Comparative study of the phage sensitivity of actinomycetes and their Nocardia-like variants

The work was aimed at studying the resistance of three streptomycetes (Streptomyces chrysomallus, S. azureus and S. roseoflavus var. roseofungini) and their spontaneous Nocardia-like variants lacking aerial mycelium and spores against nine polyphages isolated mainly from soil. Some Nocardia-like variants were found to differ from their parent cultures in the resistance against certain actinophages. S. chrysomallus VKM Ac-590 and Ac-628 variants lost resistance against the phages. S. azureus VKM Ac-719 and S. roseoflavus var. roseofungini VKM Ac-770 variants became resistant to the phages. The changed phage resistance of the streptomycetes and their Nocardia-like variants was attributed to the disorganised process of adsorption (8 and 7%, respectively, against 70 and 90% for the parent strains).     

Autoplaque formation in a Pseudomonas fluorescens strain: phage-like particles and transactivation of the defective phage

Natural bacteriophages of Pseudomonas fluorescens are rare and its temperate phages have not been described so far. In search for these phages, we have found that one of the P. fluorescens strains forms numerous small transparent autoplaques of different size and shape, which contained material reproducible on the same strains. When centrifuged in a cesium chloride gradient, this material yielded a band in the density zone of about 1.3 g/cm3, where protein components or bacteriophages with a relatively low content of nucleic acid are usually located. In the band material, electron microscopy revealed phagelike particles with empty and mostly undamaged heads and tails carrying in their distal region a formation resembling contracted sheath. DNA isolated from the preparation consisted of two components: a distinct 54-kb fragment, and a diffuse fragment ranging in size from 20 to 9.5 kb. Treatment of the large DNA fragment with various endonucleases yielded 42.2- and 29.5-kb fragments (on average for different endonucleases); whereas the same treatment of the diffuse fragment yielded two- to three distinct fragments with the overall molecular sizes of 8.9 and 6.2 kb (for different nucleases). We have suggested that cells harbor two different genetic elements whose interaction results in the autoplaque appearance and in the formation of negative colonies after infection with the autoplaque material. One of the two elements displays properties of a defective prophage with disturbed DNA synthesis and assembly, whereas the other exhibits the properties of a transposable phage. After complementation or some other interaction between these elements (transactivation, prophage induction caused by repressor inactivation), a bulk of defective phage particles devoid of DNA and a few DNA-containing particles were produced. It remains unclear whether both DNA types are contained in the same or different particles. The phage (or a system of elements) referred to as PT3 is noninducible. The phage mutants forming larger negative colonies (NCs) were also revealed. Some of bacterial mutants resistant to PT3 infection produce the mutant phage with small and turbid NCs. PT3 produces no NCs on the lawns of other strains of the same or other pseudomonade species. This is the first case of describing a natural temperate bacteriophage in P. fluorescens. The two different elements of this phage may represent the same genome of the defective prophage divided into two portions within a bacterial chromosome, each of which is capable of packaging into the phage head.     

Autoplaque Formation in a Pseudomonas fluorescensStrain: Phagelike Particles and Transactivation of the Defective Phage

Natural bacteriophages ofPseudomonas fluorescensare rare and its temperate phages have not been described so far. In search for these phages, we have found that one of the P. fluorescensstrains forms numerous small transparent autoplaques of different size and shape, which contained material reproducible on the same strains. When centrifuged in a cesium chloride gradient, this material yielded a band in the density zone of about 1.3 g/cm³, where protein components or bacteriophages with a relatively low content of nucleic acid are usually located. In the band material, electron microscopy revealed phagelike particles with empty and mostly undamaged heads and tails carrying in their distal region a formation resembling contracted sheath. DNA isolated from the preparation consisted of two components: a distinct 54-kb fragment, and a diffuse fragment ranging in size from 20 to 9.5 kb. Treatment of the large DNA fragment with various endonucleases yielded 42.2- and 29.5-kb fragments (on average for different endonucleases); whereas the same treatment of the diffuse fragment yielded two- to three distinct fragments with the overall molecular sizes of 8.9 and 6.2 kb (for different nucleases). We have suggested that cells harbor two different genetic elements whose interaction results in the autoplaque appearance and in the formation of negative colonies after infection with the autoplaque material. One of the two elements displays properties of a defective prophage with disturbed DNA synthesis and assembly, whereas the other exhibits the properties of a transposable phage. After complementation or some other interaction between these elements (transactivation, prophage induction caused by repressor inactivation), a bulk of defective phage particles devoid of DNA and a few DNA-containing particles were produced. It remains unclear whether both DNA types are contained in the same or different particles. The phage (or a system of elements) referred to as PT3 is noninducible. The phage mutants forming larger negative colonies (NCs) were also revealed. Some of bacterial mutants resistant to PT3 infection produce the mutant phage with small and turbid NCs. PT3 produces no NCs on the lawns of other strains of the same or other pseudomonad species. This is the first case of describing a natural temperate bacteriophage in P. fluorescens.The two different elements of this phage may represent the same genome of the defective prophage divided into two portions within a bacterial chromosome, each of which is capable of packaging into the phage head.     

