Systematic discovery of antiphage defense systems in the microbial pangenome

Genomic insights into the rapid rise of Pseudomonas aeruginosa ST463: A high-risk lineage's adaptive strategy in China

High-risk lineages of Pseudomonas aeruginosa pose a serious threat to public health, causing severe infections with high mortality rates and limited treatment options. The emergence and rapid spread of the high-risk lineage ST463 in China have further exacerbated this issue. However, the basis of its success in China remains unidentified. In this study, we analyzed a comprehensive dataset of ST463 strains from 2000 to 2023 using whole genome sequencing to unravel the epidemiological characteristics, evolutionary trajectory, and antibiotic resistance profiles. Our findings suggest that ST463 likely originated from a single introduction from North America in 2007, followed by widespread domestic dissemination. Since its introduction, the lineage has undergone significant genomic changes, including the acquisition of three unique regions that enhanced its metabolism and adaptability. Frequent recombination events, along with the burden of bacteriophages, antibiotic resistance genes, and the spread of c1-type (blaKPC-2) plasmid-carrying strains, have played crucial roles in its expansion in China. Mutation analysis reveals adaptive responses to antibiotics and selective pressures on key virulence factors, indicating that ST463 is evolving toward a more pathogenic lifestyle.

Comparative genomics of Salmonella enterica serovars Paratyphi A, Typhi and Typhimurium reveals distinct profiles of their pangenome, mobile genetic elements, antimicrobial resistance and defense systems repertoire

Salmonella enterica (S. enterica) is a highly ubiquitous and diverse animal and human pathogen. Distinct S. enterica serovars may present varying host-specificity and cause different diseases. While the human-restricted serovars S. Typhi (STY) and S. Paratyphi A (SPA) cause in humans a systemic life-threatening enteric fever, the host-generalist serovar, S. Typhimurium (STM) causes in immunocompetent individuals a self-limited gastroenteritis. Here, we have performed whole-genome sequencing and hybrid assembly of new SPA and STY typhoidal strains and took a comparative genomics approach to examine their phylogeny, pangenome structure and accessory genome content in comparison to the reference non-typhoidal serovar, STM. Our results identified previously uncharacterized lineages of SPA and refined the presence and distribution of core pseudogenes in typhoidal serovars. Pangenome analysis showed that while these serovars have a relatively similar core-genome size, the accessory genome of STM is more than four times larger than those of typhoidal Salmonellae and that STY and SPA display a more closed pangenome than STM. Unexpectedly, we demonstrate that STY and SPA present distinct differences in their pangenome composition, with a noticeable lower number of prophages, conjugative elements and antimicrobial genes per genome in SPA vs. STY. These results suggest that although SPA and STY are closely related at the DNA level, share a similar lifestyle and cause a symptomatic-indistinguishable disease, their genomic evolution and accessory genomes are markedly different. Moreover, these results may provide genomic explanation to phenotypic and epidemiological differences in antimicrobial resistance profiles associated with these serovars globally.

Recent advancements in bacterial anti-phage strategies and the underlying mechanisms altering susceptibility to antibiotics

The rapid spread of multidrug-resistant bacteria and the challenges in developing new antibiotics have brought renewed international attention to phage therapy. However, in bacteria-phage co-evolution, the rapid development of bacterial resistance to phage has limited its clinical application. This review consolidates the latest advancements in research on anti-phage mechanisms, encompassing strategies such as systems associated with reduced nicotinamide adenine dinucleotide (NAD+) to halt the propagation of the phage, symbiotic bacteria episymbiont-mediated modulation of gene expression in host bacteria to resist phage infection, and defence-related reverse transcriptase (DRT) encoded by bacteria to curb phage infections. We conduct an in-depth analysis of the underlying mechanisms by which bacteria undergo alterations in antibiotic susceptibility after developing phage resistance. We also discuss the remaining challenges and promising directions for phage-based therapy in the future.

Phage DisCo: targeted discovery of bacteriophages by co-culture

Phages interact with many components of bacterial physiology from the surface to the cytoplasm. Although there are methods to determine the receptors and intracellular systems a specified phage interacts with retroactively, finding a phage that interacts with a chosen piece of bacterial physiology a priori is very challenging. Variation in phage plaque morphology does not to reliably distinguish distinct phages, and therefore many potentially redundant phages may need to be isolated, purified, and individually characterized to find phages of interest. Here, we present a method in which multiple bacterial strains are co-cultured on the same screening plate to add an extra dimension to plaque morphology data. In this method, phage discovery by co-culture (Phage DisCo), strains are isogenic except for fluorescent tags and one perturbation expected to impact phage infection. Differential plaquing on the strains is easily detectable by fluorescent signal and implies that the perturbation made to the surviving strain in a plaque prevents phage infection. We validate the Phage DisCo method by showing that characterized phages have the expected plaque morphology on Phage DisCo plates and demonstrate the power of Phage DisCo for multiple targeted discovery applications, from receptors to phage defense systems.IMPORTANCEIn this work, we describe a targeted phage discovery method that allows immediate isolation of phages with specific traits. Currently, to find a phage with specific properties, huge libraries of phages must be collected and screened retroactively. This assay, Phage Discovery by Co-culture (Phage DisCo), works by co-culture of host strains that are identical except for one perturbation that may interfere with phage infection and a unique fluorescent marker. These strains are co-cultured with an environmental sample of interest in traditional plaque assay format, making phage characteristics easily identifiable by fluorescent signal after imaging of the screening plate. We validate that Phage DisCo can identify phages with specific properties, even when these phages are rare in samples. This approach allows rapid exploration of the diversity within phage samples with vastly streamlined processes, and we anticipate it will be widely adopted within the phage discovery field.

Metaproteomics in the One Health framework for unraveling microbial effectors in microbiomes

One Health seeks to integrate and balance the health of humans, animals, and environmental systems, which are intricately linked through microbiomes. These microbial communities exchange microbes and genes, influencing not only human and animal health but also key environmental, agricultural, and biotechnological processes. Preventing the emergence of pathogens as well as monitoring and controlling the composition of microbiomes through microbial effectors including virulence factors, toxins, antibiotics, non-ribosomal peptides, and viruses holds transformative potential. However, the mechanisms by which these microbial effectors shape microbiomes and their broader functional consequences for host and ecosystem health remain poorly understood. Metaproteomics offers a novel methodological framework as it provides insights into microbial dynamics by quantifying microbial biomass composition, metabolic functions, and detecting effectors like viruses, antimicrobial resistance proteins, and non-ribosomal peptides. Here, we highlight the potential of metaproteomics in elucidating microbial effectors and their impact on microbiomes and discuss their potential for modulating microbiomes to foster desired functions.

West African-South American pandemic Vibrio cholerae encodes multiple distinct phage defence systems

Our understanding of the factors underlying the evolutionary success of different lineages of pandemic Vibrio cholerae remains incomplete. The West African-South American (WASA) lineage of V. cholerae, responsible for the 1991-2001 Latin American cholera epidemic, is defined by two unique genetic signatures. Here we show that these signatures encode multiple distinct anti-phage defence systems. Firstly, the WASA-1 prophage encodes an abortive-infection system, WonAB, that renders the lineage resistant to the major predatory vibriophage ICP1, which, alongside other phages, is thought to restrict cholera epidemics. Secondly, a unique set of genes on the Vibrio seventh pandemic island II encodes an unusual modification-dependent restriction system targeting phages with modified genomes, and a previously undescribed member of the Shedu defence family that defends against vibriophage X29. We propose that these anti-phage defence systems likely contributed to the success of a major epidemic lineage of the ongoing seventh cholera pandemic.

