TABLE 2.
The primer sequences used in this study.
| Primers | Sequences (5′–3′) | Functions or target genes |
| Tn5-seqF | CAGCAACACC TTCTTCACGA | For Tn5 Sequence |
| Tn5-seqR | AACAAGCCAGG GATGTAACG | For Tn5 Sequence |
| Crp-D5F | CTCAAAGAATTCTAAG ATGAGTCCAATCACTGTGCCC | crp deletion |
| Crp-D5R | GTATACTCTAGAGGTAC CCGTTAAGTTAGTCTTCAGC | crp deletion |
| Crp-D3F | TTTTACTCTAGAGATGTAA TAAAGGGTATCTGAATCT | crp deletion |
| Crp-D3R | AGGCAGAAGCTTCAGCGA GGTTATCTAAATTAGTGGG | crp deletion |
| Crp-UF | GTTGGATACACCAGTG CGAACAGAC | crp deletion |
| Crp-DR | TCTAAACTAAGACT TCTATCAAGTT | crp deletion |
| Crp-OF | CCAGCATGATATG TTCAAGATCTT | crp deletion |
| Crp-OR | GCAGCACTAAAAT CACCAATTTCT | crp deletion |
| Crp-InF | CCAATCTCTTGA CGAGTGATCTTG | crp deletion |
| Crp-InR | AAGGTTCTGTTG CCGTATTGATTAA | crp deletion |
| Crp-CF | CAAAGGGATCCCGA CCACACCATAAAGTTAGCCTG | crp complementation |
| Crp-CR | TTTAATGAATTCGAA ACAGGCTTAAATCAAGCTGAAG | crp complementation |
| Crp-EF | ATCAACGGATCCATGGC TCTGATTGGTAAGCCAAAACC | express His6-Crp protein |
| Crp-ER | TGGCCTAAGCTTAGAAT TTATGCTAGGCCACTTTAATG | express His6-Crp protein |
| CymA-D5F | CCGGAATTCCCATTG CAGTATCGCTTATG | cymA deletion |
| CymA-D5R | GATACAGAACT GATCCGTACTTG | cymA deletion |
| CymA-D3F | GCTCACCCATA TCCAAAAG | cymA deletion |
| CymA-D3R | AAAACTGCAGC TACCTATCCAAGATCTCGAAG | cymA deletion |
| CymA-UF | TATTGTCCTGAT AGTTAGAGCT | cymA deletion |
| CymA-DR | CCTGTTAGTTTA TCGTCAGC | cymA deletion |
| CymA-OF | GCCGAAGACAAA GAGATAG | cymA deletion |
| CymA-OR | AAACCGCCAAAA ATAAAC | cymA deletion |
| CymA-InF | CCTGTCACAGC AACCATT | cymA deletion |
| CymA-InR | CTGCGGAAATA CTTAAGTGC | cymA deletion |
| CymA-CF | TTCTAAGGATCCTAAGTGAAAT AGCATAAACTAGACTT | cymA complementation |
| CymA-CR | GTTCAAGAATTCGAATGAATCG CTAAAACCTATTATCC | cymA complementation |
| CymA-PF | GACTAAGAGTTTG ATGCATAAGTATT | cymA EMSA probe |
| CymA-PR | AATCATCAAACA ATCGCAAGTTAT | cymA EMSA probe |
| CymA-QF | GAACTGGCGT GCACTATT | cymA RT-qPCR |
| CymA-QR | ATACAGAACT GATCCGTACTTG | cymA RT-qPCR |
| 16S QF | GCAGGCGGTTT GTTAAGCGAGATG | internal standard for RT-qPCR |
| 16S QR | CTTCGCCACCGG TATTCCTCCAGA | internal standard for RT-qPCR |
| CymA-FootF | TGTAAAACGACGGCCA GTAATAATGAACGGCTCGAT | cymA DNase I footprinting |
| CymA-FootR | CAGGAAACAGCTATGACCAAT AGTGCACGCCAGTTC | cymA DNase I footprinting |
| MtrC-D5F | AAAACTGCAGCTGTGTTAG CTGTCATAATGA | mtrC deletion |
| MtrC-D5R | AAACTTGAAAT ATTGAAGCC | mtrC deletion |
