Kinetic investigation of the mechanism of RNA polymerase binding to mutant lac promoters

Kinetics of promoter escape by bacterial RNA polymerase: effects of promoter contacts and transcription bubble collapse

Promoter escape by RNA polymerase, the transition between the initiation and elongation, is a critical step that defines transcription output at many promoters. In the present study we used a real-time fluorescence assay for promoter melting and escape to study the determinants of the escape. Perturbation of core promoter-polymerase contacts had opposing effects on the rates of melting and escape, demonstrating a direct role of core promoter elements sequence in setting not only the kinetics of promoter melting, but also the kinetics of promoter escape. The start of RNA synthesis is accompanied by an enlargement of the transcription bubble and pulling in of the downstream DNA into the enzyme, resulting in DNA scrunching. Promoter escape results in collapse of the enlarged bubble. To test whether the energy that could be potentially released by the collapse of the bubble plays a role in determining escape kinetics, we measured the rates of promoter escape in promoter constructs, in which the amount of this energy was perturbed by introducing sequence mismatches. We found no significant changes in the rate of promoter escape with these promoter constructs suggesting that the energy released upon bubble collapse does not play a critical role in determining the kinetics of promoter escape.

Monitoring abortive initiation

Abortive initiation, when first discovered, was an enigmatic phenomenon, but fully three decades hence, it has been shown to be an integral step in the transcript initiation process intimately tied to the promoter escape reaction undergone by RNA polymerase at the initiation-elongation transition. A detailed understanding of abortive initiation-promoter escape has brought within reach a full description of the transcription initiation mechanism. This enormous progress was the result of convergent biochemical, genetic, and biophysical investigations propelled by parallel advances in quantitation technology. This chapter discusses the knowledge gained through the biochemical approach and a high resolution method that yields quantitative and qualitative information regarding abortive initiation-promoter escape at a promoter.

Promoter Escape by Escherichia coli RNA Polymerase

Promoter escape is the process that an initiated RNA polymerase (RNAP) molecule undergoes to achieve the initiation-elongation transition. Having made this transition, an RNAP molecule would be relinquished from its promoter hold to perform productive (full-length) transcription. Prior to the transition, this process is accompanied by abortive RNA formation-the amount and pattern of which is controlled by the promoter sequence information. Qualitative and quantitative analysis of abortive/productive transcription from several Escherichia coli promoters and their sequence variants led to the understanding that a strong (RNAP-binding) promoter is more likely to be rate limited (during transcription initiation) at the escape step and produce abortive transcripts. Of the two subelements in a promoter, the PRR (the core Promoter Recognition Region) was found to set the initiation frequency and the rate-limiting step, while the ITS (the Initial Transcribed Sequence region) modulated the ratio of abortive versus productive transcription. The highly abortive behavior of E. coli RNAP could be ameliorated by the presence of Gre (transcript cleavage stimulatory) factor(s), linking the first step in abortive RNA formation by the initial transcribing complexes (ITC) to RNAP backtracking. The discovery that translocation during the initiation stage occurs via DNA scrunching provided the source of energy that converts each ITC into a highly unstable "stressed intermediate." Mapping all of the biochemical information onto an X-ray crystallographic structural model of an open complex gave rise to a plausible mechanism of transcription initiation. The chapter concludes with contemplations of the kinetics and thermodynamics of abortive initiation-promoter escape.

Roles for inhibitory interactions in the use of the -10 promoter element by sigma 70 holoenzyme

A panel of seven -10 region DNA mutants was tested for holoenzyme binding against a panel of 13 region 2 mutants of sigma 70. No patterns were noticed that would indicate unique interactions between individual amino acids and individual -10 region bases. Instead, certain amino acid substitutions led to increased holoenzyme binding to DNA, implying that the wild type interactions are associated with an inhibitory component. These inhibitory interactions were stronger on DNA containing non-consensus sequences, like those of typical promoters. In addition, the DNA segment downstream from the -10 element was also inhibitory to binding when in duplex form but stimulated binding when in single strand form. Overall, the data suggest that -10 region duplex recognition and melting have a large component of overcoming unfavorable protein:DNA base interactions, particularly when the bases are non-consensus, and that this contributes to setting physiologically appropriate variations in transcription rate.