Deciphering the Causes of IbfA-Mediated Abortive Infection in the P22-like Phage UAB_Phi20

The study of bacterial defense mechanisms against phages is becoming increasingly relevant due to their impact on the effectiveness of phage therapy. Employing a multifaceted approach that combines bioinformatics, molecular microbiology, TEM microscopy, and conventional microbiology techniques, here, we identify the ibfA gene as a novel defense factor targeting the virulent phage UAB_Phi20, acquired by Salmonella Typhimurium through lateral transfer on the IncI1α conjugative plasmid pUA1135 after oral phage therapy in broilers. IbfA, a two-domain protein containing ATPase and TOPRIM domains, significantly reduces UAB_Phi20 productivity, as indicated by decreased EOP, ECOI, and a diminished burst size, potentially reducing cellular viability without causing observable lysis. Our results indicate that IbfA enhances the transcription of early genes, including the antirepressor ant, which inhibits the C2 repressor of the lytic cycle. This may cause an imbalance in Cro/C2 concentration, leading to the observed reduction in the transcription of late genes encoding structural and cellular lysis proteins, and resulting in the abortion of UAB_Phi20 infection.

E. coli prophages encode an arsenal of defense systems to protect against temperate phages

In recent years, dozens of anti-phage defense systems have been identified. However, efforts to find these systems have focused predominantly on lytic phages, leaving defense against temperate phages poorly understood. Here, we isolated 33 temperate phages from a diverse collection of E. coli to create a library of single lysogens, which were tested for defense against the same set of temperate phages. We found that the majority of lysogens offer protection against at least one additional phage from the collection, often displaying broad defense against various phages. Defense efficacy varies based on growth media and host background, suggesting that some systems are context dependent. Using an iterative deletion-based strategy, we identify 17 systems responsible for the prophage-encoded defense, including 5 toxin-antitoxin modules. Collectively, our work uncovers a diverse array of phage-phage interactions and indicates that temperate phages encode a previously unrecognized arsenal of anti-phage defense systems.

Evolutionarily ancient functions of enzymatic TIR proteins in innate immunity

Proteins with a Toll/interleukin-1 receptor/resistance (TIR) domain are among the most ancient immune regulators and include well-known pattern recognition receptors (PRRs). A specialized subset of TIR domain proteins are enzymes that predominantly use nicotinamide adenine dinucleotide (NAD+) to generate second messenger metabolites. These enzymatic TIR proteins have essential roles in bacteria, plant, and animal immunity. The mechanism of activation of these TIR proteins, conserved across Kingdoms, involves oligomerization into higher-ordered structures, which activates their intrinsic enzymatic activity. Here, we review the functions of enzymatic TIR proteins in innate immunity in bacteria, plants, and animals. This work offers insights into the evolutionary origins of immunity itself and defines fundamental principles of immune surveillance across the Tree of Life.

Prophage transduction promotes the transmission of phage resistance interfering with adsorption among Chinese foodborne Staphylococcus aureus

Although bacteriophages have proven to be efficient biocontrol agents for foodborne Staphylococcus aureus, the transmission of phage resistance resulting in the reduced efficacy of phage therapy remains to be explored. In this study, phage resistance and adsorption of 91 Chinese foodborne S. aureus isolates by 18 phages were estimated, and the distribution and transmission of phage resistance genes were investigated. The isolated 91 S. aureus comprised 50 multidrug-resistance isolates, all of which showed sensitivity to more than two phages. However, 9.9 % (9/91) of S. aureus isolates were resistant to all 18 phages, and the majority of phages (83.3 %, 15/18) did not adsorb to all foodborne S. aureus strains. Whole-genome analysis revealed that the 91 isolates comprised 101 phage resistance genes, including 24 genes were found in prophages (intact prophages, 19.8 %, 20/101; incomplete prophages, 16.8 %, 17/101). Notably, a temperate phage SapYZUs631 was successfully induced and exhibited better biological characteristics compared to other isolated S. aureus temperate phages, including higher titre (6.2 × 109 PFU/mL), stronger pH (4-11) and thermal (60 °C for 60 min) stability, and a wider host range (80.2 %, 73/91). The SapYZUs631 genome contained phage resistance gene tarP interfering with adsorption and virulence genes. The lysogeny of SapYZUs631 into S. aureus strains YZUstau27, YZUstau31, and YZUstau35 resulted in increased phage resistance and decreased adsorption. Therefore, our analysis suggests that the interruption of adsorption is the main reason for the phage resistance of foodborne S. aureus in China, which resulted from the transmission of phage resistance by prophage transduction.

Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA

Prokaryotic Argonaute proteins (pAgos) from the long-A clade are stand-alone immune systems that use small interfering DNA (siDNA) guides to recognize and cleave invading plasmid and virus DNA. Certain long-A pAgos are co-encoded with accessory proteins with unknown functions. Here, we show that cyanobacterial long-A pAgos act in conjunction with Argonaute-associated Cas4 family enzyme 1 (ACE1). Structural and biochemical analyses reveal that ACE1-associated pAgos mediate siDNA-guided DNA interference, akin to stand-alone pAgos. ACE1 is structurally homologous to the nuclease domain of bacterial DNA repair complexes and acts as a single-stranded DNA endonuclease that processes siDNA guides. pAgo and ACE1 form a heterodimeric long-A pAgo-ACE1 (APACE1) complex, which modulates ACE1 activity. Although ACE1-associated pAgos alone interfere with plasmids and bacteriophages, plasmid interference is boosted when pAgo and ACE1 are co-expressed. Our study reveals that pAgo-mediated immunity is enhanced by accessory proteins and broadens our mechanistic understanding of how pAgo systems interfere with invading DNA.

Advances in Diversity, Evolutionary Dynamics and Biotechnological Potential of Restriction-Modification Systems

Restriction-modification systems (RMS) are ubiquitous in prokaryotes and serve as primitive immune-like mechanisms that safeguard microbial genomes against foreign genetic elements. Beyond their well-known role in sequence-specific defense, RMS also contribute significantly to genomic stability, drive evolutionary processes, and mitigate the deleterious effects of mutations. This review provides a comprehensive synthesis of current insights into RMS, emphasizing their structural and functional diversity, ecological and evolutionary roles, and expanding applications in biotechnology. By integrating recent advances with an analysis of persisting challenges, we highlight the critical contributions of RMS to both fundamental microbiology and practical applications in biomedicine and industrial biotechnology. Furthermore, we discuss emerging research directions in RMS, particularly in light of novel technologies and the increasing importance of microbial genetics in addressing global health and environmental issues.

Unveiling the multifaceted domain polymorphism of the Menshen antiphage system

Recent advances have significantly enriched our understanding of complex bacteria-phage interactions. To date, over one hundred bacterial antiphage systems have been identified, yet the mechanisms of many, including the recently discovered Menshen system, remain elusive. We employed comparative genomics and protein bioinformatics for a systematic investigation of the Menshen system, focusing on its organization, structure, function, and evolution. By delineating six primary domain determinants and predicting their functions, we propose that the three components (NsnA-B-C) of Menshen likely act as sensor, transducer, and effector modules, respectively. Notably, we unveil remarkable polymorphism in domain composition within both NsnA and NsnC. NsnA proteins universally share ParB-DUF262 and DNA-binding ParBDB domains, and often include additional DNA-binding modules at their N-termini. NsnC effectors exhibit diverse inactive PIN (inPIN)-like domains for target recognition in their N-termini, and multiple nuclease domains for toxicity in their C-termini. We demonstrate that this multifaceted polymorphism results from the independent integration of various sensor domains into NsnA, alongside constant shuffling and diversification of the inPIN and effector domains in NsnC. These findings not only elucidate the functional diversity and inter-subunit interactions of the Menshen system, but also underscore its exceptional capacity for adaptability and versatility in the ongoing arms race between bacteria and phages.

