Anti-CRISPR protein AcrIF4 inhibits the type I-F CRISPR-Cas surveillance complex by blocking nuclease recruitment and DNA cleavage

Gao, Zhengyu; Zhang, Laixing; Ge, Zihao; Wang, Hao; Yue, Yourun; Jiang, Zhuobing; Wang, Xin; Xu, Chenying; Zhang, Yi; Yang, Maojun; Feng, Yue

doi:10.1016/j.jbc.2022.102575

Cited by 7 publications

(3 citation statements)

References 32 publications

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“…It is worth noting that AcrIF4 expression still caused a slight decrease in transformation efficiency (∼50%; P = 0.0059) and resulted in smaller colonies on selective plates (Fig. 5c), which coincides with an in vitro study that showed AcrIF4 only reduces, but does not completely abolish, the binding between Csy and target DNA 27 . Additionally, the mechanism of AcrIF12 remains unknown, but its expression was found to induce the toxicity of CrePA (Fig.…”

Section: Resultssupporting

confidence: 84%

CRISPR-repressed toxin-antitoxin provides population-level immunity against diverse anti-CRISPR elements

Shu,

Wang,

et al. 2024

Preprint

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Prokaryotic CRISPR-Cas systems are highly vulnerable to phage-encoded anti-CRISPR (Acr) factors. How CRISPR-Cas systems protect themselves remains unclear. Here, we uncovered a broad-spectrum anti-anti-CRISPR strategy involving a phage-derived toxic protein. Transcription of this toxin is normally reppressed by the CRISPR-Cas effector, but is activated to halt cell division when the effector is inhibited by any anti-CRISPR proteins or RNAs. We showed that this abortive infection-like effect efficiently expels Acr elements from bacterial population. Furthermore, we exploited this anti-anti-CRISPR mechanism to develop a screening method for specific Acr candidates for a CRISPR-Cas system, and successfully identified two distinct Acr proteins that enhance the binding of CRISPR effector to non-target DNA. Our data highlight the broad-spectrum role of CRISPR-repressed toxins in counteracting various types of Acr factors, which illuminates that the regulatory function of CRISPR-Cas confers host cells herd immunity against Acr-encoding genetic invaders, no matter they are CRISPR-targeted or not.

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Section: Resultssupporting

confidence: 84%

CRISPR-repressed toxin-antitoxin provides population-level immunity against diverse anti-CRISPR elements

Shu,

Wang,

et al. 2024

Preprint

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“…Later, the research group found that there was always an Aca (anti-CRISPR-associated) gene downstream of the anti-CRISPR gene, which inspired the identification of numerous Acr genes (Pawluk et al, 2016;Borges et al, 2017). Subsequent structural and biological characterization found that most Acr proteins directly target Cas protein-crRNA complexes, such as Cascade (Yang et al, 2021;Gao Z. et al, 2022;Wang et al, 2022;Yang et al, 2022), Cas9-sgRNA (Dong et al, 2017;Rauch et al, 2017), Cas12-crRNA (Marino et al, 2018;Zhang et al, 2019), Cas13-crRNA (Lin et al, 2020;Meeske et al, 2020), and play a role by shielding the domain of recognition or binding nucleic acid substrate. A small amount of Acr proteins target apo Cas proteins, for instance, AcrIIC2 targets Cas9 and impedes the loading of sgRNA onto Cas9 proteins and the subsequent assembly of complexes (Zhu et al, 2019).…”

Section: Directly Binding Immune Proteinsmentioning

confidence: 99%

Bacteriophage strategies for overcoming host antiviral immunity

Gao

Feng

2023

Front. Microbiol.

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Phages and their bacterial hosts together constitute a vast and diverse ecosystem. Facing the infection of phages, prokaryotes have evolved a wide range of antiviral mechanisms, and phages in turn have adopted multiple tactics to circumvent or subvert these mechanisms to survive. An in-depth investigation into the interaction between phages and bacteria not only provides new insight into the ancient coevolutionary conflict between them but also produces precision biotechnological tools based on anti-phage systems. Moreover, a more complete understanding of their interaction is also critical for the phage-based antibacterial measures. Compared to the bacterial antiviral mechanisms, studies into counter-defense strategies adopted by phages have been a little slow, but have also achieved important advances in recent years. In this review, we highlight the numerous intracellular immune systems of bacteria as well as the countermeasures employed by phages, with an emphasis on the bacteriophage strategies in response to host antiviral immunity.

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“…Importantly, binding of the target DNA induces a ∼180-degree rotation of the C-terminal helical bundle (HB) of the ‘‘large’’ Cas8f subunit of the Csy complex to expose a ‘‘nuclease recruitment helix’’ in Cas8f-HB, which is responsible for further recruitment of the target DNA degrading endonuclease Cas2/3 24 . Cas8f-HB is crucial for the type I-F CRISPR-Cas immunity in P. aeruginosa , and phages also encode several anti-CRISPR proteins that antagonize the CRISPR-Cas immunity through targeting or mimicking Cas8f-HB, including AcrIF3 24 , AcrIF4 27 and AcrIF5 28 . In addition, target DNA binding-induced conformational changes of Cascade for recruitment of Cas nucleases have also been demonstrated in many other type I CRISPR-Cas systems 29–31 .…”

Section: Introductionmentioning

confidence: 99%

Cas1 mediates the interference stage in a phage-encoded CRISPR-Cas system

Zhang,

Wang,

Zeng

et al. 2024

Preprint

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CRISPR-Cas systems are prokaryotic adaptive immune systems against invading phages and other mobile genetic elements, which function in three stages: adaptation, expression and interference. Interestingly, phages were also found to encode CRISPR-Cas systems to antagonize their hosts and establish infection. The Vibrio cholerae-infecting ICP1 phage was the first discovered phage with a functional CRISPR-Cas system against an antiphage region in the host genome. Nevertheless, this system lacks a domain essential for recruitment of helicase-nuclease Cas2/3 during target DNA cleavage, and how this system accomplishes the interference stage remains unknown. Here, surprisingly, we found that Cas1, a highly conserved component known to exclusively work in the adaptation stage, also mediates the interference stage through connecting Cas2/3 to the DNA bound-Cascade (Csy) complex of the ICP1 CRISPR-Cas system. A series of structures of Csy, Csy-dsDNA, Cas1-Cas2/3 and Csy-dsDNA-Cas1-Cas2/3 complexes collectively reveal the whole process of Cas1-mediated target DNA cleavage by the ICP1 CRISPR-Cas system. Together, these data support an unprecedented model in which Cas1 mediates the interference stage in a phage-encoded CRISPR-Cas system and also shed light on a unique model of primed adaptation.

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Anti-CRISPR protein AcrIF4 inhibits the type I-F CRISPR-Cas surveillance complex by blocking nuclease recruitment and DNA cleavage

Cited by 7 publications

References 32 publications

CRISPR-repressed toxin-antitoxin provides population-level immunity against diverse anti-CRISPR elements

CRISPR-repressed toxin-antitoxin provides population-level immunity against diverse anti-CRISPR elements

Bacteriophage strategies for overcoming host antiviral immunity

Cas1 mediates the interference stage in a phage-encoded CRISPR-Cas system

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