Interaction of bacterial RNA-polymerase with two different promoters of phage T7 DNA. Conformational analysis

Using a rifampicin-resistant RNA polymerase with altered specificity to different promoters, the D promoter of T7 phage DNA with increased affinity to the mutant enzyme was chosen. This promoter and the T7 A1 promoter with unchanged affinity as well as some nonpromoter DNA fragments were used to compare temperature-induced conformational transitions of RNA polymerase in the course of complex formation. Conformational alterations of RNA polymerase were monitored by the fluorescent label method. It was shown that RNA polymerase undergoes a set of conformational transitions during complex formation with each promoter, some of which were similar by the character of change to spectral parameters of the label (reflecting RPi and, probably, RPo formation). The local structure of complexes formed above 33 degrees C differs for A1 and D. The conformational analysis reveals at least one temperature-dependent stage upon nonspecific interaction of the enzyme with nonpromoter DNA at 13-16 degrees C. Models of functional organization of the enzyme recognizing center and some features of the structure of the promoters which may be essential for their recognition are discussed.

Mechanism of initiation of transcription by Bacillus subtilis RNA polymerase at several promoters

The behavior of the major vegetative cell RNA polymerase of Bacillus subtilis, E sigma A, during initiation of transcription was compared to that of its Escherichia coli counterpart, E sigma 70, at several promoters known to be actively transcribed by both RNA polymerases. Challenge experiments using heparin, restriction endonucleases, and competing promoter DNA under various conditions showed that, at several promoters, complexes with B. subtilis RNA polymerase formed in the absence of nucleoside triphosphates were unstable. These complexes produced DNase I footprints that were less extended than those produced by the E. coli enzyme at the same promoters. Further, in the presence of certain combinations of nucleoside triphosphates, conditions that allow production of abortive oligonucleotides, these B. subtilis RNA polymerase complexes remained dissociable. Thus, at these promoters, the B. subtilis enzyme interacted with the DNA and reached a catalytically active initial transcribing complex without becoming committed to the template. At these same promoters, E. coli RNA polymerase formed stable open complexes before forming any phosphodiester bonds. B. subtilis initial transcribing complexes also remained sensitive to the drug rifampicin until a later stage in the initiation process than did the corresponding E. coli complexes. At one promoter, B. subtilis E sigma A and E. coli E sigma 70 behaved similarly, forming stable open complexes in the absence of any nucleoside triphosphates.

Transcription and decay of the lac messenger: role of an intergenic terminator

Prior work has indicated that the polycistronic lacZYA mRNA of Escherichia coli is cleaved during decay at approximately intergenic sites (L. W. Lim and D. Kennell, J. Mol. Biol. 135: 369-390, 1979). In this work, we characterized the products by using probes specific for the different cistrons. This analysis indicated that six lac mRNA species are present in the following order of decreasing abundance: lacZ, -A, -ZYA, -ZY, -YA, and -Y. Very little lacYA and lacY mRNAs were present, whereas in cells induced to steady state, there was 10 times more lacZ than lacZYA mRNA. The lacZ mRNA appeared as a discrete species extending to a site in the lacZ-Y intergenic space (ca. residue 3150). This site is just distal to a potential rho-independent termination sequence. We examined the function of this sequence to determine whether it contributes to the distribution of the mRNAs. Although the termination sequence was shown to function in vitro, when it was recloned into an expression vector, no termination was seen in vivo. Moreover, direct examination of the kinetics of lac messenger synthesis revealed that after initiation, most transcription continued to the end of the operon. We conclude that during normal growth, the operon is transcribed in its entirety and that the individual lac mRNAs are formed by cleavage. These results confirm earlier work implying that the lac operon is transcribed in its entirety but are in conflict with several recent reports suggesting that internal termination occurs. Our findings indicate that the natural polarity of the operon (lacZ is expressed sixfold more strongly than lacA) is based on posttranslational effects and not on polarity of transcription.