Mechanism of DNA capture by the MukBEF SMC complex and its inhibition by a viral DNA mimic

Ring-like structural maintenance of chromosome (SMC) complexes are crucial for genome organization and operate through mechanisms of DNA entrapment and loop extrusion. Here, we explore the DNA loading process of the bacterial SMC complex MukBEF. Using cryoelectron microscopy (cryo-EM), we demonstrate that ATP binding opens one of MukBEF's three potential DNA entry gates, exposing a DNA capture site that positions DNA at the open neck gate. We discover that the gp5.9 protein of bacteriophage T7 blocks this capture site by DNA mimicry, thereby preventing DNA loading and inactivating MukBEF. We propose a comprehensive and unidirectional loading mechanism in which DNA is first captured at the complex's periphery and then ingested through the DNA entry gate, powered by a single cycle of ATP hydrolysis. These findings illuminate a fundamental aspect of how ubiquitous DNA organizers are primed for genome maintenance and demonstrate how this process can be disrupted by viruses.

Activation of bacterial programmed cell death by phage inhibitors of host immunity

Bacterial and archaeal viruses are replete with diverse uncharacterized accessory genes (AGs), which likely interface with host processes. However, large-scale discovery of virus AG functions remains challenging. Here, we developed an integrated computational and experimental discovery platform to identify viral AGs and assign functions. We show that multiple AGs activate unexpected programmed cell death (PCD) activity of distinct restriction-modification (R-M) systems. We describe an exapted type I R-M decoy that kills the host upon sensing several different anti-defense AGs and a self-guarded type III R-M system that restricts phages but also induces PCD when bound by anti-R-M proteins. Other phage counter-defense genes additionally activate non-R-M-based abortive infection systems encoded by prophages. This defense strategy creates a conundrum: lose AGs and be exposed to immunity or keep AGs and trigger PCD. Strategies employed by viruses to avoid this double bind could be an important factor in virus evolution that remains to be explored.

Developing a robust genome editing tool based on an endogenous type I-B CRISPR-Cas system in Saccharopolyspora spinosa

Saccharopolyspora spinosa is an industrial rare actinomycete capable of producing important environmental-friendly biopesticides, spinosyns. However, exploitation of S. spinosa has been limited due to its genetic inaccessibility and lack of effective genome engineering tools. In this work, we characterized the activity of an endogenous type I-B CRISPR-Cas system as well as its recognized protospacer adjacent motifs (PAMs) based on bioinformatics analysis combined with a plasmid interference assay in S. spinosa. By delivering editing plasmids containing a designed miniCRISPR array (repeat+self-targeting spacer+repeat) and repair templates, we achieved 100% editing efficiency for gene deletion. Using this tool, the genetic barrier composed of the restriction-modification (RM) systems was systematically disarmed. We showed that by disarming one type I RM system (encoded by A8926_1903/1904/1905) and two type II RM systems (encoded by A8926_1725/1726 and A8926_2652/2653) simultaneously, the transformation efficiency of the replicative and integrative plasmids (pSP01 and pSI01) was increased by approximately 3.9-fold and 4.2-fold, respectively. Using the engineered strain with simultaneous knock-out of these three RM genes as the starting strain, we achieved the deletion of 75-kb spinosyns biosynthetic gene cluster (BGC) as well as gene insertion at high efficiency. Collectively, we developed a reliable and highly efficient genome editing tool based on the endogenous type I CRISPR-Cas system combined with the disarmament of the RM systems in S. spinosa. This is the first time to establish an endogenous CRISPR-Cas-based genome editing tool in the non-model industrial actinomycetes.

Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns

Reference genomes of root microbes are essential for metagenomic analyses and mechanistic studies of crop root microbiomes. By combining high-throughput bacterial cultivation with metagenomic sequencing, we constructed comprehensive bacterial and viral genome collections from the roots of wheat, rice, maize, and Medicago. The crop root bacterial genome collection (CRBC) significantly expands the quantity and phylogenetic diversity of publicly available crop root bacterial genomes, with 6,699 bacterial genomes (68.9% from isolates) and 1,817 undefined species, expanding crop root bacterial diversity by 290.6%. The crop root viral genome collection (CRVC) contains 9,736 non-redundant viral genomes, with 1,572 previously unreported genus-level clusters in crop root microbiomes. From these, we identified conserved bacterial functions enriched in root microbiomes across soils and host species and uncovered previously unexplored bacteria-virus connections in crop root ecosystems. Together, the CRBC and CRVC serve as valuable resources for investigating microbial mechanisms and applications, supporting sustainable agriculture.

Surface-mediated bacteriophage defense incurs fitness tradeoffs for interbacterial antagonism

Bacteria in polymicrobial habitats are constantly exposed to biotic threats from bacteriophages (or "phages"), antagonistic bacteria, and predatory eukaryotes. These antagonistic interactions play crucial roles in shaping the evolution and physiology of bacteria. To survive, bacteria have evolved mechanisms to protect themselves from such attacks, but the fitness costs of resisting one threat and rendering bacteria susceptible to others remain unappreciated. Here, we examined the fitness consequences of phage resistance in Salmonella enterica, revealing that phage-resistant variants exhibited significant fitness loss upon co-culture with competitor bacteria. These phage-resistant strains display varying degrees of lipopolysaccharide (LPS) deficiency and increased susceptibility to contact-dependent interbacterial antagonism, such as the type VI secretion system (T6SS). Utilizing mutational analyses and atomic force microscopy, we show that the long-modal length O-antigen of LPS serves as a protective barrier against T6SS-mediated intoxication. Notably, this competitive disadvantage can also be triggered independently by phages possessing LPS-targeting endoglycosidase in their tail spike proteins, which actively cleave the O-antigen upon infection. Our findings reveal two distinct mechanisms of phage-mediated LPS modifications that modulate interbacterial competition, shedding light on the dynamic microbial interplay within mixed populations.

TIR domains produce histidine-ADPR as an immune signal in bacteria

Toll/interleukin-1 receptor (TIR) domains are central components of pattern recognition immune proteins across all domains of life1,2. In bacteria and plants, TIR-domain proteins recognize pathogen invasion and then produce immune signalling molecules exclusively comprising nucleotide moieties2-5. Here we show that the TIR-domain protein of the type II Thoeris defence system in bacteria produces a unique signalling molecule comprising the amino acid histidine conjugated to ADP-ribose (His-ADPR). His-ADPR is generated in response to phage infection and activates the cognate Thoeris effector by binding a Macro domain located at the C terminus of the effector protein. By determining the crystal structure of a ligand-bound Macro domain, we describe the structural basis for His-ADPR and its recognition and show its role by biochemical and mutational analyses. Our analyses furthermore reveal a family of phage proteins that bind and sequester His-ADPR signalling molecules, enabling phages to evade TIR-mediated immunity. These data demonstrate diversity in bacterial TIR signalling and reveal a new class of TIR-derived immune signalling molecules that combine nucleotide and amino acid moieties.

