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[Genetic study of bacteriophage phi81. II. Gene localization in the right arm of the phage chromosome and a comparison of phage phi81 with phages lambda and phi80 in regard to gene functions].

Data on genetic investigation on lambdoid bacteriophage phi81 made possible to localize the cos site on the prophage genetic map. Four essential genes and the gene c1 are located in the right arm of the phage genetic map. Regulatory genes of phage phi81 are found to be uncapable of functional substitution of lambda phages regulatory genes N and Q. It is discovered that some late genes of phage phi80 can be substituted with respective phage phi81 genes. No substitution possibility was observed for a number of early genes of phage phi80.

Chromosome Mapping

The strategy of infection as a criterion for phylogenetic relationships of non-coli phages morphologically similar to phage T7.

Five phages which are morphologically similar to coliphage T7 but attack other host bacteria have been compared to T7 and to its relative, T3, by the following criteria: (a) cross-reactivity with antisera against T7 and T3, (b) DNA base sequence homologies, as determined by the C0t technique, (c) synthesis of two phage-coded enzymes: RNA polymerase and SAMase, (d) patterns of phage-directed protein synthesis, as determined by SDS-polyacrylamide gel electrophoresis of phage coat subunits. As judged by all these criteria, Pseudomonas phage PX3 is not related to T7; thus, morphological similarity was attributed to convergent evolution. The other phages, i.e. Serratia phage IV, Psuedomonas phage gh-1, Citrobacter phage ViIII and Klebsiella phage No. 11, were considered to be related to T7 on the basis of similarities in the patterns of phage-coded proteins and because, early after infection, these phages induced, as T7 does, an RNA polymerase which specifically transcribes the DNA of thehomologous phage. Phages IV and No. 11 also induced the early synthesis of SAMase (previously only known to occur upon T3 infection). With the exception of phage IV, however, DNA base sequence homologies with T7 or T3 seem to be poor or non-existent. The tested phages, again with the exception of phage IV, did not react with antiserum against T3 or T7. It is concluded that a particular pattern of phage-directed protein synthesis (as characterized by polyacrylamide gel electrophoresis and enzyme tests) may provide evidence for phylogenetic relationships between phages, even in cases where other criteria, such as genetic recombination, serological cross-reaction, and DNA base sequence homologies, fail to indicate relatedness.

Adenosylmethionine Decarboxylase

Exploring phage-host interactions in Burkholderia cepacia complex bacterium to reveal host factors and phage resistance genes using CRISPRi functional genomics and transcriptomics.

Complex interactions of bacteriophages with their bacterial hosts determine phage host range and infectivity. While phage defense systems and host factors have been identified in model bacteria, they remain challenging to predict in non-model bacteria. In this paper, we integrate functional genomics and transcriptomics to investigate phage-host interactions, revealing active phage resistance and host factor genes in Burkholderia cenocepacia K56-2. Burkholderia cepacia complex species are commonly found in soil and are opportunistic pathogens in immunocompromised patients. We studied infection of B. cenocepacia K56-2 with Bcep176, a temperate phage isolated from Burkholderia multivorans. A genome-wide dCas9 knockdown library targeting B. cenocepacia K56-2 was constructed, and a pooled infection experiment identified 63 novel genes or operons coding for candidate host factors or phage resistance genes. The activities of a subset of candidate host factor and resistance genes were validated via single-gene knockdowns. Transcriptomics of B. cenocepacia K56-2 during Bcep176 infection revealed that expression of genes coding for host factor and resistance candidates identified in this screen was significantly altered during infection by 4 h post-infection. Identifying which bacterial genes are involved in phage infection is important to understand the ecological niches of B. cenocepacia and its phages, and for designing phage therapies.IMPORTANCEBurkholderia cepacia complex bacteria are opportunistic pathogens inherently resistant to antibiotics, and phage therapy is a promising alternative treatment for chronically infected patients. Burkholderia bacteria are also ubiquitous in soil microbiomes. To develop improved phage therapies for pathogenic Burkholderia bacteria, or engineer phages for applications, such as microbiome editing, it's essential to know the bacterial host factors required by the phage to kill bacteria, as well as how the bacteria prevent phage infection. This work identified 65 genes involved in phage-host interactions in Burkholderia cenocepacia K56-2 and tracked their expression during infection. These findings establish a knowledge base to select and engineer phages infecting or transducing Burkholderia bacteria.

