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PubMed2003

The Bacillus thuringiensis linear double-stranded DNA phage Bam35, which is highly similar to the Bacillus cereus linear plasmid pBClin15, has a prophage state.

Bam35, a 15-kbp double-stranded DNA phage, infects Bacillus thuringiensis. Recently, sequencing of the related Bacillus cereus revealed a 15.1-kbp linear plasmid, pBClin15. We show that pBClin15 closely resembles Bam35 and demonstrate conversion of Bam35 to a prophage. This state is common, as several B. thuringiensis strains release Bam35-related viruses.

Amino Acid Sequence↗
PubMed2005

Increased excision of the Salmonella prophage ST64B caused by a deficiency in Dam methylase.

Salmonella enterica mutants defective in Dam methylase are strongly attenuated in virulence and release a large amount of proteins to the extracellular medium. The extent to which these two phenotypes are linked is unknown. Using a proteomic approach, we identified Sb6, Sb13, and Sb36 as proteins present in larger amounts in culture supernatants of an S. enterica serovar Typhimurium dam mutant than in those of the wild-type strain. These three proteins are encoded in the Salmonella prophage ST64B. Higher amounts of ST64B phage DNA and tailless viral capsids were also detected in supernatant extracts of the dam mutant, suggesting that Dam methylation negatively regulates the excision of ST64B. Reverse transcription-PCR analysis revealed that the expression of two ST64B genes encoding a putative antirepressor and a phage replication protein increases in the dam mutant. The SOS response also augments the excision of ST64B. Infection assays performed with phage-cured strains demonstrated that ST64B does not carry genes required for virulence in the mouse model. Evidence was also obtained discarding a relationship between the high excision of ST64B and the envelope instability or virulence attenuation phenotype. Taken together, these data indicate that ST64B excises at a high rate in dam mutants due to the loss of repression exerted by Dam on phage genes and induction of the SOS response characteristic of these mutants. The exacerbated excision of ST64B does not however contribute to the incapacity of dam mutants to cause disease.

Animals↗
PubMed2004

Insights into the genome of the enteric bacterium Escherichia blattae: cobalamin (B12) biosynthesis, B12-dependent reactions, and inactivation of the gene region encoding B12-dependent glycerol dehydratase by a new mu-like prophage.

The enteric bacterium Escherichia blattae has been analyzed for the presence of cobalamin (B12) biosynthesis and B12-dependent pathways. Biochemical studies revealed that E. blattae synthesizes B12 de novo aerobically and anaerobically. Genes exhibiting high similarity to all genes of Salmonella enterica serovar Typhimurium, which are involved in the oxygen-independent route of B12 biosynthesis, were present in the genome of E. blattae DSM 4481. The dha regulon encodes the key enzymes for the anaerobic conversion of glycerol to 1,3-propanediol, including coenzyme B12-dependent glycerol dehydratase. E. blattae DSM 4481 lacked glycerol dehydratase activity and showed no anaerobic growth with glycerol, but the genome of E. blattae DSM 4481 contained a dha regulon. The E. blattaedha regulon is unusual, since it harbors genes for two types of dihydroxyacetone kinases. The major difference to dha regulons of other enteric bacteria is the inactivation of the dehydratase-encoding gene region by insertion of a 33,339-bp prophage (MuEb). Sequence analysis revealed that MuEb belongs to the Mu family of bacteriophages. The E. blattae strains ATCC 33429 and ATCC 33430 did not contain MuEb. Accordingly, both strains harbored an intact dehydratase-encoding gene region and fermented glycerol. The properties of the glycerol dehydratases and the correlating genes (dhaBCE) of both strains were similar to other B12-dependent glycerol and diol dehydratases, but both dehydratases exhibited the highest affinity for glycerol of all B12-dependent dehydratases characterized so far. In addition to the non-functional genes encoding B12-dependent glycerol dehydratase, the genome of E. blattae DSM 4481 contained the genes for only one other B12-dependent enzyme, the methylcobalamin-dependent methionine synthase.

Amino Acid Sequence↗
PubMed2006

Use of the lambda Red recombinase system to produce recombinant prophages carrying antibiotic resistance genes.

BACKGROUND: The Red recombinase system of bacteriophage lambda has been used to inactivate chromosomal genes in E. coli K-12 through homologous recombination using linear PCR products. The aim of this study was to induce mutations in the genome of some temperate Shiga toxin encoding bacteriophages. When phage genes are in the prophage state, they behave like chromosomal genes. This enables marker genes, such as antibiotic resistance genes, to be incorporated into the stx gene. Once the phages' lytic cycle is activated, recombinant Shiga toxin converting phages are produced. These phages can transfer the marker genes to the bacteria that they infect and convert. As the Red system's effectiveness decreased when used for our purposes, we had to introduce significant variations to the original method. These modifications included: confirming the stability of the target stx gene increasing the number of cells to be transformed and using a three-step PCR method to produce the amplimer containing the antibiotic resistance gene. RESULTS: Seven phages carrying two different antibiotic resistance genes were derived from phages that are directly involved in the pathogenesis of Shiga toxin-producing strains, using this modified protocol. CONCLUSION: This approach facilitates exploration of the transduction processes and is a valuable tool for studying phage-mediated horizontal gene transfer.

