Systematic discovery of antiphage defense systems in the microbial pangenome

Structural insights into signaling promiscuity of the CBASS anti-phage defense system from a radiation-resistant bacterium

Radiation-resistant bacteria are of great application potential in various fields, including bioindustry and bioremediation of radioactive waste. However, how radiation-resistant bacteria combat against invading phages is seldom addressed. Here, we present a series of crystal structures of a sensor and an effector of the cyclic oligonucleotide-based anti-phage signaling system (CBASS) from a radioresistant bacterium Deinococcus wulumuqiensis. We found that the sensor CD-NTase enzyme, DwCdnB, can bind all four ribonucleotides and synthesize a variety of cyclic di-nucleotides, including the novel second messenger 3'3'-cyclic di-CMP. Crystal structures of DwCdnB in complex with ATP and dATP provide structural explanations for specific recognition of ribonucleotides via metal coordination with ribose 2'-OH. Crystal structures of DwCdnB in complex with purine and/or pyrimidine nucleotides in the presence of Mg2+ revealed similar binding modes; however, in the presence of Mn2+, the UTP/CTP rotates and flips into the donor pocket and make extensive contacts with additional five residues, suggesting essential role of Mn2+ for catalytic production of cyclic di-pyrimidines. Finally, structural analysis of the downstream effector DwCap5 further provides a structural explanation for its non-specific recognition of a broad range of cyclic di-nucleotides. In sum, this work provides key structural insights into the immune mechanisms of radioresistant bacteria.

CARD domains mediate anti-phage defence in bacterial gasdermin systems

Caspase recruitment domains (CARDs) and pyrin domains are important facilitators of inflammasome activity and pyroptosis1. Following pathogen recognition by nucleotide binding-domain, leucine-rich, repeat-containing (NLR) proteins, CARDs recruit and activate caspases, which, in turn, activate gasdermin pore-forming proteins to induce pyroptotic cell death2. Here we show that CARD domains are present in defence systems that protect bacteria against phage. The bacterial CARD domain is essential for protease-mediated activation of certain bacterial gasdermins, which promote cell death once phage infection is recognized. We further show that multiple anti-phage defence systems use CARD domains to activate a variety of cell death effectors, and that CARD domains mediate protein-protein interactions in these systems. We find that these systems are triggered by a conserved immune-evasion protein used by phages to overcome the bacterial defence system RexAB3, demonstrating that phage proteins inhibiting one defence system can activate another. Our results suggest that CARD domains represent an ancient component of innate immune systems conserved from bacteria to humans, and that CARD-dependent activation of gasdermins is shared in organisms across the tree of life.

Cyanobacterial type I CRISPR-Cas systems: distribution, mechanisms, and genome editing applications

Cyanobacteria, renowned for their photosynthetic capabilities, serve as efficient microbial chassis capable of converting carbon dioxide into a spectrum of bio-chemicals. However, conventional genetic manipulation strategies have proven incompatible with the precise and systematic modifications required in the field of cyanobacterial synthetic biology. Here, we present an in-depth analysis of endogenous CRISPR-Cas systems within cyanobacterial genomes, with a particular focus on the Type I systems, which are the most widely distributed. We provide a comprehensive summary of the reported DNA defense mechanisms mediated by cyanobacterial Type I CRISPR-Cas systems and their current applications in genome editing. Furthermore, we offer insights into the future applications of these systems in the context of cyanobacterial genome editing, underscoring their potential to revolutionize synthetic biology approaches.

Lineage-specific variation in frequency and hotspots of recombination in invasive Escherichia coli

BACKGROUND

The opportunistic bacterium Escherichia coli can invade normally sterile sites in the human body, potentially leading to life-threatening organ dysfunction and even death. However, our understanding of the evolutionary processes that shape its genetic diversity in this sterile environment remains limited. Here, we aim to quantify the frequency and characteristics of homologous recombination in E. coli from bloodstream infections.

RESULTS

Analysis of 557 short-read genome sequences revealed that the propensity to exchange DNA by homologous recombination varies within a distinct population (bloodstream) at narrow geographic (Dartmouth Hitchcock Medical Center, New Hampshire, USA) and temporal (years 2016 - 2022) scope. We identified the four largest monophyletic sequence clusters in the core genome phylogeny that are represented by prominent sequence types (ST): BAPS1 (mainly ST95), BAPS4 (mainly ST73), BAPS10 (mainly ST131), BAPS14 (mainly ST58). We show that the four dominant clusters vary in different characteristics of recombination: number of single nucleotide polymorphisms due to recombination, number of recombination blocks, cumulative bases in recombination blocks, ratio of probabilities that a given site was altered through recombination and mutation (r/m), and ratio of rates at which recombination and mutation occurred (ρ/θ). Each sequence cluster contains a unique set of antimicrobial resistance (AMR) and virulence genes that have experienced recombination. Common among the four sequence clusters were the recombined virulence genes with functions associated with the Curli secretion channel (csgG) and ferric enterobactin transport (entEF, fepEG). We did not identify any one recombined AMR gene that was present in all four sequence clusters. However, AMR genes mdtABC, baeSR, emrKY and tolC had experienced recombination in sequence clusters BAPS4, BAPS10, and BAPS14. These differences lie in part on the contributions of vertically inherited ancestral recombination and contemporary branch-specific recombination, with some genomes having relatively higher proportions of recombined DNA.

CONCLUSIONS

Our results highlight the variation in the propensity to exchange DNA via homologous recombination within a distinct population at narrow geographic and temporal ranges. Understanding the sources of the genetic variation in invasive E. coli will help inform the implementation of effective strategies to reduce the burden of disease and AMR.

Activation of the bacterial defense-associated sirtuin system

The NADase activity of the defense-associated sirtuins (DSRs) is activated by the phage tail tube protein (TTP). Herein, we report cryo-EM structures of a free-state Bacillus subtilis DSR2 tetramer and a fragment of the tetramer, a phage SPR tail tube, and two DSR2-TTP complexes. DSR2 contains an N-terminal SIR2 domain, a middle domain (MID) and a C-terminal domain (CTD). The DSR2 CTD harbors the α-solenoid tandem-repeats like the HEAT-repeat proteins. DSR2 assembles into a tetramer with four SIR2 clustered at the center, and two intertwined MID-CTD chains flank the SIR2 core. SPR TTPs self-assemble into a tube-like complex. Upon DSR2 binding, the D1 domain of SPR TTP is captured between the HEAT-repeats domains of DSR2, which conflicts with TTPs self-assembly. Binding of TTPs induces conformational changes in DSR2 tetramer, resulting in increase of the NAD+ pocket volume in SIR2, thus activates the NADase activity and leads to cellular NAD+ depletion.

