Cryptic Prophage (phage 🧬🪤 in 🦠)

A prophage-encoded abortive infection protein preserves host and prophage spread - Nature A Gifsy-1 prophage–encoded higher eukaryotes and prokaryotes nucleotide-binding protein, HepS, senses Siphoviridae infection, activates abortive defence by cleaving host transfer RNAs, blocks rival ph...

nature.com/articles/s41586-025-10070-6
Brilliant work from former lab undergrad Sargen showing Salmonella prophage single HEPN protein HepS is activated by Gifsy-1 J tip protein then cleaves tRNAs. But Abi data not compelling and probably just shuts down host metabolism to form persisters.

The disputed identity of Pseudomonas putida KT2440: when taxonomists rename your favorite microbe | mBio Names matter; they are not mere labels. They operate as anchors of memory, social coordinates, and references of collective identity. When a name becomes established through long-term use and broad ad...

How do you react when your favorite microbe is renamed by taxonomists who are completely outside your field—and who ignore the community that actually works with it? Here is our clear answer re the case of Pseudomonas putida KT2440 👉🏻 journals.asm.org/doi/10.1128/...

#microsky

Persistent virulent phages exist across bacterial isolates - Nature Microbiology The long-term existence of diverse virulent phages within cultures of Escherichia coli and others challenges the virulent–temperate dichotomy and points to non-canonical phage lifestyles.

nature.com/articles/s41564-025-02207-0
We found one of these pseudo-lysogenic phages, also for E. coli, named SW1, that is T1-related, provides a benefit to kin that carry it, and depends on cryptic prophage protein YfdM: doi 10.1016/j.celrep.2019.03.070 (Cell Reports 2019).

Persister Cells Form Based on Low Ribosome Content Persister cells survive any severe stress including antibiotics, starvation, heat, oxidative conditions, and phage attack, by entering a dormant physiological state. They arise without genetic change ...

biorxiv.org/content/10.64898/2025.12.18.695105v1
Previously, we discovered ribosomes dictate persister resuscitation (Environ Micro 2018, doi:10.1111/1462-2920.14093); now we show low ribosome levels in single cells increase persister formation 80-fold, cementing the ribosome-persister mechanism.

Stress Can Induce Transcription of Toxin-Antitoxin Systems without Activating Toxin Toxin-antitoxin (TA) systems are ubiquitous genetic elements in bacterial genomes, but their functions are controversial. Although they are frequently…

I am curious why this work overlooks the most-prevalent anti-phage system, toxin/antitoxins, whose transcription response to stress has been well-studied and which are induced hundreds of fold by similar stresses (see www.sciencedirect.com/science/arti...), including mqsRA (known to inhibit T2).

More toxin/antitoxin systems 😉

Congratulations to Joy for all of her hard work and to all the visitors to my lab including Daniel, Rodolfo, and Michael, who had an incredible impact and thanks to Maria!

Thanks also to the three reviewers that provided excellent insights to improve the paper.

Adsorption of phage T2 is inhibited due to inversion of cryptic prophage DNA by the serine recombinase PinQ Abstract. Recombinases catalyze site-specific integration, excision, and inversion of DNA and are often found adjacent to anti-phage system genes clustered

academic.oup.com/nar/article/...
We discovered a new, wide-spread phage defense system based on serine recombinase PinQ in E. coli cryptic prophage Qin that inverts 1,797 bp in another cryptic prophage, e14, to encode two chimeric proteins that block adsorption of T2 phage. @NAR_Open

Adsorption of phage T2 is inhibited due to inversion of cryptic prophage DNA by the serine recombinase PinQ Abstract. Recombinases catalyze site-specific integration, excision, and inversion of DNA and are often found adjacent to anti-phage system genes clustered

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

#pjagesky #phage defence

nature.com/articles/s41564-025-02124-2
BPOET: 1st high-throughput search (10,000 cmpds), resuscitates persisters (2020) with mechanism of activating hibernating ribosomes via 23S rRNA pseudouridine synthase RluD (E. coli, doi:10.1111/1462-2920.14828), cited, but not in context vs. new search:

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).