Effect of circularity and superhelicity on transcription from bacteriophagelambda DNA

Torsional stress and local denaturation in supercoiled DNA

It is shown that local denaturation can be a natural consequence of supercoiling, even in environments where base pairing of linear DNA is energetically favored. Any change in the molecular total twist from its unstressed value is partitioned between local denaturation and smooth twisting in both the native and coil regions so as to minimize the total conformational free energy involved. Threshold degrees of torsional deformation are found for the existence of stable, locally melted conformations. As these thresholds are surpassed, the number of denatured bases increase smoothly from zero. Existing experimental evidence regarding denaturation in supercoiled DNA is in good agreement with the predictions of this theory. In addition, from existing data one can estimate the partitioning of superhelicity between twisting and writhing. Possible consequences of stress-induced strand separation on the accessibility of the DNA to enzyme attack are discussed. Control of local melting by DNA topoisomerases and DNA gyrases could regulate diverse events involved in transcription, replication, recombination, and repair.

Modulation of gene expression by drugs affecting deoxyribonucleic acid gyrase

Nalidixic acid (Nal), a drug which affects deoxyribonucleic acid gyrase activity, inhibits the expression of catabolite-sensitive genes: the three maltose operons, the lactose and galactose operons, and the tryptophanase gene. A correlation between the degree of sensitivity to Nal and that to catabolite repression has been observed. The expression of the threonine and tryptophan operons, insensitive to catabolite repression, is insensitive to Nal. The expression of the lacZ gene under the control of the IQ promoter is activated by Nal. Strains carrying a mutation in the nalA locus are resistant to these effects. Novobiocin, which inhibits the negative supercoiling activity of deoxyribonucleic acid gyrase, affects expression of the operons similarly to Nal. The involvement of promoters in Nal and novobiocin action, as well as a possible role of in vivo negative supercoiling in the selectivity of gene expression, are discussed.

Fluctuations in superhelical DNA

The effect of superhelicity on the base-pair opening probability and on the probability of occurrence of cruciform states in palindromic regions is theoretically treated. The calculations show that below the superhelix density value of -sigma=0.05 superhelicity does not appreciably affect the characteristics of DNA secondary structure fluctuations. In the range of physiological superhelix densities sigma (-sigma=0.05-0.09) the base-pair opening probability markedly increases. However, within this range of sigma the base-pairs are opened only transiently and permanently open regions are not formed. Permanently opened regions appear at higher negative superhelix densities (-sigma greater than 0.10). At the values of -sigma higher than 0.06 a cruciform structure in the palindromic region centred in position 3965 proves to be the most probable fluctuational disturbance in the 0x174 duplex DNA. Different experimental approaches used for probing the fluctuations in superhelical DNA have been analysed. The results suggest that most direct quantitative information can be derived from data on the nicking of closed DNA by single strand-specific endonucleases. Such data (Wang, 1974) accord with the results of theoretical calculations. Calculations show that, due to base-pair opening, the total free energy of superhelical DNA should depend parabolically on sigma only up to some critical value of sigma=sigmac. If negative superhelicity exceeds this critical value, which under physiological conditions proves to be -sigma=0.085, the free energy should increase linearly with -sigma. The biological role of supercoiling is discussed in the light of obtained results.

Involvement of DNA gyrase in replication and transcription of bacteriophage T7 DNA

Growth of bacteriophage T7 is inhibited by the antibiotic coumermycin A1, an inhibitor of the Escherichia coli DNA gyrase. Since growth of the phage is insensitive to the antibiotic in strains containing a coumermycin-resistant DNA gyrase, this enzyme appears to be required for phage growth. We have investigated the effect of coumermycin on the kinetics of DNA, RNA, and protein synthesis during T7 infection. DNA synthesis is completely inhibited by the antibiotic. In addition, coumermycin significantly inhibits transcription of late but not early genes. Thus, E. coli DNA gyrase may play an important role in transcription as well as in replication of T7 DNA.

The interaction of RNA polymerase II from wheat with supercoiled and linear plasmid templates

Interactions between a plant RNA polymerase II and ColE1 based plasmid DNA templates have been studied. Gel electrophoresis indicates that the enzyme binds to both supercoiled and linear species. Using the totally double stranded pMB9/SmaI fragment it is shown that transcription of completely base paired DNA is ten-fold lower than that of denatured or supercoiled plasmid, and reflects the presence of fewer initiation sites. A small proportion of the transcript remains tightly bound to supercoiled templates. 3' oligodeoxycytidine extensions on pMB9/SmaI serve to promote transcription of the linear double stranded form. Using restriction kinetics it is shown that there is a small enhancement of polymerase binding at the pMB9 tetracycline promoter, but that the selectivity of binding at this locus is lower than for the natural bacterial polymerase.