Exploring Mobile Genetic Elements in Vibrio cholerae

Members of the bacterial species Vibrio cholerae are known both as prominent constituents of marine environments and as the causative agents of cholera, a severe diarrheal disease. While strains responsible for cholera have been extensively studied over the past century, less is known about their environmental counterparts, despite their contributions to the species' pangenome. This study analyzed the genome compositions of 46 V. cholerae strains, including pandemic and nonpandemic, toxigenic, and environmental variants, to investigate the diversity of mobile genetic elements (MGEs), embedded bacterial defense systems, and phage-associated signatures. Our findings include both conserved and novel MGEs across strains, pointing to shared evolutionary pathways and ecological niches. The defensome analysis revealed a wide array of antiphage/antiplasmid mechanisms, extending well beyond the traditional CRISPR-Cas and restriction-modification systems. This underscores the dynamic arms race between V. cholerae and MGEs and suggests that nonpandemic strains may act as reservoirs for emerging defense strategies. Moreover, the study showed that MGEs are integrated into genomic hotspots, which may serve as critical platforms for the exchange of defense systems, thereby enhancing V. cholerae's adaptive capabilities against phage attacks and other invading MGEs. Overall, this research offers new insights into V. cholerae's genetic complexity and potential adaptive strategies, offering a better understanding of the differences between environmental strains and their pandemic counterparts, as well as the possible evolutionary pathways that led to the emergence of pandemic strains.

Base-modified nucleotides mediate immune signaling in bacteria

Signaling from pathogen sensing to effector activation is a fundamental principle of cellular immunity. Whereas cyclic (oligo)nucleotides have emerged as key signaling molecules, the existence of other messengers remains largely unexplored. In this study, we reveal a bacterial antiphage system that mediates immune signaling through nucleobase modification. Immunity is triggered by phage nucleotide kinases, which, combined with the system-encoded adenosine deaminase, produce deoxyinosine triphosphates (dITPs) as immune messengers. The dITP signal activates a downstream effector to mediate depletion of cellular nicotinamide adenine dinucleotide (oxidized form), resulting in population-level defense through the death of infected cells. To counteract immune signaling, phages deploy specialized enzymes that deplete cellular deoxyadenosine monophosphate, the precursor of dITP messengers. Our findings uncover a nucleobase modification-based antiphage signaling pathway, establishing noncanonical nucleotides as a new type of immune messengers in bacteria.

Cell-Autonomous Immunity: From Cytosolic Sensing to Self-Defense

As an evolutionarily conserved and ubiquitous mechanism of host defense, non-immune cells in vertebrates possess the intrinsic ability to autonomously detect and combat intracellular pathogens. This process, termed cell-autonomous immunity, is distinct from classical innate immunity. In this review, we comprehensively examine the defense mechanisms employed by non-immune cells in response to intracellular pathogen invasion. We provide a detailed analysis of the cytosolic sensors that recognize aberrant nucleic acids, lipopolysaccharide (LPS), and other pathogen-associated molecular patterns (PAMPs). Specifically, we elucidate the molecular mechanisms underlying key signaling pathways, including the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway, the retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs)-mitochondrial antiviral signaling (MAVS) axis, and the guanylate-binding proteins (GBPs)-mediated pathway. Furthermore, we critically evaluate the involvement of these pathways in the pathogenesis of various diseases, including autoimmune disorders, inflammatory conditions, and malignancies, while highlighting their potential as therapeutic targets.

Efficient genetic manipulation of Shewanella through targeting defense islands

The Shewanella genus is widely recognized for its remarkable respiratory adaptability in anaerobic environments, exhibiting potential for bioremediation and microbial fuel cell applications. However, the genetic manipulation of certain Shewanella strains is hindered by defense systems that limit their genetic modification in biotechnology processes. In this study, we present a systematic method for predicting, mapping, and functionally analyzing defense islands within bacterial genomes. We investigated the genetically recalcitrant strain Shewanella putrefaciens CN32 and identified several defense systems located on two genomic islands integrated within the conserved chromosomal genes trmA and trmE. Our experimental assays demonstrated that overexpression of excisionases facilitated the excision of these islands from the chromosome, and their removal significantly enhanced the genetic manipulation efficiency of S. putrefaciens CN32. Further analysis revealed that these defense islands are widespread across various Shewanella strains and other gram-negative bacteria. This study presents an effective strategy to circumvent genetic barriers and fully exploit the potential of Shewanella for environmental and microbial engineering applications.

IMPORTANCE

Efficiently modifying bacterial genomes is critical for advancing their industrial applications. However, bacteria in complex environments naturally develop defense mechanisms in response to bacteriophages and exogenous DNA, which pose significant challenges to their genetic modification. Several methods have emerged to tackle these challenges, including in vitro methylation of plasmid DNA and targeting specific restriction-modification (R-M) and CRISPR loci. Nevertheless, many bacteria harbor multiple, often uncharacterized defense mechanisms, limiting these strategies. Our study differs from previous approaches by specifically targeting defense islands-clusters of defense systems located within mobile genetic elements. Here, we investigated Shewanella putrefaciens CN32 and identified two key defense islands responsible for these protective functions. By selectively deleting these defense islands, we significantly enhanced the efficiency of genetic manipulation in S. putrefaciens. Our findings not only demonstrate a promising strategy for improving genetic engineering in Shewanella but also suggest broader applicability across other bacterial species. This work opens new opportunities for optimizing microbial processes in biotechnology, highlighting the potential of defense island-targeted genetic modification.

Advancing RNA phage biology through meta-omics

Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in the 1960s, they have been used as important models to understand the principal processes of life, including translation and the genetic code. While RNA phages were generally thought of as rare oddities in nature, meta-omics methods are rapidly changing this simplistic view by studying diverse biomes with unprecedented resolution. Metatranscriptomics dramatically expanded the number of known RNA phages from tens to tens of thousands, revealed their widespread abundance, and discovered several new families of potential RNA phages with largely unknown hosts, biology, and environmental impact. At the same time, (meta)genomic analyses of bacterial hosts are discovering an arsenal of defense systems bacteria employ to protect themselves from predation, whose functions in immunity against RNA phages we are only beginning to understand. Here, I review how meta-omics approaches are advancing the field of RNA phage biology with a focus on the discovery of new RNA phages and how bacteria might fight them.

Discovery of diverse and high-quality mRNA capping enzymes through a language model-enabled platform

Mining and expanding high-quality genetic parts for synthetic biology and bioengineering are urgent needs in the research and development of next-generation biotechnology. However, gene mining has relied on sequence homology or ample expert knowledge, which fundamentally limits the establishment of a comprehensive genetic part catalog. In this work, we propose SYMPLEX (synthetic biological part mining platform by large language model-enabled knowledge extraction), a universal gene-mining platform based on large language models. We applied SYMPLEX to mine enzymes responsible for messenger RNA (mRNA) capping, a key process in eukaryotic posttranscriptional modification, and obtained thousands of diverse candidates with traceable evidence from biomedical literature and databases. Of the 46 experimentally tested integral capping enzyme candidates, 14 demonstrated in vivo cross-species capping activity, and 2 displayed superior in vitro activity over the commercial vaccinia capping enzymes currently used in mRNA vaccine production. SYMPLEX provides a distinct paradigm for functional gene mining and offers powerful tools to facilitate knowledge discovery in fundamental research.

