Table 2 Oligonucleotides used in this study
Oligo | aF/R | Sequence 5'-3' | bSpecificity |
|---|---|---|---|
oliRN110 | F | CGCTGCGTAAAAGATACG | aphIII |
oliRN111 | R | AATGGAGTGTCTTCTTCC | Â |
oliRN130 | F | TTGAAATGACAAAAGAAGTT | luxS |
oliRN129 | R | AAAGAGGCTATGATCCTTAT | Â |
OLEC287OLEC288 | F | AGTTAAGTGACGATAGCCTAG | 5S rRNA |
| Â | R | CTAAGCGACTACCTTATCTCA | Â |
oliRN242 | F | CGGTAACTAACCAGAAAGGG | 16S rRNA |
oliRN243 | R | CGTTGTACCAACCATTGTAGC | Â |
| Â | Â | Â | Virulence genes |
OLEC137 | F | GACCTACTCAGGCAAATC | fbp54 |
OLEC138 | R | CTTGTCTAAGGCAATCTC | Â |
oliRN204oliRN203 | F | TGGTAAAAATGCCTATACCC | isp2 |
| Â | R | GACCTCGTGAAAACTTAGCC | Â |
oliRN248 | F | AGGAATAAATTGGTCCTCTT | nga |
oliRN249 | R | GGCAGTTTCAATAAACTCAT | Â |
OLEC268 | F | AAGAGATCGAAGAAAGTCTT | scl |
OLEC269 | R | TTTGGTTAGCTTCTTTGTCA | Â |
oliRN202oliRN201 | F | AGTTAAGGCACAAGAACAGG | sibA (psp) |
oliRN246 | R | TACTTGAGGCACTTTGAACC | Â |
oliRN247 | F | ACTAGGAGCTACACAACCAG | sic |
oliRN263 | R | TACCCTGTACCTAATGCTTC | Â |
oliRN264 | F | ACATCTCAAGAATTACTAGC | ska |
oliRN279 | R | TTGTTGTAGAGTAGTTTAGC | Â |
oliRN50 | F | ATGGAAAATATTCTGATATCTTAG | slo |
oliRN47 | R | CCCAAAGGATTTCATATTGAGC | Â |
| Â | F | CATAATTACAGTCACTGATT | speC |
oliRN48 | R | ATCGAAATGACTAAAGTTCTTCAT | Â |
oliRN55 | F | TTTTCAATGGTAGCTCTTG | speF (mf) |
oliRN56 | R | TTCTTGAGCTCTTTGTTCG | Â |
| Â | Â | Â | Stand-alone regulators |
OLEC274 | F | ATAGCCTAGAAACAGAATTA | codY |
OLEC275 | R | TTCTGAATAAGAAAGCGTAT | Â |
oliRN170 | F | TAAGTAAGTTGTTTACAAGTCAAC AGTGGAG | mga |
oliRN136 | R | AAAGGCGTAGATCAATTGG | Â |
OLEC337 | F | ATGACGCCTAATAAAGAAGA | mtsR |
OLEC338 | R | CTGTGACATAAAGTTGCTTA | Â |
OLEC315 | F | TGGACATTCATTCACATCAG | perR (spf) |
OLEC316 | R | ATCAGGTTGGTCTTTTGCTT | Â |
oliRN73 | F | AAATACTTGGAATCATCAATCG | rofA |
oliRN74 | R | TTTTCTTGAGCTAATGCAACCG | Â |
OLEC278 | F | TAGACAACTTGAATGTCAAT | ropB |
OLEC279 | R | AAGCTTTATCATACTCTTGT | Â |
OLEC276 | F | ACATTTTGCAACGGTATATT | srv |
OLEC277 | R | AATAGGGTCATTAAGTCATA | Â |
| Â | Â | Â | Two-component systems |
oliRN175 | F | CTGCTTGACTTAATGTTACC | covR (CovRS) |
oliRN176 | R | TTTGACAATAATTCTTCACG | Â |
OLEC182 | F | GAGCAATAACATTTTAGG | fasX (effector molecule, FasBCA) |
OLEC183 | R | TTACAATCAGCTGATGTG | Â |
OLEC270 | F | ATTCGAAAGACATCAGATGT | Irr (Ihk/Irr) |
OLEC271 | R | CATATGTCATCCATCAATTG | Â |
OLEC339 | F | GATATCATGATGCCGATTAA | sptR (SptRS) |
OLEC340 | R | TAGCTAGTATCTTTATCACC | Â |
OLEC280 | F | TACTTATTGTGGATGATGAA | vicR (VicRK) |
OLEC281 | R | AATCATATCCCCAAACAATT | Â |
oliRN23 | F | AATTGTGAATTC TATCATAATTGTGG (Eco RI) | Cassette aphIII for luxS- deficient mutants |
oliRN24 | R | TAAATCAAGCTT CTAAAACAATTCATCCAG (Hin dIII) | Â |
oliRN20 | F | ACTAGTGAATTC TCAAACATAACAATCC (Eco RI) | Fragment luxS down for luxS- deficient mutants |
oliRN19 | R | TTCTGAGGATCC CCACCATCCAGCC (Bam HI) | Â |
oliRN22 | F | AATCAAGCATGC TTACTTGGAAAAGAACCCAACC (Sph I) | Fragment luxS up for luxS- deficient mutants |
oliRN21 | R | AAGTGGAAGCTT GTGGAGGAGAAAAGGC (Hin dIII) | Â |
oliRN267 | F | CATCGCTGCGCCTCTTGCTAC | Confirmation of the luxS- deficient mutants |
oliRN268 | R | GGGTCATTCCAGAACCACAGA | Â |
oliRN70 | F | GCTATTTTTTGACTTACTGGG | Â |
oliRN69 | R | TCCGTATCTTTTACGCAGCGG | Â |
oliRN205 | F | GTCAATGGATCC CCAGCTCTATTGCACC (Bam HI) | PluxS-luxS-TT insert for luxS complementation plasmid pEC83 |
oliRN280 | R | TATCTAGAGCTC TAGATTACTGAGAAAATC (Sac I) | Â |
oliRN250 | R | ATTCTTCAGAAATAAGACG | Primer extension |