TABLE 2.
Oligonucleotides used in this study
| Primer name | 5′–3′ sequence | Source or function |
|---|---|---|
| recTU-Fa | CCGGAATTCGGCGTACACCTCCTGAAGAT | A 1-kb fragment upstream of the recT gene |
| recTU-R | CGCGGATCCGCTGCTGTCTCCTTGTAACC | |
| recTD-F | CGCGGATCCCATGCCCAGCCGAACCATT | A 1-kb fragment downstream of the recT gene |
| recTD-R | CCCAAGCTTATGGCTCACTCCAGGTCGA | |
| recTA-F | GCGGTAGGTGTTCAGTTCG | A 3-kb fragment includes recT |
| recTA-R | TGAACGGCGAGCCTATCAG | |
| recT-F | CCGGAATTCCGGATTCACCACGAATACGG | Cloning the recT gene into pUCP18 |
| recT-R | CGCGGATCCATGAGCGAACCCACCCAAC | |
| PP9-1F | CTTCTGGAACTGCCGACTACT | Plaque PCR identification of the fragment of PP9W2 |
| PP9-1R | CGCTGGATTATCAACGTGAACA | |
| PP9-2F | CAACTGAGCTGAAGAAGGA | Plaque PCR identification of the fragment of PP8-1 or PP9-2 |
| PP9-2R | ATCTTGAACAGGAACGACAT | |
| PP8-2F | CGCAACTGCATACATTCTGGT | Plaque PCR identification of the fragment of PP8-2 |
| PP8-2R | AGTTCTTCGTCGTCCTCGTC | |
| PP9-3F | GTGGACAACGCTCAGAACAG | Plaque PCR identification of the fragment of PP9W |
| PP9-3R | AAGTGCGGCTGGCAGTAA | |
| PP9-4F | CATGGCAAGACCACTCTGAC | Plaque PCR identification of the fragment of PP8-3 or PP9-4 |
| PP9-4R | TGACGACCACCTTCTTCCTT | |
| PP9-5F | TCCAATCAGAACCGCCTAGC | Plaque PCR identification of the fragment of PP8-4 or PP9-5 |
| PP9-5R | CGCTTGCTCCGTTGATGGT | |
| P9L-F | CACGACAGGTTGAGGACGAT | Linear form in P9W when PP9W is excised |
| P9L-R | GCGAAGGTGCGGATCATCA | |
| P9I-F | AGCAGGCACGACAGGTTGA | I fragment in P9W when PP9W is integrated |
| P9I-R | CGTTCTTGCATCCTCCCTCTG | |
| PP9C-F | CGCTGAGATGGGCAGATATTG | Circular form in phage PP9W |
| PP9C-R | AATCCATCACATCGGGCATG | |
| PP9T-F | AACCCACCCAACTGGAGCA | Identification of the existence of the recT gene |
| PP9T-R | TTTCGCCCGTCTCGGTGTT | |
| pg47-F | GCATATCGGCGACAACATCA | Cloning pg47 into pEASY-T1 |
| pg47-R | GATTCCAGGACTCGACAAGATC | |
| rpoD-F | CGTCCTCAGCGGCTATATCG | Internal reference gene in RT-qPCR assay |
| rpoD-R | TCTTCCTCGTCGTCCTTCTCT | |
| pg10-F | AGACGAACCAAGGACCACATT | RT-qPCR assay for pg10 |
| pg10-R | CGGCATGGCACAGTATCATC | |
| pg26-F | CGAGGAGATGAAGGGCTTGT | RT-qPCR assay for pg26 |
| pg26-R | CGGAGAGCGGTTGTGACTT | |
| pg29-F | GGTGTGGTTCTCGTTCTCC | RT-qPCR assay for pg29 |
| pg29-R | GTTCCAGGTGATCCAGACTTC | |
| pg30-F | GACATCACATCCGCCATCCA | RT-qPCR assay for pg30 |
| pg30-R | TCGAAGCCGCTGAGGTACT | |
| pg40-F | TGATGCCGACCAAGAAGTGA | RT-qPCR assay for pg40 |
