Table 3.
Primers used in this study
| Designation | Sequence (5` - 3`) | Comment and reference |
|---|---|---|
| Primers for the mobilisation experiments | ||
| Cm_fw_PstI | CTGCAGGCTTGTCAGGGGGGCGGAG | cat cassette in pGP704 |
| Cm_rev_PstI | CTGCAGACCCTGCCCTGAACCGACGA | " |
| pir_fw_SacI | TTTGAGCTCCCGTCAAGTCAGCGTAATGCTC | Introduction of a stop codon into pir |
| pir_revStop_ EcoRI | TTTGAATTCTCAAGCTTCATCATCTTTATCGCCAGA | " |
| paiII_1XhoI | TTTCTCGAGGGGAAGCACGATATGCAGCC | Labelling of PAI II536 by homologous recombination with pSG704 |
| paiII_1SacI | TTGAGCTCGATATTTTTTGGCTGCTTCAGCTTTACG | " |
| paiII_2SacI | TTTGAGCTCGGACAAGAACACAAAATCACTCTACTGA | " |
| paiII_2XhoI | TTTCTCGAGCCCGGCTTCATCGACAATGA | " |
| ATT1 | GAGGTACCAGCGCGGTTTGATC | Confirmation of pir integration into the λ attachment site (E. coli) |
| ATT2 | CAGATGGCGCAATGCCATCTGG | " |
| 17 kD up | CCCGGCTGAACAGACGATT | Screening PCRs for PAI II536 |
| 17 kD in | GCAGCGGAGAGTCATTGTC | " |
| hlyDup | CGCGATAATCCGCTACATC | " |
| hlyDin | GGGTATGGCTGTCACTGCA | " |
| hec_down1 | CACACTGAAAGGCCGCAGC | " |
| hec_down2 | GTACAGCGTGCCGTTCTGC | " |
| dsdXin | GCTGTATCCCGACATCAGC | " |
| dsdAup | GCCACATCATTCTCCCGTA | " |
| ORFAin | CATCCCCTTCACTACAGGA | " |
| Na-Anti_pdo | CAGCGATGCTGGACCGTAT | " |
| PaiII_1fw | CAACCGTAGAAATACGTGCCG | Overlapping PCRs of PAI II536 |
| PaiII_1rev | CCAGTATGAGGCAAACCCTAAAG | " |
| PaiII_2fw | GACAATAGCTGTCCATACGGTG | " |
| PaiII_2rev | CAATGCTGGCCATATCCATCAG | " |
| PaiII_3fw | GACTCACTACTGGGAAGGTC | " |
| PaiII_3rev | GATGGTCATGTGCAGGGAGG | " |
| PaiII_4fw | GTGATGTCACTGGCGGTAATAATC | " |
| PaiII_4rev | GGCGATGACCATGATACGGTA | " |
| PaiII_5fw | CGGAATACTGAACTGCGGATAA | " |
| PaiII_5rev | GCTGGATGCCAATCAATGATCG | " |
| PaiII_6fw | GCATCCATCTCCGTTCACAG | " |
| PaiII_6rev | GCATGGCTGGTTGTTCCTAAAC | " |
| PaiII_7fw | CCTCCTTTGGACTGAAGTTCA | " |
| PaiII_7rev | GCACAGGCGCTCTTTTATTGTTTG | " |
| PaiII_8fw | GGACACATGGCAGGGTCTG | " |
| PaiII_8rev | GGAACACGTCTTCTTGTTGACA | " |
| PaiII_9fw | CAGCGATTTGTCACCACCTG | " |
| PaiII_9rev | GTACTTGACGCGGCGGACA | " |
| PaiII_10fw | GCTTCTGAAAAACGGGTGAAGTC | " |
| PaiII_10rev | CATGGCGCATCATGAAATCATCA | " |
| PaiII_11fw | CTCTCGCGTATATTCAGCAAAAAC | " |