Novel template requirements of N4 virion RNA polymerase

A DNA-dependent RNA polymerase has been purified from disrupted virions of the Escherichia coli bacteriophage N4. The RNA polymerase is phage-coded and is required for class I N4 RNA synthesis, which is defined as RNA synthesized in vivo in the absence of post-infection protein synthesis. A polypeptide of molecular weight 350,000 is detected when the purified enzyme is analyzed by sodium dodecyl sulfate/polyacrylamide gel electrophoresis. N4 RNA polymerase requires denatured DNA as a template in vitro and shows a strong preference for denatured N4 DNA. With this template, transcription is asymmetric. The RNA product is complementary to only the H strand of N4 DNA. Furthermore, only class I N4 RNA is synthesized. In vivo transcription by the N4 virion RNA polymerase is inhibited by coumermycin. This result suggests that the activity of E. coli DNA gyrase, an enzyme that introduces negative supertwists into DNA, is required for N4 transcription.

Assembly of new nucleosomal histones and new DNA into chromatin

The assembly of chromatin from newly synthesized nucleosomal histones (labeled with [3H]arginine) and new DNA (density-labeled with [125I]iododeoxyuridine)was studied in growing cultured mouse cells. The nucleosomal histones were specifically examined by dissociating histone H1 and nonhistone proteins from unsheared chromatin either by incubation in 0.6 M NaCl or by digestion with micrococcal nuclease to release nucleosomes. In both cases, the four nucleosomal histones (H2A, H2B, H3, and H4) are essentially the only proteins that remain bound to DNA and that are labeled by [3H]arginine. After formaldehyde fixation, H1-depleted chromatin containing dense DNA can be completely resolved in CsCl buoyant density gradients from that containing unreplicated DNA; separation of nucleosomes is satisfactory although less complete. New DNA and new histones are already assembled into chromatin possessing characteristic nucleosomal structure after 3 min of synthesis (the shortest time studied), as shown by the kinetics of digestion of new DNA by micrococcal nuclease, by the distribution of new DNA and new histones in nucleosomes. However, after 3-30 min of synthesis most new nucleosomal histones are associated with unreplicated DNA rather than with new DNA. It is concluded that new nucleosomes are assembled on DNA at some distance from DNA replication sites, with concomitant migration of preexisting nucleosomes onto new DNA.

Effect of chemical modification of supercoiled simian virus 40 DNA on the rate of in vitro transcription

Superhelical simian virus 40 FI DNA could be modified with the single-strand-specific reagent N-cyclohexyl-N'-beta-(4-methylmorpholinium)ethylcarbodiimide (CMC). A limited reaction, of less than 2% of the base pairs, resulted in almost total inhibition of in vitro transcription by DNA-dependent RNA polymerase from Escherichia coli. This effect was shown to be due to DNA modification and not to inhibition of polymerase activity by the reagent. Inhibition of enzyme activity occurred if the contaminating reagent was not absorbed with another protein before polymerase addition. No inhibition was observed when DNA and polymerase were incubated together to allow the formation of pre-initiation complexes before CMC was added. Studies of template saturation with polymerase showed that the inhibition of transcription by DNA modification was due to a loss of binding ability of the enzyme to the reacted, supercoiled DNA when reaction times of less than 2 h were used.

Binding and transcription of simian virus 40 DNA by DNA-dependent RNA polymerase from Escherichia coli

Supercoiled simian virus 40 was transcribed more efficiently than nonsupercoiled DNA. The effect was increased from two- to fivefold by the addition of rifampin with triphosphates. The number and locations of polymerase binding sites with respect to Hin II-III restriction fragments were determined. The total number of binding sites was nine, as determined by UV difference spectroscopy. The locations of these binding sites were on the A, B, D, E, F, and G fragments, as determined by gel electrophoresis. The number of sites was the same for both supercoiled and relaxed or Hin II-III-digested DNA, and the point of saturation of supercoiled DNA by polymerase remained the same with increasing concentrations of rifampin from 0 to 8 microgram/ml.

