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At least 127 records · Page 7Linked to original sources
PubMed1997

Cloning of anti-Gal Fabs from combinatorial phage display libraries: structural analysis and comparison of Fab expression in pComb3H and pComb8 phage.

Anti-Gal is the most abundant natural antibody in humans. It interacts specifically with the carbohydrate epitope Gal alpha1-3Galbeta1-4GlcNAc-R (termed the alpha-galactosyl epitope). In an attempt to characterize the Ig genes encoding anti-Gal, two combinatorial phage display libraries in phagemid pComb3H were screened for anti-Gal Fabs. For this purpose, phages were incubated with biotinylated BSA coupled with alpha-galactosyl epitopes (designated alpha-Gal-BSA). Subsequently, phages complexed with alpha-Gal-BSA were isolated by streptavidin-coupled magnetic beads. Because of the low affinity of this antibody, a characteristic shared with other anti-carbohydrate antibodies, only two clones displaying anti-Gal activity were isolated. Clone G9 contained the VH gene V3-43 and VL gene DPK15, whereas clone P19 contained the VH gene V3-15 and VL gene DPL16. Both clones contained between five and 14 mutations in their H and L chain V genes. The affinity of clone G9 was found to be higher than that of clone P19, as only the former could bind to solid-phase alpha-galactosyl epitopes in an enzyme-linked immunosorbent assay. This interaction could be increased by expressing Fabs in phagemid pComb8 grown in the presence of IPTG. Under such conditions, the IPTG-activated Lac-Z promoter induces an increased expression of Fabs that are linked to phage envelope protein VIII, resulting in multiple Fab display on the phage. The data suggest that screening combinatorial phage display libraries for anti-carbohydrate antibodies may be more effective with pComb8 phage grown in the presence of IPTG.

Amino Acid Sequence↗
PubMed1999

A phagemid vector using the E. coli phage shock promoter facilitates phage display of toxic proteins.

Phage display is a powerful tool with which to adapt the specificity of protease inhibitors. To this end, a library of variants of the potato protease inhibitor PI2 was introduced in a canonical phagemid vector. Although PI2 is a natural trypsin inhibitor, we were unable to select trypsin-binding variants from the library. Instead, only mutants carrying deletions or amber stop codons were found. Bacteria carrying these mutations had a much faster growth rate than those carrying the wt PI2-encoding gene, even when the promoter was repressed. To overcome these problems, two new phagemid vectors for g3-mediated phage display were constructed. The first vector has a lower plasmid copy number, as compared to the canonical vector. Bacteria harboring this new vector are much less affected by the presence of the PI2-g3 fusion gene, which appears from a markedly reduced growth retardation. A second vector was equipped with the promoter of the Escherichia coli psp operon, instead of the lac promoter, to control the PI2-g3 gene fusion expression. The psp promoter is induced upon helper phage infection. A phagemid vector with this promoter controlling a PI2-g3 gene fusion did not affect the viability of the host. Furthermore, both new vectors were shown to produce phage particles that display the inhibitor protein and were therefore considered suitable for phage display. The inhibitor library was introduced in both new vectors. Trypsin-binding phages with inhibitory sequences were selected, instead of sequences with stop codons or deletions. This demonstrates the usefulness of these new vectors for phage display of proteins that affect the viability of E. coli.

Amino Acid Sequence↗
PubMed1994

Clonal selection and amplification of phage displayed antibodies by linking antigen recognition and phage replication.

The immune response generates a tremendous array of antibody specificities by VDJ-gene rearrangements. A similar diversity can be obtained by expressing entire V-gene repertoires on the surface of filamentous bacteriophages creating large antibody libraries. Here we describe how the clonal selection mechanisms of the humoral immune response can also be mimicked in the phage display system by linking antigen-recognition and phage replication. We have achieved this by displaying antibody libraries on engineered, non-infectious phage with gene 3 deletions. Individual, antigen-specific phage are made replication competent by allowing a fusion protein, consisting of the antigen and phage coat protein 3, to bind the displayed antibody fragment. This fusion protein bridges the phage and F-pili of the bacteria and allows infection to be initiated and the phage to be clonally amplified with specific enrichment factors of approximately 10(10) after only two rounds.