Phage parasites targeting phage homologous recombinases provide antiviral immunity

Bacteria often carry multiple genes encoding anti-phage defense systems, clustered in defense islands and phage satellites. Various unrelated anti-phage defense systems target phage-encoded homologous recombinases (HRs) through unclear mechanisms. Here, we show that the phage satellite SaPI2, which does not encode orthodox anti-phage defense systems, provides antiviral immunity mediated by Stl2, the SaPI2-encoded transcriptional repressor. Stl2 targets and inhibits phage-encoded HRs, including Sak and Sak4, two HRs from the Rad52-like and Rad51-like superfamilies. Remarkably, apo Stl2 forms a collar of dimers oligomerizing as closed rings and as filaments, mimicking the quaternary structure of its targets. Stl2 decorates both Sak rings and Sak4 filaments. The oligomerization of Stl2 as a collar of dimers is necessary for its inhibitory activity both in vitro and in vivo. Our results shed light on the mechanisms underlying antiviral immunity against phages carrying divergent HRs.

Chemical inhibition of a bacterial immune system 1

The rise of antibiotic resistance motivates a revived interest in phage therapy. However, bacteria possess dozens of anti-bacteriophage immune systems that confer resistance to therapeutic phages. Chemical inhibitors of these anti-phage immune systems could be employed as adjuvants to overcome resistance in phage-based therapies. Here, we report that anti-phage systems can be selectively inhibited by small molecules, thereby sensitizing phage-resistant bacteria to phages. We discovered a class of chemical inhibitors that inhibit the type II Thoeris anti-phage immune system. These inhibitors block the biosynthesis of a histidine-ADPR intracellular 'alarm' signal by ThsB and prevent ThsA from arresting phage replication. These inhibitors promiscuously inhibit type II Thoeris systems from diverse bacteria-including antibiotic-resistant pathogens. Chemical inhibition of the Thoeris defense improved the efficacy of a model phage therapy against a phage-resistant strain of P. aeruginosa in a mouse infection, suggesting a therapeutic potential. Furthermore, these inhibitors may be employed as chemical tools to dissect the importance of the Thoeris system for phage defense in natural microbial communities.

Antiviral signaling of a type III CRISPR-associated deaminase

Prokaryotes have evolved diverse defense strategies against viral infection, including foreign nucleic acid degradation by CRISPR-Cas systems and DNA and RNA synthesis inhibition through nucleotide pool depletion. Here, we report an antiviral mechanism of type III CRISPR-Cas-regulated adenosine triphosphate (ATP) depletion in which ATP is converted into inosine triphosphate (ITP) by CRISPR-Cas-associated adenosine deaminase (CAAD) upon activation by either cA4 or cA6, followed by hydrolysis into inosine monophosphate (IMP) by Nudix hydrolase, ultimately resulting in cell growth arrest. The cryo-electron microscopy structures of CAAD in its apo and activated forms, together with biochemical evidence, revealed how cA4 or cA6 binds to the CRISPR-associated Rossmann fold (CARF) domain and abrogates CAAD autoinhibition, inducing substantial conformational changes that reshape the structure of CAAD and induce its deaminase activity. Our results reveal the mechanism of a CRISPR-Cas-regulated ATP depletion antiviral strategy.

Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer

Prokaryotes have evolved a wide repertoire of defense systems to prevent invasion by mobile genetic elements (MGEs). However, because MGEs are vehicles for the exchange of beneficial accessory genes, defense systems could consequently impede rapid adaptation in microbial populations. Here, we study how defense systems impact horizontal gene transfer (HGT) in the short term and long term. By combining comparative genomics and phylogeny-aware statistical methods, we quantify the association between the presence of seven widespread defense systems and the abundance of MGEs in the genomes of 196 bacterial and one archaeal species. We also calculate the differences in the rates of gene gain and loss between lineages that possess and lack each defense system. Our results show that the impact of defense systems on HGT is highly taxon and system dependent and, in most cases, not statistically significant. Timescale analysis reveals that defense systems must persist in a lineage for a relatively long time to exert an appreciable negative impact on HGT. In contrast, for shorter evolutionary timescales, frequent coacquisition of MGEs and defense systems results in a net positive association of the latter with HGT. Given the high turnover rates experienced by defense systems, we propose that the inhibitory effect of most defense systems on HGT is masked by their strong linkage with MGEs. These findings help explain the contradictory conclusions of previous research by pointing at mobility and within-host retention times as key factors that determine the impact of defense systems on genome plasticity.

Bacteria- and Phage-Derived Proteins in Phage Infection

Phages have exerted severe evolutionary pressure on prokaryotes over billions of years, resulting in major rearrangements. Without every enzyme involved in the phage-bacterium interaction being examined; bacteriophages cannot be used in practical applications. Numerous studies conducted in the past few years have uncovered a huge variety of bacterial antiphage defense systems; nevertheless, the mechanisms of most of these systems are not fully understood. Understanding the interactions between bacteriophage and bacterial proteins is important for efficient host cell infection. Phage proteins involved in these bacteriophage-host interactions often arise immediately after infection. Here, we review the main groups of phage enzymes involved in the first stage of viral infection and responsible for the degradation of the bacterial membrane. These include polysaccharide depolymerases (endosialidases, endorhamnosidases, alginate lyases, and hyaluronate lyases), and peptidoglycan hydrolases (ectolysins and endolysins). Host target proteins are inhibited, activated, or functionally redirected by the phage protein. These interactions determine the phage infection of bacteria. Proteins of interest are holins, endolysins, and spanins, which are responsible for the release of progeny during the phage lytic cycle. This review describes the main bacterial and phage enzymes involved in phage infection and analyzes the therapeutic potential of bacteriophage-derived proteins.

Antiviral defence arsenal across members of the Bacillus cereus group

Bacteria co-evolve with bacteriophages to overcome each other's defence arsenal. Bacillus cereus group gathers bacteria of medical and agricultural importance, including foodborne pathogens. So far, few studies have portrayed a complete defence arsenal of microorganisms, and the role of antiviral systems in the Bacillus cereus group has been overlooked. Here, we investigate the repertoire of defence systems in 6354 B. cereus group's genomic assemblies, using bioinformatics tools DefenseFinder and PADLOC. Our analyses provide an overview of the diversity and abundance of defence systems in this group, with 83,738 systems distributed by 2 to 33 within each assembly. Comparing PADLOC and DefenseFinder predictions showed that the most prevalent strategy is Restriction-Modification, but many abortive infection systems also intervene in the group's defence, such as Septu, Gabija and Lamassu. Most defences were encoded on both plasmids and the chromosome, though some tend to have a preferential genomic location. We also studied the defence systems associations within the genomic assemblies. Overall, our results establish a baseline picturing the rich and complex antiviral arsenal encoded by B. cereus group's species and provide clues for studying co-existing strategies displayed by these bacteria to subvert phages and other MGEs invasions.

