SEARCH · PubMed Health

Results for “Prophages”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7Linked to original sources

PubMed2004

The role of prophage-like elements in the diversity of Salmonella enterica serovars.

The Salmonella enterica serovar Typhi CT18 (S.Typhi) chromosome harbours seven distinct prophage-like elements, some of which may encode functional bacteriophages. In silico analyses were used to investigate these regions in S.Typhi CT18, and ultimately compare these integrated bacteriophages against 40 other Salmonella isolates using DNA microarray technology. S.Typhi CT18 contains prophages that show similarity to the lambda, Mu, P2 and P4 bacteriophage families. When compared to other S.Typhi isolates, these elements were generally conserved, supporting a clonal origin of this serovar. However, distinct variation was detected within a broad range of Salmonella serovars; many of the prophage regions are predicted to be specific to S.Typhi. Some of the P2 family prophage analysed have the potential to carry non-essential "cargo" genes within the hyper-variable tail region, an observation that suggests that these bacteriophage may confer a level of specialisation on their host. Lysogenic bacteriophages therefore play a crucial role in the generation of genetic diversity within S.enterica.

Amino Acid Sequence↗

PubMed2003

Co-expression of a prophage system and a plasmid system in Bacillus subtilis.

A dual expression system for overexpressing two proteins by a single cell strain has been developed in Bacillus subtilis. This dual expression system combines the phi105MU331 prophage system and a plasmid system within a single cell. Protein expression by the prophage system is heat inducible, while that of the plasmid system is constitutive. Three candidate genes, BPN, BT, and amyE, all of Bacillus origin, were used as test models. Seven strains (BPN, BT, AMY, BS168K, MU331K, BPNK, and BTK) were constructed to investigate the influences of the prophage system and the plasmid system on each other, and to compare the efficiency of the individual expression systems with that of the dual expression system. Individually, the yield of the plasmid system is higher than that of the prophage system, which could be attributed to the constitutive nature of the expression of the plasmid system. Nonetheless, for the dual expression strains, the expression of two enzymes in a single fermentation run can reduce costs in facilities, manpower, and utilities. Fed-batch fermentation of BPNK strains confirmed the feasibility of applying this dual expression system in industrial-scale production.

Amylases↗

PubMed2004

The prophages of Lactobacillus johnsonii NCC 533: comparative genomics and transcription analysis.

Two non-inducible, but apparently complete prophages were identified in the genome of the sequenced Lactobacillus johnsonii strain NCC 533. The 38- and 40-kb-long prophages Lj928 and Lj965 represent distinct lineages of Sfi11-like pac-site Siphoviridae unrelated at the DNA sequence level. The deduced structural proteins from Lj928 demonstrated aa sequence identity with Lactococcus lactis phage TP901-1, while Lj965 shared sequence links with Streptococcus thermophilus phage O1205. With the exception of tRNA genes, inserted between DNA replication and DNA packaging genes, the transcription of the prophage was restricted to the genome segments near both attachment sites. Transcribed genes unrelated to phage functions were inserted between the phage repressor and integrase genes; one group of genes shared sequence relatedness with a mobile DNA element in Staphylococcus aureus. A short, but highly transcribed region was located between the phage lysin and right attachment site; it lacked a protein-encoding function in one prophage.

Attachment Sites, Microbiological↗

PubMed2003

Mechanisms of replication and telomere resolution of the linear plasmid prophage N15.

The prophage of coliphage N15 is not integrated into the bacterial chromosome but exists as a linear plasmid molecule with covalently closed ends. Upon infection of an Escherichia coli cell, the phage DNA circularizes via cohensive ends. A phage-encoded enzyme, protelomerase, then cuts at another site, telRL, and forms hairpin ends (telomeres). Purified protelomerase alone processes circular and linear plasmid DNA containing the target site telRL to produce linear double-stranded DNA with covalently closed ends in vitro. N15 protelomerase is necessary for replication of the linear prophage through its action as a telomere-resolving enzyme. Replication of circular N15-based miniplasmids requires the only gene repA that encodes multidomain protein homologous to replication proteins of bacterial plasmids replicated by theta-mechanism, particularly, phage P4 alpha-replication protein. Replication of the N15 prophage is initiated at an internal ori site located within repA. Bidirectional replication results in formation of the circular head-to-head, tail-to-tail dimer molecule. Then the N15 protelomerase cuts both duplicated telomeres generating two linear plasmid molecules with covalently closed ends. The N15 prophage replication thus appears to follow the mechanism distinct from that employed by poxviruses and could serve as a model for other prokaryotic replicons with hairpin ends, and particularly, for linear plasmids and chromosomes of Borrelia burgdorferi.