Bacteriophages

[New lambdoid phages of Escherichia coli. II. Comparison of several genetic characteristics with lambda phages].

Functions of some newly isolated lambdoid phages and phage lambda genes were compared by their ability to interact with unrelated phages and the product of the bacterial gene gro P. 19 of 23 lambdoid phages studied interfere with prophage P2, that points out the presence of functionally active genes, essential for spi+ phenotype in their genomes. The development of 4 lambdoid phages with spi- phenotype is independent on the prophage P2 presence. Most of lambdoid phages show the reduced growth ability on the C600 groP- bacterial lawn. This indicates that they have a function similar to the gene P of phage lambda. The development of phage phi M417 in bacterial mutants groP- is not disturbed, which indicates that the gene P of phage phi M417 is different from that of the phage lambda. Newly isolated phages, that are homoimmune to phage lambda, restrict the development of T4 rII phage. The rest lambdoid phages have no rex function. The growth efficiency of lampodid phages on E. coli C cells, carrying Eco R1 plasmid, varies from 10(-6) to 10(-8) that presumbaly indicates on different amounts of restionci strites in DNA of these phages.

Coliphages

Filamentous cheater phages drive bacterial and phage populations to lower fitness.

Many bacteria carry phage genome(s) in their chromosome, which intertwines the fitness of the bacterium and the phage. Most Pseudomonas aeruginosa strains carry filamentous phages called Pf that establish chronic infections and do not require host lysis to spread. However, spontaneous mutations in the Pf repressor gene (pf5r) can allow extreme phage production that slows bacterial growth and increases cell death, violating an apparent détente between bacterium and phage. We observed this paradoxical outcome in an evolution experiment with P. aeruginosa in media simulating nutrients from the cystic fibrosis airway. Bacteria containing pf5r mutant phage grow to a lower density but directly outcompete their ancestor and convert them into pf5r mutants via phage superinfection. Reduced fitness therefore spreads throughout the bacterial population, driven by weaponized Pf. Yet high intracellular phage replication facilitates another evolutionary conflict: "cheater miniphages" lacking capsid genes and the superinfection exclusion gene (pfsE) invade populations of full-length phages within cells. Although bacteria containing both full-length phages and miniphages are most immune to superinfection by limiting the Pf receptor, this hybrid vigor is extremely unstable, as a classic Tragedy of the Commons scenario ensues that causes complete prophage loss. The entire cycle - from phage hyperactivation to miniphage invasion to prophage loss - can occur within 24h, showcasing rapid coevolution between bacteria and their filamentous phages. This study demonstrates that P. aeruginosa, and potentially many other bacterial species that carry filamentous prophages, risk being exploited by these phages in a runaway process that reduces fitness of both host and virus.

Inoviridae

[New lambdoid Escherichia coli phages. I. Isolation, group immunity and recombination with lambda phage].

550 bacterial strains were isolated from sewage. 69 of them were lysogenic by phages active on Escherichia coli. The phages were divided into two groups on the basis of UV-inducibility, the ability to form plaques on Rep-E. coli mutants and particle morphology: lambdoid (23 phages) and related to P2 (46 phages). Hybrid phages isolated from the crosses of lambdoid phages with phage lambda harboured the region imm lambda and the gene of adsorption specificity from other parent. Ten groups of heteroimmune phages were found in the collection of new temperate phages are homoimmune with known phages: lambda, phi 80, phi 81, 434. Another 7 phages involved in 6 groups of immunity which were heteroimmune to known phages. Diversity of lambdoid phage genes determining the structure of repressor is discussed.

Coliphages

Phage and defective phage of strains of Myxococcus.

