TABLE 1.
Bacterial strains, plasmids, and oligonucleotide primers used in this work
| Strain, plasmid, or oligonucleotide | Characteristics or description | Source and/or reference |
|---|---|---|
| E. coli strains | ||
| Top10 | F−mcrA Δ(mrr-hsdRMS-mcrBC) φ80lacZΔΜ15 ΔlacX74 deoR recA1 araD139 Δ(ara-leu)7697 galU galK rpsL (Strr) endA1 nupG λ− | Invitrogen |
| BL21(DE3) | F−ompT hsdSB(rB− mB−) gal dcm (DE3) | Novagen |
| N99 | Wild type; λ− F−sup0galK2 | M. Gottesman (9) |
| N7193 | N99 Δhip-3::CAT | M. Gottesman (9) |
| BW25113 | lacIqrrnB3 ΔlacZ4787 hsdR514 Δ(araBAD)567 Δ(rhaBAD)568 rph-1 | H. Aiba (21) |
| BW28878 | BW25113 Δ(atoSC)569 | H. Aiba (21) |
| Plasmids | ||
| pZErO 2.1 | Cloning vector | Invitrogen |
| pZero-patoD1 | atoD1p PCR product (−206 to +73 of atoDAEB) cloned into the EcoRV site of pZErO 2.1 | This work |
| pZero-patoD2 | atoD2p PCR product (−120 to +73 of atoDAEB) cloned into the EcoRV site of pZErO 2.1 | This work |
| pZero-patoD3 | atoD3p PCR product (−47 to +73 of atoDAEB) cloned into the EcoRV site of pZErO 2.1 | This work |
| pMLB1034 | Medium-copy-number vector containing a promoterless lacZ | 34 |
| pMLB-atoD1 | atoD1p (EcoRI-BamHI fragment from pZero-patoD1) cloned into pMLB1034 | This work |
| pMLB-atoD2 | atoD2p (EcoRI-BamHI fragment from pZero-patoD2) cloned into pMLB1034 | This work |
| pMLB-atoD3 | atoD3p (EcoRI-BamHI fragment from pZero-patoD3) cloned into pMLB1034 | This work |
| pCPG3 | rcsC regulatory sequences (−656 to +570) cloned into pMLB1034 | This work |
| pCPG4 | atoS regulatory sequences (−729 to +189) cloned into pMLB1034 | This work |
| pCPG5 | atoDAEB regulatory sequences (−419 to +1186) cloned into pMLB1034 | This work |
| pCPG6 | atoC regulatory sequences (−1150 to +187) cloned into pMLB1034 | This work |
| Oligonucleotides | ||
| U1patoD | 5′-TCGGAATTCATTGATGTATAAACTCCAGGAA-3′ | This work |
| U2patoD | 5′-AGGGAATTCAATTTTCTGCATAGCCGCTCAT-3′ | This work |
| U3patoD | 5′-TACGAATTCAACTAAATCCAATAATCTCATT-3′ | This work |
| LpatoD | 5′-AAGGGATCCGTGGCGTCTTGTAATGTCAT-3′ | This work |