Algorithms↗
PubMed2026

The value of a prophage-borne defense system in phage-phage competition.

Temperate phages that incorporate into their bacterial hosts' genomes often encode defense systems that protect their hosts from superinfection by unrelated phages. Yet the evolutionary value of such defenses to the phage remains unclear. We present a minimal theoretical framework to quantify the selective advantage of a prophage-borne defense system in competition between temperate phages infecting the same bacterial host. The model reveals regimes in which a "defensive phage" can invade and persist despite growth costs, regimes of bistability, and others in which all phage types coexist due to a rock-paper-scissors-like dynamic between defensive, non-defensive, and defense-loss variants. Because defense systems can be non-transitive, true rock-paper-scissors relations can lead to persistent oscillations. These results identify simple conditions under which phage-encoded defense systems are evolutionarily stable, providing testable predictions for the prevalence and maintenance of these systems in natural microbial communities.

Prophages↗
PubMed2005

[Effects of the recombinant plasmid carrying the genes of cholera prophages CTX and RS1 on the expression of virulence and immunogenicity genes in the cholera pathogen].

Using toxin-coregulated adhesion pili (TCP), the etiologic agent of cholera is able to colonize human small intestine, where this pathogen proceeds with the production of the secreted cholera toxin (CT), inducing the development of severe diarrhea. At the same time, TCP and CT are not only the major factors of pathogenicity but also form a part of the group of key protective antigens. Immunoenzyme, immunoblotting, self-agglutination investigations, electron-microscopic studies, and electrophoretic assay of the outer membrane proteins showed that the recombinant plasmid carrying a number of cloned genes of two prophages, CTX and RS1, introduced into model Vibrio cholerae strains classical biovariant, resulted in the formation of strains with an enhanced rate of synthesis of three protective antigens: CT, TCP, and an outer membrane protein, OmpU. A simultaneous increase in the level of biosynthesis of the three antigens in V. cholerae was demonstrated to be specified by alterations in the expression of the toxR regulatory gene. Information was obtained suggesting that the transcriptional activity of toxR gene was dependent on the activity of rstC antirepressor gene derived from RS1 pro-phage and localized in the cloned fragment. Strains hyperproducing the three protective antigens can be used to construct more efficient non-living cholera vaccines, and to isolate the indicated proteins applicable to the development of diagnostic test-systems.

Adhesins, Bacterial↗
PubMed1983

Effects of antimutagens on prophage induction in E coli lysogenic for lambda.

The effects of caffeine, acriflavine, spermine, quinacrine, and adenosine on spontaneous and UV-induced prophage induction in repair-proficient and -deficient strains of lysogenic Escherichia coli were examined. Caffeine caused a coinducing effect on UV induction in KMBL 160 (repair proficient) and KMBL 163 (uvrA), an anti-inducing effect in KMBL 161 (uvrE), and had no detectable effect in KMBL 164 (uvrC). Acriflavine increased UV induction in KMBL 160 and decreased it in all three repair-deficient mutant strains. Spontaneous induction was reduced by acriflavine in all four strains. Spermine caused a decrease in UV induction in KMBL 160 and KMBL 164, while it had limited effect in KMBL 161 and KMBL 163. For spontaneous induction spermine caused an increase in KMBL 160 and KMBL 163, a decrease in KMBL 164 and no detectable effect in KMBL 161. Quinacrine had no significant effect on spontaneous induction in KMBL 160 and KMBL 164, but caused a decrease in spontaneous induction in KMBL 161 and KMBL 163. Quinacrine produced no effect on UV induction in KMBL 160; however, it decreased UV induction in the three repair-deficient strains to some extent. A significant increase in spontaneous induction in KMBL 160 was caused by adenosine, while it had little effect in the repair-deficient strains. UV induction was not affected by adenosine.

Acriflavine↗
PubMed1984

Enhancing activity of rat tissue extracts for induction of lambda prophage by L-azaserine.