Cat1 forms filament networks to degrade NAD+ during the type III CRISPR-Cas antiviral response

Type III CRISPR-Cas systems defend against viral infection in prokaryotes using an RNA-guided complex that recognizes foreign transcripts and synthesizes cyclic oligo-adenylate (cOA) messengers to activate CARF immune effectors. Here we investigated a protein containing a CARF domain fused Toll/interleukin-1 receptor (TIR) domain, Cat1. We found that Cat1 provides immunity by cleaving and depleting NAD+ molecules from the infected host, inducing a growth arrest that prevents viral propagation. Cat1 forms dimers that stack upon each other to generate long filaments that are maintained by bound cOA ligands, with stacked TIR domains forming the NAD+ cleavage catalytic sites. Further, Cat1 filaments assemble into unique trigonal and pentagonal networks that enhance NAD+ degradation. Cat1 presents an unprecedented chemistry and higher-order protein assembly for the CRISPR-Cas response.

Reduced prevalence of phage defense systems in Pseudomonas aeruginosa strains from cystic fibrosis patients

Cystic fibrosis is a genetic disorder that affects mucus clearance, particularly of the lungs. As a result, cystic fibrosis patients often experience infections from bacteria, which contribute to the disease progression. Pseudomonas aeruginosa is one of the most common opportunistic pathogens associated with cystic fibrosis. The presence of P. aeruginosa complicates the treatment due to its high antibiotic resistance. Thus, research is ongoing to treat these infections with bacterial viruses instead, known as bacteriophages. Notably, P. aeruginosa clinical strains possess a variety of phage defense mechanisms that may limit the effectiveness of phage therapy. In this study, we compared the defense system repertoire of P. aeruginosa strains isolated from cystic fibrosis patients with those from non-cystic fibrosis patients. Our findings reveal that P. aeruginosa strains isolated from cystic fibrosis patients have fewer phage defense mechanisms per strain than from non-cystic fibrosis patients, suggesting altered phage selection pressures in strains colonizing CF patient lungs.IMPORTANCECystic fibrosis patients often experience chronic Pseudomonas aeruginosa lung infections, which are challenging to treat with antibiotics and contribute to disease progression and eventual respiratory failure. Phage therapy is being explored as an alternative treatment strategy for these infections. However, assessing strain susceptibility to phage treatment is essential for ensuring efficacy. To address this, we investigated whether CF-associated clinical P. aeruginosa strains have a distinct phage defense repertoire compared with those isolated from other lung patients. We observed that CF-associated P. aeruginosa strains have significantly fewer phage defenses, possibly affecting the susceptibility of these strains to phage infection.

Mono- and multidomain defense toxins of the RelE/ParE superfamily

Toxin-antitoxin (TA) modules are widely distributed across prokaryotes, often existing in large numbers despite their associated fitness costs. Most type II TA modules are bicistronic operons encoding a monodomain toxin and its cognate protein antitoxin. The RelE/ParE superfamily encompasses toxins with a conserved Barnase-EndoU-ColicinE5/D-RelE (BECR) fold. Yet, their cellular targets differ remarkably: RelE toxins function as ribosome-dependent RNases, while ParE toxins act as DNA gyrase inhibitors. Using a comprehensive bioinformatics approach, this study analyzed 13 BECR-fold toxin families as classified in the Pfam database. Intriguingly, the ParE family was found to include a subcluster of mRNA-cleaving toxins, challenging its conventional role as solely DNA-targeting. This study identified a novel tripartite operon encoding a PtuA-like defense ATPase, a homolog of type IV restriction endonucleases, and a RelE homolog, suggesting a coordinated role in defense mechanisms. Multidomain BECR-fold toxins, including transmembrane variants, were also discovered, extending the functional repertoire of type II TA modules to membrane-associated systems. These findings clarify the evolutionary relationships and functional diversity within the RelE/ParE superfamily and discover novel, putative defense systems that can now be investigated experimentally.IMPORTANCEToxin-antitoxin modules play critical roles in prokaryotic survival and adaptation, contributing to genome stabilization and defense against phages and invading plasmids. The RelE/ParE superfamily exemplifies the structural and functional diversity of these systems, with members targeting distinct cellular processes, such as translation and DNA supercoiling. By elucidating the relationships among the 13 BECR-fold toxin families, this study enhances our understanding of microbial resistance mechanisms and reveals potential new opportunities for research into prokaryotic defense and regulation. These insights may have significant implications for medical and biotechnological applications, particularly in understanding bacterial responses to genetic invaders.

Structural basis for Lamassu-based antiviral immunity and its evolution from DNA repair machinery

Bacterial immune systems exhibit remarkable diversity and modularity, as a consequence of the continuous selective pressures imposed by phage predation. Despite recent mechanistic advances, the evolutionary origins of many antiphage immune systems remain elusive, especially for those that encode homologs of the Structural Maintenance of Chromosomes (SMC) superfamily, which are essential for chromosome maintenance and DNA repair across domains of life. Here, we elucidate the structural basis and evolutionary emergence of Lamassu, a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor. Using cryo-EM, we determined structures of the Vibrio cholerae Lamassu complex in both apo- and dsDNA-bound states, revealing unexpected stoichiometry and topological architectures. We further demonstrate how Lamassu specifically senses dsDNA in vitro and phage replication origins in vivo , thereby triggering the formation of LmuA tetramers that activate the Cap4 nuclease domain. Our findings reveal that Lamassu evolved via exaptation of the bacterial Rad50-Mre11 DNA repair system to form a compact, modular sensor for viral replication, exemplifying how cellular machinery can be co-opted for novel immune functions.

Proteomic Analysis of Marine Bacteriophages: Structural Conservation, Post-Translational Modifications, and Phage-Host Interactions

Marine bacteriophages, the most abundant biological entities in marine ecosystems, are essential in biogeochemical cycling. Despite extensive genomic data, many phage genes remain uncharacterised, creating a gap between genomic diversity and gene function knowledge. This gap limits our understanding of phage life cycles, assembly, and host interactions. In this study, we used mass spectrometry to profile the proteomes of 13 marine phages from diverse lifestyles and hosts. The analysis accurately annotated hypothetical genes, mapped virion protein arrangements, and revealed structural similarities among phages infecting the same host, particularly in tail fibre proteins. Protein structure comparisons showed conservation and variability in head and tail proteins, particularly in key domains involved in virion stabilisation and host recognition. For the first time, we identified post-translational modifications (PTMs) in marine phage proteins, which may enhance phage adaptability and help evade host immune systems. These findings suggest that phages optimise their infection strategies through structural variations and PTM modifications, improving their adaptability and host interactions.

A miniature CRISPR-Cas10 enzyme confers immunity by an inverse signaling pathway

Microbial and viral co-evolution has created immunity mechanisms involving oligonucleotide signaling that share mechanistic features with human anti-viral systems 1 . In these pathways, including CBASS and type III CRISPR systems in bacteria and cGAS-STING in humans, oligonucleotide synthesis occurs upon detection of virus or foreign genetic material in the cell, triggering the antiviral response 2-4 . In a surprising inversion of this process, we show here that the CRISPR-related enzyme mCpol synthesizes cyclic oligonucleotides constitutively as part of an active mechanism that maintains cell health. Cell-based experiments demonstrated that the absence or loss of mCpol-produced cyclic oligonucleotides triggers cell death, preventing spread of viruses that attempt immune evasion by depleting host cyclic nucleotides. Structural and mechanistic investigation revealed mCpol to be a di-adenylate cyclase whose product, c-di-AMP, prevents toxic oligomerization of the effector protein 2TMβ. Analysis of cells by fluorescence microscopy showed that lack of mCpol allows 2TMβ-mediated cell death due to inner membrane collapse. These findings unveil a powerful new defense strategy against virus-mediated immune suppression, expanding our understanding of oligonucleotides in cell health and disease. These results raise the possibility of similar protective roles for cyclic oligonucleotides in other organisms including humans.