1. Phage-like particles were found in the supernatants of cultures of strains of Myxococcus xanthus, M. virescens and M. fulvus. The largest number of such particles was associated with M. virescens V2. Most of the particles were similar in morphology to the virulent Myxococcus phage, MX-1. 2. Several new phages were isolated from soil and animal droppings. A new phage was isolated from cultures of M. virescens V2. All resembled phage MX-1 in morphology and were related to phage MX-1 serologically. One of these phage, om, was characterized by fractionation of its proteins by SDS-polyacrylamide gel electrophoresis and by analysis of restriction fragments of its DNA. The very close relatedness with MX-1 was confirmed by these techniques. Phage om, was found to exist in a state of pseudolysogeny with strains of M. virescens and M. fulvus. 3. Two types of bacteriocin-like activity were found associated with Myxococcus strains. In one case, the activity was extracted from chloroformkilled or from sonicated cells. In the second case it was associated with extracellular material. Strains of Salmonella and Cytophaga were found to be good indicators for this latter activity. These strains were found to be killed by phage MX-1. 4. The significance of these data for origin of the phages of myxococci are discussed and it is proposed that MX-1 and the newly isolated phages may be virulent mutants of a family of lysogenic phages.

Bacteriocins

Phage-typing of Salmonella weltevreden based on lysogeny. II. Epidemiological usefulness of the system and geographical distribution of its phage-types.

Nine hundred and forty-six strains of Salmonella weltevreden isolated in different states of India during 1958-1974 and 124 strains from Australia, Burma, Holland, Hong Kong, New Zealand, Papua New Guinea, the Philippines, Thailand, the United States and Vietnam during 1953-1971 were phage-typed according to the phage-typing scheme described in the first part of this paper (Sood and Basu, 1977). The epidemiological incidence and geographical distribution of phage-types of Salmonella weltevreden were studied. All the phage-types were present in India, the predominant phage-types being b, d and i. Phage-type g was isolated exclusively from India. All the 14 strains from Hawaii belonged to phage-type i. Phage-type h was the most predominant phage-type in Vietnam. The 15 strains isolated from Papua New Guinea in 1965, which were supposed to have originated from a single source, belonged to 3 phage-types. Except these cultures all the available epidemiologically related strains were of uniform phage-types - a finding which establishes the epidemiological validity of the scheme.

Animals

Phage typing of Vibrio cholerae using a new collection of phages.

The authors formed a collection of typing phages in order to differentiate cholera vibrios of both biotypes. The collection consists of 7 phages proposed by Mukerjee for typing vibrios of the classical biotype and 3 El Tor phages isolated at the period of the 7th pandemy of cholera. In forming the typing collection the authors observed the following principles: 1) to crate a single set of typing phages and a single scheme of phage type differentiation of classical cholera and El Tor vibrios; 2) to use virulent phages; 3) to form a collection of serologically different phage types. The proposed collection allows to reveal a larger number of phage types as compared with phages proposed by Mukerjee phage typing a larger number of strains enhancing thus the epidemiological significance of the method of phage typing cholera vibrios.

Bacteriophage Typing

Effects of the phage P1 restriction system on coliphage phi W: degradation and complex formation of phage phi W DNA.

Growth of phages phi W and T7 was restricted in Escherichia coli lysogenic for phage P1. Only a fraction of the infected cells gave burst of phages. Cells permitting phage growth gave normal burst size. Host strains carrying P1 mutants with defective endonuclease gave no restriction of phages T7 and phi 3, the latter a host-range mutant of phi W. Degradation but not modification of parental phage DNA could be demonstrated. Although no DNA, RNA or protein was synthesized in phi W infected P1 lysogenic cells, the parental phage DNA was found in increasingly larger complexes during the course of infection. At early times after infection, parental phage DNA was found to sediment about twice as fast as mature phage DNA. At later times during the infection the parental phage DNA was recovered as a very rapidly sedimenting material. Such material was also found in alkaline sucrose gradient centrifugation after treatment of the cell extract with sodium dodecyl sulphate, pronase digestion and phenol extractions.