| PaiII_11rev | CGTCACATCGGATAACATTCGG | " |
| PaiII_12fw | CTGATATCTCTTTCAGACTTCAGAAC | " |
| PaiII_12rev | GTCACCTCAAGAACGTCTAACC | " |
| PaiII_13fw | CTGGCACCTATGGATCAGGT | " |
| PaiII_13rev | GTTCAGCAACTGAAGGTTCATACT | " |
| PaiII_14fw | GATGACCATCAGTGTTTCCGCT | " |
| PaiII_14rev | CGGGGATTTAAGTATTGGTCAGTT | " |
| PaiII_15fw | GCAACAATCTGACCTGCAAGCAT | " |
| PaiII_15rev | GGATGATGAGCTTCAGGTTCAG | " |
| PaiII_16fw | TGCCGTACAGCTTGTCATTACC | " |
| PaiII_16rev | CTGGGTACTGCACTTTCCTCA | " |
| PaiII_17fw | CTGACATTGCCACCAGATTTTTGT | " |
| PaiII_17rev | GGTGTAATGCGCTAACCTGTTTC | " |
| PaiII_18fw | CTACAAATGTTCAATATGGTGGGTATATC | " |
| PaiII_18rev | CGCTGTTGCCACTGGATTAATG | " |
| PaiII_19fw | GCCATCCACTACATATCATGCC | " |
| PaiII_19rev | CGACGGGTTTCTATGCTGAG | " |
| PaiII_20fw | CCTCAACTGGAGCAATTTTCTGTC | " |
| PaiII_20rev | GGACTTGGATCACTGAAGCTTTAC | " |
| PaiII_21fw | CCACAAGCTGTTGATTTTGGTACG | " |
| PaiII_21rev | GCGATAGTGGGCAATTTGCTATTG | " |
| PaiII_22fw | CGTAAACGTCCTCCAGAATTTATATC | " |
| PaiII_22rev | GGACGATGGCGATATGTCTG | " |
| PaiII_23fw | GTTCTTCATTTCTACGTTGCTTTGTC | " |
| PaiII_23rev | CCTACCAGAGATAACCCATGG | " |
| PaiII_24fw | CGGTTTCTCCTGAACATAACTTTG | " |
| PaiII_24rev | GGTGAAGTCCGTAACCAGAATG | " |
| PaiII_25fw | GCCTGTTTTTGCTGCTGTTCAC | " |
| PaiII_25rev | GCAGGACTAAAGTTGCAGAGC | " |
| PaiII_26fw | CGCTTTCGCCCCGATTTCTA | " |
| PaiII_26rev | ATGACCGTCGTACTGTGGAC | " |
| PaiII_27fw | GTCAGCCCGCTTTTCTTCTG | " |
| PaiII_27rev | GCTCCGTCGTATACCGATGA | " |
| PaiII_28fw | CGGTCAAGAAAATACGATGAGCC | " |
| PaiII_28rev | GAACGACAGCAAAATCCTCTCC | " |
| PaiII_29fw | CAGCACCTGCGCCGTCA | " |
| PaiII_29rev | GCGATGCCACGGTGAAAACC | " |
| PaiII_30fw | CCGGTATTACTGAATGTCCCG | " |
| PaiII_30rev | GAACATGAAGACAGCACTGACC | " |
| PaiII_31fw | CCTGAAGCAGAACATCATCCAG | " |
| PaiII_31rev | CGGCTGATATCCTGAGACTG | " |
| PaiII_32fw | CTCGCTTCCACGGACGTTG | " |
| PaiII_32rev | GTTGGCAGTGCTGAAAGCAG | " |
| PaiII_33fw | GGTCAGAATGTCCTCAGTGAG | " |
| PaiII_33rev | CAATGAAATTGACAGGAGAGATACC | " |
| PaiII_34fw | CCACTGGCATGATTTTTACCCTG | " |
| PaiII_34rev | CGGGCACATTCCTGCTGTC | " |
| PaiII_35fw | GGATACTGGGCGATGAGCG | " |
| PaiII_35rev | GAGCACGGTGAGCGAAATAG | " |
