Revisiting the stringent response, ppGpp and starvation signaling.

Microbial adaptation to environmental stress plays an important role in survival. It is necessary to understand the mechanisms underlying the survival of microbes under stress, as they may eventually aid in the successful control of the growth and persistence of these organisms. During nutrient starvation, Escherichia coli elicits a stringent response to conserve energy. The hallmark of the stringent response is the accumulation of guanosine tetra- (ppGpp) and pentaphosphates (pppGpp), which probably bind RNA polymerase to regulate gene expression at certain promoters. Recently, there has been renewed interest in the stringent responses of other microbes, with a view to correlating it with sporulation, virulence and long-term persistence.

A point mutation at the junction of domain 2.3/2.4 of transcription factor sigma 70 abrogates productive transcription and restores its expected mobility on a denaturing gel.

Region 2 of eubacterial sigma factors is highly conserved and the subdomain 2.4 is involved in -10 promoter recognition. An evolutionary conserved "RpoD box" has been identified at the junction of subdomain 2.3/2.4 in class I and class II sigma factors and there are two tryptophan residues at position 433 and 434 which can be used as intrinsic fluorescent markers to study their structure-function relationship. Site-directed mutagenesis of these two tryptophan residues has been carried out to generate three variants of sigma 70 of Escherichia coli RNA polymerase. These are W433F, W433G and W434G. sigma 70-W433F is found to be indistinguishable from the native sigma factor by both structural and functional analysis. sigma 70-W433G shows anomalous mobility on SDS-PAGE like the native sigma factor, is alpha-helical in conformation (50% helicity) although found to be less active in total transcription when reconstituted with core RNA polymerase. Free sigma 70-W434G, unlike the native sigma factor, shows the expected mobility of a 70 kDa protein on SDS-PAGE and has 20% helicity. Time-resolved fluorescence analysis indicates that free sigma 70-W434G has DNA binding ability, and displays a normal abortive initiation reaction but a decreased level of productive transcription after reconstitution with core RNA polymerase. A model is proposed in which tryptophan at position 434 interacts with the hydrophobic 1.1 domain of sigma 70 giving rise to the stability of the protein under denaturing conditions.

Carbamazepine and its -10,11-epoxide metabolite in plasma and CSF. Relationship to antidepressant response.

Levels of carbamazepine and its -10,11-epoxide metabolite were measured in plasma and CSF of affectively ill patients treated only with carbamazepine for an average of 33 days at an average dosage of 1,055 mg/day. The CSF levels of carbamazepine were 2.06 micrograms/mL (ie, 31% of plasma levels, which equaled 6.55 micrograms/mL); CSF -10,11-epoxide concentrations averaged 0.91 micrograms/mL in 18 subjects (63% of those found in plasma). Carbamazepine levels in plasma or CSF were not related to degree of antidepressant or antimanic response. In contrast, concentrations of the -10,11-epoxide metabolite were correlated with the degree of antidepressant response. This preliminary study suggests the possibility that the -10,11-epoxide metabolite of carbamazepine may be related to the degree of clinical efficacy in affectively ill patients and may thus possess active psychotropic properties in man in addition to its reported anticonvulsant effects in animals.

Non-invasive vaccine delivery in transfersomes, niosomes and liposomes: a comparative study.

Non-invasive vaccine delivery is a top priority for public health agencies because conventional immunization practices are unsafe and associated with numerous limitations. Recently, the skin has emerged as a potential alternative route for non-invasive delivery of vaccine. Topical immunization (TI), introduction of antigen through topical application onto the intact skin, has many practical merits compared to injectable routes of administration. One of the possibilities for increasing the penetration of bioactives through the skin is the use of vesicular systems. Specially designed lipid vesicles are attracting intense attention and can be used for non-invasive antigen delivery. In the present study, elastic vesicle transfersomes, non-ionic surfactant vesicles (niosomes) and liposomes were used to study their relative potential in non-invasive delivery of tetanus toxoid (TT). Transfersomes, niosomes and liposomes were prepared and characterized for shape, size and entrapment efficiency. These vesicles were extruded through polycarbonate filter (50-nm pore size) to assess the elasticity of the vesicles. The immune stimulating activity of transfersomes, niosomes and liposomes were studied by measuring the serum anti-TT IgG titre following topical immunization. The immune response elicited by topical immunization was compared with that elicited by same dose of alum-adsorbed tetanus toxoid (AATT) given intramuscularly. The results indicate that optimal formulations of transfersomes, niosomes and liposomes could entrap 72.7+/-3.4, 42.5+/-2.4 and 41.3+/-2.2% of antigen and their elasticity values were 124.4+/-4.2, 29.3+/-2.4 and 21.7+/-1.9, respectively. In vivo study revealed that topically given TT containing transfersomes, after secondary immunization, could elicit immune response (anti-TT-IgG) that was equivalent to one that produced following intramuscularly alum-adsorbed TT-based immunization. In comparison to transfersomes, niosomes and liposomes elicited weaker immune response. Thus transfersomes hold promise for effective non-invasive topical delivery of antigen(s).

