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Bacteriophage S-PM2 infects several strains of the abundant and ecologically important marine cyanobacterium Synechococcus. A large lytic phage with an isometric icosahedral head, S-PM2 has a contractile tail and by this criterion is classified as a myovirus ( Strains of unicellular cyanobacteria of the genera Synechococcus and Prochlorococcus are abundant in the world's oceans and constitute the prokaryotic component of the picophytoplankton. Together, these photosynthetic bacteria contribute a significant proportion of primary production in oligotrophic regions of the oceans (21,35,37,68). Viral infection of marine unicellular cyanobacteria was first reported in 1990 (53, 63), and cyanovirus isolates were first characterized in the laboratory in 1993 (62,69,74). The majority of these phages belong to the myoviruses. Myoviruses are physically robust and remarkably versatile; this virion design can apparently be easily adapted to a variety of different ecological niches (64). S-PM2 is a lytic cyanomyovirus with an icosahedral head and long contractile tail that infects marine Synechococcus strains. The genome has been shown to have a size of ϳ194 kb (27). Bacteriophage T4 that infects Escherichia coli is the archetype myovirus, and S-PM2 was shown to have a genetic module that encodes distant homologues of most of the major virion proteins of T4 (27). T4 has been extensively studied and is extremely well understood; it serves as a superb, if somewhat complex, model for S-PM2.A previous phylogenetic analysis of the sequences of the major head and tail genes of a wide range of T4-type bacteriophages indicated at least three distinct phylogenetic subgroups of these phages (64). There is a large cluster of phages, termed the T-evens, members of which are all closely related to T4, the archetype of the Myoviridae. The second subgroup is surprisingly phylogenetically divergent from the T-evens, but morphologically similar; these are called the pseudoT-evens (47), and they includes phages such as RB49 and RB42 that infect E. coli. The third cluster includes Aeromonas phages and vibriophages such as nt-1, KVP20, KVP40, 65, and Aeh1. Such phages have heads that are more elongated than those of both T-evens and the pseudoT-evens and thus are called the schizoT-evens (64). Phylogenetic analysis based on the major capsid protein gp23 has shown that S-PM2 and the related cyanomyovirus S-PWM3 are quite distinct from the other characterized T4-like phages and form a new discrete group, the exoT-evens (27). These marine T4-type phages have apparently diverged significantly from the T4 archetype. Beyond the fact that they have a contractile tail, these phages have little morphological resemblance to the other T4-type phages. Among the many differences between the exoT-evens and the other T-type phages are those that relate to the photosynthetic physiology of their hosts. It is clear that S-PM2 (41) and several other marine cyanomyoviruses (36, 43) encode homologues of the D1 and D2 proteins of the host photosystem II that presum...
The discovery of ∼20-kb gene clusters containing a family of paralogs of tRNA guanosine transglycosylase genes, called tgtA5, alongside 7-cyano-7-deazaguanine (preQ 0 ) synthesis and DNA metabolism genes, led to the hypothesis that 7-deazaguanine derivatives are inserted in DNA. This was established by detecting 2'-deoxy-preQ 0 and 2'-deoxy-7-amido-7-deazaguanosine in enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative bacteria Salmonella enterica serovar Montevideo. These modifications were absent in the closely related S. enterica serovar Typhimurium LT2 and from a mutant of S. Montevideo, each lacking the gene cluster. This led us to rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA. Similar gene clusters were analyzed in ∼150 phylogenetically diverse bacteria, and the modifications were detected in DNA from other organisms containing these clusters, including Kineococcus radiotolerans, Comamonas testosteroni, and Sphingopyxis alaskensis. Comparative genomic analysis shows that, in Enterobacteriaceae, the cluster is a genomic island integrated at the leuX locus, and the phylogenetic analysis of the TgtA5 family is consistent with widespread horizontal gene transfer. Comparison of transformation efficiencies of modified or unmodified plasmids into isogenic S. Montevideo strains containing or lacking the cluster strongly suggests a restriction-modification role for the cluster in Enterobacteriaceae. Another preQ 0 derivative, 2'-deoxy-7-formamidino-7-deazaguanosine, was found in the Escherichia coli bacteriophage 9g, as predicted from the presence of homologs of genes involved in the synthesis of the archaeosine tRNA modification. These results illustrate a deep and unexpected evolutionary connection between DNA and tRNA metabolism.DNA modification | restriction-modification | 7-deazaguanine | comparative genomics | queuosine H ypermodifications of DNA requiring more than one synthetic enzyme are not as prevalent and chemically diverse as RNA hypermodifications, but around a dozen have been identified in DNA to date (1). The functions of most DNA hypermodifications are still not known, but some have roles in protection against restriction enzymes, whereas others affect thermal stability temperature, DNA packaging, or transcription regulation (2). For example, the hypermodified DNA base β-D-glucosyl-hydroxymethyluracil, or base J, is an epigenetic factor that regulates Pol II transcription initiation in kinetoplastids of trypanosomes (3). The recently discovered phosphorothioate (PT) modification of the DNA backbone in bacteria was found to perform different functions in different organisms (4-6). In Salmonella Cerro 87, PT occurs on each strand of a GAAC/GTTC motif as part of a restriction-modification (R-M) system, whereas in Vibrio cyclitrophicus FF75, which lacks PT restriction enzymes, PT occurs on one strand of C ps CA motifs, and the function remains unclear (6). In 2013, Iyer et al. described the computational prediction of 12 novel DNA hypermodificat...