Defective bacteriophages

Naturally occurring defective phage particles, which do not form plaques on any known host, but have a restricted host killing range, appear to be widely distributed. The defective phages are produced spontaneously but can be induced, at much higher levels, by chemical and physical agents which interfere with metabolism or structure of DNA. The defective phages discussed in this article have been divided into various categories on the basis of their structural complexity, which ranges from what appears to be phage tail components through to intact phage particles, and the source of the DNA packaged into the heads of the phage-like particles. The evolution of the defective phages is discussed and the possibility is entertained that they may have originated from temperate phages.     

Isolation of specialized transducing bacteriophage lambda carrying genes of the L-arabinose operon of Escherichia coli B/r.

A heat-inducible lysis-defective phage lambda (lambdacI857S7) has been integrated at multiple sites within the L-arabinose region (araCOIBAD) of a strain of Escherichia coli K-12 deleted for the normal lambda attachment site (lambdaattdelta). The lambda phage has become integrated with opposite orientations at two different loci within the aratb gene and with the "normal" orientation (clockwise N-RA-J) at a single site in the araC gene. The burst size, spontaneous-curing frequencies, and number of prophage harbored by each of the ara secondary-site lysogens have been determined. From these secondary-site lysogens it has been possible to generate plaque-forming ara-transducing phage (lambdapara) and defective ara-transducing phage (lambdadara), as well as defective leucine-transducing particles (lambdadleu). The construction and characterization of these lambdaara-transducing phage and their derivatives which carry genetically defined portions of the L-arabinose region are presented.     

Association of Microcyst Formation in Spirillum itersonii with the Spontaneous Induction of a Defective Bacteriophage

Mitomycin C and ultraviolet light were found to induce the formation of microcysts in Spirillum itersonii. These forms, as well as spontaneously occurring microcysts in this species, were found to contain phage tail parts, rhapidosomes, and a granular substance not seen in normal cells. It is suggested that microcysts are formed as the result of the induction of a defective phage. The production of phage lysozyme within the cell could lead to the formation of spherical forms as the cells lose their structural mucopeptide layer. Complete virus particles were not seen, nor was any biological activity demonstrated when the induced cultures were tested against two other strains of S. itersonii. The other strains of this bacterium also formed microcysts and phage tail parts when induced with mitomycin. Attempts to isolate an organism lacking the defective phage have been unsuccessful.     

A minor pathway leading to plaque-forming particles in bacteriophage lambda. Studies on the function of gene D

Lysates of bacteriophage λ, mutant in the head gene D, contain a minor amount of defective particles which can be isolated and complemented to infective particles by adding purified gene D product. The defective particles contain DNA with a specific infectivity in the helper assay of about 10% of phage DNA. This DNA is firmly held in the capsid and a tail is attached. Although the particles adsorb to sensitive bacteria, the DNA is not injected. The complemented, infectious particles differ from normal phage by having a lower density. After growing in a permissive host, phage particles of normal density are produced. The implications of the ability of gene D protein to bind to otherwise complete particles as a last step are discussed.     

Phage particles infecting branchial Rickettsiales-like organisms in banded carpet shell Polititapes virgineus (Bivalvia) from Galicia (NW Spain)

Basophilic intracellular prokaryotic-like colonies were observed in the gills of banded carpet shell Polititapes virgineus (= Tapes rhomboides) (Linnaeus, 1767) from a natural bed in Galicia (NW Spain). Light microscope observations suggested the presence of 2 types of colonies, but transmission electron microscopy revealed that these were the same Rickettsiales-like colonies, one infected and the other uninfected by phage particles. This is the first report of the presence of phage particles in Rickettsiales-like organisms in the gills of P. virgineus.     

