Table 2.
Primers used in this study
| Plasmid | Primer | Sequence | Description |
|---|---|---|---|
| pCovRKO | LW 2-1 | GCGTGGCGGCCGCGAGAATATCTAGCTGATGCTA | Sense primer, covR upstream flanking region; NotI |
| LW 2-2 | GCGTGGGATCCTTATACCAACCCTTATCCTC | Antisense primer, covR upstream flanking region; BamHI | |
| LW 2-3 | GCGTGGGATCCTAAGTCATATGGAAAATCAG | Sense primer, covR downstream flanking region; BamHI | |
| LW 2-4 | GCGTGGGTACCCTTCTTGTTTGCCAGTCACTGAAAG | Antisense primer, covR downstream flanking region; KpnI | |
| pJC227 | JC195 | CATGGCGGCCGCAGAAGCTCAAGAGATGACC | Sense primer, shp3 upstream flanking region; NotI |
| JC284 | CATGAGATCTTTACCCACCAACAATAATG | Antisense primer, shp3 upstream flanking region; BglII | |
| JC273 | CATGACGCGTTACTTAGGTGTATACCTAAG | Sense primer, shp3 downstream flanking region; MluI | |
| Spy0533_S2 | GCGTGGCGGCCGCGAAAAAAAATATT | Antisense primer, shp3 downstream flanking region; NotI | |
| JC285 | CATGAGATCTATTAATCACCAAAAAG | Sense primer for luxA; BglII | |
| JC275 | CATGACGCGTTTATGGTAAATTCATTTCGAT | Antisense primer for luxB; MluI | |
| pJC258 | JC256 | CATGGCGGCCGCGGTTATATTGCTAGTGGTGC | Sense primer; spyCEP upstream flanking region; NotI |
| JC259 | CATGGCGGCCGCAGGCATCAAAGCATACTCG | Antisense primer; spyCEP downstream flanking region; NotI | |
| JC344 | CATGTTAATTAACCTGACGAGTACCAGTGC | Antisense primer; spyCEP upstream flanking region; PacI | |
| JC345 | CATGTTAATTAAGCAGACTGGCTTGTCACT | Sense primer; spyCEP downstream flanking region; PacI | |
| JC320 | CATGTTAATTAACGATACTATGTTATACGC | Sense primer for aphA3 cassette; PacI | |
| JC321 | CATGTTAATTAAAGCGAACTTTTAGAAAAG | Antisense primer for aphA3 cassette; PacI | |
| pJC273 | JC369 | CATGGCGGCCGCTGCTGGTATAGAGATTTCTG | Sense primer, shp3 upstream flanking region; NotI |
| JC284 | See above | ||
| JC342 | CATGTTAATTAAGTTACTTAGGTGTATACCTAAG | Sense primer, shp3 downstream flanking region; PacI | |
| Spy0533_S2 | See above | ||
| JC340 | CATGAGATCTAGAAGGAGGAAAAATATGTTA | Sense primer for gus; BglII | |
| JC343 | CATGTTAATTAATCATTGTTTGCCTCCCTG | Antisense primer for gus; PacI | |
| pRVW14 | JC147 | CATGGAATTCGTGTCGGAAAGTAAACATGC | Sense primer for shp3 promoter; EcoRI |
| RW13 | GTATGTAAGCAAAAAGTTTCCAAATTTCATAAGTGGACTTCCTTTCAG | Antisense primer for shp3 promoter; luxA overlap underlined | |
| JC106 | ATGAAATTTGGAAACTTTTTGCTTACATAC | Sense primer for luxA | |
| RW14 | CATGGGATCCACTAGTGACTATCAAACGCTTCGG | Antisense primer for luxE; BamHI | |
| pRVW19 | RW36 | ATCGGAATTCTCAGAAATGGACTATTATGGCTTT | Sense primer, pepO upstream flanking region; EcoRI |
| RW37 | ATCGTTAATTAATCGTATCTCCTTATATCATTTTAAAT | Antisense primer, pepO upstream flanking region; PacI | |
