Table 1.
List of Clostridium perfringens strains used in this study.
Table 2.
Summary of C. perfringens genome sequences used in this study.
Figure 1.
Genetic organization of NE-specific loci.
The genetic organization of (A) NELoc-1, (B) NELoc-2 and (C) NELoc-3 is shown, each arrow representing a predicted gene and the total size given below each locus. Predicted functional annotations and locus tags are shown above and below each gene, respectively. Genes are colour-coded by their putative role based upon sequence analyses.
Table 3.
Summary of predicted genes in NE pathogenicity locus NELoc-1.
Table 4.
Summary of predicted genes in NE pathogenicity locus 2.
Table 5.
Summary of predicted genes in NE pathogenicity locus 3.
Figure 2.
Identification of VirR boxes in NE strain genomes.
(A). A modified VirR-box consensus sequence was produced based on the alignment of known VirR-boxes with the VirR-box upstream from netB. The VirR-box consensus previously reported by Cheung et al. (2004) [79] is shown in bold, and absolutely conserved nucleotides are in boxes. (B) VirR-boxes identified in CP4, including one novel element upstream of the internalin-like protein gene. Nucleotides that conform with the previously reported VirR-box consensus are in green, and those that do not conform in red.
Figure 3.
PFGE and Southern blot analyses of plasmids from C. perfringens poultry strains.
(A). Agarose plugs containing DNA isolated from the eight sequenced poultry strains were digested with NotI and subjected to PFGE. (B). Southern blotting was performed with DIG-labelled probes for netB and hdhA. Results from both netB and hdhA probes are shown overlayed. In all lanes with two bands, the upper band represents netB and the lower band hdhA. Both probes hybridized to the same band in CP2. In CP6, only the hdhA probe hybridized, while in JGS4143, only the netB probe hybridized.
Figure 4.
Plasmid location of NELoc-1 and -3.
Nucleotide sequence alignments of pCPF5603, pCP8533etx and (A) NELoc-1 or (B) NELoc-3 were generated with Artemis Comparison Tool (ACT). The small boxes represent ORFs, with toxin genes colored in red and IS1151 or IS1469 genes in yellow. Grey boxes connecting the different sequences represent regions with sequence similarity. Colored bars underneath each sequence represent different loci as follows: blue, tcp; green, cpe; red, cpb2; black, pCPF5603-specific; light blue, etx. Orange bars represent the sequence found duplicated in pCP8533etx and NELoc-1 and -3 sequences.