hat is the relevance of ACE? Jolly et al. and Kuzmenko et al., demonstrated that DNA repair complexes AddAB/RecBCD are major drivers of guide DNA generation for long-A pAgos.

In another study, we recently showed that cyanobacteria lack RecBCD/AddAB:
sciencedirect.com/science/arti...

But what does it mean in vivo? We show that, in E. coli, while the cyanobacterial pAgo alone can provide defense against plasmids and phages, ACE can enhance the interference phenotype (at least for plasmids) demonstrating these proteins function in conjunction.

Co-expression of the cyanobacterial pAgo and ACE in E. coli reveals that pAgo-associated guide DNAs are (further) processed (shortened) by ACE. We show that longer guide DNAs are not functional, which shows that ACE contributes to guide DNA generation in coli.

The cyanobacterial pAgo and its ACE partner form a heterodimeric complex in which activity of ACE1 is modulated. But this still leaves a question: Is ACE1 important for guide generation or (further) target DNA a degradation?

Structural and biochemical characterization of ACE shows it is a DNA nuclease. Its catalytic site is buried in a channel that can only be accessed by single stranded DNA. Analysis of sequencing products show that ACE preferentially cleaves ssDNA upstream of guanine residues.

Investigation of the cyanobacterial pAgos shows that they are DNA-guided DNA cleaving pAgos, akin to various other long-A pAgos (TtAgo, CbAgo, PfAgo).

Those experiments as well as the crystal structure of CtAgo do not reveal why they would need ACE as partner.

Cyanobacterial long-A pAgos are co-encoded with Cas4 family proteins (from hereon: ACE for Argonaute associated Cas4-like enzyme).

Our analysis shows that despite their family name, ACEs look more like the nuclease domains of AdnAB and AddAB than like CRISPR-Cas4.

Out now: Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA
cell.com/molecular-ce...

Most long-A pAgos interfere with invading DNA solo. Why then are cyanobacterial pAgos co-encoded with a Cas4-like protein?

Finally, we discuss ecological drivers and consequences of interactions between defence and anti-defence systems.

We review the origins of anti-defence mechanisms, e.g. through co-option of prokaryotic proteins by plasmids and phages, defence component co-option and mutation, and de novo evolution.

We also discuss the selective pressure that acts on anti-defence system maintenance.

Recently very good reviews provided elaborate overviews of different anti-defence mechansms were published, so that is not the focus of this review.

You can find a selection here:
www.cell.com/cell-reports...
www.nature.com/articles/s41...
www.cell.com/trends/micro...

🚨New review🚨

Evolution and ecology of anti-defence systems in phages and plasmids

Link: www.cell.com/current-biol...

...and finally also co-occurrence with prokaryotic immune systems was analyzed. We report co-occurrences of certain DNA repair proteins with immune systems, including specific CRISPR-Cas subtypes, prokaryotic Argonautes (pAgos), dGTPases, GAPS2, and Wadjet.

Further analyses shows which proteins co-occur and/or are mutually exclusive, and whether such DNA repair proteins cluster on the genome (to my surprise often they are not clustered)...

Together with @patrickbarendse.bsky.social Sumanth performed a systematic analysis of taxonomic distribution and co-occurrence of DNA repair proteins.

To my surprise, in some bacterial taxa RecBCD, AddAB, and AdnAB are almost completely absent...

Sumanth developed a bioinformatics pipeline that (by using reciprocal searches and ranking) facilitates accurate identification and classification of DNA repair proteins without overlap that accurately cluster in distinct phylogenetic clades.

Distribution of bacterial DNA repair proteins and their co-occurrence with immune systems (cell.com/cell-reports...

It started with a simple question: Are certain prokaryotic immune systems always (or never) encoded with specific DNA repair proteins?...