Coliphages

[New transducing phage with RNA polymerase beta- and beta'-subunit genes derived from a hybrid phage lambda att80: isolation, genetic analysis and physical mapping].

A hybrid lambda att 80 phage with the genetic structure lambda (A-J) phi 80 (att-int-xis) imm lambda..cI857s7 is shown to be a convenient vector for creating transducing phages. On the one hand, the restriction analysis indicates that it has 3 restriction sites for EcoRI in comparison with 5 and 9 sites for parental phages lambda and phi 80 respectively. On the other hand, its buoyant density is less than that of phage lambda and under centrifugation it is easier separated from the phage transducing particles. When lambda att 80 prophage was excluded from the bfe locus of Escherichia coli, transducing phages with genes of two RNA polymerase beta-subunits (rpoB and rpoC) were isolated. To identify the latter, a convenient genetic test was worked out. A physical map of lambda att 80 drifd 35 transducing phage, carrying rpoB and rpoC genes has been constructed using endonucleases EcoRI and HindIII. A comparison of this map and the corresponding maps of transducing phages lambda drifd 18 and lambda drifd 47, studied earlier, led to the discovery of two integration sites of phage lambda within the locus bfe spaced apart by about 1800 nucleotide pairs. At all the sites both phages (lambda and lambda att 80) have integrated in the locus bfe in the counter clockwise order.

Bacteriophage lambda

[Results of typing staphylococci isolated from cows and their milk products using the basic set of phages and local phages].

The basic set of phages recommended for typing staphylococci from cattle and also of local phages were approbated. Staphylococci cultures (950 in all) isolated in various regions of the Soviet Union from milk, milk produce and from cows suffering from mastitis were studied. Percentage of cultures typed by the phages of the basic set proved to be 78.3. Thirty different phage patterns were revealed among staphylococcal cultures lysed by phages. Lytic activity was the greatest in phages of group IV of the basic set. It is suggested that local phage 34k can be used as an additional phage permitting to subdivide the prevailing phage types within group IV into a number of new ones.

Animals

[Functional interactions of the genomes of Shigella sonnei phages and Escherichia coli phage T4 in mixed infection].

A comparative study of Shigella sonnei phages U and G and Escherichia coli phage T4 has shown that enzymes coded for by the Sh. sonnei phages can functionally substitute for some T4-coded products. This finding in indicative of an evolutionary relationship between T-even phages and disenteric phages U and G. The U phage is uncapable to compensate amber mutants for the genes that control the conversion of cytosine into 5-hydroxymethyl cytosine (5-HMC) and the glucosylation of the latter, which agrees with our earlier finding that the U phage DNA contains no 5-HMC. U and G phages are also found to exclude the T4 phage in the course of mixed infection.

Bacteriophages

Primary structure of an EcoRI fragment of lambda imm434 DNA containing regions cI-cro of phage 434 and cII-o of phage lambda.

Digestion of phage lambda imm434 DNA with restriction endonuclease EcoRI yields 7 fragments. The shortest among them (1287 bp) contains the right part of the phage 434 immunity region and the phage DNA portion proximal to it. The complete primary structure of this fragment has been determined using the chemical method of DNA sequencing. Hypothetical amino-acid sequences of proteins coded by the cro gene of phage 434 and the cII gene of phage lambda, as well as NH2-terminal amino-acid sequences of the cI protein of phage 434 and the O protein of phage lambda, have been deduced solely on the basis of the DNA sequence. The fragment studied contains also the pR and probably prm promoters and the oR operator of phage 434. The sequence coding for them differs from the respective DNA sequence of phage lambda.

Base Sequence

Adenosine triphosphate content in Lactobacillus casei and the blender-resistant phage-cell complex-forming ability of cells on infection with PL-1 phage.