Stabilizing interactions in the dimer interface of alpha-subunit in Escherichia coli RNA polymerase: a graph spectral and point mutation study.

The formation of alpha(2) dimer in Escherichia coli core RNA polymerase (RNAP) is thought to be the first step toward the assembly of the functional enzyme. A large number of evidences indicate that the alpha-subunit dimerizes through its N-terminal domain (NTD). The crystal structures of the alpha-subunit NTD and that of a homologous Thermus aquaticus core RNAP are known. To identify the stabilizing interactions in the dimer interface of the alpha-NTD of E. coli RNAP, we identified side-chain clusters by using the crystal structure coordinates of E. coli alpha-NTD. A graph spectral algorithm was used to identify side-chain clusters. This algorithm considers the global nonbonded side-chain interactions of the residues for the clustering procedure and is unique in identifying residues that make the largest number of interactions among the residues that form clusters in a very quantitative way. By using this algorithm, a nine-residue cluster consisting of polar and hydrophobic residues was identified in the subunit interface adjacent to the hydrophobic core. The residues forming the cluster are relatively rigid regions of the interface, as measured by the thermal factors of the residues. Most of the cluster residues in the E. coli enzyme were topologically and sequentially conserved in the T. aquaticus RNAP crystal structure. Residues 35F and 46I were predicted to be important in the stability of the alpha-dimer interface, with 35F forming the center of the cluster. The predictions were tested by isolating single-point mutants alpha-F35A and alpha-I46S on the dimer interface, which were found to disrupt dimerization. Thus, the identified cluster at the edge of the dimer interface seems to be a vital component in stabilizing the alpha-NTD.

Cytosine arabinoside cerebrospinal fluid kinetics.

To better characterize the disposition of cytosine arabinoside (Ara-C) in cerebrospinal fluid (CSF), its kinetics were studied in seven patients with meningeal leukemia in complete remission. After intraventricular injection of 30 mg Ara-C, CSF and plasma samples were obtained over a 24-hr period. Ara-C levels were measured by a reverse-phase HPLC assay (with a sensitivity of 0.5 microM in CSF and 1.0 microM in plasma) that readily separated Ara-C from its major metabolite uracil arabinoside (Ara-U). Elimination of Ara-C from CSF followed a biphasic pattern, with an initial t1/2 of 1 hr and a terminal t1/2 of 3.4 hr. Ara-C clearance from CSF was 0.42 ml/min, suggesting that drug elimination was primarily by CSF bulk flow. The ratio of the AUC of Ara-U to the AUC of Ara-C was 0.08, indicating only minor metabolism of Ara-C to Ara-U in CSF, in contrast to that after systemic Ara-C. Despite initial CSF Ara-C concentrations exceeding 2 mM, Ara-C was not detectable in plasma in any patient. Intraventricular Ara-C results in very high levels in CSF, but systemic tissues are relatively spared from exposure to Ara-C.

The presence of two tightly bound Zn2+ ions is essential for the structural and functional integrity of yeast RNA polymerase II.

DNA-dependent RNA polymerases (RNApol) are Zn2+ metalloproteins where the Zn2+ ion plays both catalytic and structural roles. Although the ubiquitous presence of Zn2+ with the RNApol from eukaryotes had already been established, the exact stoichiometry of Zn2+ ion(s) per mole enzyme is not well documented, and its role in enzymatic function remains elusive. We show here that RNApolII from Saccharomyces cerevisiae has two Zn2+ ions tightly associated with it which are necessary for its transcriptional activity. Upon prolonged dialysis against 10 mM EDTA for 4-5 h, the enzyme loses one Zn2+, as well as partial activity. However, Zn2+ can be added back to the enzyme, but without recovering its total activity. 5 mM orthophenanthroline (OP) removes one Zn2+ within 2 h; the enzyme, however, cannot be reconstituted back with Zn2+. Circular dichroism (CD) studies showed that the conformation of the native enzyme is unique and cannot be reproduced with Zn2+-reconstituted RNApolII. Similarly, the rate of abortive synthesis of a dinucleotide product over a non-specific template is faster when catalyzed by two Zn2+-native enzymes. Zn2+-reconstituted RNApolII or one Zn2+-RNApolII showed a slower abortive synthesis rate. 65Zn2+-blotting experiments indicated that the removal of one Zn2+ from the enzyme destroys the Zn2+-binding ability of the larger subunits of yeast RNApolII. In order to check whether the presence of Zn2+ ions has any effect on substrate recognition, we followed the binding of (gamma-AmNS)UTP, a fluorescent substrate analog to RNApolII. It was observed that OP-treated enzyme showed non-specific substrate recognition, whereas two Zn2+-native RNApol binds substrate at a single site.

