Table 1. Specialized metabolic clusters and their control by Lsr2.
| Predicted specialized metabolic gene cluster# (characterized product) |
1st gene | Last gene | Number of upregulated genes (q-value < 0.01; >4 fold change) |
% of upregulated genes in each cluster | Number of Lsr2- associated sites (q-value < 0.01) |
|---|---|---|---|---|---|
| Ectoine | SVEN_0223 | SVEN_0234 | 1 | 8.33 | 0 |
| Terpene | SVEN_0261 | SVEN_0306 | 1 | 0 | 0 |
| T1PKS-T3PKS-NRPS (venemycin/watasemycin/thiazostatin) | SVEN_0463 | SVEN_0531 | 28 | 42.65 | 2 (SVEN_0502*, 506) |
| Lantipeptide – terpene | SVEN_0540 | SVEN_0561 | 0 | 0 | 1 (SVEN_0557) |
| Lantipeptide (venezuelin) | SVEN_0612 | SVEN_0630 | 3 (1 repressed) | 16.67 | 0 |
| Indole (acryriaflavin) | SVEN_0755 | SVEN_0772 | 0 | 0 | 0 |
| Chloramphenicol | SVEN_0913 | SVEN_0928 | 14 | 93.33 | 1 (SVEN_0926) |
| Other | SVEN_1844 | SVEN_1884 | 0 | 0 | 0 |
|
Siderophore
(desferrioxamine-like) |
SVEN_2566 | SVEN_2577 | 5 | 41.67 | 1 (SVEN_2576) |
| Lassopeptide | SVEN_3103 | SVEN_3132 | 2 | 6.90 | 1 (SVEN_3116*−7) |
| Other | SVEN_4061 | SVEN_4110 | 1 | 2.04 | 1 (SVEN_4069–70) |
| Butyrolactone (gaburedin) | SVEN_4179 | SVEN_4189 | 0 | 0 | 0 |
| Melanin | SVEN_4620 | SVEN_4662 | 0 | 0 | 4 (SVEN_4629–30, 4632, 4634–5, 4651) |
| Butyrolactone | SVEN_5076 | SVEN_5111 | 3 | 11.54 | 2 (SVEN_5091–92, 5106*−07) |
| Thiopeptide | SVEN_5119 | SVEN_5145 | 3 | 11.54 | 3 (SVEN_5127–8, 5129–31, 5132–3) |
| T3pks | SVEN_5351 | SVEN_5383 | 0 | 0 | 0 |
| Siderophore | SVEN_5413 | SVEN_5426 | 0 | 0 | 0 |
| Siderophore | SVEN_5471 | SVEN_5482 | (1 repressed) | 9.09 | 0 |
| Bacteriocin | SVEN_5817 | SVEN_5840 | 3 | 15.15 | 1 (SVEN_5817*) |
| Butyrolactone – T2PKS | SVEN_5951 | SVEN_6002 | 19 | 45.10 | 6 (SVEN_5963*−4, 5968*−9, 5972–3, 5974, 5975–6, 5979) |
| Other | SVEN_6112 | SVEN_6204 | 3 (1 repressed) | 3.26 | 1 (SVEN_6199) |
| NRPS-ladderane | SVEN_6134 | SVEN_6282 | 50 | 36.49 | 7 (SVEN_6199, 6216–7, 6219–20, 6225*, 6230, 6247–8, 6251) |
| Terpene | SVEN_6436 | SVEN_6490 | 6 | 16.67 | 1 (SVEN_6458) |
| Bacteriocin | SVEN_6527 | SVEN_6535 | (1 repressed) | 0 | 0 |
| T2PKS | SVEN_6767 | SVEN_6814 | 2 | 4.26 | 0 |
| Melanin | SVEN_6833 | SVEN_6842 | 4 | 44.44 | 0 |
| NRPS | SVEN_7032 | SVEN_7080 | 0 | 0 | 0 |
| Terpene | SVEN_7101 | SVEN_7119 | (two repressed) | 0 | 1 (SVEN_7109–10*) |
| T3PKS | SVEN_7223 | SVEN_7259 | 1 | 2.78 | 2 (SVEN_7235, 7237*−8) |
| Terpene-NRPS | SVEN_7417 | SVEN_7452 | 0 | 0 | 4 (SVEN_7427–8, 7440,7447–9, 7449–50) |
#:Cluster prediction by antiSMASH; * Asterisks indicate regulatory genes bound by Lsr2.
Bold: clusters containing an Lsr2 binding site.
Gray shading: clusters containing differentially expressed genes.