Negatively charged amino acid residues play an active role in orienting the Sec-independent Pf3 coat protein in the Escherichia coli inner membrane

The coat protein of Pseudomonas aeruginosa phage Pf3 is transiently inserted into the bacterial inner membrane with a single transmembrane anchor sequence in the N(out)C(in) orientation. The N-terminal sequence immediately flanking the membrane anchor contains one negatively charged residue, whereas the C-terminal hydrophilic segment has two positively charged residues. To investigate how the orientation of this protein is achieved, the three flanking charged amino acid residues were altered. Membrane insertion was analyzed in vivo using the accessibility to externally added protease and in vitro by testing the insertion into inverted Escherichia coli membrane vesicles. In both systems, the orientation of the protein was completely reversed for the oppositely charged mutant coat protein (RD mutant). In addition, we show in vivo that the electrochemical membrane potential is necessary for the translocation of both the wild-type and the mutant Pf3 coat proteins, suggesting that membrane insertion is driven by electrophoretic forces.

Mutational analysis of bacteriophage phi CTX cos site

The DNA of phi CTX contains the gene ctx, located closely downstream of cos. This encodes for the pore-forming cytotoxin protein, CTX. phi CTX converts some Pseudomonas aeruginosa strains into CTX producers. After different periods of phi CTX infection, two distinct forms of phage DNA were isolated: circular DNA from bacterial cytosol and later linear DNA from phi CTX particles. When circular phi CTX DNA was transfected into the P. aeruginosa strains CF5 and E40, phi CTX was amplified and ctx expressed. phi CTX induced a protein fraction in CF5 cells that cleaved the 0.477 kb cos fragment at the cos site, indicating terminase activity. Deletion and point mutation variants of the cos DNA were prepared. Protein binding to DNA in vitro and competition experiments in vivo showed that portions of the cos site and its flanking sequences are differentially critical to the binding of phi CTX-induced proteins.

Genetic and sequence analysis of the cos region of the temperate Pseudomonas aeruginosa bacteriophage, D3

The location and structure of the cos ends of bacteriophage D3, which infects Pseudomonas aeruginosa strain PAO, has been determined using a combination of deletion analysis, transposon mutagenesis, and sequencing directly off the phage DNA. Phage D3 was found to have 9-bp 3' cos ends, making it the first phage of a Gram-negative organism known to have 3' cos ends. A 700-bp region flanking the cos site was necessary for efficient transduction of D3 cosmid derivatives. This region was found to contain incomplete inverted repeat sequences flanking the cos site, along with adenine-rich repeats homologous to coliphage gama Ter binding sites. Possible IHF binding sites were also present.

[Interaction between Pseudomonas aeruginosa phages-transposons: genetic analysis of the trait of inhibition by prophage D3112 of phage B39 development]

A novel, previously unknown cip gene of Pseudomonas aeruginosa phage D3112 was discovered. The cip gene is responsible for inhibiting the intracellular growth of the related heteroimmune phage B39 of P. aeruginosa. It was shown that the cip gene product inhibits replication of the B39 genome, interacting, apparently, with the definite s+ site in the phage B39 genome. Mutants cip- of phage D3112, incapable of inhibiting the growth of phage B39, and B39 mutants, insensitive to the action of the cip gene product of phage D3112, were isolated.

Damage to Pseudomonas aeruginosa PAO1 bacteriophage F116 DNA by biocides

The mechanism of action of biocides against viruses has not been widely studied, although two main targets are viral proteins (capsids, enzymes) and the viral genome. This study was undertaken in order to investigate the efficacy of several disinfectants against the nucleic acid of the Pseudomonas aeruginosa PAO bacteriophage F116. Of all the biocides tested, only peracetic acid affected significantly the phage genome. However, it is not clear whether the nucleic acid was damaged inside the phage capsid or when released into the surrounding medium.

Isolation and characterization of the recA gene of Xanthomonas campestris pv. campestris

A 1.8-kb NsiI-StuI fragment containing the recA gene of Xanthomonas campestris pv. campestris was cloned by a PCR-based approach and complementation of Escherichia coli HB 101. Sequence analysis of this fragment revealed an ORF (orf343) of 1,032 bp able to encode a protein of 343 amino acids with a calculated MW of 37,021 Da, a size similar to the values detected by in vitro system and Western blotting. It showed 69.6% identity to the E. coli RecA in amino acid sequence. Amino acid residues of the E coli RecA associated with functional activities are conserved in this Xc17 RecA. The recA mutant, L1, constructed by gene replacement, was sensitive to ultraviolet irradiation and methyl methanesulfonate, and deficient in homologous recombination.

