Transposons are powerful drivers of genome evolution, but we lack a clear understanding of how these selfish genetic elements evolve and co-evolve with their hosts. Here, we develop a new general model of transposon–host co-evolution that incorporates key details of transposon and host biology. Our model reveals that the way that transposons replicate is critical for their evolutionary prognosis. Publicly-replicating transposons (such as DNA transposons), which cooperatively share their replication machinery, are predicted to be self-limiting. However, privately-replicating transposons (such as long interspersed nuclear elements, or LINEs), which do not replicate cooperatively, are under continual selection to increase their duplication rate even to the point of host extinction, a so-called tragedy of the commons. Neither selection against transposons’ deleterious effects nor exploitation by parasitic elements is sufficient to prevent host extinction. Instead, our analysis shows that only active suppression by hosts avoids population collapse. In particular, suppression must act post-transcriptionally in order to prevent continuous escalation of the transposon–host genetic conflict. We argue that only with host enforcement of transposons can complex life exist. Transposons are genetic parasites that have had far-reaching effects on eukaryotic evolution. This modelling study shows that host defences against transposon activity are necessary to prevent species extinction.

Defence against viral infection is a conserved feature of all cellular life. From single-cell bacteria to humans and complex multicellular animals, constitutive and inducible forms of immunity are required to inhibit viruses and safeguard cellular fitness. Recent studies reveal that the components of human antiviral immunity are surprisingly ancient, originating billions of years ago in bacteria as pathways that defend against phage replication. The unification of previously disparate fields of human and bacterial immunity creates a foundation to explain key features of host–virus interactions. This Review defines principles of pathogen recognition, signal amplification and immune effector function that shape mechanisms of antiviral immunity that are shared across kingdoms of life. Shared forms of immunity, including cGAS–STING, inflammasomes, argonautes and viperin, reveal ancient features of antiviral defence. Similarly, direct comparisons of pattern recognition receptors and interferon-stimulated genes in human cells with CRISPR immunity and antiphage defence systems in bacteria explain prevalent strategies to effectively sense and inhibit viral replication. Cross-kingdom analysis reveals universal rules that control host–virus interactions and highlights open questions in understanding of antiviral immunity. The Review describes shared ancient, conserved mechanisms between human antiviral immunity and bacterial anti-phage systems, outlining universal principles of pathogen sensing, signalling and effector function that reveal common rules governing host–virus interactions across life.

Cell surface display (CSD) elements are a major class of bioengineering modules, but systematic rules linking CSD sequence to functional potency are lacking. Here we develop DeepSCan, a suite of deep learning and artificial intelligence models to systematically map CSD sequence–function relationships to reliably capture potent elements’ conserved features and iteratively design and develop potent de novo CSD modules for mRNA antigen display. We experimentally quantify surface expression across >570 chimeric antigens, derive cell surface translocation strength labels for ~310 CSD elements and compile ~45 independent training datasets. We train three generations of DeepSCan models and evaluate their performance. Guided by these models, we computationally design 3,700 and experimentally validate approximately 120 generative CSDs, identifying 7 generative CSDs that match or exceed the cell surface translocation strength of the most potent naturally occurring CSDs. Enhanced surface displays are validated across multiple cell types and are functional in an antigen-specific CAR-T cytotoxicity assay. A systematic artificial intelligence-guided approach designs cell surface display elements for therapeutic applications.

Industrial adoption of microbial cell-free protein synthesis (CFPS), an in vitro protein production platform that uses transcription and translation machinery from lysed cells, remains limited despite sustained technical progress across the field. This perspective positions microbial CFPS within a manufacturing context, focusing on its current capabilities, the limits of those capabilities and the concrete steps required for industrial adoption. In CFPS, the absence of cell growth constraints supports rapid protein production, simplified upstream workflows and direct control over reaction conditions, while also lending itself to formats such as lyophilized reagents for storage and transport. Beyond basic protein expression, microbial CFPS is increasingly used as an adaptable production environment in which reaction composition can be tuned, accessory enzymatic functions can be introduced and post-translational modification strategies can be engineered to better align with product requirements. The expanding range of microbial chassis further broadens the design space, allowing platform choice to be guided by functional, regulatory and deployment considerations rather than yield alone. However, increased capability has not yet translated into routine manufacturing use, and persistent barriers include reproducibility, vulnerable supply chains, limited scale-up practice, downstream purification suitable for therapeutic products and the absence of CFPS-specific quality and regulatory expectations. Overall, microbial CFPS is best evaluated not as a replacement for existing biomanufacturing but as a complementary manufacturing paradigm whose industrial relevance will depend on establishing standardization, economics and regulatory readiness.

Bacterial toxin-antitoxin (TA) systems are classically viewed as stress-activated toxic switches. Specifically, ribonucleolytic toxins are thought to indiscriminately cleave RNA to halt cellular growth. We recently showed that the MazF toxin of Bacillus subtilis targets an unusually strict 6bp RNA cleavage sequence, but the implications of this stringent specificity were unknown. Here, we demonstrate that the MazEF system functions as a non-lethal post-transcriptional regulator in B. subtilis. Using a specialized single cell fluorescent reporter and transcriptome profiling, we show that MazF is uniformly activated across the population upon entry into the stationary phase, where it cleaves a narrow mRNA regulon to reshape gene expression. Rather than inhibiting growth, MazF activation tunes down the Spo0A stress response by repressing the mRNA level of its kinases. Reduced stress leads to an adaptive shortening of the lag phase upon nutrient replenishment. Furthermore, MazEF’s structural architecture, cleavage specificity, and impact on growth recovery are highly conserved across Gram-positive bacteria. Altogether, our findings redefine a paradigmatic toxin as a precision global mRNA stress regulator that primes cells for rapid regrowth.

