TABLE 2.
Oligonucleotide primers
| Primer | Sequence (5′ → 3′)a | Reference |
|---|---|---|
| Preparation of NAP gene disruption mutants | ||
| Gm-F | CGAATTAGCTTCAAAAGCGCTCTGA | 30 |
| Gm-R | CGAATTGGGGATCTTGAAGTTCCT | 30 |
| pmr_del_up_F | GGATCCAGGAATCACTGTTCGGCAAG | This study |
| pmr_del_up_R2 | TCAGAGCGCTTTTGAAGCTAATTCGCTTGTCTCCTTGGTCTGGG | This study |
| pmr_del_down_F2 | AGGAACTTCAAGATCCCCAATTCGGTTTGCGCTACCGCGGATCT | This study |
| pmr_del_down_R | AAGCTTGTGAGCCAAGGCTTCTTCAG | This study |
| pnd_del_up_F | GGATCCCGGAGTCCCAAACCGTAATA | This study |
| pnd_del_up_R | TCAGAGCGCTTTTGAAGCTAATTCGGAGCAAAGTCCTTGTAGTTT | This study |
| pnd_del_down_F | AGGAACTTCAAGATCCCCAATTCGAAAAATGCCCCGTCCATCTC | This study |
| pnd_del_down_R | AAGCTTGGATCAATTCCAGCCTCAAA | This study |
| phu_del_up_F | GGATCCTAGACGATCGACGCAAAGTG | This study |
| phu_del_up_R2 | TCAGAGCGCTTTTGAAGCTAATTCGTCGCTTTTACTCCTTGGTTG | This study |
| phu_del_down_F2 | AGGAACTTCAAGATCCCCAATTCGGCCCCCTCCAGCCGCCCCGA | This study |
| phu_del_down_R | AAGCTTGCGATGAGAAGGGCAAATAG | This study |
| Preparation of pmr-complemented strains | ||
| Gm-F-SalI | GTCGACCGAATTAGCTTCAAAAGCGCTCTG | This study |
| Gm-R-PstI | CTGCAGCGAATTGGGGATCTTGAAGTTCCT | This study |
| ORF98_COMP_up_F | GGATCCACCTGGGTACTGGCTCATTG | This study |
| ORF98_COMP_up_R | CTGCAGGCCCGTTTTCCTACGCAGCT | This study |
| ORF99_COMP_down_F | CCCGGGCTGGTGGCACGCGTCGGCCC | This study |
| ORF99_COMP_down_R | AAGCTTCATATCGCATGGGATTTTCC | This study |
| pmr_COMP_F | CCCGGGCGCATTCTGGCCTTCCGCCG | This study |
| pmr_COMP_R | GTCGACCTCACAAAAAAGGCCGGGTT | This study |
| pCAR1 stability assay | ||
| recT-ox-F | GGATCCAAGGAGACCTTCGGGTGCGTTTTC | This study |
| recT-ox-R | TCTAGACTATCACTCGCCTTGCG | This study |
| 5′-RACE analysis | ||
| M13-F | GTAAAACGACGGCCAGT | 38 |
| M13-R | GGAAACAGCTATGACCATG | 38 |
| pnd308 | CCGGTTGAGAGGTTCGATTCTTCCAT | This study |
| pnd498 | GGACTGCTTGTTGTTCTGCCATTCG | This study |
| phu157 | TTGACTCGAAAGTACCAAAGCCCACGAG | This study |
| phu258 | CTTGAAGGACTTGCCAGGGGTGAACT | This study |
| phu_up395 | CATTACCACACTTCGGACAGAGCAATCC | This study |
| phu_up564 | GAGGTTCCCGGAGTGGTCAATGATAATG | This study |
| qRT-PCR | ||
| pmr_qRT_F | GATCCGGACTATCGAAAGCA | 35 |
| pmr_qRT_R | TTCCACTCCTTGAGCGTCTT | 35 |
| pnd_qRT_F | TGGCAGAACAACAAGCAGTC | This study |
| pnd_qRT_R | GTCTACACCCTCCTGGCAAC | This study |
| phu_qRT_F | TCGTGGGCTTTGGTACTTTC | This study |
| phu_qRT_R | GGTGAACTTTGGCTTGATCG | This study |
| univ16S-F | ACACGGTCCAGACTCCTACG | 35 |
| univ16S-R | TACTGCCCTTCCTCCCAACT | 35 |
a
Underlined nucleotides represent artificial restriction sites.