Terbium(III)-induced conformational transition in poly(dG-dC) fluorescence and circular dichroic studies.

Poly(dG-dC) in 60% aqueous alcohol exhibits the characteristic inversion of the circular dichroism spectrum associated with the formation of left-handed helix. Upon complexation with Tb3+, poly(dG-dC) in this medium induces marked enhancement of the Tb(III) fluorescence emission at 488 and 545 nm, when excited at 290 nm. The degree of fluorescence enhancement is dependent on the concentration of Tb(III) at a fixed poly(dG-dC) concentration. Neither poly(dG-dC) in water nor poly(dA-dT) in water or 60% alcohol, causes any significant fluorescence spectral changes of Tb3+. Tb(III)-poly(dG-dC) in 60% alcohol shows circular dichroic spectra associated with a broad positive molar ellipticity ranging from 6000 to 10 000 degree X cm2 X dmol-1 between 270 and 280 nm, and a small negative band around 240 nm.

Spectroscopic studies on the mode of binding of ATP, UTP and alpha-amanitin with yeast RNA polymerase II.

The binding affinity between the substrates ATP and UTP with the purified yeast RNA polymerase II have been studied here in the presence and absence of Mn2+. In the absence of template DNA, both ATP and UTP showed tight binding with the enzyme without preference for any specific nucleotide, unlike Escherichia coli RNA polymerase. Fluorescence titration of the tryptophan emission of the enzyme by nucleoside triphosphate substrates gave an estimated Kd value around 65 microM in the absence of Mn2+ whereas in the presence of Mn2+, the Kd was 20 microM. The effect of substrates on the longitudinal relaxation of the HDO proton in enzyme-substrate complex also yielded a similar Kd value.

Inhibition of the first phosphodiester bond formation catalyzed by Escherichia coli RNA polymerase in the presence of bovine seminal plasmin: promoter dependency.

Inhibition of the abortive initiation of transcription catalyzed by E. coli RNA polymerase has been studied here in the presence of bovine seminal plasmin. Seminal plasmin, which is known to be a stronger inhibitor than rifampicin binds at the same site as rifampicin to RNA polymerase. However, unlike rifampicin, seminal plasmin showed the inhibition of the formation of both the first and second phosphodiester bonds. We observed, in vitro, that the degree of inhibition of transcription was different at different promoters. Thus, the percent of inhibition of transcription initiation by seminal plasmin was much less at r-RNA promoters in comparison to that at the early promoters of bacteriophage T7.

DNA intervention in transcriptional activation.

Accurate initiation of eukaryotic mRNA synthesis takes place as a result of the interplay between general transcription factors and RNA polymerase II. Activation of transcription from the basal level involves a number of promoter-specific trans-acting factors which interact with cis elements in the promoter DNA. In this paper we have emphasized the importance of even those portions of the promoter stretch which do not have any identifiable binding sites for regulatory proteins. The length and structure of the DNA between cognate binding sites of trans-acting factors may interfere with the level of transcriptional activation. Depending upon the length of the intervening DNA we describe three cases of transcriptional activation. In addition, based on this classification we propose a new third domain, the other two being DNA binding and transcriptional activation domains, which is involved in bending the intervening DNA so that activation from a distance can take place successfully.

Interaction of bovine seminalplasmin with Escherichia coli RNA polymerase in the presence of rifampicin.

The interaction of bovine seminalplasmin and rifampicin with E. coli RNA polymerase was studied using fluorescence spectroscopy. Both seminalplasmin and rifampicin are known to be the inhibitors for the initiation of RNA synthesis in E. coli. Rifampicin quenced the intrinsic fluorescence of RNA polymerase and seminalplasmin when excited at 280 nm. However, excess of seminalplasmin reversed the quenching of RNA polymerase fluorescence by rifampicin. Upon addition of rifampicin to the seminalplasmin-RNA polymerase complex, no change in fluorescence spectrum was observed. It appeared that although rifampicin could form complexes with RNA polymerase and seminalplasmin alone, no binding domain was available for rifampicin in the RNA polymerase-seminalplasmin complex. These observations are discussed in the light of the 'initiation site' of E. coli RNA polymerase.