Construction and analysis of a bacteriophage phi 6 gene 14 nonsense mutant

The production of a small low-abundance protein encoded by the large dsRNA genome segment of bacteriophage phi 6 in extracts of phage-infected Pseudomonas phaseolicola has been reported previously. Construction and analysis of a phage containing a nonsense mutation in this gene, designated gene 14, indicates that its product is not essential for growth in the laboratory. However, since early protein synthesis is delayed, burst sizes are reduced, and plaques are smaller than wild type, P14 is needed for optimal phage development.

[Cryptic transposable phages of Pseudomonas aeruginosa]

Frequencies of nucleotide sequences homologous to phage transposons (PT) of two species, D3112 and B3, were assessed in genomes of natural Pseudomonas aeruginosa strains by the dot-blot hybridization method. These strains were incapable of liberating viable phages on a lawn of the PA01 standard indicator strain of P. aeruginosa. It was shown that the homologies detected belong to two groups, high and intermediate, with respect to homology level. Homology patterns were classified as high when they provided signals comparable to those for hybridization in a positive control; they were classified as intermediate when the hybridization level higher than the background level, but lower than in the positive control. Homologous PT sequences were designated as cryptic PT. Intact cryptic PT prophages were shown to exist in genomes of particular natural strains manifesting a high level of hybridization. However, the growth of these phages was limited by the restriction system of strain PA01. It is possible to isolate strains maintaining the growth of a portion of cryptic PT. These strains differed from P. aeruginosa with respect to the specificity of the restriction and modification system. Nevertheless, in most cases, the attempt to identify a novel host capable of maintaining growth of a cryptic PT failed. Natural strains often carry cryptic PT related to both known PT species, D3112 and B3. The frequency of cryptic PT is extremely high, reaching 30% in only strains with a high level of homology and up to 50% in all strains exhibiting homology. This high PT frequency is assumed to be associated with the considerable variation of P. aeruginosa.

Nucleotide sequence of a single-stranded RNA phage from Pseudomonas aeruginosa: kinship to coliphages and conservation of regulatory RNA structures

We report the complete nucleotide sequence of the single-stranded RNA phage PP7 from Pseudomonas aeruginosa. There are three open reading frames which code for apparent protein homologues of the single-stranded RNA coliphages, i.e., maturation protein, coat protein, and replicase. A fourth overlapping reading frame exists that probably encodes a lysis protein, similar to what has been found in the group A coliphages such as MS2. The genetic map of PP7 is colinear with group A coliphages and we accordingly classify the phage as a levivirus. There is, generally speaking, no significant nucleotide sequence identity between PP7 and the coliphages except for a few regions where homologous parts of proteins are encoded, most notable in the replicase gene. In these regions the nucleotide sequence similarity between PP7 and MS2 is no greater than between PP7 and the group B coliphages such as Q beta. Surprisingly, Q beta and MS2 are no closer to each other than they are to PP7. Several regulatory RNA secondary structure features that are present in the coliphages were identified also in PP7 RNA although the sequences involved cannot be aligned. Among these are the coat protein binding helix at the start of the replicase gene, structures at the 5' and 3' terminus of the RNA, a replicase binding site, and the structure of the coat protein cistron start. Some of these features resemble MS2 type coliphages but others the Q beta type. These findings suggest that PP7 is related to the coliphages but branched off before the coliphages diverged into separate groups.

Site-specific integration of the phage phi CTX genome into the Pseudomonas aeruginosa chromosome: characterization of the functional integrase gene located close to and upstream of attP

The site-specific integration of the phage phi CTX genome, which carries the gene for a pore-forming cytotoxin, into the Pseudomonas aeruginosa chromosome was analysed. The 1,167 bp integrase gene, int, located immediately upstream of the attachment site, attP, was characterized using plasmid constructs, harbouring the integration functions, and serving as an integration probe in both P. aeruginosa and Escherichia coli. The attP plasmids p1000/p400 in the presence of the int plasmid pIBH and attP-int plasmids pINT/pINTS can be stably integrated into the P. aeruginosa chromosome. Successful recombination between the attP plasmid p1000 and the attB plasmid p5.1, in the presence of the int plasmid pIBH in E. coli HB101 showed that the int gene is active in trans in E. coli. The int gene product was detected as a 43 kDa protein in E. coli maxicells harbouring pINT. Proposed integration arm regions downstream of attP are not necessary for the integration process. pINT and phage phi CTX could be integrated together into P. aeruginosa chromosomal DNA, yielding double integrates.

