The ‘mobile’ VirR regulon Our analysis identified three targets located on plasmids, one coding for ϵ-toxin (pCP8533etx_p28) in plasmid pCP8533etx from strain NCTC 8533B4D, in addition with two hypothetical proteins, sharing 98% identity, in pCP8533etx (pCP8533etx_p40) and in pCPF5603 (pCPF5603_50) of strain F5603, respectively. Concerning plasmid pCP8533etx, we noticed that it is also present in the shotgun sequences from ATCC3626 (data not shown based on blastn comparisons) and also in that case we were

able to find a VirR motif upstream of the gene encoding ϵ-toxin. selleck Plasmid analysis Plasmids can be transferred between species, and gene content similarities between plasmids can be used to trace gene flow between different strains. To evaluate evolutionary relationships relating plasmids Ro 61-8048 datasheet from C. perfringens species, we performed an analysis to quantify the number of genes shared by each pair of plasmids. For this reason, we built the phylogenetic profiles of

the proteomes encoded by plasmids in these strains. The phylogenetic profiles for each group of proteins were obtained by comparing all those proteins one against each other with the package Blast2Network [13]. A phylogenetic profile, or phyletic pattern, is represented by a matrix where each row corresponds to a plasmid molecule and each column to a given protein family. The cell at the intersection between row i and column j indicates the presence of a component of protein family j in plasmid i. A phylogenetic profile can be thus interpreted as a graph with two types of nodes: those corresponding to plasmid molecules are connected to nodes of protein families if the corresponding plasmids contains the gene encoding that protein. These matrices can become very

large when many plasmids and proteins are involved, so that their analysis and biological interpretation is difficult. A strategy for dimensionality reduction can be through deletion of nodes corresponding to protein families and connection of plasmids directly, through edges that reflect the number of shared protein families (see [Additional file 2] for a scheme). The obtained hypergraph Phosphoribosylglycinamide formyltransferase is reported in figure 3, where plasmids are connected by links weighted on the basis of the number of common genes. A group of four connected plasmids (i.e. sharing several genes), including pCP8533etx and pCPF5603, was found. This finding is in agreement with previous data showing that plasmids pCPF5603 and pCP8533etx evolved from insertion of mobile genetic elements carrying enterotoxin or etx genes, respectively, onto a common progenitor plasmid [14]. This group of plasmids is connected to a second group, composed of three plasmids (plasmid 1, plasmid 2 and pBCNF5603) through a bridge represented by pCP13. This implies that pCP13 shares different genes with plasmids from both groups i.e.