TABLE 2.
Primers used in this study
| Primer function and name | Sequence (5′–3′) |
|---|---|
| 77bpIR mutant construction, verification, and complementation | |
| ErmF | CCGATAGCTTCCGCTATTGC |
| ErmR | GAAGCTGTCAGTAGTATACC |
| Ermchk1 | CGTAAATGTTCAACCAAAGCTGTG |
| Ermchk2 | CTCAAGTCTCGATTCAGCAATTGC |
| R2-77bpIR | TGTAGATAAATTATTAGGTATACTACTGACAGCTTCTGGAATTATTACATTCTTTGTGCA |
| F2-77bpIR | ACCGATGAGCAAAAAAGCAATAGCGGAAGCGATCGGATCATTCCACTGGGATTTAGGA |
| F3-77bpIR | GCTCCGCGATGCCCTCAAA |
| R3-77bpIR | CCC AAG CAA CCA ATA ACAGACACA |
| 77bpIR complementation strain construction | |
| F3-77bpIR | GCTCCGCGATGCCCTCAAA |
| R1-77bpIR | TAACATCCCCAGAAGCACCAGACT |
| TetQ-F | CGTTCCATTGGCCCTCAAAC |
| TetQ-R | CTCCTGCCATTCATAGAGGC |
| Knock-in-R1 | GGAGCACAAGTGCTGTTGAC |
| pTloop1 plasmids | |
| Loop1Hind-Forw | CAAGAAGCTTTCCATATGTCAGAGATTCAAATCATAGAG |
| Loop1Eag-Rev | CAAGCGGCCGTTAATGGGACCTTTGCACAATAAGCA |
| Loop2Ale-Forw | CATTCACTGACGTGTGACAATCAAATCCTTTCAACG |
| Loop2Eag-Rev | TGATCGGCCGTCTGCACTGGCAATGTAACC |
| 5′/3′ RACE | |
| First-round PCR | |
| sORF + 140Rev | CGGATTTCCACAAGTGGAAAGATAG |
| sORF + 170Fwd | ACCAAATAGTCGCCTGACACA |
| Second-round PCR | |
| sORF + 130Rev | GTGGAAAGATAGCTTTCCACCG |
| sORF + 210Fwd | AAAGTGCCTGCTTATTGTGCAAAG |
| Third-round PCR | |
| sORF + 28Rev | ACATCCAACGACATGACCGT |
| 0106p1-Rev | GAGCGTAGCAATCGTTAGATC |
| qRT-PCR | |
| PG0108-Forw | CATGTGTAGAGGCTGCAAC |
| PG0108-Rev | GACGCTCTCGATAGATTAGATCAG |
| PG0113-Forw | CGTCCAGGAGATAGACTGATTGTTAC |
| PG0113-Rev | TGGTGGATAATAAGGCATCATAATCA |
| PG0118-Forw | GCGATGAATTGACAGAACAGCAT |
| PG0118-Rev | TTGCGTAATTTGGCTCATAATAACTG |
| PG0121-F2 | TGTAGCTGAAAAGGCCAACC |
| PG0121-R2 | GCACGCTCGCTCACTGAGAA |
| PG1138-F1 | GCTGCGAAAAAGTTCTGTCC |
| PG1138-R1 | GTATATCCCCCTCCCATTGC |
| PG_1141-Forw | GGCAGCAGATTATGCCATCA |
| PG_1141-Rev | GAGGCAAATCAGTGGCTACAA |
| 16S-Forw | TGTTACAATGGGAGGGACAAAGGG |
| 16S-Rev | TTACTAGCGAATCCAGCTTCACGG |
| asRNA RT-PCR | |
| asRNA-Forw | GATTGGAGGAGCACAAGTGCTGTT |
| asRNA-Rev | AGTGGAAAGATAGCTTTCCACCGG |