DNA end sensing and cleavage by the Shedu anti-phage defense system

The detection of molecular patterns associated with invading pathogens is a hallmark of innate immune systems. Prokaryotes deploy sophisticated host defense mechanisms in innate anti-phage immunity. Shedu is a single-component defense system comprising a putative nuclease SduA. Here, we report cryoelectron microscopy (cryo-EM) structures of apo- and double-stranded DNA (dsDNA)-bound tetrameric SduA assemblies, revealing that the N-terminal domains of SduA form a clamp that recognizes free DNA ends. End binding positions the DNA over the PD-(D/E)XK nuclease domain, resulting in dsDNA nicking at a fixed distance from the 5' end. The end-directed DNA nicking activity of Shedu prevents propagation of linear DNA in vivo. Finally, we show that phages escape Shedu immunity by suppressing their recombination-dependent DNA replication pathway. Taken together, these results define the antiviral mechanism of Shedu systems, underlining the paradigm that recognition of pathogen-specific nucleic acid structures is a conserved feature of innate immunity across all domains of life.

Bacterial Shedu immune nucleases share a common enzymatic core regulated by diverse sensor domains

Prokaryotes possess diverse anti-bacteriophage immune systems, including the single-protein Shedu nuclease. Here, we reveal the structural basis for activation of Bacillus cereus Shedu. Two cryoelectron microscopy structures of Shedu show that it switches between inactive and active states through conformational changes affecting active-site architecture, which are controlled by the protein's N-terminal domain (NTD). We find that B. cereus Shedu cleaves near DNA ends with a 3' single-stranded overhang, likely enabling it to specifically degrade the DNA injected by certain bacteriophages. Bioinformatic analysis of Shedu homologs reveals a conserved nuclease domain with remarkably diverse N-terminal regulatory domains: we identify 79 distinct NTD types falling into eight broad classes, including those with predicted nucleic acid binding, enzymatic, and other activities. Together, these data reveal Shedu as a broad family of immune nucleases with a common nuclease core regulated by diverse NTDs that likely respond to a range of signals.

Compact RNA editors with natural miniature Cas13j nucleases

Clustered regularly interspaced short palindromic repeats-Cas13 effectors are used for RNA editing but the adeno-associated virus (AAV) packaging limitations because of their big sizes hinder their therapeutic application. Here we report the identification of the Cas13j family, with LepCas13j (529 aa) and ChiCas13j (424 aa) being the smallest and most highly efficient variants for RNA interference. The miniaturized Cas13j proteins enable the development of compact RNA base editors. Chi-RESCUE-S, by fusing dChiCas13j with hADAR2dd, demonstrates high efficiency and specificity in A-to-G and C-to-U conversions. Importantly, this system is compatible with single-AAV packaging without the need for protein sequence truncation. It successfully corrected pathogenic mutations, such as APOC3D65N and SCN9AR896Q, to the wild-type forms. In addition, we developed an optimized system, Chi-RESCUE-S-mini3, which pioneered efficient in vivo C-to-U RNA editing of PCSK9 in mice through single-AAV delivery, resulting in reduced total cholesterol levels. These results highlight the potential of Cas13j to treat human diseases.

Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress

BACKGROUND

The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. We established microcosm systems with varying concentrations of hexavalent chromium (Cr(VI)) to investigate the adaptive modifications of prokaryotic antiviral defense systems under abiotic stress.

RESULTS

Utilizing hybrid metagenomic assembly with long-read and short-read sequencing, we discovered that antiviral defense systems were more diverse and prevalent in heavily polluted soils, which was corroborated by meta-analyses of public datasets from various heavy metal-contaminated sites. As the Cr(VI) concentration increased, prokaryotes with defense systems favoring prokaryote-virus mutualism gradually supplanted those with defense systems incurring high adaptive costs. Additionally, as Cr(VI) concentrations increased, enriched antiviral defense systems exhibited synchronization with microbial heavy metal resistance genes. Furthermore, the proportion of antiviral defense systems carried by mobile genetic elements (MGEs), including plasmids and viruses, increased by approximately 43% and 39%, respectively, with rising Cr concentrations. This trend is conducive to strengthening the dissemination and sharing of defense resources within microbial communities.

CONCLUSIONS

Overall, our study reveals the adaptive modification of prokaryotic antiviral defense systems in soil ecosystems under abiotic stress, as well as their positive contributions to establishing prokaryote-virus mutualism and the evolution of microbial heavy metal resistance. These findings advance our understanding of microbial adaptation in stressful environments and may inspire novel approaches for microbiome manipulation and bioremediation. Video Abstract.

Role of phage therapy in acute gastroenteritis

The gut ecosystem, comprising the gut microbiota and its interactions, plays a crucial role in human health and disease. This complex ecosystem involves a diverse array of microorganisms such as viruses, fungi, and bacteria, collectively known as the gut microbiota. These microorganisms contribute to various functions, including nutrient metabolism and immune modulation, thereby impacting human health. Dysbiosis, or an imbalance in the gut microbiota, has been associated with the pathogenesis of several diseases, ranging from intestinal disorders such as inflammatory bowel disease to extra-intestinal conditions such as metabolic and neurological disorders. The implications of dysbiosis in the gut ecosystem are far-reaching, affecting not only gastrointestinal health but also contributing to the development and progression of conditions such as autoimmune gastritis and gastric cancer. Furthermore, the burden of antimicrobial use and subsequent side effects, including antibiotic resistance, poses additional challenges in managing gastrointestinal diseases. In light of these complexities, investigating the role of bacteriophages as regulators of the gut ecosystem and their potential clinical applications presents a promising opportunity to tackle antibiotic resistance and fight infectious diseases.

Exploring Viral Interactions in Clavibacter Species: In Silico Analysis of Prophage Prevalence and Antiviral Defenses

Clavibacter is a phytopathogenic genus that causes severe diseases in economically important crops, yet the role of prophages in its evolution, pathogenicity, and adaptation remains poorly understood. In this study, we used PHASTER, Prophage Hunter, and VirSorter2 to identify prophage-like sequences in publicly available Clavibacter genomes. Prophage predictions were checked by hand to make them more accurate. We identified 353 prophages, predominantly in chromosomes, with some detected phage-plasmids. Most prophages exhibited traits of advanced domestication, such as an unimodal genome length distribution, reduced numbers of integrases, and minimal transposable elements, suggesting long-term interactions with their bacterial hosts. Comparative genomic analyses uncovered high genetic diversity, with distinct prophage clusters showing species-specific and interspecies conservation patterns. Functional annotation revealed prophage-encoded genes were involved in sugar metabolism, heavy metal resistance, virulence factors, and antibiotic resistance, highlighting their contribution to host fitness and environmental adaptation. Defense system analyses revealed that, despite lacking CRISPR-Cas, Clavibacter genomes harbor diverse antiviral systems, including PD-Lambda-1, AbiE, and MMB_gp29_gp30, some encoded within prophages. These findings underscore the pervasive presence of prophages in Clavibacter and their role in shaping bacterial adaptability and evolution.

