Yamei Yu

Bacteria employ diverse defense strategies against phage infection, yet mechanisms directly targeting viral proteins remain scarcely documented. In this study, we characterize two bacterial defense systems: TFAD1 featuring a serine protease and TFAD2 featuring a Ser/Thr kinase. We show that TFAD1 and TFAD2 act on phage long tail fiber proteins via protein degradation and phosphorylation, respectively. Intriguingly, both systems allow complete phage replication cycles but generate non-infective progeny—a mechanism distinct from classical abortive infection (Abi), which we term “passive Abi”. Our findings expand the paradigm of bacterial immunity by unveiling protease- and kinase-mediated incapacitation of phage structural proteins, offering insights into the molecular arms race between bacteria and phages.

Retrons represent a novel class of bacterial defense systems that employ reverse transcriptase (RT), noncoding RNA, and effector proteins to counteract phage infections. In this study, we elucidate the molecular mechanism of a retron system, Retron–Eco8. Biochemical experiments reveal that the Retron–Eco8 holocomplex, rather than the effector alone, exhibits double-stranded DNA cleavage activity, triggering abortive infection and therefore effectively halting phage propagation. Cryo-electron microscopy (cryo-EM) analysis reveals a supramolecular assembly comprising four RT subunits, four multicopy single-stranded DNA molecules, and four overcoming lysogenization defect (OLD) nucleases—a configuration critical for antiphage defense. Notably, we examine the activation of Retron–Eco8 by diverse single-stranded DNA-binding (SSB) proteins, and phylogenetic analysis of these SSB proteins elucidates the phage resistance specificity. Collectively, our findings delineate the structural architecture of the Retron–Eco8 defense complex and provide mechanistic insights into retron-mediated bacterial immunity.

The evolutionary arms race between bacteria and phages drives the development of bacterial antiviral defense systems and phage counter-defense strategies. Restriction–modification (RM) systems protect bacteria by methylating ‘self’ DNA and cleaving unmodified phage DNA. Phages like T-even coliphages evade RM systems by substituting cytosine with 5-hydroxymethyl cytosine (5hmC) or 5-glucosylated hmC (5ghmC). Here, we characterize ‌a single-component antiviral defense system featuring a GIY-YIG endonuclease domain. Biochemical and structural analyses demonstrate that this defense system is a type IV modification-dependent restriction endonuclease that specifically degrades 5hmC- or 5ghmC-modified DNA, and we accordingly name it CMoRE ( C ytosine Mo dification ‌R ‌estriction E ndonuclease). The crystal structures reveal an N-terminal GIY-YIG nuclease domain and a C-terminal modification-sensing domain. Unique features, including a ‘GIYxY-YIG’ motif and an inhibitory negatively charged loop, distinguish CMoRE as an additional member of the GIY-YIG family. This system not only highlights the evolutionary interplay between phages and bacteria but also presents CMoRE as a potential tool for precise genomic detection of 5hmC in mammals, with implications for epigenetics research and disease diagnostics.

EMPIAR, the Electron Microscopy Public Image Archive centered at EMBL-EBI, is a public resource for raw electron microscopy images related to EMDB, contains micrographs, particle sets and tilt-series.

The rising prevalence of multidrug-resistant (MDR) bacterial infections, coupled with the diminishing efficacy of antibiotics, has reinvigorated interest in bacteriophage (phage) therapy as a promising alternative, leveraging its unique bactericidal mechanisms and precise targeting capabilities. Concurrently, phage display technology has advanced tumor diagnostics and targeted drug delivery through high-throughput peptide screening. This review systematically evaluates the mechanisms, strategies, and clinical progress of phage-based applications in anti-infective and oncological therapies. Clinical evidence highlights its efficacy against respiratory, oral, wound, bloodstream, and urinary tract infections, alongside solid tumors. However, challenges persist, including limited host range, bacterial resistance, immunogenicity, inefficient delivery systems, and regulatory uncertainties. Future efforts should prioritize AI-driven phage optimization, standardized pharmacokinetic assessment, and interdisciplinary collaboration to accelerate clinical translation. Despite current limitations, phage therapy represents a transformative and scalable approach for combating antimicrobial resistance and advancing precision oncology, positioning it as a pivotal tool in addressing global health crises.

Widespread in bacteria and archaea, toxin-antitoxin (TA) systems have been recently demonstrated to function in phage defense. Here we characterize the anti-phage function of a type IV TA system, ShosTA. Using structural and biochemical approaches, we show that ShosT couples phosphoribosyltransferase and pyrophosphatase activities to disrupt purine metabolism, resulting in DNA duplication, cell filamentation and ultimate cell death. ShosA binds DNA and likely recruits other proteins to facilitate DNA homologous recombination to antagonize ShosT’s toxicity. We identify Gp0.7 of T7 phage as a trigger for ShosTA system via shutting off the protein synthesis, and the C-terminus-mediated intrinsic instability of ShosA releases the toxicity of the existing ShosT proteins. Collectively, our results provide a novel toxin-antitoxin mechanism for anti-phage immunity and shed light on the triggering of this TA system.