TABLE 1.
Bacterial strains and plasmids used
| Strain or plasmid | Characteristic(s)a | Source or reference |
|---|---|---|
| Strains | ||
| P. denitrificans | ||
| PD1222 | Wild type, G−, Rifr | David Schleheck |
| ΔpdeI mutant | pdeI deletion mutant of PD1222 | This study |
| ΔpdeR mutant | pdeR deletion mutant of PD1222 | This study |
| PD0786 | PD1222 derivative with PpdeR-lacZ | This study |
| PD0787 | PD1222 derivative with PpdeI-lacZ | This study |
| PD4202 | PD1222 derivative with Phmu-lacZ | This study |
| PD1077 | PD1222 derivative with Pfbp-lacZ | This study |
| E. coli | ||
| DH5α | Host strain for cloning vectors | Lab stock |
| SM10λpir | Conjugation strain | Lab stock |
| BL21(DE3) | F− ompT hsdS(rB− mB−) gal dcm lacY1 (DE3) | Lab stock |
| A. tumefaciens | ||
| KYC55 | AHL bioassay strain | Huiming Zheng |
| Plasmids | ||
| For gene expression | ||
| pMD19T | T-A cloning vector | Lab stock |
| pET-30(a) | Expression vector, Kanr | Lab stock |
| pET-pdeI | pET-30(a) derivative carrying pdeI | This study |
| pET-pdeR | pET-30(a) derivative carrying pdeR | This study |
| For gene knockout | ||
| pJQ200SK | Gmr, Mob+, lacZα, SacB | Zhongli Cui |
| pJQ-pdeI | pdeI deletion construct in pJQ200SK | This study |
| pJQ-pdeR | pdeR deletion construct in pJQ200SK | This study |
| pRK2013 | Helper plasmid, mob+ tra+, Kanr | Zhongli Cui |
| For lacZ fusion | ||
| pVIK112 | lacZ transcriptional fusion vector, R6K origin | Zhongli Cui |
| pPD0787 | pVIK112 derivative, PpdeI-lacZ | This study |
| pPD0786 | pVIK112 derivative, PpdeR-lacZ | This study |
| pPD4202 | pVIK112 derivative, Phmu-lacZ | This study |
| pPD1077 | pVIK112 derivative, Pfbp-lacZ | This study |
a
G−, Gram negative; Rifr, rifampin resistant; Kanr, kanamycin resistant; Gmr, gentamicin resistant.