Incomplete prophage tolerance by type III-A CRISPR-Cas systems reduces the fitness of lysogenic hosts

Goldberg, Gregory W.; McMillan, Elizabeth A.; Varble, Andrew; Modell, Joshua W.; Samai, Poulami; Jiang, Wenyan; Marraffini, Luciano A.

doi:10.1038/s41467-017-02557-2

Cited by 38 publications

(37 citation statements)

References 79 publications

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“…Similarly, in Listeria monocytogenes , a small-colony phenotype was observed following transformation of a CRISPR-targeted plasmid ( 46 ). Furthermore, tolerance of transcriptionally repressed targets has been directly demonstrated in a type III-A CRISPR-Cas system in Staphylococcus aureus , which only efficiently cleaves target DNA that is transcribed ( 47 ). This suggests that CRISPR-tolerant phenotypes occur in organisms other than E. faecalis .…”

Section: Discussionmentioning

confidence: 99%

An Attenuated CRISPR-Cas System in Enterococcus faecalis Permits DNA Acquisition

Hullahalli

Rodrigues

Nguyen

et al. 2018

mBio

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Antibiotic-resistant bacteria are critical public health concerns. Among the prime causative factors for the spread of antibiotic resistance is horizontal gene transfer (HGT). A useful model organism for investigating the relationship between HGT and antibiotic resistance is the opportunistic pathogen Enterococcus faecalis, since the species possesses highly conjugative plasmids that readily disseminate antibiotic resistance genes and virulence factors in nature. Unlike many commensal E. faecalis strains, the genomes of multidrug-resistant (MDR) E. faecalis clinical isolates are enriched for mobile genetic elements (MGEs) and lack clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) genome defense systems. CRISPR-Cas systems cleave foreign DNA in a programmable, sequence-specific manner and are disadvantageous for MGE-derived genome expansion. An unexplored facet of CRISPR biology in E. faecalis is that MGEs that are targeted by native CRISPR-Cas systems can be maintained transiently. Here, we investigate the basis for this “CRISPR tolerance.” We observe that E. faecalis can maintain self-targeting constructs that direct Cas9 to cleave the chromosome, but at a fitness cost. Interestingly, DNA repair genes were not upregulated during self-targeting, but integrated prophages were strongly induced. We determined that low cas9 expression contributes to this transient nonlethality and used this knowledge to develop a robust CRISPR-assisted genome-editing scheme. Our results suggest that E. faecalis has maximized the potential for DNA acquisition by attenuating its CRISPR machinery, thereby facilitating the acquisition of potentially beneficial MGEs that may otherwise be restricted by genome defense.

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Section: Discussionmentioning

confidence: 99%

An Attenuated CRISPR-Cas System in Enterococcus faecalis Permits DNA Acquisition

Hullahalli

Rodrigues

Nguyen

et al. 2018

mBio

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“…One of the postulated explanations is that type III systems enable bacteria to distinguish between lytic and lysogenic phage infection. Tolerating lysogenic infections while still being able to neutralize lytic infections would provide immunity without blocking the influx of potentially beneficial genes via horizontal gene transfer [45].…”

Section: Figurementioning

confidence: 99%

RNA-Targeting CRISPR–Cas Systems and Their Applications

Burmistrz

Krakowski

Krawczyk‐Balska

2020

IJMS

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Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)–CRISPR-associated (Cas) systems have revolutionized modern molecular biology. Numerous types of these systems have been discovered to date. Many CRISPR–Cas systems have been used as a backbone for the development of potent research tools, with Cas9 being the most widespread. While most of the utilized systems are DNA-targeting, recently more and more attention is being gained by those that target RNA. Their ability to specifically recognize a given RNA sequence in an easily programmable way makes them ideal candidates for developing new research tools. In this review we summarize current knowledge on CRISPR–Cas systems which have been shown to target RNA molecules, that is type III (Csm/Cmr), type VI (Cas13), and type II (Cas9). We also present a list of available technologies based on these systems.

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“…Acquisition of perfectly matching spacers in lysogens amplified these fitness costs, since this programs the immune system to attack the prophage inside the bacterial genome even more strongly. Such self-targeting by CRISPR-Cas is well known to be highly toxic (92)(93)(94)(95)(96)(97)(98)(99), even for Type III CRISPR-Cas systems that target only transcriptionally active DNA (100,101). Finally, a recent and exciting study showed that R. intestinalis in the mouse gut can evolve high levels of CRISPR-based immunity when one of its active prophages evolves to become hypervirulent (i.e.…”

Section: -Temperate Phagementioning

confidence: 99%

How important is CRISPR-Cas for protecting natural populations of bacteria against infections by mobile genetic elements?

Westra

Levin

2020

Preprint

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Articles on CRISPR commonly open with some variant of the phrase 'these short-palindromic repeats and their associated endonucleases (Cas) are an adaptive immune system that exists to protect bacteria and archaea from viruses and infections with other deleterious ("badass") DNAs'.There is an abundance of genomic data consistent with the hypothesis that CRISPR plays this role in natural populations of bacteria and archaea, and experimental demonstrations with a few species of bacteria and their phage and plasmids show that CRISPR-Cas systems can play this role in vitro.Not at all clear are the ubiquity, magnitude and nature of the contribution of CRISPR-Cas systems to the ecology and evolution of natural populations of microbes, and the strength of selection mediated by different types of phage and plasmids to the evolution and maintenance of CRISPR-Cas systems. In this perspective, with the aid of heuristic mathematical-computer simulation models, we explore the a priori conditions under which exposure to lytic and temperate phage and conjugative plasmids will select for and maintain CRISPR-Cas systems in populations of bacteria and archaea. We review the existing literature addressing these ecological and evolutionary questions and highlight the experimental and other evidence needed to fully understand the conditions responsible for the evolution and maintenance of CRISPR-Cas systems and the contribution of these systems to the ecology and evolution of bacteria, archaea and the mobile genetic elements that infect them. SignificanceThere is no question about the importance and utility of CRISPR-Cas for editing and modifying genomes. On the other hand, the mechanisms responsible for the evolution and maintenance of these systems and the magnitude of their importance to the ecology and evolution of bacteria, archaea and their infectious DNAs, are not at all clear. With the aid of heuristic mathematical/simulation models and reviews of the existing literature, we raise questions that have to be answered to elucidate the contribution of selection -mediated by phage and plasmids -to the evolution and maintenance of this adaptive immune system and its consequences for the ecology and evolution of prokaryotes and their viruses and plasmids.

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Incomplete prophage tolerance by type III-A CRISPR-Cas systems reduces the fitness of lysogenic hosts

Cited by 38 publications

References 79 publications

An Attenuated CRISPR-Cas System in Enterococcus faecalis Permits DNA Acquisition

An Attenuated CRISPR-Cas System in Enterococcus faecalis Permits DNA Acquisition

RNA-Targeting CRISPR–Cas Systems and Their Applications

How important is CRISPR-Cas for protecting natural populations of bacteria against infections by mobile genetic elements?

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