Analysis of bacteriophage T4 chloramphenicol RNA by DNA-RNA hybridization and by cell-free protein synthesis, and the effect of Escherichia coli polarity-suppressing alleles on its synthesis

T4-induced antipolarity: temporal heterogeneity in response of early transcription units

When T4 infects Escherichia coli in the absence of protein synthesis, rho-mediated termination takes place on early polycistronic transcription units. During the early period of development, the appearance of delayed early transcripts becomes insensitive to the inhibition of protein synthesis. In the absence of the T4 gene product mot, an inducer for the middle mode of transcription, only the early polycistronic messengers are synthesized. In mot- -infected cells, the synthesis of the distal transcripts still becomes completely insensitive to the polar effect of chloramphenicol. This happens because potential rho-sensitive termination sites are not used in these cells. In this respect, overcoming polarity induced by chloramphenicol can be called a process of antitermination. The mot-independent antitermination can be studied by addition of chloramphenicol during infections with mot- bacteriophage. The effect is stable; it allows a constant percentage of rho-sensitive termination sites in the cell to be traversed by RNA polymerase for at least 10 min at 42 degrees C. By examining six different transcription units on the T4 genome, we find that each transcription unit has a cis-acting component (or components) which determines when its rho-sensitive termination site stops functioning. In extreme cases, rho acts with 100% efficiency in some transcription units, whereas it is almost inactive in others.

In vitro transcription of phage T4 late genes on purified DNA by partially purified RNA polymerase from T4-infected Escherichia coli b cells

RNA polymerase was purified from 'late' phage T4-infected Escherichia coli B cells by DNA-cellulose affinity chromatography and high salt agarose filtration. The DNA-cellulose-purified RNA polymerase preparation contained T4-coded DNA endonuclease activity and several proteins, some with sizes comparable with the known T4 maturation factors, essential for late RNA synthesis. Some of these proteins, and the DNA endonuclease utilizing native, parental T4 DNA and supercoiled phi X 174 DNA as substrates, were partially separated from the RNA polymerase as a complex during agarose filtration. In vitro RNA was made by the DNA-cellulose-purified RNA polymerase using native, parental T4 DNA as template. About 26% of the in vitro RNA was transcribed from the DNA r-strand; 75% from the same r-strand region as in vivo late after infection. Both the abundancy and specificity of the in vitro r-strand transcription were markedly reduced after agarose filtration of the enzyme. Addition of the proteins separated from the RNA polymerase during agarose filtration caused a restoration of in vitro r-strand transcription abundance, but not its specificity. These results show that partially purified RNA polymerase from T4-infected E. coli B cells was able to transcribe late T4 genes in vitro with some abundancy and specificity on purified, parental T4 DNA, but further purification of the enzyme caused an irreversible reduction of this ability.

Sizes of bacteriophage T4 early mRNA's separated by preparative polyacrylamide gel electrophoresis and identified by in vitro translation and by hybridization to recombinant T4 plasmids

We determined the sized of specific T4 prereplicative nRNA's by preparative polyacrylamide gel electrophoresis, and we used the following two techniques to identify specific gene transcripts; cell-free protein synthesis accompanied by sodium dodecyl sulfate-polyacrylamide gel electrophoresis to distinguish T4 polypeptides and hybridization to recombinant plasmids containing T4 DNA of known genetic composition. In our first analysis, the use of nonsense and in-phase deletion mutants allowed unambiguous identification of the functional transcripts that encoded genes 32, rIIB, and rIIA. In addition, we identified the functional transcript that encoded genes 43, 45, 30, 39, and 52, the beta-glucosyl transferase gene, and the deletion 293 region. A single peak of mRNA activity that coded for gp43, gp39, gprIIA, beta-glucosyl transferase, and the polypeptide encoded in the deletion 293 region was present; the other polypeptides were encoded in multiple mRNA species, gp46 and gp32 were encoded by two mRNA's and gp52 and gprIIB were encoded by three nRNA's. By hybridizing fractionated, pulse-labeled early RNA to cloned restriction fragments of T4 DNA, we identified the same specific transcripts for genes 43, 52, and rIIB. In addition, a lower-molecular-weight RNA (presumably degraded nRNA) was present even in pulse-labeled RNA preparations. The distribution of pulse-labeled RNAs that hybridized to gene 39, gene 30, gene rIIA, gene 40 plus gene 41, and gene 42 plus the beta-glucosyl transferase gene indicated extensive degradation. We detected cotranscription of genes rIIA and rIIB by rehybridization of RNA first annealed to an rIIB plasmid and then eluted and annealed to an rIIA plasmid. The size distributions of normal and chloramphenicol-treated RNAs that hybridized to plasmids containing T4 immediate early gene 30, gene 39, gene 40 plus gene 41, and gene 42 plus the beta-glucosyl transferase gene were not significantly different.

