Gene transfer agents, bacteriophages, and bacteriocins of Rhodopseudomonas capsulata.

Thirty-three wild type strains of Rhodopseudomonas capsulata were examined for ability to engage in genetic recombination through mediation by "gene transfer agent" (GTA) particles. The genetic exchange assays were based on capacity of strains to produce or receive GTA required for restoration of photosynthetic growth competence to a non-photosynthetic "white" mutant or for acquisition of resistance to rifampicin. A majority of the strains could either produce or receive GTA, and it was demonstrated that the agent is species specific. Possible relations between GTA and bacteriophages or bacteriocins were investigated. Sixteen types of virulent phages active on Rps. capsulata were isolated and their host ranges determined. Tests for transduction by the phages gave uniformly negative results. The viruses showed strict species specificity, but there was no apparent correlation between capacity of the Rps. capsulata strains to donate or receive GTA and susceptibility to the phages. A comparable survey disclosed that most of the bacterial strains were sensitive to or capable of producing bacteriocins; the latter also appear to be unrelated to GTA activity. The collection of bacterial strains was also screened for detection of lysogenic properties. None of the isolates is a "true" lysogen, but phages were detected in cultures of two strains, which may be "phage carriers" or pseudolysogens.     

Characterization of the gene transfer agent made by an overproducer mutant of Rhodopseudomonas capsulata.

Most wild-type isolates of the photosynthetic bacterium Rhodopseudomonas capsulata spontaneously produce nucleoprotein particles that act as vectors of genetic exchange in this species. The low yield of these particles, termed gene transfer agents, has made their characterization difficult. We have utilized a new screening technique to select a mutant, Y262, which produces about three orders of magnitude more GTA² per culture. The GTA produced by Y262 seem to be identical to those of wild type by immunological, genetic and sedimentation analyses, and they have been further characterized by a variety of techniques. GTA resemble tailed bacteriophage, although GTA with a head diameter of 30 nm are smaller than most morphologically similar viruses. DNA isolated from GTA is in the form of linear duplex molecules of about 3 × 10⁶ molecular weight. There is no phage-like DNA in GTA particles as judged by C_ot and restriction endonuclease analyses. Instead, GTA DNA shows the same kinetic complexity and restriction endonuclease digestion pattern as the R. capsulata genome. The GTA of ten independently isolated wild-type strains of R. capsulata show a high degree of immunological cross-reactivity; thus this genetic exchange system, while not a species-wide trait, does seem to be the product of a conservative evolutionary process.     

The gene transfer agent of Rhodopseudomonas capsulata,: Purification and characterization of its nucleic acid

Photosynthetic bacteria of the species Rhodopseudomonas capsulata are capable of exchanging genetic information via a recently discovered gene transfer agent (GTA). The 70S particle mediating the genetic exchange was purified and its nucleic acid was analyzed. Cell-free filtrates containing GTA were prepared by filtration of stationary cultures of R. capsulata on an Amicon thin-channel filtration apparatus. Purification of this filtrate was achieved by successive membrane filtration, diafiltration, agarose-gel filtration, ion-exchange chromatography on diethylaminoethyl cellulose, and sucrose gradient sedimentation, resulting in an overall purification of 4000-fold with a yield of 2–4%. [³H]thymidine-labeled nucleic acid isolated from this material was identified as deoxyribonucleic acid on the basis of its resistance to alkaline hydrolysis and its buoyant density of 1.718 g/ml in CsCl. The double-stranded nature of the deoxyribonucleic was demonstrated by its resistance to degradation by the single-strand-specific S₁-nuclease and the density shift in CsCl of +0.016 g/ml upon denaturation. Its molecular weight was estimated to be 3.6 × 10⁶ from sucrose gradient sedimentation in the presence of markers, and the linear, unnicked nature of the molecule was evident from sedimentation in an alkaline sucrose gradient.     

Characterization of Rhodopseudomonas capsulata

Thirty-three strains of Rhodopseudomonas capsulata have been studied in order to develop a more comprehensive characterization of the species. On the basis of morphological, nutritional, physiological and other properties, the characteristics of an ideal biotype have been defined, which can be used to distinguish Rps. capsulata from similar purple bacteria. In this connection, two properties of Rps. capsulata are of particular note: a) sensitivity to penicillin G is 10³–10⁵ times greater than that shown by closely related species, and b) all strains examined are susceptible to lysis by one or more strains of host species-specific virulent bacteriophages. It appears that members of the species Rps. capsulata form a stringent taxonomic grouping.     

