TABLE 2.
Primers used in this work
| Primer name | Sequence (5′–3′)a | Function or description |
|---|---|---|
| OTn1 | GATCCTGGAAAACGGGAAAG | Identification of Tn5G insertion sites |
| OTn2 | CCATCTCATCAGAGGGTAGT | |
| lfsTU-F | CCGGAATTCCGGTCAGTCATGGCGAAAC | 1-kb fragment upstream of lfsT |
| lfsTU-R | CGCGGATCCAACCAAGATGACAGCCCATTG | |
| lfsTD-F | CGCGGATCCGTTGGCGTGTGGTACTGAAT | 1-kb fragment downstream of lfsT |
| lfsTD-R | CCCAAGCTTGCGTCCTTGTCTTGTTGTGA | |
| lfsT-F | CCGGAATTCGTGGCAGCGAAGAACTCATTG | Cloning of the lfsT gene into pUCP18 |
| lfsT-R | CGCGGATCCCTAAGGCGTGTCGGGCTCTT | |
| 72N-F | CCGGAATTCGGAAGCTATGACCACCATCTAC | Cloning of the gp72 gene into pUCP18 |
| 72N-R | CGCGGATCCGCTGTCATGTCAGGCAACC | |
| 71N-F | CCGGAATTCTTCGGATGGAACTCAAAGAC | Cloning of the gp71 gene into pUCP18 |
| 71N-R | CGCGGATCCGCGATCTCCTATCCAATGC | |
| OEX-F | CGCGGATCCGTGGCAGCGAAGAACTCATTG | Expression of lfsT in pET32a(+) |
| OEX-R | CCCAAGCTTCTAAGGCGTGTCGGGCTCTT | |
| gp02-Fb | AATTACGGAGTGTCGGTCTTC | DNA probe synthesis for Southern blotting |
| gp02-R | GGATGGATGTGTTGGAGAGTC | |
| gp71-F | AGCATGGAGCCTTACATATTCG | RT-qPCR assay for gp71 |
| gp71-R | ATAAGCGGACTTGTCTGGATTG | |
| gp72-F | TTTGGGACTCAAGACGAGACC | RT-qPCR assay for gp72 |
| gp72-R | CAACCGCCGACAGCATTTC | |
| gp75-F | GCGATTATTACCTGTCCGTAGA | RT-qPCR assay for gp75 |
| gp75-R | GGTGTTCAGTCGGCAGATG | |
| gp77-F | GCGTTCCTGTGATTCTCCTAAG | RT-qPCR assay for gp77 |
| gp77-R | ACTCGGTATGCTCGTTGTAGA | |
| gp58-F | AGCAGCGTAGTGATGAATGGT | RT-qPCR assay for gp58 |
| gp58-R | AATCGGCTCCAGGTCGGTA | |
| gp36-F | CCACACTAAGGCAGGCAAG | RT-qPCR assay for gp36 |
| gp36-R | CGCAGGTCGTGAATCGTAA | |
| faoA-F | GCAAGCCGAAGAAGGTCAC | RT-qPCR assay for faoA |
| faoA-R | GGAAGCCGATGCCGTAGAT | |
| 2550-F | GCGGCAACATAGACCACATC | RT-qPCR assay for PA2550 |
| 2550-R | TGCATGGCGTACCAGTAGG | |
| potA-F | CAGCCTGACGATCAACACC | RT-qPCR assay for potA |
| potA-R | GCTCTGGAACACCGTATGC | |
| popN-F | GGACATCCTCCAGAGTTCCTC | RT-qPCR assay for popN |
| popN-R | AAGGCGAAGGTCAGCTCTT | |
| rpoD-F | CGTCCTCAGCGGCTATATCG | Reference gene for RT-qPCR assay |
| rpoD-R | TCTTCCTCGTCGTCCTTCTCT | |
| E71-F | ATGGGAACGCCCATGATAA | Promoter region of gp71 for EMSA |
| E71-R | CTGAGCAATATACGCCGATC | |
| E72-F | CCCTGCTGTACCGTATGAGT | Promoter region of gp72 for EMSA |
| E72-R | GACACAGGTCCTCTTTCTTGAA | |
| E75-F | GCGATTACTACAGGGCTTTGT | Promoter region of gp75 for EMSA |
| E75-R | GTTCTGTCATGCCGATCTTGT | |
| E13-F | GGACAGCCTGGAGCACATT | Promoter region of gp13 for EMSA |
| E13-R | CGCACCATCCGATCAAACC | |
| E09-F | TCTGCGGTGAGCTTCTGAC | Promoter region of gp09 for EMSA |
