Comparative Metabolic Potential of Select Rickettsiales

<p>Metabolic pathways of E. chaffeensis (magenta arrows), A. phagocytophilum (green arrows), N. sennetsu (gold arrows), W. pipientis (lavender arrows), and R. prowazekii (cyan arrows) were reconstructed and compared. The networks of some of the more important pathways are shown with metabolites color coded: red and purple, central and intermediary metabolites; blue, cofactors; green, amino acids; and black, cell structures. Transporters are shown in the membrane and are grouped by predicted substrate specificity: green, inorganic cations; magenta, inorganic anions; red, carbohydrates and carboxylates; blue, amino acids/peptides/amines; yellow, nucleotides/nucleosides; and black, drug/polysaccharide efflux or unknown.</p

Representative Illustrations of <i>p44</i> Genes

<p>Full-length <i>p44</i> genes contain conserved start and stop codons, an ORF longer than 1,000 bp, and a central hypervariable region of approximately 280 bp containing a signature of four conserved amino acid regions (C, C, WP, A). These genes can be expressed at their respective current genome location or can recombine into the expression locus (<i>p44ES</i>/APH_1221). A silent/reserve <i>p44</i> is less than 1,000 bp. It may have either the conserved or alternative start and/or stop codons. A silent/reserve <i>p44</i> is not likely to be expressed at its current genome location, but can recombine into the expression locus (<i>p44ES</i>/APH_1221). Truncated <i>p44</i>s carry the complete hypervariable region, or a portion thereof, but only one of the two conserved regions. Fragments of <i>p44</i> have only a conserved region and no hypervariable region. Each annotated <i>p44</i> is longer than 60 bp. It should be noted that smaller fragments can be identified throughout the genome. These, as well as <i>p44</i> truncations and fragments, are likely to be nonfunctional remnants of previous recombination events.</p

Synteny of the Rickettsiales

<p>Regions of conserved synteny were identified using the ortholog clusters (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020021#s3" target="_blank">Materials and Methods</a>) and visualized with Sybil. The genes along each ordered chromosome were colored on a gradient from yellow to blue. The ortholog clusters for each query genome were then plotted relative to the order of the reference genome. Regions of synteny are then seen as continuous gradients across large regions of the genome. Above the synteny gradient display is the atypical nucleotide composition. Below the gradient display are the predicted coding regions on the plus strand and the minus strand, and the GC-skew. Representatives of all the Rickettsiales (A) and representative <i>Ehrlichia</i> spp. and <i>Anaplasma</i> spp. (B) were compared separately. AMA, A. marginale St. Maries; APH, A. phagocytophilum HZ; ECH, E. chaffeensis Arkansas; ERU, E. ruminantium Welgevonden; NES, N. sennetsu Miyayama; RPR, R. prowazekii Madrid E; WOL, <i>W. pipientis w</i>Mel.</p

Phylogenetic Tree of the α-Proteobacteria

<p>The protein sequences of select conserved genes were concatenated and aligned, and a phylogenetic tree was inferred of all sequenced α-Proteobacteria (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020021#s3" target="_blank">Materials and Methods</a>). The Anaplasmataceae (purple) and the Rickettsiaceae (yellow) are highlighted.</p

Comparison of the Rickettsiales Gene Sets

<p>The composition of ortholog clusters (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020021#s3" target="_blank">Materials and Methods</a>) of representative Rickettsiales (A), <i>Ehrlichia</i> spp. (B), and <i>Anaplasma</i> spp. (C) were compared. Numbers within the intersections of different ovals indicate ortholog clusters shared by 2, 3, 4, or 5 organisms. Species compared are indicated in diagram intersections as follows. A, <i>R. prowazekii;</i> B, <i>N. sennetsu;</i> C, <i>W. pipientis;</i> D, <i>A. phagocytophilum;</i> E, <i>E. chaffeensis;</i> F, <i>A. marginale;</i> G, E. ruminantium Gardel; and H, E. ruminantium Welgevonden.</p