Cytotoxin-converting phages, phi CTX and PS21, are R pyocin-related phages

phi CTX is a temperate phage of Pseudomonas aeruginosa harbouring the ctx gene that encodes cytotoxin (CTX). We identified phi CTX as an R pyocin-related phage, by serological and molecular analysis, based on the findings that the infectivity of the phage was inhibited with the antisera directed R pyocins and R pyocin-related phages and that the phi CTX genome showed DNA homology to the genome of PS17 (a representative of the R pyocin-related phages) as well as to the pyocin R2 genes. Another new CTX-converting, R pyocin-related phage named PS21 was isolated from a CTX-producing strain of P. aeruginosa, suggesting the distribution of the ctx gene by certain members of R pyocin-related phage family.

Transduction of imipenem resistance by the phage F-116 from a nosocomial strain of Pseudomonas aeruginosa isolated in Slovakia

Generalized transducting Pseudomonas aeruginosa phage F-116 was propagated in an Imipenem (IMI)-resistant clinical isolate of P. aeruginosa No. 191 and the phage was then used to transduce the IMI-resistance to a susceptible auxotrophic mutant strain of the same species. Transduction seems to be a suitable method for study of resistance determinant(s) and mechanism of resistance in this important species. It was found that the IMI-resistance of the clinical strain No. 191 is caused by production of a betalactamase specifically hydrolyzing this antibiotic.

Cloning of the early promoters of Pseudomonas aeruginosa bacteriophage D3: sequence of the immunity region of D3

The early promoters of bacteriophage D3 of Pseudomonas aeruginosa were cloned and physically mapped to the right 25% of the phage genome. The promoters were cloned into promoter selection vector pQF26, and their relative strengths, the direction of transcription, and whether they were directly regulated by repressor were determined. A 3.3-kb fragment of the genome containing the immunity region was sequenced and analyzed (GenBank accession number: L22692). The promoter activity associated with this region was determined to be bidirectional and repressible, indicating that this region contains operator-promoter complexes. Sequence and functional analyses suggest that this region is analogous to the immunity region of coliphage lambda. Two strong promoters, one of which was repressible, were found to be located adjacent to the immunity region. Clear-plaque mutant phage D3c contains insertion element IS222, which causes it to behave as a repressor-negative (c1) variant. The site of insertion of IS222 was sequenced and determined to lie within the c1 gene open reading frame. This phage shows remarkable similarity in genomic organization to coliphage lambda and its relatives.

Transduction of a freshwater microbial community by a new Pseudomonas aeruginosa generalized transducing phage, UT1

A pseudolysogenic, generalized transducing bacteriophage, UT1, isolated from a natural freshwater habitat, is capable of mediating the transfer of both chromosomal and plasmid DNA between strains of Pseudomonas aeruginosa. Several chromosomal alleles from three different P. aeruginosa strains were found to transduce at frequencies from 10(-8) to 10(-10) transductants per PFU at multiplicities of infection (MOI) between 0.1 and 1. Transduction frequencies of certain alleles increased up to 1000-fold as MOIs were decreased to 0.01. UT1 is also capable of transducing plasmid DNA to indigenous populations of microorganisms in natural lake-water environments. Data obtained in this study suggest that environmentally endemic bacteriophages such as UT1 are formidable transducers of naturally occurring microbial communities. It should be possible to develop model systems to test transduction in freshwater environments using components derived exclusively from these environments.

[The phenotype of rpi mutant of Pseudomonas aeruginosa phage-transposon D3112 expressed in a heterologous Escherichia coli host]

A clone of Escherichia coli II-16 with unique properties was isolated upon incorporation of hybrid plasmid RP4::D3112 with an integrated genome of phage-transposon D3112 Pseudomonas aeruginosa into E. coli C600 cells. The cells of this clone produce viable phage and are not sensitive to growth under low temperatures, which is characteristic of the majority of E. coli (RP4::D3112) clones with the genome of wild type phage. The clone E. coli II-16 contains phage genome both in an integrated state within the chromosome and in plasmid RP4. The properties of phage D3112 in the clone II-16 demonstrated that the phage carried a mutation. The mutation was designated RP4-phage interaction (rpi). The phenotypic effect of this mutation is expressed as phage inability to replicate in response to the presence of plasmid RP4 at 30 C (Tcs phenotype). The mutant rpi differs in its characters from the previously described mutants in the early regulator gene cip, the analog of the ner gene of E. coli phage Mu1, and from the known mutations in the A gene. Plasmid RP4::D3112 rpi exerts an inhibitory effect on the burst size of RP4::D3112 in E. coli.