Advances in phage therapy and novel applications of phages in biotechnology encourage interest in phage impact on human and animal immunity. Here we present comparative studies of immunogenic properties of T4 phage head surface proteins gp23*, gp24*, Hoc, and Soc, both as elements of the phage capsid and as isolated agents. Studies comprise evaluation of specific antibodies in the human population, analysis of the proteins' impact on the primary and secondary responses in mice, and the effect of specific antibodies on phage antibacterial activity in vitro and in vivo in mice. In humans, natural antibodies specific to T4-like phages were abundant (81% of investigated sera). Among those, significantly elevated levels of IgG antibodies only against major head protein (gp23*) were found, which probably reflected cross-reactions of T4 with antibodies induced by other T4-like phages. Both IgM and IgG antibodies were induced mostly by gp23* and Hoc, while weak (gp24*) and very weak (Soc) reactivities of other head proteins were noticed. Thus, T4 head proteins that markedly contribute to immunological memory to the phage are highly antigenic outer capsid protein (Hoc) and major capsid protein (gp23*). Specific anti-gp23* and anti-Hoc antibodies substantially decreased T4 phage activity in vitro and to some extent in vivo. Cooperating with antibodies, the immune complement system also contributed to annihilating phages.
Bacteriophages recognize and bind to their hosts with the help of receptor-binding proteins (RBPs) that emanate from the phage particle in the form of fibers or tailspikes. RBPs show a great variability in their shapes, sizes, and location on the particle. Some RBPs are known to depolymerize surface polysaccharides of the host while others show no enzymatic activity. Here we report that both RBPs of podovirus G7C - tailspikes gp63.1 and gp66 - are essential for infection of its natural host bacterium E. coli 4s that populates the equine intestinal tract. We characterize the structure and function of gp63.1 and show that unlike any previously described RPB, gp63.1 deacetylates surface polysaccharides of E. coli 4s leaving the backbone of the polysaccharide intact. We demonstrate that gp63.1 and gp66 form a stable complex, in which the N-terminal part of gp66 serves as an attachment site for gp63.1 and anchors the gp63.1-gp66 complex to the G7C tail. The esterase domain of gp63.1 as well as domains mediating the gp63.1-gp66 interaction is widespread among all three families of tailed bacteriophages.
Summary Felix d’Herelle first demonstrated, about 90 years ago, the presence of bacteriophages in human and animal body microbiota. Our comprehension of the impact of naturally occurring bacteriophages on symbiotic bacteria, and of their role in general homeostasis of macro‐organism, nevertheless remains quite fragmentary. Analysis of data in various human‐ and animal body‐associated microbial systems on phage occurrence, diversity, host specificity and dynamics, as well as host occurrence, specificity and dynamics, suggests that mechanisms which stabilize phage–bacteria coexistence are not identical for either different species or different body sites. Regulation by phage infection instead probably depends on specific physical, chemical and biological conditions, e.g. pH, nutrient densities, host prevalence, relation to mucosa and other surfaces and presence of phage inhibiting substances. In some animal species intestinal bacteriophages thus appear to exert significant selective pressure over at least some resident bacterial populations, resulting in phages playing important roles in the self‐regulation of these microbial systems while at the same time contributing to maintenance of bacterial diversity (i.e. ‘killing the winner’). Emerging data additionally suggest that bacteriophage particles could play roles in regulating the immune reactions of the macro‐organism. Alternatively, for many systems links between phages and community characteristics have not been established.
