Fragmentation of Bacillus bacteriophage phi105 DNA by complementary single-stranded DNA in the cohesive ends of the molecule

Complete Genome Sequence of Enterococcus faecalis Siphophage Sigurd

Enterococcus faecalis is associated with antibiotic-resistant infections, and this study presents E. faecalis siphophage Sigurd. The 41,811-bp Sigurd genome is divided into two arms defined by long convergent predicted transcription units that are separated by a bidirectional rho-independent terminator. Sigurd has a small terminase that is closely related to Bacillus subtilis cos phage phi105.

An efficient expression and secretion system based on Bacillus subtilis phage phi 105 and its use for the production of B. cereus beta-lactamase I

A novel expression system based on the Bacillus subtilis bacteriophage phi 105 has been developed to permit the high-level synthesis and secretion of beta-lactamase I (BlaI) from Bacillus cereus. Shotgun insertion of a promoterless lacZ gene into the phage genome permitted the identification of a clone producing large amounts of beta-galactosidase (beta Gal), indicating the transcription of the reporter gene from a strong phage promoter. The insertion also blocked lysis of the host cell. Although the insertion in the original prophage was complex, plasmid vectors and prophage derivatives have been developed to facilitate the replacement of lacZ with other genes for expression. The new prophages contain two additional mutations: an ind mutation, which greatly enhances the normally poor transformability of phi 105 lysogens, and a cts mutation, which allows thermo-induction of phage development and protein production. Induction of a derivative prophage containing the blaI gene from B. cereus resulted in the production of up to 500 micrograms of secreted BlaI per ml of culture supernatant.

Transactivation of both early and late simian virus 40 promoters by large tumor antigen does not require nuclear localization of the protein

The early gene product of simian virus 40, large tumor antigen (T antigen), is required for the onset of viral replication. This protein has also been reported to transactivate viral late gene expression, independently of replication. In this study I have used a vector that permits simultaneously a precise quantitation of simian virus 40 early and late promoter activity with a single nuclease S1 mapping probe. The results show that T antigen can activate the early promoter as well as the late promoter and that only on replicating templates does a shift occur in the ratio of late-to-early transcription. This simultaneous transactivation of early and late promoters occurs in human (HeLa) and monkey (CV-1) cells but does not occur in mouse embryonal carcinoma cells. It is seen with either wild-type T antigen or with a T antigen protein that carries a mutation in the nuclear localization signal. The mutant protein cannot bring about an early-to-late shift, consistent with its inability to support viral replication.

Comeasurement of simian virus 40 early and late promoter activity in HeLa and 293 cells in the presence of T antigen

Transcription of the simian virus 40 (SV40) late promoter is strongly activated by SV40 T antigen. We were interested in examining this process in relation to other T-antigen functions such as replication and repression of early transcription. To quantitate the various T-antigen effects, we used a vector which has a promoterless beta-globin gene flanking the early and late sides of the SV40 promoter region. Following cotransfection with a plasmid encoding T antigen, transcription from the two promoters can be measured with a single S1 mapping probe and replication can be assayed by Southern blot analysis of DNA recovered in Hirt extracts. In this study, transactivation was examined in HeLa and 293 cells, since these cells differ in their ability to support SV40 replication. The strength of the late promoter relative to the early promoter was approximately three- to fourfold higher in 293 cells. Replication in 293 cells was also more efficient, by the same margin. In both cell lines, late promoter transactivation was barely detectable on replication-defective templates. Taken together, the results suggest that T-antigen activation of late transcription occurs only on replicated, or replicating, DNA. T antigen also activated the late-early start sites, and while in HeLa cells they were seen to be only 30% as strong as the late promoter, in 293 cells late and late-early activities were almost equal.