Interaction of bacteriophage T4 AsiA protein with Escherichia coli sigma70 and its variant.

Bacteriophage T4 produces a small protein AsiA, which inhibits transcription from sigma70-dependent promoters in E. coli by tightly binding to sigma70 and is therefore termed as anti-sigma factor. We observed that there was no inhibition of single round transcription at lac UV5 promoter when AsiA was added to preformed open complex between RNA polymerase and template DNA. However, transcription was found to proceed normally at 'extended -10' promoters in the presence of AsiA. It appears therefore that AsiA binds sigma70 at its 4.2-subdomain or in its close vicinity. Further experiments on immunoprecipitation of sigma70 and a mutant sigma70-V576G with AsiA seem to corroborate such conclusion.

Detection of putative Zn(II) binding sites within Escherichia coli RNA polymerase: inconsistency between sequence-based prediction and 65Zn blotting.

The availability of repeating 'Cys' and/or 'His' units in a particular order prompts the prediction of Zn(II) finger motifs in a protein. Escherichia coli RNA polymerase has two tightly bound Zn(II) per molecule of the enzyme as detected by atomic absorption spectroscopy. One Zn(II) was identified to be at the beta subunit, whereas the other putative Zn(II) binding site has recently been predicted to be at the N-terminal half of the beta' subunit, from primary sequence analysis. We show here that the beta' subunit has no ability to bind 65Zn(II). On the other hand, the N-terminal domain of the alpha subunit has strong Zn(II) binding ability with no obvious functional implications.

Differential inhibition of abortive transcription initiation at different promoters catalysed by E. coli RNA polymerase. Effect of rifampicin on purine or pyramidine-initiated phosphodiester synthesis.

The action of rifampicin on the RNA chain initiation catalysed by E. coli RNA polymerase over different templates has been studied. The steady-state formation of dinucleoside tetraphosphate under the condition of abortive initiation reaction was assayed. It was observed that rifampicin shows a spectrum of inhibitory effects on transcription initiation at different promoters. At two different promoters with a pyrimidine nucleotide at the 5'-initiation site, e.g. rrnB P2 having CTP and lacP2 having UTP, the effect of rifampicin on the abortive synthesis of the first phosphodiester bond was found to be total, even at low concentrations of the antibiotic. On the other hand, in most cases the effect of rifampicin on the abortive synthesis with a purine nucleotide at the 5'-initiation site was found to be only partial, with the exception of the T7A2 promoter, where rifampicin stimulates the abortive synthesis of pppGpC. It was also noticed that if there was a purine nucleotide at the second position of a dinucleotide which had already been synthesised by the enzyme, then further addition of the third nucleotide was not blocked in the presence of rifampicin. It appeared that a purine nucleotide at the initiation site or at the product terminus site of a translocated dinucleotide behaved similarly towards rifampicin. In the same way, if this position was occupied by a pyrimidine, rifampicin would inhibit further phosphodiester synthesis, even at a very low concentration. The stimulatory effect of rifampicin at the T7A2 promoter was presumably because here a ternary complex containing the promoter, enzyme and the abortive transcript pppGpC was initially stable, but dissociated upon addition of rifampicin, resulting in the rapid turn-over of the product.

Bovine seminalplasmin [corrected] is a DNA unwinding protein.

The duplex DNA unwinding ability of seminalplasmin [corrected] from bovine semen was examined by treatment of plasmid-protein complexes with calf thymus topoisomerase I and resolution of the topoisomer distributions by agarose gel electrophoresis. Binding of seminalplasmin [corrected] results in a moderate degree of unwinding of supercoiled plasmid. The elongation of the RNA chain by E. coli RNA polymerase over promoter containing template is not inhibited by seminalplasmin [corrected]. However, the reinitiation of transcription is blocked in such cases indicating that seminalplasmin [corrected] inhibits transcription by binding to the initiation site of RNA polymerase.

Correlation between the DNA supercoiling and the initiation of transcription by Escherichia coli RNA polymerase in vitro: role of the sequences upstream of the promoter region.