Antibodies↗
PubMed1955

The effect of iodoacetate and other inhibitors on phage production and lysis in three phage systems.

The minimal bacteriostatic concentration of iodoacetate, azide, or proflavine was added at intervals during the latent periods of virus in three different bacterium-bacteriophage systems (M. aureus, B. mycoides, E. coli). For each interval at which inhibitor was added, the occurrence of lysis and the final yield of phage were determined. In the B. mycoides and E. coli systems, when added during the first part of the latent period, inhibitor prevented lysis and no phage was released. Introduction of inhibitor during the last part of the latent period resulted in normal lysis and in a linear increase in phage that progressively approached the yield obtained in the absence of inhibitor (the later the introduction, the higher the yield). In the M. aureus system, phage production and lysis in the presence of inhibitor followed the same general pattern, except that release of phage and normal lysis occurred in infected cells to which inhibitor had been added quite early in the latent period. Our results, when compared with those of Foster (1948) with proflavine and Bozeman et al. (1954) with chloramphenicol, suggest that (1) the final phage yields represent the amount of mature intracellular virus present at the time of addition of inhibitor and (2) the reactions leading to lysis proceed independently of those leading to the formation of mature virus once phage infection has reached a critical point in time.

Azides↗
PubMed1981

Effect of defective phages on the cell membrane of Bacillus subtilis and partial characterization of the phage protein involved in killing.

In order to investigate whether defective phages of Bacillus subtilis killed sensitive bacteria by a lysis from without mechanism, the minimal number of phages required for killing was determined. This figure was found to vary with the m.o.i., giving a value of 1 on extrapolation to an m.o.i. of 0. This excluded lysis from without as the only killing mechanism, although it might play a role at high m.o.i.s. This was confirmed by experiments on leakage of ATP and u.v.-absorbing material, the uptake of oxygen and the effect of the phages on the membrane potential. Apart from a short, initial leakage of ATP, the cell membrane was not affected at low m.o.i.s. These results lead to the conclusion that at low m.o.i.s. the phages acted on a cytoplasmic component. Treatment of defective phages for 10 min at pH 2.5 resulted in breakdown of the phages without complete abolition of the killing activity. The active component, which was shown not to be DNA, could not be isolated from the mixture, but SDS gel electrophoresis of PBS X and a non-killing mutant of this phage suggested that a protein with a mol. wt. of 85000 was involved in killing.

Bacillus subtilis↗
PubMed1984

A phage-resistant mutant of Lactobacillus casei which permits phage adsorption but not genome injection.

A phage-resistant mutant of Lactobacillus casei (strain YIT 9021) was capable of adsorbing both PL-1 and J-1 phages, but did not yield phage-infected cells. The mutant and wild-type strains were identical in morphology and sugar composition of the cell walls. Attempts to induce prophages from strain YIT 9021 were unsuccessful. Electron microscopic examination of negatively stained mixtures of phage PL-1 and YIT 9021 bacteria revealed that the phages were adsorbed to the cells in a tail-first orientation. All the absorbed phages had DNA-filled heads. It was concluded that PL-1 adsorbed normally but was blocked in the injection of the phage genome into the cell.

Bacteriophages↗
PubMed1987

Recombinant derivatives of Bacillus subtilis phage Z containing the DNA methyltransferase genes of related methylation-proficient phages.

The DNA methyltransferase (Mtase) genes of temperate Bacillus subtilis phages SPR, phi 3T, SP beta and rho 11 can be transferred by transfection and recombination to the genome of the related non-modifying phage Z. Integration of the Mtase genes occurs in phage Z DNA at a unique location which is homologous with the flanking regions of the Mtase genes of the related phages. In lysogenic cells carrying recombinant phages, expression of the Mtase genes is repressed, irrespective of whether the Mtase genes were derived from phage donors which were homo- or heteroimmune to phage Z.

