A phage weaponizes a satellite recombinase to subvert viral restriction

A phage satellite manipulates the viral DNA packaging motor to inhibit phage and promote satellite spread

ICP1, a lytic bacteriophage of Vibrio cholerae, is parasitized by phage satellites, PLEs, which hijack ICP1 proteins for their own horizontal spread. PLEs' dependence on ICP1's DNA replication machinery and virion components results in inhibition of ICP1's lifecycle. PLEs are expected to depend on ICP1 factors for genome packaging, but the mechanism(s) PLEs use to inhibit ICP1 genome packaging is currently unknown. Here, we identify and characterize Gpi, PLE's indiscriminate genome packaging inhibitor. Gpi binds to ICP1's large terminase (TerL), the packaging motor, and blocks genome packaging. To overcome Gpi's negative effect on TerL, a component PLE also requires, PLE uses two genome packaging specifiers, GpsA and GpsB, that specifically allow packaging of PLE genomes. Surprisingly, PLE also uses mimicry of ICP1's pac site as a backup strategy to ensure genome packaging. PLE's pac site mimicry, however, is only sufficient if PLE can inhibit ICP1 at other stages of its lifecycle, suggesting an advantage to maintaining Gpi, GpsA and GpsB. Collectively, these results provide mechanistic insights into another stage of ICP1's lifecycle that is inhibited by PLE, which is currently the most inhibitory of the documented phage satellites. More broadly, Gpi represents the first satellite-encoded inhibitor of a phage TerL.

Sporadic phage defense in epidemic Vibrio cholerae mediated by the toxin-antitoxin system DarTG is countered by a phage-encoded antitoxin mimic

Bacteria and their viral predators (phages) are constantly evolving to subvert one another. Many bacterial immune systems that inhibit phages are encoded on mobile genetic elements that can be horizontally transmitted to diverse bacteria. Despite the pervasive appearance of immune systems in bacteria, it is not often known if these immune systems function against phages that the host encounters in nature. Additionally, there are limited examples demonstrating how these phages counter-adapt to such immune systems. Here, we identify clinical isolates of the global pathogen Vibrio cholerae harboring a novel genetic element encoding the bacterial immune system DarTG and reveal the immune system's impact on the co-circulating lytic phage ICP1. We show that DarTG inhibits ICP1 genome replication, thus preventing ICP1 plaquing. We further characterize the conflict between DarTG-mediated defense and ICP1 by identifying an ICP1-encoded protein that counters DarTG and allows ICP1 progeny production. Finally, we identify this protein, AdfB, as a functional antitoxin that abrogates the toxin DarT likely through direct interactions. Following the detection of the DarTG system in clinical V. cholerae isolates, we observed a rise in ICP1 isolates with the functional antitoxin. These data highlight the use of surveillance of V. cholerae and its lytic phages to understand the co-evolutionary arms race between bacteria and their phages in nature.IMPORTANCEThe global bacterial pathogen Vibrio cholerae causes an estimated 1 to 4 million cases of cholera each year. Thus, studying the factors that influence its persistence as a pathogen is of great importance. One such influence is the lytic phage ICP1, as once infected by ICP1, V. cholerae is destroyed. To date, we have observed that the phage ICP1 shapes V. cholerae evolution through the flux of anti-phage bacterial immune systems. Here, we probe clinical V. cholerae isolates for novel anti-phage immune systems that can inhibit ICP1 and discover the toxin-antitoxin system DarTG as a potent inhibitor. Our results underscore the importance of V. cholerae and ICP1 surveillance to elaborate novel means by which V. cholerae can persist in both the human host and aquatic reservoir in the face of ICP1.

Genomic analysis of hyperparasitic viruses associated with entomopoxviruses

Polinton-like viruses (PLVs) are a diverse group of small integrative dsDNA viruses that infect diverse eukaryotic hosts. Many PLVs are hypothesized to parasitize viruses in the phylum Nucleocytoviricota for their own propagation and spread. Here, we analyze the genomes of novel PLVs associated with the occlusion bodies of entomopoxvirus (EPV) infections of two separate lepidopteran hosts. The presence of these elements within EPV occlusion bodies suggests that they are the first known hyperparasites of poxviruses. We find that these PLVs belong to two distinct lineages that are highly diverged from known PLVs. These PLVs possess mosaic genomes, and some essential genes share homology with mobile genes within EPVs. Based on this homology and observed PLV mosaicism, we propose a mechanism to explain the turnover of PLV replication and integration genes.

