[Coupling of bacteriophage T7 DNA penetration with its transcription, during infection]

Further research on bacteriophage T7 DNA penetration mechanism into E. coli cells during the infection was carried out. The DNA-RNA-hybridization on nitrocellulose filters revealed that in the presence of chloramphenicol the T7 DNA penetration from the virion into a host cell was coupled with its transcription by the bacterial RNA polymerase. The data obtained indicate that in the absence of antibiotics the penetration of a part of T7 genome which correspondes to class II and III genes is coupled with its transcription by a phage-specific RNA polymerase. Along with this the host restriction-modification system when its activity is not inhibited by the phage-induced proteins will be able to cleave the penetrated T7 DNA just after its transcription was accomplished. Considering these data along with our conception on direct involvement of transcription in T7 DNA penetration process during the infection one can suggest that E. coli RNA polymerase molecules which provide the phage DNA transport, are localized at the inner surface of cytoplasmic membrane.

RNA polymerase-dependent mechanism for the stepwise T7 phage DNA transport from the virion into E. coli

The influence of rifampicin, streptolydigin, tetracycline and chloramphenicol on phage DNA transport from the T7 virion into the E. coli cell was studied. It has been found that the DNA transport proceeds in at least three stages. During the initial stage the phage injects into the host cell the left approximately 10 per cent of its DNA molecule. The entrance of the next 50 per cent of 17 DNA molecule is blocked by inhibitors which block transcription but not translation. Moreover, the entrance time of this part of the T7 DNA increases in the case of the T7 mutant D111 (which contains a deletion of the A2 and A3 promoters) and decreases in the case of the D53 mutant (which contains a deletion in the region of the early gene transcription terminator). It would appear, that the second stage of the phage DNA transport is tightly coupled with its transcription and that a mechanical function is carried out by RNA polymerase. The translation inhibitors completely block the entrance of the remaining 40 per cent of the 17 DNA molecule (class III genes) into the host cell. It would appear that some class I and (or) II gene product(s) are obligatory components of the final stage of 17 DNA transport. Some probable consequences of this virus DNA transport model as well as its agreement with the functional structure of T7 chromosome and with T7 development are discussed.

[Discontinuous transfer of phage T7 DNA molecules into Escherichia coli cells during infection]

HpaI restriction analysis of the part of T7 DNA molecule which comes off from E. coli after ultrasonic desorption of virion had been carried out. In such a way it was possible to follow the transfer of labelled T7 DNA into the host cell after the phage adsorption under different conditions. It was established that in the presence of chloramphenicol the left 60% of T7 chromosome is gradually (during 20 min) transferred into the cell and further transport is stopped. This suggests that some T7 gene(s) of I or (and) II class(es) is (are) necessary to transfer the last 40% of T7 DNA molecule containing the genes encoding capsid proteins. Also some new results are obtained which support thr idea about the tight coupling of the processes of T7 DNA transport and its transcription, and about the possibility for RNA polymerase to carry a mechanical function as well. All these results suggest a rather complicated mechanism of the process of T7 DNA transfer into the host cell consisting of at least three stages tightly connected with T7 gene expression temporal control. Some probable consequences of this model as well as its agreement with functional structure of T7 chromosome and with T7 development are discussed.

[Kinetic determination of the non-specific constants for the binding of Escherichia coli RNA polymerase to T7 phage DNA]

The kinetics of promoter complex formation of E. coli RNA polymerase with T7 phage DNA was studied under different ionic strengths at DNA concentrations 0.15, 1.5 and 20 microns/ml. Based on the results obtained the non-specific binding constants, Keq, and the promoter complex formation rate constants, kp, were estimated. Within ionic strength range 0 + 125 mM NaCl the Keq and kp vary from 5.10(6) to 9.10(5) M-1 and from 0.8 x 0.26 x 10(9) M-1 S-1, respectively. The results are discussed from the view point of the one-dimensional diffusion sliding of the enzyme along DNA in the process of phomoter site selection.

[Gradual penetration of T7 phage DNA molecules into Escherichia coli cells during infection in the presence of chloramphenicol]

The cell-attached T7 phage DNA has been analyzed when E. coli was infected in the presence of chloramphenicol or rifampicin followed by sonication to provide phage desorption. Sucrose gradient sedimentation of the cell T7-DNA followed by HpaI digestion and agarose gel electrophoresis were performed. The results obtained suggest a gradual entrance of the T7-DNA molecule into the host cell starting on its left end bearing early genes. These data support the conception that the T7-DNA entrance into host cell is directly coupled with its transcription by RNA polymerase. At the same time one more HpaI fragment was found even in the cells, infected with the phage in the process of rifampicin. It may be that this fragment corresponds to the right end of the T7 chromosome, thus suggesting that short fragment of the T7-DNA right end can also enter the host cell early in infection.