We studied the effect of rat tissue extracts on induction of lambda prophage in Escherichia coli (lambda) by L-azaserine. Hepatic and pancreatic extracts, primarily the cytosolic fraction, markedly increased the rate of induction. Hepatic extracts from lipotrope-deficient rats were somewhat more active than extracts from normal rats. The enhancing activity in normal rat hepatic cytosol was partially characterized. It reduced by about one-half the dose of azaserine required for a given purpose. The enhancement was increased by preincubating the bacterial cells with cytosol; cells retained the effect after cytosol was removed. Enhancing activity was inhibited strongly by the amino acids phenylalanine, tryptophan, and tyrosine; to lesser extents by leucine, methionine, and serine; and not at all by proline or glutamine. It was eliminated by dialysis of the cytosol and reduced by omission of nicotinamide adenine dinucleotide phosphate (NADP) from the reaction mixture. Heating the cytosol to 60 degrees C or 80 degrees C or varying the pH of the reaction mixture from 6 to 8 had no significant effect. Treating the cytosol with trypsin appeared to release an inhibitor of the activity. Glutathione, cysteine, and beta-mercaptoethanol also enhanced lambda induction by azaserine, but the cytosolic activity was not affected by the thiol-inactivating compound diethylmaleate (DEM). The results suggest that factors in cytosol interact with bacterial cells to facilitate transport of azaserine into the cells, primarily through the aromatic amino acid transport system. A small molecule, not a free thiol compound, appears to be involved. It may serve to establish reducing conditions protective for azaserine, the probable mechanism of action of sulfhydryl compounds.

Animals↗
PubMed1996

Different restriction profiles of kappa prophage in Serratia marcescens K and HY.

Temperate phage kappa originated from the defectively lysogenic Serratia marcescens strain K, from where it was liberated after uv irradiation with low efficiency. The phage is usually indicated on strain HY that can be easily lysogenized by it and rather efficiently uv-induced. Comparing the Eco RI restriction profiles of the kappa prophage in HY revealed a DNA rearrangement, by which the precursor structure in K is converted into the non-defective form. Apparently the fragment containing the pac sequence is concerned since a phage DNA probe prepared from the assumed initiation fragments of the first particles of the packaging series gave two signals instead of one with genomic K DNA. Since several independent new kappa isolates showed the same Eco RI restriction pattern as the original phage of ELLMAUER and KAPLAN (1959), the generation of kappa is a reproducible event.

Bacteriophages↗
PubMed1996

Regulation of the Serratia marcescens extracellular nuclease: positive control by a homolog of P2 Ogr encoded by a cryptic prophage.

The Serratia marcescens extracellular nuclease is a secreted protein that is subject to growth phase and SOS control. Regulatory mutants affecting nuclease expression have been isolated that define a new locus, nucC, essential for transcription of the nuclease gene nucA. The cloned nucC gene is able to activate efficient expression from the nucA promoter in Escherichia coli, where it normally is poorly expressed. NucC is very similar to the bacteriophage P2 Ogr protein, a transcriptional activator essential for P2 late gene expression. NucC is able to replace P2 Ogr to support the growth of P2 ogr- mutants in E. coli. Ogr is a poor activator of the nuclease promoter in E. coli, but the related delta gene product from satellite phage P4 is highly effective. The presence of genes encoding a lysozyme and a putative porin or holin in the nucC operon suggests that nucC may be part of a cryptic prophage genome. The putative holin-like membrane protein is required in E. coli for extracellular secretion of the S. marcescens nuclease.

Amino Acid Sequence↗
PubMed1998

An evolutionary link between sporulation and prophage induction in the structure of a repressor:anti-repressor complex.

Spore formation is an extreme response of some bacteria to adversity. In Bacillus subtilis the proteins of the sin, sporulation inhibition, region form a component of an elaborate molecular circuitry that regulates the commitment to sporulation. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer. The interactions governing this curious quaternary transition are revealed in the crystal structure of the SinI-SinR complex. The most striking, and unexpected, finding is that the tertiary structure of the DNA-binding domain of SinR is identical with that of the corresponding domains of the repressor proteins, CI and Cro, of bacteriophage 434 that regulate lysis/lysogeny. This structural similarity greatly exceeds that between SinR and any bacterial protein or between the 434 repressor proteins and their homologues in the closely related bacteriophage lambda. The close evolutionary relationship implied by the structures of SinR and the 434 repressors provokes both comparison of their functions and a speculative consideration of the intriguing possibility of an evolutionary link between the two adaptive responses, sporulation and prophage induction.

Amino Acid Sequence↗
PubMed2002

Bacteriophage Mu genome sequence: analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus.

