Table 1 Distribution of B. cenocepacia J2315 strain σ70 factors among other Burkholderia genome sequences and P. aeruginosa.
Bcc | pseudomallei lineage | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Bcen σ 70 factor | associated name | cds position in J2315 genome | locus tag | B. cenocepacia | B. vietnamiensis | B. sp. 383 | B. ambifaria | B. dolosa | B. mallei | B. pseudomallei | B. thailandensis | B. xenovorans | P. aeruginosa |
Bcen-SigE | RpoD | chr.2 1009395*-1011812 | BCAM0918 | 4/4 | 1/1 | 1/1 | 1/1 | 1/1 | 4/4 | 6/6 | 1/1 | 1/1 | 2/2 |
Bcen-SigI | chr.2 2666931-2668817 | BCAM2371 | 4/4 | 1/1 | 0/1 | 1/1 | 1/1 | 0/4 | 0/6 | 0/1 | 0/1 | 0/2 | |
Bcen-SigJ | chr.2 1383611-1382085 | BCAM1259 | 3/4 | 1/1 | 1/1 | 1/1 | 1/1 | 4/4 | 6/6 | 1/1 | 0/1 | 0/2 | |
Bcen-SigL | RpoH-like | chr.1 2088369-2089457 | BCAL1892 | 4/4 | 1/1 | 1/1 | 1/1 | 1/1 | 4/4 | 6/6 | 1/1 | 1/1 | 2/2 |
Bcen-SigM | FliA-like | chr.1 860723-859788 | BCAL0787 | 4/4 | 1/1 | 1/1 | 1/1 | 1/1 | 4/4 | 6/6 | 1/1 | 1/1 | 2/2 |
Bcen-SigK | RpoS | chr.1 168141-168872 | BCAL0144 | 4/4 | 1/1 | 1/1 | 1/1 | 1/1 | 4/4 | 6/6 | 1/1 | 1/1 | 2/2 |
Bcen-EcfA1 | RpoE | chr.1 1085335-1085934 | BCAL0998 | 4/4 | 1/1 | 1/1 | 1/1 | 1/1 | 4/4 | 6/6 | 1/1 | 1/1 | 2/2 |
Bcen-EcfA2 | RpoE | chr.1 153677-153078 | BCAL2872 | 1/4 | 0/1 | 0/1 | 0/1 | 0/1 | 0/4 | 0/6 | 0/1 | 0/1 | 0/2 |
Bcen-EcfB | PrtI-like | chr.1 3817661-3818182 | BCAL3478 | 4/4 | 1/1 | 1/1 | 1/1 | 1/1 | 0/4 | 6/6 | 1/1 | 0/1 | 0/2 |
Bcen-EcfC | FecI-like | chr.1 1506330-1506836 | BCAL1369 | 4/4 | 0/1 | 1/1 | 0/1 | 0/1 | 4/4 | 6/6 | 1/1 | 0/1 | 2/2 |
Bcen-EcfD | chr.1 2615164-2615727 | BCAL2360 | 4/4 | 1/1 | 1/1 | 1/1 | 1/1 | 4/4 | 6/6 | 1/1 | 1/1 | 0/2 | |
Bcen-EcfE | chr.1 2728250-2727696 | BCAL2462 | 4/4 | 0/1 | 1/1 | 0/1 | 1/1 | 0/4 | 0/6 | 0/1 | 1/1 | 0/2 | |
Bcen-EcfF | chr.1 3441702-3441187 | BCAL3151 | 4/4 | 1/1 | 1/1 | 1/1 | 1/1 | 4/4 | 6/6 | 1/1 | 1/1 | 0/2 | |
Bcen-EcfG | chr.1 2146519*-2145818 | BCAL1947 | 4/4 | 0/1 | 1/1 | 1/1 | 1/1 | 4/4 | 6/6 | 1/1 | 1/1 | 0/2 | |
Bcen-EcfH | chr.2 1846346-1845561 | BCAM1661 | 4/4 | 0/1 | 1/1 | 1/1 | 0/1 | 0/4 | 0/6 | 0/1 | 1/1 | 0/2 | |
Bcen-EcfI | OrbS | chr.1 1846454-1847122 | BCAL1688 | 4/4 | 1/1 | 1/1 | 1/1 | 1/1 | 4/4 | 6/6 | 1/1 | 1/1 | 2/2• |
Bcen-EcfJ | chr.2 230-829 | BCAM0001 | 4/4 | 1/1 | 1/1 | 1/1 | 1/1 | 4/4 | 6/6 | 1/1 | 0/1 | 0/2 | |
Bcen-EcfK | chr.2 3109088-3109981 | BCAM2748 | 4/4 | 0/1 | 1/1 | 0/1 | 1/1 | 4/4 | 6/6 | 1/1 | 0/1 | 0/2 | |
Bcen-EcfL | chr.2 934738-936006 | BCAM0849 | 4/4 | 1/1 | 1/1 | 1/1 | 1/1 | 4/4 | 6/6 | 1/1 | 1/1 | 0/2 | |
Bcen-EcfM | chr.1 3824313-3823432 | BCAL3486 | 4/4 | 1/1 | 1/1 | 1/1 | 1/1 | 0/4 | 0/6 | 0/1 | 0/1 | 0/2 | |
- TBLASTN searches of Bce-J2315 σ factors were performed on fully sequenced Burkholderia genomes. In accordance with phylogenetic inferences shown in Fig. 3 and 4, TBLASTN were considered to reveal homologs or orthologs of a same σ70 lineage when showing identity values above 50% and similarity higher than 63%, and when being part of a phylogenetic cluster supported by high bootstrap values. • P. aeruginosa OrbS homologs, named PvdS, showed 38% identity and 56% similarity with Bcen-J2315 homolog. Sequences were retrieved from [51-54]. Genomes of the following strains were analysed: B. cenocepacia, strains J2315, AU1054, HI2424, PC184 (negative for Bcen-SigJ); B. vietnamiensis, G4; Burkholderia sp., 383 ; B. ambifaria, AMMD, B. dolosa, AU0158; B. xenovorans, LB400; B. mallei, ATCC23344, 10229, GB8 horse 4, SAVP1; B. pseudomallei, 1710a, 1710b, S13, 1655, 668, K96243; B. thailendensis, E264; P. aeruginosa, PAO1, PA14. * indicates an ORF different from the one of the annotated genome.
Distribution limited to Burkholderia genomes, see Fig. 4.