Coliphages↗

PubMed2005

Prophage association of mef(A) elements encoding efflux-mediated erythromycin resistance in Streptococcus pyogenes.

OBJECTIVES: To compare different mef(A) elements of Streptococcus pyogenes for a possible chimeric genetic nature, i.e. a transposon inserted into a prophage. METHODS: Eleven S. pyogenes isolates with efflux-mediated erythromycin resistance were used. The isolates were typed using several genotypic approaches. Gene detection was performed by PCR using specific primer pairs. The mef(A) elements of the test strains were induced with mitomycin C and phage DNA was extracted. Induction was monitored by PCR using primers targeting mef(A). RESULTS: Six tetracycline-susceptible isolates had PCR evidence of all of the eight open reading frames (ORFs) of the Tn1207.1 element; their mef(A) element was consistent with the Tn1207.3 element in four isolates and with the 58.8 kb chimeric element in two. Five tetracycline-resistant isolates had no PCR evidence of orf1 and orf2 and showed variable patterns as to orf3, orf7, and orf8. Three ORFs placed along the conserved region downstream of Tn1207.1 in the 58.8 kb mef(A) chimeric element were detected in the six tetracycline-susceptible, but not in the five tetracycline-resistant isolates. Induction assays with mitomycin C demonstrated that the mef(A) elements of all strains tested were present in culture supernatants in a DNAse-resistant form, such as a phage capsid. CONCLUSIONS: All recognized mef(A) elements of S. pyogenes appear to be prophage-associated. Whereas the two elements detected in tetracycline-susceptible isolates (Tn1207.3 and the 58.8 kb one) were apparently inserted into the same prophage, the tet(O)-mef(A) element was inserted into a different prophage. Phage transfer is likely to play a critical role in the dissemination of erythromycin resistance in S. pyogenes populations.

Bacterial Proteins↗

PubMed2003

Bidirectional replication from an internal ori site of the linear N15 plasmid prophage.

The prophage of coliphage N15 is not integrated into the chromosome but exists as a linear plasmid molecule with covalently closed hairpin ends (telomeres). Upon infection the injected phage DNA circularizes via its cohesive ends. Then, a phage-encoded enzyme, protelomerase, cuts the circle and forms the hairpin telomeres. N15 protelomerase acts as a telomere-resolving enzyme during prophage DNA replication. We characterized the N15 replicon and found that replication of circular N15 miniplasmids requires only the repA gene, which encodes a multidomain protein homologous to replication proteins of bacterial plasmids replicated by a theta-mechanism. Replication of a linear N15 miniplasmid also requires the protelomerase gene and telomere regions. N15 prophage replication is initiated at an internal ori site located within repA and proceeds bidirectionally. Electron microscopy data suggest that after duplication of the left telomere, protelomerase cuts this site generating Y-shaped molecules. Full replication of the molecule and subsequent resolution of the right telomere then results in two linear plasmid molecules. N15 prophage replication thus appears to follow a mechanism that is distinct from that employed by eukaryotic replicons with this type of telomere and suggests the possibility of evolutionarily independent appearances of prokaryotic and eukaryotic replicons with covalently closed telomeres.

Bacteriophages↗

PubMed2004

The Mycoplasma fermentans prophage phiMFV1: genome organization, mobility and variable expression of an encoded surface protein.

