Chao Liu
@ployaaaa.bsky.social
Ph.D., Institute of Microbiology, Chinese Academy of Sciences;
CRISPR-Cas system, defense system, TA system, phage and microbes.
CRISPR-Cas system, defense system, TA system, phage and microbes.
Reposted by Chao Liu
I am so excited to share our project with you! We find prokaryotic proteases activate toxic enzymes and pores as a modular strategy in phage defense. We studied four fascinating protease-toxin pairs that are abundant across bacterial genomes:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Proteolytic activation of diverse antiviral defense modules in prokaryotes
Linked protease–effector modules are widespread in prokaryotic antiviral defense, yet the mechanisms of most remain poorly understood. Here we show that four of the most prevalent modules—metallo-β-la...
www.biorxiv.org
November 15, 2025 at 11:49 PM
I am so excited to share our project with you! We find prokaryotic proteases activate toxic enzymes and pores as a modular strategy in phage defense. We studied four fascinating protease-toxin pairs that are abundant across bacterial genomes:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Chao Liu
New from the @doudna-lab.bsky.social and first author @owentuck.bsky.social!
Our nuclease-protease story is out! We explored a fascinating case of coevolution and modularity in prokaryotic immune systems: www.science.org/doi/10.1126/...
Thanks to wonderful coauthors/collaborators/friends, the whole @doudna-lab.bsky.social and everyone at @innovativegenomics.bsky.social
Thanks to wonderful coauthors/collaborators/friends, the whole @doudna-lab.bsky.social and everyone at @innovativegenomics.bsky.social
Recurrent acquisition of nuclease-protease pairs in antiviral immunity
Antiviral immune systems diversify by integrating new genes into existing pathways, creating new mechanisms of viral resistance. We identified genes encoding a predicted nuclease paired with a trypsin...
www.science.org
November 14, 2025 at 12:27 AM
New from the @doudna-lab.bsky.social and first author @owentuck.bsky.social!
Reposted by Chao Liu
#microsky #phagesky
Predicting host- #phage interactions from genomics.
www.biorxiv.org/content/10.1...
Predicting host- #phage interactions from genomics.
www.biorxiv.org/content/10.1...
Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes
Bacteriophages offer promising alternatives to antibiotics for treating drug-resistant infections and engineering microbiomes, but applications are limited by inability to select phages infecting spec...
www.biorxiv.org
November 16, 2025 at 9:53 AM
#microsky #phagesky
Predicting host- #phage interactions from genomics.
www.biorxiv.org/content/10.1...
Predicting host- #phage interactions from genomics.
www.biorxiv.org/content/10.1...
Reposted by Chao Liu
#microsky #phagesky #phage defence
Anti-CRISPR protein hijacks host’s enolase to tackle and block CRISPR-Cas
www.nature.com/articles/s41...
Anti-CRISPR protein hijacks host’s enolase to tackle and block CRISPR-Cas
www.nature.com/articles/s41...
A phage-encoded anti-CRISPR protein co-opts host enolase to prevent type III CRISPR immunity - Nature Microbiology
Streptococcus thermophilus phages circumvent host CRISPR defences via AcrIIIA2, which complexes with enolase, a highly abundant glycolysis enzyme, to block phage RNA binding.
www.nature.com
November 11, 2025 at 4:27 PM
#microsky #phagesky #phage defence
Anti-CRISPR protein hijacks host’s enolase to tackle and block CRISPR-Cas
www.nature.com/articles/s41...
Anti-CRISPR protein hijacks host’s enolase to tackle and block CRISPR-Cas
www.nature.com/articles/s41...
Reposted by Chao Liu
The hitchhiker’s guide to cross-species DNA delivery
@cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez
www.cell.com/trends/micro...
@cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez
www.cell.com/trends/micro...
The hitchhiker’s guide to cross-species DNA delivery
Microbial hitchhikers are rewriting the rules of horizontal gene transfer. He, Patkowski,
et al. reveal how phage satellites assemble chimeric infective particles that deliver
DNA across species bound...
www.cell.com
November 9, 2025 at 9:39 AM
The hitchhiker’s guide to cross-species DNA delivery
@cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez
www.cell.com/trends/micro...
@cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez
www.cell.com/trends/micro...
Reposted by Chao Liu
After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...