| PaiII_36fw | CCGCATTAGGTGACTTTACACG | " |
| PaiII_36rev | GACGCCGTACTGACCGATG | " |
| PaiII_37fw | CCAGGTTTGTTATCGAGGTAAGG | " |
| PaiII_37rev | GGCGCTATCGACTACGTCC | " |
| PaiII_38fw | GGCAGTATATCGATTCGGCGA | " |
| PaiII_38rev | GCTTCCCAGCCTGTCACTTC | " |
| PaiII_39fw | GGGCATCTTCAAAGTCAAAGCC | " |
| PaiII_39rev | CGCCCGTCTGTTTTTCAGTTTC | " |
| PaiII_40fw | GGGGCATCAAGGTCGCTATTT | " |
| PaiII_40rev | CAGAACCGCAGCCAGCCAT | " |
| PaiII_41fw | GCTGCGATGCGGATCCAC | " |
| PaiII_41rev | GGTTACCGCAATGGTGAAAGG | " |
| PaiII_42fw | GCTTTTACTGCGCCGACATCA | " |
| PaiII_42rev | CGTTGCACGCGGCTATCTG | " |
| PaiII_43fw | CGATGGATACATTCGGGTTTAGC | " |
| PaiII_43rev | GCAACAGCGACATCATCCTG | " |
| PaiII_44fw | CTCTCTCTTCAGCCAGTCATC | " |
| PaiII_44rev | GCCAAAATCTGATCCCCAGC | " |
| PaiII_45fw | GCAACTACGCCATTGGTTTGTC | " |
| PaiII_45rev | GAAAAACTGGCACGTCATCAACG | " |
| PaiII_46fw | GAAGGCTGCCATTCGGGTATA | " |
| PaiII_46rev | CTGTACTGACTCGTCAGCACT | " |
| PaiII_47fw | CTTGAGATTCAGCAAGGTGGC | " |
| PaiII_47rev | GGAATCCCCTAATGCTGGTG | " |
| PaiII_48fw | GTATAACGGGATGAAAGTGGGG | " |
| PaiII_48rev | GTTGAGAATGTCGGGAATGGTAC | " |
| PaiII_49fw | GGATGTGTATCAGACAAAGCAATG | " |
| PaiII_49rev | TTTCTGGCGAATTTCTTCAGGAAG | " |
| PaiII_50fw | CAGCCATTTTTCCCTCTCCG | " |
| PaiII_50rev | CCTGACCATCTTCCGTCATG | " |
| PaiII_51fw | CTGCTGTTCACTGTGGCATC | " |
| PaiII_51rev | GAGTGGCAACCAGTTGAGACT | " |
| PaiII_52fw | CGCATAATTCCACCACACCTTC | " |
| PaiII_52rev | GGCTGGTCGGTACGCAC | " |
| PaiII_53fw | GGCAGGCATTTCACTGTGTGA | " |
| PaiII_53rev | CGAAGGCCGGACTCGAACA | " |
| K12R (rev) | ATCCTGCGCACCAATCAACAA | E. coli K-12 specific [67] |
| K12L (fw) | TTCCCACGGACATGAAGACTACA | " |
| K12IS-L (fw) | CGCGATGGAAGATGCTCTGTA | " |
| orf4bico | GGAATGAATGCCACTCCATTATTGACAGAAATG | E. coli 536 (K15 capsule)- specific |
| orf5bico | GATCAAACGAGTCAGCTAAATAATCCCCAC | E. coli 536 (K15 capsule)- specific |
| M803b | GCCTGGAGTGTGACAAAGGTTAC | leuX flanking primers [17] |
| M805c | GATGTTCACCAAGGTGGGCGT | " |
| leu 2 | ACCAAGCGCTGCAAAAAGAT | Concatemer PAI II536 |
| Concat 1 | CCGGATTGGATCTATCGCGA | " |
| yjgB1 | ACTTTATCGGCACCCATCG | Downstream of leuX |
| yjgB2 | GCATGAGGTGATTGGGCG | " |