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PubMed1979

The prophage of SP beta c2dcitK1, A defective specialized transducing phage of Bacillus subtilis.

The defective specialized transducing phage SP beta c2dcitK1 carries two known bacterial genes, kauA and citK, as well as SP beta hage markers including the heat-sensitive repressor allele, c2. Some phage genes (including essential ones) are missing. When SP beta c2dcitK1 transduces SP beta-sensitive cells of Bacillus subtilis, the defective prophage is inserted into sites in the homologous bacterial DNA of the attSP beta-kauA-citK region of the recipient chromosome. During the growth of these transductants, occasional excisions occur that result in the loss of the phage genes and of the heterogenotic state. These excisions increase greatly in frequency during growth at repressor-inactivating temperatures. The kinds of insertions and excisions seen suggest that a Campbell-type (CAMPBELL 1962) circular phage genome may occur transiently. If the transductants are superinfected by SP beta c2 or by the clear-plaque mutant SP beta c1, the resulting double lysogen can be heat induced to release high-frequency-of-transduction (HFT) lysates for kauA and citK.

Bacillus subtilis↗

PubMed2001

Ribonucleotide reductase genes of Bacillus prophages: a refuge to introns and intein coding sequences.

The ribonucleotide reductase gene tandem bnrdE/bnrdF in SPbeta-related prophages of different Bacillus spp. isolates presents different configurations of intervening sequences, comprising one to three of six non-homologous splicing elements. Insertion sites of group I introns and intein DNA are clustered in three relatively short segments encoding functionally important domains of the ribonucleotide reductase. Comparison of the bnrdE homologs reveals mutual exclusion of a group I intron and an intein coding sequence flanking the codon that specifies a conserved cysteine. In vivo splicing was demonstrated for all introns. However, for two of them a part of the mRNA precursor molecules remains unspliced. Intergenic bnrdE-bnrdF regions are unexpectedly long, comprising between 238 and 541 nt. The longest encodes a putative polypeptide related to HNH homing endonucleases.

Bacillus↗

PubMed1978

Construction of recombinant plasmid carrying the lambda DNA fragment responsible for prophage integration.

The recombinant DNA molecules were constructed from plasmid RSF2124 and the EcoRI fragment of lambda DNA containing the genes responsible for prophage integration. The presence of these genes in recombinant plasmids was detected genetically. lambda int-gene was shown to be expressed in either orientation of insertion in the plasmid. We found that recombinant plasmid was able to integrate into chromosome of lambda lysogens. The integration of plasmid into host chromosome was demonstrated by contransduction of chromosome and plasmid markers using generalized transducer P1 and by specialized transduction with lambda phages.

Coliphages↗

PubMed1984

Lysogenicity and prophage type of the strains of Vibrio cholerae O-1 isolated mainly from the natural environment.

Attention has recently been given to the increasingly frequent detection of atypical Vibrio cholerae O-1 in the natural environments throughout the world. Lysogenicity of V. cholerae O-1, mainly isolated from environmental sources in nine areas, including the United States, was studied by electron microscopy and a cross-lysis test between bacteria and the culture supernatants. A total of 38 strains isolated in Texas in 1973 and in Louisiana in 1978 were lysogenic, whereas there were no lysogenic strains among those isolated in Louisiana in 1979. Because these phages were identical in terms of serology and host range, the phage in them was named T-L phage. T-L phage differed in host range from the k type phage in the epidemic strain of the seventh cholera pandemic. Although the T-L phage was neutralized by antiserum to the k type phage and vice versa, the two phage types were not serologically identical. By a prophage typing method, strains of V. cholerae O-1 isolated from the environment in Guam, Bangladesh, and Japan were classified as either of the Celebes type (epidemic strain) or the Classic-Ubon type. All strains isolated in Brazil, the Chesapeake Bay, and England were nonlysogenic and classified as Classic-Ubon type.

Bacteriophage Typing↗

PubMed1986

Prophage induction by ultraviolet light in Acinetobacter calcoaceticus.

UV-induction of prophage P78 of Acinetobacter calcoaceticus increased with the UV-dose given to the lysogenic strain from the spontaneous induction frequency of about 0.8% to a maximal frequency of 10%. This 10- to 20-fold increase of induction frequency, as measured by the number of infective centres, was accompanied by a 1000-fold increase in the yield of free phage. This effect was probably due to an increase in burst size under the conditions of lysogenic induction. Unusually, the lysogen was more resistant to UV-irradiation than the corresponding non-lysogenic strain.

