TABLE 3.
Primers used in this study
| Primer | Sequence (5′→3′)a |
|---|---|
| Primers for saeS deletion and complementation plasmid construction | |
| SaeS up BamHI (forward) | GGGGGATCCAACAACGACAACTAGCGGTAAAGA |
| SaeS up Sall (reverse) | AGTGTCGACACACCATTATCGGCTCCTTTCA |
| SaeS down EcoRI (forward) | CCCGAATTCTAGCCCATGATTTAAAAACACCTT |
| SaeS down Bglll (reverse) | CCCAGATCTTTCCTACATCTATATCACTGCTTACACTG |
| SaeRS Comp II KpnI For | TTTTTGGTACCGGTAAATTAATGCTTACTAACTACAA |
| SaeRS Comp II EcoRI Rev | CCCCCGAATTCTTATGTCGTAATGTCTAATTTGTG |
| Primers for sarA deletion and complementation plasmid construction | |
| SarA upstream For attB1 | GGGGACAAGTTTGTACAAAAAAGCAGGCTAGGTGCAGCATTAACAACACT |
| SarA upstream Revb | AATTGCCATGGTTAAAACCTC |
| SarA downstream Forb | GAACTATAATTTTGTTTAGCG |
| SarA downstream rev primer attB2 | GGGGACCACTTTGTACAAGAAAGCTGGGTTGAGGGAGGTGTCACAATGA |
| SarA complement KpnI For | TTTTTGGTACCTTTAACATTTAGCTTATCATTTTAA |
| SarA complement SacI Rev | CCCCCGAGCTCTTATAGTTCAATTTCGTTGTTTGCT |
| Primers for sequencing | |
| SaeRS screen For | CTGGGGGATATGTTTTACC |
| SaeRS screen Rev | GTCCCTATGCGTATTAAGGA |
| pMAD seq FP | GGGGAAGGCCATCCAGCCTCGCGTC |
| pMAD seq RP | AATCTAGCTAATGTTACGTTACACA |
| SarA flank For | TCTTATCATTAAAACTGCACTGGGA |
| SarA flank Rev | GCGGTGGCAATTCGTTCATT |
| pKOR1For | CAGATCCATATCCTTCTTTTCTGA |
| pKOR1 Rev | GTGTGGAATTGTGAGCGGATA |
| pALC2073 Seq For | GGTTGCATGCCTGCAGGTCGACGG |
| pALC2073 Seq Rev | CAGTCACGACGTTGTAAAACG |
| Primers for qRT-PCR analysis | |
| tst-For | CTGATGCTGCCATCTGTGTT |
| tst-Rev | GTAAGCCCTTTGTTGCTTGC |
| agrA-For (P2) | GTGAAATTCGTAAGCATGACCCAGTTG |
| agrA-Rev (P2) | TGTAAGCGTGTATGTGCAGTTTCTAAAC |
| rnaIII-For (P3) | TAGATCACAGAGATGTGA |
| rnaIII-Rev (P3) | CTGAGTCCAAGGAAACTAACTC |
| saeR-For | CCAAGGGAACTCGTTTTACG |
| saeR-Rev | ACGCATAGGGACTTCATGAC |
| sarA-For | TGTTTGCTTCAGTGATTCGTTT |
| sarA-Rev | CATCAGCGAAAACAAAGAGAAA |
| rpoB-For | TCCTGTTGAACGCGCATGTAA |
| rpoB-Rev | GCTGGTATGGCTCGTGATGGTA |
| Primers for EMSA experiments | |
| SaeP1-For-biotin | ATTAGTTAAGCGATATTTAAACGAAGTTAAGAATTAGTTAATGGCA |
| SaeP1-Rev | TGCCATTAACTAATTCTTAACTTCGTTTAAATATCGCTTAACTAAT |
| ptst-For-biotin | AAAGTGACTTTAAAGAATATAACTA |
| ptst-Rev | TTTTAATTCTCCTTCATTCAAATGT |
| Probe1-For-IRDye800 | GTAACAAACACTTTTTAATTAATATATATTTAAACAATAATTTAGA |
| Probe1-Rev | TCTAAATTATTGTTTAAATATATATTAATTAAAAAGTGTTTGTTAC |
| Probe 2-For-IRDye800 | TTTTTAATTAATATATATTTAAACAATAATTTAGAGATGGTTAATTGATT |
| Probe2-Rev | AATCAATTAACCATCTCTAAATTATTGTTTAAATATATATTAATTAAAAA |
| Probe3-For-IRDye800 | AATTTAGAGATGGTTAATTGATTCATTTAAATAATATTTATACATTCT |
| Probe3-Rev | AGAATGTATAAATATTATTTAAATGAATCAATTAACCATCTCTAAATT |
a
Restriction sites (indicated in the primer name) are underlined in the primer sequence, and attB sites are shown in boldface.
b
Primer contained a phosphate group for blunt-end ligation.