Mapping the lacZ ribosome binding site by RNA footprinting

The ribosome binding site of the Escherichia coli lacZ mRNA has been characterized by using an RNA footprinting technique. Purified E. coli 70S ribosomes and fMet-tRNA were incubated with mRNA, and the complex was treated with RNA-reactive reagents or RNases as probes. The protected sites on the mRNA were then mapped by extending a radioactive primer with reverse transcriptase. Dimethyl sulfate, diethyl pyrocarbonate, and 1,10-phenanthroline-copper ion oxidative complex were used as reagent probes; they detected interaction sites within the ribosome binding site. A region of approximately 35 nucleotides was protected by the ribosome, specifically across the Shine-Dalgarno region, around the fMet initiation codon, and at a region 7-12 nucleotides distal to the fMet codon. In addition, an enhanced reaction occurred between the fMet codon and the distal site. These results imply an internally selective interaction between the ribosome and the mRNA sequence. The enhanced reactivity of a site distal to the initiation site--flanked by the AUG codon and a site previously identified as conserved in a study of initiation sequences--may indicate a region where the mRNA is specifically exposed.

Activation of the lac promoter and its variants. Synergistic effects of catabolite activator protein and supercoiling in vitro

Escherichia coli lac promoter variants are shown to be subject to large synergistic transcriptional activation by catabolite activator protein (CRP) and DNA supercoiling in vitro. Activation was studied for the lac wild-type promoter, a promoter with a variant spacing (lac delta l) and two promoters with variant -10 regions (lac ps, lac UV5). The variant promoters respond to the simultaneous presence of CRP and supercoiling by exhibiting large multiplicative activation at the low to moderate superhelicities that are most pertinent in vivo. Although all four promoters can be activated by CRP, those made stronger by changing downstream promoter elements are less CRP-activated even though each contains an identical CRP binding site. When each of the variant promoters is made stronger by introducing DNA supercoils, the apparent CRP activation initially remains constant but eventually declines at higher superhelicities. Thus, strengthening the lac promoter through either DNA sequence changes or the introduction of high-level DNA supercoiling can lead to diminished potential for activation by CRP. These results are interpreted in terms of a role for CRP in providing extra stabilizing contacts for RNA polymerase binding that are necessary only when other stabilizing features of promoter structure are lacking.

Effect of the delta subunit of Bacillus subtilis RNA polymerase on initiation of RNA synthesis at two bacteriophage phi 29 promoters

Initiation of RNA synthesis by Bacillus subtilis RNA polymerase (sigma-43) has been examined at two early promoters of phage phi 29: the A2 promoter, which is a weak promoter, and the G2 promoter, which is a strong promoter. The delta subunit of the polymerase inhibits the rate of initiation at A2, but not G2. In addition, formation of stable complexes by the polymerase at A2, but not at G2, requires the presence of the first two nucleotides of the A2 transcript.

Determination of the promoter strength of the gene encoding Escherichia coli heat-stable enterotoxin II

We studied the promoter strength of the gene encoding the Escherichia coli heat-stable enterotoxin II (STII). The promoter region and a portion of the 5' coding sequence of the STII gene were fused to the lacZ gene so that the production of beta-galactosidase was under the control of the STII gene promoter. The strength of the STII gene promoter was compared with that of the ompF and lac operons, which were similarly fused to the lacZ gene. The beta-galactosidase produced by the hybrid genes was assayed in vitro by using cell extracts. The mRNA transcribed by each promoter was assayed by Northern blot analysis and by in vitro transcription. The results suggest that the STII gene is regulated by a relatively weak promoter.

Entry of RNA polymerase at the lac promoter

The pathway of RNA polymerase entry at the lac promoter was studied by investigating the relationship between the promoter and a weak, overlapping polymerase interaction site (P2). If polymerase is made to enter the DNA by binding in vitro at this P2 site, cyclic AMP receptor protein (CRP) actively removes polymerase and redirects it to the promoter. A template competition experiment demonstrates that RNA polymerase initially bound at P2 does not slide the 22 base pairs along the DNA from this "entry" site to the promoter, but must locate the promoter by first leaving the template. We infer that CRP works by binding DNA in a way that both clears the promoter and modifies it to assume a form that is a better receptor for the binding of RNA polymerase from free solution.

