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Background Active lysogeny is a newly characterized mechanism that the dynamic integration and excision of prophages serve as molecular switches to coordinately regulate bacterial gene expression without generating progeny virions. The Sa3int family phages, the most prevalent prophages in Staphylococcus aureus , specifically integrate into the β-toxin-coding gene hlb . While infection conditions favor the loss of Sa3int phages and the emergence of Hlb-producing variants, highlighting their potential for active lysogeny, the environmental cues and underlying mechanisms controlling the peculiar life cycle of Sa3int phages remain largely unexplored. Methods In this study, we identified a Sa3int phage, designated ΦSa3XN, from the methicillin-resistant S. aureus strain XN108. The active lysogeny feature of ΦSa3XN was analyzed by combinational PCR, plaque assay, transmission electron microscopy, and DNase protection assay. Additionally, glucose-induced active lysogeny of ΦSa3XN and its impact on S. aureus virulence were evaluated via reporter assay, electrophoretic mobility shift assay, hemolytic assay, and mouse infection models. Results ΦSa3XN acts as a genuine molecular switch, capable of excision without producing progeny phages. Glucose serves as an environmental cue that triggers ΦSa3XN excision and reinstates hlb expression, wherein the catabolite control protein A (CcpA) directly binds to the promoter region of cI and suppresses the expression of CI repressor, thus switching the phage life cycle. Moreover, glucose-induced active lysogeny of ΦSa3XN significantly enhances bacterial hemolytic activity, exacerbating skin inflammation and subcutaneous abscess formation in hyperglycemic mice. Conclusion This study illustrates a novel example of active lysogeny for Sa3int phages and elucidates a glucose-responsive CcpA pathway that regulates ΦSa3XN excision to augment S. aureus virulence, advancing our understanding of the sophisticated interactions between S. aureus and phages.

Background Temperate phages play a central role in the evolution and pathogenicity of Staphylococcus aureus . Sa3int phages provide highly human-specific virulence factors that promote immune evasion and survival within the host. The reversible excision of these phages which occurs without phage production and bacterial lysis allows the simultaneous expression of phage virulence genes and the hlb gene where they usually integrate. However, the regulatory mechanisms that control phage assembly and the cross-talk with host factors remain poorly understood. Methods and results We analyzed the regulatory mechanism controlling late gene transcription of Sa3int phage Φ13. We identified a functional promoter, P 23, located upstream of the late phage genes that control DNA processing and packaging, capsid assembly, bacterial lysis and immune evasion. SAOUHSC_02200 , the gene located upstream of P 23 , encodes for a late transcriptional regulator (Ltr). Mutating the P 23 TATA-box or the ltr gene abolished P 23 activity and formation of mature intact phage particles, thus confirming the role of Ltr in regulating P 23 activity. Four direct repeats upstream of the P 23 transcriptional start site were identified as potential Ltr binding sites. RT-qPCR analysis confirmed that Ltr-dependent P 23 activation is essential for the expression of late genes and the subsequent Φ13 propagation. Furthermore, comparative analysis of P 23 activity and ltr expression in different host strain backgrounds revealed strain-specific differences that appear to depend on the alternative sigma factor SigB and its downstream effector SpoVG. Conclusions Ltr controls the expression of late phage genes, thereby regulating phage assembly and lysis. This process is modulated by SpoVG activity.

Cold-active bacteriophages are bacterial viruses that infect and replicate at low temperatures (≤4 °C). Understanding remains limited of how cold-active phage–host systems sustain high viral abundance despite the persistently low temperatures in pelagic sediments in polar seas. In this study, two Pseudoalteromonas phages, ACA1 and ACA2, were isolated from sediment core samples of the continental shelf in the western Arctic Ocean. These phages exhibited successful propagation at a low temperature of 1 °C and displayed typical myovirus morphology with isometric icosahedral heads and contractile tails. The complete genome sequences of phages ACA1 and ACA2 were 36,825 bp and 36,826 bp in size, respectively, sharing almost the same gene content. These are temperate phages encoding lysogeny-related proteins such as anti-repressor, immunity repressor and integrase. The absence of cross-infection between the host strains, which were genomically distinct Pseudoalteromonas species, can likely be attributed to heavy divergence in the anti-receptor apparently mediated by an associated diversity-generating retroelement. HHpred searching identified genes for all of the structural components of a P2-like phage (family Peduoviridae), although the whole of the Peduoviridae family appeared to be divided between two anciently diverged tail modules. In contrast, Blast matching and whole genome tree analysis are dominated by a nonstructural gene module sharing high similarity with Pseudoalteromonas phage C5a (founder of genus Catalunyavirus). This study expands the knowledge of diversity of P2-like phages known to inhabit Peudoalteromonas and demonstrates their presence in the Arctic niche.

The finding that total viral abundance is higher than total prokaryotic abundance and that a significant fraction of the prokaryotic community is infected with phages in aquatic systems has stimulated research on the ecology of prokaryotic viruses and their role in ecosystems. This review treats the ecology of prokaryotic viruses (`phages') in marine, freshwater and soil systems from a `virus point of view'. The abundance of viruses varies strongly in different environments and is related to bacterial abundance or activity suggesting that the majority of the viruses found in the environment are typically phages. Data on phage diversity are sparse but indicate that phages are extremely diverse in natural systems. Lytic phages are predators of prokaryotes, whereas lysogenic and chronic infections represent a parasitic interaction. Some forms of lysogeny might be described best as mutualism. The little existing ecological data on phage populations indicate a large variety of environmental niches and survival strategies. The host cell is the main resource for phages and the resource quality, i.e., the metabolic state of the host cell, is a critical factor in all steps of the phage life cycle. Virus-induced mortality of prokaryotes varies strongly on a temporal and spatial scale and shows that phages can be important predators of bacterioplankton. This mortality and the release of cell lysis products into the environment can strongly influence microbial food web processes and biogeochemical cycles. Phages can also affect host diversity, e.g., by `killing the winner' and keeping in check competitively dominant species or populations. Moreover, they mediate gene transfer between prokaryotes, but this remains largely unknown in the environment. Genomics or proteomics are providing us now with powerful tools in phage ecology, but final testing will have to be performed in the environment.

Phage Mu transposes by two distinct pathways depending on the specific stage of its life cycle. A common {theta} strand transfer intermediate is resolved differentially in the two pathways. During lytic growth, the {theta} intermediate is resolved by replication of Mu initiated within the flanking target DNA; during integration of infecting Mu, it is resolved without replication, by removal and repair of DNA from a previous host that is still attached to the ends of the incoming Mu genome. We have discovered that the cryptic endonuclease activity reported for the isolated C-terminal domain of the transposase MuA [Wu Z, Chaconas G (1995) A novel DNA binding and nuclease activity in domain III of Mu transposase: Evidence for a catalytic region involved in donor cleavage. EMBO J 14:3835-3843], which is not observed in the full-length protein or in the assembled transpososome in vitro, is required in vivo for removal of the attached host DNA or \"5'flap\" after the infecting Mu genome has integrated into the E. coli chromosome. Efficient flap removal also requires the host protein ClpX, which is known to interact with the C-terminus of MuA to remodel the transpososome for replication. We hypothesize that ClpX constitutes part of a highly regulated mechanism that unmasks the cryptic nuclease activity of MuA specifically in the repair pathway.