Acinetobacter↗

PubMed1997

The site-specific recombinase encoded by pinD in Shigella dysenteriae is due to the presence of a defective Mu prophage.

The DNA inversion systems are made up of an invertible DNA segment and a site-specific recombinase gene. Five systems are known in prokaryotes: the Salmonella typhimurium H segment and hin gene (H-hin), phage Mu G-gin, phage P1 C-cin, Escherichia coli e14 P-pin, and Shigella sonnei B-pinB systems. In this report a site-specific recombinase (pinD) gene of Shigella dysenteriae was cloned and sequenced. pinD mediated inversion of five known segments at the same extent in E. coli. Although one inv sequence was identified, no invertible region was detected in a cloned fragment. The predicted amino acid sequences of PinD and three ORFs showed high homology to those of Gin and its flanking gene products. An ORF homologous to Mom of Mu conserved a functional activity to modify intracellular plasmid DNA. Southern analysis showed that the cloned fragment contains two homologous regions corresponding to the left and right ends of the Mu genome. Together these results indicated that the pinD gene in S. dysenteriae is derived from a Mu-like prophage.

Amino Acid Sequence↗

PubMed1996

Organization of the Bacillus subtilis 168 chromosome between kdg and the attachment site of the SP beta prophage: use of Long Accurate PCR and yeast artificial chromosomes for sequencing.

Within the Bacillus subtilis genome sequencing project, the region between lysA and ilvA was assigned to our laboratory. In this report we present the sequence of the last 36 kb of this region, between the kdg operon and the attachment site of the SP beta prophage. A two-step strategy was used for the sequencing. In the first step, total chromosomal DNA was cloned in phage M13-based vectors and the clones carrying inserts from the target region were identified by hybridization with a cognate yeast artificial chromosome (YAC) from our collection. Sequencing of the clones allowed us to establish a number of contigs. In the second step the contigs were mapped by Long Accurate (LA) PCR and the remaining gaps closed by sequencing of the PCR products. The level of sequence inaccuracy due to LA PCR errors appeared to be about 1 in 10,000, which does not affect significantly the final sequence quality. This two-step strategy is efficient and we suggest that it can be applied to sequencing of longer chromosomal regions. The 36 kb sequence contains 38 coding sequences (CDSs), 19 of which encode unknown proteins. Seven genetic loci already mapped in this region, xpt, metB, ilvA, ilvD, thyB, dfrA and degR were identified. Eleven CDSs were found to display significant similarities to known proteins from the data banks, suggesting possible functions for some of the novel genes: cspD may encode a cold shock protein; bcsA, the first bacterial homologue of chalcone synthase; exol, a 5' to 3' exonuclease, similar to that of DNA polymerase I of Escherichia coli; and bsaA, a stress-response-associated protein. The protein encoded by yplP has homology with the transcriptional NifA-like regulators. The arrangement of the genes relative to possible promoters and terminators suggests 19 potential transcription units.

Amino Acid Sequence↗

PubMed1990

Induction of a phi C31 prophage inhibits rRNA transcription in Streptomyces coelicolor A3(2).

A lysogen of Streptomyces coelicolor A3(2) containing a thermoinducible mutant of the temperate phage phi C31 (phi C31 cts1) was used to obtain synchronous phage development. Filter hybridization experiments indicated a marked reduction in rRNA synthesis after prophage induction. S1 nuclease mapping showed that transcription from each of the four promoters of one rRNA gene set (rrnD) was reduced to approximately the same extent, and that inhibition required protein synthesis. Crude preparations of RNA polymerase from induced lysogens had enhanced transcribing activity for phi C31 DNA which was lost upon further purification. The purified preparations were unimpaired in their ability to transcribe from the rrnD promoters in vitro and apparently unchanged in polypeptide composition. The factor(s) responsible for stimulating phage transcription, and possibly for inhibiting rRNA synthesis, may have been separated from the enzyme during purification.

Bacterial Proteins↗

PubMed1991

Response of Escherichia coli cell membranes to induction of lambda cl857 prophage by heat shock.