An updated evolutionary classification of CRISPR–Cas systems including rare variants - Nature Microbiology
An exploration of previously undescribed variants from the long tail of the CRISPR–Cas distribution.
www.nature.com
November 6, 2025 at 1:49 PM
After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...
Reposted by Chao Liu
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides.
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:00 AM
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides.
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Reposted by Chao Liu
Reposted by Chao Liu
1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Antiviral reverse transcriptases reveal the evolutionary origin of telomerase
Defense-associated reverse transcriptases (DRTs) employ diverse and distinctive mechanisms of cDNA synthesis to protect bacteria against viral infection. However, much of DRT family diversity remains ...
www.biorxiv.org
October 17, 2025 at 5:22 PM
1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Reposted by Chao Liu
This is one of the main "immune systems for the genome" - sophisticated machinery that can detect and suppress genome parasites (transposons). It's cool molecular biology and hat's off to @juliusbrennecke.bsky.social and team for working out yet more detail of it.
PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity.
But how does piRNA-guided target interaction translate into silencing?
PhD student Júlia Portell Montserrat has an intriguing answer
www.cell.com/molecular-ce...
But how does piRNA-guided target interaction translate into silencing?
PhD student Júlia Portell Montserrat has an intriguing answer
www.cell.com/molecular-ce...
September 17, 2025 at 10:48 AM
This is one of the main "immune systems for the genome" - sophisticated machinery that can detect and suppress genome parasites (transposons). It's cool molecular biology and hat's off to @juliusbrennecke.bsky.social and team for working out yet more detail of it.
Reposted by Chao Liu
🦠🧍♀️From bacterial to human immunity.
We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social
www.science.org/doi/10.1126/...
We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social
www.science.org/doi/10.1126/...
www.science.org
July 24, 2025 at 6:23 PM
🦠🧍♀️From bacterial to human immunity.
We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social
www.science.org/doi/10.1126/...
We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social
www.science.org/doi/10.1126/...
Reposted by Chao Liu
Here we show how the type III signalling molecule SAM-AMP is bound and degraded by a specialised lyase enzyme encoded in cellular and phage genomes. More great work by @haotianchi.bsky.social and the team. @uniofstandrews.bsky.social
academic.oup.com/nar/article/...
academic.oup.com/nar/article/...
SAM-AMP lyases in type III CRISPR defence
Abstract. Type III CRISPR systems detect non-self RNA and activate the enzymatic Cas10 subunit, which generates nucleotide second messengers for activation
academic.oup.com
July 14, 2025 at 11:07 AM
Here we show how the type III signalling molecule SAM-AMP is bound and degraded by a specialised lyase enzyme encoded in cellular and phage genomes. More great work by @haotianchi.bsky.social and the team. @uniofstandrews.bsky.social
academic.oup.com/nar/article/...
academic.oup.com/nar/article/...
Reposted by Chao Liu
Bacteria encode homologs of the human NACHT proteins that form inflammasomes and use them to defend against phage #infection. @amyconte.bsky.social @aaronwhiteley.bsky.social &co show that bNACHT25 detects diverse phages indirectly through interaction with the host chaperone DnaJ. 🧪
plos.io/4koXP60
plos.io/4koXP60
DnaJ mediates phage sensing by the bacterial NLR-related protein bNACHT25
Bacteria encode homologs of the human NACHT proteins that form inflammasomes, and use them to defend against phage infection. This study shows that the NLR-related protein bNACHT25 detects diverse pha...
plos.io
June 3, 2025 at 3:19 PM
Bacteria encode homologs of the human NACHT proteins that form inflammasomes and use them to defend against phage #infection. @amyconte.bsky.social @aaronwhiteley.bsky.social &co show that bNACHT25 detects diverse phages indirectly through interaction with the host chaperone DnaJ. 🧪
plos.io/4koXP60
plos.io/4koXP60
Reposted by Chao Liu
Exciting news!! Our latest paper is out in Nat. Microbiol. @natmicrobiol.nature.com
We show that a sub-lineage of 7th pandemic V. cholerae has acquired mobile genetic elements packed with phage defense systems—rendering it multi-phage resistant 😳 ..... 1/3
www.nature.com/articles/s41...
We show that a sub-lineage of 7th pandemic V. cholerae has acquired mobile genetic elements packed with phage defense systems—rendering it multi-phage resistant 😳 ..... 1/3
www.nature.com/articles/s41...
