Complementary Strands of Bacteriophage phi29 Deoxyribonucleic Acid: Preparative Separation and Transcription Studies

In vitro synthesis of late bacteriophage phi 29 RNA

A crude P-100 fraction prepared from Bacillus subtilis 21 min after infection with wild-type phage phi 29 supported the in vitro synthesis of late phi 29 RNA by added RNA polymerase. Synthesis of late RNA was also detected when purified phi 29 DNA was transcribed by RNA polymerase in the presence of an S-150 fraction obtained by lysis of phi 29-infected cells in the presence of 1 M NaCl. Late phi 29 RNA was not synthesized when either the P-100 or the S-150 fraction was prepared from cultures infected with phi 29 having a mutation in gene 4.

Transcription of the genome of bacteriophage phi 29: isolation and mapping of the major early mRNA synthesized in vivo and in vitro

The phi29 early mRNA's synthesized in infected Bacillus subtilis were studied by using sedimentation velocity analysis, polyacrylamide gel electrophoresis, and hybridization of phi29 DNA fragments generated by the restriction endonuclease Eco RI. Viral RNAs synthesized in vivo in the resence of chloramphenicol were found to hybridize to Eco RI-A, -C, and -D fragments, but not to Eco RI-B and -E fragments, of the viral genome. Major early mRNA sedimenting as 16S material in neutral sucrose gradients was examined in detail. Radioactive phi29 RNA, purified by sucrose gradient centrifugation, was hybridized to either the Eco RI-A or Eco RI-C DNA fragment. The RNA was eluted from the hybrids and then tested for complementary hybrid formation with Eco RI-A and -C fragments. RNA eluted from the Eco RI-A fragment annealed only to the Eco RI-A fragment and not to the Eco RI-C fragment. Similarly, RNA eluted from the Eco RI-C fragment hybridized to the Eco RI-C and -D fragments. Viral RNAs synthesized in vitro using B. subtilis RNA polymerase hybridized to both Eco RI-A and -C DNA fragments. Furthermore, RNA initiated with [gamma-(32)P]GTP also hybridized to both Eco RI-A and -C fragments. These results indicate that there are at least two efficient promotors for early transcription on the phi29 chromosome. In addition, a low-molecular-weight RNA initiated with [gamma-(32)P]ATP was found to hybridize exclusively with the Eco RI-A fragment. Kinetic studies of phi29 mRNA synthesis during the lytic cycle have shown that viral RNAs hybridizable to the Eco RI-A and -C fragments are synthesized immediately after phage infection. On the other hand, mRNA specific for the Eco RI-B fragment was not synthesized for several minutes after phage infection. Based on the results of the in vivo and in vitro transcription studies, a transcription map of the phi29 chromosome is proposed.

The binding of poly(rA) and poly(rU) to denatured DNA. I. Model studies with homopolymers

We have compared the properties of the poly(rA).oligo(dT) complex with those of the poly(rU).oligo(dA)n complex. Three main differences were found. First, poly(rA) and oligo(dT)n do not form a complex in concentrations of CsCl exceeding 2 M because the poly(rA) is insoluble in high salt. If the complex is made in low salt, it is destabilized if the CsCl concentration is raised. Complexes between poly(rU) and oligo(dA)n, on the other hand, can be formed in CsCl concentrations up to 6.6 M. Second, complexes between poly(rA) and oligo(dT)n are more rapidly destabilized with decreasing chain length than complexes between poly(rU) and oligo(dA)n. Third, the density of the complex between poly(rA) and poly(dT) in CsCl is slightly lower than that of poly(dT), whereas the density of the complex between poly(rU) and poly(dA) in CsCl is at least 300 g/cm3 higher than that of poly(dA). These results explain why denatured natural DNAs that bind poly(rU) in a CsCl gradient usually do not bind poly(rA).

