TABLE 2.
Oligonucleotides used in this study
| Oligonucleotide name | Sequence (5′–3′)a | Function |
|---|---|---|
| ndvBp-F-2b | cttctcctttactcatatgtatatctccttcAGAGATGAAACCAGGTTCCGG | PndvB-gfp fusion |
| ndvBp-R-2b | caaaaacgcgtaacaaaagtgtctataatcaACCCGGCAGGCCGGGTTG | PndvB-gfp fusion |
| AH-GFP-Tag-Fb | tcatccgccaaaacagccaagcttgcatgcctgcagactagtGGAGTCCAAGCTCAGCTAATTAAGC | GFP stability tag |
| AH-GFP-Tag-Rb | acagctgctgggattacacatggcatggatgaactatacaaaAGGCCTGCAGCAAACGACGAA | GFP stability tag |
| rpoSdel1 | ATCCATGGATCCTAGTCTGATCGGCCGTTTTG | rpoS deletion |
| rpoSdel2 | ATCATCGTGGTCAAACTCCG | rpoS deletion |
| rpoSdel3 | CGGAGTTTGACCACGATGATGACAAGCAGCGTGAGGTGGT | rpoS deletion |
| rpoSdel4 | ATCCATCTGCAGTGCCAGAAAACCCAGCGAAG | rpoS deletion |
| rpoScompF | AATAATGGTACCCTGCGAGCGGTAGTCTGATC | rpoS complementation |
| rpoScompR | CATCATAAGCTTATCTACTTAGGCTCACACGC | rpoS complementation |
| ndvBp-lacZ for | ATCCATCTGCAGGGACTAGACTTGCAACAGAC | PndvB-lacZ fusion |
| ndvBp-mut-lacZ forc | ATCCATCTGCAGGGAAGAGACTTGCAACAGAC | Mutant PndvB-lacZ fusion |
| ndvBp-lacZ rev | ATCCATAAGCTTAGAGATGAAACCAGGTTCCG | PndvB-lacZ fusion |
| Tn7R | CACAGCATAACTGGACTGATTTC | Tn7 insertion verification |
| glmS-down | GCACATCGGCGACGTGCTCTC | Tn7 insertion verification |
| ndvB-F | ACAAGGGCTTCTTCCACATC | ndvB qPCR |
| ndvB-R | TCTTCGGTGATGCACCATTC | ndvB qPCR |
| rpoD-F | TCCATCGCCAAGAAGTACAC | rpoD qPCR |
| rpoD-R | TTGTAGCCACGACGGTATTC | rpoD qPCR |
| rpoS-F | CGAACCTTCACCCGAAGAAA | rpoS qPCR |
| rpoS-R | AAGAGAGACGTCTACCGAAGT | rpoS qPCR |
| gfp-gsp1 | AGCACGTGTCTTGTAGTTCC | 5′ RACE |
| gfp-gsp2 | ATCTGGGTATCTCGCAAAGC | 5′ RACE |
| gfp-gsp3 | CTACAGGATCCGAAAGTAGTGACAAGTGTTGG | 5′ RACE |
| 3′ RACE adapter primer | GGCCACGCGTCGACTAGTAC(T)17 | 5′ RACE |
| AUAP | GGCCACGCGTCGACTAGTAC | 5′ RACE |
| M13R | TCACACAGGAAACAGCTATGAC | Sequencing |
a
Restriction sites are indicated in bold.
b
Primer used for yeast-recombination cloning. Uppercase in the sequence indicates sequences targeted for PCR amplification. Lowercase in the sequence indicates sequences homologous to the vector used for recombination.
c
Primer contains two changes (underlined) to the predicted ndvB promoter element.