West African–South American pandemic Vibrio cholerae encodes multiple distinct phage defence systems - Nature Microbiology
The West African–South American lineage of Vibrio cholerae contains multiple distinct anti-phage defence systems that provide resistance to various phage families, including vibriophage ICP1, a key pr...
www.nature.com
May 22, 2025 at 6:14 PM
Exciting news!! Our latest paper is out in Nat. Microbiol. @natmicrobiol.nature.com
We show that a sub-lineage of 7th pandemic V. cholerae has acquired mobile genetic elements packed with phage defense systems—rendering it multi-phage resistant 😳 ..... 1/3
www.nature.com/articles/s41...
We show that a sub-lineage of 7th pandemic V. cholerae has acquired mobile genetic elements packed with phage defense systems—rendering it multi-phage resistant 😳 ..... 1/3
www.nature.com/articles/s41...
Reposted by Chao Liu
Habemus paper! Our story on integron-encoded anti-phage defenses is now out in @science.org! 16 new systems, small versions of known ones, and a lot more in this highly-collaborative study.
Many thanks to everyone involved, especially my supervisor @epcrocha.bsky.social
bsky.app/profile/bapt...
Many thanks to everyone involved, especially my supervisor @epcrocha.bsky.social
bsky.app/profile/bapt...
White smoke, we have a new pope and also 16 new anti-phages systems in sedentary integrons (SCIs) !
In collaboration with the Rocha lab, we show in our new paper that cassettes of these large platforms encode many known anti-phage defenses, and uncovered 16 new ones.
www.science.org/doi/10.1126/...
In collaboration with the Rocha lab, we show in our new paper that cassettes of these large platforms encode many known anti-phage defenses, and uncovered 16 new ones.
www.science.org/doi/10.1126/...
Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems
Integrons are genetic systems that drive bacterial adaptation by acquiring, expressing, and shuffling gene cassettes. While mobile integrons are well known for spreading antibiotic resistance genes, t...
www.science.org
May 9, 2025 at 11:51 AM
Habemus paper! Our story on integron-encoded anti-phage defenses is now out in @science.org! 16 new systems, small versions of known ones, and a lot more in this highly-collaborative study.
Many thanks to everyone involved, especially my supervisor @epcrocha.bsky.social
bsky.app/profile/bapt...
Many thanks to everyone involved, especially my supervisor @epcrocha.bsky.social
bsky.app/profile/bapt...
Cyclic-dinucleotide-induced filamentous assembly of phospholipases governs broad CBASS immunity: Cell www.cell.com/cell/fulltex...
Cyclic-dinucleotide-induced filamentous assembly of phospholipases governs broad CBASS immunity
Phospholipase effectors of the CBASS system assemble from an inactive dimeric state
into active higher-order filamentous oligomers upon sensing cyclic dinucleotides,
facilitating membrane disruption a...
www.cell.com
May 9, 2025 at 1:30 AM
Cyclic-dinucleotide-induced filamentous assembly of phospholipases governs broad CBASS immunity: Cell www.cell.com/cell/fulltex...
Reposted by Chao Liu
🧪
Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉
Short 🧵
www.science.org/doi/10.1126/...
Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉
Short 🧵
www.science.org/doi/10.1126/...
Mobile integrons encode phage defense systems
Integrons are bacterial genetic elements that capture, stockpile, and modulate the expression of genes encoded in integron cassettes. Mobile integrons (MIs) are borne on plasmids, acting as a vehicle ...
www.science.org
May 8, 2025 at 8:27 PM
🧪
Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉
Short 🧵
www.science.org/doi/10.1126/...
Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉
Short 🧵
www.science.org/doi/10.1126/...
Reposted by Chao Liu
"That telomere phages are so prevalent means that they are a selective force, one that we know little about. We now want to understand how the telomere-toxin is secreted and also understand how this ‘telocin’ wheedles its way into unsuspecting bacterial neighbors”
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Telomere bacteriophages are widespread and equip their bacterial hosts with potent interbacterial weapons
Klebsiella host strains infected with telomere phages can grow to be the dominant lineage in mixed populations.