Intermediates in transcription initiation from the E. coli lac UV5 promoter

We have used nondenaturing polyacrylamide gel electrophoresis to separate intermediates in transcription initiation that result from action of E. coli RNA polymerase on the lac UV5 promoter. The resolved gel complexes are characterized by DNAase I footprinting, protein subunit content, RNA content, and transcription ability. There are two "open" complexes, whose equilibrium ratio is a function of temperature; they differ in their ability to escape abortive cycling, but not in their DNAase I footprints. We find three "initiated" complexes, containing RNA chains at least 11 nucleotides long, and lacking the sigma subunit of RNA polymerase. These experiments provide a detailed view of the early initiation steps and their thermal regulation at the E. coli lac promoter.

Properties of lac P2 in vivo and in vitro. An overlapping RNA polymerase binding site within the lactose promoter

The Escherichia coli lac promoter has been shown to contain an RNA polymerase binding site (P2) that overlaps with, and is shifted 22 base-pairs upstream from the normal lac promoter (P1). In this paper, we provide RNA polymerase protection data obtained in vitro that show that, in the absence of CAP-cAMP, in vitro P2 is the preferred polymerase binding site on the P+ template. In the presence of CAP-cAMP, polymerase binding to P2 is reduced and more polymerase is bound at P1. Two lac P1 "-35 region" mutations, L157 and 4, which increase the homology between this region and the consensus "-10 region" sequence, are both shown to have an increased affinity for polymerase binding at P2. CAP-cAMP is also able to decrease the amount of polymerase bound to P2 and to increase the amount bound to P1 on these mutant promoter fragments. P2 does not initiate transcription efficiently in vivo. Nuclease S1 mapping experiments detect only a low level of transcription from one of the P2 "up" mutations, but no beta-galactosidase synthesis is directed by this mutant. Mutations such as L157 and 4, which alter the P2-10 region, also alter lac P sensitivity to CAP-cAMP in vivo, suggesting that the P2 sequence plays a role in CAP-cAMP regulation of lac P. Possible roles for P2 in vivo are discussed.

Lactose promoter mutation Pr115 activates an overlapping promoter within the lactose control region

The Escherichia coli lac promoter mutation Pr115, an A X T to T X A transversion at +1 (the transcription initiation site of the lac wild-type and lac UV5 promoters), creates a new "-10 region"-like sequence starting at +1. We show that this mutation activates a new RNA polymerase binding site (P115) that overlaps with, and is shifted 12 base-pairs downstream from, the wild-type RNA polymerase binding site (P1). Nuclease S1 mapping studies and RNA polymerase protection experiments in vitro indicate that, in the absence of CAP-cAMP, this new site is used preferentially over the P1 site. In vivo, beta-galactosidase assays of the Pr115 mutation in combination with mutations of the P1 "-35 region" demonstrate that the P1 -35 region sequences are not involved in the interaction between RNA polymerase and P115 in the absence of CAP-cAMP; therefore P115 is an independent binding site. The presence of CAP-cAMP in vivo stimulates polymerase binding and initiation at P1, which serves to block polymerase from binding at P115.

Supercoiling response of the lac ps promoter in vitro

The rate of open promoter complex formation was measured on lac ps promoter DNA templates differing in negative superhelicity. The templates ranged from fully relaxed to those with numbers of superhelical turns exceeding that of form I plasmid DNA. The observed transcription response had two clearly distinguished phases: an initial rapid rise in rate followed eventually by a precipitous inhibition. The stimulation phase involved a nearly 40-fold increase in rate, which peaks at superhelical densities near that of isolated form I plasmid DNA. The introduction of more negative superhelical turns leads to inhibition. The magnitude of the response and the observation of both increases and decreases suggest that minor differences in superhelicity in vivo could lead to significant increases or decreases in transcription rate. The increase in rate was found to be directly proportional to the free energy of supercoiling; that is, to the square of the superhelical density. We suggest that the energy may be used both for enhanced DNA melting and for changes in DNA structure that alter the helical "face" with which RNA polymerase must interact. A quantitative method is presented that allows simple estimation of differences in the supercoiling response among promoters, both in the presence and in the absence of added factors.

