Repressor structure and the mechanism of positive control

Two functional domains conserved in major and alternate bacterial sigma factors

Sequences of the sigma factors of Escherichia coli and Bacillus subtilis were aligned with the sequences of two sigma-like proteins, HtpR, involved in the expression of heat-shock genes in E. coli, and SpoIIG, necessary for endospore formation in B. subtilis. An internal region is highly conserved in the four proteins and is proposed to be involved in binding of sigma factors to core RNA polymerase. The carboxy-terminal part of the four proteins presents the characteristic structure found in several prokaryotic DNA-binding proteins and is proposed to be involved in promoter recognition.

Characterization of Drosophila transcription factors that activate the tandem promoters of the alcohol dehydrogenase gene

Fractionation of a nuclear extract derived from Drosophila tissue culture cells reveals the presence of multiple components involved in accurate transcription of both distal and proximal promoters of the alcohol dehydrogenase (Adh) gene. Transcription of deletion mutants indicates that a region between -24 and -85 upstream of the distal start site contains sequences required for RNA synthesis in vitro. Moreover, sequences that overlap this same upstream control region are specifically bound and protected from DNAase digestion by a promoter-specific transcription factor, Adf-1. Analysis of proximal promoter mutants identified multiple upstream elements that influence transcription, and DNAase footprint analysis detected three specific binding regions. Adf-1 binds at least one of these proximal promoter regions but interaction at this site is not specifically required for transcription. Our results suggest that multiple sequence-specific DNA binding proteins interact differentially with the proximal and distal promoters of Adh to activate transcription.

A dimer of AraC protein contacts three adjacent major groove regions of the araI DNA site

Contact sites of AraC protein to the regulatory site araI of the Escherichia coli araBAD operon have been determined by the chemical-interference technique. DNA fragments were chemically modified an average of once per molecule, and fragments that no longer bound AraC were separated by gel electrophoresis from the DNA fragments still able to bind the protein. The contact sites were then determined by comparing the positions of modifications in the two DNA samples. Strong contacts were found with guanines in three consecutive major groove regions and the adjacent phosphates along one side of the DNA. The conserved bases of the AraC-binding DNA consensus sequence are also found in the same positions. The gel electrophoresis assay was used to determine the stoichiometry of binding, and AraC protein was found to bind the araI and araO1 regulatory sites as a dimer. Therefore, AraC appears to bind DNA differently from the other well-characterized regulatory proteins such as phage lambda repressor.

Active site and complete sequence of the suicidal methyltransferase that counters alkylation mutagenesis

The inducible resistance to alkylation mutagenesis and killing in Escherichia coli (the adaptive response) is controlled by the ada gene. The Ada protein acts both as a positive regulator of the response and as a DNA repair enzyme, correcting premutagenic O6-alkylguanine in DNA by suicidal transfer of the alkyl group to one of its own cysteine residues. We have determined the DNA sequence of the cloned ada+ gene and its regulatory region. The data reveal potential sites of ada autoregulation. Amino acid sequence determinations show that the active center for the O6-methylguanine-DNA methyltransferase is located close to the polypeptide COOH terminus and has the unusual sequence -Pro-Cys-His-, preceded by a very hydrophobic region. These same structural features are present at the active site of thymidylate synthase, suggesting a common chemical mechanism for activation of the cysteine.

Essential and nonessential sequences in malPp, a positively controlled promoter in Escherichia coli

A plasmid bearing the malPp promoter was digested with Bal31 to obtain a set of deletions with closely spaced endpoints in the upstream region of this promoter. Some of these deletions were sequenced, and their effect on malPQ expression was determined after having transferred them onto the chromosome. We found that a site which binds the cyclic AMP receptor protein in vitro and which is centered at position -93 with respect to the site of transcription initiation could be deleted without affecting malPQ expression. In contrast, the activity of the malPp promoter decreased abruptly when the deletions reached position -72. The downstream region of the promoter was analyzed by using a technique of "sequence replacement" which involved the selection of Mal+ pseudorevertants from strains which carried small deletions in the -25 region. The pseudorevertants, which expressed the malPQ operon in a manner indistinguishable from wild type, had grossly different sequences downstream from position -38, except for a few positions, some of which must be important for promoter function. By combining all presently available information, it is suggested that the malPp promoter contains three binding sites for its activator, the product of gene malT. These sites are defined by three quasi-identical hexanucleotides present in one orientation around position -37 and twice in the other orientation around positions -60 and -73.