Electron microscopy analysis of the interaction between Escherichia coli DNA-dependent RNA polymerase and the replicative form of phage fd DNA. 1. Mapping of the binding sites

The interaction of Escherichia coli DNA-dependent RNA polymerase (EC 2.7.7.6) with the replicative form of the DNA from the filamentous coliphage fd cleaved by the restriction endonuclease HindII has been studied by electron microscopy at low and high ionic strength. In the presence of ATP or GTP, and heparin, RNA polymerase binds to fd replicative-form DNA at a few specific sites which have been mapped. The map was oriented so that transcription is from right to left. Three main GTP initiator sites are found at 15%, 82% and 94% of the genome length. One main ATP initiator site is found which cannot be mapped with the same accuracy, and which is localized between 38% and 50%. In the absence of initiator triphosphates and heparin, the binding of the enzyme to fd DNA is much more heterogeneous and therefore the mapping is more difficult. Nevertheless it seems that the preferential binding regions correspond to the specific sites mapped in the presence of GTP or ATP. The mean number of polymerase molecules bound to DNA as a function of the molecular ratio enzyme to DNA present in the mixture has been determined. From these results a binding isotherm can be obtained. The apparent equilibrium constant (K approximately 10(9) M-1) which is derived certainly represents an under-estimated value, as discussed.

Inhibition of transcription of supercoiled PM2 DNA by carbodiimide modification

PM2 superhelican DNA (form I), which as been reacted with the single strand specific reagent, N-cyclohexyl-N'-beta-(methylmorpholinium)ethyl carbodiimide (CMC) is more than 95% inhibited in its ability to support transcription with E. coli B RNA polymerase in vitro. Almost complete inhibition of transcription was achieved after 2 hours of reaction with FI when only 1% of the bases were modified. A large increase in S20,* (from 26.8 S to 33.6 S) of FI DNA was observed during the course of reaction. Rifampicin resistant transcription is more susceptible to inhibition by CMC than total transcription, suggesting that the CMC is preferentially binding at promoter sites. These results clearly are in accord with the observation that supercoiled DNA contains localized regions of unpaired bases. The promotor sites for E. coli RNA polymerase in FI PM2 DNA appear to be located at or near these unpaired sites.

Specificity of initiation of transcription of simian virus 40 DNA I by Escherichia coli RNA polymerase: identification and localization of five sites for initiation with [gamma-32P]ATP

Simian virus 40 (SV40) DNA I was transcribed with Escherichia coli RNA polymerase in the presence of gamma-32P-labeled ribonucleoside triphosphates in order to investigate the specificity of initiation of in vitro transcription. ATP and GTP served as predominant initiating nucleotides, the former being incorporated about twice as much as the latter. Cleavage of [gamma-32P]ATP-labeled SV40 complementary RNA (cRNA) with T1 RNase followed by homochromatographic analysis of the resultant 5' initiation fragments revealed the presence of four specific initiation fragments 6 to 9 nucleotides in length, designated AI, AII, AIIIa, and AIIIb. By means of hybridization of [gamma-32P]ATP-labeled SV40 cRNA to DNA from specific adenovirus 2-SV40 hybrids and specific restriction endonuclease fragments of SV40 DNA before chromatographic analysis, it was possible to identify and determine approximate localizations of five [gamma-32P]ATP initiation sites on the SV40 genome: one in Hin-G close to the Hin-G-B junction, giving rise to the AII fragment, two in the overalpping fragment Hin-A-Hae-A,giving rise to AI and AIII fragments, and two in the fragment Hin-A-Hae-E, also giving rise to AI and AIII fragments. All five sites either fall within or lie near regions of the genome that are cleaved by S1 nuclease and subject to partial alkaline denaturation. These five sites lie on the minus strand of SV40 DNA and initiate RNAs that are copied in a leftward direction. Cleavage of [gamma-32P]GTP-labeled cRNA with pancreatic RNase liberated three major 5' initiation fragments of short length, GI, GII, and GIII, suggesting the presence of three principal GTP initiation sites.

In vitro transcription of the ribosomal RNA genes of E. coli DNA

Bacterial ribosomal RNA synthesis was studied in an in vitro system in which the presence of heparin prevented reinitiation of transcription. The number of heparin-resistant binary complexes of RNA-polymerase and E. coli DNA depended strongly on the quality of the template. High-molecular weight DNA was a much superior template than DNA prepared by conventional techniques. Using this high-molecular weight DNA as template the amount of ribosomal RNA synthetized in one round of transcription was found to be 4-5 fold higher than the amount of rDNA present. Controls have shown that the transcription probably started at the proper initiation sites and no significant read-through form distant promoters contributed to this effect. If the binary polymerase-DNA complexes were dissociated in the presence of 0.5 M KC1 prior to transcription all RNA synthesis was strongly reduced but the proportion of rRNA increased in the transcript. However, in this case the amount of rRNA did not exceed the amount of rDNA. We propose that the promoters of the rRNA genes are complex structures, able to store 4-5 molecules of RNA polymerase and of these several polymerase only one is bound in an extremely salt-resistant form.