Transduction of resistance to Imipenem, Aztreonam and Ceftazidime in nosocomial strains of Pseudomonas aeruginosa by wild-type phages

Two wild-type bacteriophages, designated AP-2 (for P. aeruginosa phage) and AP-12, have been isolated and propagated from two multiple drug resistant strains of P. aeruginosa. Both phages were found to transduce Imipenem- (IMI), Aztreonam- (AZA) and Ceftazidime- (CTZ) resistance as well as resistance determinants to other drugs. Genetic analysis showed that resistance determinants to newest anti-pseudomonal antibiotics IMI, AZA and CTZ could be separated by transduction. Thus the resistance to these antibiotics is presumably coded by different genes. In some transductans also the presence of the tra+ has been demonstrated, indicating that they can transfer the resistance to other strains by conjugation.

The cloning and characterization of phage promoters, directing high expression of luciferase in Pseudomonas syringae pv. phaseolicola, allowing single cell and microcolony detection

Regions of DNA containing promoter sequences from a Pseudomonas syringae pv. phaseolicola-specific phage (phi 11P) were identified by shotgun cloning into a broad-host-range promoter-probe vector (pQF70). When used in conjunction with the luciferase reporter genes, one of these DNA fragments, 19H, directed gene expression at a level which enabled the subsequent light output (bioluminescence) of single cells of P. syringae pv. phaseolicola to be detected and visualized using a charge-coupled device (CCD). The P. syringae pv. phaseolicola phi 11P, 19H and P. aeruginosa phi PLS27, HcM promoters gave a 50-fold increase in bioluminescence (maximum relative light output) compared to similar constructs containing other well-characterized promoters, for example, tetracycline. Similar bioluminescent characteristics of the transformed bacterium, were observed during growth with and without antibiotic-selection. When lux+ bacteria were inoculated onto French bean leaf (Phaseolus vulgaris L.), the resultant secondary halo blight lesions were bioluminescent and during phylloplane colonization by the lux+ bacterium, bioluminescence on leaf surfaces was detected and imaged by the CCD. Use of these newly identified promoters, combined with the greatly increased sensitivity of bioluminescence detection by the CCD, thus provided a new dimension for the study of natural ecological populations during the bacterial colonization of plants.

[The effect of certain Escherichia coli genes on the appearance of the TCS phenotype, conferred by plasmid RP4 with an integrated genome of the D3112 Pseudomonas aeruginosa phage]

The possibility of the SOS system activation caused by introduction of a hybrid plasmid RP4::D3112 (where D3112 is a genome of the transposable phage of Pseudomonas aeruginosa) into Escherichia coli was examined. It has been shown previously that the presence of this plasmid confers to E. coli a so called TCS phenotype: E. coli (RP4::D3112) forms normal colonies and grows at 42 degrees C but does not divide and becomes filamentous at 30 degrees C, probably because of E. coli DNA damages generated in the course of D3112 replication-transposition. It was shown that the level of prophage lambda induction is not elevated during the growth of E. coli (lambda) (RP4::D3112) cells at 30 degrees C. The character of the TCS phenotype was not affected by lex A3 or lex A51 mutations (which cause correspondingly non-inducibility or constitutive expression of the SOS regulon). It was concluded therefore that the TCS phenotype is not related to induction of the SOS response. It was found also that the mutation to heat shock gene dnaJ (dnaJ259) is a cause for significant decrease in phage D3112 production in E. coli dnaJ259 (RP4::D3112) cells. The DNA hybridization data of labelled RP4 and D3112 DNA with total E. coli dnaJ259 (RP4::D3112) DNA suggest that the dnaJ259 probably affected the late D3112 functions.

[Transduction of Pseudomonas mallei bacteria]

The transducing ability of 17 Pseudomonas pseudomallei bacteriophages has been studied. Five of them were found to be capable of transducing the transposon Tn7 markers TpR, SmR into the strain Pseudomonas mallei C-5. The transduced bacterial recipients became lysogenic and acquired resistance to trimethoprim and streptomycin. Transduction of transposon Tn7 has been confirmed by DNA-DNA hybridization.

