TABLE 1.
Primers used in this study
| Primer purpose and name | Sequence (5′–3′) | Overhanging restriction sitea |
|---|---|---|
| Plasmid construction for gene deletion | ||
| araA-ML-U-F | GCTCTAGAGTGCTGACGATGATGGCGGA | XbaI |
| araA-ML-U-R | CTCTACTAGTTCCATGTCGATCGAAGACCA | SpeI |
| araA-ML-D-F | GCTCTAGAAGTGCTATGGCAGTGCAACT | XbaI |
| araA-ML-D-R | CTCTACTAGTACTCACTGCGAACAAGGTCA | SpeI |
| araE-ML-U-F | GCTCTAGATCGCTCGGACACCGTCACAT | XbaI |
| araE-ML-U-R | GCGGATCCACCGAAGAAGTAGATGTACG | BamHI |
| araE-ML-D-F | CGGGATCCATCCCGCTCATCGTCGAGAA | BamHI |
| araE-ML-D-R | GCGATATCTGAGAGATGCCGTTGGTGCT | EcoRV |
| Plasmid construction for gene expression | ||
| AraR-Ex-F | GGAATTCCATATGAGCTCCACCCAG | NdeI |
| AraR-Ex-R | GGAATTCTCAGAGCTGTGTGAAATC | EcoRI |
| RT-PCR analysis | ||
| 16S-F | CAGGTCTCTGGGCAGTAACTGA | |
| 16S-R | CGTTTACGGCATGGACTACCA | |
| araA-F | GCGCCAATGACAACGTCAT | |
| araA-R | TCATTAGCCTGGGTGTGAAGGT | |
| araB-F | GGATCGAGCTCTTCAGTGAGGTT | |
| araB-R | CACCGGAGACGAAGTTGTAGGT | |
| araD-F | GCGATGGTGGTGTGCAACA | |
| araD-R | GGTCGAATGAGTGTGCACGAT | |
| araE-F | CATGTGGCCGATCATCCA | |
| araE-R | CGGCGATGACCATGAACA | |
| araR-F | GCACGCTGTCAAGCATTGA | |
| araR-R | GGTCTCTTCGGCATTTTTCATC | |
| galM-F | GGTCTTCGCCACCTTCTCTCT | |
| galM-R | GTGGTGTCGCCGACATTGT | |
| 5′-RACE | ||
| araB-RA-RTb | TGAGAACTAGGTCG | |
| araB-RA-F1 | ACGGAGTTGAAAGTATGGAG | |
| araB-RA-R1 | GTTCGGTTCCTTGATGAC | |
| araB-RA-F2 | AATTCGGATCGACCCGCATT | |
| araB-RA-R2 | TTTGAGAGCGGAGCTTCGTA | |
| araE-RA-RTb | GATCATCGTCTGGT | |
| araE-RA-F1 | CGACCGTACATCTACTTCTT | |
| araE-RA-R1 | GTTGAACAGTCTCTGTCATC | |
| araE-RA-F2 | TCCTCTTCTCTGCGCTGGTA | |
| araE-RA-R2 | GCTGTCTGAGCGGATGATGT | |
| galM-RA-RTb | TGCCATCGGTGTAGA | |
| galM-RA-F1 | TCCACGGTGGTGTTCTCGTT | |
| galM-RA-R1 | TTGATCGTGACCTGTTTTCC | |
| galM-RA-F2 | CCGACGGCATCTACACCGAT | |
| galM-RA-R2 | CTTCTGGGGCGATGTGTCAT | |
| Electrophoretic mobility shift assay | ||
| PA-F | TGGTGCTGCCATCGGTGTAG | |
| PA-R | AGCTTCGTATTGGTGTTATCGCT | |
| PB-F | CCTCGAGTGAGTAGCTCCAG | |
| PB-R | CTTCTGGGGCGATGTGTCAT | |
| PC-F | TCTGGGTTCTCGGGTGATAA | |
| PC-R | GCTGTCTGAGCGGATGATGT | |
| PD-F | ACCGTCTCCTCCCGATCAGA | |
| PD-R | TGGGTGGAGCTCATGGTGAT | |
| P2-F | TGCGATCCGGTCACT | |
| P3-F | AATGCGGGTCGATCCGAA | |
| P4-F | ACGGTCCACGACACT | |
| P5-F | GTTCGGTTCCTTGATGAC | |
| P6-R | GTGTGATGCTTGCTTGAC | |
| P7-R | GATGGCCGTTAAGAAC | |
| P8-R | CTCAAATGTGATCCGAAGC | |
| P9-R | ACGGAGTTGAAAGTATGGAG | |
| DNase I footprinting analysis | ||
| pUC-IR-Fw | TTGTAAAACGACGGCCAGTG | |
| pUC-IR-Rvc | GGAAACAGCTATGACCATGA | |
| araB-DF-F | CTTCTGGGGCGATGTGTCAT | |
| araB-DF-R | AGCTTCGTATTGGTGTTATCGCT | |
| araE-DF-F | CGAGCGACAAACACGACA | |
| araE-DF-R | TTGTCCTGGTTCTTCGAC |
a
The restriction site overhangs used in the cloning procedure are underlined in the sequences.
b
5′-Phosphorylated primer.
c
5′-IRD700-labeled primer.