The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation

A quantitative model has been developed for processes in the bacteriophage lambda that control the switchover from lysogenic to lytic modes of growth. These processes include the interactions of cI repressor and cro proteins at the three DNA sites of the right operator, OR, the binding of RNA polymerase at promoters PR and PRM, the synthesis of cI repressor and cro proteins, and the degradative action of recA during induction of lysis. The model is comprised of two major physical-chemical components: a statistical thermodynamic theory for relative probabilities of the various molecular configurations of the control system; and a kinetic model for the coupling of these probabilities to functional events, including synthesis of regulatory proteins cI and cro. Using independently evaluated interaction constants and rate parameters, the model was found capable of predicting essential physiological characteristics of the system over an extended time. Sufficiency of the model to predict known physiological properties lends credence to the physical-chemical assumptions used in its construction. Several major physiological characteristics were found to arise as "system properties" through the non-linear, time-dependent, feedback-modulated combinations of molecular interactions prescribed by the model. These include: maintenance of the lysogenic state in the absence of recA-mediated cI repressor degradation; induction of lysis and the phenomenon of subinduction; and autogenous negative control of cro. We have used the model to determine the roles, within the composite system, of several key molecular processes previously characterized by studies in vitro. These include: co-operativity in cI repressor binding to DNA; interactions between repressors and RNA polymerase (positive control); and the monomer-dimer association of cI repressor molecules. A major role of cI repressor co-operativity is found to be that of guaranteeing stability of the lysogenic state against minor changes in cI repressor levels within the cell. The role of positive control seems to be that of providing for a peaked, rather than monotonic, dependence of PRM activity on cI repressor level, while permitting PR activity to be a step function. The model correlates an immense body of studies in vivo and in vitro, and it makes testable predictions about molecular phenomena as well as physiological characteristics of bacteriophage lambda. The approach developed in this study can be extended to include more features of the lambda system and to treat other systems of gene regulation.

"N" transcription antitermination proteins of bacteriophages lambda, phi 21 and P22

Comparison is made among the amino acid sequences of three transcription antitermination proteins, based upon the DNA sequences of their genes in bacteriophages lambda, phi 21 and P22. The three proteins are all small (about 100 amino acids), hydrophilic and basic, but otherwise show little homology. A basic region near the amino terminus has several amino acid positions common to all three proteins and is the locus of mutations that alter six different amino acid positions inactivating the lambda N protein. A less basic region near the center is the locus of three mutations affecting the interaction of lambda N with host nusA protein. The N gene of phi 21 has an amino terminus more like that of P22, and a carboxy terminus clearly related to that of lambda.

Molecular basis of DNA sequence recognition by the catabolite gene activator protein: detailed inferences from three mutations that alter DNA sequence specificity

Previously, we reported that substitution of Glu-181 of the catabolite gene activator protein (CAP) by lysine, leucine, or valine results in a protein that has specificity for A X T base pairs at positions 7 and 16 of the DNA recognition site, rather than G X C base pairs as is the case with the wild-type CAP. In this paper, we deduce from these genetic data both (i) the specific chemical interactions by which amino acid side chains at position 181 interact with base pairs 7 and 16 and (ii) the precise alignment between the structures of the CAP and DNA in the intermolecular CAP-DNA complex. Our analysis supports the idea that the two symmetry-related F alpha-helices of the CAP dimer interact with successive major grooves of right-handed B-type DNA [Pabo, C. & Lewis, M. (1982) Nature (London) 298, 443-447; and Steitz, T., Weber, I. & Matthew, J. (1983) Cold Spring Harbor Symp. Quant. Biol. 47, 419-426].

