TABLE 2.
Primers used in this study
| Primer function and gene or primer name | Primer directiona | Primer sequence (5′→3′)b | Efficiencyc | Restriction site added |
|---|---|---|---|---|
| Expression studies | ||||
| rpoA | F | AAACCGCGCCTGGTAGATA | 1.78 | |
| R | CCTTTCAGGTTGAGCAGGAT | |||
| rhlA | F | GCATATTTCCGATCCTGCAC | 1.93 | |
| R | CCCAGGAAATCGACAGGATA | |||
| virK | F | CGTCCAAGTCGCTGAAAAGC | 1.93 | |
| R | CCTGATAACGCATGAACTGC | |||
| nipE | F | CAACATTCCCCCTCTGGATT | 1.94 | |
| R | GTGCAACGTGTTGGATTTGT | |||
| avrL | F | GCTTGTCGCAGGCAGTTTAC | 1.94 | |
| R | CGGGAACTTGATCTGGTTGA | |||
| avrM | F | GATTATCGGCGGCTTATTCA | 1.96 | |
| R | CGGCCTCGACATCTTTTATG | |||
| ahpC | F | AGAAAAGCATCGAAGGCAAA | 1.92 | |
| R | CATGCCAGGCTTTGTGAGTA | |||
| fabI | F | CATCTTCCGCAACATCACAC | 1.94 | |
| R | ACGGTAAGCGCATTCTGGTA | |||
| indA | F | TACGGCCAGAAAGATTGAGG | 1.95 | |
| R | GCCAGAATCACCGGAATATC | |||
| fadR | F | GGATTCGCGGAAGAGTACAT | 1.80 | |
| R | GGTTTACCGTGCTGAATCGT | |||
| rsmA | F | GAGTTGGCGAAACCCTCAT | 1.96 | |
| R | GCTGAGACTTCTCTGCCTGAA | |||
| hns | F | GCGAAGCACTTAAGATTCTAAACA | 1.86 | |
| R | CTTTACCGGCAACTTTGCTT | |||
| rpmE2 | F | CGGGTATCCATCCCAACTAC | 1.94 | |
| R | CGCTACCTTCTTTGGCGTAT | |||
| ffh | F | TGGTGCGTGATTTCATCAAT | ||
| R | CTTACCAACGCTGGTGGTTT | 1.92 | ||
| Gene cloning | ||||
| rhlAdeb | GCTCTAGACTGTCTGAAGACACAGTCAGATTC | XbaI | ||
| rhlAstop | CCGTGATAGCGCTGGTTATTC | |||
| virKdeb | GCTCTAGACTGCTGAGTCCCGACAGCGG | XbaI | ||
| virKstop | CGATGGCTGCCGGAACCGGC | |||
| nipEdeb | CAGATGTTCGAGTTGGCG | |||
| nipEstop | CGCCAGTTACAGCCAGAC | |||
| ahpCdeb | GCTCTAGATGGGCCGCATCTGTGCCG | XbaI | ||
| ahpCstop | CGTCCAGCGTCGCCACTAAC | |||
| avr1B1 | CAACGATATCATCCGAATCATG | |||
| avr1B2 | CTTAAGTCCGTTTTCCGAGCATG | |||
| avr2B1 | CTTAAGTGCTGGATGGAACGGTATTCAC | |||
| avr2B2 | TGATCAGGCGAAATTCGGCACGCAGTTC | |||
| Regulatory region cloning | ||||
| RRrhlA5′ | GCTCTAGACTGTCTGAAGACACAGTCAGATTC | XbaI | ||
| RRrhlA3′ | GGAATTCAATAATGGTTTCATGTGCAGG | EcoRI | ||
| RRvirK5′ | GCTCTAGACTGCTGAGTCCCGACAGCGG | XbaI | ||
| RRvirK3′ | GGAATTCGACTTGGACGCCACGGCC | EcoRI | ||
| RRnipE5′ | GCTCTAGAGAATATTATCCCTCATGGGTG | XbaI | ||
| RRnipE3′ | GGAATTCCAGTTTGTCAAAATCATCG | EcoRI | ||
| RRavrL5′ | GCTCTAGACAACGATATCATCCGAATCATG | XbaI | ||
| RRavrL3′ | GGAATTCGCATAAGCGGCTCTCGCCGCC | EcoRI | ||
| RRaphC5′ | GCTCTAGATGGTGCCGCATCTGTTGCCG | XbaI | ||
| RRahpC3′ | GGAATCGTAAAGTCAGCCGGATAGAAG | EcoRI | ||
| mfhR5′ | CCGTTTTGGTGAATTGCGCAAAG | |||
| mfhR3′ | GCAGATCTTTTAGCCTTGCGCCCGCGCG | BglII | ||
| Primer extension | ||||
| rhlA-pExt1 | GACAATGCATTTTTCTATGG | |||
| virK-pExt1 | GCAGCACAGGGGTAATACG | |||
| nipE-pExt1 | GCCAGTACAGCTGTCTTCTT | |||
| avrL-pExt1 | GCGCCCCAGAGAAATATGC | |||
| ahpC-pExt2 | GTAAAGTCAGCCGGATAGAAG |
a
F, forward; R, reverse.
b
Restriction sites are underlined.
c
Primer PCR efficiency was estimated via a calibration dilution curve and slope calculation. Efficiency = 10−1/slope.