Have they found the key to missing oriT?

Please read the original article at: https://doi.org/10.1038/s41564-024-01844-1

Disclaimer: Below is an interpretation of the article thus do not necessarily represent the views of the authors.

Have they found the key to missing oriT?

Yes! At least for an exciting amount of plasmids.

But let’s take a step back: what are oriTs, and why do they matter?

As we know, plasmids are major culprits in spreading antibiotic resistance and virulence genes among pathogenic bacteria. For two bacteria to swap DNA directly, three components are essential: mating-pair formation machinery (MPF), a relaxase (MOB), and an oriT on a plasmid. The relaxase interacts with the oriT to initiate the transfer. While some plasmids can borrow on MPF and MOB produced by other plasmids, as far as we know*, a plasmid must have an oriT to transfer itself.

The thing is, we don't actually know that many oriT types. In fact, most known plasmids, including transferrable ones, have no identifiable oriT. That's not because they don't exist. It's because we didn't know what to look for.

In general, we rely too much on homology. We find something in a model organism, e.g. E. coli, and look for similar sequences in other bacteria. Since every organism is related to each other, thus their DNA, this is a very powerful method. But it produces a strong bias towards these model organisms. If an oriT has a completely different DNA sequence, we might miss it.

Ares-Arroyo et. al. went one further. Instead of just considering sequence similarity, what about their genomic context? What are oriT normally near to? Are they always found with something else? Which plasmids are they found in?

By identifying these patterns, they predicted oriTs in many known plasmids, including those from high-priority pathogenic bacteria, that previously lacked recognisable oriTs. They also experimentally validated several of their predictions.

Interestingly, no oriTs were predicted in some plasmids known to be transferable, including clinically significant ones. This suggests that their deduced patterns aren’t universal and highlights how oriT diversity is even more complex than we thought. While much work remains to fully unravel the genealogy of oriTs, this study represents a major step forward in understanding plasmid mobility and its role in AMR epidemiology.

Note: * there is some evidence that oriT may not be necessary for rolling-circle replication plasmids