Enzymatic digestion of operator DNA in the presence of the lac repressor tryptic core

The trypsin-resistant core protein of the lac repressor was utilized in protecting operator DNA from two types of enzymatic digestion. Core repressor protects and enhances operator DNA digestion by DNase I in the same fashion as intact repressor, though to a lesser degree on the lower strand. DNase I patterns found for the ternary complexes (protein-sugar-operator) were consistent with the expected affinity alterations of the protein species in response to binding these ligands. The 3' boundaries obtained by exonuclease III digestion for the intact repressor-operator complex varied slightly from those reported by Shalloway et al. (1980). Asymmetric binding to operator by the core repressor fragment was suggested by differences in the 3' boundary for the core compared to intact repressor on the promoter-distal side of the complex. A composite picture of repressor structure and function emerges from the protection studies reported here and in the accompanying paper. In light of these and other results, models for repressor binding are examined.

Regulation of the Escherichia coli L-arabinose operon studied by gel electrophoresis DNA binding assay

DNA binding properties of the proteins required for induction of the Escherichia coli L-arabinose operon were measured using a polyacrylamide gel electrophoresis assay. The mechanisms of induction and repression were studied by observing the multiple interactions of RNA polymerase, cyclic AMP receptor protein and araC protein with short DNA fragments containing either the araC or araBAD promoter regions. These studies show that binding of araC protein to the operator site, araO1, directly blocks RNA polymerase binding at the araC promoter, pC. We find that cyclic AMP receptor protein and araC protein do not bind co-operatively at their respective sites to linear DNA fragments containing the pBAD promoter. Nevertheless, both these positive effectors must be present on the DNA to stimulate binding of RNA polymerase. Additionally, binding of the proteins to the DNA is not sufficient; araC protein must also be in the inducing state, for RNA polymerase to bind. Equilibrium binding constraints and kinetics were determined for araC protein binding to the araI and the araO1 sites. In the presence of inducer, L-arabinose, araC protein binds with equal affinity to DNA fragments containing either of these sites. In the presence of anti-inducer, D-fucose, the affinity for both sites is reduced 40-fold. The apparent equilibrium binding constants for both states of the protein vary in parallel with the buffer salt concentration. This result suggests that the inducing and repressing forms of araC protein displace a similar number of cations upon binding DNA.

Mutants of the gamma delta resolvase: a genetic analysis of the recombination function

The resolvase protein encoded by the gamma delta transposon has two functions. It catalyzes a site-specific recombination, and it negatively regulates the expression of two transposon genes. Both functions involve the action of resolvase at the res site. To define regions of resolvase that are involved specifically in the recombination reaction, we have isolated and characterized mutants that are defective in cointegrate resolution but retain the ability to bind to res (as measured by regulatory activity). Nine independent mutants were found to contain six different amino acid substitutions among just four distinct residues. The altered residues all lie within the 140 amino acid amino-terminal domain of resolvase and fall within two clusters of amino acids that are highly conserved in other related recombinases. The regulatory properties of the mutants suggest that one of these clusters may be involved in the interaction of the catalytic domain with the crossover site.

Sequence of a Drosophila segmentation gene: protein structure homology with DNA-binding proteins

Mutations in the fushi tarazu (ftz) locus of Drosophila result in embryos with half the usual number of body segments. The sequences of the wild-type gene, a temperature-sensitive allele and a dominant mutant allele are presented. A portion of the conserved protein domain present in ftz and several homoeotic genes resembles the DNA-binding region of prokaryotic DNA-binding proteins, and is also similar to products of the yeast mating-type locus.