Structural and mechanistic insights into the activation of a short prokaryotic argonaute system from archaeon Sulfolobus islandicus

Prokaryotic Argonaute proteins (pAgos) defend the host against invading nucleic acids, including plasmids and viruses. Short pAgo systems confer immunity by inducing cell death upon detecting invading nucleic acids. However, the activation mechanism of the SiAgo system, comprising a short pAgo from the archaeon Sulfolobus islandicus and its associated proteins SiAga1 and SiAga2, remains largely unknown. Here, we determined the cryo-electron microscopy structures of the SiAgo-Aga1 apo complex and the RNA-DNA-bound SiAgo-Aga1 complex at resolutions of 2.7 and 3.0 Å, respectively. Our results revealed that a positively charged pocket is generated from the interaction between SiAgo and SiAga1, exhibiting an architecture similar to APAZ-pAgo of short pAgo systems and accommodating the nucleic acids. Further investigation elucidated the conserved mechanism of nucleic acid recognition by SiAgo-Aga1. Both the SiAgo-Aga1 interaction and nucleic acid recognition by the complex are essential for antiviral defense. Biochemical and structural analyses demonstrated that SiAgo-Aga1 undergoes extensive conformational changes upon binding to the RNA-DNA duplex, thereby licensing its interaction with the effector SiAga2 to trigger the immune response. Overall, our findings highlight the evolutionary conservation of Agos across phylogenetic clades and provide structural insights into the activation mechanism of the SiAgo system.

Kiwa is a bacterial membrane-embedded defence supercomplex activated by phage-induced membrane changes

Bacteria and archaea deploy diverse, sophisticated defence systems to counter virus infection, yet many immunity mechanisms remain poorly understood. Here, we characterise the Kiwa defence system as a membrane-associated supercomplex that senses changes in the membrane induced by phage infection and plasmid conjugation. This supercomplex, comprising KwaA tetramers bound to KwaB dimers, as its basic repeating unit, detects structural stress via KwaA, activating KwaB, which binds ejected phage DNA through its DUF4868 domain, stalling phage DNA replication forks and thus disrupting replication and late transcription. We show that phage-encoded DNA mimic protein Gam, which inhibits RecBCD, also targets Kiwa through KwaB recognition. However, Gam binding to one defence system precludes its inhibition of the other. These findings reveal a distinct mechanism of bacterial immune coordination, where sensing of membrane disruptions and inhibitor partitioning enhance protection against phages and plasmids.

Novel adaptive immune systems in pristine Antarctic soils

Antarctic environments are dominated by microorganisms, which are vulnerable to viral infection. Although several studies have investigated the phylogenetic repertoire of bacteria and viruses in these poly-extreme environments with freezing temperatures, high ultra violet irradiation levels, low moisture availability and hyper-oligotrophy, the evolutionary mechanisms governing microbial immunity remain poorly understood. Using genome-resolved metagenomics, we test the hypothesis that Antarctic poly-extreme high-latitude microbiomes harbour diverse adaptive immune systems. Our analysis reveals the prevalence of prophages in bacterial genomes (Bacteroidota and Verrucomicrobiota), suggesting the significance of lysogenic infection strategies in Antarctic soils. Furthermore, we demonstrate the presence of diverse CRISPR-Cas arrays, including Class 1 arrays (Types I-B, I-C, and I-E), alongside systems exhibiting novel gene architecture among their effector cas genes. Notably, a Class 2 system featuring type V variants lacks CRISPR arrays, encodes Cas1 and Cas2 adaptation module genes. Phylogenetic analysis of Cas12 effector proteins hints at divergent evolutionary histories compared to classified type V effectors and indicates that TnpB is likely the ancestor of Cas12 nucleases. Our findings suggest substantial novelty in Antarctic cas sequences, likely driven by strong selective pressures. These results underscore the role of viral infection as a key evolutionary driver shaping polar microbiomes.

Nucleic acid recognition during prokaryotic immunity

Parasitic elements often spread to hosts through the delivery of their nucleic acids to the recipient. This is particularly true for the primary parasites of bacteria, bacteriophages (phages) and plasmids. Although bacterial immune systems can sense a diverse set of infection signals, such as a protein unique to the invader or the disruption of natural host processes, phage and plasmid nucleic acids represent some of the most common molecules that are recognized as foreign to initiate defense. In this review, we will discuss the various elements of invader nucleic acids that can be distinguished by bacterial host immune systems as "non-self" and how this signal is relayed to activate an immune response.

Pseudomonas aeruginosa as a model bacterium in antiphage defense research

Bacteriophages, or phages, depend on their bacterial hosts for proliferation, leading to a coevolutionary relationship characterized by on-going arms races, where bacteria evolve diverse antiphage defense systems. The development of in silico methods and high-throughput screening techniques has dramatically expanded our understanding of bacterial antiphage defense systems, enormously increasing the known repertoire of the distinct mechanisms across various bacterial species. These advances have revealed that bacterial antiphage defense systems exhibit a remarkable level of complexity, ranging from highly conserved to specialized mechanisms, underscoring the intricate nature of bacterial antiphage defense systems. In this review, we provide a concise snapshot of antiphage defense research highlighting two preponderantly commandeered approaches and classification of the known antiphage defense systems. A special focus is placed on the model bacterial pathogen, Pseudomonas aeruginosa in antiphage defense research. We explore the complexity and adaptability of these systems, which play crucial roles in genome evolution and adaptation of P. aeruginosa in response to an arsenal of diverse phage strains, emphasizing the importance of this organism as a key emerging model bacterium in recent antiphage defense research.

Domainator, a flexible software suite for domain-based annotation and neighborhood analysis, identifies proteins involved in antiviral systems

The availability of large databases of biological sequences presents an opportunity for in-depth exploration of gene diversity and function. Bacterial defense systems are a rich source of diverse but difficult to annotate genes with biotechnological applications. In this work, we present Domainator, a flexible and modular software suite for domain-based gene neighborhood and protein search, extraction and clustering. We demonstrate the utility of Domainator through three examples related to bacterial defense systems. First, we cluster CRISPR-associated Rossman fold (CARF) containing proteins with difficult to annotate effector domains, classifying most of them as likely transcriptional regulators and a subset as likely RNases. Second, we extract and cluster P4-like phage satellite defense hotspots, identify an abundant variant of Lamassu defense systems and demonstrate its in vivo activity against several T-even phages. Third, we integrate a protein language model into Domainator and use it to identify restriction endonucleases with low similarity to known reference sequences, validating the activity of one example in vitro. Domainator is made available as an open-source package with detailed documentation and usage examples.

In silico characterization of defense system hotspots in Acinetobacter spp

The bacteria-phage arm race drives the evolution of diverse bacterial defenses. This study identifies and characterizes the defense hotspots in Acinetobacter baumannii using a reference-free approach. Among 4383 high-quality genomes, we found a total of 17,430 phage defense systems and with 54.54% concentrated in 21 hotspots. These hotspots exhibit distinct preferences for different defense systems, and co-occurrence patterns suggest synergistic interactions. Additionally, the mobile genetic elements are abundant around these hotspots, likely facilitating horizontal transfer and evolution of defense systems. The number of hotspots increases in species phylogenetically closer to Acinetobacter baumannii, but the number of defense systems per hotspot varies due to particular selective pressures. These findings provide critical insights into the genetic organization of phage defense systems, contributing to a broader understanding of bacterial immunity and the evolutionary dynamics that shape Acinetobacter genomes. This knowledge lays the foundation for developing targeted interventions  to combat antibiotic resistance Acinetobacter baumannii.