Completing the BASEL phage collection to unlock hidden diversity for systematic exploration of phage-host interactions

Research on bacteriophages, the viruses infecting bacteria, has fueled the development of modern molecular biology and inspired their therapeutic application to combat bacterial multidrug resistance. However, most work has so far focused on a few model phages which impedes direct applications of these findings in clinics and suggests that a vast potential of powerful molecular biology has remained untapped. We have therefore recently composed the BASEL collection of Escherichia coli phages (BActeriophage SElection for your Laboratory), which made a relevant diversity of phages infecting the E. coli K-12 laboratory strain accessible to the community. These phages are widely used, but their assorted diversity has remained limited by the E. coli K-12 host. We have therefore now genetically overcome the two major limitations of E. coli K-12, its lack of O-antigen glycans and the presence of resident bacterial immunity. Restoring O-antigen expression resulted in the isolation of diverse additional viral groups like Kagunavirus, Nonanavirus, Gordonclarkvirinae, and Gamaleyavirus, while eliminating all known antiviral defenses of E. coli K-12 additionally enabled us to isolate phages of Wifcevirus genus. Even though some of these viral groups appear to be common in nature, no phages from any of them had previously been isolated using E. coli laboratory strains, and they had thus remained largely understudied. Overall, 37 new phage isolates have been added to complete the BASEL collection. These phages were deeply characterized genomically and phenotypically with regard to host receptors, sensitivity to antiviral defense systems, and host range. Our results highlighted dominant roles of the O-antigen barrier for viral host recognition and of restriction-modification systems in bacterial immunity. We anticipate that the completed BASEL collection will propel research on phage-host interactions and their molecular mechanisms, deepening our understanding of viral ecology and fostering innovations in biotechnology and antimicrobial therapy.

A phage-encoded counter-defense inhibits an NAD-degrading anti-phage defense system

Bacteria contain a diverse array of genes that provide defense against predation by phages. Anti-phage defense genes are frequently located on mobile genetic elements and spread through horizontal gene transfer. Despite the many anti-phage defense systems that have been identified, less is known about how phages overcome the defenses employed by bacteria. The integrative and conjugative element ICEBs1 in Bacillus subtilis contains a gene, spbK, that confers defense against the temperate phage SPβ through an abortive infection mechanism. Using genetic and biochemical analyses, we found that SpbK is an NADase that is activated by binding to the SPβ phage portal protein YonE. The presence of YonE stimulates NADase activity of the TIR domain of SpbK and causes cell death. We also found that the SPβ-like phage Φ3T has a counter-defense gene that prevents SpbK-mediated abortive infection and enables the phage to produce viable progeny, even in cells expressing spbK. We made SPβ-Φ3T hybrid phages that were resistant to SpbK-mediated defense and identified a single gene in Φ3T (phi3T_120, now called nip for NADase inhibitor from phage) that was both necessary and sufficient to block SpbK-mediated anti-phage defense. We found that Nip binds to the TIR (NADase) domain of SpbK and inhibits NADase activity. Our results provide insight into how phages overcome bacterial immunity by inhibiting enzymatic activity of an anti-phage defense protein.

Structural basis of antiphage defense by an ATPase-associated reverse transcriptase

Reverse transcriptases (RTs) have well-established roles in the replication and spread of retroviruses and retrotransposons. However, recent evidence suggests that RTs have been conscripted by cells for diverse roles in antiviral defense. Here we determine structures of a type I-A retron, which explain how RNA, DNA, RT, HNH-nuclease and four molecules of an SMC-family ATPase assemble into a 364 kDa complex that provides phage defense. We show that phage-encoded nucleases trigger degradation of the retron-associated DNA, leading to disassembly of the retron and activation of the HNH nuclease. The HNH nuclease cleaves tRNASer, stalling protein synthesis and arresting viral replication. Taken together, these data reveal diverse and paradoxical roles for RTs in the perpetuation and elimination of genetic parasites.

PglZ from Type I BREX phage defence systems is a metal-dependent nuclease that forms a sub-complex with BrxB

BREX (Bacteriophage Exclusion) systems, identified through shared identity with Pgl (Phage Growth Limitation) systems, are a widespread, highly diverse group of phage defence systems found throughout bacteria and archaea. The varied BREX Types harbour multiple protein subunits (between four and eight) and all encode a conserved putative phosphatase (PglZ aka BrxZ) and an equally conserved, putative ATPase (BrxC). Almost all BREX systems also contain a site-specific methyltransferase (PglX aka BrxX). Despite having determined the structure and fundamental biophysical and biochemical behaviours for the PglX methyltransferase, the BrxL effector, the BrxA DNA-binding protein and the BrxR transcriptional regulator, the mechanism by which BREX impedes phage replication remains largely undetermined. In this study, we identify a stable BREX sub-complex of PglZ:BrxB, validate the structure and dynamic behaviour of that sub-complex, and assess the biochemical activity of PglZ, revealing it to be a metal-dependent nuclease. PglZ can cleave cyclic oligonucleotides, linear oligonucleotides, plasmid DNA and both non-modified and modified linear phage genomes. PglZ nuclease activity has no obvious role in BREX-dependent methylation, but does contribute to BREX phage defence. BrxB binding does not impact PglZ nuclease activity. These data contribute to our growing understanding of the BREX phage defence mechanism.

The LAMP-CRISPR-Cas13a technique for detecting the CBASS mechanism of phage resistance in bacteria

Introduction

Antimicrobial resistance (AMR) is a major public health threat, driving the need for alternative treatments such as phage therapy. However, bacterial defense mechanisms, often regulated by the quorum sensing (QS) network and encoded in genomic islands (GIs), can generate phage-resistant mutants. Understanding these resistance mechanisms is essential for optimizing phage therapy.

Methods

This study analyzed 48 Klebsiella pneumoniae strains to identify pathogenicity islands (PAIs) containing anti-phage defense (APD) proteins. We constructed a knockout strain lacking the cyclase gene from the type II CBASS defense systems present in PAIs to investigate QS regulation and its role in cell viability. The LAMP-CRISPR-Cas13a technique was used to confirm gene knockout and to detect the main cyclase in type I CBASS systems, i.e., APECO1.

Results

A total of 309 pathogenicity islands (PAIs), containing 22.1% of anti-phage defense (APD) proteins, were identified. Type I and II CBASS APD systems were also detected in the genome of the 48, K. pneumoniae strains, and only two type II CBASS systems were located in PAIs. Alluding to these defense mechanisms, the QS revealed to be involved in the regulation of the type II CBASS systems contained in PAIs. Finally, the LAMP-CRISPR-Cas13a technology successfully detected the main cyclases habored in type I and II CBASS systems, respectively.

Discussion

The study findings highlight the regulatory role of the QS network in APD systems. Notably, this is the first study to develop an innovative biotechnological application for the LAMP-CRISPR-Cas13a rapid-technique (<2 h), thereby helping to optimize phage therapy by detecting bacterial resistance mechanisms and predicting the potential inefficacy of therapeutic phages and thus improving patient prognosis.