The approximately 16 kb genome of the Mycoplasma fermentans phiMFV1 prophage is described, and its mobility, replication and effect on the mycoplasma surface phenotype are demonstrated. In various M. fermentans strains, phiMFV1 was either absent or integrated at diverse (and sometimes multiple) chromosomal sites, each marked by a conserved TTTTTA target sequence that is duplicated upon integration. Precise excision, replication of an extrachromosomal form and loss of phiMFV1 from the mycoplasmal genome were documented in a series of clonal derivatives of M. fermentans propagated in culture. Of 18 open reading frames (ORFs) encoded by phiMFV1, most can be ascribed functions related to phage biology, whereas one encodes a unique coiled-coil membrane surface protein, Mem, that was confirmed to be expressed in propagating populations of M. fermentans. With the exception of Mem and other minor ORFs, the striking similarity between the deduced proteomes of phiMFV1 and the recently described phiMAV1 of arthritogenic strains of Mycoplasma arthritidis, along with the prominent gene synteny between these elements, provides the taxonomic basis for a new family of prophage. Their coding features are consistent with long-term residence in mycoplasma genomes and the divergence of species within a phylogenetic clade of mycoplasmas. The unique Mem protein expressed from phiMFV1 and the unique hypothetical surface lipoproteins encoded by phiMAV1 and phiMFV1 also suggest that prophage-associated genes may provide specific, selectable phenotypic traits during co-evolution of mycoplasma species with their respective mammalian hosts. Retention of these labile prophage elements in organisms with such drastically reduced genome sizes implies a significant role in adaptation and survival.

Adaptation, Biological↗

PubMed2004

Polylysogeny and prophage induction by secondary infection in Vibrio cholerae.

Strains of Vibrio cholerae O1, biotypes El Tor and classical, were infected with a known temperate phage (PhiP15) and monitored over a 15-day period for prophage induction. Over the course of the experiment two morphologically and three genomically distinct virus-like particles were observed from the phage-infected El Tor strain by transmission electron microscopy and field inversion gel electrophoresis, respectively, whereas only one phage, PhiP15, was observed from the infected classical strain. In the uninfected El Tor culture one prophage was spontaneously induced after 6 days. No induction in either strain was observed after treatment with mitomycin C. Data indicate that El Tor biotypes of V. cholerae may be polylysogenic and that secondary infection can promote multiple prophage induction. These traits may be important in the transfer of genetic material among V. cholerae by providing an environmentally relevant route for multiple prophage propagation and transmission.

Bacterial Typing Techniques↗

PubMed1964

ULTRAVIOLET SENSITIVITY OF ESCHERICHIA COLI CONTAINING HEAT-INDUCIBLE LAMBDA PROPHAGES.

The c1-t mutants of bacteriophage lambda can form prophage at 36 degrees C but cause lysis of sensitive bacteria at temperatures above 42 degrees C. Growth of cultures at 42 degrees to 46 degrees C induces prophage replication and lysis in Escherichia coli K12 (lambda c1-t); lysogenic strains containing wild-type prophage are not induced to lyse at these temperatures. Heat induction is prevented by chloramphenicol. Strains containing heatinducible prophage are much more sensitive to killing by ultraviolet light than is K12 (lambda+).

Bacteriophage lambda↗

PubMed2004

The pKO2 linear plasmid prophage of Klebsiella oxytoca.

Temperate bacteriophages with plasmid prophages are uncommon in nature, and of these only phages N15 and PY54 are known to have a linear plasmid prophage with closed hairpin telomeres. We report here the complete nucleotide sequence of the 51,601-bp Klebsiella oxytoca linear plasmid pKO2, and we demonstrate experimentally that it is also a prophage. We call this bacteriophage phiKO2. An analysis of the 64 predicted phiKO2 genes indicate that it is a fairly close relative of phage N15; they share a mosaic relationship that is typical of different members of double-stranded DNA tailed-phage groups. Although the head, tail shaft, and lysis genes are not recognizably homologous between these phages, other genes such as the plasmid partitioning, replicase, prophage repressor, and protelomerase genes (and their putative targets) are so similar that we predict that they must have nearly identical DNA binding specificities. The phiKO2 virion is unusual in that its phage lambda-like tails have an exceptionally long (3,433 amino acids) central tip tail fiber protein. The phiKO2 genome also carries putative homologues of bacterial dinI and umuD genes, both of which are involved in the host SOS response. We show that these divergently transcribed genes are regulated by LexA protein binding to a single target site that overlaps both promoters.

