Table 1.
The structure of 14 putative PAIs.
| Putative PAI | Position | No. of genes | Characteristics |
| I | gbs0211-0235 | 25 | Island I is adjacent to tRNA-Ala, begins with a phage integrase family site-specific recombinase (gbs0211) and a Cro/CI transcriptional regulator (gbs0212), and harbors other mobilization genes. The region contains rgg (gbs0230), a homologue of a virulence regulator in S. pyogenes. |
| II | gbs0236-0254 | 19 | Inserted into the proximal end of island II, adjacent to tRNA-Leu, are 9 genes in strain NEM316 (gbs0236-0244) not present in strain 2603VR, and 7 genes in strain 2603VR (sag0245-0251) not present in strain NEM316. Gbs0236-0244 consists of genes encoding a phage integrase and other phage proteins. Sag0245-0251 consists of genes encoding hypothetical proteins and a Cro/CI family regulator. Neither of these two regions harbor known virulence genes. In the remainder of island II (gbs0245-0254 or sag0252-0264), there are no other mobilization genes or known virulence genes. |
| III, VII, VIII | gbs0361-0410 gbs0692-0740 gbs0969-1016 |
50 49 48 |
Islands III, VII, VIII are near-identical copies of a chromosomally integrated plasmid, designated pNEM316-1. |
| IV | gbs0458-0482 (gbs0458-0486*) | 25 (29)* | Gbs0458-0470 (or sag0423-0433) contains several transcriptional regulators, including araC family members, and the virulence factor alp, but does not harbor any identifiable mobilization genes. Inserted into the distal end of island IV, adjacent to tRNA-Thr, are 16 genes in strain NEM316 (gbs0471-0486) not present in strain 2603VR, and 6 genes in strain 2603VR (sag0434-0439) not present in strain NEM316. Gbs0471-0486 contains an integrase (gbs0482) and a Cro/CI transcriptional regulator (gbs0475). Sag0434-0439 contains an IS256 family transposase (sag0434), a phage family site-specific recombinase (sag0438). Neither of these elements contain known virulence genes. |
| V | gbs0588-0598 | 11 | Inserted into the proximal end of island V, adjacent to tRNA-Arg, is a single gene in strain NEM316 (gbs0588; an integrase) that is not present in strain 2603VR, and 65 genes in strain 2603VR (sag0545-0609) that are not present in strain NEM316. Sag0545-0609 contains numerous prophage lambda genes. The remainder of island V (gbs0589-0598 or sag0610-0617) harbors genes encoding a cell membrane protein complex and a two-component regulator, vncSR, flanked by two transposase genes (for instance, sag0611 a degenerate transposase and sag0618 a truncated transposase). There are no genes known to be involved in virulence in island V. |
| VI | gbs0616-0678 | 63 | Island VI contains the cyl locus (gbs0644-0655; sag0662-0673), encoding a β-hemolysin that has been shown unequivocally to be involved in virulence. The region preceding the cyl locus (gbs0616-0639) in strain NEM316 contains Tn5252 transposon genes, and is identical in strain 2603VR (sag0636-0657). Downstream of the cyl locus, in strain NEM316, there are neither mobilization genes nor other known virulence genes. In the middle of the island, three genes in strain NEM316 (gbs0656-0658; encoding a permease and hypothetical proteins) are not present in strain 2603VR, and 10 genes in strain 2603VR (sag0674-0683; protease, endopeptidase and permease genes) are not present in strain NEM316. The distal half of island VI contains genes encoding core metabolic enzymes, and does not contain mobile elements or virulence determinants. |
| IX | gbs1049-1076 | 28 | Island IX contains genes with homology to those encoding a two-component regulatory system, a carbon starvation protein, and secreted proteins, but it does not contain any mobilization genes. |
| X | gbs1118-1153 (gbs1118-1152*) | 36 (35)* | Island X appears to be mobile in that it is present in strain NEM316 but not in strain 2603VR, and it contains transferase, relaxase and some genes homologous with those in Tn5252. It also contains 3 LPXTG genes and a DNA methyltransferase. There are no known virulence genes. |
| XI | gbs1214-1224 | 11 | Island XI is composed of three genes that are present in both strains NEM316 and 2603VR, and these are involved in murein hydrolase export. Eight genes in island XI are present in strain NEM316, but not in strain 2603VR. One of these is an integrase, and the element is adjacent to a tRNA gene. None of the 8 genes appears to have a role in virulence. |
| XII | gbs1296-1373 | 78 | Island XII is a good candidate for a pathogenicity island. The virulence genes lmb (gbs1307), and scpB (gbs1308), encoding laminin binding protein and C5a peptidase, respectively, are at the proximal end of island XII, and are part of a large compound transposon. Upstream of lmb/scpB, gbs1296-1306, are five transposon (ISSdy1) or phage related genes, and downstream of lmb/scpB, gbs1309-1313 and gbs1338-1340, are other transposon (Tn5252) genes. In the distal half of island XII, 24 genes are present in strain NEM316 (gbs1314-1337; encoding phage and plasmid replication genes and the lac operon) that do not occur in strain 2603VR. In the same relative location in the genome, 20 genes (sag1253-1272; encoding heavy metal transporters) are present in strain 2603VR that do not occur in strain NEM316. |
| XIII | gbs1965-2011 | 47 | Inserted into the proximal end of island XIII, adjacent to tRNA-Lys, are 20 genes in strain NEM316 (gbs1965-1984; function mostly unknown, but not obvious virulence genes) that is not present in strain 2603VR, and 47 genes in strain 2603VR (sag1979-2025; containing several phage genes) that are not present in strain NEM316. The downstream half of the island (gbs1987-2011) is identical in strains NEM316 and 2603VR and contains genes encoding the CAMP factor, two proteases, core metabolic enzymes, two transporters, and a two-component regulator. There are no mobilization genes in this half of the island. |
| XIV | gbs2071-2092 (gbs2064*-2092) | 22 (29)* | Inserted into the proximal end of island XIV are 16 genes in strain NEM316 (gbs2064-2079; containing numerous phage genes) that are not present in strain 2603VR, and 10 genes in strain 2603VR (sag2111-2120; containing phage genes) that are not present in strain NEM316. The remainder of the island contains genes encoding 2 two-component regulators, 2 membrane proteins and enzymes involved in metabolism, but no obvious virulence or mobilization genes. |
* Re-annotation of putative pathogenicity islands based upon the location of mobile DNA present in strain NEM316 but absent from strain 2603VR.