Critical Anti-CRISPR Locus Repression by a Bi-functional Cas9 Inhibitor

Osuna, Beatriz A.; Karambelkar, Shweta; Mahendra, Caroline; Sarbach, Anne; Johnson, Matthew C.; Kilcher, Samuel; Bondy‐Denomy, Joseph

doi:10.1016/j.chom.2020.04.002

Cited by 53 publications

(45 citation statements)

References 32 publications

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“…Although no known aca genes form part of the P. aeruginosa acrIF23-24 locus, the C-terminus of AcrIF24 contains an HTH domain, implying a possible dual Acr-Aca function (Figure 4d, Supplementary Figure S8). A similar binary role was previously shown for AcrIIA1 (Osuna, Karambelkar, Mahendra, Sarbach, et al, 2020) and AcrIIA13-15 (Watters et al, 2020), suggesting that self-regulation by Acrs may be widespread. Our results reveal two additional I-F inhibitors associated with genes encoding proteins containing different HTH domains.…”

Section: Identification Of a Previously Undescribed Aca And Two Type supporting

confidence: 82%

Discovery of multiple anti-CRISPRs uncovers anti-defense gene clustering in mobile genetic elements

Pinilla‐Redondo

Shehreen

Marino

et al. 2020

Preprint

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Many prokaryotes employ CRISPR-Cas systems to combat invading mobile genetic elements (MGEs). In response, some MGEs have evolved Anti-CRISPR (Acr) proteins to bypass this immunity, yet the diversity, distribution and spectrum of activity of this immune evasion strategy remain largely unknown. Here, we uncover 11 new type I anti-CRISPR genes encoded on numerous chromosomal and extrachromosomal mobile genetic elements within Enterobacteriaceae and Pseudomonas. Candidate genes were identified adjacent to anti-CRISPR associated gene 5 (aca5) and assayed against a panel of six type I systems: I-F (Pseudomonas, Pectobacterium, and Serratia), I-E (Pseudomonas and Serratia), and I-C (Pseudomonas), revealing the type I-F and/or I-E acr genes and a new aca (aca9). We find that acr genes not only associate with other acr genes, but also with inhibitors of distinct bacterial defense systems. These genomic regions appear to be "anti-defense islands", reminiscent of the clustered arrangement of "defense islands" in prokaryotic genomes. Our findings expand on the diversity of CRISPR-Cas inhibitors and reveal the potential exploitation of acr loci neighborhoods for identifying new anti-defense systems.

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Section: Identification Of a Previously Undescribed Aca And Two Type supporting

confidence: 82%

Discovery of multiple anti-CRISPRs uncovers anti-defense gene clustering in mobile genetic elements

Pinilla‐Redondo

Shehreen

Marino

et al. 2020

Preprint

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“…[77] Importantly, AcrIIA1 and its homologs promote induction through the HTH domain, independent of Cas9 inhibition, demonstrating that this bifunctional protein connects CRISPR-Cas regulation with the lysislysogeny switch. [78] The above data support the central role of the lysis-lysogeny decision of the prophage in governing the activity of CRISPR-Cas in the cell through the Aca protein. During lysogeny, Aca is principally located at operator sites within its cognate promoter in the prophage genome and inhibits Acr production [78] (Figure 2E).…”

Section: Anti-crispr Proteins Couple Crispr-cas With the Lysis-lysogesupporting

confidence: 59%

Phage lysis‐lysogeny switches and programmed cell death: Danse macabre

Benler

Koonin

2020

BioEssays

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Exploration of immune systems in prokaryotes, such as restriction-modification or CRISPR-Cas, shows that both innate and adaptive systems possess programmed cell death (PCD) potential. The key outstanding question is how the immune systems sense and "predict" infection outcomes to "decide" whether to fight the pathogen or induce PCD. There is a striking parallel between this life-or-death decision faced by the cell and the decision by temperate viruses to protect or kill their hosts, epitomized by the lysis-lysogeny switch of bacteriophage Lambda. Immune systems and temperate phages sense the same molecular inputs, primarily, DNA damage, that determine whether the cell lives or dies. Because temperate (pro)phages are themselves components of prokaryotic genomes, their shared "interests" with the hosts result in coregulation of the lysis-lysogeny switch and immune systems that jointly provide the cell with the decision machinery to probe and predict infection outcomes, answering the life-or-death question.

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“…This is also the case for acrI genes carried by Pseudomonas prophages, which are able to inhibit the type I CRISPR response (Bondy-Denomy et al, 2013). Following robust transcription at the onset of phage infection, acr genes are repressed by anti-CRISPR associated (Aca) transcription factors to prevent the deleterious effects of the acr high transcription on the downstream phage genes (Osuna et al, 2020;Stanley et al, 2019). The acr region of ΦAP1.1 contains two genes, orf3 and orf4, which are transcribed during lysogeny.…”

Section: Discussionmentioning

confidence: 97%

Integration of prophages into CRISPR loci remodels viral immunity inStreptococcus pyogenes

Varble

Campisi

Euler

et al. 2020

Preprint

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SummaryCRISPR loci are composed of short DNA repeats separated by sequences that match the genomes of phages and plasmids, known as spacers. Spacers are transcribed and processed to generate RNA guides used by CRISPR-associated nucleases to recognize and destroy the complementary nucleic acids of invaders. To counteract this defense, phages can produce small proteins that inhibit these nucleases. Here we demonstrate that the ΦAP1.1 temperate phage utilizes an alternate approach to antagonize the type II-A CRISPR response in Streptococcus pyogenes. Immediately after infection this phage expresses a canonical anti-CRISPR, AcrIIA23 that prevents Cas9 function, allowing ΦAP1.1 to integrate into the direct repeats of the CRISPR locus and neutralizing immunity. However, acrIIA23 is not transcribed during lysogeny and phage integration/excision cycles can result in the deletion and/or transfer of spacers, enabling a complex modulation of the type II-A CRISPR immune response.

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Critical Anti-CRISPR Locus Repression by a Bi-functional Cas9 Inhibitor

Cited by 53 publications

References 32 publications

Discovery of multiple anti-CRISPRs uncovers anti-defense gene clustering in mobile genetic elements

Discovery of multiple anti-CRISPRs uncovers anti-defense gene clustering in mobile genetic elements

Phage lysis‐lysogeny switches and programmed cell death: Danse macabre

Integration of prophages into CRISPR loci remodels viral immunity inStreptococcus pyogenes

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