Binding of Escherichia coli RNA polymerase and the abortive initiation of transcription at the A2 promoter of bacteriophage T7, separately cloned in pBR322, was found to be strongly dependent on the degree of supercoiling of the plasmid. Supercoiling does not seem to play any role in the initiation of transcription at the T7A1 promoter under identical conditions. Plasmid containing T7A2 promoter was found to be less amenable to S1 nuclease in comparison to that having T7A1. Sequence comparison reveals a high G/C content upstream to the -35 region of T7A2 which by extra duplex stability probably renders the initiation of transcription more dependent on the state of supercoiling of the template.

Guanosine tetraphosphate-induced dissociation of open complexes at the Escherichia coli ribosomal protein promoters rplJ and rpsA P1: nanosecond depolarization spectroscopic studies.

We have measured the fluorescence anisotropy decays of various transcription complexes formed between Escherichia coli RNA polymerase (RNAP) and the rplJ, rpsA P1 and lacUV5 promoters, where the sigma 70-subunit of RNAP is covalently labeled with the fluorescent probe 1,5-IAEDANS. The observed changes in the rotational correlation times (phi r) of the sigma 70-bound probe upon ppGpp or NTP addition to preformed open complexes, were used to directly infer the extent of association of the sigma-subunit with these transcription complexes. At the rplJ and rpsA P1 promoters, the addition of ppGpp (in the absence of heparin and nucleotides), results in the dissociation of RNAP from the binary complex. This is either accompanied by, or leads to the dissociation of a fraction of the holoenzyme-bound sigma 70. At the lacUV5 promoter, only a marginal dissociation of RNAP is observed. We propose a model where two types of ppGpp-bound RNAP interact with the ribosomal protein promoters. One is transcription-competent and releases sigma 70 upon elongation, while the other dissociates from the open complex. A fraction of the latter species releases the sigma 70 subunit and is unable to form a transcription-competent holoenzyme. Our data supports the mechanism of open complex-destabilization at stringent promoters by ppGpp.

The differential effects of guanosine tetraphosphate on open complex formation at the Escherichia coli ribosomal protein promoters rplJ and rpsA P1.

The effects of guanosine tetraphosphate (ppGpp) on inhibition of single-round in vitro transcription and on the kinetics of open complex formation were investigated at the Escherichia coli ribosomal protein promoters rplJ and rpsA P1. The two promoters differ in their saturation characteristics and sensitivities to ppGpp. With a 10:1 molar ratio of RNA polymerase (RNAP) to DNA, saturation of transcription activity and weak inhibition (approximately 30%) are observed at rplJ, in contrast to the weak activity and strong inhibition (approximately 80%) at rpsA P1. In the absence of ppGpp, the two promoters show a threefold difference in the overall rate constants of association (ka) (6.5 x 10(7) M-1 s-1 at rplJ and 2.0 x 10(7) M-1 s-1 at rpsA P1), while the dissociation rate constants (kd) are similar (approximately 4.8 x 10(-5) s-1). The addition of ppGpp causes a twofold reduction in k2 (isomerisation constant) rplJ and a threefold decrease in KB (equilibrium constant of RNAP binding) at rpsA P1. There is a significant twofold increase in kd at rplJ, compared with smaller changes at rpsA P1 and at the non-stringent lacUV5 promoter. These results indicate that ppGpp affects the formation and stability of the open complex at the rplJ promoter, in contrast to the inhibition of RNAP binding to the rpsA P1 promoter.

Reduced systemic drug exposure by combining intra-arterial chemotherapy with hemoperfusion of regional venous drainage.

Four patients with malignant cerebral gliomas received 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU) into the internal carotid artery (ICA) while the ipsilateral jugular drainage was pumped extracorporeally through a hemoperfusion cartridge containing a nonionic adsorbant resin. Each patient received 220 mg/sq m BCNU, infused over 45 minutes through a toposcopic catheter positioned with the tip in the ICA beyond the origin of the ophthalmic artery. Jugular blood was pumped extracorporeally at 300 ml/min through a large-bore catheter in the jugular bulb. Plasma samples were obtained for BCNU measurement at frequent intervals from the right atrium. During a separate treatment, 6 weeks before or after the hemoperfusion treatment, the same dose of BCNU was infused into the ICA and atrial samples were obtained on a similar schedule. Hemoperfusion of the jugular blood during intracarotid infusion reduced the systemic exposure by 56% to 87% and increased total body clearance of BCNU by two- to eightfold. The calculated pharmacokinetic advantage (brain:body exposure ratio) was between 21 and 55:1 when the combined treatment was used.