Mean amino acid distances within the 1^st 600 amino acids of each Pmp.

<p>Mean amino acid distances within the 1^st 600 amino acids of each Pmp.</p

Mean amino acid distances within the 1^st 600 amino acids of each Pmp.

<p>Mean amino acid distances within the 1^st 600 amino acids of each Pmp.</p

Global polymorphism analysis.

<p>A) Sliding-window analysis of the genetic variability throughout each <i>pmp</i> (window and step size of 15 bp). For each <i>pmp</i>, the black plot represents the polymorphism among all strain collection, while the remainder plots represent the impact of removing strains from the ocular group (red plot) and from the LGV group (magenta plot) on the global polymorphism. The region highlighted in yellow encompasses the 1^st 600 amino acids (used in vaccine attempts) where further analyses were performed. The horizontal bars below the plots represent the typical domains of these autotransporter proteins: passenger domain (magenta), middle domain (green), and C-terminal autotransporter domain (blue). B) Impact in both the number and percentage of variable sites found among <i>C</i>. <i>trachomatis</i> strains after the successive addition of LGV and ocular strains to the epithelial-genital group.</p

Pmp alignments showing examples of protein regions containing high concentration of FxxN motifs (purple), GGA(I, L) motifs (orange), and cysteine residues (blue).

<p>MHC class II (I-Ab)-bound <i>C</i>. <i>trachomatis</i> peptides are highlighted in yellow.</p

Expression profile of the nine <i>pmp</i> genes and <i>ompA</i> throughout the development of <i>C. trachomatis.</i>

<p>Reference strain L₂/434 is represented in panel A and E/Bour in panel B. Values represent the mean±SEM based on three independent experiments for time points of 2, 6, 12, 18, 24, 36, and 48 h post infection. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000878#s2" target="_blank">methods</a> for details.</p

Predicted <i>pmpF</i> promoter sequence for reference and clinical strains.

<p>Sequences are for reference strains E/Bour and L₂/434, and clinical strains E/537C-05, E/S-141, E/CS-500-96, and L₂. The predicted transcription promoter for <i>pmpF</i> is located within a 100% conserved region of the <i>pmpG/pmpF</i> IGR, where putative -10 and -35 elements are in blue characters and boxed. Potential A/T spacer region is underlined, and the predicted transcription start site is shown in a larger font below a red asterisk. The putative RBS for <i>pmpF</i> is in orange characters, and the putative RNase E cleavage sites are highlighted in grey. Numbers represent positions relative to the start codon of <i>pmpF</i> (highlighted in yellow). The start codon of <i>pmpG</i> is highlighted in blue.</p

Distribution/Location of the putative RNase E cleavage sites within the <i>pmpFE</i> operon coding sequence.

<p>The sequence is for reference strains E/Bour and L₂/434 and for clinical strains E/537C-05, E/S-141, E/CS-500-96 and L₂. Black vertical lines represent all RNase E cleavage sites conserved among all strains under study; green vertical lines show the ones only conserved among the four “E” strains; orange vertical lines represent those specific solely for both L₂ strains. Numbers represent nucleotide positions relative to the start codon of <i>pmpF.</i></p

Dot-Blot of serum immunoreactivity against recombinant (r)PmpD and rPmpF.

<p>Sera was obtained from adolescents singly infected and uninfected with a different <i>C. trachomatis</i> clinical strain as described previously <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000878#pone.0000878-Gomes3" target="_blank">[17]</a> (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000878#s2" target="_blank">methods</a>). rPmpD and rPmpF concentrations were standardized for use on the blots. Immunoreactivity to each fusion protein for sera from patients infected with strain Ba (n = 3), D (n = 3), E (n = 8), F (n = 5), G (n = 1), Ia (n = 1), J (n = 2) or K (n = 3) are shown. Of note is that immunoreactivity was consistent for sera from patients infected with the same clinical strain except for strain F (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000878#pone-0000878-t002" target="_blank">Table 2</a>); all eight patients infected with strain E were reactive to rPmpD.</p

Expression profile of <i>pmp</i> and <i>ompA</i> genes throughout the development of <i>C. trachomatis</i> clinical strains.

<p>(A) Strain L₂ shares the same <i>ompA</i> genotype as L₂/434; and strains E/537C-05 (B), E/S-141 (C) and E/CS-500-96 (D) share the same <i>ompA</i> genotype as E/Bour. Values represent the mean±SEM based on three independent experiments for time points of 2, 6, 12, 18, 24, 36, and 48 h post infection. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000878#s2" target="_blank">methods</a> for details.</p

Oligonucleotide primers used for kRT-PCR

a<p>Primers designed based on each <i>pmp</i> sequence of reference strains E/Bour and L₂/434 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000878#pone.0000878-Gomes1" target="_blank">[12]</a>.</p>b<p>Primers designed only for strain L₂.</p>c<p>Primers designed based on the <i>ompA</i> sequence of reference strains E/Bour and L₂/434 (GenBank Accession No. X52557 and M14738, respectively).</p>d<p>Primers designed based on the <i>16SrRNA</i> sequence of reference strains E/Bour and L₂/434 (GenBank Accession No. D85722 and U68443, respectively).</p