TABLE 2.
Primers used in this study
| Primer | Sequence (5′–3′)a | Purpose |
|---|---|---|
| pnpA-F | GACTGACATATGGAAACGCTTGAAGGAG | Amplification of pnpA gene for expression |
| pnpA-R | GGTCTCGAGTTACGCTGCAAGCTTAAGAGG | |
| pnpA1-F | AGGAGACATATGATGGAGACGCTAGAAGG | Amplification of pnpA1 gene for expression |
| pnpA1-R | GGCCTCGAGTCACTTCAGGACGACTTGCG | |
| pnpB-F | AGAAACCATATGGCAACTAAGATTCAGATTGTG | Amplification of pnpB gene for expression |
| pnpB-R | GGTCTCGAGTTACTTGGACTGCGCGACCAGC | |
| pnpCD-F | AGGCACCATATGCAAGAAACGGTGTTCG | Amplification of pnpCD gene for expression |
| pnpCD-R | GGACTCGAGGAACTGGATCGGATTGGC | |
| pnpE-F | AGGCACCATATGCAAACCCAACTCTTCATTG | Amplification of pnpE gene for expression |
| pnpE-R | GGAGAATTCTCAGCGGGGGAAGTACG | |
| pnpF-F | AGGCACCATATGGAACCTTTCGTATATCAAAGC | Amplification of pnpF gene for expression |
| pnpF-R | GGACTCGAGCTACCTCGGTGCCCGCC | |
| RTA-F | GAAGGAGTGGTCGTTGTTGGTGGAG | Amplification of 725 bp of pnpA by RT-PCR |
| RTA-R | TCGGGCATACGACGACGCACTTC | |
| RTB-F | AACTCGTGCCCGAAGAAGTCCTG | Amplification of 445 bp of pnpB by RT-PCR |
| RTB-R | CGAGCGATTGCCAGTTCGTTTTC | |
| RTA1-F | GCCTATGTGACGATTGAAACCCG | Amplification of 555 bp of pnpA1 by RT-PCR |
| RTA1-R | TGCCGACTCTTTGATGACTGCG | |
| RTAB-F | TGCTTACACACGCAGGCACGGAC | Amplification of 743 bp of pnpA-pnpB-spanning region |
| RTAB-R | CGATAGCCCTTCATTCCGCTCTTAACC | |
| RTBA1-F | TGGTCATCGTTGGTGTGCCGTATT | Amplification of 665 bp of pnpB-pnpA1-spanning region |
| RTBA1-R | TCCGCCAACTACGACCACGCCTT | |
| RTA1C-F | CGGAAAACATTCAGAGCAGAG | Amplification of 440 bp of pnpA1-pnpC-spanning region |
| RTA1C-R | CCTTGCCTGTGATGATTTCG | |
| RTCD-F | CCGAAGGGAAAGCCGATG | Amplification of 421 bp of pnpC-pnpD-spanning region |
| RTCD-R | ACCGTAAAAGAAGCCCCAAGC | |
| RTDE-F | ACCAAATCATCTGGGACATCGC | Amplification of 459 bp of pnpD-pnpE-spanning region |
| RTDE-R | ACGGCACGGTCGATGTCG | |
| RTEF-F | AGCCCTGGTTCGCCTTTTG | Amplification of 514 bp of pnpE-pnpF-spanning region |
| RTEF-R | GGTCGGGATCGCAATGATAG | |
| RTFG-F | ATGGTCCGCAGGCTGTTTTC | Amplification of 679 bp of pnpF-pnpG-spanning region |
| RTFG-R | ACTTCTTCCCAGTTGCGGTCAG | |
| RTq16S-F | CGTGTAGCAGTGAAATGCGTAGAG | Amplification of 142-bp fragment of 16S rRNA genes for real-time qPCR |
| RTq16S-R | GACATCGTTTAGGGCGTGGAC | |
| RTq-pnpA-F | CGTCGCAACGAATGTCTTCTATG | Amplification of 172-bp fragment of pnpA for real-time qPCR |
| RTq-pnpA-R | CATACGACGACGCACTTCCTC | |
| RTq-pnpA1-F | CTGCCTATGTGACGATTGAAACC | Amplification of 134-bp fragment of pnpA1 for real-time qPCR |
| RTq-pnpA1-R | CCAGGTGGTGCCATCAAAAG | |
| W-pnpB-F | TACAAGATGGCCGAAGC | Amplification of fragment of pnpB for genomic walking |
| W-pnpB-R | AGGAAGTTGCGCATTTG | |
| GC-pnpA-F | GACGGTACCGATGGAAACGCTTGAAGGAGTGG | Amplification of pnpA for gene complementation |
| GC-pnpA-R | GGTGAATTCTTACGCTGCAAGCTTAAGAGGC | |
| KO-pnpAu-F | CCATGATTACGAATTGAGGGTTTCTAATCGGTTTCGC | Amplification of upstream fragment of pnpA for gene knockout |
| KO-pnpAu-R | AGAGATTTTGAGACATTTTCAGTCTCCTGTCACAACGC | |
| KO-pnpAd-F | GATGAGTTTTTCTAAATTTTGACCGCAATTTGGGAC | Amplification of downstream fragment of pnpA for gene knockout |
| KO-pnpAd-R | GGCCAGTGCCAAGCTTTGACGCGAACCATCTGCAC | |
| KO-pnpA1u-F | CCATGATTACGAATTGATGGCCGAAGCTATCGCG | Amplification of upstream fragment of pnpA1 for gene knockout |
| KO-pnpA1u-R | AGAGATTTTGAGACAGTGTCTCCTTTCAACTCGCGTTTC | |
| KO-pnpA1d-F | GATGAGTTTTTCTAAGCGTTTGCCTTCGGAACG | Amplification of downstream fragment of pnpA1 for gene knockout |
| KO-pnpA1d-R | GGCCAGTGCCAAGCTTGGTGCGTCCGAATTTGTCC | |
| KO-kan-F | TGTCTCAAAATCTCTGATGTTAC | Amplification of kanamycin resistance gene for gene knockout |
| KO-kan-R | TTAGAAAAACTCATCGAGCATC |
a
Specified restriction sites are underlined.