Complete genome sequence of the Q-fever pathogen Coxiella burnetii

Abstract

The 1,995,275-bp genome of Coxiella burnetii, Nine Mile phase I RSA493, a highly virulent zoonotic pathogen and category B bioterrorism agent, was sequenced by the random shotgun method. This bacterium is an obligate intracellular acidophile that is highly adapted for life within the eukaryotic phagolysosome. Genome analysis revealed many genes with potential roles in adhesion, invasion, intracellular trafficking, host-cell modulation, and detoxification. A previously uncharacterized 13-member family of ankyrin repeat-containing proteins is implicated in the pathogenesis of this organism. Although the lifestyle and parasitic strategies of C. burnetii resemble that of Rickettsiae and Chlamydiae, their genome architectures differ considerably in terms of presence of mobile elements, extent of genome reduction, metabolic capabilities, and transporter profiles. The presence of 83 pseudogenes displays an ongoing process of gene degradation. Unlike other obligate intracellular bacteria, 32 insertion sequences are found dispersed in the chromosome, indicating some plasticity in the C. burnetii genome. These analyses suggest that the obligate intracellular lifestyle of C. burnetii may be a relatively recent innovation.

Figure 1

(a) Schematic representation of the 5S-23S-16S components of the rRNA operon in C. burnetii. The intervening sequences (IVSs) located in the 23S rRNA gene are indicated. (b) Phylogenetic clustering of the C. burnetii group I intron endonuclease with other sequenced endonucleases. Amino acid sequences were aligned by using CLUSTALW, and a neighbor-joining tree was generated from the alignment by using the PAUP program. All nodes had bootstrap values >85%. The C. burnetii endonuclease clusters with intron-associated endonucleases from the mitochondrial genomes of Monomastix spp., Acanthamoeba castellani, and other single-celled eukaryote mitochondrial and chloroplast genomes.

Figure 2

Circular representation of the C. burnetii RSA493 overall genome structure. The outer scale designates coordinates in base pairs. The first circle shows predicted coding regions on the plus strand color-coded by role categories: violet, amino acid biosynthesis; light blue, biosynthesis of cofactors, prosthetic groups, and carriers; light green, cell envelope; red, cellular processes; brown, central intermediary metabolism; yellow, DNA metabolism; light gray, energy metabolism; magenta, fatty acid and phospholipid metabolism; pink, protein synthesis and fate; orange, purines, pyrimidines, nucleosides, and nucleotides; olive, regulatory functions and signal transduction; dark green, transcription; teal, transport and binding proteins; gray, unknown function; salmon, other categories; blue, hypothetical proteins. The second circle shows predicted coding regions on the minus strand color-coded by role categories: third circle, pseudogenes in green; fourth circle, IS elements in red; fifth circle, tRNA genes in violet; sixth circle, rRNA genes in dark brown; seventh circle, trinucleotide composition in black; eighth circle, GC-skew curve in blue (positive residues) and gray (negative residues).

Figure 3

(a) Average and median pI values of all predicted proteins for C. burnetii and a subset of sequenced γ-proteobacteria and intracellular bacterial genomes. (b) Percentage of total proteins in given pI ranges for C. burnetii and various sequenced bacterial genomes.

Figure 4

Linear representation of the locus encoding a putative type IV secretion system in C. burnetii with relation to L. pneumophila icm-dot genes. Genes are shown as arrowheads and colored by predicted function: orange, putative type IV secretion system components; black, hypothetical protein; gray, conserved hypothetical protein; red, IS1111 element transposase. Black lines connect genes with best matches to L. pneumophila genes (shown in white) at a P-value cutoff of <10⁻⁵. Both CBU1629 and CBU1630 show significant similarity to IcmL; however, they are not identical to each other.