level because forward mutations are easily isolated, the target size is small, and the DNA sequence changes of mutations can be determined rapidly.

Nucleotide sequence of the CytR regulatory gene of E. coli K-12

We have determined the nucleotide sequence of the cytR gene, which codes for the Cyt repressor (CytR). The coding region consists of 1023 or 1029 bp. The subunits of CytR are thus predicted to consist of 341 or 343 residues. It is shown that the N-terminal segment of the polypeptide is structurally similar to the DNA-binding region of known DNA-binding proteins. In addition, there exists an exceptionally high amino acid sequence homology between CytR and the Gal repressor, indicating a common origin of evolution.

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.

Requirement of stereospecific alignments for initiation from the simian virus 40 early promoter

The distance between the simian virus 40 early promoter elements has been altered by inserting either odd or even multiples of half a DNA turn. There are marked differences in the in vivo effects of these two types of insertions on initiation of transcription from this promoter.

Yeast adenylate cyclase catalytic domain is carboxy terminal

Subcloning of DNA fragments from the gene coding for yeast adenylate cyclase has permitted, after complementation studies in S. cerevisiae cdc35 mutants as well as E. coli cya mutants, to identify the sequence coding for the catalytic domain of the protein. No homology is found between the yeast cyclase catalytic domain and the homologous domain found in E. coli adenylate cyclase. Analysis by Northern blotting of yeast polyA mRNA has shown the existence of multiple transcriptional products of the gene. A putative origin of a major transcript (3.5 kb) would allow synthesis of a ca. 100,000 dalton protein exhibiting cyclase activity in its carboxy terminal domain, and having 7 repeats of 17 amino acids at its amino terminal end. Several note-worthy features, including the possibility of transcriptional control by the general control of amino acids biosynthesis, are present at this putative origin. Data are presented suggesting that a much longer gene product might also be synthesized from the CDC35 gene. Neither the gene organization nor the amino acid sequence of the protein does display any homology with the adenylate cyclase gene and protein of Escherichia coli. This suggests a case of evolutionary convergence for the synthesis of cAMP in prokaryotes and eukaryotes.

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.

Phage lambda repressor revertants. Amino acid substitutions that restore activity to mutant proteins

We have isolated same-site and second-site revertants that restore partial activity, wild-type activity, or greater than wild-type activity, to lambda repressor proteins bearing different mutations in the DNA binding domain. In some cases the revertant repressors contain same-site substitutions that are similar to the wild-type side-chain (e.g. Tyr22----Phe, Ser77----Thr). The activity of these revertants makes it possible to assess the role of specific hydrogen bonds and/or packing interactions in repressor structure and function. In other same-site revertants, a very different type of residue is introduced (e.g. Ser35----Leu, Gly48----Asn). This indicates that the chemical and steric requirements at these side-chain positions are relaxed. Two of the second-site revertants, Glu34----Lys and Gly48----Ser, restore activity to more than one primary mutant. Both substitutions apparently increase the affinity of the repressor-operator interaction by introducing new contacts with operator DNA. These results suggest that reversion may be a generally applicable method for identifying sequence changes that increase the activity of a protein to greater than wild-type levels.

Lambda repressor mutations that increase the affinity and specificity of operator binding

Intragenic, second-site reversion has been used to identify amino acid substitutions that increase the affinity and specificity of the binding of lambda repressor to its operator sites. Purified repressors bearing the second-site substitutions bind operator DNA from 3 to 600 fold more strongly than wild type; these affinity changes result from both increased rates of operator association and decreased rates of operator dissociation. Three of the revertant substitutions occur in the alpha 2 and alpha 3 DNA binding helices of repressor and seem to increase affinity by introducing new salt-bridges or hydrogen bonds with the sugar-phosphate backbone of the operator site. The fourth substitution alters the alpha 5 dimerization helix of repressor and appears to increase operator affinity indirectly.

Changing the binding specificity of a repressor by redesigning an alpha-helix

We replaced amino acids on the 'outside', or solvent-exposed, surface of the DNA recognition alpha-helix of 434 repressor with the corresponding amino acids from the recognition helix of P22 repressor. The binding specificity of the resulting hybrid protein, as measured in vivo and in vitro, was that of P22 repressor.