The intracellular ATP content of Lactobacillus casei ATCC 27092 grown in a glucose-containing medium was almost constant (2 to 3 microgram/mg dry wt. cells) through the early to middle stage of logarithmic phase, but it was lowered to less than 0.1 microgram/mg after cessation of growth owing to the exhaustion of available glucose. All the cells in the early stage of stationary phase were still viable and thus considered to be in a starved state. When such starved cells were infected with PL-1 phages in a tris-maleate buffer of pH 6.0, the process of forming blender-resistant phage-cell complexes signifying the complete injection of phage genomes into the cells was much inhibited. There was a good correlation between the ATP content of cells and the extent of the formation of blender-resistant phage-cell complexes and the correlation coefficient between them was 0.89 + 0.09 at the 95% confidence limit. On the other hand, the process of forming both the phage-adsorbed cells and the anti-phage serum-resistant phage-cell complexes were not affected by the ATP content of cells. Feeding of glucose to such starved cell cultures caused the cells to restore both the ATP content and the ability to form blender-resistant phage-cell complexes. Such restoration was also observed when the starved cells collected by centrifugation were incubated in a glucose-containing medium. The significance of the intracellular level of high energy compounds such as ATP for the mechanism of the injection of phage genomes into the cells is discussed.

Adenosine Triphosphate

Bacteriophage phiNS11: a lipid-containing phage of acidophilic thermophilic bacteria. IV. Sedimentation coefficient, diffusion coefficient, partial specific volume, and particle weight of the phage.

The particle weight (molecular weight) of phiNS11 was determined from the sedimentation coefficient, diffusion coefficient, and partial specific volume of the phage. The sedimentation coefficient of the phage (S(0)20, W) is 416 +/- 2.7S. The diffusion coefficient D(0)20, W), which was determined by quasielastic light scattering measurement, is (0.57 +/- 0.03) x 10(-7) cm2/s. The partial specific volume was determined by the mechanical oscillation technique to be 0.747 +/- 0.007 cm3/g. Based on these values, the particle weight of the phage was calculated to be (70.3 +/- 4.3) x 10(6) daltons, which agrees well with the particle weight (69--72 x 10(6) daltons) estimated from the molecular weight of phage DNA and the content of DNA. The Stokes radius of the phage particle was calculated to be 37.7 +/- 2 nm and hydration of the phage was estimated to be 1.18 cm3/g of dry phage. From the particle weight and the chemical composition of the phage, we estimated that one phage particle contains one double-stranded DNA molecule, 16,000 residues of fatty acid, 72 protein I molecules, 920 protein II, 42 protein III, 48 protein IV, 290 protein V molecules, and 3,700 molecules of polyamines.

Bacteria

[Chemotypes of "Shigella flexneri" R mutants and related phage receptors. II. -- Localization of phage receptors (author's transl)].

Receptor sites for phages FP3, V, P1kcvir, H+, C21, T4, T3, T7 and 6SR have been investigated, by comparing the lytic activity of these phages on R mutants of strain F6 (F6R) and of various serotypes (FH) of Shigella flexneri with their inhibition by the lipopolysaccharides isolated from these mutants. The results suggest the following localizations for the receptor sites: phage FP3: lipid A-KDO; phage V: heptose or glucose; phage C21: heptose-glucose; phages H+, P1kcvir, T4 and T3: glucose; phage T7: glucose-galactose; phage 6SR: complete core structure.

Bacteriophages

Use of phage F-phi WJ-1 of Mycobacterium fortuitum to discern more phage types of Mycobacterium tuberculosis.

A total of 125 strains of Mycobacterium tuberculosis from the Southeastern area of the United States was subjected to phage typing. In addition to the five major mycobacteriophages, a new phage, F-phi WJ-1, was used in the study. The results obtained with the five major phages were: type A0, 35.2%; TYPE B, 29.6%, and type C, 4.0%. The remaining 21.2% of the strains phaged typed as subgroups A1 through A6. These percentages were similar to the typing results of earlier studies. The new phage, F-phi WJ-1, subdivided each of the phage types, with the exception of type C, into two subgroups. The possible role of host modification-restriction of the phages used in phage typing of strains of M. tuberculosis is discussed.

Bacteriophage Typing