Determination of phase variable expression of<i>S. enterica</i> subspecies I Gtr families.

<p>N/A: not applicable due to absence of detectable phase variation.</p><p>N/D: not determined.</p>*<p>Data taken from <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003568#pgen.1003568-Broadbent1" target="_blank">[20]</a>.</p

Regulatory regions from 8<i>gtr</i> operons illustrating degrees of conservation and variation in <i>gtr</i> phase variation sequence elements

<p><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003568#pgen.1003568-Broadbent1" target="_blank">[<b>20</b>]</a><b>.</b> Top of the figure is a schematic representation of the phase variable <i>gtr</i> regulatory region showing the location of three OxyR dimer binding sequences (thick black line), GATC sequences (open rectangle), −35 and −10 promoter sequences, transcription start site (+1) and the <i>gtrA</i> open reading frame. The presence of these elements is a signature of <i>gtr</i> phase variation. Below the schematic is an alignment of seven <i>gtr</i> regulatory region sequences showing consensus OxyR dimer binding sequence, GATC sequences in bold and the −35 of the promoter shaded in grey. Sequence “SIN S1326/28_III” is shown as comparison to illustrate lack of phase variation sequence elements. This sequence was aligned based on conserved sequence surrounding the +1 site (not shown). Acronyms represented: STM, <i>S.</i> Typhimurium; SCH, <i>S.</i> Choleraesuis; SIN, <i>S.</i> Infantis. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003568#pgen.1003568.s001" target="_blank">Figure S1</a> shows the alignment and conserved nucleotides of 128 bp of regulatory sequence from 43 <i>gtr</i> operons.</p

Heterogeneity of Gtr families localized within locus 2 of<i>Salmonella</i> serovars.

<p>Represented is an alignment and sequence comparison of the <i>cysS</i> to <i>pheP</i> genomic region encompassing locus 2 (SPI-16, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003568#pgen-1003568-g003" target="_blank">Figure 3</a>) from nine <i>gtr</i> positive <i>Salmonella</i> serovars. The phage-associated locus 2 is defined by a pair of direct repeats (pink) and a 5′ Arg-tRNA <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003568#pgen.1003568-Vernikos1" target="_blank">[25]</a>. Black coding sequences refer to those located within locus 2 boundaries, while white coding sequences are located outside locus 2. The <i>gtr</i> operon located within locus 2 is colored on the basis of GtrC family clustering (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003568#pgen-1003568-g001" target="_blank">Figure 1</a>). A different colored GtrC family likely reflects a functionally different <i>gtr</i> operon. <i>S.</i> Schwarzengrund contains a <i>gtr</i> positive lambda-like prophage and <i>S.</i> Dublin harbors a large remnant P22-like phage <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003568#pgen.1003568-Villafane1" target="_blank">[11]</a> within locus 2. Regions of genetic similarity between genome sequences are shaded in grey and were determined by BLASTn analysis using Easyfig <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003568#pgen.1003568-Sullivan1" target="_blank">[52]</a>.</p

Extensive recombination within<i>gtr</i> operons.

<p>A) Schematic representation of a BLAST comparison between the <i>gtr</i> operons from three Kaufmann-White serogroup C₁ genomes; <i>S.</i> Paratyphi C, <i>S.</i> Infantis and <i>S.</i> Choleraesuis. Red shaded regions indicate gene products with >98% protein similarity; blue regions <90% similarity; yellow regions <80% similarity and Grey regions <50% similarity as determined by ClustalW2 amino acid alignments <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003568#pgen.1003568-Larkin1" target="_blank">[42]</a>. A possible <i>gtr</i> recombination is evident between the <i>gtrA</i> or <i>gtrBC</i> of <i>S.</i> Choleraesuis <i>gtr</i>^SCB67_I and the <i>gtrA</i> or <i>gtrBC</i> of <i>S.</i> Paratyphi C <i>gtr</i>^RKS4594_I<i>gtr</i> operons. <i>S.</i> Choleraesuis <i>gtr</i>^SCB67_I is encompassed within a full-length P22-like prophage termed Scho1 <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003568#pgen.1003568-Villafane1" target="_blank">[11]</a>. Genome integration sites as depicted in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003568#pgen-1003568-g003" target="_blank">Figure 3</a> are represented above the Figure. IS refers to insertion-like sequences. B) Mapping of homoplasic SNPs within <i>gtrA</i> and <i>gtrB</i> gene sequences. On the left of the figure is the mid-point rooted phylogeny of the <i>gtrA</i> and <i>gtrB</i> gene sequences with gene names colored according to GtrC Family designation (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003568#pgen-1003568-g001" target="_blank">Figure 1</a>). Colored vertical lines depict homoplasic bases (red:A, blue:T, green:C, orange:G) that differ from the ancestral sequence and are shown relative to the concatenated <i>gtrAB</i> gene sequence shown on top. The pattern of lines represents a homoplasic ‘barcode’ of similarity between strains and is used to indicate recombined regions. High homoplasic SNP density across both <i>gtrA</i> and <i>gtrB</i> genes indicates a dynamic and complex evolutionary history driven by extensive recombination. Some examples of recombined regions are indicated by blue boxes. In the case of <i>S.</i> Agona <i>gtr</i>^SL483_I and <i>S.</i> Hadar <i>gtr</i>^18_I/<i>S.</i> Newport <i>gtr</i>^SL254_I, recombination is not restricted by <i>gtrAB</i> gene boundaries.</p