Recombinational-type transfer of viral DNA during bacteriophage 2C replication in Bacillus subtilis

The Bacillus subtilis phage 2C contains one molecule of double-stranded DNA of about 100 x 10(6) daltons in which thymine is replaced by hydroxymethyluracil; the two strands have different buoyant densities. Parental DNA, labeled with either [3H]uracil of [32P]phosphate, was quite effectively transferred to offspring phage, and the efficiency of transfer was the same for the two strands. Labeled nucleotide compositions of the H and L strands from parental and progeny virions were very close. These data exclude a degradation of the infecting DNA and reutilization of nucleotides. Upon infection of light unlabeled cells with heavy radioactive viruses, no DNA with either heavy or hybrid density was extracted from offspring phage. Instead, an heterogeneous population of DNA molecules of densities ranging from that of almost hybrid to that of fully light species was obtained. Shear degradation of such progeny DNA to fragments of decreasing molecular weight produced a progressive shift to the density of hybrid molecules. Denaturation of sheared DNA segments caused the appearance of labeled and heavy single-stranded segments. These findings indicate that 2C DNA replicates semiconservatively and then undergoes extensive genetic recombination with newly formed viral DNA molecules within the vegatative pool, thus mimicking a dispersive transfer of the infecting viral genome. The pieces of transferred parental DNA have an average size of 10 x 10(6) daltons.

Bacteriophages of Bacillus subtilis

Images

Analysis of bacteriophage phi 29 gene function: protein synthesis in suppressor-sensitive mutant infection of Bacillus subtilis

Phage phi29 suppressor-sensitive (sus) mutants of 14 cistrons have been examined for production of (14)C-labeled viral-specific proteins in restrictive infections of Bacillus subtilis. Proteins specified by four cistrons (H, J, L, and N) have been resolved and identified by sodium dodecyl sulfate gel electrophoresis and autoradiography, and fragments of the normal polypeptides were detected. Mutants of six cistrons (C, D, E, F, I, and M) demonstrated two or more missing bands in the gel profiles, and thus some of these gene products may have regulatory functions. Mutation was detected in at least five genes coding for low-molecular-weight proteins, but a conditionally lethal mutant in only one of these genes has been isolated. Preliminary evidence that a precursor protein is cleaved to generate the neck appendage structural protein and a low-molecular-weight product has been obtained.

Viral protein synthesis in bacteriophage phi 29-infected Bacillus subtilis

Twenty-three (14)C-labeled phage phi29-specific proteins in lysates of UV-irradiated Bacillus subtilis have been resolved by sodium dodecyl sulfate polyacrylamide gel electrophoresis and identified by autoradiography. Included in this group of proteins are the six major structural proteins of the virion. Analysis of the temporal sequence of viral protein synthesis indicates that three groups of proteins can be identified by time of appearance, beginning at 2 to 4, 4 to 6, or 8 to 10 min after infection, respectively. These proteins account for approximately 90% of the coding capacity of the phi29 genome.

RNA polymerase from Bacillus amyloliquefaciens infected with phi29 bacteriophage

DNA-dependent RNA polymerase was purified from uninfected and varphi29-infected Bacillus amyloliquefaciens. Differences were observed in the specific activities, template specificities, stability, and sedimentation properties of the two enzymes. A polypeptide of 30,000 molecular weight was found in association with the polymerase of high specific activity from phage-infected cells and was absent from polymerase isolated from uninfected cells. The change in polymerase properties and the appearance of the polypeptide occurred early in phage infection.

Genetic study of suppressor-sensitive mutants of the Bacillus subtilis bacteriophage phi 29

With bacteriophage phi29 of Bacillus subtilis 133, suppressor-sensitive (sus) hydroxylamine mutants have been isolated. Intracistronic and intercistronic quantitative complementation placed the mutants in 13 cistrons, and three-factor crosses have been used to assign an unambiguous order for 10 cistrons. Recombination frequencies have been presented for several regions of the genome to facilitate comparison of the sus system with the previously published temperature-sensitive mapping systems.

Gene expression during the development of Bacillus subtilis bacteriophage phi 29. I. Analysis of viral-specific transcription by deoxyribonucleic acid-ribonucleic acid competition hybridization

The ribonucleic acid (RNA) specified by bacteriophage phi29 was analyzed to determine its composition at various times in the viral lytic cycle. Although viral-specific RNA was detected immediately after infection, a large increase in the rate was observed at 10 min when DNA synthesis began. phi29 was found to resemble other viruses in that gene expression occurred in two stages which could be defined temporally as "early" and "late." Early RNA appeared before the onset of viral deoxyribonucleic acid (DNA) replication and accounted for approximately 40% of the viral genetic potential. This RNA was also present late in the infectious cycle because of the slow turnover rate of phi29-specific RNA (approximately 10 min half-life) and the continued synthesis of much early viral RNA throughout infection. Late RNA was first detected at approximately the same time as viral DNA replication, although late transcription was not dependent upon DNA synthesis. This RNA was only partially displaced by early RNA in the appropriate competition experiments, suggesting that it contained sequences not present in the early class. Expression of viral genes was sensitive to rifamycin throughout the lytic cycle, the sensitivity resulting from a dependence upon the rifamycin phenotype of the host RNA polymerase.