Asymmetry of an energy transducing membrane. The location of cytochrome c2 in Rhodopseudomonas spheroides and Rhodopseudomonas capsulata

Monospecific antibodies have been prepared against cytochrome c₂ from Rhodopseudomonas spheroides and Rhodopseudomonas capsulata, and against cytochrome c′ from Rps. capsulata. These antibodies precipitated their respective antigens, but did not cross react with a wide range of procaryotic or eucaryotic cytochromes, or with other bacterial proteins. The cytochromes produced during aerobic growth were immunologically indistinguishable from those produced during photosynthetic growth.Cytochrome c₂ is located in vivo in the periplasmic space between the cell wall and the cell membrane, and when chromatophores are prepared from whole cells the cytochrome becomes trapped inside these vesicles. The implications of these results to energy coupling in the photosynthetic bacteria are discussed.     

Purification and molecular properties of a soluble ferredoxin from Rhodopseudomonas capsulata

A soluble ferredoxin was purified from the photosynthetic bacterium Rhodopseudomonas capsulata and characterized. Unlike Rhodospirillum rubrum, where two soluble ferredoxins have been found, only a single species was found in Rps. capsulata. The amino acid composition, ultraviolet-visible spectral properties, molecular weight (12000) and biological activity were determined. The ultraviolet-visible spectrum is similar to that of other bacterial ferredoxins, with a maximum when oxidized at 380 nm (? = 26.1 · 10³ M^-1 · cm^-1). The possible roles of this ferredoxin in the cellular metabolism are discussed.     

Magnetic field effects on the fluorescence of mutant strains of Rhodopseudomonas capsulata

The magnetic field effects on bacteriochlorophyll fluorescence in six strains of Rhodopseudomonas capsulata were investigated. All strains exhibit an increase in fluorescence upon application of a magnetic field. Large magnetic field effects are shown to arise in mutants which contain the B800–850 complex as the only bacteriochlorophyll-containing protein. These fluorescence increases are observed only with carotenoid excitation and are best described by a carotenoid singlet heterofission mechanism. Variations in the magnitudes of the magnetic field effects for the Rps. capsulata strain arise from energy differences in the excited states of the molecules involved in the process. In order to determine the contribution from reaction centers to the magnetic field effects observed in the mutants which contain all three pigment-protein complexes, reaction centers were isolated from these strains. The reaction center contribution to the magnetic field effect on fluorescence in whole cells was determined to be smaller than the antenna contribution when carotenoid excitation was employed.     

Properties and regulation of synthesis of two ferredoxins from Rhodopseudomonas capsulata

Two ferredoxins from nitrogen-fixing cells of the phototrophic bacterium Rhodopseudomonas capsulata, strain B10, are purified to a homogeneous state and characterized. The molecular mass of ferredoxin I is about 12 kDa and that of ferredoxin II, 18 kDa. Ferredoxin I contains 8 Fe²⁺ and 8 S^2?; ferredoxin II has 4 Fe²⁺ and 4 S^2? per molecule. The redox potential of ferredoxin I is about ?270 mV and that of ferredoxin II ?419 mV. Ferredoxin I is more labile to the action of O₂, O^?₂, H₂O₂ and heating. The ferredoxins are also different in their absorption and EPR spectra, amino acid composition and electron-transfer activity to Rps. capsulata nitrogenase: both C₂H₂ reduction and H₂ evolution by Rps. capsulata nitrogenase proceed faster in the presence of ferredoxin I than in case of ferredoxin II. Synthesis of ferredoxin I takes place only in Rps. capsulata nitrogen-fixing cells grown in light under anaerobic conditions whereas ferredoxin II formation does not depend on the source of nitrogen or the growth medium, though the amount of ferredoxin II varies with the growth conditions. Its highest level has been found in the cells grown in lactate-limited medium in the presence of CO₂ and light or in the presence of glutamate in darkness under anaerobic conditions.     