Isolation and characterization of new facultatively alkalophilic strains of Bacillus species

Four facultatively alkalophilic isolates were purified from enrichment cultures initiated with lime-treated garden soil. Four isolates, OF1, OF3, OF4, and OF6, were obligately aerobic, spore-forming, gram-positive, motile rods which were capable of growth at both pH 7.5 and pH 10.5. Strains OF1 and OF6 grew best at the lower pH value; and whereas growth of these strains at pH 10.5 was completely dependent on added Na+, growth at pH 7.5 was only partially dependent on added Na+. Strains OF3 and OF4 grew better at pH 10.5 than at pH 7.5, with strain OF3 growing modestly over its entire pH range, while OF4 grew well. Growth of OF3 and OF4 was completely dependent on added Na+ at both pH 7.5 and pH 10.5. DNA-DNA hybridization studies indicated that OF1 and OF6 are closely related strains but are not related to the other isolates, Bacillus subtilis, or two previously studied obligately alkalophilic bacilli. OF3 was unrelated to any of the other organisms examined in the study, whereas OF4 showed complete homology with obligately alkalophilic Bacillus firmus RAB. All four isolates maintained a cytoplasmic pH that was considerably lower than the external pH when the latter was 10.5. Although substantial transmembrane electrical potentials were observed, the total electrochemical proton gradient (delta mu H+) was low at pH 10.5 in all the strains. By contrast, delta mu H+ was substantial at pH 7.5 and at that pH was composed entirely of an electrical potential. These results are in contrast to previous findings that obligately alkalophilic bacilli generate only small electrical potentials at near neutral pH. All the isolates exhibited substantial rates of respiration as measured by oxygen consumption. Neither respiration nor NADH oxidation by everted membrane vesicles was significantly stimulated by Na+. Analyses of reduced versus oxidized difference spectra of membranes from OF4 showed that the total membrane cytochrome content was considerably higher in cells grown at pH 10.5 than at pH 7.5, with the levels of c- and a-type cytochromes exhibiting the largest pH-dependent differences. Initial examination of membrane protein profiles on gel electrophoresis also indicated a number of changes in pattern in each isolate, depending on the growth pH.

Temperate Bacillus bacteriophage SP16 genome is circularly permuted and terminally redundant

The physical nature of temperate Bacillus bacteriophage SP16 DNA was analyzed by electron microscopy, exonuclease digestion, denaturation-renaturation experiments, and restriction enzyme analysis. The SP16 genome is a linear molecule 60.0 +/- 2.0 kilobases in length without cohesive ends. Electron micrographs of denatured and renatured SP16 DNA showed that the DNA is circularly permuted. The genome possesses terminal redundancy, as demonstrated by electron microscopy of exonuclease III-digested DNA.

Evidence for circular permutation of the prophage genome of Bacillus subtilis bacteriophage phi 105

Analysis of DNA extracted from Bacillus subtilis lysogenic for bacteriophage phi 105 was performed by restriction endonuclease digestion and Southern hybridization using mature phi 105 DNA as a probe. The data revealed that the phi 105 prophage is circularly permuted. Digests using the enzymes EcoRI, SmaI, PstI, and HindIII localized the bacteriophage attachment site (att) to a region 63.4 to 65.7% from the left end of the mature bacteriophage genome. The phi 105 att site-containing SmaI C, PstI J, and HindIII L fragments were not present in digests of phi 105 prophage DNA. phi 105-homologous "junction" fragments were visualized by probing digests of prophage DNA with the purified PstI J fragment isolated from the mature bacteriophage genome. The excision of the phi 105 prophage was detected by observing the appearance of the mature PstI J fragment and the concomitant disappearance of a junction fragment during the course of prophage induction.