Structural and bioinformatics analyses identify deoxydinucleotide-specific nucleases and their association with genomic islands in gram-positive bacteria

Dinucleases of the DEDD superfamily, such as oligoribonuclease, Rexo2 and nanoRNase C, catalyze the essential final step of RNA degradation, the conversion of di- to mononucleotides. The active sites of these enzymes are optimized for substrates that are two nucleotides long, and do not discriminate between RNA and DNA. Here, we identified a novel DEDD subfamily, members of which function as dedicated deoxydinucleases (diDNases) that specifically hydrolyze single-stranded DNA dinucleotides in a sequence-independent manner. Crystal structures of enzyme-substrate complexes reveal that specificity for DNA stems from a combination of conserved structural elements that exclude diribonucleotides as substrates. Consistently, diDNases fail to complement the loss of enzymes that act on diribonucleotides, indicating that these two groups of enzymes support distinct cellular functions. The genes encoding diDNases are found predominantly in genomic islands of Actinomycetes and Clostridia, which, together with their association with phage-defense systems, suggest potential roles in bacterial immunity.

Exploring the diversity of anti-defense systems across prokaryotes, phages and mobile genetic elements

The co-evolution of prokaryotes, phages and mobile genetic elements (MGEs) has driven the diversification of defense and anti-defense systems alike. Anti-defense proteins have diverse functional domains, sequences and are typically small, creating a challenge to detect anti-defense homologs across prokaryotic and phage genomes. To date, no tools comprehensively annotate anti-defense proteins within a desired sequence. Here, we developed 'AntiDefenseFinder'-a free open-source tool and web service that detects 156 anti-defense systems of one or more proteins in any genomic sequence. Using this dataset, we identified 47 981 anti-defense systems distributed across prokaryotes and their viruses. We found that some genes co-localize in 'anti-defense islands', including Escherichia coli T4 and Lambda phages, although many appear standalone. Eighty-nine per cent anti-defense systems localize only or preferentially in MGE. However, >80% of anti-Pycsar protein 1 (Apyc1) resides in nonmobile regions of bacterial genomes. Evolutionary analysis and biochemical experiments revealed that Apyc1 likely originated in bacteria to regulate cyclic nucleotide (cNMP) signaling, but phage co-opted Apyc1 to overcome cNMP-utilizing defenses. With the AntiDefenseFinder tool, we hope to facilitate the identification of the full repertoire of anti-defense systems in MGEs, the discovery of new protein functions and a deeper understanding of host-pathogen arms race.

A Class 1 OLD family nuclease encoded by Vibrio cholerae is countered by a vibriophage-encoded direct inhibitor

Bacteria are constantly threatened by their viral predators (phages), which has resulted in the development of defense systems for bacterial survival. One family of defense systems found widely across bacteria are OLD (for overcoming lysogeny defect) family nucleases. Despite recent discoveries regarding Class 2 and 4 OLD family nucleases and how phages overcome them, Class 1 OLD family nucleases warrant further study as there has only been one anti-phage Class 1 OLD family nuclease described to date. Here, we identify the Vibrio cholerae-encoded Class 1 OLD family nuclease Vc OLD and describe its disruption of genome replication of the lytic vibriophage ICP1. Furthermore, we examine its in vitro activity, identifying Vc OLD as a DNA nickase. Finally, we identify the first direct inhibitor of a Class 1 OLD family nuclease, the ICP1-encoded Oad1. Our research further illuminates Class 1 OLD family nucleases' role in phage defense and explores the dynamic arms race between V. cholerae and its predatory phage ICP1.

Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities

Bacteria have evolved various antiviral defense systems (DSs) to protect themselves, but how DSs respond to the variation of bacteriophages in complex bacterial communities and whether DSs function effectively in maintaining the stability of bacterial community structure and function remain unknown. Here, we conducted a long-term metagenomic investigation on the composition of bacterial and phage communities of monthly collected activated sludge (AS) samples from two full-scale wastewater treatment plants over 6 years and found that DSs were widespread in AS, with 91.1% of metagenome-assembled genomes (MAGs) having more than one complete DS. The stability of the bacterial community was maintained under the fluctuations of the phage community, and DS abundance and phage abundance were strongly positively correlated; there was a 0-3-month time lag in the responses of DSs to phage fluctuations. The rapid turnover of clustered regularly interspaced short palindromic repeat spacer repertoires further highlighted the dynamic nature of bacterial defense mechanisms. A pan-immunity phenomenon was also observed, with nearly identical MAGs showing significant differences in DS composition, which contributed to community stability at the species level. This study provides novel insights into the complexity of phage-bacteria interactions in complex bacterial communities and reveals the key roles of DSs in stabilizing bacterial community structure and function.

Loop-extrusion-mediated plasmid DNA cleavage by the bacterial SMC Wadjet complex

Structural maintenance of chromosomes (SMC) complexes play pivotal roles in genome organization and maintenance across all domains of life. In prokaryotes, SMC-family Wadjet complexes structurally resemble the widespread MukBEF but serve a defensive role by inhibiting plasmid transformation. We previously showed that Wadjet specifically cleaves plasmid DNA; however, the molecular mechanism underlying plasmid recognition remains unclear. Here, we use in vitro single-molecule imaging to directly visualize DNA loop extrusion and plasmid cleavage by Wadjet. We find that Wadjet is a symmetric loop extruder that simultaneously reels in DNA from both sides of a loop and that this activity requires a dimeric JetABC supercomplex. On surface-anchored plasmid DNAs, Wadjet extrudes the full length of a 44-kb-pair plasmid, stalls, and cleaves DNA. Our findings reveal the role of loop extrusion in the specific recognition and elimination of plasmids by Wadjet and establish loop extrusion as an evolutionarily conserved mechanism among SMC complexes across all kingdoms of life.

Making waves: Intelligent phage cocktail design, a pathway to precise microbial control in water systems

Current practices in water and wastewater treatment to control unwanted microbes have led to new problems, including health effects from disinfection byproducts, growth of opportunistic pathogens resistant to residual disinfectants (e.g., chlorine), and antibiotic resistance. These challenges are spurring interest in rethinking our practices of microbial control. Simultaneously, advances in molecular biology and computation power are driving renewed interest in using phages (viruses that infect bacteria) to precisely control microbial growth (aka, phage biocontrol). In this Making Waves article, I begin by reviewing the current state of research into phage cocktail design, emphasizing our limited understanding of the features of successful phage cocktails (combinations of multiple types of phages). I describe the state of modeling phage-bacteria interactions and underscore the need for increasing research efforts to predict phage cocktail success, a key gap slowing the application of phage biocontrol. I also detail how research must also focus on techniques for engineering more effective phages to offer a more rapid alternative to phage discovery from natural environments. In this way, phage cocktails comprised of phages with complementary infection strategies may be designed. The final area for increased research effort that I highlight is the need for phage cocktail design to account for possible unintended environmental effects, a risk that is increasingly acknowledged in phage ecology studies but mostly ignored by those developing phage biocontrol technologies. By focusing more research effort towards the areas necessary for intelligent phage cocktail design, we can accelerate the development of phage-based biocontrol in water systems and improve public health.

