Phylogenetic analysis of initiating glycosyltransferases.

<p>Phylogeny of ItrA related protein sequences. <i>A. baumannii</i> ItrA are indicated by bold-face type, and ItrA for which biochemistry is available are boxed. Bootstrap values based on 100 replicate trees are shown. Abbreviations and GenPept accessions are as follows: <i>P. cryohalolentis</i> K5 is <i>Psychrobacter cryohalolentis</i> K5 [YP_579903.1]; <i>P. multocida</i> P1059 is <i>Pasturella multocida</i> P1059 [EJZ79825]; <i>V. cholerae</i> O5 is <i>Vibrio cholerae</i> CO545 [ADF80985.1]; <i>N. gonorrhoeae</i> PglB is <i>Neisseria gonorrhoeae</i> MS11 [ZP_06132416.1]; <i>Neiserria sp</i> PglB [EFI22895.1]; <i>V. vulnificus</i> YJ016 [NP_933154.1]; <i>V. cholerae</i> HE-45 [EJH66138.1]; <i>C. jejuni</i> PglC is <i>Campylobacter jejuni</i> NCTC 11168 [CAL35241.1]. Both PglB and PglC are specific for UDP-D-Qui<i>p</i>NAc4NAc <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062160#pone.0062160-Hartley1" target="_blank">[66]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062160#pone.0062160-Glover1" target="_blank">[67]</a>.</p

Map of the genome of GC1 isolate AB0057 showing positions of genes and loci.

<p>The genes and loci described in this study are indicated by boxes, with their names shown inside the circle. Locations of genes included in the Oxford MLST scheme are indicated by the ovals with names outside the circle. The <i>gpi</i> gene is within the K locus. The arrow indicates the <i>comM</i> gene, the location at which transposons carrying resistance to antibiotics are often inserted. The numbers represent megabases from origin, and a scale bar is shown. The AB0057 sequence was chosen as the representative genome [GenBank accession CP001182] because it begins at the origin of replication (0/4) and this position differs in other genomes. Genes outside the K and OC loci that code for PglL, GlmS, GlmM, GlmU, Gne, and Wzi are found in the at locus tags AB57_3633, AB57_3845, AB57_3769, AB57_3844, AB57_2335, and AB57_1078 respectively.</p

<i>A. baumannii</i> completed genome sequences^a.

a<p>As of 30^th September, 2012.</p>b<p>GC: Global clone.</p

Pathways for biosynthesis of common UDP-linked sugar precursors.

<p>Common UDP-linked sugar precursors derived from glucose-6-phophate are boxed. Arrows denote the direction of each reaction, and the enzyme name is adjacent. Enzymes highlighted in bold are encoded by genes in module B (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062160#pone-0062160-g003" target="_blank">Figure 3</a>). Abbreviations: UDP-D-Glc<i>p</i>NAc is UDP-<i>N</i>-acetyl-D-glucosamine; UDP-D-Glc<i>p</i> is UDP-D-glucose; UDP-D-Glc<i>p</i>A is UDP-D-glucuronic acid; UDP-D-Gal<i>p</i> is UDP-D-galactose; D-Glc<i>p</i>-6-P is glucose-6-phosphate; L-Fru<i>p</i>-6-P is fructose-6-phosphate; D-Glc<i>p</i>-1-P is glucose-1-phosphate; UDP-D-Gal<i>p</i>NAc is UDP-<i>N</i>-acetyl-D-galactosamine; UDP-D-Glc<i>p</i>NAcA is UDP-<i>N</i>-acetyl-D-glucosaminuronic acid; UDP-D-Gal<i>p</i>NAcA is UDP-<i>N</i>-acetyl-D-galactosaminuronic acid.</p

Key to gene names used.

a<p>Genes in the OC loci.</p

Location of K and OC loci in completed genomes.

a<p>GC: Global clone.</p>b<p><i>fkpA</i> and <i>lldP</i> are divergently transcribed, with start codons closest to the K locus.</p>c<p><i>aspS</i> and <i>ilvE</i> are transcribed in opposite directions, with stop codons closest to the OC locus.</p>d<p>Some ORFs with potential frameshifts (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062160#pone-0062160-g003" target="_blank">Figure 3</a>).</p

Genes and pathways involved in the synthesis of UDP-D-QuipNAc4NHb, UDP-D-Qui<i>p</i>NAc and UDP-L-Fuc<i>p</i>NAc.

<p>KL1 regions 5 and 6 are compared to a region from the K locus of <i>A. venetianus</i> RAG-1 [GenBank accession AJ243431], and to KL4 regions 5 and 6. A region from KL9 is compared to KL4 and a region in the O11 O-antigen locus from <i>P. aeruginosa</i> [GenBank accession AF147795]. The biosynthesis pathways of UDP-D-QuipNAc4NHb <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062160#pone.0062160-Nakar1" target="_blank">[23]</a>, UDP-L-Fuc<i>p</i>NAc <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062160#pone.0062160-Kneidinger1" target="_blank">[45]</a> and UDP-D-Qui<i>p</i>NAc <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062160#pone.0062160-Belanger1" target="_blank">[40]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062160#pone.0062160-Pinta1" target="_blank">[65]</a> are shown on the right. Horizontal arrows represent genes showing the direction of transcription, with gene names shown above. Genes are coloured by the predicted function of their gene product and the colour scheme is shown the below. The% identity between predicted gene products is shown between aligned pairs of gene clusters. Regions are defined in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062160#pone-0062160-g003" target="_blank">Figure 3</a>. The figure is drawn to scale from the GenBank entries listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062160#pone-0062160-t001" target="_blank">Table 1</a> and above.</p

PCR scheme for the detection of OC locus arrangements.

<p>PCR scheme for the detection of OC locus arrangements.</p

OC locus forms found in single draft genomes.

a<p> ST is sequence type – Institut Pasteur scheme.</p>b<p> NEW is ST with known alleles but an unregistered MLST profile.</p>c<p> The accession number is for the contig containing the OC locus.</p><p>OC locus forms found in single draft genomes.</p

Group B OC locus arrangements.

<p>Arrows represent genes showing direction of transcription. Gene annotations are shown above, as defined in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107833#pone-0107833-t003" target="_blank">Table 3</a>. Modules shared between arrangements are boxed. Colour scheme key is below, and the figure is drawn to scale from GenBank accession numbers HM590877 (OCL5), AMFS01000036 (OCL6), AMTB01000027 (OCL7), ABXK01000027 (OCL8), and ALOH01000183 (OCL9).</p