| MtrC-D3F | GCAGTGCAG TCAGAAACC | mtrC deletion |
| MtrC-D3R | CCGGAATTCT GCTCACCTCCATGACAT | mtrC deletion |
| MtrC-UF | GCATTAACTTA AGTCGCCTC | mtrC deletion |
| MtrC-DR | TGTTCTTCATA ATAGGCTTCC | mtrC deletion |
| MtrC-OF | GTGGTTGTAGCA GTTGTCATAC | mtrC deletion |
| MtrC-OR | ATAATGCCCCTT ACTACTGG | mtrC deletion |
| MtrC-InF | GGTACCTACAG CTATGACTTCG | mtrC deletion |
| MtrC-InR | TGGTGTAATGT TTGGCGT | mtrC deletion |
| MtrA-D5F | CCGGAATTCAA GTATTGTTGACGGTAAGCT | mtrA deletion |
| MtrA-D5R | ATAACTCCCTT CAGCGAAC | mtrA deletion |
| MtrA-D3F | AATTGCCATA GTCAGGTTCA | mtrA deletion |
| MtrA-D3R | AAAACTGCAG CCAGATATCACATTGGTATTGTC | mtrA deletion |
| MtrA-UF | GCAGTGCAGTC AGAAACCT | mtrA deletion |
| MtrA-DR | AGCCCTTACAG CTCCATG | mtrA deletion |
| MtrA-OF | TTGAAATTATT ACTAACGTTGGCC | mtrA deletion |
| MtrA-OR | CTTGGCTCATT TGTCCCG | mtrA deletion |
| MtrA-InF | GCAATGAACC GATGATCAC | mtrA deletion |
| MtrA-InR | CGTGACAGGC ATAACAGGT | mtrA deletion |
| MtrB-D5F | CCGGAATTCG CCACCTTAGATAAAAAGTTCG | mtrB deletion |
| MtrB-D5R | AACGATGCA GCCCTTACAG | mtrB deletion |
| MtrB-D3F | GACGCCGCGA ATGATATC | mtrB deletion |
| MtrB-D3R | AAAACTGCAG TGCTAATAAAGATGTCATGGATGC | mtrB deletion |
| MtrB-UF | GCTGCTTAAAT TGCCATAGT | mtrB deletion |
| MtrB-DR | CTTGTCGTAGC GCTTAAAC | mtrB deletion |
| MtrB-OF | TTGCTACGAGT GCTCATG | mtrB deletion |
| MtrB-OR | GGCGACTTGCT TGTAATAT | mtrB deletion |
| MtrB-InF | GGCAAATTT GACGCTGAC | mtrB deletion |
| MtrB-InR | TACTATCCA GTTATCAGGCAATGT | mtrB deletion |
| UndA-D5F | AAAACTGCAGA CTGCGCCTATTGTAGCT | undA deletion |
| UndA-D5R | GGTCAGTACTA TATCAACGCTG | undA deletion |
| UndA-D3F | AACGGTGGTGT GTACAATG | undA deletion |
| UndA-D3R | TTGGATCCGCG AACATAGTTATTCAGTACAAT | undA deletion |
| UndA-UF | TGATGATGATTA CAACTATTGC | undA deletion |
| UndA-DR | TCTGTCAACTAT TGCTGCTT | undA deletion |
| UndA-OF | CCGATTTCAGA AATAATGC | undA deletion |
| UndA-OR | AGTAAAGACA GGTAGCGTGG | undA deletion |
| UndA-InF | TGGATCAGC TATATCAACTCAGT | undA deletion |
| UndA-InR | GGTGTATCAA GGTCGGGT | undA deletion |
| MtrC-D5F1 | CCCAAGCTTC TGTGTTAGCTGTCATAATGA | mtrCAB deletion |
| MtrC-D5R1 | TTGGATCCAAACT TGAAATATTGAAGCC | mtrCAB deletion |
| UndA-D5F1 | CCCAAGCTTACTGCGCC TATTGTAGCT | mtrCAB/undA deletion |
| UndA-D5R1 | TTGGATCCGGTCAGTA CTATATCAACGCTG | mtrCAB/undA deletion |
| MtrB-D3F1 | TTGGATCCGACGCCGC GAATGATATC | mtrCAB/undA deletion |
| MtrB-D3R1 | AAAACTGCAGTGCTAA TAAAGATGTCATGGATGC | mtrCAB/undA deletion |