Characterization of Inducible Bacteriophages in Bacillus licheniformis

Two morphologically distinct and physically separable defective phages have been found in Bacillus licheniformis NRS 243 after induction by mitomycin C. One of them (PBLB) is similar to the defective phage PBSX of B. subtilis, which has a density of 1.373 g/cm(3) in CsCl and a sedimentation coefficient of 160S. PBLB incorporates into its head mainly bacterial deoxyribonucleic acid (DNA) which has a sedimentation coefficient of 22S and a buoyant density in CsCl of 1.706 g/cm(3). The other phage (PBLA) has a morphology similar to the temperate phage phi105 of B. subtilis; the head diameter is about 66 nm, and it possesses a long and noncontractile tail. PBLA has a density of 1.484 g/cm(3) in CsCl and the phage-specific DNA, which is exclusively synthesized after induction by mitomycin C, has a density of 1.701 g/cm(3). PBLA DNA is double-stranded and has a sedimentation coefficient of 36S, corresponding to a molecular weight of 34 x 10(6) to 35 x 10(6) daltons. The phage DNA has one interruption per single strand, giving single-stranded segments with molecular weights of 13 x 10(6) and 4 x 10(6) daltons. Common sequences between the two phage DNA species and with their host DNA have been demonstrated by DNA-DNA hybridization studies. Both phage particles kill sensitive bacteria. However, all attempts thus far to find an indicator strain to support plaque formation have been unsuccessful.     

Characterization of a defective phage system for the analysis of bacteriophage T4 DNA replication origins

We have developed a defective phage system for the isolation and analysis of phage T4 replication origins based on the T4-mediated transduction of plasmid pBR322. During the initial infection of a plasmid-containing cell, recombinant plasmids with T4 DNA inserts are converted into fully modified linear DNA concatamers that are packaged into T4 phage particles, to create defective phage (transducing particles). In order to select T4 replication origins from genomic libraries of T4 sequences cloned into the plasmid pBR322, we searched for recombinant plasmids that transduce with an unusually high efficiency, reasoning that this should select for T4 sequences that function as origins on plasmid DNA after phage infection. We also selected for defective phage that can propagate efficiently with the aid of a coinfecting helper phage during subsequent rounds of phage infection. which should select for T4 sequences that can function as origins on the linear DNA present in the defective phage. Several T4 inserts were isolated repeatedly in one or both of these selective procedures, and these were mapped to particular locations on the T4 genome. When plasmids were selected in this way from genomic libraries constructed using different restriction nucleases, they contained overlapping segments of the T4 genome, indicating that the same T4 sequences were selected. The inserts in two of the selected plasmids permit a very high frequency of transduction from circular plasmids: these have been shown to contain a special type of T4 replication origin.     

Analysis of genomic similarity in Streptomycetes belonging to the fluorescent subgroup as a confirmation of their taxonomic revision using a population method

Genomic similarity was analysed in streptomycetes belonging to the fluorescent subgroup: Streptomyces chrysomallus, S. fluorescens, S. galbofluorescens and S. citreofluorescens. The degree of reference S. chrysomalius DNA hybridization with S. fluorescens and S. galbofluorescens DNAs was 75 and 82%, respectively, thus being within the limits of the intraspecial hybridization level. S. citreofluorescens DNA showed a 55% homology with reference S. chrysomallus DNA, which corresponded to the range of interspecies hybridization. These conclusions were confirmed by the results obtained in analysing the thermostability of hybrid duplexes. Therefore, these findings are consistent with the data of revising the species taxonomy of this streptomycetes subgroup which was done using the method of comparative population analysis. The population model proposed by one of the authors can be used to assess the intraspecies level of DNA-DNA hybridization.     