Amino Acid Sequence↗

PubMed2006

Prophagic DNA fragments in Streptococcus agalactiae strains and association with neonatal meningitis.

We identified-by randomly amplified polymorphic DNA (RAPD) analysis at the population level followed by DNA differential display, cloning, and sequencing-three prophage DNA fragments (F5, F7, and F10) in Streptococcus agalactiae that displayed significant sequence similarity to the DNA of S. agalactiae and Streptococcus pyogenes. The F5 sequence aligned with a prophagic gene encoding the large subunit of a terminase, F7 aligned with a phage-associated cell wall hydrolase and a phage-associated lysin, and F10 aligned with a transcriptional regulator (ArpU family) and a phage-associated endonuclease. We first determined the prevalence of F5, F7, and F10 by PCR in a collection of 109 strains isolated in the 1980s and divided into two populations: one with a high risk of causing meningitis (HR group) and the other with a lower risk of causing meningitis (LR group). These fragments were significantly more prevalent in the HR group than in the LR group (P < 0.001). Our findings suggest that lysogeny has increased the ability of some S. agalactiae strains to invade the neonatal brain endothelium. We then determined the prevalence of F5, F7, and F10 by PCR in a collection of 40 strains recently isolated from neonatal meningitis cases for comparison with the cerebrospinal fluid (CSF) strains isolated in the 1980s. The prevalence of the three prophage DNA fragments was similar in these two populations isolated 15 years apart. We suggest that the prophage DNA fragments identified have remained stable in many CSF S. agalactiae strains, possibly due to their importance in virulence or fitness.

Base Sequence↗

PubMed2026

Pan genome clustering identifies a novel mosaic prophage specific to Salmonella Enteritidis lineage associated with the invasive disease in India.

Salmonella enterica serovar Enteritidis is a leading cause of invasive non-typhoidal Salmonella (iNTS) disease globally, particularly in sub-Saharan Africa. In contrast, the epidemiology and population structure of invasive S. Enteritidis in South Asia remain poorly characterized. This study investigates the clinical presentation, phylogenetic relationships and genomic characteristics of S. Enteritidis bloodstream infections (BSIs) in India. Clinical data were collected from 101 patients with S. Enteritidis BSI between 2012 and 2022. Whole-genome sequencing was performed on representative bloodstream isolates together with isolates from non-blood clinical specimens and poultry sources. Comparative genomic analyses included phylogenetic reconstruction, invasiveness index prediction, and prophage characterization. Infants and immunosuppressed individuals were disproportionately affected by iNTS disease. Phylogenetic analysis identified four major lineages of S. Enteritidis. Most BSI isolates clustered in a previously unrecognized lineage, designated the Global Intermediate Clade, which occupied a phylogenetic position between the Global outlier and Global epidemic clades. Bayesian inference dated its most recent common ancestor to around 1789 AD (95% HPD: 1692-1941), with global circulation confirmed by European and Asian isolates. The Global Intermediate clade exhibited the second-highest invasiveness index (median 0.221, SD 0.013) after the West African clade; however, this index reflects genomic signatures associated with invasiveness and should not be interpreted as a direct measure of virulence. Poultry isolates clustered separately from the dominant bloodstream-associated lineage. Pan-genome analysis identified a lineage-specific mosaic prophage composed of modules homologous to prophages found in diverse Enterobacterales. This study provides the first detailed genomic insight into invasive S. Enteritidis in India and identifies a previously unrecognized Global Intermediate Clade associated with bloodstream infection. The distinct phylogenetic placement and genomic features of this lineage, including a lineage-specific mosaic prophage, warrant further investigation and support the need for expanded One Health genomic surveillance.

Humans↗

PubMed1990

Induction of prophage lambda by chlorophenols.