Genotypic and Phenotypic Diversity among Induced, stx2-Carrying Bacteriophages from Environmental Escherichia coli Strains

Shiga toxin 2 (stx₂) gene-carrying bacteriophages have been shown to convert Escherichia coli strains to Shiga toxin-producing Escherichia coli (STEC). In this study, 79 E. coli strains belonging to 35 serotypes isolated from wastewaters of both human and animal origin were examined for the presence of stx₂-carrying bacteriophages in their genomes. The lytic cycle of the bacteriophages was induced by mitomycin, and the bacteriophage fraction was isolated and used for morphological and genetic characterization. The induced bacteriophages showed morphological diversity, as well as restriction fragment length polymorphism variation, in the different strains belonging to different serotypes. The ability to infect new hosts was highly variable, although most of the induced phages infected Shigella sonnei host strain 866. In summary, in spite of carrying either the same or different stx₂ variants and in spite of the fact that they were isolated from strains belonging to the same or different serotypes, the induced bacteriophages were highly variable. The high level of diversity and the great infectious capacity of these phages could enhance the spread of the stx₂ gene and variants of this gene among different bacterial populations in environments to which humans may be exposed.     

Some theoretical aspects of protein coevolution in the ecosystem “phage-bacteria” I. The problem

The possibility of prolonged coevolution of bacterial reception protein and viral adsorption one is questioned in this paper. A general deterministic model of ecosystem “phage-bacteria” is formulated. Analysis of the model accentuates the problem of clearing up conditions that provide steady regimes not of coexistence but coevolution, i.e. successive mutational changes of mutually “coadaptive” pairs of mutant strains of bacteria and phages. Heuristic validity of this model in a framework of some actual problems and paradoxes of molecular evolution theory is particularly emphasized.     

Isolation and characterization of Rhodobacter capsulatus strains lacking endogenous plasmids

Phodobacter capsulatus (formerly Rhodopseudomonas capsulata) strain B10 was found to contain a single plasmid of molecular weight 86×10⁶. Strains lacking this plasmids were isolated by various methods from strains containing the mutant R plasmid, pTH10. With the exception of two strains, which were found to contain chromosomal insertions of R plasmid DNA, strains lacking the endogenous plasmid appeared to be unaffected in any of the following metabolic or genetic functions: photosynthetic, autotrophic, diazotrophic, and dark, anaerobic growth; the production of bacteriocin; homologous recombination; the restriction of foreign DNA; and the production of gene transfer agent. DNA-DNA hybridization experiments confirmed that the plasmid had been eliminated from these strains and not become integrated into the chromose. However, sequences homologous to those of the endogenous plasmid were found to be present in the chromosome of R. capsulatus B10. This suggests, among other possibilities, that the endogenous plasmid may have originated in the chromosome, and might serve to duplicate certain chromosomal functions.Abbreviations kb kilobase-pair - GTA gene transfer agent - Cma chromosome mobilizing ability     

Occurrence of Strains Producing Specific Antibacterial Inhibitory Agents in Five Genera of Enterobacteriaceae

Striking differences in the production of specific inhibitory agents affecting other strains of the same (or of related) species were found between genera of the family Enterobacteriaceae. We tested 50–163 strains each of the potentially pathogenic genera: Escherichia, Citrobacter, Enterobacter, Kluyvera, and Leclercia for their ability to produce bacteriophages, high-molecular-weight (HMW) and low-molecular-weight (LMW) bacteriocins and siderophores against the same sets of strains, using the cross-test method. The genus Escherichia differs substantially from all other Enterobacteriaceae, harboring a notable proportion of lysogenic (36.6%) and colicinogenic (13.9%) strains. Only 18.2% of the Citrobacter strains are lysogenic and only rarely are they colicinogenic, although in 7.3%, they produce phage tail-like bacteriocins. On the other hand, Kluyvera strains were only in 1.8% lysogenic, no colicinogenic strains were found, but in 7.3%, they produced siderophores causing zones of growth inhibition in agar cultures of strains of the same genus. In Leclercia, 10.0% of the strains were lysogenic, 2.0% produced HMW bacteriocins, no colicinogenic strains were found and 2.0% produced siderophores. Enterobacter has shown 23.1% of strains producing siderophores, whereas merely 7.7% were lysogenic, 1.9% colicinogenic and 3.8% formed phage tail-like bacteriocins. HMW bacteriocins of Enterobacter strains disposed of an unusually wide spectrum of activity. The siderophore activity spectrum was rather wide in any genus, but the siderophores were usually not produced by strains producing phages or colicins.     

