Our current model is that the matured lanthivirin interacts with a phage-encoded GNAT and the phage DNA primase, and may act as a molecular glue that could lock them in a non-productive complex, thereby blocking phage DNA replication.

7/10 15 independent escapers, isolated from 4 phages, carried mutations in homologs of the same phage-encoded GNAT acetyltransferase. Interaction experiments further connected lanthivirin precursor with phage GNAT and DNA primase. The GNAT therefore appears central to lanthivirin sensitivity.

How do they work? Lanthivirins do not detectably harm the host, trigger cell death, or block phage adsorption. They act after entry: phage DNA accumulation drops early, followed by reduced phage transcripts, proteins, and particle production.

The biosynthetic chemistry is essential for the antiviral activity. Deleting the LanB-like dehydratase or LanC-like cyclase abolished defense. So did mutations in conserved residues predicted to form the lanthionine rings. Lanthivirin maturation is required for antiviral activity.

Genomics gave us candidates; then came a lot of Streptomyces work, thx to a lot of collaborators for helping us with that! Six diverse lanthivirin systems protected against phages in heterologous hosts. In S. coelicolor, activating cryptic lanthivirin cluster reduced phage titers by 10^4.

3/10 We combined antiSMASH and DefenseFinder predictions across 29,401 actinobacterial genomes. One clade of class I lanthipeptide clusters was strongly enriched near known defense systems. It contains >2,000 systems across diverse Actinobacteria. We named them lanthivirins

2/10 The biological roles of most bacterial natural products remain unknown. A few were shown to provide antiphage phenotypes, as early as 1945 by Doris Jones and more recently by the @themaxwelllab.bsky.social and @frunzkelab.bsky.social labs. Ex: www.nature.com/articles/s41...

Great piece and cover @science.org about how our field is uncovering the evolutionary and mechanistic connections between bacterial and eukaryotic immunity ! www.science.org/content/article/ancient-wars-between-microbes-gave-us-key-immune-defenses

To explore this crazy diversity, we’re incredibly excited to share all these predictions with the community! Not just as huge tables, but also through an interactive web atlas defensefinder.mdmlab.fr/wiki/refseq_.... Search by sequence, PFAM, and more — and have fun hunting for new mechanisms.

Bacterial antiphage systems often function as multi-gene operons. To make this diversity easier to explore , we developed a method to automatically infer candidate operons for experimental follow-up. We call them PAPO (Predicted AntiPhage Operons).

At pangenome scale, the models predict 2.39 million antiphage proteins across >32,000 bacterial genomes. More than 85% of predicted defense-associated protein families had no prior link to immunity. In other words: we are still only exploring a fraction of bacterial immune diversity.

Yes!! We developed GeneCLR, a model that integrates both context and function. It performed better than all of our other models, reaching 99% precision and 92% recall for prediction of antiphage proteins. So what does GeneCLR-DF tell us about bacterial immunity ?

Then, we fined tuned ESM-DF, a protein language model classifier. Here the underlying signal would be homology (capturing domains and very distant variants). We validated its predictions in E. coli uncovering six additional systems. But could we get the best of both worlds? Context AND sequence ?

We first developed ALBERT-DF, a model trained on genomic context, hypothesizing it would recognize defense islands or MGE. We validated its predictions in Streptomyces Albus, uncovering six novel antiphage systems, including only proteins with completely novel domains.

Finally, we explore how expression differences are functionally relevant: by tuning conditions and strain background, we found conditions where famously repressed native E. coli CRISPR-Cas system becomes active.

What about the famous defense islands ?🛡️🏝️ They emerge as key regulatory units, frequently associated with candidates local transcription factors that could coordinate multiple systems.

What could be the drivers of this variability ? Antiphage system expression correlates with cellular physiology and mobile element activity, e.g. repression during SOS, association with IS activity.

This variability is not noise. Most systems show multi-fold expression changes across environmental (low or high temperatures🌡️), physiological (growth stage), or spatial gradients. For examples, some systems seem expressed at the center of biofilms, others on the biofilm edges

What did we learn ? Across species and strains, antiphage systems are typically moderately expressed, but expression is highly variable across conditions. We put it in context with highly expressed genes (ribosomal proteins) or repressed ones (famous lac operon!).

To study this, we combine: - ~10,000 public RNA-seq samples across 14 species - a new, high-resolution dataset corresponding to 540 RNA seq samples: 15 E. coli strains, 6 environments, 2 growth stages, surveilling the expression of over 230 antiphage systems. We love complex datasets ❤️💻

Where did such a system come from? Phylogenetic & structural comparisons point to a clear origin: the SbcCD DNA-repair complex. Lamassu emerged through sequential step including coiled-coil shortening, loss of SbcCD nuclease and integration of modular effectors into LmuA.

Overall, Lamassu keeps its nuclease (LmuA) inactive within the LmuA₁B₂C₁ complex. When viral replication begins, Lamassu senses the replication intermediates, triggering an ATP-dependent rearrangement that releases LmuA. LmuA tetramerizes into an active nuclease that dregades cellular DNA.

How is detection linked to activation? Conserved interfaces between LmuB, LmuC, and the LmuA C-terminus keep LmuA inactive. When viral replication is sensed, LmuA disengages from the complex and tetramerizes into a nuclease with a single catalytic pocket.

What DNA ends and when ? ChIP-seq during λ infection shows Lamassu accumulates specifically at the phage origin of replication, but only during the early, transient stage when replication intermediates form. We propose that it recognizes DNA structures generated during early viral replication.

To explore this, we solved Lamassu structures in two states: apo and dsDNA-bound. The architecture that emerged was striking: a shortened, kinked SMC-like scaffold, reorganized with LmuC and LmuA into a complex capable of recognizing double-stranded DNA ends.

We looked for Lamassu across ~23,000 genomes, and found 3,829 Lamassu ! They are present in ~15% of prokaryotes. They fall into two major clades, long and short, with short Lamassu being far more diverse, modular and widespread. How can such modularity evolve at the structural level ?

Overall we discovered a novel family of immune genes conserved across bacteria and eukaryotes. SIRal, a human homolog, is a novel actor of the TLR pathway. Much remains to be understood about SIRal and Sirims in immunity, but 🦠 will help us along the way.

How does this family of proteins function? Like their bacterial relatives, eukaryotic SIRims — including human SIRal — use NAD+ in vitro. This enzymatic activity (NADase) seems ancient and conserved across the tree of life.

What about pathogens? We demonstrate that SIRal limits infection by herpes virus and by the bacteria Salmonella in mouse macrophages.

We analyzed SIRal’s function in human and mouse cells. Through numerous experiments (yay bar graphs!), we show that SIRal is required for a key immune pathway in animals (Toll-like receptor/TLR). SIRal mediates the up-regulation of interferon-stimulated genes (ISGs) and proinflammatory cytokines.