| JC397 | GCATGTTAATTAAATGGCTAAAATGAGAATATCACC | Sense primer for aphA3; PacI | |
| JC304 | GCATGACGCGTCCCTCCTTGTATTTTCAATAAT | Antisense primer for aphA3; MluI | |
| RW38 | ATCGACGCGTTTAGGTAGTTGATAAACCTTCAAATGC | Sense primer, pepO downstream flanking region; MluI | |
| RW49 | CTAGGTCGACCGTTGCTGCTGTTGTTGA | Antisense primer, pepO downstream flanking region; SalI | |
| pRVW21 | RW44 | ATCGAGATCTAATATGGTCCGTAAAACTTTATTAAAACTTG | Sense primer for recA promoter; BglII |
| RW41 | TTGATAAGTTGTCATTACTTTCTCCTCTTTTTTAACAAACCATCG | Sense primer for pepO; recA promoter overlap underlined | |
| RW43 | AAAGAGGAGAAAGTAATGACAACTTATCAAGATGATTTTTACCAG | Antisense primer for recA promoter; pepO overlap underlined | |
| RW42 | ATCGGAATTCTTACCAAATAATCACACGGTCTTT | Antisense primer for pepO; PstI | |
| pRVW23 | RW58 | TTTAAGAAGGAGATATACAATGACAACTTATCAAGATGATTTTTAC | Sense primer for pepO. Upstream plasmid flanking region underlined |
| RW59 | CAGTGGTGGTGGTGGTGGTGCTCGAGCCAAATAATCACACGGTC | Antisense primer for pepO. Downstream plasmid flanking region underlined | |
| pRVW24 | RW55 | ATCGGAATTCCTAAAAGCCTGAGGTTAGGCGAATTC | Sense primer for pepO promoter region; EcoRI |
| RW56 | AAGTTTCCAAATTTCATTCGTATCTCCTTATATC | Antisense primer for pepO promoter region fusion to luxA | |
| RW57 | GATATAAGGAGATACGAATGAAATTTGGAAACTTTTTGCT | Sense primer for luxA. pepO promoter region overlap underlined | |
| RW14 | CATGGGATCCACTAGTGACTATCAAACGCTTCGG | Antisense primer to amplify luxE; BamHI | |
| pRVW25 | RW60 | CATGACGCGTGCGAAAAAGGAGAAGTCGGTTCAGAA | Sense primer to amplify cat; MluI |
| RW61 | CATGTTAATTAAGCTTGATGAAAATTTGTTTGATTT | Antisense primer to amplify cat; PacI | |
| pRVW27 | RW66 | CCTCTAGACTCGAGGTAAAACAGACAAAAACCTCTG | Sense primer for spyCEP promoter; flanking plasmid region underlined |
| RW67 | CAAATTTCATCTGATACCCTCCTAAATGTTTTAAC | Antisense primer for prtS promoter; flanking luxA region underlined. | |
| RW68 | GGTATCAGATGAAATTTGGAAACTTTTTGC | Sense primer for luxA. Flanking prtS promoter region in lowercase. | |
| RW69 | GTTGGGAGCTCTCCGACTATCAAACGCTTCGGTTAAG | AS primer for luxE. Flanking plasmid region underlined. | |
| Other Primers | |||
| RW62 | CAGGATGATTCGTTTATGAC | Sense primer, 1100 bp upstream pepO, for deletion verification | |
| RW63 | GATGGTGACATGGACAAAG | Antisense primer, 1100 bp downstream pepO, for deletion verification | |
| ISS1-FOUT1 | GCAAGAACCGAAGAAATGGAACG | Sense primer for ISS1 amplification, (Maguin et al., 1996) | |
| ISS1-ROUT1 | GATTGTAACGTAGATAATAACCAACAGC | Antisense primer for ISS1 amplification, (Maguin et al., 1996) | |
| ISS1-ROUT2 | AATAGTTCATTGATATATCCTCGCTGTCA | Sequencing primer for ISS1 junction site identification, (Maguin et al., 1996) |