Table 2.
DNA oligonucleotide sequences used in this work
| Primers | Primer sequences | Purposes |
|---|---|---|
| crp_she-F (BamHI) | 5′-CG GGATCC ATG GCT CTG ATT GGT AAG CC-3′ | Gene cloning |
| crp_she-R (XhoI) | 5′-CCG CTCGAG TTA ACG GGT ACC ATA TAC CAC-3′ | |
| crp_she-ck1 | 5′-GTG AAT CCA GTG AGT TTG ACA-3′ | PCR detection for the crp mutant of Shewanella |
| crp_she-ck2 | 5′-CAG AGT TGA CTA ACG CCT TG-3′ | |
| PlipBA-F (SalI) | 5′-CCG GTCGAC GAT GAA CTG ATG GAG TTC CCC-3′ | PCR amplification and cloning of the lipBA promoter |
| PlipBA-R (EcoRI) | 5′-AACC GAATTC CAA GGG CAA CCT CTC CCC TA-3′ | |
| lipBA_she CRP site-F (43 bp) | 5′-CAA GGT CAT AAA GTG TGA TCT ATC TTACATTTA TGG CCA AGA G-3′ | Synthesis of the predicted CRP site of Shewanella lipBA |
| lipBA_she CRP site-R (43 bp) | 5′-CTC TTG GCC ATA AATGTA AGA TAG ATC ACACTT TAT GAC CTT G-3′ | |
| lipA_ec CRP site-F (42 bp) | 5′-ACG GAG TAA TAGATG TTA TCC GTA ATG CATTTT GAA AAA GTA-3′ | Synthesis of the suspected CRP site of E. coli lipA |
| lipA_ec CRP site-R (42 bp) | 5′-TAC TTT TTC AAA ATG CAT TAC GGA TAA CAT CTA TTA CTC CGT-3′ | |
| fadD_ec CRP site-F (48 bp) | 5′-GTA AAG ATA AAA ATA AAT AGT GAC GCG CTTCGC AACCTT TTC GTT GGG-3′ | Synthesis of the known CRP site of E. coli fadD |
| fadD_ec CRP site-R (48 bp) | 5′-CCC AAC GAA AAG GTT GCG AAG CGC GTC ACTATT TAT TTT TAT CTT TAC-3′ | |
| ybeD_ec CRP site-F(42 bp) | 5′-AAA CAC TTG AAAGTG TAA TTT CCG TCC CCATAT ACT AAG CAT-3′ | Synthesis of the anticipated CRP site of E. coli ybeD |
| ybeD_ec CRP site-R(42 bp) | 5′-ATG CTT AGT ATATGG GGA CGG AAA TTA CACTTT CAA GTG TTT-3′ | |
| ybeD_es CRP site-F(42 bp) | 5′-GAA CAC TTG AAA GTG TGA TTT CCA TCC CCA TAT ACT AGG TAT-3′ | Synthesis of the CRP site of ybeD gene from Enterobacter sp. 638 |
| ybeD_es CRP site-R(42 bp) | 5′-ATA CCT AGT ATA TGG GGA TGG AAA TCA CAC TTT CAA GTG TTC-3′ | |
| ybeD_kp CRP site-F(42 bp) | 5′-GAACACTTGAAA GTG TGA TTT CCA TCC CCA TATACTATTCAT-3′ | Synthesis of the CRP site of ybeD gene from Klebsiella pneumonia |
| ybeD_kp CRP site-R(42 bp) | 5′-ATG AAT AGT ATATGG GGA TGG AAA TCA CACTTT CAA GTG TTC-3′ | |
| ybeD_st CRP site1-F(42 bp) | 5′-GAA CGCTTGAAA GTG TGA TTT TCG TCC CCA TAT ACTATGCAT-3′ | Synthesis of the CRP site 1 of ybeD gene from Salmonella typhimurium LT2 |
| ybeD_st CRP site1-R(42 bp) | 5′-ATG CAT AGT ATA TGG GGA CGA AAA TCA CACTTT CAA GCG TTC-3′ | |
| ybeD_st CRP site2-F(42 bp) | 5′-CTG TGG CGG GAG TTG TTA TTT TTT TTA CGT AAT GCC GGA GCT-3′ | Synthesis of the CRP site 2 of the ybeD gene from Salmonella typhimurium LT2 |
| ybeD_st CRP site2-R(42 bp) | 5′-AGC TCC GGC ATTACG TAA AAA AAA TAACAACTC CCG CCA CAG-3′ | |
| ybeD_yp CRP site-F (42 bp) | 5′-ATT GGC CCC ATATTG TGA TTA ATC TTA TAT TGC AAA TAA GCT-3′ | Synthesis of the CRP site of the ybeD gene from Yersinia pestis |
| ybeD_yp CRP site-R (42 bp) | 5′-AGC TTA TTT GCA ATA TAA GAT TAA TCA CAA TAT GGG GCC AAT-3′ | |
| LacZ-R | 5′-CAG TGA ATC CGT AAT CAT GGT C-3′ | PCR assay for the lipBA-lacZ junction |
| crp_ec-F | 5′-CAG GTA GCG GGA AGC ATA TTT C-3′ | PCR assay for the E. coli crp |
| crp_ec-R | 5′-CAG CGT TTG TCG AAG TGC ATA G-3′ | |
| ybeD-F (19-39) | 5′-GAT GAA CTG ATG GAG TTC CCC-3′ | PCR (RT-PCR) assay for the S. oneidensis ybeD |
| ybeD-R (223-243) | 5′-GAT GTT GGC GAG CTC TGT GTA-3′ | |
| lipB-F (471-491) | 5′-CTG TGG ATC GTT GAA CAT CCA-3′ | PCR (RT-PCR) assay for the S. oneidensis lipB |
| lipB-R (760-780) | 5′-GAC CTA AGG AAG CCA CTT TGC-3′ | |
| lipA-F (1020-1040) | 5′-CTG AAC GTT TAC AAC CCG GAG-3′ | PCR (RT-PCR) assay for the S. oneidensis lipA |
| lipA-R (1253-1273) | 5′-CAT AAA GGT TGC TGT GCC GTG-3′ | |
| ybeD-lipB-F (208-229) | 5′-CAT ATC GAA ACC CTG TAC ACA G-3′ | PCR (RT-PCR) assay for the ybeD-lipB junction of S. oneidensis |
| ybeD-lipB-R (471-492) | 5′-GTG GAT GTT CAA CGA TCC ACA G-3′ | |
| lipB-lipA-F (910-930) | 5′-GCC CAC AAA CTG TGA TAG AAG-3′ | PCR (RT-PCR) assay for the lipA-lipB junction of S. oneidensis |
| lipB-lipA-R (1160-1181) | 5′-CTT GCT TAA TGT CGA GAA TGC G-3′ | |
| lipBA-Nest (769-789) | 5′-GGA TCC TAA GAC CTA AGG AAG-3′ | 5′-RACE of S. neidensis lipBA |
| lipBA-GSP (868-898) | 5′-CTG CAT TGC ACC ATT TCA AGG-3′ | |
| 16S_she-F | 5′-GAT AAC AGT TGG AAA CGA CTG-3′ | PCR (RT-PCR) assay |
| 16S_she-R | 5′-CTT TCC TCC CTA CTG AAA GTG-3′ |
The underlined italic letters represent restriction sites, and the bold letters denote the known (and/or predicted) CRP-binding sites. RT-PCR, reverse transcription-polymersase chain reaction; CRP, cAMP-receptor protein.