Chlorinated phenols, which are used primarily as wood preservatives and fungicides, are present in most air, water, and soil samples in industrialized areas as well as in the urine of most people. We have examined the ability of phenol and the 19 isomers of chlorophenol to induce DNA damage using the Microscreen prophage-induction assay in Escherichia coli. Seven of the isomers (2,3,4,-tri, 2,4,5-tri, 3,4,5-tri, 2,3,4,5-tetra, 2,3,6-tri, 2,4,6-tri, and pentachlorophenol) induced prophage lambda in the presence of S9, with the first three being approximately 10 times more potent than the last three. The more potent isomers have either one or no chlorine atom ortho to the OH group; whereas the less potent isomers have two chlorine atoms ortho to the OH group. Although none of the 20 compounds is mutagenic in Salmonella, the prophage-induction results agree with findings by others that most of these seven isomers are clastogenic, are associated with cancer and chromosomal aberrations in humans (pentachlorophenol), and are carcinogenic in rodents (2,4,6-tri and pentachlorophenol). A likely basis for the genotoxicity of the seven isomers involves the metabolism of the parent isomer to a chlorohydroquinone, which can form a chlorobenzosemiquinone in the presence of oxygen. These two metabolites can produce free radicals that can cause DNA strand breaks, resulting in prophage induction in E. coli or, possibly, the chromosomal aberrations/cancer associated with human exposure to chlorophenols.

Bacteriophage lambda↗

PubMed1983

Ham22, a mini-F mutation which is lethal to host cell and promotes recA-dependent induction of lambdoid prophage.

A mini-F region 800 bp long, located between the two F origin sites, plays an essential role in the relationship between the F plasmid and its host. This region comprises two sets of overlapping coding sequences: the first set codes for the newly identified H1 and H2 polypeptides; the second set codes for polypeptides G1 and G2. A mini-F amber mutation (Ham22) causes the virtual disappearance of polypeptides H1 and H2 but only slightly reduces synthesis of polypeptides G1 and G2. This mutation: (i) renders mini-F hybrids lethal to the host cells (conditional Hos- phenotype for host survival) and (ii) causes the induction of a resident prophage in recA+ strains (conditional Map- phenotype for maintenance of the prophage). When an additional mutation prevents the synthesis of polypeptides G1 and G2, both the lethal character and the induction of the prophage are abolished. We conclude: (i) that polypeptides G1 and/or G2 are specific mini-F polypeptides involved in the plasmid-mediated killing effect and in the recA-dependent induction of the resident prophage and (ii) that, in normal conditions, polypeptides H1 and/or H2 negatively control (directly or indirectly) the action of polypeptides G1 and/or G2. In relation to the analysis of indirect induction mediated by u.v.-irradiated lambda mini-F hybrids, we propose that polypeptides G1 and/or G2 are specific mini-F products involved in the activation of the bacterial SOS pathway. The H1/H2 and G1/G2 polypeptides could constitute the controlled mini-F signal enabling the coordination between cell division and F plasmid replication.

Bacteriophage lambda↗

PubMed1987

Transactivation of several genes of two native Serratia prophages after superinfection by phage kappa.

Serratia marcescens HY bacteria must be lysogenic with either prophage y or psi to make it possible for phage kappa to form plaques unless they carry a so-called ink mutation. Genes in y and psi termed any and anp were identified that after infection of ink+ cells are necessary for an effective propagation of these phages as well as of coinfecting kappa phage. When kappa infects y and/or psi-lysogenic cells it transactivates the respective prophage genes by means of two early genes termed tay and tap. It appears that on infection of nonlysogenic ink+ cells kappa damps its own development, provided the regulatory region of the responsible gene is undermethylated. After kappa infection duly to achieve the special methylation of this region seems to be the function of any and anp. There are some more genes in y and psi prophage under the control of tay and tap, concerning in both cases a Dam methylation (recognition sequence GATC) of kappa DNA, a recombination proneness under restricting conditions of kappa DNA not modified by the modification enzyme of HY, and the kappa plaque size. By hybridization studies a region of homology common to y and psi was demonstrated which from its size might comprise all the transactivated genes. The view is supported by genetic data indicating an affinity among the any and anp genes. Investigation of various any mutants were indicative of DNA inversions in this region of the y genome. Surprisingly some of the any mutants had become sensitive in their plaque forming ability to an inhibitory activity exerted by prophage psi. Mutants of psi unable to interfere but still able to lysogenize were isolated. A model is presented accounting for the formation of pleiotropic and nonpleiotropic mutations with Any phenotype and their reversion types. Possible functions of the y genes and their counterparts in psi are discussed.

