Also with the collaboration of the Sequence Bioinformatics lab (Kristen Curry & @rayanchikhi.bsky.social ) & the @mdmlab.bsky.social (@ftesson.bsky.social Arthur Lobat, Jean Cury and @audeber.bsky.social) , all at @pasteur.fr
Great collaborative work from our lab (Marie Touchon & @alicemaestri.bsky.social @raphael-microb.bsky.social @epcrocha.bsky.social) and the Synthetic Biology lab (Florence Depardieu & @dbikard.bsky.social)
What we can say from these results is that the defence genes carried by P4/P2 are "quasi-independent" of their genomic context. This makes P4 and P2 very dynamic platforms that accumulate, diversify, generate and then spread (to other bacterial hosts) both known and novel antiviral defence systems
So many questions left! How does defence swapping occur, mechanistically? How flexible is it? Can defective elements still swap genes, or are their defences fixed in the host? And what is up with P4 and P2 not sharing defence genes? Alas, we had no more space in this one. Stay tuned for follow ups!
Many homologs of P4/P2 defences are in genomic regions that are not classified as… well, anything really (could they be novel MGEs? 🤔)
But some regions are defective P4 or P2. Mobility genes gone, so we couldn’t identify them as such. Their hosts, smartly, kept the defence genes intact, though 😎
Defence genes aren’t swapped only between P4s or between P2s. P4/P2 have defence homologs in very different MGEs like plasmids or other types of phages. Surprisingly, no defence homologs between P4 and P2 🤨 Super strange, because they often coincide (and replicate/package) within the same bacterium
In this fast swap of defences, new systems might be created. We find many variants, minimizations or chimeras of known systems. We tested if these can protect against phages, and many do! And genes of unknown function, randomly picked from the where we expect P4/P2 defences to be? They work too!
Ok, so what about the turnover of defences in P4 and P2? Well, we had trouble finding similar defence genes even in other, very similar P4/P2. And we couldn’t find inactivated (pseudogene) defences either. This suggests that the defence systems in P4 and P2 are very quickly swapped by new ones!
So, not only defence genes (even just the known ones) are a very large fraction of the P4 and P2 pangenomes, the defences in P4 and P2 are an important part of the whole set of bacterial antiviral defences. In some bacteria, up to 50% of their known defences are in a P4 satellite or a P2 phage!
Moreover, and adding to the defence hotspot we already knew about, we found secondary hotspots that also accumulate defence genes (gene in orange in the figure below) in these elements. Many P2 (and a few P4) also have 2 or 3 different defence systems.
We first confirmed that yes, most P4 satellites and P2 phages have known defence genes. But we saw that these defences are more abundant and diverse than previously thought!
We focused on 2 “linked” MGEs: P2 phages and P4 satellites. P4 is a hitcher, a non-autonomous MGE that depends on its P2 helper to move. We already knew that P4 and P2 carry defence genes (see 🔗), but with SatelliteFinder + P4s detected in metagenomes, we could explore thousands of elements!
➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔
🧵👇
Also in collaboration with the Sequence Bioinformatics lab (Kristen Curry & @rayanchikhi.bsky.social) and the @mdmlab.bsky.social (@ftesson.bsky.social, Arthur Lobat, Jean Cury and @audeber.bsky.social)
An all @pasteur.fr collaboration!
New preprint out on bioRxiv!
www.biorxiv.org/content/10.6...
Can conjugative plasmids be used to control plasmid and pathogen spread?
Follow me down the rabbit hole that led to this story 🧵
Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive.
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
Had a fantastic time and very fun discussions writing this with @coluzzic.bsky.social, @aresarroyom.bsky.social and @epcrocha.bsky.social!
New paper from the lab, the mysteries involving the genetic elements that move by being mobilized by other MGEs. Hitcher Genetic Elements are distinctive, ancient and diverse.
ecoevorxiv.org/repository/v...
New from the lab. We were stuck studying plasmid mobility because we ignored most origins of transfer by conjugation. Using the occurrences of known oriT, we developed a method to find novel unrelated families. Works well. We now cover most conjugative plasmids of E coli, K pneumo & A baumannii.
