A New Group of Phage Anti-CRISPR Genes Inhibits the Type I-E CRISPR-Cas System of Pseudomonas aeruginosa

Pawluk, April; Bondy‐Denomy, Joseph; Cheung, Vivian H. W.; Maxwell, Karen L.; Davidson, Alan R.

doi:10.1128/mbio.00896-14

Cited by 240 publications

(262 citation statements)

References 22 publications

(47 reference statements)

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“…Alternatively, other molecular regulations employed by bacterial host or phage may be important for CRISPR-mediated resistance and may contribute to the infection outcome. Such regulation mechanisms potentially include transcriptional and/or translational regulation of CRISPR RNA and Cas genes and anti-CRISPR genes encoded by phages (Bondy-Denomy et al, 2013;Pawluk et al, 2014). Interactions between P. acnes and phages may also depend on additional mechanisms involved in phage binding, entry, replication or release.…”

Section: Phage Strainsmentioning

confidence: 99%

The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin

et al. 2015

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The viral population, including bacteriophages, is an important component of the human microbiota, yet is poorly understood. We aim to determine whether bacteriophages modulate the composition of the bacterial populations, thus potentially playing a role in health or disease. We investigated the diversity and host interactions of the bacteriophages of Propionibacterium acnes, a major human skin commensal implicated in acne pathogenesis. By sequencing 48 P. acnes phages isolated from acne patients and healthy individuals and by analyzing the P. acnes phage populations in healthy skin metagenomes, we revealed that P. acnes phage populations in the skin microbial community are often dominated by one strain. We also found phage strains shared among both related and unrelated individuals, suggesting that a pool of common phages exists in the human population and that transmission of phages may occur between individuals. To better understand the bacterium-phage interactions in the skin microbiota, we determined the outcomes of 74 genetically defined Propionibacterium strains challenged by 15 sequenced phages. Depending on the Propionibacterium lineage, phage infection can result in lysis, pseudolysogeny, or resistance. In type II P. acnes strains, we found that encoding matching clustered regularly interspaced short palindromic repeat spacers is insufficient to confer phage resistance. Overall, our findings suggest that the prey-predator relationship between bacteria and phages may have a role in modulating the composition of the microbiota. Our study also suggests that the microbiome structure of an individual may be an important factor in the design of phage-based therapy.

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Section: Phage Strainsmentioning

confidence: 99%

The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin

et al. 2015

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“…Having both RNA-and DNA-targeting systems could provide silencing of different types of viruses and other mobile genetic elements that for Pfu remain largely uncharacterized. Furthermore, we speculate that having multiple, and potentially redundant, CRISPR-Cas immune systems would be highly beneficial in the event that a virally encoded "anti-CRISPR" gene functions to inactivate a specific CRISPR-Cas type as has been observed for phages that infect Pseudomonas aeruginosa (Bondy-Denomy et al 2013;Pawluk et al 2014). The identification of the Csa and Cst crRNPs described in this study lays the foundation for a (pre-crRNA)…”

Section: Advantages Of Multiple Crispr-cas Systemsmentioning

confidence: 99%

Three CRISPR-Cas immune effector complexes coexist in Pyrococcus furiosus

Majumdar

Zhao

Pfister

et al. 2015

RNA

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CRISPR-Cas immune systems function to defend prokaryotes against potentially harmful mobile genetic elements including viruses and plasmids. The multiple CRISPR-Cas systems (Types I, II, and III) each target destruction of foreign nucleic acids via structurally and functionally diverse effector complexes (crRNPs). CRISPR-Cas effector complexes are comprised of CRISPR RNAs (crRNAs) that contain sequences homologous to the invading nucleic acids and Cas proteins specific to each immune system type. We have previously characterized a crRNP in Pyrococcus furiosus (Pfu) that contains Cmr (Type III-B) Cas proteins associated with one of two size classes of crRNAs and cleaves complementary target RNAs. Here, we have isolated and characterized two additional native Pfu crRNPs containing either Csa (Type I-A) or Cst (Type I-G) Cas proteins and distinct profiles of associated crRNAs. For each complex, the Cas proteins were identified by mass spectrometry and immunoblotting and the crRNAs by RNA sequencing and Northern blot analysis. The crRNAs associated with both the Csa and Cst complexes originate from all seven Pfu CRISPR loci and contain identical 5 ′ ends (8-nt repeat-derived 5 ′ tag sequences) but heterogeneous 3 ′ ends (containing variable amounts of downstream repeat sequences). These crRNA forms are distinct from Cmr-associated crRNAs, indicating different 3 ′ end processing pathways following primary cleavage of common pre-crRNAs. Like other previously characterized Type I CRISPR-Cas effector complexes, we predict that the newly identified Pfu Csa and Cst crRNPs each function to target invading DNA, adding an additional layer of protection beyond that afforded by the previously characterized RNA targeting Cmr complex.