The diversity of coliphages and indigenous coliform strains (ICSs) simultaneously present in horse feces was investigated by culture-based and molecular methods. The richness of coliforms (as estimated by the Chao1 method) is about 1,000 individual ICSs distinguishable by genomic fingerprinting present in a single sample of feces. This unexpectedly high value indicates that some factor limits the competition of coliform bacteria in the horse gut microbial system. In contrast, the diversity of phages active against any selected ICS is generally limited to one to three viral genotypes present in the sample. The sensitivities of different ICSs to simultaneously present coliphages overlap only slightly; the phages isolated from the same sample on different ICSs are usually unrelated. As a result, the titers of phages in fecal extract as determined for different Escherichia coli strains and ICSs may differ by several orders of magnitude. Summarizing all the data, we propose that coliphage infection may provide a selection pressure that maintains the high level of coliform diversity, restricting the possibility of a few best competitors outgrowing other ICSs. We also observed high-magnitude temporal variations of coliphage titers as determined using an E. coli C600 test culture in the same animal during a 16-day period of monitoring. No correlation with total coliform count was observed. These results are in good agreement with our hypothesis.Bacteriophages exert a significant influence on natural microbial communities (2, 24, 33). They are responsible for 20 to 80% of bacterial mortality in freshwater and marine ecosystems (25, 33) and increase bacterial biodiversity (references 14, 15, 31, and 33 and references therein) due to preferential attack on the dominant species or strains and redistribution of the organic matter. The role of bacteriophages could be even more important in microbial systems where high densities of active bacteria are achieved. Among these systems are intestinal microbial populations of animals and humans where bacteria (17, 28) and bacteriophages (5,6,9,10,13,16,17) are present at high densities. The gut is the natural habitat for Escherichia coli and for coliphages, which are highly suitable for work in culture, making this system attractive as a model for phage ecology.For our study, we selected the horse as the macro host. The cellulolytic microbial community localized in the horse large intestine is very complex and includes bacteria, archaea, fungi, and protozoa (18). In contrast to rumen communities, the microbial biomass in the horse intestine is not subjected to digestion and is excreted with the feces. The conditions in the horse gut seem more stable than those in the intestines of many other species, as the time taken to digest grass is about 72 h (18), and the intervals between food intake and defecation are normally much shorter. A spatial complexity is present in the gut (9). The mucosal surface and the lumen contents are different ecological niches for bacteria. It has been show...
The O antigen (O polysaccharide), composed of many oligosaccharide repeats (O units), is a part of the lipopolysaccharide (LPS) of Gram-negative bacteria and the most structurally variable cell surface constituent. The O-antigen diversity is due to variations of O-antigen biosynthesis genes and is believed to offer various bacterial clones selective advantages in their specific ecological niches (1). The O antigen plays important and various roles in bacteriophage interactions with the host. Many bacteriophages employ the O antigen as a primary receptor that ensures reversible adsorption to the host cell followed by irreversible adsorption to a secondary receptor, most frequently an outer membrane protein (2-4). O-antigen modifications may prevent bacteriophage binding. For instance, phage SPC35 uses the Salmonella O12 antigen receptor, and phase-variable glucosylation of the O antigen confers transient SPC35 resistance to the bacteria (5). A temperate podovirus, Sf6, also uses O antigen of its host, Shigella flexneri, as a primary receptor (4). Interestingly, the Sf6 genome harbors the oac gene for O-antigen acetylase that causes O-serotype conversion of Sf6 lysogens, which precludes bacteriophage Sf6 adsorption to these cells (6). On the other hand, the O-antigen-carrying LPS of E. coli is able to prevent the access of phages and colicins to their outer membrane protein receptors, which are otherwise sufficient for a successful attack of the cell (7). O-antigen deficiency also enhances the sensitivity of E. coli to Shiga toxin 2-converting bacteriophages (3,8). A phage T5 mutant lacking L-shaped tail fibers that recognize polymannose O antigens showed a reduced rate of adsorption to the O-antigen-producing hosts but infected O-antigen-less strains as efficiently as the wild-type phage (9, 10).These data indicate that the O-antigen layer represents an effective shield that nonspecifically protects the bacteria from interactions of bacteriophages with their cell surface receptors. In order to penetrate this shield, the phages need to acquire the proteins that specifically recognize the O antigen, thus becoming dependent on a given O-polysaccharide type. Many bacteriophages that use the O antigen as a primary receptor possess enzymes that degrade or modify it (11, 12).N4-like bacteriophage G7C and its host E. coli 4s were isolated from horse feces in the course of an investigation of coliphage ecology in the equine gut ecosystem (13). In addition to G7C, E. coli 4s was used as a host for the isolation and propagation of several other G7C-related phages (14; A. K. Golomidova, unpublished data). Currently, E. coli 4s remains the only known host for bacteriophage G7C, but despite the extremely narrow host range, G7C-related phages persisted in the same horse population for several years (14). The mechanisms that help G7C avoid extinction despite the small fraction of the total E. coli population that is suitable for its growth are poorly understood (9). Elucidation of the molecular details of the initial steps of th...
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