| E09-R | ACCATGCCAGTGAGACATCC | |
| E04-F | TCGTGGACTTCAACCAGACA | Promoter region of gp04 for EMSA |
| E04-R | TTTCCTTGGCGTCGATCTTTG | |
| E01-F | GAAATAGTCGGGTTCCATCAGC | Promoter region of gp01 for EMSA |
| E01-R | GGTGTCCTAGCGAAAGGTTCT | |
| Epot-F | GGCGAAGGAACATCGAAGAC | Promoter region of potA for EMSA |
| Epot-R | CGCATCCCGCTCTAACTAGA | |
| Efao-F | GGCGTATGAATCGAGCGTTT | Promoter region of faoA for EMSA |
| Efao-R | CAAGAGGCTTAACCGTGATGG | |
| Epop-F | GCGACGAATTTCAGTGCCA | Promoter region of popN for EMSA |
| Epop-R | CGGAGGAACTCTGGAGGATG | |
| E255-F | TCAGGTTGGCTTCGGTATAGAT | Promoter region of PA2550 for EMSA |
| E255-R | TGGTAACGATGCCGGAACA | |
| M13-47 | CGCCAGGGTTTTCCCAGTCACGAC | Amplification of the promoter regions cloned into pMD19 |
| RV-M | GAGCGGATAACAATTTCACACAGG | |
| L71-F | CCGGAATTCATGGGAACGCCCATGATAA | Promoter region of gp71 for lacZ fusion |
| L71-R | CGCGGATCCCTGAGCAATATACGCCGATC | |
| L75-F | CCGGAATTCGCGATTACTACAGGGCTTTGT | Promoter region of gp75 for lacZ fusion |
| L75-R | CGCGGATCCGTTCTGTCATGCCGATCTTGT | |
| L13-F | CCGGAATTCGGACAGCCTGGAGCACATT | Promoter region of gp13 for lacZ fusion |
| L13-R | CGCGGATCCCGCACCATCCGATCAAACC | |
| L09-F | CCGGAATTCTCTGCGGTGAGCTTCTGAC | Promoter region of gp09 for lacZ fusion |
| L09-R | CGCGGATCCACCATGCCAGTGAGACATCC | |
| L04-F | CCGGAATTCTCGTGGACTTCAACCAGACA | Promoter region of gp04 for lacZ fusion |
| L04-R | CGCGGATCCTTTCCTTGGCGTCGATCTTTG | |
| L01-F | CCGGAATTCGAAATAGTCGGGTTCCATCAGC | Promoter region of gp01 for lacZ fusion |
| L01-R | CGCGGATCCGGTGTCCTAGCGAAAGGTTCT | |
| Lpot-F | CCGGAATTCGGCGAAGGAACATCGAAGAC | Promoter region of potA for lacZ fusion |
| Lpot-R | CGCGGATCCCGCATCCCGCTCTAACTAGA | |
| Lfao-F | CCGGAATTCGGCGTATGAATCGAGCGTTT | Promoter region of faoA for lacZ fusion |
| Lfao-R | CGCGGATCCCAAGAGGCTTAACCGTGATGG | |
| Lpop-F | CCGGAATTCGCGACGAATTTCAGTGCCA | Promoter region of popN for lacZ fusion |
| Lpop-R | CGCGGATCCCGGAGGAACTCTGGAGGATG | |
| L255-F | CCGGAATTCTCAGGTTGGCTTCGGTATAGAT | Promoter region of PA2550 for lacZ fusion |
| L255-R | CGCGGATCCTGGTAACGATGCCGGAACA | |
| LC-F | AGCCACAATCCTGTGCTCTAC | Quantification of lysogenic copies |
| LC-R | AAAGGAATTTCACGATTGGCAC | |
| TC-Fc | AGGAAGGCTACAGCGTCTC | Quantification of total copies |
| TC-R | GGCGGTCTTGGTCATCAGT | |
a
The underlined sequences represent the sites of recognition of different restriction enzymes.
b
Primers gp02-F and gp02-R were used to amplify the designed probe region of gp02 (502 bp).
c
Primers TC-F and TC-R were used to amplify the specific fragment of phage PP9W2 integrated into the genome of P8W.