Bacillus subtilis↗
PubMed1984

Characterization of generalized transducing phage phi w39 heteroimmune to phage P1 in Escherichia coli W39.

Generalized transducing phage similar to phage P1 in Escherichia coli was isolated from E. coli W39, an antigenic test strain of the O121 group. This phage, designated phi w39, was reciprocally heteroimmune to phages P1 and P7, but nonreciprocally heteroimmune to phage D6. Transduction experiments using various R plasmids with different molecular weights suggested that phage phi w39 could transduce at least 65 megadaltons DNA. As in the case of P1 prophage, phi w39 prophage existed as a plasmid belonging to incompatibility group Y and carried a dnaB-like function. The molecular weight of phi w39 plasmid was nearly the same as that of plasmid, i.e., 58.6 megadaltons. Despite the pronounced structural and functional similarity of phages phi w39 and P1, restriction cleavage patterns of their genomes differed considerably.

Coliphages↗
PubMed2000

Identification of a DNA region from lactococcal phage sk1 protecting phage 712 from the abortive infection mechanism AbiF.

Bacteriophage 712 is a small isometric-headed phage which is sensitive to the lactococcal abortive infection mechanism AbiF. Its 29.6-kb DNA genome was characterized by restriction mapping and transcriptional analysis. Construction of a gene bank of lactococcal phage sk1, which is insensitive to the action of AbiF, in Lactococcus lactis containing AbiF resulted in the identification of a 324-bp DNA fragment which reduced the effect of the abortive infection mechanism on phage 712. Analysis of this region provided evidence that the action of AbiF is related to the cos ends of small isometric-headed phages. Sequence analysis of a 3.2-kb segment containing the middle operon and the cos ends of phage 712 genome allowed comparison of this part of the phage 712 genome with the equivalent sequences of four other small isometric-headed phages.

Cloning, Molecular↗
PubMed2006

Genome sequence and global gene expression of Q54, a new phage species linking the 936 and c2 phage species of Lactococcus lactis.

The lytic lactococcal phage Q54 was previously isolated from a failed sour cream production. Its complete genomic sequence (26,537 bp) is reported here, and the analysis indicated that it represents a new Lactococcus lactis phage species. A striking feature of phage Q54 is the low level of similarity of its proteome (47 open reading frames) with proteins in databases. A global gene expression study confirmed the presence of two early gene modules in Q54. The unusual configuration of these modules, combined with results of comparative analysis with other lactococcal phage genomes, suggests that one of these modules was acquired through recombination events between c2- and 936-like phages. Proteolytic cleavage and cross-linking of the major capsid protein were demonstrated through structural protein analyses. A programmed translational frameshift between the major tail protein (MTP) and the receptor-binding protein (RBP) was also discovered. A "shifty stop" signal followed by putative secondary structures is likely involved in frameshifting. To our knowledge, this is only the second report of translational frameshifting (+1) in double-stranded DNA bacteriophages and the first case of translational coupling between an MTP and an RBP. Thus, phage Q54 represents a fascinating member of a new species with unusual characteristics that brings new insights into lactococcal phage evolution.

Amino Acid Sequence↗
PubMed2006

Abortive phage resistance mechanism AbiZ speeds the lysis clock to cause premature lysis of phage-infected Lactococcus lactis.

