CRISPR-Cas, DNA Supercoiling, and Nucleoid-Associated Proteins

Dorman, Charles J.; Bhriain, Niamh Ní

doi:10.1016/j.tim.2019.08.004

Cited by 26 publications

(18 citation statements)

References 92 publications

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“…MGE-encoded H-NS-like proteins are often considered "stealth proteins" that tamper with host gene expression (Shintani, Suzuki-Minakuchi and Nojiri, 2015;Vial and Hommais, 2019). Given the H-NS-mediated silencing of CRISPR-Cas adaptive immunity in E. coli (Pul et al, 2010;Westra et al, 2010), the lateral acquisition of H-NS homologs may help MGEs evade adaptive immunity, as previously proposed for certain plasmids (Dorman, 2014;Dorman and Ní Bhriain, 2020) and phages (Skennerton et al, 2011). Finally, we also found close ties between type II acrs (e.g.…”

Section: Acrs Cluster With Anti-rm and Other Anti-defense Genessupporting

confidence: 81%

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: Acrs Cluster With Anti-rm and Other Anti-defense Genessupporting

confidence: 81%

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

Pinilla‐Redondo

Shehreen

Marino

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…MGE-encoded H-NS-like proteins are often considered “stealth proteins” that tamper with host gene expression 41 , 42 . Given the H-NS-mediated silencing of CRISPR–Cas adaptive immunity in E. coli 43 , 44 , the lateral acquisition of H-NS homologs may help MGEs evade adaptive immunity, as previously proposed for certain plasmids 45 , 46 and phages 47 . Finally, we also found close ties between type II acrs (e.g., AcrIIA9 and AcrIIA7) and anti-RM components in other types of MGEs, including a conjugative transposon and a putative phage (Fig.…”

Section: Resultsmentioning

confidence: 73%

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

et al. 2020

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Many prokaryotes employ CRISPR–Cas systems to combat invading mobile genetic elements (MGEs). In response, some MGEs have developed strategies to bypass immunity, including anti-CRISPR (Acr) proteins; yet the diversity, distribution and spectrum of activity of this immune evasion strategy remain largely unknown. Here, we report the discovery of new Acrs by assaying candidate genes adjacent to a conserved Acr-associated (Aca) gene, aca5, against a panel of six type I systems: I–F (Pseudomonas, Pectobacterium, and Serratia), I–E (Pseudomonas and Serratia), and I–C (Pseudomonas). We uncover 11 type I–F and/or I–E anti-CRISPR genes encoded on chromosomal and extrachromosomal MGEs within Enterobacteriaceae and Pseudomonas, and an additional Aca (aca9). The acr genes not only associate with other acr genes, but also with genes encoding inhibitors of distinct bacterial defense systems. Thus, our findings highlight the potential exploitation of acr loci neighborhoods for the identification of previously undescribed anti-defense systems.

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“…For example, it was shown that the DNA polymerase I is necessary for both na ve and primed adaptation (pre sumably to fill single stranded repeats that arise during spacers embedding) [68]. Dorman and Bhriain hypothe sized that the negative supercoiling could alter various stages of the CRISPR proteins interaction with DNA, including adaptation, expression of cas genes and CRISPR loci, and, in fact, interference [65].…”

Section: Crispr Cas Adaptive Immunity Systemsmentioning

confidence: 99%

Microbial Arsenal of Antiviral Defenses. Part II

Musharova

Severinov

2021

Biochemistry Moscow

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Bacteriophages or phages are viruses that infect bacterial cells (for the scope of this review we will also consider viruses that infect Archaea). The constant threat of phage infection is a major force that shapes evolution of microbial genomes. To withstand infection, bacteria had evolved numerous strategies to avoid recognition by phages or to directly interfere with phage propagation inside the cell. Classical molecular biology and genetic engineering had been deeply intertwined with the study of phages and host defenses. Nowadays, owing to the rise of phage therapy, broad application of CRISPR-Cas technologies, and development of bioinformatics approaches that facilitate discovery of new systems, phage biology experiences a revival. This review describes variety of strategies employed by microbes to counter phage infection. In the first part defense associated with cell surface, roles of small molecules, and innate immunity systems relying on DNA modification were discussed. The second part focuses on adaptive immunity systems, abortive infection mechanisms, defenses associated with mobile genetic elements, and novel systems discovered in recent years through metagenomic mining.

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CRISPR-Cas, DNA Supercoiling, and Nucleoid-Associated Proteins

Cited by 26 publications

References 92 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

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

Microbial Arsenal of Antiviral Defenses. Part II

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