Cryptic Prophage (phage 🧬🪤 in 🦠)

Uracil first shown 2009 to be a QS signal in P. a. & UMP path important for QS & virulence. Moreover, 5-fluorouracil is a potent QS quencher & is the first QQ compound used commercially (for catheters). Uracil also is a signal in the Drosophila GI tract.

Quite insane if true

Using DefenseFinder misses nearly all of the toxin/antitoxin systems; i.e., the most prevalent phage defense system is missing to a large degree from this database. I recommend running TAFinder or TADB. etc., too, to search for TAs, which likely are anti-phage systems.

Using DefenseFinder misses nearly all of the toxin/antitoxin systems; i.e., the most prevalent phage defense system is missing to a large degree from this database. I recommend running TAFinder or TADB. etc., too, to search for TAs, which likely are anti-phage systems.

I am excited to announce a fantastic collaboration! We thank the U.S.-Israel #BSF and the National Science Foundation #NSF for funding our project with Prof. Hadar Ben-Yoav and @crypticprophage.bsky.social. We will be studying #mucin- associated #biofilms using innovative mucin-on-chip systems.

Congratulations Ilana!

The E. coli CRISPR-Cas conundrum: are they functional immune systems or genomic singularities? | EcoSal Plus The story spanning the first recognition of peculiar repeat sequences in the genomes of Escherichia coli (1), to the functional description of what is today known as CRISPR-Cas, has been detailed in s...

doi.org/10.1128/ecos...
Balanced review from Ed Dudley considering whether CRISPR-Cas is active in E. coli K-12. We discovered it silences lysis transcripts from cryptic prophages in 2022 (doi 10.3390/ijms232416195).

A quinolone N-oxide antibiotic selectively targets Neisseria gonorrhoeae via its toxin–antitoxin system - Nature Microbiology Pseudomonas aeruginosa-derived 2-nonyl-4-quinolone N-oxide exerts bactericidal effects on Neisseria gonorrhoea via zeta1–epsilon1 toxin–antitoxin activation in vitro and abrogates experimental infecti...

nature.com/articles/s41...
On the basis of sex: another important link of toxin/antitoxin systems to the stress response. Here, P. aeruginosa-derived NQNO inhibits N. gonorrhoeae by increasing oxidative stress, activating Zeta1 toxin, without affecting vaginal lactobacilli.

Serine Recombinase PinR Inverts Cryptic Prophage DNA to Block Adsorption of Phages Recombinases catalyze site-specific integration, excision, and inversion of DNA and are found in myriad defense islands; however, their function in phage-defense is unknown as they are frequently dism...

biorxiv.org/content/10.1...
We found ubiquitous recombinases from cryptic prophages may invert DNA to form new, chimeric proteins that inhibit phages by blocking adsorption. Congratulations to Joy, Daniel, Rodolfo and Michael for their strong efforts.

Viable but non‐culturable and persistence describe the same bacterial stress state Bacteria are often thought of as having two dormant phenotypes: the viable but non-culturable (VBNC) state and the persister state. Here we investigate the relatedness of the two stress-induced pheno...

Cryptic Prophage (phage 🧬🪤 in 🦠)
(2/2) Not cited: doi:10.1111/1462-2920.14075 where it was shown the few live VBNCs = persisters. Also, there is no proof of differences in dormancy, i.e., no differences in persister cells (enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...).

doi.org/10.1016/j.ti...
(1/2) Fantastic summary of flawed research. As published, there are no differences between persisters & the live fraction of VBNCs & one of the clear indications of death is protein aggregation, so increased aggregation simply means the cells are dead.

🧐Yes, indeed, there is a continuum of dormancy: Persisters revive based on ribosomes almost instantaneously with food and VBNCs never revive since they are dead, which is the ultimate dormant state...i.e., protein aggregation = death.

A noncanonical intrinsic terminator in the HicAB toxin–antitoxin operon promotes the transmission of conjugative antibiotic resistance plasmids Abstract. Conjugative plasmids, major vehicles for the spread of antibiotic resistance genes, often contain multiple toxin–antitoxin (TA) systems. However,

A noncanonical intrinsic terminator in the HicAB toxin–antitoxin operon promotes the transmission of conjugative antibiotic resistance plasmids

in @narjournal.bsky.social by Lin et al.

academic.oup.com/nar/article/...

DUF4297 and HerA form abortosome to mediate bacterial immunity against phage infection Immune receptors form higher-order complexes known as inflammasomes in animals and resistosomes in plants to mediate immune signaling. Here, we report…

www.sciencedirect.com/science/arti...
🧐106 claims of cell death ('Abi', 'PCD', 'abortosome', 'death') upon phage induction of Hailibu system (DUR4297 DNase + HerA ATPase), but extraordinarily weak data to support claims: just system fails 3 MOI but works at 100X less phage.

Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins Despite ongoing efforts to study CRISPR systems, the evolutionary origins giving rise to reprogrammable RNA-guided mechanisms remain poorly understood…

www.sciencedirect.com/science/arti...
Chicken or egg? Looks like toxin/antitoxins were first, and a type III TA system (HEPN RNase toxin inhibited by ncRNA) evolved into CRISPR-Cas13 (RNA-degrading).

A plasmid-encoded inactive toxin–antitoxin system MtvT/MtvA regulates plasmid conjugative transfer and bacterial virulence in Pseudomonas aeruginosa Abstract. Plasmid-encoded toxin–antitoxin (TA) systems are known for their role in plasmid maintenance via post-segregational killing. Here, we identified

academic.oup.com/nar/article/...
Excellent additional proof of the regulatory nature of toxin/antitoxin modules by binding promoters other than the ones that encode the TA locus. Here, MtvT/MvtA decrease conjugation and increase virulence of P. aeruginosa.

Limited impact of Salmonella stress and persisters on antibiotic clearance - Nature Experiments in infected mice and tissue-mimicking chemostats show that resilience of Salmonella against antimicrobial compounds is largely a result of starvation-induced general resilience rather than...

www.nature.com/articles/s41...
Results are in-line with the first single-cell persister resuscitation work of 2018 (not cited) which showed many persister cells lyse upon waking due to internalized ampicillin (doi 10.1111/1462-2920.14093).

Composition and liquid-to-solid maturation of protein aggregates contribute to bacterial dormancy development and recovery - Nature Communications Recalcitrant infections are often caused by dormant bacteria, including persisters and viable but nonculturable cells. Here, the authors explore how composition and structure of protein aggregates affect dormancy and exit from this state.

www.nature.com/articles/s41...
🧐Yes, indeed, there is a continuum of dormancy: Persisters revive based on ribosomes almost instantaneously with food and VBNCs never revive since they are dead, which is the ultimate dormant state...i.e., protein aggregation = death.

I am sorry to hear that Vivek. I hope the pain diminishes.

DefensePredictor: A Machine Learning Model to Discover Novel Prokaryotic Immune Systems Anti-phage defense systems protect bacteria from viruses. Studying defense systems has begun to reveal the evolutionary roots of eukaryotic innate immunity and produced important biotechnologies such ...

www.biorxiv.org/content/10.1...
Most 'novel' systems described here after prediction from machine learning, are related to toxin/antitoxin systems (e.g., DS-11, DS6AB, DS-3, DS-32, HEPN motifs, etc.) cementing the idea that TAs are the most prevalent phage defense system.

Fun read. And yes, persistence (dormancy via ribosome inactivation) should be recognized as an universal state, conserved across kingdoms and for bacteria, like lag, exponential, and stationary phases.

Congratulations and Happy New Year!

DNA end sensing and cleavage by the Shedu anti-phage defense system The detection of molecular patterns associated with invading pathogens is a hallmark of innate immune systems. Prokaryotes deploy sophisticated host d…

www.sciencedirect.com/science/arti...
Yet another phage defense system that detects free DNA ends and provides immunity without causing 'programmed cell death'.

What a great way to end the year! ✨

Today in @cellpress.bsky.social we report the structure and function of the Shedu anti-phage defense system.

tinyurl.com/4crj6dnx

A long 🧵...

www.nature.com/articles/s41...
Another phage inhibition system (Zorya) that does not cause cell death or what has been termed 'abortive infection'. Congratulations to the authors for discerning the lovely mechanism of detecting phage disruption of the cell envelope then DNase activity.

doi.org/10.1038/s415...
Just my opinion, based on what I consider sound research in a field with much noise due to studying dying cells, but please see the attached list of the usual errors from this lab in their Nature Rev Micro persister review.

A prophage competition element protects Salmonella from lysis Most bacteria are polylysogens that carry multiple prophages integrated into the chromosome. These prophages confer advantages to their bacterial host…

sciencedirect.com/science/arti...
I'ing tripartite TA system identified in Salmonella Gifsy-1 prophage (not called this but toxin is common HEPN protein & TAs are prevalent in prophages). No survival phenotype upon TA deletion (Fig. 1M), but less lysis from other prophages (due to slower growth?).

Adenosine derivatives and adenosine has been shown to be important for signaling to P. aeruginosa by several labs (e.g., doi:10.1111/j.1751-7915.2012.00338.x).

Great list; thanks. I also still do dabble in the field...