www.science.org
May 1, 2025 at 10:04 PM
"That telomere phages are so prevalent means that they are a selective force, one that we know little about. We now want to understand how the telomere-toxin is secreted and also understand how this ‘telocin’ wheedles its way into unsuspecting bacterial neighbors”
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Chao Liu
🧬🧫🦠 @science.org Bacterial reverse transcriptase synthesizes long poly-A–rich cDNA for antiphage defense | Science www.science.org/doi/10.1126/... #microbiology #bacteriophage #antiphage #immunity #DNA #RNAsky #RT #Cryo-EM #DRT9
May 2, 2025 at 9:02 PM
🧬🧫🦠 @science.org Bacterial reverse transcriptase synthesizes long poly-A–rich cDNA for antiphage defense | Science www.science.org/doi/10.1126/... #microbiology #bacteriophage #antiphage #immunity #DNA #RNAsky #RT #Cryo-EM #DRT9
Reposted by Chao Liu
Elegant prokaryote-style innate immunity revealed in Nature paper led by 🇱🇹 team
Histidine+ADP-ribose = His-ADPR
New bacterial “danger” molecule made during phage infection
Produced by TIR domains, recognized by Macro domains, and blocked by viral evasion proteins
www.nature.com/articles/s41...
Histidine+ADP-ribose = His-ADPR
New bacterial “danger” molecule made during phage infection
Produced by TIR domains, recognized by Macro domains, and blocked by viral evasion proteins
www.nature.com/articles/s41...
May 1, 2025 at 10:48 AM
Elegant prokaryote-style innate immunity revealed in Nature paper led by 🇱🇹 team
Histidine+ADP-ribose = His-ADPR
New bacterial “danger” molecule made during phage infection
Produced by TIR domains, recognized by Macro domains, and blocked by viral evasion proteins
www.nature.com/articles/s41...
Histidine+ADP-ribose = His-ADPR
New bacterial “danger” molecule made during phage infection
Produced by TIR domains, recognized by Macro domains, and blocked by viral evasion proteins
www.nature.com/articles/s41...
Reposted by Chao Liu
Circular 23S rRNA within archaeal ribosomes https://www.biorxiv.org/content/10.1101/2025.04.27.650855v1
April 29, 2025 at 2:36 PM
Circular 23S rRNA within archaeal ribosomes https://www.biorxiv.org/content/10.1101/2025.04.27.650855v1
Reposted by Chao Liu
Base-modified nucleotides mediate immune signaling in bacteria | Science www.science.org/doi/10.1126/...
Base-modified nucleotides mediate immune signaling in bacteria
Signaling from pathogen sensing to effector activation is a fundamental principle of cellular immunity. Whereas cyclic (oligo)nucleotides have emerged as key signaling molecules, the existence of othe...
www.science.org
April 25, 2025 at 6:55 AM
Base-modified nucleotides mediate immune signaling in bacteria | Science www.science.org/doi/10.1126/...
Reposted by Chao Liu
#weekendreading📑🔬
Base-modified nucleotides mediate immune signaling in bacteria
@science.org #microsky
www.science.org/doi/10.1126/...
Base-modified nucleotides mediate immune signaling in bacteria
@science.org #microsky
www.science.org/doi/10.1126/...
Base-modified nucleotides mediate immune signaling in bacteria
Signaling from pathogen sensing to effector activation is a fundamental principle of cellular immunity. Whereas cyclic (oligo)nucleotides have emerged as key signaling molecules, the existence of othe...
www.science.org
April 25, 2025 at 8:35 AM
#weekendreading📑🔬
Base-modified nucleotides mediate immune signaling in bacteria
@science.org #microsky
www.science.org/doi/10.1126/...
Base-modified nucleotides mediate immune signaling in bacteria
@science.org #microsky
www.science.org/doi/10.1126/...
Reposted by Chao Liu
Gene editing and many other useful biotechnology tools came from studies of bacteria fighting off viral invaders.
But scientists have only begun to unlock the secrets of this ancient arms race
https://go.nature.com/4lD4LOa
But scientists have only begun to unlock the secrets of this ancient arms race
https://go.nature.com/4lD4LOa
Microbial warfare brought us CRISPR. What big breakthroughs could be next?
Gene editing and many other useful biotechnology tools came from studies of bacteria fighting off viral invaders. But scientists have only begun to unlock the secrets of this ancient arms race.
go.nature.com
April 9, 2025 at 11:51 AM
Gene editing and many other useful biotechnology tools came from studies of bacteria fighting off viral invaders.
But scientists have only begun to unlock the secrets of this ancient arms race
https://go.nature.com/4lD4LOa
But scientists have only begun to unlock the secrets of this ancient arms race
https://go.nature.com/4lD4LOa