Sulfide utilization by purple nonsulfur bacteria

Summary The purple nonsulfur bacteria Rhodospirillum rubrum SMG 107, Rhodopseudomonas capsulata SMG 155, Rps. sphaeroides SMG 158 and Rps. palustris SMG 124 were tested for a possible utilization of sulfide. The first three strains were found to oxidize sulfide to extracellular elemental sulfur only, whereas Rps. palustris SMG 124 converted sulfide into sulfate without intermediate accumulation of elemental sulfur. Growth ceased at lower sulfide concentrations than usually found with purple sulfur bacteria. In consequence of the low sulfide tolerance information on the specific growth rates obtainable with sulfide as photosynthetic electron donor could not be provided by cultivation in batch cultures. Sulfide-limited chemostat cultures of Rps. capsulata SMG 155 showed that the maximum specific growth rate was close to 0.14 h^-1 (doubling time 5 h). Sulfide was converted into extracellular elemental sulfur at all dilution rates tested. The maximum specific growth rate of Rps. palustris SMG 124 was found to be much lower (less than 0.03 h^-1). Sulfate was the only product of the conversion of sulfide.These data show that at least some purple nonsulfur bacteria may play a role in the dissimilatory sulfur cycle in nature. Taxonomic implications of our results are discussed.Abbreviation SMG Sammlung für Mikroorganismen, Göttingen     

Prophages integrating into prophages: A mechanism to accumulate type III secretion effector genes and duplicate Shiga toxin-encoding prophages in Escherichia coli

Bacteriophages (or phages) play major roles in the evolution of bacterial pathogens via horizontal gene transfer. Multiple phages are often integrated in a host chromosome as prophages, not only carrying various novel virulence-related genetic determinants into host bacteria but also providing various possibilities for prophage-prophage interactions in bacterial cells. In particular, Escherichia coli strains such as Shiga toxin (Stx)-producing E. coli (STEC) and enteropathogenic E. coli (EPEC) strains have acquired more than 10 prophages (up to 21 prophages), many of which encode type III secretion system (T3SS) effector gene clusters. In these strains, some prophages are present at a single locus in tandem, which is usually interpreted as the integration of phages that use the same attachment (att) sequence. Here, we present phages integrating into T3SS effector gene cluster-associated loci in prophages, which are widely distributed in STEC and EPEC. Some of the phages integrated into prophages are Stx-encoding phages (Stx phages) and have induced the duplication of Stx phages in a single cell. The identified attB sequences in prophage genomes are apparently derived from host chromosomes. In addition, two or three different attB sequences are present in some prophages, which results in the generation of prophage clusters in various complex configurations. These phages integrating into prophages represent a medically and biologically important type of inter-phage interaction that promotes the accumulation of T3SS effector genes in STEC and EPEC, the duplication of Stx phages in STEC, and the conversion of EPEC to STEC and that may be distributed in other types of E. coli strains as well as other prophage-rich bacterial species.     

Isolation of Nine Bacteriophages Shown Effective against Erwinia amylovora in Korea

Erwinia amylovora is a devastating bacterial plant pathogen that infects Rosaceae including apple and pear and causes fire blight. Bacteriophages have been considered as a biological control agent for preventing bacterial infections of plants. In this study, nine bacteriophages (ΦFifi011, ΦFifi044, ΦFifi051, ΦFifi067, ΦFifi106, ΦFifi287, ΦFifi318, ΦFifi450, and ΦFifi451) were isolated from soil and water samples in seven orchards with fire blight in Korea. The genetic diversity of bacteriophage isolates was confirmed through restriction fragment length polymorphism pattern analysis. Host range of the nine phages was tested against 45 E. amylovora strains and 14 E. pyrifoliae strains and nine other bacterial strains. Among the nine phages, ΦFifi044 and ΦFifi451 infected and lysed E. amylovora only. And the remaining seven phages infected both E. amylovora and E. pyrifoliae. The results suggest that the isolated phages were different from each other and effective to control E. amylovora, providing a basis to develop biological agents and utilizing phage cocktails.     

Observations on lysogeny in glutamic acid bacteria.

Induced lysis occurred in a number of different strains of glutamic acid bacteria. Mixed culture experiments indicated that induced cultures produce phages or bacteriocins. Temperate phages were isolated from two related strains of Brevibacterium divaricatum.     

Gut Microbiota is an Important Source of Bacteriocins and Their In Situ Expression Can Be Explored for Treatment of Bacterial Infections

Bacteriocins are interesting natural antimicrobial peptides that could be deployed quickly to combat certain antimicrobial-resistant bacterial infections. These molecules could be used in conjunction with traditional antibiotics, or even to replace them in some circumstances. To strengthen the concept of “bacteriocinotherapy,” we discuss here the benefits associated with production in situ of bacteriocins by commensal bacteria. This on sites production capacity could augment the gut microbiota global resistance plan and provide a backup for bacterial infection treatments.

