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CCOOMMMMEENNTTAARRYY COMMENTARY Mobile Genetic Elements 2:3, 145-148; May/June, 2012; © 2012 Landes Bioscience The flexible gene pool of Propionibacterium acnes Holger Brüggemann,* Hans B. Lomholt and Mogens Kilian Department of Biomedicine; Aarhus University; Aarhus, Denmark . e t Propionibacterium acnes is a Gram- at similar frequencies from skin sites of u positive bacterium that is intimately healthy individuals. b associated with humans. The nature Recent research has highlighted the ri and consequences of this symbiosis are population structure of P. acnes.6-8 It is a st poorly understood; it might comprise species with relatively little diversity with i d both mutualistic and parasitic proper- respect to the core genome. As judged from ties. Recent advances in distinguishing MLST analyses the species can be divided t o phylotypes of P. acnes have revealed that in three main lineages (termed types I, II n certain type I lineages are predominantly and III). Type I strains are further divided o associated with acne vulgaris. Genome into several subtypes (types I-1a, I-1b, I-26,8 D analyses revealed a highly conserved core or type IA, IA , IB, IC7), and each sub- 1 2 genome and the existence of island-like type consists of clonal complexes (CC). It . e genomic regions and possible mobile has been suggested and partly confirmed c genetic elements as part of the flex- that certain CCs of P. acnes are associated n ible gene pool. The analysis of clustered with acne vulgaris, e.g., CC18 strains (type e regularly interspaced short palindromic I-1a), whereas others are more often isolated i c repeats (CRISPR), found exclusively in from healthy individuals.6 There is some s type II P. acnes, recently revealed the circumstantial evidence indicating that o presence of CRISPR spacers that derived strains of individual CCs have distinguish- i B from mobile genetic elements. These ele- able inflammatory and host tissue inter- ments are present in a subset of P. acnes action properties.6,7,9,10 However, despite s type I lineages. Their significance for extensive genome sequencing the genetic e type-specific host-interacting properties basis for these unique properties is unclear. d and their contribution to pathogenicity One possible factor explaining phenotypic n Keywords: Propionibacterium acnes, acne is currently under investigation. differences between strains is the absence a vulgaris, mobile genetic element, tight and presence of genomic islands encod- L adherence, multilocus sequence typing, P. acnes is ubiquitously found on human ing CC-specific properties. Even within a 2 clustered regularly interspaced short pal- skin, and has been mainly regarded as a given CC, strains could vary with respect 1 indromic repeats (CRISPR) commensal. It is also part of the human to genomic island-encoding features, since 0 Submitted: 06/15/12 microbiota at other body sites, including the MLST-based schemes, according to 2 Revised: 06/21/12 the upper respiratory and gastrointestinal principles of population genetics, relies on © tracts. The organism is mostly known for genes from the core genome, thus neglect- Accepted: 06/21/12 its association with acne vulgaris, a skin ing the flexible gene pool. The horizontal http://dx.doi.org/ disorder affecting around 80% of humans acquisition of genomic islands could be a *Correspondence to: Holger Brüggemann; at some time in their life.1,2 In addition, relatively recent event in the evolution- Email: [email protected] P. acnes is isolated from a variety of other ary history of P. acnes, thus it might not disease sites, including foreign body infec- be reflected in the phylogenetic tree of Comment on: Brüggemann H, Lomholt HB, tions, sarcoidosis and prostate patholo- P. acnes. Tettelin H, Kilian M. CRISPR/cas loci of type II gies.3-5 However, so far clear-cut evidence We have identified a number of genomic Propionibacterium acnes confer immunity of causal relationships is lacking. Even a regions that harbor signs of horizontal against acquisition of mobile elements present in type I P. acnes. PLoS One 2012; 7:e34171; role of P. acnes in acne vulgaris could not acquisition, such as an aberrant G + C con- PMID:22479553; http://dx.doi.org/10.1371/journal. be unambiguously assigned, mainly due to tent and the presence of flanking insertion pone.0034171. the fact that the microorganism is isolated sequences (Fig. 1).10-12 The gene content of www.landesbioscience.com Mobile Genetic Elements 145 such encoding genes of the Gram-negative Aggregatibacter actinomycetemcomitans; the TAD system in A. actinomycetemcomitans was shown to be important for host colonization and pathogenesis.20 It was further analyzed in which strains these islands occur: whereas the BCN locus is found in a phylogeneti- cally distinct subtype of P. acnes (in CC3 strains), the TAD locus is present in a subset of diverse type I-1a strains (CC3, CC18, CC28 and CC31). The fact that . e all tested CC3 strains were positive for the t BCN locus indicates that this locus was u acquired by an ancestor strain of CC3. b The TAD locus most likely spread more ri recently, since it is not restricted to strains st of a specific phylogenetic clade. Moreover, i d the TAD locus was found also in other organisms, i.e., in the tentatively