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CRISPR/cas loci of type II Propionibacterium acnes confer immunity against acquisition of mobile elements present in type I P. acnes.

Brüggemann H, Lomholt HB, Tettelin H, Kilian M - PLoS ONE (2012)

Bottom Line: The population structure of this species shows three main lineages (I-III).While type I strains are mainly associated with sebaceous follicles of human skin and inflammatory acne, types II and III strains are more often associated with deep tissue infections.Sequence analyses of the CRISPR spacers revealed that the system confers immunity to P. acnes-specific phages and to two mobile genetic elements.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedicine, Aarhus University, Aarhus, Denmark. brueggemann@microbiology.au.dk

ABSTRACT
Propionibacterium acnes is a skin commensal that occasionally acts as an opportunistic pathogen. The population structure of this species shows three main lineages (I-III). While type I strains are mainly associated with sebaceous follicles of human skin and inflammatory acne, types II and III strains are more often associated with deep tissue infections. We investigated the occurrence and distribution of the clustered regularly interspaced short palindromic repeats (CRISPR) in P. acnes, assessed their immunological memory, and addressed the question if such a system could account for type-specific properties of the species. A collection of 108 clinical isolates covering all known phylotypes of P. acnes was screened for the existence of CRISPR/cas loci. We found that CRISPR loci are restricted to type II P. acnes strains. Sequence analyses of the CRISPR spacers revealed that the system confers immunity to P. acnes-specific phages and to two mobile genetic elements. These elements are found almost exclusively in type I P. acnes strains. Genome sequencing of a type I P. acnes isolate revealed that one element, 54 kb in size, encodes a putative secretion/tight adherence (TAD) system. Thus, CRISPR/cas loci in P. acnes recorded the exposure of type II strains to mobile genetic elements of type I strains. The CRISPR/cas locus is deleted in type I strains, which conceivably accounts for their ability to horizontally acquire fitness or virulence traits and might indicate that type I strains constitute a younger subpopulation of P. acnes.

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The CRISPR/cas-harboring locus is a genomic island in P. acnes.(A) A 16 kb gene cluster containing the CRISPR/cas locus is inserted as an island-like region in type II P. acnes genomes (strain J139) between two genes of the core genome, encoding HutH (histidine ammonia-lyase) and a Sir2 family protein (highlighted in yellow). Some type II strains (shown here: HL050PA2 [GenBank:ADYC00000000]) have no insertion at this genomic location. In contrast, all tested type I strains have cas gene fragments (cas2 and the 3′-end of cas1) inserted at this site (shown here: KPA), indicating that a functional CRISPR/Cas system was lost in the evolutionary history of type I strains. Red, >97% nucleotide sequence identity. (B) Deletion of the CRISPR locus and downstream genes in KPA occurred within the first CRISPR repeat sequence (red).
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pone-0034171-g005: The CRISPR/cas-harboring locus is a genomic island in P. acnes.(A) A 16 kb gene cluster containing the CRISPR/cas locus is inserted as an island-like region in type II P. acnes genomes (strain J139) between two genes of the core genome, encoding HutH (histidine ammonia-lyase) and a Sir2 family protein (highlighted in yellow). Some type II strains (shown here: HL050PA2 [GenBank:ADYC00000000]) have no insertion at this genomic location. In contrast, all tested type I strains have cas gene fragments (cas2 and the 3′-end of cas1) inserted at this site (shown here: KPA), indicating that a functional CRISPR/Cas system was lost in the evolutionary history of type I strains. Red, >97% nucleotide sequence identity. (B) Deletion of the CRISPR locus and downstream genes in KPA occurred within the first CRISPR repeat sequence (red).

Mentions: In all analyzed CRISPR/cas-positive P. acnes genomes the CRISPR/cas locus is located on a 16 kb genomic region, which is inserted between genes encoding a histidine ammonia-lyase (HutH = PPA2170 in genome KPA) and a Sir2 family protein (PPA2172) (Figure 5A). The 16 kb CRISPR/cas-containing genomic region harbors additional genes downstream of the CRISPR locus, including a putative restriction-modification system. This indicates that resistance mechanisms to control incoming DNA are apparently clustered and have likely been horizontally acquired and inserted into the core genome, as it was suggested for CRISPR/cas loci in other bacteria [29]–[31]. Interestingly, there is a genetic fragment in almost all CRISPR/cas-negative genomes (i.e. type I strains), composed of cas2 and the 3′-end of cas1 (PPA2171 in the KPA genome) (Figure 5A). These cas gene fragments of type I strains are identical to the corresponding genes in the complete CRISPR/cas loci of type II strains, indicating that the CRISPR/cas gene cluster was partially deleted in type I strains. Two deletion events could have taken place, deleting the cas genes located on a 8.4 kb fragment (cas3-casA-casB-casC-casD-casE and the 5′-end of cas1) and the downstream region of cas2 (7 kb fragment containing CRISPR and downstream genes). A hybrid-like pattern of the CRISPR/cas-containing 16 kb locus is supported by the analysis of the respective locus in Propionibacterium avidum (see below). Looking closer at the second site of deletion, it occurred within the first copy of the CRISPR repeat (Figure 5B), indicating that the repeats are associated with genomic instability. PCR analyses revealed that a few strains (HL050PA2, 34.1.A1, 39.3.R1 and CCUG33206) did not contain cas gene fragments; these were all type II strains (Figure 5A). Among the type II strains one strain (CCUG38203, ST 53) was exceptional, since it contained cas1/cas2 gene fragments as seen in type I strains.