Temperature dependence of the rate constants of the Escherichia coli RNA polymerase-lambda PR promoter interaction. Assignment of the kinetic steps corresponding to protein conformational change and DNA opening

The kinetics of formation and of dissociation of open complexes (RPo) between Escherichia coli RNA polymerase (R) and the lambda PR promoter (P) have been studied as a function of temperature in the physiological range using the nitrocellulose filter binding assay. The kinetic data provide further evidence for the mechanism R + P in equilibrium I1 in equilibrium I2 in equilibrium RPo, where I1 and I2 are kinetically distinguishable intermediate complexes at this promoter which do not accumulate under the reaction conditions investigated. The overall second-order association rate constant (ka) increases dramatically with increasing temperature, yielding a temperature-dependent activation energy in the range 20 kcal (near 37 degrees C) to 40 kcal (near 13 degrees C) (1 kcal = 4.184 kJ). Both isomerization steps (I1----I2 and I2----RPo) appear to be highly temperature dependent. Except at low temperatures (less than 13 degrees C) the step I1----I2, which we attribute to a conformational change in the polymerase with a large negative delta Cp degrees value, is rate-limiting at the reactant concentrations investigated and hence makes the dominant contribution to the apparent activation energy of the pseudo first-order association reaction. The subsequent step I2----RPo, which we attribute to DNA melting, has a higher activation energy (in excess of 100 kcal) but only becomes rate-limiting at low temperature (less than 13 degrees C). The initial binding step R + P in equilibrium I1 appears to be in equilibrium on the time-scale of the isomerization reactions under all conditions investigated; the equilibrium constant for this step is not a strong function of temperature and is approximately 10(7) M-1 under the standard ionic conditions of the assay (40 mM-Tris . HCl (pH 8.0), 10 mM-MgCl2, 0.12 M-KC1). The activation energy of the dissociation reaction becomes increasingly negative at low temperatures, ranging from approximately -9 kcal near 37 degrees C to -30 kcal near 13 degrees C. Thermodynamic (van't Hoff) enthalpies delta H degrees of open complex formation consequently are large and temperature-dependent, increasing from approximately 29 to 70 kcal as the temperature is reduced from 37 to 13 degrees C. The corresponding delta Cp degrees value is approximately -2.4 kcal/deg. We propose that this large negative delta Cp degrees value arises primarily from the burial of hydrophobic surface in the conformational change (I1 in equilibrium I2) in RNA polymerase in the key second step of the mechanism.(ABSTRACT TRUNCATED AT 400 WORDS)

Interaction of RNA polymerase with lacUV5 promoter DNA during mRNA initiation and elongation. Footprinting, methylation, and rifampicin-sensitivity changes accompanying transcription initiation

We have used enzymatic and chemical probes to follow the movement of Escherichia coli RNA polymerase along lacUV5 promoter DNA during transcription initiation. The RNA polymerase does not escape from the promoter but remains tightly bound during the synthesis of the initial bases of the transcript. This initial phase of RNA synthesis involves the reiterative synthesis and release of RNA chains up to ten bases long via the RNA polymerase cycling reaction and the enzyme remains sensitive to rifampicin inhibition. When longer chains are made, promoter-specific binding is disrupted and the enzyme forms a rifampicin-resistant elongation complex with downstream DNA sequences. This elongation complex covers less than half as much DNA and lacks the DNase I-hypersensitive sites and the base-specific contacts that characterize promoter-bound RNA polymerase. These results lead us to suggest that lacUV5 mRNA synthesis is primed by a promoter-bound enzyme complex that synthesizes the initial nine or ten bases in the mRNA chain. Subsequently, when a chain of ten bases, or slightly longer, is made, contacts with promoter DNA are irreversibly disrupted, sigma subunit is lost, and a "true" elongation complex is formed.

In vitro characterization of hybrid promoters and altered tryptophan operon promoters

This study examines the in vitro interaction of hybrid and altered Escherichia coli promoters and other promoters with purified E. coli RNA polymerase. Three parameters of polymerase activity were examined: the time for open complex formation; the temperature of transitions; and the time required for productive initiation. The results indicate the rate of in vitro binding as measured by the filter binding technique does not completely correlate with the in vivo activities among these diverse promoters. Transition temperatures ranged from 13 to 27 degrees C with the lowest transition temperatures associated with the relatively weak in vivo beta-lactamase and anti-tet promoters. The productive initiation studies showed a dependence on labeled nucleoside triphosphate concentration when that nucleotide was present early and frequently in the transcript. Promoters containing the -10 region of the lac promoter had slow productive initiation rates while trp -10 promoter derivatives were generally very fast. In the promoters studied here, a trend was noted between the binding rate and transition temperature studies in that the promoters with the lower transition temperatures tended to bind more rapidly.

