TABLE 2.
Primers for RT-qPCR and gene knockout
| Primer paira | Sequences (5′–3′)b | Product length (bp) |
|---|---|---|
| Primers for RT-qPCR | ||
| 16S-F, 16S-R | CACACTGGAACTGAGACACG, TGCTTTACAATCCGAAGACC | 127 |
| qspmA1-F, qspmA1-R | AACGTGCCCAGTTTCCGTA, TGACTCAGGCAATCACCAGT | 122 |
| qspmA2-F, qspmA2-R | ACACCACCATGGAAACCGAA, CGGCTGGAATGGAAGGTGAA | 106 |
| qsirA2-F, qsirA2-R | GGCGAAAGTGCGGAAGTCG, ACTGCTCAAGGCCAAGATGGA | 103 |
| qald1-F, qald1-R | TGCTGGCGGTGGATGAAT, CTTGCCTGTGAATGGCTTCC | 155 |
| qald2-F, qald2-R | CAGCCAGTTTCGCTGGATT, TCTTCGTTGCGCAGGCT | 168 |
| Primers for gene knockout | ||
| spm1-UF, spm1-UR | ctatgacatgattacgaattcGCAACTGCGATGACAAGGCT, tttagcccagCCAATCTCTGTAGATTTTATGGAAGATT | 459 |
| spm1-DF, spm1-DR | cagagattggCTGGGCTAAATCTCCTGCAATG, caggtcgactctagaggatccGGGCGTGATTTCGTAGAGCG | 524 |
| spm2-UF, spm2-UR | ctatgacatgattacgaattcACAACTCTTTGCGGGTCTGC, cagcattgcaTTGCGCAAGACTCAAAGCCA | 450 |
| spm2-DF, spm2-DR | tcttgcgcaaTGCAATGCTGGTCCTTAACGT, caggtcgactctagaggatccGAGCGAAACCTTGGAGCAATC | 532 |
| sirA2-UF, sirA2-UR | gagctcggtacccggggatccGCATCAAGTCGCACGAGAACT, ctgcgGTCTTTTCCAAGGATCGTCAATG | 1,383 |
| sirA2-DF, sirA2-DR | atccttggaaaagacCGCAGGGTCTCCAAAGGC, acgacggccagtgccaagcttGGTTACGGGTGTCGGCAAT | 873 |
| ald1-UF, ald1-UR | gagctcggtacccggggatccGCTACCGTATTCGCGGGTAA, tgagccGGCTTTCTCCGGGTCTCG | 724 |
| ald1-DF, ald1-DR | acccggagaaagccGGCTCAGCGGCGCAAGCC, acgacggccagtgccaagcttTGGCAGTGTTGGCTATCTGGC | 682 |
| ald2-UF, ald2-UR | gagctcggtacccggggatccTGGCTTCGAGACGGAGATTG, ttgtgcgaTCAGGCTTGCTCCCCCTG | 771 |
| ald2-DF, ald2-DR | agcaagcctgaTCGCACAAGGGACGCCTC, acgacggccagtgccaagcttCTGTCATCCAGCGCCTTTTC | 695 |
| Verification primers for gene knockout | ||
| yz-spm1-F, yz-spm1-R | CCGCCCTTTAGGTGCAATTT, TTTCAGGTCGCACTCCCGAA | 1,408 |
| yz-spm2-F, yz-spm2-R | CCGTTCATCCCTAGCACCTC, AAAGATGCCACGCCTCCAAT | 1,615 |
| yz-sirA2-F, yz-sirA2-R | CAGCAGGTGGTGGTGTACTT, CGATTTGCGCCAGGTTGTAG | 2,674 |
| yz-ald1-F, yz-ald1-R | ATTTCCACCGGCCGTTCA, AACGCACCTGTCCGATAACC | 1,947 |
| yz-ald2-F, yz-ald2-R | ATGTCTTCGGGCAGTTCGAC, TAGCGATTCGGCCTGGTATT | 1,999 |
| Primers for gene expression | ||
| nicAB-CF, nicAB-CR | gtcgacggtatcgataagcttgaATGCAAACAACCGTCTCCCTG, cgctctagaactagtggatccTCAGTGGCTGCCAGGGTTG | 4,034 |
| ald2-CF, ald2-CR | gtcgacggtatcgataagcttgaATGGAACTACGCATCAACCAGAA, cgctctagaactagtggatccTCAGCTGAAGGTGTGGCGG | 2,711 |
| nicAB-yzF, nicAB-yzR | GTGTGGTCAGGTACGCAGAA, TGGTGGACTGGATGACGTTG | 889 |
a
Primer designations are based on the Pseudomonas sp. strain JY-Q genome (GenBank accession number CP011525).
b
Underlined nucleotide abbreviations indicate restriction cleavage sites, and lowercase nucleotide abbreviations indicate homologous segments for plasmid-bearing sequences.