     

The growth,toxicity and genetic characterization of seven strains of Alexandrium catenella (Whedon and Kofoid) Balech 1985 (Dinophyceae) isolated during the 2009 summer outbreak in southern Chile

The dinoflagellate Alexandrium catenella causes recurrent harmful algal blooms in southern Chile. This species belongs to the “Alexandrium tamarense/catenella/fundyense species complex” (the “tamarensis complex”), defined by morphological attributes. Ribosomal sequences serve to differentiate five evolutionary lineages (clades) in this species complex. These distinctions reflect the geographic distribution and toxicity of the populations rather than their morphological designations. Despite the social and economic impact that harmful blooms produce in Chile, few strains of A. catenella have been isolated. Moreover, physiological and/or genetic studies of the group are scarce. The aim of this work was to examine possible physiological and genetic variability among populations of A. catenella having different geographical origins but isolated from the same toxic event. Seven strains of A. catenella were isolated and established from phytoplankton samples collected in the Aysén and Los Lagos regions of southern Chile during a recent outbreak (February–March 2009). Growth, toxicity, and ITS sequences were compared among these strains. All the strains included in this study were grouped with strains belonging to the previously described “North America” clade. The genetic diversity detected among Chilean strains was 3%, a much higher value than those reported for comparisons among strains from other parts of the world. In addition, a remarkable variability of growth parameters and toxicity was detected among strains. Strain PFB45 showed the highest PSP toxin content, whereas strain PFB41 had the lowest value of this parameter but had the highest maximum cell density. In strains PFB38, PFB42, and PFB37, more than 98% of the total PSP toxin content occurred in the form of gonyautoxins (primarily GTX-4,1 and GTX-3,2). In strains PFB39, PFB36, and PFB45, neoSTX, and STX toxins were detected. These results demonstrated remarkable variability at the genetic and physiological level among strains of A. catenella isolated from the same outbreak. No correlations were found between the phenotypic traits (growth and toxicity) and the genetic affiliation of the strains studied.     

Wide-Inhibitory Spectra Bacteriocins Produced by Lactobacillus gasseri K7

The aim of our study was to determine the genetic characterization and classification of Lb. gasseri K7 bacteriocins, comparison with bacteriocins of the Lb. gasseri LF221 strain and other related strains. Bacteriocin-encoding genes were amplified by PCR, subjected to DNA sequencing, and BLAST sequence analysis was performed to search the database for homologous peptides. Lb. gasseri K7 produces two two-peptide bacteriocins, named gassericin K7 A and gassericin K7 B. Their nucleotide sequences were deposited at GenBank, under accession numbers EF392861 for the gassericin K7 A and AY307382 for the gassericin K7 B. Analysis of gene clusters of bacteriocins in Lb. gasseri K7 strain revealed a 100 percent sequence identity with bacteriocins in LF221 strain. An active peptide of gassericin K7 B is homologous to the complementary peptide of gassericin T, and a complementary peptide of gassericin K7 B is homologous to the active peptide of gassericin T. Another surprising finding was that the sakacin T-beta peptide is partly homologous to the active peptide of gassericin K7 A, while the other sakacin T peptide (alfa) is partly homologous to the complementary peptide of gassericin K7 B. Gassericins of Lb. gasseri K7 strain were both classified as two-peptide bacteriocins. Human probiotic strains Lb. gasseri K7 and LF221 are different isolates but with identical bacteriocin genes. They produce wide-inhibitory spectra bacteriocins that are new members of two-peptide bacteriocins with some homologies to other bacteriocins in this group. Described bacteriocins offer a great potential in applications in food industry, pharmacy and biomedicine.     

Isolation of Plaque-Forming, Galactose-Transducing Strains of Phage Lambda

Plaque-forming, galactose-transducing lambda strains have been isolated from lysogens in which bacterial genes have been removed from between the galactose operon and the prophage by deletion mutation.—A second class has been isolated starting with a lysogenic strain which carries a deletion of the genes to the right of the galactose operon and part of the prophage. This strain was lysogenized with a second lambda phage to yield a lysogen from which galactose-transducing, plaque-forming phages were obtained. These plaque-forming phages were found to be genetically unstable, due to a duplication of part of the lambda chromosome. The genetic instability of these partial diploid strains is due to homologous genetic recombindation between the two identical copies of the phage DNA comprising the duplication. The galactose operon and the duplication of phage DNA carried by these strains is located between the phage lambda P and Q genes.