Adaptive loss of tRNA gene expression leads to phage resistance in a marine Synechococcus cyanobacterium

Synechococcus is a significant primary producer in the oceans, coexisting with cyanophages, which are important agents of mortality. Bacterial resistance against phage infection is a topic of significant interest, yet little is known for ecologically relevant systems. Here we use exogenous gene expression and gene disruption to investigate mechanisms underlying intracellular resistance of marine Synechococcus WH5701 to the Syn9 cyanophage. The restriction-modification and Gabija defence systems possessed by Synechococcus WH5701 did not contribute to resistance. Instead, resistance was primarily driven by insufficient levels of LeuTAA tRNA, preventing translation of key phage genes in a passive, intracellular mode of resistance. Restoring cellular tRNA expression rendered the cyanobacterium sensitive to infection. We propose an evolutionary scenario whereby changes in cell codon usage, acquisition of tRNAs by the phage and loss of cell and phage tRNA expression resulted in an effective means of resistance, highlighting the dynamic interplay between bacteria and phages in shaping their co-evolutionary trajectories.

A widespread family of viral sponge proteins reveals specific inhibition of nucleotide signals in anti-phage defense

Cyclic oligonucleotide-based antiviral signaling systems (CBASS) are bacterial anti-phage defense operons that use nucleotide signals to control immune activation. Here we biochemically screen 57 diverse E. coli and Bacillus phages for the ability to disrupt CBASS immunity and discover anti-CBASS 4 (Acb4) from the Bacillus phage SPO1 as the founding member of a large family of >1,300 immune evasion proteins. A 2.1 Å crystal structure of Acb4 in complex with 3'3'-cGAMP reveals a tetrameric assembly that functions as a sponge to sequester CBASS signals and inhibit immune activation. We demonstrate Acb4 alone is sufficient to disrupt CBASS activation in vitro and enable immune evasion in vivo. Analyzing phages that infect diverse bacteria, we explain how Acb4 selectively targets nucleotide signals in host defense and avoids disruption of cellular homeostasis. Together, our results reveal principles of immune evasion protein evolution and explain a major mechanism phages use to inhibit host immunity.

Unusual Genomic and Biochemical Features of Paenarthrobacter lasiusi sp. nov-A Novel Bacterial Species Isolated from Lasius niger Anthill Soil

The black garden ant (Lasius niger) is a widely distributed species across Europe, North America, and North Africa, playing a pivotal role in ecological processes within its diverse habitats. However, the microbiome associated with L. niger remains poorly investigated. In the present study, we isolated a novel species, Paenarthrobacter lasiusi, from the soil of the L. niger anthill. The genome of P. lasiusi S21 was sequenced, annotated, and searched for groups of genes of physiological, medical, and biotechnological importance. Subsequently, a series of microbiological, physiological, and biochemical experiments were conducted to characterize P. lasiusi S21 with respect to its sugar metabolism, antibiotic resistance profile, lipidome, and capacity for atmospheric nitrogen fixation, among others. A notable feature of the P. lasiusi S21 genome is the presence of two prophages, which may have horizontally transferred host genes involved in stress responses. P. lasiusi S21 synthesizes a number of lipids, including mono- and digalactosyldiacylglycerol, as well as steroid compounds that are typically found in eukaryotic organisms rather than prokaryotes. P. lasiusi S21 exhibits resistance to penicillins, lincosamides, fusidins, and oxazolidinones, despite the absence of specific genes conferring resistance to these antibiotics. Genomic data and physiological tests indicate that P. lasiusi S21 is nonpathogenic to humans. The genome of P. lasiusi S21 contains multiple operons involved in heavy metal metabolism and organic compound inactivation. Consequently, P. lasiusi represents a novel species with an intriguing evolutionary history, manifesting in distinctive genomic, metabolomic, and physiological characteristics. This species may have potential applications in the bioaugmentation of contaminated soils.

Multi-conflict islands are a widespread trend within Serratia spp

Bacteria carry numerous anti-phage systems in "defense islands" or hotspots. Recent studies have delineated the content and boundaries of these islands in various species, revealing instances of islands that encode additional factors, including antibiotic resistance genes, stress genes, type VI secretion system (T6SS)-dependent effectors, and virulence factors. Our study identifies three defense islands in the Serratia genus with a mixed cargo of anti-phage systems, virulence factors, and different types of anti-bacterial modules, revealing a widespread trend of co-accumulation that extends beyond T6SS-dependent effectors to colicins and contact-dependent inhibition systems. We further report the identification of four distinct anti-phage system/subtypes, including a previously unreported Toll/interleukin (IL)-1 receptor (TIR)-domain-containing system with population-wide immunity, and two loci co-opting a predicted T6SS-related protein for phage defense. This study enhances our understanding of the protein domains that can be co-opted for phage defense, resulting in a highly diversified anti-phage arsenal.

Phage detection by a bacterial NLR-related protein is mediated by DnaJ

Bacteria encode a wide range of antiphage systems and a subset of these proteins are homologous to components of the human innate immune system. Mammalian nucleotide-binding and leucine-rich repeat containing proteins (NLRs) and bacterial NLR-related proteins use a central NACHT domain to link detection of infection with initiation of an antimicrobial response. Bacterial NACHT proteins provide defense against both DNA and RNA phages. Here we determine the mechanism of RNA phage detection by the bacterial NLR-related protein bNACHT25 in E. coli. bNACHT25 was specifically activated by Emesvirus ssRNA phages and analysis of MS2 phage escaper mutants that evaded detection revealed a critical role for Coat Protein (CP). A genetic assay confirmed CP was sufficient to activate bNACHT25 but the two proteins did not directly interact. Instead, we found bNACHT25 requires the host chaperone DnaJ to detect CP. Our data suggest that bNACHT25 detects a wide range of phages by guarding a host cell process rather than binding a specific phage-derived molecule.

A bacterial NLR-related protein recognizes multiple unrelated phage triggers to sense infection

Immune systems must rapidly sense viral infections to initiate antiviral signaling and protect the host. Bacteria encode >100 distinct viral (phage) defense systems and each has evolved to sense crucial components or activities associated with the viral lifecycle. Here we used a high-throughput AlphaFold-multimer screen to discover that a bacterial NLR-related protein directly senses multiple phage proteins, thereby limiting immune evasion. Phages encoded as many as 5 unrelated activators that were predicted to bind the same interface of a C-terminal sensor domain. Genetic and biochemical assays confirmed activators bound to the bacterial NLR-related protein at high affinity, induced oligomerization, and initiated signaling. This work highlights how in silico strategies can identify complex protein interaction networks that regulate immune signaling across the tree of life.