Hin D restriction mapping of upaired regions in simian virus 40 superhelical DNA I: considerations regarding structure-function relationships

Superhelical simian virus 40 (SV40) DNA I was reacted with N-cyclohexyl-N'-beta-(4-methylmorpholinium)ethylcarbodiimide (CMC), and the location of CMC sites was mapped using the Hin D restriction endonuclease. The use of 14C-labeled CMC allows a quantitative analysis of the binding to the respective Hin D restriction endonuclease fragments. The percentage of reactivity was 6.54% for fragment A, 3.87% for fragment B, and 2.74% for fragment G. No CMC radioactivity was detected in other fragments. This reactivity is in agreement with the evaluation of binding by buoyant density measurements. The above fragments also contain the sites susceptible to S1 endonuclease action. This adds further support to the view that superhelical DNA can contain regions of localized interrupted secondary structure which may be capable of forming intrastrand hairpin structures if sequence relationships are favorable. The possible structure-function relationships for this model are discussed with the emphasis on transcription.

Conformational analysis of deoxyribonucleic acid from PM2 bacteriophage. The effect of size on supercoil shape

Laser light-scattering studies of bacteriophage PM2 DNA showed the molecule to have mol.wt. 5.9 X 10(6) and root-mean -square radius 125 nm at an ionic strength of 0.2 mol/litre. Computer-generated curves compatible with these data were compared with the experimental interference curve for several structural models of the molecules. The data fit best to an asymmetric four-armed planar molecule in which all four arms emerge from or close to the one area of the molecule. This contrasts with the smaller DNA molecules investigated, which have shown a three-armed molecule, whose symmetry varies with primary structure.

Tertiary structure and function of closed-circular mitochondrial DNA and its transcription in vivo

The conformation of the closed circular mitochondrial DNA in cultured human cells is changed by the addition of berenil to the culture medium in such a way that the 34-S mitochondrial DNA is converted into a 29-S DNA and finally into a 24-S DNA. The superhelix density of the covalently closed 29-S mitochondrial DNA is sigma O = -1.5 times 10(-2) (turns/10 base pairs) and consequently is intermediate between the superhelix density of the 34-S DNA (sigma0 = -2.8 times 10(-2)) and that of the closed circular 24-S DNA (sigmao appromiately 0). Removal of the drug reverses the transition, covalently closed circular 34-S DNA to covalently closed circular 29-S DNA to covalently closed circular 24-S DNA. The covalently closed circular 24-S mitochondrial DNA is not replicated. Transcription of this DNA is also inhibited as indicated by the fact that no synthesis of the mitochondrial ribosomal RNAs occurs as long as the mitochondrial DNA is in this conformation. The covalently closed circular 29-S mitochondrial DNA is replicated but not transcribed in vivo.

Interaction of f1 histone with superhelical DNA

The superhelicity of double-stranded, closed circular SV40 DNA was altered by the addition of various amounts of ethidium bromide. The interaction of f1 histone with the series of molecules of various superhelicities was studied. The extent of interaction increases with increasing superhelicity regardless of whether it is of the positive or negative sense. The interaction of f1 histone with superhelical DNA is shown to be reversible.

The activation of RNA polymerase by alkylammonium ions

Tetramethylammonium and tetraethylammonium ions both lower the melting temperature of DNA. We have shown that these ions increase the activity of E. Coli RNA polymerase. When the base composition of the DNA template was varied, there was a correlation between the decrease in melting temperature and increase in RNA polymerase activity. No stimulation was observed when heat denatured DNA was used as template. It was shown that initiation of RNA synthesis was stimulated but to a smaller degree than was total RNA synthesis. The lag observed at low temperatures before RNA synthesis commences was found to be shorter in the presence of these alkyl ammonium ions. All these results are consistent with an unwinding of the double helix being an important step in transcription.

Synthesis in vitro of phi29-specific early proteins directed by phage DNA

The RNA and proteins synthesized in an Escherichia coli cell-free system of protein synthesis directed by Bacillus subtilis phage phi29 DNA were studied. Hybridization-competition experiments showed that most of the RNA species synthesized in vitro are early RNAs. Many of the early proteins induced after phage infection were also synthesized in the E. coli cell-free system. None of the late proteins, structural or non-structural, were synthesized in the system in vitro.