Alkalophilic Bacillus firmus RAB generates variants which can grow at lower Na+ concentrations than the parental strain

Obligately alkalophilic Bacillus firmus RAB cannot grow well on media containing less than 5 mM Na+. However, variant strains can be isolated on plates containing 2 to 3 mM Na+. These variants are observed only rarely in cultures that are plated before being subjected to repeated transfers in liquid medium. Cultures which have been transferred several times produce variants at an apparent frequency of 2 X 10(-4). Most of these variants are unstable, generating parental types at the high frequency of 10%; however, stable variants can be isolated. These strains grow better than the parental strain at very high pH values in the presence of 5 mM Na+ and have enhanced activity of the Na+ -H+ antiporter that has been implicated in pH homeostasis. By contrast, Na+ -coupled solute uptake is indistinguishable from that of the parental strain, and no obvious changes in the respiratory chain components are apparent in reduced versus oxidized difference spectra. The membranes of the variants show a marked enhancement, on sodium dodecyl sulfate-polyacrylamide gradient electrophoresis, in one polypeptide band with a molecular weight in the range of 90,000. The findings are discussed from the point of view of genetic mechanisms that might confer adaptability to even more extreme environments than usual and in view of earlier models relating the Na+ -translocating activities of the alkalophiles.

Nucleotide sequence of the immunity region of Bacillus subtilis bacteriophage phi 105: identification of the repressor gene and its mRNA and protein products

A gene involved in the regulation of lysogeny in the temperate Bacillus subtilis phage phi 105 has been identified and isolated. A plasmid, pDC4, was constructed that contains a 740-bp HindIII-PvuII fragment that is derived from the phi 105 immunity region and is capable of rendering B. subtilis immune to infection by phi 105. Three different hybrid plasmids that contain the 740-bp fragment, pAG101 [Cully and Garro, J. Virol. 34 (1980) 789-791], pDC1 and pDC2, were found to synthesize a common 18-kDal polypeptide in B. subtilis minicells and Escherichia coli maxicells. The nucleotide (nt) sequence of this region revealed three open reading frames (ORFs) that predict proteins with Mrs of 16521, 7332, and 5516. In vivo synthesized phi 105 prophage RNA was mapped by primer extension and shown to be transcribed from the DNA strand coding for the Mr 16521 protein. The 5' end of the phi 105 lysogen RNA was mapped to a region that contains conserved sequences for RNA polymerase recognition.

Nucleotide sequence of the temperate Bacillus subtilis bacteriophage SPO2 DNA polymerase gene L

Temperate Bacillus subtilis phage SPO2 codes for a phage-specific DNA polymerase. The polymerase gene has been cloned, and its nucleotide sequence has been determined. Within the sequence there is an open reading frame starting with a TTG and ending with three consecutive translational stop codons. Ten base pairs upstream from the proposed TTG initiation codon there is a probable ribosome-binding site with a calculated free energy of interaction with the 3' end of B. subtilis 16S rRNA of -15 kcal (-63 kJ)/mol. Based on the sequence and the expression of the polymerase gene in three different hybrid plasmids, we conclude that this open reading frame is the structural gene for SPO2 DNA polymerase. The predicted molecular weight of the polymerase is 72,486. In hybrid plasmid pJB74, the terminal triplet of an open reading frame with coding capacity for a protein of ca. 10 kilodaltons overlaps with the translational initiation triplet TTG of the polymerase gene. We speculate that transcription and translation of this open reading frame can influence the amount of phage DNA polymerase made in SPO2-infected bacteria.

Characterization of bacteriophage N3 DNA

The DNA from Haemophilus influenzae temperate phage N3 was characterized by centrifugation and by electrophoresis after nuclease digestion. The double-stranded DNA, with a mass of 25.8 X 10(6) daltons, had single-strand cohesive ends. Strand association through cohesion was reduced by heat and removed by S1 nuclease digestion. N3 DNA contained five EcoRI, one KpnI, two SacI, six XbaI, and four XhoI cleavage sites. The cohesive end segments were identified by heating the digests before electrophoresis. This was the first step in the construction of the physical maps of this DNA.

Expression of superinfection immunity to bacteriophage phi 105 by Bacillus subtilis cells carrying a plasmic chimera of pUB110 and EcoRI fragment F of phi 105 DNA

A 2.1-megadalton, EcoRI-generated fragment of Bacillus subtilis phage phi 105 DNA was cloned into plasmid pUB110. The hybrid plasmid produces a biologically active product which renders B. subtilis immune to infection by phi 105.