Bacterial WYL domain transcriptional repressors sense single-stranded DNA to control gene expression

Bacteria encode a wide array of immune systems to protect themselves against ubiquitous bacteriophages and foreign DNA elements. While these systems' molecular mechanisms are becoming increasingly well known, their regulation remains poorly understood. Here, we show that an immune system-associated transcriptional repressor of the wHTH-WYL-WCX family, CapW, directly binds single-stranded DNA to sense DNA damage and activate expression of its associated immune system. We show that CapW mediates increased expression of a reporter gene in response to DNA damage in a host cell. CapW directly binds single-stranded DNA by-products of DNA repair through its WYL domain, causing a conformational change that releases the protein from double-stranded DNA. In an Escherichia coli CBASS system with an integrated capW gene, we find that CapW-mediated transcriptional activation is important for this system's ability to prevent induction of a λ prophage. Overall, our data reveal the molecular mechanisms of WYL-domain transcriptional repressors, and provide an example of how bacteria can balance the protective benefits of carrying anti-phage immune systems against the inherent risk of these systems' aberrant activation.

Genome Analysis of Anti-Phage Defense Systems and Defense Islands in Stenotrophomonas maltophilia: Preservation and Variability

Anti-phage defense systems are widespread in bacteria due to the latter continuous adaptation to infection by bacteriophages (phages). Stenotrophomonas maltophilia has a high degree of intrinsic antibiotic resistance, which makes phage therapy relevant for the treatment of infections caused by this species. Studying the array of anti-phage defense systems that could be found in S. maltophilia helps in better adapting the phages to the systems present in the pathogenic bacteria. Pangenome analysis of the available S. maltophilia strains with complete genomes that were downloaded from GenBank, including five local genomes, indicated a wide set of 72 defense systems and subsystems that varied between the strains. Seven of these systems were present in more than 20% of the studied genomes and the proteins encoded by the systems were variable in most of the cases. A total of 27 defense islands were revealed where defense systems were found; however, more than 60% of the instances of systems were found in four defense islands. Several elements linked to the transfer of these systems were found. No obvious associations between the pattern of distribution of the anti-phage defense systems of S. maltophilia and the phylogenetic features or the isolation site were found.

Protein disulfide isomerase A4 binds to Brucella BtpB and mediates intracellular NAD+/NADH metabolism in RAW264.7 cells

The Toll/interleukin-1 receptor (TIR) signaling domain is distributed widely in mammalian Toll-like receptors and adaptors, plant nucleotide-binding leucine-rich repeat receptors, and specific bacterial virulence proteins. Proteins that possess TIR domain exhibit NADase activity which is distinct from the canonical signaling function of these domains. However, the effects of bacterial TIR domain proteins on host metabolic switches and the underlying mechanism of NADase activity in these proteins remain unclear. Here, we utilized Brucella TIR domain-containing type IV secretion system effector protein, BtpB, to explore the mechanism of NADase activity in host cells. We showed that using ectopic expression BtpB not only generates depletion of NAD+ but also loss of NADH and ATP in RAW264.7 macrophage cells. Moreover, immunoprecipitation-mass spectrometry, co-immunoprecipitation, and confocal microscope assays revealed that BtpB interacted with host protein disulfide isomerase A4 (PDIA4). The Brucella mutant strain deleted the gene for BtpB, significantly decreased PDIA4 expression. Furthermore, our data revealed that PDIA4 played an important role in regulating intracellular NAD+/NADH levels in macrophages, and PDIA4 overexpression restored the decline of intracellular NAD+ and NADH levels induced by Brucella BtpB. The results provide new insights into the metabolic regulatory activity of TIR domain proteins in the critical human and animal pathogen Brucella.

Unveiling Hidden Allies: In Silico Discovery of Prophages in Tenacibaculum Species

Tenacibaculosis, caused by Tenacibaculum species, is a significant disease in aquaculture, leading to high mortality and economic losses. Antibiotic treatment raises concerns about resistance, making phage therapy an interesting alternative. Analyzing phage traces in Tenacibaculum genomes is crucial for developing these bacteriophage-based strategies.

METHODS

We assessed the presence of prophages in 212 Tenacibaculum genomes/assemblies available in the NCBI repository, comprising several species and global locations, using the PHASTEST program. Then, we focused on those regions classified as intact, evaluating the most common phages found using VICTOR. The protein of interest discovered in the prophages was evaluated using the ProtParam, DeepTMHMM, InterPro, and Phyre2 tools. In addition, we evaluated the presence of antiphage defense systems in those genomes with intact prophages using the DefenseFinder tool.

RESULTS

We identified 25 phage elements in 24 out of the 212 Tenacibaculum genomes/assemblies analyzed, with 11% of the assemblies containing phage elements. These were concentrated in T. maritimum and T. mesophilum, which harbored 10 and 7 prophage regions, respectively. Of the identified elements, six were classified as intact, including four in T. maritimum, with the most common phages belonging to the Pippivirus and Siphoviridae families. Bioinformatic analysis showed that the putative endolysin is a stable protein of 432 amino acids and 49.8 kDa, with three transmembrane helices and a CHAP domain, structurally similar to the CHAP lytic domain of S. aureus bacteriophage K.

CONCLUSIONS

Key prophage elements in Tenacibaculum, especially in T. maritimum, show promise for phage therapy against tenacibaculosis, supporting sustainable, antibiotic-free treatments in aquaculture.

Gamma-Mobile-Trio systems are mobile elements rich in bacterial defensive and offensive tools

The evolutionary arms race between bacteria and phages led to the emergence of bacterial immune systems whose diversity and dynamics remain poorly understood. Here we use comparative genomics to describe a widespread genetic element, defined by the presence of the Gamma-Mobile-Trio (GMT) proteins, that serves as a reservoir of offensive and defensive tools. We demonstrate, using Vibrio parahaemolyticus as a model, that GMT-containing genomic islands are active mobile elements. Furthermore, we show that GMT islands' cargoes contain various anti-phage defence systems, antibacterial type VI secretion system (T6SS) effectors and antibiotic-resistance genes. We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy. Our findings underscore the need to broaden the concept of 'defence islands' to include defensive and offensive tools, as both share the same mobile elements for dissemination.

The growing repertoire of phage anti-defence systems

The biological interplay between phages and bacteria has driven the evolution of phage anti-defence systems (ADSs), which evade bacterial defence mechanisms. These ADSs bind and inhibit host defence proteins, add covalent modifications and deactivate defence proteins, degrade or sequester signalling molecules utilised by host defence systems, synthesise and restore essential molecules depleted by bacterial defences, or add covalent modifications to phage molecules to avoid recognition. Overall, 145 phage ADSs have been characterised to date. These ADSs counteract 27 of the 152 different bacterial defence families, and we hypothesise that many more ADSs are yet to be discovered. We discuss high-throughput approaches (computational and experimental) which are indispensable for discovering new ADSs and the limitations of these approaches. A comprehensive characterisation of phage ADSs is critical for understanding phage-host interplay and developing clinical applications, such as treatment for multidrug-resistant bacterial infections.