proposed t o species “Propionibacterium humerusii”21 n Figure 1. Island-like regions inserted into the core genome of P. acnes. Only islands larger than and in Clostridium leptum, a bacterium 10 kb are shown. The islands are named according to their gene content and/or most interest- o ing function: BCN, bacteriocin synthesis cluster; Hya, hyaluronidase; Thio, thiopeptide synthesis isolated from the human gastrointestinal D cluster; NRPS, non-ribosomal peptide synthetases; phage, cryptic prophage; sugar, sugar-uptake tract.22 The origin of this mobile genetic and -degrading systems; CRISPR, clustered regularly interspaced short palindromic repeats; TAD, element is so far unclear. It has a G + C . tight adherence system. The genomic insertion site of the TAD locus is not known, it might be an e content (63%) that is closer to propi- extrachromosomal element. For each island, the P. acnes type is given in which it most often oc- c onibacteria (ca. 60%) than to C. leptum curs (e.g., the NRPS island is present mainly in type I-1a strains, in particular of clonal complex (CC) n 28; it is occasionally present in I-2 strains). (50.2%). Interesting open questions are if e these mobile elements are still active and i c if their gene content contributes to strain- s genomic regions is enriched with fitness strains (Fig. 2). CRISPR/cas systems are specific properties, e.g., if TAD locus- o functions such as antimicrobial defense, present in a variety of bacteria and archaea positive strains have special or stronger i B stress resistance, adhesion and metabolic and have been identified as a prokaryotic adherence properties and if BCN locus– functions (e.g., import/export and degra- “adaptive immune” system; they provide positive strains are able to kill competi- s dation of sugars and oligopeptides). For acquired immunity against invasion of tors (either BCN locus-negative P. acnes e example, one island (designated “Thio” in mobile genetic elements, phages and plas- strains or other species present on the skin, d Fig. 1) harbors genes for the biosynthesis mids.14-18 The CRISPR regions of P. acnes e.g., Staphylococcus epidermidis). n of a thiopeptide similar to berninamycin of type II strains thus provide a record of The investigation of the CRISPR/cas a Streptomyces bernensis13; thiopeptides often the genome parasites that these organisms containing genomic region in P. acnes L act as potent inhibitors of protein synthesis have encountered. Like most CRISPR/cas also provides some hints about the evolu- 2 in Gram-positive bacteria. Another region systems, it contains sequence fragments tion of the species. Analysis of all avail- 1 (“NRPS” in Fig. 1) harbors a gene cluster (CRISPR spacers) of phages, more pre- able genomes of P. acnes and additional 0 for non-ribosomal peptide synthetases and cisely of P. acnes-specific siphoviruses.19 PCR-based analysis of our strain collec- 2 genes involved in the synthesis of a cyclic Surprisingly, sequence analyses of the tion revealed that there are type II strains © lipopeptide.10 The genomic islands depicted CRISPR spacers also revealed the presence that lack the entire CRISPR/cas harboring in Figure 1 are only present in a subset of of sequence fragments from two genomic locus (Fig. 2). In contrast, all tested type P. acnes strains; these strains often, but not islands that are found in other types of I and type III strains have gene fragments exclusively, belong to the same CC. P. acnes, in particular in type I strains. of the locus inserted in their core genome. Another island-like region was Apparently, these islands are mobile Type I strains harbor only a small locus recently investigated in more detail.12 It genetic elements. They are designated fragment, whereas type III strains pos- contains clustered regularly interspaced BCN (bacteriocin) and TAD (tight adher- sess larger locus remnants. As a possible short palindromic repeats (CRISPRs) ence) loci, respectively (Fig. 1). The BCN evolutionary scenario, type II strains have and CRISPR-associated genes (cas). The island contains genes related to streptoly- apparently acquired the locus by horizon- CRISPR/cas region is located on a 16 kb sin biosynthesis (sagBCD) of streptococcal tal gene transfer. Subsequently, the locus locus that is inserted into the core genome species. The TAD locus contains genes was partially deleted, giving rise to type III and exclusively present in type II P. acnes with homology to the tight adherence strains; further deletion events occurred, 146 Mobile Genetic Elements Volume 2 Issue 3 . e t u b Figure 2. The CRISPR/cas-containing locus in P. acnes. The 16 kb genomic region is present in most type II strains (such as in strain J139), inserted ri between hutH (encoding a histidine ammonia-lyase) and sir2 (encoding a Sir2 family protein). A few type II strains (e.g., HL050PA2) are CRISPR/cas t s locus-negative. Type III and type I strains possess fragments of this genomic island-like region inserted between hutH and sir2, indicative of deletion i events (marked by the double-headed arrow). d t 9. Nagy I, Pivarcsi A, Koreck A, Széll M, Urbán E, o resulting in type I strains. Alternatively, References Kemény L. Distinct strains of Propionibacterium n the partial CRISPR/cas locus dele- 1. 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