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“…In contrast, the VIM-2 gene seems to be extremely stable in the main VIM clade, with only one representative lacking it. The diversity of accessory genes found among representatives of this high-risk clone may reflect loss of the clustered, regularly interspaced short palindromic repeats system (CRISPR-Cas), which acts as a bacterial defense system against foreign DNA, such as phage DNA and plasmids, as a result of phage-derived anti-CRISPR proteins, encoded by elements that may also be found in mobile genetic elements in P. aeruginosa (46). Multidrug-resistant isolates of Enterococcus faecalis and P. aeruginosa are associated with compromised CRISPR-cas genome defense systems, making them better able to acquire elements carrying antibiotic resistance genes (47,48); this would also explain the marked accessory genome diversity among the set.…”

Section: Discussionmentioning

confidence: 99%

High-Resolution Analysis by Whole-Genome Sequencing of an International Lineage (Sequence Type 111) of Pseudomonas aeruginosa Associated with Metallo-Carbapenemases in the United Kingdom

et al. 2015

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(1); one isolate had VIM-2 and IMP-18, and 7 carried no metallo-beta-lactamase (MBL) gene. Single nucleotide polymorphism analysis divided the isolates into distinct clusters; the NDM-1 isolate was an outlier, and the IMP isolates and 6/7 MBL-negative isolates clustered separately from the main set of 73 VIM-2 isolates. Within the VIM-2 set, there were at least 3 distinct clusters, including a tightly clustered set of isolates from 3 hospital laboratories consistent with an outbreak from a single introduction that was quickly brought under control and a much broader set dominated by isolates from a long-running outbreak in a London hospital likely seeded from an environmental source, requiring different control measures; isolates from 7 other hospital laboratories in London and southeast England were also included. Bayesian evolutionary analysis indicated that all the isolates shared a common ancestor dating back ϳ50 years (1960s), with the main VIM-2 set separating approximately 20 to 30 years ago. Accessory gene profiling revealed blocks of genes associated with particular clusters, with some having high similarity (>95%) to bacteriophage genes. WGS of widely found international lineages such as ST-111 provides the necessary resolution to inform epidemiological investigations and intervention policies. Concern over the increasing prevalence in hospitals of multiresistant bacteria, especially those that are resistant to carbapenem antibiotics, has prompted the use of typing methods that easily allow interlaboratory comparison of isolates. As a result, it has become clear that (i) high-risk clones of various Gram-negative bacteria, including Pseudomonas aeruginosa, can be found in many disparate locations, often with no obvious epidemiological links between the affected patients, and (ii) many of these clones are adept at acquiring various antibiotic resistance determinants (1, 2). These clones are commonly referred to as international lineages since they have been described in many countries across the globe. Epidemiological investigations of apparent outbreaks and interhospital spread of such lineages are confounded by the fact that they are so widely found; microbiological evidence of the same type must be considered alongside information about patient location and movement, for example, and patient location and movement information should be sufficiently robust to allow firm conclusions to be drawn. Greater resolution than that provided by conventional molecular typing methods, such as multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and variable-number tandem repeat (VNTR) analysis, is essential if we are to infer or discount potential transmission pathways with confidence. Understanding these pathways will be critical for precise public health interventions to contain these highrisk clones effectively. Whole-genome sequencing (WGS) can provide this resolution and has been used to investigate outbreaks of Klebsiella pneumoniae ST-258 producing K. pneumoniae carbapenemase (KPC) enz...

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A New Group of Phage Anti-CRISPR Genes Inhibits the Type I-E CRISPR-Cas System of Pseudomonas aeruginosa

Cited by 240 publications

References 22 publications

The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin

The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin

Three CRISPR-Cas immune effector complexes coexist in Pyrococcus furiosus

High-Resolution Analysis by Whole-Genome Sequencing of an International Lineage (Sequence Type 111) of Pseudomonas aeruginosa Associated with Metallo-Carbapenemases in the United Kingdom

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