A widespread phage-encoded kinase enables evasion of multiple host antiphage defence systems

DNA degradation (Dnd) is a widespread bacterial antiphage defence system that relies on DNA phosphorothioate (PT) modification for self/non-self discrimination and subsequent degradation of unmodified DNA. Phages employ counterstrategies to evade host immunity, but anti-Dnd immunity has not been characterized. Here we report an immune evasion protein encoded by the Salmonella phage JSS1 that contributes to subverting Dnd and other defence systems. Using quantitative proteomic and phosphoproteomic analyses, we show that the protein JSS1_004 employs N-terminal Ser/Thr/Tyr protein kinase activity to catalyse the multisite phosphorylation of host DndFGH. Notably, JSS1_004 also phosphorylates other bacterial immune systems to varying degrees, including CRISPR‒Cas, QatABCD, SIR2+HerA and DUF4297+HerA. Given that JSS1_004 and its homologues are widespread in phylogenetically diverse phages, we suggest that this strategy constitutes a family of immune evasion proteins that increases the chances of phage proliferation even when a host deploys multiple defence systems.

Genome integrity sensing by the broad-spectrum Hachiman antiphage defense complex

Hachiman is a broad-spectrum antiphage defense system of unknown function. We show here that Hachiman is a heterodimeric nuclease-helicase complex, HamAB. HamA, previously a protein of unknown function, is the effector nuclease. HamB is the sensor helicase. HamB constrains HamA activity during surveillance of intact double-stranded DNA (dsDNA). When the HamAB complex detects DNA damage, HamB helicase activity activates HamA, unleashing nuclease activity. Hachiman activation degrades all DNA in the cell, creating "phantom" cells devoid of both phage and host DNA. We demonstrate Hachiman activation in the absence of phage by treatment with DNA-damaging agents, suggesting that Hachiman responds to aberrant DNA states. Phylogenetic similarities between the Hachiman helicase and enzymes from eukaryotes and archaea suggest deep functional symmetries with other important helicases across domains of life.

The vibriophage-encoded inhibitor OrbA abrogates BREX-mediated defense through the ATPase BrxC

Bacteria and phages are locked in a co-evolutionary arms race where each entity evolves mechanisms to restrict the proliferation of the other. Phage-encoded defense inhibitors have proven powerful tools to interrogate how defense systems function. A relatively common defense system is BREX (bacteriophage exclusion); however, how BREX functions to restrict phage infection remains poorly understood. A BREX system encoded by the sulfamethoxazole and trimethoprim (SXT) integrative and conjugative element, VchInd5, was recently identified in Vibrio cholerae, the causative agent of the diarrheal disease cholera. The lytic phage ICP1 (International Centre for Diarrhoeal Disease Research, Bangladesh cholera phage 1) that co-circulates with V. cholerae encodes the BREX-inhibitor OrbA, but how OrbA inhibits BREX is unclear. Here, we determine that OrbA inhibits BREX using a unique mechanism from known BREX inhibitors by directly binding to the BREX component BrxC. BrxC has a functional ATPase domain that, when mutated, not only disrupts BrxC function but also alters how BrxC multimerizes. Furthermore, we find that OrbA binding disrupts BrxC-BrxC interactions. We determine that OrbA cannot bind BrxC encoded by the distantly related BREX system encoded by the aSXT VchBan9, and thus fails to inhibit this BREX system that also circulates in epidemic V. cholerae. Lastly, we find that homologs of the VchInd5 BrxC are more diverse than the homologs of the VchBan9 BrxC. These data provide new insight into the function of the BrxC ATPase and highlight how phage-encoded inhibitors can disrupt phage defense systems using different mechanisms.IMPORTANCEWith renewed interest in phage therapy to combat antibiotic-resistant pathogens, understanding the mechanisms bacteria use to defend themselves against phages and the counter-strategies phages evolve to inhibit defenses is paramount. Bacteriophage exclusion (BREX) is a common defense system with few known inhibitors. Here, we probe how the vibriophage-encoded inhibitor OrbA inhibits the BREX system of Vibrio cholerae, the causative agent of the diarrheal disease cholera. By interrogating OrbA function, we have begun to understand the importance and function of a BREX component. Our results demonstrate the importance of identifying inhibitors against defense systems, as they are powerful tools for dissecting defense activity and can inform strategies to increase the efficacy of some phage therapies.

Fine-tuned spatiotemporal dynamics of DNA replication during phage lambda infection

After the ejection of viral DNA into the host cytoplasm, the temperate bacteriophage (phage) lambda integrates a cascade of expressions from various regulatory genes, coupled with DNA replication, to commit to a decision between lysis and lysogeny. Higher multiplicity of infection (MOI) greatly shifts the decision toward the lysogenic pathway. However, how the phage separates the MOI from replicated viral DNA during lysis-lysogeny decision-making is unclear. To quantitatively understand the role of viral DNA replication, we constructed a reporter system facilitating the visualization of individual copies of phage DNA throughout the phage life cycle, along with the lysis-lysogeny reporters. We showed that intracellular viral DNA diverges between the lytic and lysogenic pathways from the early phase of the infection cycle, mostly due to the synchronization and success of DNA injection, as well as the competition for replication resources, rather than the replication rate. Strikingly, we observed two distinct replication patterns during lysogenization and surprisingly heterogeneous integration kinetics, which advances our understanding of temperate phage life cycles. We revealed that the weak repression function of Cro is critical for an optimal replication rate and plays a crucial role in establishing stable lysogens.

IMPORTANCE

Temperate bacteriophages, such as lambda, incorporate environmental cues including host abundance and nutrient conditions to make optimal decisions between propagation and dormancy. A higher phage-to-host ratio or multiplicity of infection (MOI) during λ infection strongly biases toward lysogeny. However, a comprehensive understanding of this decision-making process and the impact of phage replication prior to the decision is yet to be achieved. Here, we used fluorescence microscopy to quantitatively track the spatiotemporal progression of viral DNA replication in individual cells with different cell fates. The implementation of this fluorescent reporter system and quantitative analysis workflow opens a new avenue for future studies to delve deeper into various types of virus-host interactions at a high resolution.

Acidic polymers reversibly deactivate phages due to pH changes

Bacteriophages are promising as therapeutics and biotechnological tools, but they also present a problem for routine and commercial bacterial cultures, where contamination must be avoided. Poly(carboxylic acids) have been reported to inhibit phages' ability to infect their bacterial hosts and hence offer an exciting route to discover additives to prevent infection. Their mechanism and limitations have not been explored. Here, we report the role of pH in inactivating phages to determine if the polymers are unique or simply acidic. It is shown that lower pH (=3) triggered by either acidic polymers or similar changes in pH using HCl lead to inhibition. There is no inhibitory activity at higher pHs (in growth media). This was shown across a panel of phages and different molecular weights of commercial and controlled-radical polymerization-derived poly(acrylic acid)s. It is shown that poly(acrylic acid) leads to reversible deactivation of phage, but when the pH is adjusted using HCl alone the phage is irreversibly deactivated. Further experiments using metal binders ruled out ion depletion as the mode of action. These results show that polymeric phage inhibitors may work by unique mechanisms of action and that pH alone cannot explain the observed effects whilst also placing constraints on the practical utility of poly(acrylic acid).