The conjugative plasmid pTR2030 has been used extensively to confer phage resistance in commercial Lactococcus starter cultures. The plasmid harbors a 16-kb region, flanked by insertion sequence (IS) elements, that encodes the restriction/modification system LlaI and carries an abortive infection gene, abiA. The AbiA system inhibits both prolate and small isometric phages by interfering with the early stages of phage DNA replication. However, abiA alone does not account for the full abortive activity reported for pTR2030. In this study, a 7.5-kb region positioned within the IS elements and downstream of abiA was sequenced to reveal seven additional open reading frames (ORFs). A single ORF, designated abiZ, was found to be responsible for a significant reduction in plaque size and an efficiency of plaquing (EOP) of 10(-6), without affecting phage adsorption. AbiZ causes phage phi31-infected Lactococcus lactis NCK203 to lyse 15 min early, reducing the burst size of phi31 100-fold. Thirteen of 14 phages of the P335 group were sensitive to AbiZ, through reduction in either plaque size, EOP, or both. The predicted AbiZ protein contains two predicted transmembrane helices but shows no significant DNA homologies. When the phage phi31 lysin and holin genes were cloned into the nisin-inducible shuttle vector pMSP3545, nisin induction of holin and lysin caused partial lysis of NCK203. In the presence of AbiZ, lysis occurred 30 min earlier. In holin-induced cells, membrane permeability as measured using propidium iodide was greater in the presence of AbiZ. These results suggest that AbiZ may interact cooperatively with holin to cause premature lysis.

Bacterial Proteins↗
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↗
PubMed2003

Validation of phage T7 biological dosimeter by quantitative polymerase chain reaction using short and long segments of phage T7 DNA.

Phage T7 can be used as a biological dosimeter; its reading, the biologically effective dose (BED), is proportional to the inactivation rate |ln (n/n0)|. For the measurement of DNA damage in phage T7 dosimeter, a quantitative polymerase chain reaction (QPCR) methodology has been developed using 555 and 3826 bp fragments of phage T7 DNA. Both optimized reactions are so robust that an equally good amplification was obtained when intact phage T7 was used in the reaction mixture. In the biologically relevant dose range a good correlation was obtained between the BED of the phage T7 dosimeter and the amount of ultraviolet (UV) photoproducts determined by QPCR with both fragments under the effect of five various UV sources. A significant decrease in the yield of photoproducts was detected by QPCR in isolated T7 DNA and in heated phage compared with intraphage DNA with all irradiation sources. Because the yield of photoproducts was the same in B, C and A conformational states of T7 DNA, a possible explanation for modulation of photoproduct frequency in intraphage T7 DNA is that the presence of bound phage proteins induces an alteration in DNA structure that can result in increased induction of photoproducts.

Bacteriophage T7↗
PubMed1999

Influence of phage proteins on formation of specific UV DNA photoproducts in phage T7.

Phage T7 can be used as a biological UV dosimeter. Its reading is proportional to the inactivation rate expressed in HT7 units. To understand the influence of phage proteins on the formation of DNA UV photoproducts, cyclobutane pyrimidine dimers (CPD) and (6-4)photoproducts ((6-4)PD) were determined in T7 DNA exposed to UV radiation under different conditions: intraphage T7 DNA, isolated T7 DNA and heated phage. To investigate the effects of various wavelengths, seven different UV sources have been used. The CPD and (6-4)PD were determined by lesion-specific antibodies in an immunodot-blot assay. Both photoproducts were HT7 dose-dependently produced in all three objects by every irradiation source in the biologically relevant UV dose range (1-10 HT7). The CPD to (6-4)PD ratios increased with the increasing effective wavelength of the irradiation source and were similar in intraphage T7 DNA, isolated DNA and heated phage with all irradiation sources. However, a significant decrease in the yield of both photoproducts was detected in isolated T7 DNA and in heated phage compared to intraphage DNA, the decrease was dependent on the irradiation source. Both photoproducts were affected the same way in isolated T7 DNA and heated phage, respectively. The yield of CPD and (6-4)PD was similar in B, C-like and A conformational states of isolated T7 DNA, indicating that the conformational switch in the DNA is not the decisive factor in photoproduct formation. The most likely explanation for modulation of photoproduct frequency in intraphage T7 DNA is that the presence of bound phage proteins induces an alteration in DNA structure that can result in an increased rate of dimerization and (6-4)PD production of adjacent based in intraphage T7 DNA.

Bacteriophage T7↗
PubMed1980

[Pseudomonas aeruginosa bacteriophages with DNA structure similar to the DNA structure of Mu1 phage. II. Evidence for similarity between D3112, B3, and B39 bacteriophages: analysis of DNA splits by restriction endonucleases, isolation of D3112 and B3 recombinant phages].

