Kinetics of open complex formation between Escherichia coli RNA polymerase and the lac UV5 promoter. Evidence for a sequential mechanism involving three steps

The forward and reverse kinetics of open complex formation between Escherichia coli RNA polymerase and the lac UV5 promoter have been studied in the temperature range of 15-42 degrees C. The standard two-step model, involving the formation of a closed intermediate, RPc, followed by an isomerization that leads to the active complex RPo, could not account for the present data. The promoter-enzyme lifetime measurements showed an inverse temperature dependence (apparent activation energy, -35 kcal/mol). A third step, which is very temperature dependent and which is very rapid at 37 degrees C, was postulated to involve the unstacking of DNA base pairs that immediately precedes open complex formation. Evidence for incorporating a new binary complex, RPi, in the pathway was provided by experiments that distinguished between stably bound species and active promoter after temperature-jump perturbations. These experiments allowed measurement of the rate of reequilibration between the stably bound species and determination of the corresponding equilibrium constant. They indicated that the third step became rate limiting below 20 degrees C; this prediction was checked by an analysis of the forward kinetics. A quantitative evaluation of the parameters involved in this three-step model is provided. Similar experiments were performed on a negatively supercoiled template: in this case the third equilibrium was driven toward formation of the open complex even at low temperature, and the corresponding step was not rate limiting.     

Effects of an anti-beta monoclonal antibody on the interaction of the Escherichia coli RNA polymerase with the lac and TAC promoters

The effects of an inhibitory monoclonal antibody (mAb) raised against the beta subunit of the Escherichia coli RNA polymerase were determined on the kinetics and structural interactions during formation of the open promoter complex (RPo). Analysis of the kinetics of abortive initiation on linear and supercoiled templates of the lac and TAC16 promoters showed that abortive synthesis by mAb 210E8-RNA polymerase varied as a function of DNA topology. A kinetic analysis of RPl formation on the supercoiled lac UV5 promoter showed that mAb 210E8 effected a slight alteration in the isomerization rate and no effect on the initial rate of RNA polymerase binding to the promoter. The potent inhibition of initiation with linear promoters by mAb 210E8 was not apparent when the promoters were assayed in their supercoiled forms. Abortive synthesis with the TAC16 promoter was accompanied by an mAb 210E8 induced hindrance of ApUpU but not UpGpU synthesis. The data indicate that the inhibition by mAb 210E8 with the supercoiled TAC16 promoter is further alleviated when the spacer length is shifted from 16 base pairs (ApUpU formation) to 18 base pairs (UpGpU formation). When DNase I and dimethyl sulfate were used to probe DNA structure, mAb 210E8 was found to alter polymerase interactions with the lac promoter. DNase I footprinting indicated that the structural interactions for lac P+ promoter-RNA polymerase complexes were slightly altered in the presence of mAb 210E8. Treatment of the RNA polymerase-lac UV5 complex with dimethyl sulfate revealed an alternate mode of RNA polymerase interaction with essential guanine contacts which was intermediate between a fully protected and free promoter.(ABSTRACT TRUNCATED AT 250 WORDS)     

pH-dependent charge equilibria between tyrosine-D and the S states in photosystem II. Estimation of relative midpoint redox potentials

The effect of protonation events on the charge equilibrium between tyrosine-D and the water-oxidizing complex in photosystem II has been studied by time-resolved measurements of the EPR signal IIslow at room temperature. The flash-induced oxidation of YD by the water-oxidizing complex in the S2 state is a monophasic process above pH 6.5 and biphasic at lower pHs, showing a slow and a fast phase. The half-time of the slow phase increases from about 1 s at pH 8.0 to about 20 s at pH 5.0, whereas the half-time of the fast phase is pH independent (0.4-1 s). The dark reduction of YD+ was followed by measuring the decay of signal IIslow at room temperature. YD+ decays in a biphasic way on the tens of minutes to hours time scale. The minutes phase is due to the electron transfer to YD+ from the S0 state of the water-oxidizing complex. The half-time of this process increases from about 5 min at pH 8.0 to 40 min at pH 4.5. The hours phase of YD+ has a constant half-time of about 500 min between pH 4.7 and 7.2, which abruptly decreases above pH 7.2 and below pH 4.7. This phase reflects the reduction of YD+ either from the medium or by an unidentified redox component of PSII in those centers that are in the S1 state. The titration curve of the half-times for the oxidation of YD reveals a proton binding with a pK around 7.3-7.5 that retards the electron transfer from YD to the water-oxidizing complex. We propose that this monoprotic event reflects the protonation of an amino acid residue, probably histidine-190 on the D2 protein, to which YD is hydrogen bonded. The titration curves for the oxidation of YD and for the reduction of YD+ show a second proton binding with pK approximately 5.8-6.0 that accelerates the electron transfer from YD to the water-oxidizing complex and retards the process in the opposite direction. This protonation most probably affects the water-oxidizing complex. From the measured kinetic parameters, the lowest limits for the equilibrium constants between the S0YD+ and the S1YD as well as between the S1YD+ and S2YD states were estimated to be 5 and 750-1000, respectively.(ABSTRACT TRUNCATED AT 400 WORDS)     

Effect of 1,10-phenanthroline on bacterial conjugation in Escherichia coli K-12: inhibition of maturation from preliminary mates into effective mates.