Physical mapping of Bacillus subtilis phage rho14 cloning vehicles: heteroduplex and restriction enzyme analyses

Four deletion mutants of temperate Bacillus subtilis bacteriophage rho14 have been examined utilizing restriction enzyme and DNA heteroduplex methods. This has allowed the orientation and mapping of the deletions on the rho14 physical map. A continuous 15% of the genome contains functions not essential for bacteriophage viability. A 7% subsection of this region contains phage immunity functions. The deletions were found to range in size from about 2.2-3.3 kilobases. In addition, the deletion mutants retain a single Sal I restriction site, which is currently being used as a cloning site for recombinant DNA. We have located the Sal I site to be 400 basepairs from the immunity region. Thus, the clear- and turbid-plaque deletion mutants are all capable of being utilized as molecular cloning vehicles for Bacillus subtilis.

Restriction-fragment map of the temperate Bacillus subtilis bacteriophage SPO2

The endonucleases BglI, BglII, EcoRI, SalI, SmaI, and XbaI were used to fragment the phage SPO2 DNA. Electrophoretic analysis using ethidiumbromide agarose gels showed the phage to have nine BglI sites, one BglII site, four EcoRI sites, one SalI site, one SmaI site, and six XbaI sites. Using partial digestions, multiple endonuclease digestion, and autoradiography the fragments were sized and ordered into a circular map of 23 Md. Such an analysis locates the endonuclease sites, indicates which endonucleases are potentially useful in cloning with SPO2, and allows insertions and/or deletions in the SPO2 DNA to be characterized.

Correlated genetic and EcoRI cleavage map of Bacillus subtilis bacteriophage phi105 DNA

The seven previously identified EcoRI cleavage fragments of phi 105 DNA were ordered with respect to their sites of origin on the phage genome by marker rescue. One fragment, H, did not carry any determinants essential for replication. This fragment was totally missing in a deletion mutant which exhibited a lysogenization-defective phenotype. There is a nonessential region on the phi 105 genome which begins in fragment B, spans fragment H, and ends in fragment F. The size of the nonessential region, as estimated by alterations observed in the fragmentation patterns of deletion mutant DNAs, is approximately 2.7 X 10(6) daltons. Two new EcoRI cleavage fragments with molecular weights of approximately 0.2 X 10(6) were detected by autoradiography of 32P-labeled DNA. These small fragments were not located on the cleavage map.

Restriction endonuclease mapping of bacteriophage phi105 and closely related temperate Bacillus subtilis bacteriophages rho10 and rho14

Cleavage maps of the three similar Bacillus subtilis temperate bacteriophages, phi105, rho10, and rho14, were constructed by partial digestion analysis utilizing the restriction endonuclease EcoRI. Comparison of the topography of these maps indicates that all phage DNAs posses cohesive ends and a number of EcoRI restriction sites; the fragments are conserved, and the estimated base substitution/nucleotide divergence between these phages is 0.03 to 0.07 based on conserved fragments or between 0.03 and 0.11 based on conserved cleavage sites. These lines of evidence indicate that phi105, rho10, and rho14 are closely related. Double-enzyme digestion analysis reveals that rho14 DNA has unique SalGI and BglII restriction sites and phi105 DNA has a unique SalGI restriction site, making these phages possible cloning vectors for B. subtilis.

Transfection with replicating DNA from the temperate Bacillus bacteriophage phi 105 and with T4-ligase treated phi105 DNA: the importance in transfection of being longer than genome-length

Replicating phage DNA extracted from Bacillus subtilis infected with phage phi 105 has a higher activity in transfection than mature DNA. By heteroduplex analysis it was shown that this DNA contains concatemeric molecules. Concatemers, constructed in vitro by treatment of mature DNA with T4-ligase also have an increased activity in transfection. DNA showing an increased activity in transfection does not have a requirement for more than one molecule per transfection event as is typically found for transfection with mature phi 105 DNA. An explanation is given for this difference suggesting that the structure of the ends of the transfecting molecules play an important role intransfection.