A phage satellite manipulates the viral DNA packaging motor to inhibit phage and promote satellite spread

ICP1, a lytic bacteriophage of Vibrio cholerae, is parasitized by phage satellites, PLEs, which hijack ICP1 proteins for their own horizontal spread. PLEs' dependence on ICP1's DNA replication machinery, and virion components results in inhibition of ICP1's lifecycle. PLEs' are expected to depend on ICP1 factors for genome packaging, but the mechanism(s) PLEs use to inhibit ICP1 genome packaging is currently unknown. Here, we identify and characterize Gpi, PLE's indiscriminate genome packaging inhibitor. Gpi binds to ICP1's large terminase (TerL), the packaging motor, and blocks genome packaging. To overcome Gpi's negative effect on TerL, a component PLE also requires, PLE uses two genome packaging specifiers, GpsA and GpsB, that specifically allow packaging of PLE genomes. Surprisingly, PLE also uses mimicry of ICP1's pac site as a backup strategy to ensure genome packaging. PLE's pac site mimicry, however, is only sufficient if PLE can inhibit ICP1 at other stages of its lifecycle, suggesting an advantage to maintaining Gpi, GpsA, and GpsB. Collectively, these results provide mechanistic insights into another stage of ICP1's lifecycle that is inhibited by PLE, which is currently the most inhibitory of the documented phage satellites. More broadly, Gpi represents the first satellite-encoded inhibitor of a phage TerL.

A Vibrio cholerae viral satellite maximizes its spread and inhibits phage by remodeling hijacked phage coat proteins into small capsids

Phage satellites commonly remodel capsids they hijack from the phages they parasitize, but only a few mechanisms regulating the change in capsid size have been reported. Here, we investigated how a satellite from Vibrio cholerae, phage-inducible chromosomal island-like element (PLE), remodels the capsid it has been predicted to steal from the phage ICP1 (Netter et al., 2021). We identified that a PLE-encoded protein, TcaP, is both necessary and sufficient to form small capsids during ICP1 infection. Interestingly, we found that PLE is dependent on small capsids for efficient transduction of its genome, making it the first satellite to have this requirement. ICP1 isolates that escaped TcaP-mediated remodeling acquired substitutions in the coat protein, suggesting an interaction between these two proteins. With a procapsid-like particle (PLP) assembly platform in Escherichia coli, we demonstrated that TcaP is a bona fide scaffold that regulates the assembly of small capsids. Further, we studied the structure of PLE PLPs using cryogenic electron microscopy and found that TcaP is an external scaffold that is functionally and somewhat structurally similar to the external scaffold, Sid, encoded by the unrelated satellite P4 (Kizziah et al., 2020). Finally, we showed that TcaP is largely conserved across PLEs. Together, these data support a model in which TcaP directs the assembly of small capsids comprised of ICP1 coat proteins, which inhibits the complete packaging of the ICP1 genome and permits more efficient packaging of replicated PLE genomes.

Sporadic phage defense in epidemic Vibrio cholerae mediated by the toxin-antitoxin system DarTG is countered by a phage-encoded antitoxin mimic

Bacteria and their viral predators (phages) are constantly evolving to subvert one another. Many bacterial immune systems that inhibit phages are encoded on mobile genetic elements that can be horizontally transmitted to diverse bacteria. Despite the pervasive appearance of immune systems in bacteria, it is not often known if these immune systems function against phages that the host encounters in nature. Additionally, there are limited examples demonstrating how these phages counter-adapt to such immune systems. Here, we identify clinical isolates of the global pathogen Vibrio cholerae harboring a novel genetic element encoding the bacterial immune system DarTG and reveal the immune system's impact on the co-circulating lytic phage ICP1. We show that DarTG inhibits ICP1 genome replication, thus preventing ICP1 plaquing. We further characterize the conflict between DarTG-mediated defense and ICP1 by identifying an ICP1-encoded protein that counters DarTG and allows ICP1 progeny production. Finally, we identify this protein as a functional antitoxin that abrogates the toxin DarT likely through direct interactions. Following the detection of the DarTG system in clinical V. cholerae isolates, we observed a rise in ICP1 isolates with the functional antitoxin. These data highlight the use of surveillance of V. cholerae and its lytic phages to understand the co-evolutionary arms race between bacteria and their phages in nature.