Bridge recombinases from the IS110 family of transposons, such as IS621, associate with a bridge RNA (bRNA) to mediate programmable recombination between donor DNA and target DNA. Although insertion is mediated by the recombinase–bRNA complex, it remains unknown how IS621 elements are excised from host genomes to form the circular DNA intermediates required for transposition. Here we show that bRNA is weakly expressed from IS621 loci in the E. coli genome and that the IS621 recombinase–bRNA complex mediates excision less efficiently than insertion. Furthermore, we present the cryo-electron microscopy structures of the IS621 recombinase–bRNA complex bound to excision DNA substrates, providing mechanistic insights into the excision reaction. Similar to the previously reported donor- and target-bound insertion complex, the excision complex comprises two recombinase dimers, each accommodating the target- and donor-binding loops of the bRNA. However, DNA recognition differs notably between the two complexes. Although the donor and target DNAs form a bent U-shape during insertion, the excision substrates adopt linear conformations and bind across both bRNA loops, forming an X-shaped structure. This geometry reduces the efficiency of top-strand exchange and contributes to the naturally observed bias favoring insertion over excision. Despite these differences, the efficiencies of both reactions are similarly modulated by base pairing between specific dinucleotides in the bRNA, termed handshake guides, and the top strands of the DNA substrates. Overall, this study provides mechanistic insights into the complete IS110 transposition cycle and facilitates the optimal design of programmable bridge-editing applications. Cryo-electron microscopy structures show how IS621 bridge recombinase mediates DNA excision, explaining its natural preference for insertion and informing the design of programmable bridge-editing technologies.

Sustained and controlled delivery of glucose-lowering agents using engineered designer cells is recognized as an effective strategy for diabetes therapy. However, current technologies rely on external signal control or have been programmed into mammalian cells using synthetic gene networks, which pose safety concerns arising from transplantation. Here we developed an engineered oral-deliverable glucose-sensing and functional response probiotic living drug for ‘sense-and-respond’-based control of diabetic blood glucose. We created a glucose sensor based on a synthetic gene circuit that incorporates the glucose-responsive transcriptional regulator HexR, coupled with a synthetic promoter. Upon oral administration of the engineered probiotics carrying the sensor, the cells reside temporarily in the intestine and regulate the expression of therapeutic transgenes in response to glucose levels that exceed the normal threshold. We show efficacy from the engineered probiotics for glycaemic control in multiple diabetic mouse and non-human primate models, demonstrating that long-term oral administration drives clear improvements in lipid profiles, while also attenuating development of multiple diabetic complications. Our probiotics-based living drug enables therapeutic dosing in response to real-time blood glucose levels, providing a programmable, orally deliverable sense-and-respond platform for metabolic therapy without transplantation. Engineered probiotics equipped with a synthetic glucose-responsive circuit transiently colonize the gut and secrete therapeutic factors when glucose levels increase, enabling safe, oral, sense-and-respond control of diabetes in mouse and primate models.

Sliding-window phylogenetic analyses of multiple sequence alignments (MSAs) generate sequences of phylogenetic trees that can reveal phylogenetic conflict along genomes, as can be caused by recombination and other sources, yet comparing trees across genomic windows remains challenging. Phylo-Movies is a browser-based tool—also available as a standalone desktop application—that decomposes topological differences between consecutive phylogenetic trees into interpretable rooted subtree prune-and-regraft (SPR) moves and animates these transformations. We illustrate its use in two contexts: localising candidate recombination breakpoints in norovirus genomes, where taxa change from polymerase-genotype-associated to capsid-genotype-associated placements at the ORF1/ORF2 junction, and exploring candidate rogue taxa that change position across bootstrap replicates. Phylo-Movies complements quantitative measures such as Robinson–Foulds distances, split-frequency support values, and rogue-taxon scores by showing which subtrees move and how their source and target placements differ. The animations also provide an intuitive educational tool for teaching and workshops. Phylo-Movies is freely available at https://enesberksakalli.github.io/phylo-movies, with source code at https://github.com/enesBerkSakalli/phylo-movies, and demonstration videos at https://vimeo.com/1199476378, https://vimeo.com/1199476382, https://vimeo.com/1199476534, https://vimeo.com/1199487394, and https://vimeo.com/1199495473.

Prime editing (PE) can make specific local changes to genomic DNA in living systems but its efficient application currently requires extensive optimization of PE guide RNA (pegRNA) sequences. Here we present OptiPrime, a machine learning model of PE efficiency based on current understanding of PE mechanisms. OptiPrime achieves state-of-the-art accuracy on PE efficiency prediction and enables prediction of nicking guide RNA (PE3) and dual pegRNA (twinPE) outcomes. We validate that OptiPrime has learned the determinants of mammalian mismatch repair (MMR) and is well suited for nominating MMR-evasive silent edits that improve PE efficiency. We demonstrate the use of OptiPrime in a variety of prospective therapeutic contexts in primary human and mouse cells. Lastly, we show that OptiPrime can be used to achieve streamlined and efficient in vivo correction of a pathogenic mutation in the brain of a mouse model of KIF1A-associated neurological disorder. We provide a webserver for OptiPrime ( https://optipri.me/ ) as a community resource. OptiPrime incorporates prime-editing biochemistry to predict prime-editing outcomes.