Structure-guided discovery of viral proteins that inhibit host immunity

Viruses encode proteins that inhibit host defenses, but sifting through the millions of available viral sequences for immune-modulatory proteins has been so far impractical. Here, we develop a process to systematically screen virus-encoded proteins for inhibitors that physically bind host immune proteins. Focusing on Thoeris and CBASS, bacterial defense systems that are the ancestors of eukaryotic Toll/interleukin-1 receptor (TIR) and cyclic GMP-AMP synthase (cGAS) immunity, we discover seven families of Thoeris and CBASS inhibitors, encompassing thousands of genes widespread in phages. Verified inhibitors exhibit extensive physical interactions with the respective immune protein counterpart, with all inhibitors blocking the active site of the immune protein. Remarkably, a phage-encoded inhibitor of bacterial TIR proteins can bind and inhibit distantly related human and plant immune TIRs, and a phage-derived inhibitor of bacterial cGAS-like enzymes can inhibit the human cGAS. Our results demonstrate that phages are a reservoir for immune-modulatory proteins capable of inhibiting bacterial, animal, and plant immunity.

Application of Comparative Genomics for the Development of PCR Primers for the Detection of Harmful or Beneficial Microorganisms in Food: Mini-Review

Gene markers are widely utilized for detecting harmful and beneficial microorganisms in food products. Primer sequences targeting the 16S rRNA region, recognized as a conserved region, have been conventionally employed in PCR analyses. However, several studies have highlighted limitations and false-positive results associated with the use of these primer sequences. Consequently, pan-genome analysis, a comparative genomic approach, has been increasingly applied to design more selective gene markers. This mini-review explores the application of pan-genome analysis in developing PCR primers for the detection of harmful microorganisms, such as Salmonella, Cronobacter, Staphylococcus, and Listeria, as well as beneficial microorganisms like Lactobacillus. Additionally, the review discusses the applicability, advantages, limitations, and future directions of pan-genome analysis for primer design. A comparative overview of bioinformatics tools, recent trends, and verification methods is also provided, offering valuable insights for researchers interested in leveraging pan-genome analysis for advanced primer design.

Bacterial Hachiman complex executes DNA cleavage for antiphage defense

Bacteria have developed a variety of immune systems to combat phage infections. The Hachiman system is a novel prokaryotic antiphage defense system comprising HamA and HamB proteins, which contains the DUF1837 and helicase domains, respectively. However, the defense mechanism remains only partially understood. Here, we present the cryo-electron microscopy (cryo-EM) structure of the Hachiman defense system featuring a fusion of Cap4 nuclease domain within HamA. Further structure analysis indicates that the DUF1837 domain on HamA resembles the PD-(D/E)XK nuclease but lacks active sites. Bioinformatics analysis reveals that catalytically inactive DUF1837 domains often recruit other functional domains to fulfill anti-phage defense. HamA interacts with HamB to form a heterodimer HamAB to mediate ATP hydrolysis and execute DNA cleavage, thus implementing antiphage defense. Our findings elucidate the structural basis of the Hachiman defense complex, highlighting the critical roles of the helicase and nuclease in prokaryotic immunity.

Early onset of septal FtsK localization allows for efficient DNA segregation in SMC-deleted Corynebacterium glutamicum strains

Structural maintenance of chromosomes (SMC) are ubiquitously distributed proteins involved in chromosome organization. Deletion of smc causes severe growth phenotypes in many organisms. Surprisingly, smc can be deleted in Corynebacterium glutamicum, a member of the Actinomycetota phylum, without any apparent growth phenotype. SMC in C. glutamicum is loaded in a ParB-dependent fashion to the chromosome and functions in replichore cohesion. The unexpected absence of a growth phenotype in the smc mutant prompted us to screen for synthetic interactions within C. glutamicum. We generated a high-density Tn5 library from wild-type and smc-deleted C. glutamicum strains. Transposon sequencing data revealed that the DNA translocase FtsK is essential in an smc-deletion strain. In wild-type cells, FtsK localized to the septa and cell poles, showing polar enrichment during the earlier stages of the life cycle and relocating to the septum in the later stages. However, deletion of smc resulted in an earlier onset of pole-to-septum FtsK relocation, suggesting that prolonged FtsK complex activity is both required and sufficient to compensate for the absence of SMC, thus achieving efficient chromosome segregation in C. glutamicum. Deletion of ParB increases SMC and FtsK mobility. While the change in SMC dynamics aligns with previous data showing ParB's role in SMC loading on DNA, the change in FtsK mobility suggests defects in chromosome segregation. Based on our data, we propose an efficient mechanism for reliable DNA segregation in the absence of replichore arm cohesion in smc mutant cells.IMPORTANCEFaithful DNA segregation is of fundamental importance for life. Bacteria have developed efficient systems to coordinate chromosome compaction, DNA segregation, and cell division. A key factor in DNA compaction is the SMC complex that is found to be essential in many bacteria. In members of the Actinomycetota, smc is dispensable, but the reason for the lack of an smc phenotype in these bacteria remained unclear. We show here that the divisome-associated DNA pump FtsK can compensate for SMC loss and the subsequent loss in correct chromosome organization. In cells with distorted chromosomes, FtsK is recruited and stabilized earlier to the septum, allowing for DNA segregation for a larger part of the cell cycle, until chromosomes are segregated.

Modularity of Zorya defense systems during phage inhibition

Bacteria have evolved an extraordinary diversity of defense systems against bacteriophage (phage) predation. However, the molecular mechanisms underlying these anti-phage systems often remain elusive. Here, we provide mechanistic and structural insights into Zorya phage defense systems. Using cryo-EM structural analyses, we show that the Zorya type I and II core components, ZorA and ZorB, assemble in a 5:2 complex that is similar to inner-membrane ion-driven, rotary motors that power flagellar rotation, type 9 secretion, gliding and the Ton nutrient uptake systems. The ZorAB complex has an elongated cytoplasmic tail assembled by bundling the C-termini of the five ZorA subunits. Mutagenesis demonstrates that peptidoglycan binding by the periplasmic domains of ZorB, the structured cytoplasmic tail of ZorA, and ion flow through the motor is important for function in both type I and II systems. Furthermore, we identify ZorE as the effector module of the Zorya II system, possessing nickase activity. Our work reveals the molecular basis of the activity of Zorya systems and highlights the ZorE nickase as crucial for population-wide immunity in the type II system.

Structural variants of AcrIIC5 inhibit Cas9 via divergent binding interfaces

CRISPR-Cas is a bacterial defense system that employs RNA-guided endonucleases to destroy invading foreign nucleic acids. Bacteriophages produce anti-CRISPR (Acr) proteins to evade CRISPR-Cas defense during the infection. AcrIIC5, a type II-C Cas9 inhibitor, exhibits unusual variations in the local backbone fold between its orthologs. Here we investigated how the folding variations affect the inhibition of target Cas9 using AcrIIC5 orthologs. Structural comparison of free AcrIIC5Smu and AcrIIC5Nch confirmed that the folding variation correlated with characteristic indels in the helical region. Mutagenesis and biochemical assays combined with AlphaFold2 predictions identified key residues of AcrIIC5 orthologs important for Cas9 inhibition. Remarkably, AcrIIC5 orthologs employed divergent binding interfaces via folding variations to inhibit the Cas9 targets. Our study suggests that Acr proteins have evolved structural variants to diversify key interfaces for target Cas9, which could be beneficial for the adaptation of phages to evasive mutations on the Cas9 surface.