Phylogenetic and clustering analyses of the GtrC, GtrB and GtrA gene products from<i>Salmonella</i>.

<p>A total of 59 <i>gtr</i>-like operons were identified from BLAST analysis of 22 complete <i>S. enterica</i> subspecies I complete genome sequences, 28 draft <i>S. bongori</i> genome sequences and 4 phage genome sequences. The grey bar indicates clusters of sequences that segregated on the basis of genomic sequence as determined by the Bayesian algorithm software, BAPS <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003568#pgen.1003568-Corander1" target="_blank">[23]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003568#pgen.1003568-Corander2" target="_blank">[24]</a>. 10 GtrC clusters (‘GtrC families’) are identified by clustering and colored accordingly. This GtrC family color scheme is applied to the GtrB and GtrA trees to examine evolutionary relationships between the 3 gene products. GtrB and GtrA segregate into 7 and 5 clusters accordingly and the overall clusters are more closely related compared to GtrC gene products (scale bar). The lack of congruent clustering between GtrC, GtrB and GtrA gene products reflect different evolution histories of the gene products. Maximum likelihood rectangular phylograms were derived from ClustalW2 alignments using PhyML. Horizontal distances are proportional to sequence differences per site relative to the scalebar shown for each tree. Bootstrap values, out of 1000 trials, are shown on the tree branches. Each terminal node is labeled with a Gtr acronym assigned in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003568#pgen.1003568.s002" target="_blank">Table S1</a>. Asterisk denotes sequences predicted to contain deletions or frameshift mutations. The six <i>S.</i> Typhimurium genome sequences examined in this study (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003568#pgen.1003568.s002" target="_blank">Table S1</a>) share 100% sequence identity in their family III and family IV GtrC sequences and are collectively represented in this figure as STM_I and STM_II respectively.</p

Sorties graphiques de Flotrop V : Dispersion spatiale à moyenne échelle (suite)

<p>The <i>C</i>. <i>trachomatis</i> L2 developmental cycle (<b>A</b>) and the experimental workflow for the analysis of highly purified <i>C</i>. <i>trachomatis</i> L2 EBs and RBs using 2D-RP-RP-LC-MS^E label-free technology (<b>B</b>).</p

Estimated percentage energy investment in different functional classes of proteins for proteins present in 2+ EB replicates and/or 2+ RB replicates.

<p>Blue, RB proteome; Red, EB proteome; Purple, proteins up-regulated in EB; Green, percentage of proteome in functional class.</p

Structural proteins of the Type III secretion apparatus identified.

<p>Structural proteins of the Type III secretion apparatus identified.</p

A SNP based maximum likelihood phylogeny of the seventh pandemic <i>V. cholerae</i> lineage.

<p>The phylogenetic tree shows the relation between the 2009 isolates from Chandigarh and the global collection of <i>V. cholera</i> genomes published by Mutreja et al <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002981#pntd.0002981-Mutreja1" target="_blank">[1]</a>. The positions of the isolates from Chandigarh are indicated with colour bars on the right representing the district they were isolated from (see <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002981#pntd-0002981-g001" target="_blank">Figure 1</a>). Other sub-clades that map close by on the tree to the Chandigarh isolates have been marked to highlight their global phylo-geographical context. The pre-seventh pandemic isolate M66 (2) was used as an out-group to root the tree. The scale given represents substitutions per variable site.</p

Structural variations in SXT among <i>V. cholerae</i> isolates.

<p>The structures of the SXT of <i>V. cholerae</i> isolates from Chandigarh were compared to published isolates from Nepal and Haiti. Reads were mapped to ICE<i>Vch</i>Hai1 (accession number JN648379). Plot showing presence (blue) or absence (white) of the genes of ICEVchHai1. The antibiotic resistance genes within the SXT cluster are highlighted in red.</p