Cryptic Prophage (phage 🧬🪤 in 🦠)
@crypticprophage.bsky.social
TA systems stop phages (discovered '96), phages create persisters (discovered '23), E. c. CRISPR regulates cryptic prophages (discovered '21), indole = inter-kingdom signal, AI2 increases biofilm & TqsA exports (Thomas K. Wood, endowed prof, H113, 351 pub)
Pinned
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
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
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
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
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
October 16, 2025 at 8:41 PM
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
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
Reposted by Cryptic Prophage (phage 🧬🪤 in 🦠)
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:
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:
October 12, 2025 at 12:01 PM
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:
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.
September 29, 2025 at 2:30 PM
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.
Reposted by Cryptic Prophage (phage 🧬🪤 in 🦠)
Quite insane if true
#NewResearch
Nasal colonisation by S. aureus is linked with depression in a human cohort and shown in a mouse model to cause decreased serotonin and dopamine in the brain
#MicroSky #Depression
www.nature.com/articles/s41...
Nasal colonisation by S. aureus is linked with depression in a human cohort and shown in a mouse model to cause decreased serotonin and dopamine in the brain
#MicroSky #Depression
www.nature.com/articles/s41...
Nasal Staphylococcus aureus carriage promotes depressive behaviour in mice via sex hormone degradation - Nature Microbiology
Nasal colonization by Staphylococcus aureus is linked with depression in a human cohort and shown in a mouse model to cause decreased serotonin and dopamine in the brain.
www.nature.com
September 23, 2025 at 8:33 PM
Quite insane if true
Reposted by Cryptic Prophage (phage 🧬🪤 in 🦠)
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.
September 23, 2025 at 4:07 PM
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.
Reposted by Cryptic Prophage (phage 🧬🪤 in 🦠)
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.
August 25, 2025 at 12:37 PM
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.
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).
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).
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
April 13, 2025 at 11:19 AM
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).
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).
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.
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.
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
April 4, 2025 at 7:53 AM
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.
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.
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.
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.
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
March 29, 2025 at 7:46 AM
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.
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.
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.
(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.
March 24, 2025 at 9:31 AM
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.
(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.
Reposted by Cryptic Prophage (phage 🧬🪤 in 🦠)
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/...
in @narjournal.bsky.social by Lin et al.
academic.oup.com/nar/article/...
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,
academic.oup.com
March 3, 2025 at 7:56 AM
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/...
in @narjournal.bsky.social by Lin et al.
academic.oup.com/nar/article/...
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.
🧐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.
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
February 26, 2025 at 12:12 PM
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.
🧐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.
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).
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).
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
February 19, 2025 at 6:08 AM
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).
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).
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.
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.
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
February 17, 2025 at 2:03 PM
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.
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.
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).
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).
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
February 6, 2025 at 11:50 AM
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).
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).
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.
🧐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.
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
January 28, 2025 at 2:12 PM
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.
🧐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.
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.
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.
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
January 9, 2025 at 12:30 PM
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.
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.
January 8, 2025 at 8:43 PM
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.
www.sciencedirect.com/science/arti...
Yet another phage defense system that detects free DNA ends and provides immunity without causing 'programmed cell death'.
Yet another phage defense system that detects free DNA ends and provides immunity without causing 'programmed cell death'.
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
January 1, 2025 at 1:49 PM
www.sciencedirect.com/science/arti...
Yet another phage defense system that detects free DNA ends and provides immunity without causing 'programmed cell death'.
Yet another phage defense system that detects free DNA ends and provides immunity without causing 'programmed cell death'.
Reposted by Cryptic Prophage (phage 🧬🪤 in 🦠)
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 🧵...
Today in @cellpress.bsky.social we report the structure and function of the Shedu anti-phage defense system.
tinyurl.com/4crj6dnx
A long 🧵...
December 31, 2024 at 3:38 PM
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 🧵...
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.
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.
Structure and mechanism of the Zorya anti-phage defense system - Nature
Nature - Structure and mechanism of the Zorya anti-phage defense system
www.nature.com
December 12, 2024 at 8:02 AM
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.
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.
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.
November 21, 2024 at 2:39 PM
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.
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.
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?).
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?).
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
November 21, 2024 at 8:21 AM
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?).
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?).