Model of specific complex between catabolite gene activator protein and B-DNA suggested by electrostatic complementarity

Calculation of the electrostatic potential energy surfaces of Escherichia coli catabolite gene activator protein (CAP) dimer suggests a model for the complex between CAP and a specific DNA sequence. The positive electrostatic charge density of CAP lies on the two COOH-terminal domains and about 20-30 A from the molecular 2-fold axis. Assuming that the 2-fold axes of the CAP dimer and the DNA to which it binds are coincident, the positions of the positive electrostatic potential surfaces strongly suggest the rotational orientation of the DNA relative to the protein. A specific complex between CAP and its DNA binding site in the lac operon has been built with the DNA in this orientation. The amino ends of the two protruding F alpha-helices interact in successive major grooves of the DNA. Four side chains emanating from each F helix can form hydrogen bonds with the exposed edges of four bases in the major groove. Electrostatic considerations as well as the necessity to make interactions between CAP and a DNA site as much as 20 base pairs long require us to bend or kink the DNA. In our model of CAP complexed with B-DNA, as with those proposed for Cro and lambda cI repressors, the protruding second helices of the two-helix motif from both subunits interact in successive major grooves of B-DNA. However, unlike Cro and similar to lambda cI, the protruding alpha-helices are nearly parallel to the bases rather than the groove.

A Drosophila RNA polymerase II transcription factor binds to the regulatory site of an hsp 70 gene

A Drosophila RNA polymerase II transcription factor that is specific for at least one of the heat-shock genes has been isolated (designated HSTF for heat-shock transcription factor). This factor is required for active transcription of an hsp 70 gene in addition to RNA polymerase II and another general transcription factor, the A factor. Footprint analysis of the HSTF on the hsp 70 gene reveals that it binds specifically to a 55 bp region upstream from the TATA box. Both coding and noncoding DNA strands are completely protected from DNAase I cleavage by the HSTF . HSTF binding occurs in the apparent absence of RNA polymerase II. The HSTF is present in both heat-shocked and nonshocked cells, although it is more transcriptionally active when isolated from heat-shocked cells. The previously described B factor (an RNA polymerase II transcription factor that binds to the TATA box), isolated from nonshocked cells, is significantly reduced in both binding and transcriptional activity in heat-shocked cells. The potential role of the HSTF and the B factor in the activation of heat-shock gene transcription is discussed.

The distal transcription signals of the herpesvirus tk gene share a common hexanucleotide control sequence

The two distal transcription signals of the herpesvirus tk gene share a common hexanucleotide sequence and function in a mutually dependent manner. We examined their roles by introducing corresponding base mutations into each hexanucleotide. The effects of mutations in the hexanucleotide of the first distal signal match the pattern of effects of the corresponding mutations in the second distal signal. These concordant patterns suggest that the hexanucleotide repeats are functionally analogous. There is one difference between the two distal signals. Disruption of the second distal signal concomitantly inactivates the first distal signal; disruption of the first distal signal leads to only partial inactivation of the second distal signal. When the positions of the two distal signals are switched, the partial dependence of the second distal signal is alleviated. We suggest a model for positive transcriptional control analogous to activation of the cl maintenance promoter of bacteriophage lambda by repressor.

Role of cII protein in stimulating transcription initiation at the lambda PRE promoter. Enhanced formation and stabilization of open complexes

Abortive and productive initiation assays were used to study transcription initiation at the PRE promoter of phage lambda in vitro. Two parameters were measured: k2, the rate constant for the transition between closed and open complexes; and KB, the equilibrium constant for the initial binding of RNA polymerase to promoter DNA. In the absence of cII protein (which activates PRE) the PRE promoter was extremely weak as expected, with k2 = 4.0 X 10(-4) S-1 and KB = 1.0 X 10(7) M-1. The addition of cII protein resulted in about a 15-fold increase in KB and a 40-fold increase in k2. Thus, cII activation of PRE results both in enhanced binding of RNA polymerase to DNA to form closed complexes and in an enchanced rate of isomerization of closed to open complexes. In addition, we found that open complexes formed in the presence of cII protein were at least four times as stable as those formed in its absence. This suggests that RNA polymerase and cII protein may remain in close contact even after complexes are formed.