Heat shock induces protein aggregation in Escherichia coli and E. coli (lambda cl857). The aggregates (S fraction) appear 15 min post-induction and are separable from membranes by sucrose density-gradient centrifugation. The S fraction quickly disappears in wild type strains but persists in rpoH mutant with concomitant quick inner membrane destruction. We propose that: (1) the disappearance of the S fraction reflects a rpoH-dependent processing, (2) the membrane destruction explains the lethality of the rpoH mutation at elevated temperatures; and (3) the protection of the inner membrane integrity is an important physiological function of the heat-shock response. We assume that the S fraction of aggregated proteins represents the signal inducing the heat-shock response. The prophage thermo-induction results in an increase (35 min post-induction) in the A fraction resembling that of the adhesion zones of the membranes. This fraction is greater than the corresponding fraction from uninduced cells. The increase is mediated by the lambda late genes, since it is absent in the induced E. coli (lambda cl857 Qam21). Since heat shock is widely used for induction of the lambda promoters in expression vectors it is possible that the formation of the protein aggregates (though transient in WT strains) and/or the fragility of membranes in rpoH mutants may be the cause of poor expression of cloned genes or may lead to mistaken localization of their expression products.

Bacterial Outer Membrane Proteins↗

PubMed1993

The Cro-like Apl repressor of coliphage 186 is required for prophage excision and binds near the phage attachment site.

The Apl protein of the temperature coliphage 186 represses transcription of the immunity repressor gene and down-regulates lytic transcription. It is shown here that an apl- mutant is competent for lytic development and establishes lysogeny normally but is defective in excision of the prophage. The Apl protein binds between the lytic and lysogenic promoters and also near the phage attachment site, suggesting that its role in excision is direct. Apl thus appears to act as an excisionase as well as a repressor. The pattern of Apl-induced DNase I enhancements indicates that the DNA is bent by Apl. Potential Apl recognition sequences are identified; these sequences are directly repeated several times across each binding region and are spaced 10 or 11 bases apart, suggesting that Apl binds to one face of the DNA helix.

Attachment Sites, Microbiological↗

PubMed1995

Restriction alleviation and modification enhancement by the Rac prophage of Escherichia coli K-12.

Bacteriophage lambda encodes an antirestriction function, RaI, which is able to modulate the activity of the Escherichia coli K-12 restriction and modification system, EcoKI. Here we report the characterization of an analogous function, Lar, expressed by E. coli sbcA mutants and the hybrid phage lambda reverse. E. coli sbcA mutants and lambda reverse both express genes of the Rac prophage, and we have located the lar gene immediately downstream of recT in this element. The lar gene has been cloned in an expression plasmid, and a combination of site-directed mutagenesis and labelling of plasmid-encoded proteins has enabled us to identify a number of translational products of lar, the smallest of which is sufficient for restriction alleviation. Lar, like RaI, is able both to alleviate restriction and to enhance modification by EcoKI. Lar, therefore, is functionally similar to RaI and the nucleotide sequences of their genes share 47% identity, indicating a common origin. A comparison of the predicted amino acid sequences of Lar and RaI shows only a 25% identity, but a few short regions do align and may indicate residues important for structure and/or function.

Amino Acid Sequence↗

PubMed1998

Replicating function of the RS1 element associated with Vibrio cholerae CTX phi prophage.

The RS1 element associated with Vibrio cholerae CTX phi prophage was cloned from an E1 Tor biotype Vibrio cholerae strain. We used the recA- vaccine strain Peru-15, that lacks the target for RS-mediated site-specific integration, to show that RS1 promotes autonomous replication of a suicide vector. A linker insertion in the rstR open reading frame abolished autonomous replication in Peru-15 but not in a strain containing an RS1 in the chromosome. An AT-rich region containing cis-acting elements involved in autonomous replication was identified by deletion. This region was sufficient to support autonomous replication in a strain containing an RS1 in the chromosome. DNA sequence analysis of a region present in RS1 and not RS2 revealed the presence of putative binding sites for host proteins involved in plasmid replication. These results indicate that RS1 contains a replicon distinct from RS2 which could be involved in replicative recombination events associated with tandem amplification of the CTX element.

Bacteriophages↗

PubMed1989

Induction of lambda prophage near the site of focused UV laser radiation.