Physical properties of the complementary T4 RNA

The complementary transcribed T4 RNA after self-annealing and RNAase treatment was isolated by gel chromatography and then used for further studies. From salt-dependent RNAase resistance and melting studies it is evident that this RNA represents a genuine double-stranded structure. The base content of the isolated double-stranded RNA was found to be the same as total T4 mRNA. Sucrose gradient analysis and hydroxyapatite chromatography of T4 RNA, annealed early and late RNA, and of the isolated double-stranded RNA, gave results indicating that the complementary RNA is part of a RNA molecule and further that the size of the complementary regions are independent of the RNA molecules. Partial digestion of pulse-labelled late RNA with phosphodiesterase I prior to annealing with unlabelled early RNA, showed that the complementary regions on the mRNA are not located to the 5'- or 3'-end but randomly distributed along the T4 RNA molecules.

Control of early gene expression of bacteriophage T4: involvement of the host rho factor and the mot gene of the bacteriophage

Many early mRNA species of bacteriophage T4 are not synthesized after infection of Escherichia coli in the presence of chloramphenicol. This has been interpreted as a need for T4 protein(s) to be synthesized to allow expression of some early genes, e.g., those for deoxycytidinetriphosphatase, deoxynucleosidemonophosphate kinase and UDP-glucose-DNA beta-glucosyltransferase. In the experiments described here, early mRNA of bacteriophage T4 was allowed to accumulate during chloramphenicol treatment. After the addition of rifampin to inhibit further RNA synthesis, and subsequent removal of chloramphenicol, the accumulated mRNA was permitted to express itself into measured enzyme activities. It was shown that the early mRNA species coding for deoxycytidinetriphosphatase and UDP-glucose-DNA beta-glucosyltransferase could be formed in the presence of chloramphenicol if the E. coli host cell carried a mutation in the structural gene for the RNA chain termination factor rho. This was interpreted to mean that T4 protein(s) with anti-rho activity is normally required for the expression of these two early genes. An altered rho-factor could not, however, relieve the need of phage protein synthesis for the formation of another early mRNA, that coding for deoxynucleosidemonophosphate kinase. In this case the mot gene of T4 seemed to be involved, since the primary infection of E. coli cells with the mot gene mutant tsG1 did not allow subsequent deoxynucleoside monophosphate kinase mRNA synthesis after wild-type phage infection in the presence of chloramphenicol. In control experiments, deoxynucleoside monophosphate kinase mRNA synthesis induced by wild-type phage superinfecting in the presence of chloramphenicol was facilitated by the primary infection with T4 phage containing an unmutated mot gene.

In vitro system for induction of delayed early RNA of bacteriophage T4

Concentrated lysates of Escherichia coli that had been infected with bacteriophage T4 in the presence of chloramphenicol show the same restriction of transcription in vitro as is found in vivo. Restricted lysates can be complemented with lysates from infected cells to induce production of delayed early RNA. Complementation takes place between the RNA polymerase of the restricted lysate and the DNA of the unrestricted lysate. We present evidence that delayed early RNA in these lysates is initiated at quasi-late (middle) promoters, and that such recognition is related to changes in the state of the template DNA.