CRISPR/cas loci of type II Propionibacterium acnes confer immunity against acquisition of mobile elements present in type I P. acnes.

Brüggemann H, Lomholt HB, Tettelin H, Kilian M - PLoS ONE (2012)

The CRISPR/cas-harboring locus is a genomic island in P. acnes.(A) A 16 kb gene cluster containing the CRISPR/cas locus is inserted as an island-like region in type II P. acnes genomes (strain J139) between two genes of the core genome, encoding HutH (histidine ammonia-lyase) and a Sir2 family protein (highlighted in yellow). Some type II strains (shown here: HL050PA2 [GenBank:ADYC00000000]) have no insertion at this genomic location. In contrast, all tested type I strains have cas gene fragments (cas2 and the 3′-end of cas1) inserted at this site (shown here: KPA), indicating that a functional CRISPR/Cas system was lost in the evolutionary history of type I strains. Red, >97% nucleotide sequence identity. (B) Deletion of the CRISPR locus and downstream genes in KPA occurred within the first CRISPR repeat sequence (red).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3316620&req=5

pone-0034171-g005: The CRISPR/cas-harboring locus is a genomic island in P. acnes.(A) A 16 kb gene cluster containing the CRISPR/cas locus is inserted as an island-like region in type II P. acnes genomes (strain J139) between two genes of the core genome, encoding HutH (histidine ammonia-lyase) and a Sir2 family protein (highlighted in yellow). Some type II strains (shown here: HL050PA2 [GenBank:ADYC00000000]) have no insertion at this genomic location. In contrast, all tested type I strains have cas gene fragments (cas2 and the 3′-end of cas1) inserted at this site (shown here: KPA), indicating that a functional CRISPR/Cas system was lost in the evolutionary history of type I strains. Red, >97% nucleotide sequence identity. (B) Deletion of the CRISPR locus and downstream genes in KPA occurred within the first CRISPR repeat sequence (red).
Mentions: In all analyzed CRISPR/cas-positive P. acnes genomes the CRISPR/cas locus is located on a 16 kb genomic region, which is inserted between genes encoding a histidine ammonia-lyase (HutH = PPA2170 in genome KPA) and a Sir2 family protein (PPA2172) (Figure 5A). The 16 kb CRISPR/cas-containing genomic region harbors additional genes downstream of the CRISPR locus, including a putative restriction-modification system. This indicates that resistance mechanisms to control incoming DNA are apparently clustered and have likely been horizontally acquired and inserted into the core genome, as it was suggested for CRISPR/cas loci in other bacteria [29]–[31]. Interestingly, there is a genetic fragment in almost all CRISPR/cas-negative genomes (i.e. type I strains), composed of cas2 and the 3′-end of cas1 (PPA2171 in the KPA genome) (Figure 5A). These cas gene fragments of type I strains are identical to the corresponding genes in the complete CRISPR/cas loci of type II strains, indicating that the CRISPR/cas gene cluster was partially deleted in type I strains. Two deletion events could have taken place, deleting the cas genes located on a 8.4 kb fragment (cas3-casA-casB-casC-casD-casE and the 5′-end of cas1) and the downstream region of cas2 (7 kb fragment containing CRISPR and downstream genes). A hybrid-like pattern of the CRISPR/cas-containing 16 kb locus is supported by the analysis of the respective locus in Propionibacterium avidum (see below). Looking closer at the second site of deletion, it occurred within the first copy of the CRISPR repeat (Figure 5B), indicating that the repeats are associated with genomic instability. PCR analyses revealed that a few strains (HL050PA2, 34.1.A1, 39.3.R1 and CCUG33206) did not contain cas gene fragments; these were all type II strains (Figure 5A). Among the type II strains one strain (CCUG38203, ST 53) was exceptional, since it contained cas1/cas2 gene fragments as seen in type I strains.

Bottom Line: The population structure of this species shows three main lineages (I-III).While type I strains are mainly associated with sebaceous follicles of human skin and inflammatory acne, types II and III strains are more often associated with deep tissue infections.Sequence analyses of the CRISPR spacers revealed that the system confers immunity to P. acnes-specific phages and to two mobile genetic elements.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedicine, Aarhus University, Aarhus, Denmark. brueggemann@microbiology.au.dk

ABSTRACT
Propionibacterium acnes is a skin commensal that occasionally acts as an opportunistic pathogen. The population structure of this species shows three main lineages (I-III). While type I strains are mainly associated with sebaceous follicles of human skin and inflammatory acne, types II and III strains are more often associated with deep tissue infections. We investigated the occurrence and distribution of the clustered regularly interspaced short palindromic repeats (CRISPR) in P. acnes, assessed their immunological memory, and addressed the question if such a system could account for type-specific properties of the species. A collection of 108 clinical isolates covering all known phylotypes of P. acnes was screened for the existence of CRISPR/cas loci. We found that CRISPR loci are restricted to type II P. acnes strains. Sequence analyses of the CRISPR spacers revealed that the system confers immunity to P. acnes-specific phages and to two mobile genetic elements. These elements are found almost exclusively in type I P. acnes strains. Genome sequencing of a type I P. acnes isolate revealed that one element, 54 kb in size, encodes a putative secretion/tight adherence (TAD) system. Thus, CRISPR/cas loci in P. acnes recorded the exposure of type II strains to mobile genetic elements of type I strains. The CRISPR/cas locus is deleted in type I strains, which conceivably accounts for their ability to horizontally acquire fitness or virulence traits and might indicate that type I strains constitute a younger subpopulation of P. acnes.

Show MeSH
Related in: MedlinePlus