Structure Reveals a Mechanism of CRISPR-RNA-Guided Nuclease Recruitment and Anti-CRISPR Viral Mimicry

Rollins, MaryClare F.; Chowdhury, Saikat; Carter, Joshua A.; Golden, Sarah; Miettinen, Heini M.; Santiago-Frangos, Andrew; Faith, Dominick; Lawrence, C. Martin; Lander, Gabriel C.; Wiedenheft, Blake

doi:10.1016/j.molcel.2019.02.001

Cited by 94 publications

(89 citation statements)

References 80 publications

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“…AcrIF3 is an example of such anti-CRISPR protein with a dual anti-interference and anti-adaptation activity [24]. This CRISPR-Cas inhibitor binds to the helicase/nuclease Cas3, and prevents its recruitment to the effector Cascade-crRNA complex [26][27][28]. AcrIE1 inactivates the type I-E Cas3 nuclease [29] and thereby could also inhibit the adaptation step, although further experiments are required to confirm its anti-adaptation activity.…”

Section: Inhibition Of Crispr-cas Adaptationmentioning

confidence: 99%

“…However, AcrIF3 functions as a mimic of a Cas protein, in contrast with the DNA mimics presented above. Its 3D structure is similar to the C-terminal helical bundle of Cas8, which is exposed upon target DNA binding to Cascade-crRNA complex to recruit Cas2/3 [28,37]. AcrIF3 forms homodimers that bind to Cas2/Cas3 (Figure 2A), thereby preventing its recruitment to the target-bound Cascade-crRNA complex [26,27].…”

Section: Steric Occlusion Of Cas Effector Functional Sitesmentioning

confidence: 99%

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Diversity of molecular mechanisms used by anti-CRISPR proteins: the tip of an iceberg?

Hardouin

Goulet

2020

Biochemical Society Transactions

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Bacteriophages (phages) and their preys are engaged in an evolutionary arms race driving the co-adaptation of their attack and defense mechanisms. In this context, phages have evolved diverse anti-CRISPR proteins to evade the bacterial CRISPR–Cas immune system, and propagate. Anti-CRISPR proteins do not share much resemblance with each other and with proteins of known function, which raises intriguing questions particularly relating to their modes of action. In recent years, there have been many structure–function studies shedding light on different CRISPR–Cas inhibition strategies. As the anti-CRISPR field of research is rapidly growing, it is opportune to review the current knowledge on these proteins, with particular emphasis on the molecular strategies deployed to inactivate distinct steps of CRISPR–Cas immunity. Anti-CRISPR proteins can be orthosteric or allosteric inhibitors of CRISPR–Cas machineries, as well as enzymes that irreversibly modify CRISPR–Cas components. This repertoire of CRISPR–Cas inhibition mechanisms will likely expand in the future, providing fundamental knowledge on phage–bacteria interactions and offering great perspectives for the development of biotechnological tools to fine-tune CRISPR–Cas-based gene edition.

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Section: Inhibition Of Crispr-cas Adaptationmentioning

confidence: 99%

Section: Steric Occlusion Of Cas Effector Functional Sitesmentioning

confidence: 99%

Diversity of molecular mechanisms used by anti-CRISPR proteins: the tip of an iceberg?

Hardouin

Goulet

2020

Biochemical Society Transactions

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“…The latter interacts with Cas6f, Cas7f, and Cas5f (Bondy-Denomy et al, 2015;Chowdhury et al, 2017). Cas8f hook is essential in PAM recognition and crRNA-DNA heteroduplex formation since it generates a lysinecontaining wedge (K-wedge) and an alanine-rich loop (A-loop) (Guo et al, 2017;Rollins et al, 2019). The K-wedge, indeed, reacts with the negatively charged DNA phosphatic backbone, which stabilizes the hybridization between crRNA and DNA.…”

Section: Preventing Dna Bindingmentioning

confidence: 99%

Types I and V Anti-CRISPR Proteins: From Phage Defense to Eukaryotic Synthetic Gene Circuits

Marchisio

2020

Front. Bioeng. Biotechnol.

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Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPRassociated proteins), a prokaryotic RNA-mediated adaptive immune system, has been repurposed for gene editing and synthetic gene circuit construction both in bacterial and eukaryotic cells. In the last years, the emergence of the anti-CRISPR proteins (Acrs), which are natural OFF-switches for CRISPR-Cas, has provided a new means to control CRISPR-Cas activity and promoted a further development of CRISPR-Cas-based biotechnological toolkits. In this review, we focus on type I and type V-A anti-CRISPR proteins. We first narrate Acrs discovery and analyze their inhibitory mechanisms from a structural perspective. Then, we describe their applications in gene editing and transcription regulation. Finally, we discuss the potential future usageand corresponding possible challenges-of these two kinds of anti-CRISPR proteins in eukaryotic synthetic gene circuits.

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“…In the incessant host-parasite arms race, viruses evolved multiple anti-defense mechanisms including numerous, diverse anti-CRISPR proteins (Acrs) that are currently known to comprise 46 distinct families 5,6 . The Acrs employ different mechanisms to abrogate the activity of CRISPR-Cas systems [7][8][9][10] . The majority of the Acrs that have been studied in detail to date bind to functionally important sites of CRISPR-Cas effector proteins and display high specificity towards a particular CRISPR-Cas variant from a narrow range of bacteria or archaea.…”

Section: Introductionmentioning

confidence: 99%

Vast diversity of anti-CRISPR proteins predicted with a machine-learning approach

Gussow

Shmakov

Makarova

et al. 2020

Preprint

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Bacteria and archaea evolve under constant pressure from numerous, diverse viruses and thus have evolved multiple defense systems. The CRISPR-Cas are adaptive immunity systems that have been harnessed for the development of the new generation of genome editing and engineering tools. In the incessant host-parasite arms race, viruses evolved multiple anti-defense mechanisms including numerous, diverse anti-CRISPR proteins (Acrs) that can inhibit CRISPR-Cas and therefore have enormous potential for application as modulators of genome editing tools. Most Acrs are small, highly variable proteins which makes their prediction a formidable task. We developed a machine learning approach for comprehensive Acr prediction. The model showed high predictive power when tested against an unseen test set that included several families of recently discovered Acrs and was employed to predict 2,500 novel candidate Acr families. An examination of the top candidates confirms that they possess typical Acr features. One of the top candidates was independently tested and found to possess anti-CRISPR activity (AcrIIA12). We provide a web resource (http://acrcatalog.pythonanywhere.com/) to access the predicted Acrs sequences and annotation. The results of this analysis expand the repertoire of predicted Acrs almost by two orders of magnitude and provide a rich resource for experimental Acr discovery.

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Structure Reveals a Mechanism of CRISPR-RNA-Guided Nuclease Recruitment and Anti-CRISPR Viral Mimicry

Cited by 94 publications

References 80 publications

Diversity of molecular mechanisms used by anti-CRISPR proteins: the tip of an iceberg?

Diversity of molecular mechanisms used by anti-CRISPR proteins: the tip of an iceberg?

Types I and V Anti-CRISPR Proteins: From Phage Defense to Eukaryotic Synthetic Gene Circuits

Vast diversity of anti-CRISPR proteins predicted with a machine-learning approach

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