TABLE 3.
Primers used in this study
| Primer | Sequence (5′–3′) |
|---|---|
| ΔrpoX-up-F | CTAGTGGGGCCCTTCTAGATGCAATTCATTTGAGTATCAGTTTGG |
| ΔrpoX-up-R | GCTAAAAATCTGACAGTTCATCCGTGACAGCTCGG |
| ΔrpoX-down-F | TGAACTGTCAGATTTTTAGCCCCTTATCCTAGCCG |
| ΔrpoX-down-R | CGGGAGAGCTCAGGTTACCCCTGACTTTAACCTTCAACACATCGA |
| ΔrpoX-out-F | TGCTGGAGACCGAGCAATAGTTGCC |
| ΔrpoX-out-R | ACGAGCCATTTAATGGTGCAGAGCA |
| ΔrpoX-in-F | ATGAAAGAATCGTTGTCAGTTGGGA |
| ΔrpoX-in-R | TTAAACCCAACCATCGAATCGGAGA |
| ΔN646_4611-up-F | GAGCTCAGGTTACCCGCATGCAAGATCTATTATGGACTTTGGCGCAGTCATAATG |
| ΔN646_4611-up-R | ATAACTTGGAACGTCATCTCCAGCAATTGCTGATTG |
| ΔN646_4611-down-F | TGGAGATGACGTTCCAAGTTATAACAGACTGTCAGC |
| ΔN646_4611-down-R | CCCTCGAGTACGCGTCACTAGTGGGGCCCTGACAGCTCGGAACCTAGCAAAGCAT |
| ΔN646_4611-out-F | GAGTACGCGGCGAACAACCAAATCG |
| ΔN646_4611-out-R | CGAGACAACAAATCAATGCCCAC |
| ΔN646_4611-in-F | CACCTGATTGAGCAATTGGC |
| ΔN646_4611-in-R | GTAAACTCAGGATAGTAAGC |
| rpoX-Flag-F | CCATACCCGTTTTTTTGGGCTAGCGAATTCAGGCCAATTTGCGTACAAATACTAT |
| rpoX-Flag-R1 | CTTGTCGTCGTCGTCCTTGTAGTCAACCCAACCATCGAATCGGAGACGT |
| Flag-R2 | GGTCAGCATGGGTACCTTTCTCCTCTTTAATTACTTGTCGTCGTCGTCCTTGTAGTC |
| N646_4611-Flag-F | CCATACCCGTTTTTTTGGGCTAGCGAATTCTTCAGCCGTAAAATGAAGCATAGAG |
| N646_4611-Flag-R | CTTGTCGTCGTCGTCCTTGTAGTCATTCACTTGACGAAGCGCAGGTTGA |
| rpoE-pET22b-F | ATCGGATCCGATGAACGAGCAGCTGACCGATC |
| rpoE-pET22b-R | ATATGTCGACGCGTTGCAAAAGAGGTCTGATT |
| rpoX-pET22b-F | ATCGGATCCATGAAAGAATCGTTGTCAGTTGGGA |
| rpoX-pET22b-R | ATATGTCGACAACCCAACCATCGAATCGGAGA |
| pDM8-PrpoX-F | ATCCCGGGAGGCCAATTTGCGTACAAATACTTG |
| pDM8-PrpoX-R | ATCCCGGGTGACAGTTCATCCGTGACAGCTCGG |
| rpoX-RACE-nested | TCACGAGACAACAAATCAATGCCCA |
| rpoX-RACE | CAACATTTCGCGCGCTTCTTCATCA |
| RACE-adapter | GCGCGAATTCCTGTAGA |
| RACE-adapter2 | GCGCGAATTCCTGTAGAACGAAC |
| RNA-Linker | AUAUGCGCGAAUUCCUGUAGAACGAACACUAGAAGAAA |
| PrpoXcy5-F | TGCCTGCAGGTCGACGATCGGCCAATTTGCGTACAAATACTTG |
| PrpoXcy5-R | TGACAGTTCATCCGTGACAGCTCGG |
| PN646_4603cy5-F | TGCCTGCAGGTCGACGATCTCGACTGCTGTTTTTCTTCT |
| PN646_4603cy5-R | ATTTATCATTATCCCACCGCAC |
| PN646_4601cy5-F | TGCCTGCAGGTCGACGATCAATCGACAACAAAGTATACAAACCAAGAC |
| PN646_4601cy5-R | CTCTAGTTCTGACTCCGGCACAT |
| PN646_1623cy5-F | TGCCTGCAGGTCGACGATCAGACTCTTTTGCAAATGGCTTG |
| PN646_1623cy5-R | TTTTTAAATTCCTAGAATAAACTGATACTAAATAAAT |
| gyrB cy5-F | TGCCTGCAGGTCGACGATCGCACTATCAGAGAAAGTTGAGC |
| gyrB cy5-R | CCACCTTCATACATGAAGTGATCA |
| rpoE-qRT-F | TGTTGCTCAAGGGCGTAGAC |
| rpoE-qRT-R | CGATTGCACTGAACACCACC |
| rpoX-qRT-F | TAATGAACAATGGCCGCACG |
| rpoX-qRT-R | GCTCTGCTTTCACCCCTGAG |
| rpoH-qRT-F | GCGAGTTAGGTGTTGAGCCT |
| rpoH-qRT-R | ATAGCATCGGCGCTGTGTAA |
| N646_3697qRTF | GCTCAGTTCTCGCAGGTACA |
| N646_3697qRTR | AACAAGGCCCGCTGTTGATA |
| N646_3696qRTF | AGAGAAGCGTTTTGAGCCGA |
| N646_3696qRTR | ATTCGTTTCGAAGCTGCGTG |
| N646_3695qRTF | GTCCTCGCCAGTAACCTAGC |
| N646_3695qRTR | CACCGGTTTGTTCACACCAC |
| N646_0523qRTF | CGCGTCCCTTCAACCAAATC |
| N646_0523qRTR | ACAGCTCGCACAGATGTCAA |
| N646_4604qRTF | GCAGTACCGAGACTTGGTGG |
| N646_4604qRTR | GTAAACCACGAGGCGATCCA |
| 16S RNA-qRT-F | AAAGCACTTTCAGTCGTGAGGAA |
| 16S RNA-qRT-R | TGCGCTTTACGCCCAGTAAT |