Bacteriophages↗

PubMed1978

Regional replication of the bacterial chromosome induced by derepression of prophage lambda. IV. Escape synthesis of gal operon in phage 82.

Derepression of prophage lambda in E. coli strain K12 results in constitutive synthesis of the enzymes directed by the nearby bacterial operon, gal (escape synthesis). Phage 82 fails to cause escape synthesis despite that it lysogenizes the strain K12 at the site identical to that of lambda on the host chromosome. The reason for the observed difference between 82 and lambda is studied in the light of the recent finding that escape synthesis in lambda-lysogen is closely associated to phage-promoted replication of bacterial chromosome contiguous to the prophage including gal operon (escape replication). Excision-defective mutants from 82, 82int or 82xis, do initiate escape synthesis, suggest that the prophage 82 is normally excised too quickly after induction to allow sufficient escape replication. In support of this, much more DNA hybridizable to bacterial DNA contained in lambdagal accumulates after induction if 82int than after induction of 82. Studies with various hybrid phages between 82 and lambda have suggested: 1. The occurrence of gal escape synthesis depends on the nature of the region between b2 and N in the lambda map. 2. Regions of the 82 genome on both sides of the attachment site contribute independently to prevent gal escape synthesis. Implications of these results are discussed with regard to the factors involved in the prophage excision.

Chromosomes, Bacterial↗

PubMed1982

Cell survival, UV-reactivation and induction of prophage lambda in Escherichia coli K12 overproducing RecA protein.

The effect of the cellular level of RecA protein on the ability of E. coli K12 bacteria to (i) survive UV-irradiation (ii) promote UV-reactivation of UV-damaged phage lambda (iii) induce prophage lambda was determined in bacterial mutants with discrete increasing levels of RecA protein. The various levels of RecA protein were obtained by combining lexA and recA alleles. Except for the double mutant lexA3 recAo98, whose repair ability was 25% less than that observed in wild type bacteria, bacterial survival was proportional to the level of RecA protein measured after 90 min of incubation. In lexA3 recAo98 bacteria, RecA protein, at a constitutive high basal level, failed to compensate totally for the lack of LexA repressor cleavage; UV-reactivation of UV-damaged phage lambda was not restored; yet, prophage lambda was induced with 35% efficiency. Efficient UV-induction of prophage lambda is linked to the induction of lexA-controlled host processes that repair the UV-damaged prophage.

Bacterial Proteins↗

PubMed1983

Curing and induction of the Fels 1 and Fels 2 prophages in the Ames mutagen tester strains of Salmonella typhimurium.

A method is described for curing the Ames Salmonella mutagen tester strains of their Fels 1 and Fels 2 prophages with the aid of the antitumor drug daunorubicin. Non-lysogenic derivatives corresponding to TA100 and TA1535 were isolated and designated TAQ100 and TAQ1535 respectively. In addition, the Fels 1 monolysogens TAQ100F1 and TAQ1535F1, as well as the Fels 2 monolysogens TAQ100F2 and TAQ1535F2, were obtained. Finally, strains corresponding to TA98 and TA1538 cured of Fels 2, but retaining a cryptic Fels 1 (F1d) prophage were isolated and designated TAQ98F1d and TAQ1538F1d respectively. The various cured derivatives were identified by colony hybridization with 32P-labeled probes of Fels 1 and Fels 2 DNA. Southern blot hybridizations confirmed that phage-specific Fels DNA sequences were missing from the cured strains. The Fels 2-cured strains were resistant to Fels 2, but Fels 1 grew, albeit poorly, on the Fels 1-cured strains. Strains TAQ100F1, TAQ1535F1, TAQ100F2 and TAQ1535F2 were used in prophage induction assays, in the presence of rat-liver extract where necessary. Daunorubicin, bleomycin, mitomycin C, aflatoxin B1, 2-amino-dipyrido[1,2-a:3',2'-d]imidazole (Glu-P-2) were found to induce Fels 1 and/or Fels 2 in at least one of these strains. The induction of the Fels prophages in the TAQ monolysogens may provide a useful complement to the Ames test for the detection of DNA-damaging agents and potential carcinogens.

DNA, Bacterial↗