Nucleotide sequence of attP and cos sites of phage CTX and expression of cytotoxin in Pseudomonas aeruginosa PA158

The gene for Pseudomonas aeruginosa cytotoxin (CTX) has been found to be part of a temperate phage with a total size of 35.5 kb. We have investigated several DNA fragments of this phage for CTX production. For phage integration, the phage genome cohesive (cos) ends covalently associate with host DNA of strain PA158. The cos ends and the CTX gene are found on a 3.4 kb EcoRI fragment B and are included in the 11 kb HindIII fragment A and the 8.5 kb BamHI fragment B of the phage DNA. The cos ends are 20 nucleotides long and are located at 338-357 nucleotides upstream of the CTX transcriptional initiation site. The phage attachment (attP) site is also present on the 3.4 kb EcoRI fragment B. The attP site consists of 34 bp and is located at 974-1007 nucleotides upstream of the CTX gene start site. Replication of the vegetative form of the phage is increased at 37 degrees C compared to that at 30 degrees C, while cytotoxin production in infected cells is similar at 30 degrees C and 37 degrees C. It can be concluded, therefore, that the integrated form of the CTX gene is responsible for CTX production. SDS-polyacrylamide gel electrophoresis (SDS-PAGE) showed ten proteins in purified phage preparations; however, CTX could not be detected on Western blots using an enzyme-linked immunofluorescence assay.

DNA homology in species of bacteriophages active on Pseudomonas aeruginosa

Using electron microscopy and DNA-DNA-hybridization, 113 virulent and temperate bacteriophages specific for P. aeruginosa have been assigned to 23 species. In most cases, especially in virulent phages, both particle morphology and DNA homology types were in good correlation and their use was sufficient for clear-cut definition of phage species. No virulent phages of different species had any DNA homology. DNA homology was detected between temperate phages of several species. Temperate phages formed two large groups of two and seven species, respectively. The first group included all transposable bacteriophages. The extent of interspecies DNA homology of phages belonging to each group was not more than 10-15% (except for 25% for phages D 3 and KF 1). No DNA homology was between phages of different groups. The possible origin and function of homologous sequences (genetic modules, linkers, occasional insertional sequences) are discussed. One of the phages (phi C 15) may be considered as the result of recombination between phages belonging to two different species, 295 and SM.

Molecular analysis of a cytotoxin-converting phage, phi CTX, of Pseudomonas aeruginosa: structure of the attP-cos-ctx region and integration into the serine tRNA gene

The Pseudomonas aeruginosa ctx gene encoding cytotoxin is carried by a temperate phage phi CTX. The genome of phi CTX is a 35.5 kb double-stranded DNA with cohesive ends (cos). It is unique in that the ctx gene and attP site of phi CTX exist very close to the respective cohesive ends. In this study, we determined the structure of this attP-cos-ctx region. The termini of phi CTX are 21-base 5' extended-single-stranded DNAs. The ctx gene is located 361 bp downstream of the left end (cosL). The attP core sequence of 30 bp exists only 647 bp apart from the right end (cosR). The attP-cos-ctx region contains six kinds of repeats and integration host factor-binding sequences and showed sequence-directed static bends, suggesting its potential to form a highly ordered structure. In addition, phi CTX was found to integrate into the serine tRNA gene which was mapped to the 43-45 min region on the P. aeruginosa chromosome.

Imipenem and cefotaxime resistance: transduction by wild-type phages in hospital strains of Pseudomonas aeruginosa

A wild-type bacteriophage appeared and was isolated from a Pseudomonas aeruginosa strain resistant to imipenem, cefotaxime, kanamycin and streptomycin (susceptible to carbenicillin, aztreonam, amikacin and fluoroquinolones). The best transducing properties were obtained with phage lysates prepared from bacteria growing on cefotaxime or imipenem. Transducing properties were found specific for individual recipient strain(s) susceptible to all drugs. A high-frequency of transduction was recorded for kanamycin and particularly for cefotaxime resistance determinants, followed by an imipenem determinant. This is now the fourth published wild-type bacteriophage, isolated from lysogenic nosocomial P. aeruginosa resistant to imipenem which was found to transduce this resistance determinant to susceptible pseudomonads.