Specialized transduction of the ilvD-thyB-ilvA region mediated by Bacillus subtilis bacteriophage SP beta

Specialized transducing SP beta particles were found that carried the Bacillus subtilis genes lying to the left of the prophage attachment site. Three classes of transducing particles were differentiated, depending upon whether they carried ilvA only, thyB and ilvA, or ilvD, thyB, and ilvA. Lysates prepared by the induction of strains that carried both a transducing phage and a plaque-forming phage contained the two particles in a ratio of about 1:3,000. When the transducing particles were used to transduce a phage-sensitive auxotrophic strain to prototrophy, some of the transductants carried only the transducing phage genomes which, by themselves, were defective. One putative nondefective transducing phage (for ilvA only) is also described. SP beta can mediate specialized transduction even in the absence of the major (recE) bacterial recombination system.     

Defective bacteriophage MS2 particles containing specific RNA FRAGMENTS]

Two types of MS2 particle are revealed when phage lysates are banded in CsCl density gradient. The lower band contain normal phage particles with a density of 1.46 g/cm3. The upper band with a density of 1.44 g/cm3 containes uninfective incomplete MS2 particles. Both phage types reveal no abnormalities in the content of the coat protein and A-protein. They are nearly identical in RNA content. RNA in the normal buoyant density phage particles is native. RNA in the defective particles consists of three specific fragments with molecular weights 6.5-10(5), 5.5-10(5) and 4.4-10(5) and molar ratios 5:4:9 respectively. THE 5'-TERMINAL ANALYSIS OF RNA from defective MS2 particles reveals the presence of native pppGp. THE 3'-TERMINAL ANALYSIS OF THE INDIVIDUAL RNA fragments reveals the presence of adenosine only in the shortest fragment. RNA fragmentation in defective particles can be explained by the action of intracellular RNAses on the unprotected regions on RNA chain in structurally incomplete virions.     

Is the injection of DNA enough to cause bacteriophage P22-induced changes in the cellular transport process of Salmonella typhimurium?

It was demonstrated earlier in this laboratory that phage P22 induces a transient depression in the cellular transport processes of the host Salmonella typhimurium immediately after infection and that an effective injection process is enough to cause the depression. By using defective phage particles that contain host DNA instead of phage DNA for infection, it has been demonstrated that the injection of phage-specific DNA is essential for this. The defective particles adsorbed to the host and injected their DNA, but the cellular transport processes of the host were not altered. Thus, the injection of host DNA by the phage fails to affect the transport process. Insensitivity of the phage DNA-induced depression in transport to chloramphenicol rules out the involvement of newly synthesized protein in this change and indirectly suggests the possible role of phage DNA-associated internal proteins of P22.     

Development of a system for cloning a DNA fragment, containing the determinant of resistance to actinomycin for Streptomyces chrysomallus No.2--a producer of actinomycin C]

To study the modes of actinomycin biosynthesis and the mechanism responsible for resistance to the antibiotic producing S. chrysomallus No. 2, the authors undertook an examination and studies into the cloning system for gene(s) of resistance to actinomycin from a S. chrysomallus No. 2 actinomycin C producer and the cloning of a S. chrysomallus No. DNA fragment to the actinomycin-sensitive Streptomyces Sp. 26-115 H-I on the vector plasmid pIJ702. The cloning gave rise to actinomycin-resistant strains. The character of actinomycin resistance is inheritable in a steady fashion.     

On the nature of spontaneous RNA synthesis by Q beta replicase.

Numerous RNA species of different length and nucleotide sequence grow spontaneously in vitro in Q beta replicase reactions where no RNA templates are added deliberately. Here, we show that this spontaneous RNA synthesis by Q beta replicase is template directed. The immediate source of template RNA can be the laboratory air, but there are ways to eliminate, or at least substantially reduce, the harmful effects of spontaneous synthesis. Solitary RNA molecules were detected in a thin layer of agarose gel containing Q beta replicase, where they grew to form colonies that became visible upon staining with ethidium bromide. This result provides a powerful tool for RNA cloning and selection in vitro. We also show that replicating RNAs similar to those growing spontaneously are incorporated into Q beta phage particles and can propagate in vivo for a number of phage generations. These RNAs are the smallest known molecular parasites, and in many aspects they resemble both the defective interfering genomes of animal and plant viruses and plant virus satellite RNAs.     