Control of expression of the Tn10-encoded tetracycline resistance operon. II. Interaction of RNA polymerase and TET repressor with the tet operon regulatory region

The promoter and operator sequences of the Tn10-encoded tetracycline resistance operon are determined in vitro by transcription studies of purified DNA restriction fragments, protection of guanosine from methylation by dimethylsulphate, and DNase I footprinting employing the purified TET repressor protein. In vitro transcription reveals three promoters with overlapping consensus sequences. Two of them, designated PR1 and PR2, are directed towards the tet repressor gene and the third, called PA, initiates transcription of the tet resistance gene. All three promoters are regulated simultaneously by the TET repressor protein, as demonstrated by in vitro transcription. Tetracycline functions as an inducer in these experiments. Two palindromic operator sequences in the tet operon control region, called O1 and O2, are occupied simultaneously by the TET repressor. Four guanosine residues in symmetric positions close to the centre of the palindromic operator sequences are protected from methylation in the repressor-operator complex. However, only one guanosine residue exhibits an enhanced reaction with dimethylsulphate under these conditions. Footprinting experiments reveal protection of phosphodiester bonds against DNase I slightly further than the palindromic sequence arrangement. Several phosphodiester bonds between the two operators are accessible for cleavage by DNase I in the repressor-operator complex. Two phosphodiester bonds within each operator sequence are cleaved by DNase I. This feature shows a clear assymmetry with the two inside cleavage positions of O1 and O2 being much less accessible for DNase I as compared to the two outside positions. A molecular mechanism of regulation of the Tn10-encoded tetracycline resistance operon is presented based on these and previous results.

The lambda and P22 phage repressors

The lambda cI repressor and the P22 c2 repressor contain two structural domains. In both proteins, the N-terminal domains mediate operator recognition and positive control of transcription, and the C-terminal domains mediate subunit oligomerization and recognition of the recA protein. In some cases, structural, biochemical, and genetic studies implicate particular repressor side chains in these processes.

The promoter-specific transcription factor Sp1 binds to upstream sequences in the SV40 early promoter

Fractionation of HeLa cell extracts reveals the presence of a promoter-specific transcription factor, Sp 1, which activates a class of promoters that includes the SV40 early promoter but not several others that have been tested. We analyzed SV40 early-promoter deletion mutants and determined that transcriptional activation by Sp 1 requires sequences within tandem 21 bp repeats located 70-110 bp upstream of the transcription initiation sites. In a DNAase footprinting assay, Sp 1 protected sequences in this same 21 bp repeat region, thus indicating the presence of a specific site for Sp 1 binding. During purification of Sp 1, there was a correlation between transcription-stimulatory activity and promoter-binding activity. These results suggest that direct binding of Sp 1 to sequences in the upstream promoter element is the mechanism by which this factor activates transcription by RNA polymerase II at the SV40 early promoter.

A small region of the mouse mammary tumor virus long terminal repeat confers glucocorticoid hormone regulation on a linked heterologous gene

Expression of mouse mammary tumor virus (MMTV) proviruses is transcriptionally regulated by glucocorticoid hormones. We have linked the MMTV long terminal repeat (LTR) to the coding region of the herpes simplex virus thymidine kinase gene and used this construction to characterize sequences within the LTR that are involved in glucocorticoid regulation. Our results show that 290 base pairs (bp) of the MMTV LTR, including 190 bp upstream from the start site for transcription, are sufficient to confer regulation on the downstream gene. Deletion of an additional 50 bp, leaving sequences from position -140 to +100, eliminates the response. However, the constitutive level of expression is maintained even after deletion of sequences upstream from position -80, indicating that sequences required for the hormone response can be distinguished from those required for basal expression. We also have shown, by making a 4-bp insertion or a 20-bp deletion around position -107, that the distance between the putative signal for hormone response and the start site of transcription can be varied without affecting regulation. Furthermore, replacement of MMTV sequences from position -59 to +100 with analogous sequences from the Rous sarcoma virus LTR does not change the regulation.