On the promoter complex formation rate of E. coli RNA polymerases with T7 phage DNA

Influence of ionic strength on the kinetics of the promoter complex formation between E. coli RNA polymerase and T7 phage DNA was investigated using a membrane filter assay. The enzyme-promoter association rate constant was determined. It varies from 10(9) to 3 x 10(7) M-1 sec-1 when the ionic strength is changed from zero to 0.15 M NaCl. Basing on the theoretical analysis of experimental data obtained the model for the promoter site selection assuming the enzyme sliding along the DNA is discussed.

Circular dichroism anisotrophy of DNA with different modifications at N7 of guanine

The complexex DNA-Ag1+, DNA-Cu1+, protonated DNA and DNA methylated at N7 of guanine were oriented by pumping the solutions through a multicapillary cell in the direction of a light beam. The CD components along the DNA axis, delta epsilon parallel, and normal to it, 2 delta epsilon perpendicular, were calculated from the CD spectra of the oriented samples by the method of Chung and Holzwarth, (1975) J. Mol. Biol. 92, 449--466. It was shown that in most cases, except that of the protonated DNA, the degree of orientation was only slightly less than that for pure DNA. This demonstrated the absence of aggregation and of appreciable denaturation. In all cases the modifications of DNA give rise to a negative component 2 delta epsilon perpendicular, whose magnitude increased as the extent of modification increased. From both the CD spectra of non-oriented samples and the absorption spectra, an inference is drawn that Ag1+ and Cu1+ are attached to the same site as CH3 groups i.e., to the N7 atom of guanine. Proton transfer along the H-bond from the N1 atom of G to the N3 atom of the complementary cytosine is suggested to be a result of the modifications, although the case of H+-DNA may differ from the others. Based on the CD spectra for the anisotropic components, delta epsilon parallel and 2 delta epsilon perpendicular, it is proposed that ligand binding is accompanied by winding of the DNA helix.

[Transcription initiation: influence of ionic strength and actinomycin D on the kinetics of the open promoter complex formation between Escherichia coli RNA-polymerase and T7 DNA]

A membrane filter assay has been devised to study the influence of ionic strength (0--150 mM NaCl) and actinomycin D on the kinetics of the open promoter complex formation between E. coli RNA-polymerase and [3H]DNA of T7 phage. The dependence of the complex formation rate upon the ionic strength is non-monotoneus with a maximum at 75--100 mM. The addition of one actinomycin molecule per 200 base pairs decreases the open promoter complex formation rate at ionic strength less than 100 mM. A promoter site selection model including liner diffusional selection is proposed which is in a good agreement with the experimental results obtained.

On the flexibility of the boundaries between the A-form and B-form sections in DNA molecule

The degree of orientation of DNA in a flow has been studied within the interval of the B - A transition induced by ethanol. The orientation of the B DNA (60-65% ethanol, v/v) and that of the A DNA (80-82% ethanol) are nearly identical. This means that both conformations have similar persistence lengths and that there is no aggregation in the course of formation of the A form. Within the transition range (65-78% ethanol) the orientation attains a sharp minimum which coincides with the half-transition point (73% ethanol). The cooperative character of the B - A transition presupposes the existence of boundaries between the alternating sections of the A and B conformations that may entail an increased flexibility of the DNA molecule and a corresponding drop of orientation. Theory predicts an elliptical dependence of the number of boundaries on the proportion of the A form. The experimental degree of orientation follows the same pattern. Quantitative evaluation shows that the flexibility of a boundary is small, so that several dozen of boundaries are required to simulate free rotation.

[Conformational transition of DNA within the B-family as revealed by anisotropy circular dichroism]

The native T2 DNA in solutions with different LiCl concentrations was oriented by pumping through a capillary device similar to that described in rf. 1. The change of the parallel, deltaepsilon parallel, and perpendicular, 2 delta epsilon perpendicular, components of circular dichroism tensor was studied as a function of salt concentration. Positive (delta epsilon parallel 280) and negative (2 delta epsilon perpendicular 280) components were shown to increase in absolute magnitude, so that there was a monotonous drop in the longwave band magnitude of the isotropic delta epsilon 280 as a result of compensation; the shortwave band magnitude of the isotopic delta 245 and its anisotropic components were constant. It is proposed that while the helix is winding as a result of LiCl rise progressive tilting of base pairs takes place. It was also shown that the glucosylated T2 DNA in solution is wound to a greater extent than the non-glucosylated DNA of the same GC-content.

Circular dichroism of DNA--proflavine, DNA--ethidium and DNA--distamycine flow--oriented complexes

The circular dichroism (CD) spectra of flow-oriented complexes of DNA with proflavine (PF), ethidium (ET) and distamycine (DS) have been studied in the ultraviolet region. The CD spectra with light propagating in parallel to the flow direction were measured by the method of Chung and Holzwarth [1]. Delta epsilon and delta epsilon values have been obtained by this method. It was shown that all the complexes studied exhibit a strong CD anisotropy so that "isotropic" CD spectra measured with a conventional procedure can be attributed to the mutual compensation of the two components of opposite signs.