Activation and inhibition of transcription by supercoiling

Stimulation of transcriptional activity in vitro is observed at low and moderate negative superhelical densities up to the level of the natural superhelical form of the plasmid pBR322. We have isolated and identified three specific transcription products: ampicillinR RNA, tetracyclineR RNA and "Rep" RNA. Their enhancement of transcription occurs at different levels of superhelicity, suggesting a sequence-dependent structural alteration of promoters upon changes of axial writhe, which may generate kink formation. The activation of transcription is drastically inhibited at higher specific linking differences exceeding that of the natural superhelical form of pBR322, which is correlated with a transition from the right-handed B to a left-handed DNA form of particular sequences induced by supercoiling. We have identified a new stop point in the beta-lactamase coding sequence composed of eight alternating purine-pyrimidine residues which, at higher torsional stress, causes transcription to stop, leading to the synthesis of a short RNA of about 55 nucleotides instead of AmpR RNA (about 580 nucleotides). In the "Rep" promoter, two alternating purine-pyrimidine segments are found, which conformational change at higher superhelical densities may be implicated in repression of "Rep" RNA synthesis. The enhancement and inhibition of transcription by supercoiling support the role of energetic and structural changes in topologically constrained DNA as elements of a control mechanism.

Kinetics and mechanism of the interaction of Escherichia coli RNA polymerase with the lambda PR promoter

The kinetics of formation and dissociation of specific (open) complexes between active Escherichia coli RNA polymerase holoenzyme (RNAP) and the lambda PR promoter have been studied by selective nitrocellulose filter binding assays at two temperatures (25 degrees C, 37 degrees C) and over a range of ionic conditions. Competition with a polyanion (heparin) or stabilization of open promoter complexes at PR by incubation with specific combinations of nucleoside triphosphates was employed to obtain selectivity in the filter assay. This study provides a useful example of how information about mechanism may be obtained from the quantitative analysis of the effects of salt concentration and temperature on the rate constants of a protein-DNA interaction. The association reaction between RNAP and lambda PR was investigated under ionic conditions where the process is essentially irreversible, and under pseudo first-order conditions of excess polymerase. The pseudo first-order rate constant is directly proportional to the concentration of active polymerase over the entire range investigated (2 to 10 nM) at both 25 degrees C and 37 degrees C, within experimental uncertainty. Second-order association rate constants (ka), calculated from these data at standard ionic conditions (0.12 M-KCl, 0.01 M-MgCl2, 0.04 M-Tris (pH 8)), were strongly temperature-dependent: ka = (2.6 +/- 0.4) X 10(6) M-1 S-1 at 37 degrees C and ka = (7.2 +/- 1.4) X 10(5) M-1 s-1 at 25 degrees C, corresponding to an activation energy of the association reaction of approximately 20 +/- 5 kcal. In addition, ka decreases strongly with increasing KCl concentration, corresponding to the net release of the thermodynamic equivalent of at least nine monovalent ions prior to or during the rate-limiting step of the association reaction. This strong dependence of ka on the ionic environment suggests that inorganic cations should be considered as possible regulators of in vivo transcription initiation. Dissociation rate constants (kd) were also measured under irreversible reaction conditions. At the standard ionic conditions, kd = (2.2 +/- 0.3) X 10(-5) s-1 at 37 degrees C and kd = (4.0 +/- 0.4) X 10(-5) s-1 at 25 degrees C. The increase in kd with decreasing temperature corresponds to a negative activation energy of dissociation (-9 +/- 4 kcal). In addition, kd increases with increasing KCl concentration, corresponding to the net uptake of the thermodynamic equivalent of at least six monovalent ions in or prior to the rate-limiting step of the dissociation reaction.(ABSTRACT TRUNCATED AT 400 WORDS)

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.