DNA damage from photon scatter or beam spread during UV excimer laser irradiation was investigated using the induction of bacteriophage lambda in E. coli BR339. Prophage induction in these cells leads to the production of beta-galactosidase which can be detected colorimetrically by the application of appropriate substrates. An agar surface overlayed with BR339 cells was placed at various distances from the focal point of a converging lens and exposed to either 193 or 248 nm laser radiation. Energy densities ranging from approximately 5 mJ/cm2 to 30 J/cm2 were used. Ablation with 193 nm laser radiation produced an 800 microns wide clear 'trench' surrounded by a 500 microns zone of cells in which lambda had been induced. Following ablation with 248 nm laser radiation, the zone of induction was several millimeters wide. Exposures to 193 nm radiation at 170 mJ/cm2/pulse produced visible ablation of the agar surface at 1.7 J/cm2. Lambda induction was observed surrounding cleared ablation areas. The presence of induction in this system suggests that both 248 and 193 nm excimer laser radiation delivered at high energy densities has sufficient spread or scatter to damage DNA in cells surrounding areas of ablation.

Bacteriophage lambda↗

PubMed1968

Prophage S2 mutants in Haemophilus influenzae: a technique for their production and isolation.

A procedure utilizing nitrosoguanidine has been developed to produce defective and temperature-sensitive mutants of prophage (S2) in lysogenic Haemophilus influenzae. The system should be generally applicable to all temperate phage systems. At saturating concentrations of phage DNA, more than 25 percent of recipient mutant lysogenic bacteria can be transformed to the wild type.

Bacteriophages↗

PubMed1980

Prophage-Cured Derivatives of Streptococcus lactis and Streptococcus cremoris.

Prophage curing was achieved in Streptococcus lactis and Streptococcus cremoris, and the cured derivatives were shown to be indicators for their temperate bacteriophages. Relysogenization of these cured derivatives completed the first formal demonstration of the lysogenic state in lactic streptococci.

Journal Article↗

PubMed1986

Cloning in Streptococcus lactis of plasmid-mediated UV resistance and effect on prophage stability.

Plasmid pIL7 (33 kilobases) from Streptococcus lactis enhances UV resistance and prophage stability. A 5.4-kilobase pIL7 fragment carrying genes coding for both characters was cloned into S. lactis, using plasmid pHV1301 as the cloning vector. The recombinant plasmid was subsequently transferred to three other S. lactis strains by transformation or protoplast fusion. Cloned genes were expressed in all tested strains.

Bacillus subtilis↗

PubMed1975

Prophage induction of Escherichia coli (lambda) by N-nitrosamines.

Carcinogenic N-nitrosamines were tested for their ability to induce lambda in a lysogenic strain of Escherichia coli K-12 (58-161 F+ Dimethylnitrosamine, di-n-propylnitrosamine, methyl-n-propylnitrosamine, and N-nitrosopiperidine were shown to be inducers of prophage.

Coliphages↗

PubMed2006

The Rgg regulator of Streptococcus pyogenes influences utilization of nonglucose carbohydrates, prophage induction, and expression of the NAD-glycohydrolase virulence operon.

The expression of many virulence-associated genes in Streptococcus pyogenes is controlled in a growth phase-dependent manner. Unlike the model organisms Escherichia coli and Bacillus subtilis, such regulation is apparently not dependent upon alternative sigma factors but appears to rely on complex interactions among several transcriptional regulators, including Rgg. The purpose of this study was to identify changes in gene expression associated with inactivation of the rgg gene in S. pyogenes strain NZ131 (serotype M49). To this end, the transcriptomes of wild-type and rgg mutant strains were analyzed during both the exponential and postexponential phases of growth using Affymetrix NimbleExpress gene chips. Genomewide differences in transcript levels were identified in both phases of growth. Inactivation of rgg disrupted coordinate expression of genes associated with the metabolism of nonglucose carbon sources, such as fructose, mannose, and sucrose. The changes were associated with an inability of the mutant strain to grow using these compounds as the primary carbon source. Bacteriophage transcript levels were also altered in the mutant strain and were associated with decreased induction of at least one prophage. Finally, transcripts encoding virulence factors involved in cytolysin-mediated translocation of NAD-glycohydrolase, including the immunity factor IFS and the cytolysin (streptolysin O [SLO]), were more abundant in the mutant strain, which correlated with the amount of NADase and SLO activities in culture supernatant fluids. The results provide further evidence that Rgg contributes to growth phase-dependent gene regulation in strain NZ131.

Bacterial Proteins↗