High resolution structural studies of Cro repressor protein and implications for DNA recognition

Cro repressor is a small dimeric protein that binds to specific sites on the DNA of bacteriophage lambda. The structure of Cro has been determined and suggests that the protein binds to its sequence-specific sites with a pair of two-fold related alpha-helices of the protein located within successive major grooves of the DNA. From the known three-dimensional structure of the repressor, model building and energy refinement have been used to develop a detailed model for the presumed complex between Cro and DNA. Recognition of specific DNA binding sites appears to occur via multiple hydrogen bonds between amino acid side chains of the protein and base pair atoms exposed within the major groove of DNA. The Cro:DNA model is consistent with the calculated electrostatic potential energy surface of the protein. From a series of amino acid sequence and gene sequence comparisons, it appears that a number of other DNA-binding proteins have an alpha-helical DNA-binding region similar to that seen in Cro. The apparent sequence homology includes not only DNA-binding proteins from different bacteriophages, but also gene-regulatory proteins from bacteria and yeast. It has also been found that the conformations of part of the presumed DNA-binding regions of Cro repressor, lambda repressor and CAP gene activator proteins are strikingly similar. Taken together, these results strongly suggest that a two-helical structural unit occurs in the DNA-binding region of many proteins that regulate gene expression. However, the results to date do not suggest that there is a simple one-to-one recognition code between amino acids and bases. Crystals have been obtained of complexes of Cro with six-base-pair and nine-basepair DNA oligomers, and X-ray analysis of these co-crystals is in progress.

Solution NMR studies of intact lambda repressor

Using a combination of two and one-dimensional NMR spectroscopy, it is shown that in the intact bacteriophage lambda repressor, the N-terminal domain assumes the same global structure as when it remains isolated. It is further shown that the N-terminal domain is only loosely attached to the C-terminal domain in the intact repressor.

DNA-binding proteins

The structures of three proteins that regulate gene expression have been determined recently and suggest how these proteins may bind to their specific recognition sites on the DNA. One protein (Cro) is a repressor of gene expression, the second (CAP) usually stimulates gene expression, and the third (lambda repressor) can act as either a repressor or an activator. The three proteins contain a substructure consisting of two consecutive alpha helices that is virtually identical in each case. Structural and amino acid sequence comparisons suggest that this bihelical fold occurs in a number of proteins that regulate gene expression, and is an intrinsic part of the DNA-protein recognition event. The modes of repression and activation by Cro and lambda repressor are understood reasonably well, but the mode of action of CAP is still unclear.

DNA sequences bound specifically by glucocorticoid receptor in vitro render a heterologous promoter hormone responsive in vivo

Glucocorticoids stimulate transcriptional initiation within integrated mammary tumor virus (MTV) DNA sequences in infected cells. We report here that production of herpes simplex virus thymidine kinase (tk) RNA is stimulated as much as 50-fold by the glucocorticoid, dexamethasone, when sequences from a particular region of MTV DNA are fused upstream of the normally constitutive tk promoter region. Three cloned fragments of MTV DNA were tested, each itself lacking the sequences required for transcription initiation. We monitored the effects of dexamethasone on the efficiency with which these recombinants transfect a tk- rat cell line to a tk+ phenotype, and measured tk enzymatic activity, the size and abundance of tk mRNA, and the 5' termini of tk transcripts in the transfectants. We conclude that the MTV promoter region contains a "glucocorticoid response element" that can be separated from a second element essential for MTV transcription initiation. The hormone response element maps within a 340-base pair MTV DNA fragment that contains specific binding sites for purified glucocorticoid receptor protein in vitro, implying that receptor binding at these sites in vivo may mediate hormone responsiveness. Comparison of several different constructions indicates that the location and orientation of the glucocorticoid response element relative to the transcription start site is not rigidly constrained.

The effect of a lambda repressor mutation on the activation of transcription initiation from the lambda PRM promoter

Wild-type lambda repressor activates transcription from the lambda PRM promoter by stimulating the rate-limiting isomerization step in the initiation reaction. The positive-control mutants of lambda repressor retain the ability to bind operator DNA normally, but fail to activate transcription from the lambda PRM promoter in vivo. We have characterized one of these mutants in vitro, and have determined the biochemical nature of the defect. We show that the mutant repressor was deficient in its ability to stimulate the isomerization step in transcription initiation. The initial binding of RNA polymerase to PRM was only slightly reduced by the mutant repressor. We also found that the mutant and wild-type repressors had similar affinities for all three binding sites in the rightward operator. These results provide support for the hypothesis that direct repressor-RNA polymerase interactions are important in the PRM activation mechanism.