Comparative genomics and transcriptomics of Propionibacterium acnes

Abstract

The anaerobic gram-positive bacterium Propionibacterium acnes is a human skin commensal that is occasionally associated with inflammatory diseases. Recent work has indicated that evolutionary distinct lineages of P. acnes play etiologic roles in disease while others are associated with maintenance of skin homeostasis. To shed light on the molecular basis for differential strain properties, we carried out genomic and transcriptomic analysis of distinct P. acnes strains. We sequenced the genome of the P. acnes strain 266, a type I-1a strain. Comparative genome analysis of strain 266 and four other P. acnes strains revealed that overall genome plasticity is relatively low; however, a number of island-like genomic regions, encoding a variety of putative virulence-associated and fitness traits differ between phylotypes, as judged from PCR analysis of a collection of P. acnes strains. Comparative transcriptome analysis of strains KPA171202 (type I-2) and 266 during exponential growth revealed inter-strain differences in gene expression of transport systems and metabolic pathways. In addition, transcript levels of genes encoding possible virulence factors such as dermatan-sulphate adhesin, polyunsaturated fatty acid isomerase, iron acquisition protein HtaA and lipase GehA were upregulated in strain 266. We investigated differential gene expression during exponential and stationary growth phases. Genes encoding components of the energy-conserving respiratory chain as well as secreted and virulence-associated factors were transcribed during the exponential phase, while the stationary growth phase was characterized by upregulation of genes involved in stress responses and amino acid metabolism. Our data highlight the genomic basis for strain diversity and identify, for the first time, the actively transcribed part of the genome, underlining the important role growth status plays in the inflammation-inducing activity of P. acnes. We argue that the disease-causing potential of different P. acnes strains is not only determined by the phylotype-specific genome content but also by variable gene expression.

Figure 1. Comparison of five P. acnes genomes.

(A) All CDS of the reference genome of strain KPA171202 are shown in the two outer rings (cyan, depending on strand location). The subsequent rings depict Bi-Blast results for each CDS of the reference genome in the following genomes (exterior to interior): 266, SK187, SK137, J139 and P. freudenreichii (the unfinished genome of P. acnes J165 was not taken into consideration due to insufficient quality of CDS prediction). The innermost ring depicts the GC content variation from the mean (60%) of the reference genome. CDS of the KPA genome which have a Bi-Blast hit with > = 25% protein sequence identity in the subject genome are depicted in grey, those with a protein sequence identity <25% are shown in red. (B) The genome of strain 266 was taken as the reference genome (two outer rings in green). The subsequent rings, depicting Bi-Blast hits of each CDS of the reference genome are (exterior to interior): KPA, SK187, SK137, J139 and P. freudenreichii. The numbers 1 to 9 represent main genomic islands identified in the reference genomes (see Table S1).

Figure 2. Transcription of the four large island-like genomic regions of P. acnes.

The transcriptional profiles of the main four genomic islands are shown. The upper panels (A) represents the expression profiles in strain KPA compared to strain 266. The yellow bar depicts the genomic regions that are absent in strain 266 (islands 1, 3 and 4). The first profile depicts the log₂ intensities (brown, KPA; green, 266), and the second profile the log₂ ratios (blue, higher in KPA; red, higher in 266). Note that the predicted non-ribosomal peptide biosynthesis gene cluster (PPA1284-1292, green bar) of island 2 is upregulated in strain KPA, albeit present also in strain 266. The lower panel (B) depicts the growth phase-dependent transcription of the genomic regions in strain KPA. Again, the first profile depicts the log₂ intensities (lilac, exponential phase; cyan, stationary phase), and the second profile the log₂ ratios (blue, higher in exponential phase; red, higher in stationary phase). Note that the predicted thiopeptide synthesis gene cluster (PPA0859-PPA0866, orange bar) of island 1 is strongly transcribed and upregulated in the exponential growth phase of KPA. The black arrows mark the boundaries of each island-like genomic region.

Figure 3. Growth phase-dependent utilization of amino acid-metabolizing pathways in P. acnes.

The schematic representation includes amino acid-metabolizing enzymes whose genes were strongly deregulated between the exponential (green) and stationary (yellow) growth phases. The arginine deiminase pathway (PPA0582-0585) is an exponential phase trait, whereas the pathways for the interconversion of glutamate to ornithine (PPA1347-1350) and of glutamine/aspartate to dihydroorotate (PPA0997-1000) are stationary growth phase traits. Please note also the connected fumarate-producing reactions selectively upregulated in strain 266 (in grey). Fumarate respiration is a major source of energy conservation in P. acnes; most likely, reducing equivalents are delivered by the NADH dehydrogenase (PPA1922-1936). The enzyme-attributed numbers correspond to the gene nomenclature of the KPA genome. For simplicity reasons inorganic and organic phosphate cosubstrates were omitted from the scheme.

Figure 4. The expression profile of the arginine deiminase gene cluster of P. acnes.

The most highly deregulated genes in the entire P. acnes transcriptome are shown here. The gene cluster PPA0582-0585 encodes the arginine deiminase pathway, and PPA0580/PPA0581 encode stress response genes. Note the opposing expression of PPA0580/0581 and PPA0582-0585. The upper panels (A) represents the expression profiles in strain KPA compared to strain 266. The first profile depicts the log₂ intensities (brown, KPA; green, 266), and the second profile the log₂ ratios (blue, higher in KPA; red, higher in 266). The lower panel (B) depicts the growth-phase dependent transcription of this genomic region in strain KPA. The first profile depicts the log₂ intensities (lilac, exponential phase; cyan, stationary phase), and the second profile the log₂ ratios (blue, higher in exponential phase; red, higher in stationary phase).