Signalling by co-operative higher-order assembly formation: linking evidence at molecular and cellular levels

The concept of higher-order assembly signalling or signalling by co-operative assembly formation (SCAF) was proposed based on the structures of signalling assemblies formed by proteins featuring domains from the death-fold family and the Toll/interleukin-1 receptor domain family. Because these domains form filamentous assemblies upon stimulation and activate downstream pathways through induced proximity, they were envisioned to sharpen response thresholds through the extreme co-operativity of higher-order assembly. Recent findings demonstrate that a central feature of the SCAF mechanism is the nucleation barrier that allows a switch-like, digital or 'all-or-none' response to minute stimuli. In agreement, this signalling mechanism features in cell-death and innate immunity activation pathways where a binary decision is required. Here, we broaden the concept of SCAF to encapsulate the essential kinetic properties of open-ended assembly in signalling, compare properties of filamentous assemblies and other co-operative assemblies such as biomolecular condensates, and review how this concept operates in cells.

Study of the probability of resistance to phage infection in a collection of clinical isolates of Pseudomonas aeruginosa in relation to the presence of Pf phages

Pseudomonas aeruginosa is a bacterial pathogen that is a major cause of lung infections in cystic fibrosis (CF) and other patients. Isolates of P. aeruginosa from CF patients commonly carry filamentous phages (Pf phages), which constitute a family of temperate phages known to be related to biofilm production and antibiotic sequestration. In this study, we identified 12 new Pf phage genomes in a collection of clinical isolates of P. aeruginosa from CF patients. Study of the anti-phage defense systems in the bacterial isolates revealed the presence of 89 such systems, of which eight were encoded in the Pf phage genomes. Finally, although a weak relation between resistance to phage infection and the number of anti-phage defense systems was detected, it was observed that the phage resistance was related to the presence of Pf phages and the anti-phage defense systems encoded in these phages.IMPORTANCEBacteria harbor a wide range of defense mechanisms to avoid phage infections that hamper the application of phage therapy because they can lead to the rapid acquisition of phage resistance. In this study, eight anti-phage defense systems were found in the genome of 12 Pf phages that were presents in 56% of the CF isolates of P. aeruginosa. The high prevalence of these phages underlines the importance of our findings about newly discovered filamentous phages and the role of these phages in resistance to phage infections. Thus, the knowledge of the anti-defense system in the Pf phage genomes could be useful in assessing the possible application of phage therapy to treat an infectious disease.

Temperate bacteriophage SapYZUs7 alters Staphylococcus aureus fitness balance by regulating expression of phage resistance, virulence and antimicrobial resistance gene

Temperate bacteriophages are crucial for maintaining the pathogenicity and fitness of S. aureus, which also show promise as a biocontrol agent for S. aureus. However, the fitness benefit and cost of lysogeny by S. aureus temperate phages and their underlying mechanisms remain unexplored. In this study, phage resistance, virulence, antimicrobial resistance (AMR), transcriptome, and metabolome of phage SapYZUs7 lysogenic and non-lysogenic S. aureus strains were compared. Whole-genome analysis revealed that SapYZUs7 harbouring smaII associated with a single-protein MazF-like antiphage system could be integrated into the genome of S. aureus isolates. Notably, lysogenic S. aureus exhibited higher phage resistance, a lower growth rate, and inhibited metabolic activity compared to the parental strains, indicating interference of phage reproduction by smaII. Moreover, prophages carrying smaII are widely distributed across S. aureus and harboured other virulence factor (VF) and AMR genes. Besides, the SapYZUs7-integration increased phagocytosis resistance but decreased adhesion, biofilm formation, and AMR. The combined use of SapYZUs7 and antibiotics exhibited a better bactericidal effect than SapYZUs7 or the antibiotics alone. Consistently, integrated omics analysis suggested that SapYZUs7-lysogeny downregulated multiple VF and AMR genes. Our analysis suggests that SmaII drives mutualistic phage-host interactions through lysogenic conversion. The fitness cost of SapYZUs7-integration is the downregulated expression of VF and AMR genes, serving as an alternative candidate as a biocontrol agent for methicillin-resistant S. aureus and multidrug-resistant S. aureus.

Structure and mechanism of the Zorya anti-phage defence system

Zorya is a recently identified and widely distributed bacterial immune system that protects bacteria from viral (phage) infections. Three Zorya subtypes have been identified, each containing predicted membrane-embedded ZorA-ZorB (ZorAB) complexes paired with soluble subunits that differ among Zorya subtypes, notably ZorC and ZorD in type I Zorya systems1,2. Here we investigate the molecular basis of Zorya defence using cryo-electron microscopy, mutagenesis, fluorescence microscopy, proteomics and functional studies. We present cryo-electron microscopy structures of ZorAB and show that it shares stoichiometry and features of other 5:2 inner membrane ion-driven rotary motors. The ZorA5B2 complex contains a dimeric ZorB peptidoglycan-binding domain and a pentameric α-helical coiled-coil tail made of ZorA that projects approximately 70 nm into the cytoplasm. We also characterize the structure and function of the soluble Zorya components ZorC and ZorD, finding that they have DNA-binding and nuclease activity, respectively. Comprehensive functional and mutational analyses demonstrate that all Zorya components work in concert to protect bacterial cells against invading phages. We provide evidence that ZorAB operates as a proton-driven motor that becomes activated after sensing of phage invasion. Subsequently, ZorAB transfers the phage invasion signal through the ZorA cytoplasmic tail to recruit and activate the soluble ZorC and ZorD effectors, which facilitate the degradation of the phage DNA. In summary, our study elucidates the foundational mechanisms of Zorya function as an anti-phage defence system.

Integrons are anti-phage defence libraries in Vibrio parahaemolyticus

Bacterial genomes have regions known as defence islands that encode diverse systems to protect against phage infection. Although genetic elements that capture and store gene cassettes in Vibrio species, called integrons, are known to play an important role in bacterial adaptation, a role in phage defence had not been defined. Here we combine bioinformatic and molecular techniques to show that the chromosomal integron of Vibrio parahaemolyticus is a hotspot for anti-phage defence genes. Using bioinformatics, we discovered that previously characterized defences localize to integrons. Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence. Our work reveals that integrons are an important reservoir of defence systems in V. parahaemolyticus. As integrons are of ancient origin and are widely distributed among Proteobacteria, these results provide an approach for the discovery of anti-phage defence systems across a broad range of bacteria.

Overcoming Bacteriophage Contamination in Bioprocessing: Strategies and Applications

Bacteriophage contamination has a devastating impact on the viability of bacterial hosts and can significantly reduce the productivity of bioprocesses in biotechnological industries. The consequences range from widespread fermentation failure to substantial economic losses, highlighting the urgent need for effective countermeasures. Conventional prevention methods, which focus primarily on the physical removal of bacteriophages from equipment, bioprocess units, and the environment, have proven ineffective in preventing phage entry and contamination. The coevolutionary dynamics between phages and their bacterial hosts have spurred the development of a diverse repertoire of antiviral defense mechanisms within microbial communities. These naturally occurring defense strategies can be harnessed through genetic engineering to convert phage-sensitive hosts into robust, phage-resistant cell factories, providing a strategic approach to mitigate the threats posed by bacteriophages to industrial bacterial processes. In this review, an overview of the various defense strategies and immune systems that curb the propagation of bacteriophages and highlight their applications in fermentation bioprocesses to combat phage contamination is provided. Additionally, the tactics employed by phages to circumvent these defense strategies are also discussed, as preventing the emergence of phage escape mutants is a key component of effective contamination management.