The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129

Abstract

Corynebacterium diphtheriae is a Gram-positive, non-spore forming, non-motile, pleomorphic rod belonging to the genus Corynebacterium and the actinomycete group of organisms. The organism produces a potent bacteriophage-encoded protein exotoxin, diphtheria toxin (DT), which causes the symptoms of diphtheria. This potentially fatal infectious disease is controlled in many developed countries by an effective immunisation programme. However, the disease has made a dramatic return in recent years, in particular within the Eastern European region. The largest, and still on-going, outbreak since the advent of mass immunisation started within Russia and the newly independent states of the former Soviet Union in the 1990s. We have sequenced the genome of a UK clinical isolate (biotype gravis strain NCTC13129), representative of the clone responsible for this outbreak. The genome consists of a single circular chromosome of 2 488 635 bp, with no plasmids. It provides evidence that recent acquisition of pathogenicity factors goes beyond the toxin itself, and includes iron-uptake systems, adhesins and fimbrial proteins. This is in contrast to Corynebacterium's nearest sequenced pathogenic relative, Mycobacterium tuberculosis, where there is little evidence of recent horizontal DNA acquisition. The genome itself shows an unusually extreme large-scale compositional bias, being noticeably higher in G+C near the origin than at the terminus.

Figure 1

Circular representation of the C.diphtheriae NCTC13129 chromosome. From the outer to the inner circle: Circle 1, DNA bases (counting clockwise); circles 2 and 3, all genes (forward and reverse strands); circle 4, PAIs; circle 5, genes with orthologues in M.tuberculosis; circle 6, metal-ion transport systems (orange), phage-related genes (navy blue), DT (black); circle 7, putative sortases (red), putative sortase substrates (green); circle 8, repX (brown), IS element pairs (purple); circle 9, G+C content (plotted using a 10 kb window); circle 10, GC skew [(G–C) / (G+C)] (plotted using a 10 kb window). Colour coding for circles 2, 3 and 5: dark blue, pathogenicity/adaptation; black, energy metabolism; red, information transfer; dark green, surface associated; cyan, degradation of large molecules; magenta, degradation of small molecules; yellow, central/intermediary metabolism; pale green, unknown; pale blue, regulators; orange, conserved hypothetical; brown, pseudogenes; pink, phage and IS elements; grey, miscellaneous.

Figure 2

G+C content of the C.diphtheriae genome. (a) Total G+C content (using 20 kb window). (b) Frame-specific G+C content of CDSs (using 20 kb window): green, frame 1; blue, frame 2; red, frame 3. (c) G+C content of non-protein-coding regions (using 2 kb window). The predicted origin of replication is situated on the left-hand side of the figures.

Figure 3

Linear genomic comparison of C.diphtheriae (top) with C.efficiens (bottom). The coloured ticks represent the genes in the six reading frames; those in C.diphtheriae are colour coded as for Figure 1. The red lines in between the genomes represent DNA:DNA similarities (BLASTN matches) between the two DNA sequences. The plots above and below the genomes represent G+C content plotted over a 50 kb window.

Figure 4

Linear representation of the inserted corynephage (CDSs from DIP0180 to tox-DIP0222), showing the DNA (black central line) and flanking tRNAs (blue), the phage-related CDSs (pink), CDSs with no significant database matches (light green), putative membrane-associated proteins (dark green), a pseudogene (brown) and the toxin gene (tox, black). The top graph represents the CG content in this region (calculated with a window size of 500 bp), highlighting the low-G+C region encoding tox on the right-hand side.