The addition of 1 mM orthophenanthroline (OP) into a mating mixture drastically reduced the production of recombinants. Examination of the effect of OP on each step of conjugation showed that the effect on the following steps could not account for the up to 500-fold reduction of recombinant formation: (i) preliminary mate formation and (ii) deoxyribonucleic acid transfer and integration. Taking these results and additional experiments together, we conclude that OP inhibits the maturation of preliminary mates into effective mates. Kinetic experiments showed that there were two phases in the maturation of preliminary (OP-sensitive) mates into effective (OP-resistant) mates. The half-time (the time required to reach 50% OP-resistant mates) was 2.5 min for the first phase and 4 min for the second phase, with an overall half-time of 7.5 min. In contrast, only 3 min was required to reach 50% Zn2+-resistant mates. The difference in half-time suggests that there is an intermediate step involved to form an effective mate from a preliminary mate.     

From stand-by to decoding site. Adjustment of the mRNA on the 30S ribosomal subunit under the influence of the initiation factors.

The hypothesis of an adjustment of the mRNA in its ribosomal channel under the influence of the initiation factors has been tested by site-directed crosslinking experiments. Complexes containing 30S subunits with bound mRNA having 4-thio-uracil at specific positions were prepared in the presence or absence of initiation factors and/or fMet-tRNA and subjected to UV irradiation to obtain specific crosslinks of the radioactively labeled mRNA with bases of the 16S rRNA and with ribosomal proteins. The subsequent identification of the specific sites of both mRNA and rRNA and individual ribosomal proteins involved in the crosslinking, obtained under different conditions of complex formation, provide direct evidence for the occurrence of a partial relocation of the mRNA on the 30S ribosomal subunits under the influence of the factors. The nature of this mRNA relocation is compatible with our previous proposal of a shift of the template from an initial ribosomal "stand-by site" to a second site closer to that occupied when the initiation triplet of the mRNA is decoded in the P-site.     

DNA supercoiling promotes formation of a bent repression loop in lac DNA

Titration experiments on supercoiled lac DNA show that one repressor tetramer can bind simultaneously to the primary lac operator and to the very weak lac pseudo-operator, located 93 base-pairs apart. The formation of this complex is accompanied by the appearance of an extreme hypersensitive site in a five base-pair sequence located approximately midway between the operators. This remote sequence is hypersensitive to attack by two different chemical probes, dimethyl sulfate and potassium permanganate, the latter of which is a new probe for distorted DNA. We interpret these results in terms of a complex in which lac repressor holds two remote operators together in a DNA loop. The formation of this bent DNA loop requires negative DNA supercoiling. In vivo, both lac operators bind repressor even though the presence of multiple operator copies has forced the two operators to compete for a limited amount of repressor. This suggests that the operator and pseudo-operator have similar affinities for repressor in vivo. Such similar affinities were observed in vitro only when DNA supercoiling forced formation of a repression loop.     

Specialized transduction with lambda plac5: dependence on recB.

Genetically disabled lambda plac5 transducing phage derivatives were used to study the recB dependence of recombination during specialized transduction. The frequency of transduction was normalized to colony-forming units, and the end product of recombination was monitored by scoring for addition and substitution transductants. When a chromosomal lac gene was the recipient DNA substrate molecule, both the normalized transduction frequency and the proportion of addition and substitution transductants showed essentially no recB dependence. There was a pronounced recB dependence for both normalized transduction frequency and recombination end product formation when F42 lac was the recipient DNA substrate. recB appears to have no significant role in the recombination that occurs between the two lac regions in an addition transductant. UV irradiation of the transducing phages increased the absolute level of both addition and substitution transductants obtained with a chromosomal lac gene but resulted in a considerable change in the relative frequency of addition versus substitution transductants.     

Bacteriophage T4-induced shut-off of host-specific translation.

To study the mechanism by which bacteriophage T4 inhibits the synthesis of inducible host enzymes we measured the formation of beta-galactosidase from preformed lac mRNA. Beta-Galactosidase was induced with isopropyl-beta-D-thiogalactopyranoside in the presence of 7-azatryptophan, a tryptophan analogue that is incorporated into proteins and renders the beta-galactosidase formed inactive. The accumulated las mRNA was measured by capacity to form active beta-galactosidase after a chase of the analogue with excess tryptophan. After T4 infection the ability to form beta-galactosidase from the preformed lac mRNA was rapidly lost even when T4 infection took place in the presence of rifampin. This restriction was dependent on the multiplicity of infection. At a multiplicity of infection of 8.6, 90% of the ability to express preformed lac mRNA was lost within 30 s. The kinetics of cessation of beta-galactosidase synthesis after T4 infection indicate that infection blocks initiation of lac mRNA translation.     

Post-translational processing of the epidermal growth factor receptor. Glycosylation-dependent acquisition of ligand-binding capacity

The post-translational processing of the epidermal growth factor receptor in human A431 epidermoid carcinoma cells has been investigated. By employing the affinity matrix epidermal growth factor Affi-Gel in conjunction with immunoprecipitation, it has been demonstrated that core oligosaccharide addition is essential for the acquisition of epidermal growth factor-binding activity. Furthermore, the initial 160-kDa translation product was observed to undergo a processing step by which ligand-binding activity was acquired with a half-time of approximately 30 min while exhibiting no apparent change in mobility on sodium dodecyl sulfate-polyacrylamide gels. This was shown not to involve the conversion of high-mannose chains to complex chains which have been capped with fucose and sialic acid. Possible explanations for this activation in terms of translocation of intermediates and/or formation of disulfide bonds are discussed.