Bacteriophage of Haemophilus influenzae III. Morphology, DNA Homology, and Immunity Properties of HP1c1, S2, and the Defective Bacteriophage from Strain Rd

The phages HP1c1 and S2 and a defective phage of Haemophilus influenzae have been compared. The morphology of the phages and the mol wt of their DNAs are similar, although the defective phage appears to have a different tail plate region. Electron microscope observation indicates that the defective phage does not attach to the cell surface, and its DNA appears to lack cohesive ends. The homology of the DNAs of the phages has been measured by hydridization. DNA from the defective phage shows little or no homology with the other phage DNAs. HP1c1 and S2 DNAs show a high level of homology. Each of these phages can form plaques on lawns of the lysogen of the other phage but at reduced plating efficiencies, suggesting that the two phages have related but not identical immunity systems.     

Effect of Spermine on Host-Cell Lysis and Reproduction by a Lactic Streptococcal Bacteriophage

A method was tested for protecting a Streptococcus lactis strain, ML3, used as a starter in the manufacture of Cheddar cheese, against the lytic activity of its homologous phage, ml(3). At a concentration of 10(-2)m, a naturally occurring polyamine, spermine, in the form of its hydrochloride, protected ML3 against lysis-from-without and lysozyme activity and against lysis by the phage when added at the time of infection or up to 21 min after infection. It was found that the latter protective effect could be accounted for in terms of the spermine preventing the formation of mature particles rather than preventing the escape of viable phage. Single colonies selected from a culture of ML3 cells that had been previously infected with phage ml(3), in the presence of spermine, were all found to have acquired resistance to phage ml(3). They retained this resistance during a 3-month period of daily subculture in broth and, in the absence of spermine, could not be induced to liberate phage or phage components either by the techniques normally used for inducing lysogens or by artificial disruption of the cells. It is concluded that when spermine is added to ML3 cells before a certain critical stage of the phage infection cycle, the process of phage synthesis is irreversibly halted and the cells retain the infecting phage as a defective prophage that confers on the cells immunity to infection by the homologous phage. Phage-resistant cultures did not inherit reduced starter activity in association with their acquired resistance characteristic.     

Assembly of bacteriophage phi X174: identification of a virion capsid precursor and proposal of a model for the functions of bacteriophage gene products during morphogenesis.

A capsomeric structure sedimenting with an S value of 108 in sucrose gradients was isolated from Escherichia coli infected with bacteriophage phi X174. The 108S material contained viral proteins F, G, H, and D, and the relative amounts of these proteins in the 108S material were similar to those in the infectious 132S particle, which has previously been described as a possible intermediate in the assembly of 114S phage particles. Electron micrographs indicated that the size and shape of the 108S material resemble those of the 132S particle. The 108S material contained no DNA, and its formation occurred independently of DNA synthesis. The 108S material accumulated in infected cells when viral DNA replication was prevented either by mutation in phage genes A or C or by removal of thymidine from a culture infected with wild-type phage or with a lysis gene E mutant. Upon restoration of thymidine to cells infected with the lysis gene E mutant and then starved of thymidine, the accumulated 108S material was converted to 132S particles and to 114S phage particles, implying that the 108S material is a precursor of phage particles. A model that proposes possible functions for the products of phi X174 genes A, B, C, D, F, and G during viral replication and phage maturation is described.     

Stability of the transformants obtained by phage particle-mediated gene transfer

Recombinant lambda phage DNA, encapsulated in phage particles and coprecipitated with calcium phosphate, efficiently transforms cultured mammalian cells without a requirement for carrier DNA. The present paper analyzes the stability of the transformants obtained by the phage transfer method. lambda phage particles containing recombinant DNA that includes the thymidine kinase (TK) gene of herpes simplex virus type 1 as a selective marker were introduced into Ltk- cells deficient in TK activity, and TK+ transformants were selected in HAT medium. To test the stability of the TK+ phenotype of the transformants, seven individual transformant clones were isolated, cultured in HAT selective medium and then in non-selective medium for various lengths of time. After such culture, transformants were allowed to develop colonies in both selective and non-selective medium. For all seven transformant clones, the numbers of colonies obtained in the two types of medium were almost identical, irrespective of whether or not each transformant clone had been previously cultured for 15 to 50 days in non-selective medium. This result suggests that most transformants obtained by the phage transfer method maintain the TK+ phenotype stably, for at least 50 days, when grown in non-selective medium.