It is found that bacteriophages B3 and B39 specific for Pseudomonas aeruginosa have the same genome structure as previously described phage D3112. On the right (S) end of their genomes a variable non-phage DNA is located (approximately 0.9-2.5 kilobases for different phages). It is probable that this variable DNa has its origin from different regions of bacterial chromosome. In genome of one of the phages, B3 phage, such variable DNA (not more than 150 base pairs) was found on the left end of DNA molecule. Isolation of a viable B3XD3112 recombinant phage and analysis of its genome with restriction technique and with studies of homo- and heteroduplex molecules had confirmed genetical relationship of B3 and D3112. Some essential non-homology of B3 and D3112 DNAs have been found on the right ends of genomes of the phages.

Bacteriophages↗
PubMed1978

[Phage-typing modifications induced by "in vitro" transfer of R plasmids. I.--Phage typing of Salmonella typhi (author's transl)].

The phage-typing modifications induced by transfer of antibiotic-resistance plasmids wre studied in two S. typhi Vi+ strains: n 2411 (phage-type A) and Ty2 (phage-type E1a). Forty-one R plasmids belonging to twenty-two incompatibility groups were investigated. Twenty-two plasmids were unable to produce any phage typing modifications. Among the groups of plasmids with phage-typing restriction capacity,four (I1, 10.B.O., N and W) groups were found heterogeneous with regard to this property and one (F1 group) caused significant modifications of the phage-types defined by the Vi phage-typing international system.

Anti-Bacterial Agents↗
PubMed1963

INHIBITORY ACTION OF PHAGE K ON STAPHYLOCOCCAL DEHYDROGENASES. I. EFFECT ON VARIOUS STRAINS OF STAPHYLOCOCCUS AUREUS, INCLUDING MEMBERS OF THE PHAGE-TYPING SERIES.

Ralston, D. J. (University of California, Berkeley) and B. S. Baer. Inhibitory action of phage K on staphylococcal dehydrogenases. I. Effect on various strains of Staphylococcus aureus, including members of the phage-typing series. J. Bacteriol. 86:666-672. 1963.-The polyvalent phage K was found to depress the dehydrogenase activities of a large number of Staphylococcus aureus strains, as measured by the reduction of triphenyl tetrazolium chloride to the insoluble red formazan. The inhibition occurred immediately after the absorption of a multiplicity of phage particles, and was independent of the infectibility of the strains and of the killing ability of the phage. It appeared to be closely associated with the phenomenon of sensitization-a change in the cell surface which increased the susceptibility of the wall to digestion by soluble staphylococcal lysins and simultaneously abolished the capacity to synthesize phage. The inhibitory effect occurred both in nutrient media and in a nongrowth glucose - phosphate buffer supplemented with cysteine.

Bacteriophage Typing↗
PubMed1980

Complementation of T4 phage am mutations by hybrid phages lambda-T4.

EcoRI fragments of the T4 cytosine-containing DNA (dC-DNA) were cloned in the lambda XIII vector phage carrying the only restriction site for EcoRI in the repressor gene of lambda. 38 genes of T4 were identified in the cloned fragments by means of marker rescue technique. All cloned early genes and some late genes of T4 were able to complement a corresponding am mutations of T4 phage when nonpermissive cells of E.coli were simultaneously infected with hybrid phages lambda-T4 and am mutants of T4. An average burst size for am mutants from su- cells (when complemented by corresponding hybrid phage) was 20-70 pfu for early genes and 1-3 to 20 pfu for late ones. When the extract of cells infected with hybrid phage lambda-T4-22 containing T4 genes 57, 1, 2, 64 was mixed with the extract of cells infected with T4N51 mutant, the complementation in vitro was observed. So, it was shown that normal product of late gene 2 is synthesized in the cells infected with hybrid phage lambda-T4-22 in the absence of positive regulators of transcription coded by early T4 genes.

Bacteriophage lambda↗