| pg40-R | GCCAAACGATACGACCGATAA | |
| pg48-F | TTCAGCAACGCGCAACTC | RT-qPCR assay for pg48 |
| pg48-R | TCGTCGTCCTCCTGCTCTT | |
| pg49-F | GCGGTTCGGATGATTGAGG | RT-qPCR assay for pg49 |
| pg49-R | TGTTCGTGCTCCTGAGTTCT | |
| pg50-F | AGCTCGACGACCTGGTGAT | RT-qPCR assay for pg50 |
| pg50-R | CGCTTGATGGTCAGTGCCA | |
| pg55-F | CCGAACCATTGAAGAGCAGTT | RT-qPCR assay for pg55 |
| pg55-R | GGACTCGCTGAGGAACATC | |
| pg56-F | ACAAGGATTGCCTGCTCATCAT | RT-qPCR assay for pg56 |
| pg56-R | TCGCTGTCGTCTGCTGGTT | |
| pg57-F | CGCTGTTCGAGAAGGTGAAG | RT-qPCR assay for pg57 |
| pg57-R | GCCGATTCCAGTTCCTCCT | |
| pg66-F | GGCAGTAGTAGAGGAATCCATC | RT-qPCR assay for pg66 |
| pg66-R | CGTTACGCAGATACAGCACTA | |
| fliM-F | GCGGTGCTGGAGATGAACT | RT-qPCR assay for fliM |
| fliM-R | TCGTGGTCGGACTGGAAAC | |
| pilB-F | AGTCGTATCTCTGCTCGTCTC | RT-qPCR assay for pilB |
| pilB-R | TCCTTCTGGTCCTCCTCGTA | |
| pctA-F | ACAAAGAGCAGGTGATGAAGAC | RT-qPCR assay for pctA |
| pctA-R | GGATGGCGACGATGGAGAT | |
| rmd-F | TGACTCAGCGTCTGTTCGT | RT-qPCR assay for rmd |
| rmd-R | GTGCCAAGGAGGTTGATCTG | |
| mexT-F | TCTGAACCTGCTGATCGTGTT | RT-qPCR assay for mexT |
| mexT-R | ATGGCGGTGGAGATGGAATC | |
| arnB-F | CCTGGCACCTGTTCATCCT | RT-qPCR assay for arnB |
| arnB-R | GAGTTCCACTCGCTGTTGG | |
| 19.1Sb | cggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccac | 50-bp single-strand DNA of pUC19 |
| 19.2S | gtggcgataagtcgtgtcttaccgggttggactcaagacgatagttaccg | Reverse fragment to 19.1S |
| 19.3S | ttcggtcctccgatcgttgtcagaagtaagttggccgcagtgttatcact | Another 50-bp single-strand DNA of pUC19 |
| CIP-F | ATTCATACGGCTGCCTCCAT | The promoter region of pg40 for EMSA dsDNA binding assay |
| CIP-R | CGCTGGTTGAGTCTGTCTGA | |
| 50P-F | AGAACTCAGGAGCACGAACA | The promoter region of pg50 for EMSA dsDNA binding assay |
| 50P-R | AGATTCACCACCAGGGTCTC | |
| 55P-F | GTCAACGACTTCATCGAACCG | The promoter region of pg55 for EMSA dsDNA binding assay |
| 55P-R | GGCTCGTCTCCATCGTCTTC | |
| 57P-F | CGAAATCACCAATTTCCAAGGG | The promoter region of pg57 for EMSA dsDNA binding assay |
| 57P-R | CCATAGCCACGCCATCAAG | |
| 59P-F | ACCCTGCTGGACCTCTTCA | The promoter region of pg59 for EMSA dsDNA binding assay |
| 59P-R | GCTGATGAACACGGCATCC | |
| M13-47 | CGCCAGGGTTTTCCCAGTCACGAC | Amplification of the promoter regions |
| RV-M | GAGCGGATAACAATTTCACACAGG |
a
The underlined sequences represent the recognition sites of different restriction enzymes.
b
The primers 19.1S, 19.2S, and 19.3S are also used for EMSA ssDNA binding assay.