Transcription during the development of bacteriophage phi29: definition of "early" and "late" phi29 ribonucleic acid

Bacteriophage phi29 messenger ribonucleic acid (mRNA) production following infection of Bacillus subtilis has been analyzed. Early (e) phi29 RNA, made prior to the onset of phage deoxyribonucleic acid (DNA) replication and exclusively from the light (L) phi29 DNA strand, has been shown by RNA-DNA hybridization-competition experiments to be present throughout the phage latent period. No repression of e RNA production during phi29 development could be demonstrated. Unmodified host RNA polymerase molecules appear to be sufficient for the synthesis of e RNA since phage-specific RNA made in the presence of chloramphenicol hybridizes only to the L strand of phi29 DNA, and this RNA can be effectively competed during hybridization by e RNA. The appearance of late (l) phi29 RNA is coincident with the onset of viral DNA replication. This RNA consists of L DNA strand transcripts which are identical to e RNA and a new class of mRNAs made exclusively from the "heavy" (H) phi29 DNA strand (lH). Protein synthesis in infected cells is required for lH RNA production. Studies with the antibiotic rifamycin demonstrated that synthesis of the major phi29 structural proteins is dependent on production of lH RNA.

Transcription during the development of bacteriophage phi 29: production of host- and phi 29-specific ribonucleic acid

The synthesis of ribonucleic acid (RNA) during development of the virulent Bacillus subtilis bacteriophage phi29 has been analyzed. Transcription of host deoxyribonucleic acid (DNA) continues at the preinfection rate throughout the latent period of viral growth. RNA-DNA hybridization was used to show that host messenger RNA synthesis continues late into the phage lytic cycle. Amino acid-labeling experiments show that this RNA is continuously used to produce protein. Ribosomal RNA production is not inhibited by phage infection. Small quantities of phage-specific RNA first appear between min 6 and 9 after infection. This RNA is made exclusively from one of the phi29 DNA strands. At 12 min postinfection, when phage DNA replication commences, large quantities of viral RNA start to be synthesized. This RNA appears to be transcribed from both strands of phi29 DNA. Studies with rifamycin and rifamycin-resistant host strains showed that the production of all phage phi29-specific RNA requires those components of the host RNA polymerase which are sensitive to this antibiotic. Thus, phage phi29 does not stop transcription of host DNA and may produce only one element for regulation of transcription of its own DNA. These findings may reflect the limited amount of genetic information carried by this phage.

Transfecting deoxyribonucleic acid of Bacillus bacteriophage phi 29 that is protease sensitive

The transfecting activity of Bacillus phage varphi29 DNA, extracted either by sodium lauroyl sarcosine-phenol or by 2 M perchlorate, was destroyed by treatment with proteolytic enzymes, although these enzymes did not effect transfecting DNAs of SPP1, SPO1, and SP50. These facts suggest that a protein is associated with transfective varphi29 DNA. Stabilization of protease-resistance during transfection appeared earlier than that of DNaseresistance, indicating that the protein associated with varphi29 DNA is necessary for initiation of the incorporation of DNA molecules into competent cells. The physical nature of varphi29 DNA before and after the trypsin treatment was investigated by sucrose and CsCl density gradient centrifugations. The trypsin treatment did not alter the sedimentation rate of the unit varphi29 DNA; however, it did convert the sedimentation rate of the aggregated material in the untreated DNA to that of the unit varphi29 DNA. The density of the trypsinized DNA was 0.009 g/cm(3) greater than that of the untreated DNA. The possible location of the protein on the DNA is discussed.

Temperature-shift analysis of bacteriophage phi 29 gene expression in Bacillus amyloliquefaciens

Temperature shift-up experiments with conditional lethal mutants of Bacillus phage phi29 have allowed placement of early, middle, and late functions on the linear phi29 genetic map Most of the phi29 cistrons are late and are found at the ends of the map.