TABLE 2.
List of oligonucleotides used in this study
| Oligonucleotide function and target gene(s) or region | Forward primer (5′-3′) | Reverse primer (5′-3′) | Probe |
|---|---|---|---|
| Construction of mutant strains | |||
| relE1 upstream | GGGAAGCTTTCTGCCCGGATCGAACGC | GGGGCGGCCGCCGCGCGGTGTAACGGTTGCG | |
| relE1 downstream | GGGGCGGCCGCGCCGTACCCCGGGTACCGG | GGTTAATTAAGCTGGCTCGCCGAACACC | |
| relE2 upstream | GGAAGCTTGGCGGGTCGGCTCGTAGCG | GGAGGCCTCGCTCAGTGGGGGCGTCGC | |
| relE2 downstream | GGAGGCCTCAACTCACCGACGGGCGCTC | GGTTAATTAACGCGGCGGACCGATCGACC | |
| relE3 upstream | GGGAAGCTTAGAACCCCGGCCGGTATCAG | GGGGATATCTCTCACTCCTCGCCGCCGGC | |
| relE3 downstream | GGGGATATCGATTTGGGGGCTGGTGGTATTC | GGGTTAATTAACGTGGATTTCACGCTCGCCG | |
| mazF1 upstream | GGAAGCTTCCGGCGAGGACGCCATCG | GGGAGGCCTCGACTCCGTCGCCGACGGTC | |
| mazF1 downstream | GGGAGGCCTCTCTCGCAGGTTCCGCGTCG | GGGTTAATTAACGATCCGTTCTGGGACCGAC | |
| mazF5 upstream | GGGAAGCTTCACGGCGATGGCGG | GGGAGGCCTCCCGATATCACGTCAGCAAAC | |
| mazF5 downstream | GGGAGGCCTGAGTCTCCAGCCGCCC | GGGTTAATTAAATCTCCTTAATGTGTTCTCGG | |
| mazF6 upstream | GGGAAGCTTTGGTGTGCGACGGGTCGTGG | GGGAGGCCTTAGGTCTACAGCACTGCACC | |
| mazF6 downstream | GGGAGGCCTCGTACGACCTCGCGGG | GGGTTAATTAAGCTATGAGCCGCTGTTCAC | |
| Construction of overexpression strains | |||
| relE1 | GGGCATATGAGCGACGACCATCCCTAC | GGGGCGGCCGCTTAACGTGGCCGGCACGGGa | |
| relB1 and relE1 | GGGCATATGGCTGTTGTCCCACTGGGCG | GGGGCGGCCGCTTAACGTGGCCGGCACGGG | |
| relE2 | GGGCATATGCCTTACACCGTGCGGTTC | GGGGCGGCCGCCTATCGGCGGTAGATGTCCGCGa | |
| relB2 and relE2 | GGGCATATGCGGATACTGCCGATTTCG | GGGGCGGCCGCCTATCGGCGGTAGATGTCCGCG | |
| relE3 | GGGCATATGGTGAGAAGCGTCAACTTCG | GGGGCGGCCGCTCAGTAGTGGTATCGGGCCa | |
| relB3 and relE3 | GGGCATATGAGCATCAGTGCGAGCGAG | GGGGCGGCCGCTCAGTAGTGGTATCGGGCC | |
| mazF1 | GGGCATATGGTGATGCGCCGCGGTGAG | GGGGCGGCCGCCTACGACCATAAGTCGAGATGC | |
| mazF2 | GGGCATATGCTGCGCGGTGAGATCTG | GGGGCGGCCGCTCAGCTCGGCAGGGGAGACG | |
| mazF3 | GGGCATATGGTGATTAGTCGTGCCG | GGGGCGGCCGCTCAAAGGTCCAGTACGCGAC | |
| mazF4 | GGGCATATGATGCGGCGCGGTGAATTGTG | GGGGCGGCCGCTCAACACCCCGTGCTCGCCC | |
| mazF5 | GGGCATATGACCGCACTTCCGGCGCG | GGGGCGGCCGCTCATCGAGAGCAATCGACGG | |
| mazF6 | GGGCATATGCGACCTATCCACATCGC | GGGGCGGCCGCCTATGCCACCACCCAATCG | |
| mazF7 | GGGCATATGAACGCGCCGTTGCGTG | GGGGCGGCCGCTCATGGCCACGGTAGCCCCA | |
| RT-PCR analysis | |||
| relB1 | CGCCGAAGTTGAGCTGACA | GATGACCGTGCCGGGTTA | ACGAGCGCATCACG |
| relE1 | AATGACCTTGAAGGCCTCCA | GATGGCGTAGACGACGCG | TCAGCCCGCCGCGGTGATT |
| relB2 | TGCGGATACTGCCGATTTC | CGCGTCGACGAACTCATTG | ACGATCAAGGGCAAGC |
| relE2 | CACGTTCAGCGCGCG | AGGATCACTACCGTTGTGTGCTC | CGCCTGCTGTACCGGATTGACGA |
| relB3 | CGAGGCAGCGCCTGTT | CGGCTGGTGATCGGTATTG | CCACTCATCGAACAGG |
| relE3 | TGCCTGGGAGGACTTCTTGT | ATCCGACGGGCCGTTT | CTGGCTGGCCGCTGATCGC |
| sigA | GACGAGGAGATCGCTGAACC | TCGTCTTCATCCCAGACGAAA | CCGAAAAGGACAAGGCCTCCGG |
a
This primer was also used for synthesis of cDNA from mycobacterial RNA, done using Superscript reverse transcriptase.