We report the complete 36,717 bp genome sequence of bacteriophage Mu and provide an analysis of the sequence, both with regard to the new genes and other genetic features revealed by the sequence itself and by a comparison to eight complete or nearly complete Mu-like prophage genomes found in the genomes of a diverse group of bacteria. The comparative studies confirm that members of the Mu-related family of phage genomes are genetically mosaic with respect to each other, as seen in other groups of phages such as the phage lambda-related group of phages of enteric hosts and the phage L5-related group of mycobacteriophages. Mu also possesses segments of similarity, typically gene-sized, to genomes of otherwise non-Mu-like phages. The comparisons show that some well-known features of the Mu genome, including the invertible segment encoding tail fiber sequences, are not present in most members of the Mu genome sequence family examined here, suggesting that their presence may be relatively volatile over evolutionary time. The head and tail-encoding structural genes of Mu have only very weak similarity to the corresponding genes of other well-studied phage types. However, these weak similarities, and in some cases biochemical data, can be used to establish tentative functional assignments for 12 of the head and tail genes. These assignments are strongly supported by the fact that the order of gene functions assigned in this way conforms to the strongly conserved order of head and tail genes established in a wide variety of other phages. We show that the Mu head assembly scaffolding protein is encoded by a gene nested in-frame within the C-terminal half of another gene that encodes the putative head maturation protease. This is reminiscent of the arrangement established for phage lambda.

Amino Acid Sequence↗
PubMed1996

The Escherichia coli retrons Ec67 and Ec86 replace DNA between the cos site and a transcription terminator of a 186-related prophage.

Retrons are unusual, reverse transcriptase-encoding elements found in bacteria. Although there are a number of indications that retrons are mobile elements, their transposition has not been observed. The Escherichia coli retrons Ec67 and Ec86 are different retrons inserted at the same site and we have further characterized this site in search of clues to the mechanism of retron transposition. We confirm, by extending previous sequence analysis, that Ec67 and Ec86 are inserted into prophages related to coliphage 186. Comparison with the recently published sequence of the 186 96-2% region indicates that the retrons have replaced approximately 180 bp of DNA between the phage cohesive end site (cos) and the transcription terminator of a phage DNA-packaging gene. These features--DNA replacement at the insertion site and the location of retron junctions near transcription terminators or DNA cleavage sites--are shared with other retrons and suggest ways in which retron transposition might have occurred.

Amino Acid Sequence↗
PubMed1990

Nucleotide sequence of the region encompassing the int gene of a cryptic prophage and the dna Y gene flanked by a curved DNA sequence of Escherichia coli K12.

The nucleotide sequence of a 2.5 kb region encompassing a curved DNA segment (BENT-9) randomly cloned from the total Escherichia coli chromosome was determined. This region was found to contain the dna Y gene encoding a transfer RNA. The curved DNA structure was demonstrated to be located just upstream of the dna Y promoter. The results of sequencing further revealed that the int gene of a cryptic prophage, qsr', which has been shown to be present in the E. coli genome, is located next to the dna Y gene.

Amino Acid Sequence↗
PubMed1980

Transfer-deficient cointegrates of Flac and lambda prophage.

Twelve transfer-deficient mutants of the plasmid Flac were obtained by insertion of prophage lambda into secondary attachment sites within the transfer region. Insertions into eight different tra genes were identified. These mutations were strongly polar on expression of tra genes previously mapped "downstream", and thus confirmed that the genes traA through traD form a single operon. However, some continued expression of traI suggested that this was transcribed in part from a promoter located between traD and traI, and in part from the transfer operon promoter. One insertion early in the transfer operon produced a plasmid-specific tra mutation not complemented by R100-1 or R1-19: this insertion was into a new gene (traY), located before traA as the first member of the transfer operon. Partial tra deletion mutants were obtained as 42 degrees C--survivors from several of the Flac tra::ED lambda 4 plasmids, and their properties are described.

Bacteriophage lambda↗
PubMed1981

Genetic analysis of mu or mini-mu containing F' pro lac episomes after prophage induction.

We have investigated the fate of different F pro lac episomes carrying a Mu or mini-Mu, after induction of the Mu or mini-Mu prophage, by looking at the frequencies of transfer of the episome and of one chromosomal marker. During the first 10 min after induction the frequency of chromosome mobilization increases while the frequency of episome transfer decreases. This suggests that the F interacts with the chromosome through some kind of Mu mediated process. Later the transfer of both the episome and chromosomal markers is inhibited. Possible reasons for this inhibition are discussed.

Bacteriophage mu↗
PubMed1976

Isolation of lambda prophage mutants defective in structural genes: their use for the study of bacteriophage morphogenesis.

Mutants of coliphage lambda defective in structural genes were isolated and characterized. The isolation method consisted in lysogenizing bacteria with mutagenized phage and testing for inability to form plaques after heat induction. The mutants were propagated as prophages in the lysogens. Mutants in the region of the tail-genes U, V, G and H were enriched for by a selection method based on recombination and complementation with known mutants, and they were mapped by deletion mapping with newly isolated lambdadg's. The lysates of all the mutants were examined by electron microscopy. Some of the mutants showed phenotypes different from those of known amber mutants in the same genes. They are interpreted as producing partially active, altered gene products and might be useful for the studies of morphogenesis and of the mechanism of infection.

Coliphages↗