A Vibrio cholerae viral satellite maximizes its spread and inhibits phage by remodeling hijacked phage coat proteins into small capsids

Phage satellites commonly remodel capsids they hijack from the phages they parasitize, but only a few mechanisms regulating the change in capsid size have been reported. Here, we investigated how a satellite from Vibrio cholerae, PLE, remodels the capsid it has been predicted to steal from the phage ICP1 (1). We identified that a PLE-encoded protein, TcaP, is both necessary and sufficient to form small capsids during ICP1 infection. Interestingly, we found that PLE is dependent on small capsids for efficient transduction of its genome, making it the first satellite to have this requirement. ICP1 isolates that escaped TcaP-mediated remodeling acquired substitutions in the coat protein, suggesting an interaction between these two proteins. With a procapsid-like-particle (PLP) assembly platform in Escherichia coli, we demonstrated that TcaP is a bona fide scaffold that regulates the assembly of small capsids. Further, we studied the structure of PLE PLPs using cryogenic electron microscopy and found that TcaP is an external scaffold, that is functionally and somewhat structurally similar to the external scaffold, Sid, encoded by the unrelated satellite P4 (2). Finally, we showed that TcaP is largely conserved across PLEs. Together, these data support a model in which TcaP directs the assembly of small capsids comprised of ICP1 coat proteins, which inhibits the complete packaging of the ICP1 genome and permits more efficient packaging of replicated PLE genomes.

Nuclease genes occupy boundaries of genetic exchange between bacteriophages

Homing endonuclease genes (HEGs) are ubiquitous selfish elements that generate targeted double-stranded DNA breaks, facilitating the recombination of the HEG DNA sequence into the break site and contributing to the evolutionary dynamics of HEG-encoding genomes. Bacteriophages (phages) are well-documented to carry HEGs, with the paramount characterization of HEGs being focused on those encoded by coliphage T4. Recently, it has been observed that the highly sampled vibriophage, ICP1, is similarly enriched with HEGs distinct from T4's. Here, we examined the HEGs encoded by ICP1 and diverse phages, proposing HEG-driven mechanisms that contribute to phage evolution. Relative to ICP1 and T4, we found a variable distribution of HEGs across phages, with HEGs frequently encoded proximal to or within essential genes. We identified large regions (> 10kb) of high nucleotide identity flanked by HEGs, deemed HEG islands, which we hypothesize to be mobilized by the activity of flanking HEGs. Finally, we found examples of domain swapping between phage-encoded HEGs and genes encoded by other phages and phage satellites. We anticipate that HEGs have a larger impact on the evolutionary trajectory of phages than previously appreciated and that future work investigating the role of HEGs in phage evolution will continue to highlight these observations.

Everything OLD is new again: How structural, functional, and bioinformatic advances have redefined a neglected nuclease family

Overcoming lysogenization defect (OLD) proteins are a conserved family of ATP-powered nucleases that function in anti-phage defense. Recent bioinformatic, genetic, and crystallographic studies have yielded new insights into the structure, function, and evolution of these enzymes. Here we review these developments and propose a new classification scheme to categorize OLD homologs that relies on gene neighborhoods, biochemical properties, domain organization, and catalytic machinery. This taxonomy reveals important similarities and differences between family members and provides a blueprint to contextualize future in vivo and in vitro findings. We also detail how OLD nucleases are related to PARIS and Septu anti-phage defense systems and discuss important mechanistic questions that remain unanswered.

Nuclease genes occupy boundaries of genetic exchange between bacteriophages

Homing endonuclease genes (HEGs) are ubiquitous selfish elements that generate targeted double-stranded DNA breaks, facilitating the recombination of the HEG DNA sequence into the break site and contributing to the evolutionary dynamics of HEG-encoding genomes. Bacteriophages (phages) are well-documented to carry HEGs, with the paramount characterization of HEGs being focused on those encoded by coliphage T4. Recently, it has been observed that the highly sampled vibriophage, ICP1, is similarly enriched with HEGs distinct from T4’s. Here, we examined the HEGs encoded by ICP1 and diverse phages, proposing HEG-driven mechanisms that contribute to phage evolution. Relative to ICP1 and T4, we found a variable distribution of HEGs across phages, with HEGs frequently encoded proximal to or within essential genes. We identified large regions (> 10kb) of high nucleotide identity flanked by HEGs, deemed HEG islands, which we hypothesize to be mobilized by the activity of flanking HEGs. Finally, we found examples of domain swapping between phage-encoded HEGs and genes encoded by other phages and phage satellites. We anticipate that HEGs have a larger impact on the evolutionary trajectory of phages than previously appreciated and that future work investigating the role of HEGs in phage evolution will continue to highlight these observations.