Huge thanks to @aharms485.bsky.social who made this work possible. It has been a privilege to tackle something this ambitious together. And big thanks to all co-authors Jessica Ransome, @damienpiel.bsky.social , @veeninglab.com for their amazing contributions!

We also uncovered hidden roles for known proteins. For example T4 Alt, a protein that is injected together with the phage DNA which is long known for its role in phage infection, seems to also act as anti-defense factor against Mokosh type I bacterial defense system.🔦

We then moved this into more real-world complexity: clinical bacterial strains. We found phage genes that are conditionally essential only in specific hosts. Some of those genes with previously unknown function we could match to bacterial immunity systems of the respective hosts. 🛡️⚔️

For example, some T4 genes become essential only when the host expresses specific defense systems like rIIA/B for the RexAB, dmd for RnlAB etc.

But essentiality is not static. A gene can be essential in one context and irrelevant in another. HIDEN-SEQ is very sensitive and detects this context-dependent essentiality - genes that matter only under specific challenges.

First test: can HIDEN-SEQ reproduce knowledge that we have for classical phage models like T4 🤔? YES and with remarkably high resolution. It recapitulates an essentiality map that took decades of work to assemble.

In bacteria, TnSeq revolutionized genetics by linking genes to phenotypes at scale. But for phages nothing equivalent exists. So we built HIDEN-SEQ, the first TnSeq approach for phages, enabled by a hide-and-seek interplay between the host CRISPR-Cas13a and a phage anti-CRISPR protein.

Phages are major players in microbial ecosystems but most of their genes have no known function. This ”viral dark matter” has been hard to study because we have lacked scalable ways to link phage genes to what they actually do.

First the link to the preprint: www.biorxiv.org/content/10.1...

Huge thanks to @aharms485.bsky.social who made this work possible. It has been a privilege to tackle something this ambitious together. And big thanks to all co-authors Jessica Ransome, @damienpiel.bsky.social , @veeninglab.com for their amazing contributions!

Most people fail to appreciate just how groundbreaking McClintock's work truly was. Her transposon work was first presented in 1950 - before we knew, for example, "DNA is the genetic material." Long before most discoveries that we consider fundamental to the question of: "What is a gene?"