The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation

Abstract

The obligate intracellular bacterial pathogen Chlamydophila abortus strain S26/3 (formerly the abortion subtype of Chlamydia psittaci) is an important cause of late gestation abortions in ruminants and pigs. Furthermore, although relatively rare, zoonotic infection can result in acute illness and miscarriage in pregnant women. The complete genome sequence was determined and shows a high level of conservation in both sequence and overall gene content in comparison to other Chlamydiaceae. The 1,144,377-bp genome contains 961 predicted coding sequences, 842 of which are conserved with those of Chlamydophila caviae and Chlamydophila pneumoniae. Within this conserved Cp. abortus core genome we have identified the major regions of variation and have focused our analysis on these loci, several of which were found to encode highly variable protein families, such as TMH/Inc and Pmp families, which are strong candidates for the source of diversity in host tropism and disease causation in this group of organisms. Significantly, Cp. abortus lacks any toxin genes, and also lacks genes involved in tryptophan metabolism and nucleotide salvaging (guaB is present as a pseudogene), suggesting that the genetic basis of niche adaptation of this species is distinct from those previously proposed for other chlamydial species.

Figure 1.

Circular representation of the Cp. abortus chromosome. The outer scale shows the size in base pairs. From the outside in, circles 1 and 2 show the position of genes transcribed in a clockwise and anticlockwise direction, respectively (for color codes, see below); circles 3 and 4 CDS encoding all membrane proteins (green) minus the Pmp and TMH/Inc-family proteins in the clockwise and anticlockwise directions, respectively; circles 5 and 6 show members of the Pmp (purple) and TMH/Inc protein families (blue) in the clockwise and anticlockwise directions, respectively. Circle 7 shows a plot of G+C content (in a 10-kb window); circle 8 shows a plot of GC skew ([G–C]/[G+C]; in a 10-kb window). Genes in circles 1 and 2 are color coded according to the function of their gene products: (dark green) membrane or surface structures; (yellow) central or intermediary metabolism; (cyan) degradation of macromolecules; (red) information transfer/cell division; (purple) degradation of small molecules; (pale blue) regulators; (dark blue) pathogenicity or adaptation; (black) energy metabolism; (orange) conserved hypothetical; (pale green) unknown; (brown) pseudogenes. The position of the plasticity zone (PZ) is shown as a red arc outside of the scale ring.

Figure 2.

Global comparison between Cp. caviae (GPIC), Cp. abortus (S26/3), and Cp. pneumoniae (AR39). The figure shows ortholog matches (see Methods; displayed using ACT http://www.sanger.ac.uk/Software/ACT/) of the three sequenced Chlamydophila genomes. Gray bars represent the forward and reverse strands of DNA with the scale marked in base pairs. The red bars between the DNA lines represent individual forward ortholog matches, with inverted matches colored blue. The positions of the PZ region (green), pmp clusters (purple; numbered 1–4), tmh cluster (blue), and biotin biosynthetic operon (yellow) are shown as colored boxes on the DNA lines. All the genomes have been oriented at the origin of replication to start at the hemB gene.

Figure 3.

(A) Comparison of the tmh locus of Cp. caviae (GPIC), Cp. abortus (S26/3), C. muridarum (Nigg), C. trachomatis (serovar D), and Cp. pneumoniae (AR39). ACT (see Fig. 2) comparison of amino acid matches between the complete six-frame translations (computed using TBLASTX) of representatives of the five sequenced Chlamydiaceae species. The red bars spanning between the genomes represent individual TBLASTX matches. CDS are marked as colored boxes positioned on the gray DNA lines: tmh family (green for intact genes, brown for pseudogenes), pmpD (pink), those carrying both DUF1539 and DUF1548 motifs (yellow), CDS encoding products with paired N-terminal TM domains (dark blue), lipid A biosynthesis (white), and all others (light blue). The scale is marked in base pairs. The region shown for Cp. pneumoniae strain AR39 is identical in all of the other sequenced Cp. pneumoniae strains (data not shown). (B) Architecture of the proteins encoded at the tmh locus of Cp. abortus. The amino acid sequences of the two pseudogenes CAB762 and CAB768 have been artificially reconstructed for the purpose of this analysis. See key for color codes. (DUF) Domain of unknown function.

Figure 3.

(A) Comparison of the tmh locus of Cp. caviae (GPIC), Cp. abortus (S26/3), C. muridarum (Nigg), C. trachomatis (serovar D), and Cp. pneumoniae (AR39). ACT (see Fig. 2) comparison of amino acid matches between the complete six-frame translations (computed using TBLASTX) of representatives of the five sequenced Chlamydiaceae species. The red bars spanning between the genomes represent individual TBLASTX matches. CDS are marked as colored boxes positioned on the gray DNA lines: tmh family (green for intact genes, brown for pseudogenes), pmpD (pink), those carrying both DUF1539 and DUF1548 motifs (yellow), CDS encoding products with paired N-terminal TM domains (dark blue), lipid A biosynthesis (white), and all others (light blue). The scale is marked in base pairs. The region shown for Cp. pneumoniae strain AR39 is identical in all of the other sequenced Cp. pneumoniae strains (data not shown). (B) Architecture of the proteins encoded at the tmh locus of Cp. abortus. The amino acid sequences of the two pseudogenes CAB762 and CAB768 have been artificially reconstructed for the purpose of this analysis. See key for color codes. (DUF) Domain of unknown function.

Figure 4.

(A) Clustering of the Pmp-family proteins of sequenced chlamydial species. Phylogenetic tree of the Pmp-family proteins from Cp. abortus (S26/3), Cp. caviae (GPIC), Cp. pneumoniae (AR39), C. muridarum (Nigg), and C. trachomatis (serovar D). The Pmp protein families (A–I) are marked as previously assigned (Grimwood and Stephens 1999). (B) Architecture of the Pmp-family proteins of Cp. abortus. Conserved domains are color coded: signal sequence (light blue), transmembrane domain (dark purple), Pmp-repeat region (green), central PMP_M region (light purple), and autotransporter-like domain (yellow). The amino acid sequences of the pseudogenes CAB270 and CAB273 and the phase-variable genes CAB279 and CAB596 have been reconstructed in silico for the purpose of this analysis. CAB267 is a gene remnant.

Figure 4.

(A) Clustering of the Pmp-family proteins of sequenced chlamydial species. Phylogenetic tree of the Pmp-family proteins from Cp. abortus (S26/3), Cp. caviae (GPIC), Cp. pneumoniae (AR39), C. muridarum (Nigg), and C. trachomatis (serovar D). The Pmp protein families (A–I) are marked as previously assigned (Grimwood and Stephens 1999). (B) Architecture of the Pmp-family proteins of Cp. abortus. Conserved domains are color coded: signal sequence (light blue), transmembrane domain (dark purple), Pmp-repeat region (green), central PMP_M region (light purple), and autotransporter-like domain (yellow). The amino acid sequences of the pseudogenes CAB270 and CAB273 and the phase-variable genes CAB279 and CAB596 have been reconstructed in silico for the purpose of this analysis. CAB267 is a gene remnant.