TABLE 1.
PCR detection and DNA sequencing of degradation genes in R. wratislaviensis and R. aetherivorans
| Primer set | Target gene (protein encoded) | Reference | Primers used | Length (bp) of PCR fragment sequenced (expected amplicon size) | GenBank accession no. |
|---|---|---|---|---|---|
| R. wratislaviensis | |||||
| alk-H1F, alk-H3R | alkB (alkane hydroxylase) | 8 | alk-H1F, 5′-CIG IIC ACG AII TIG GIC ACA AGA AGG-3′; alk-H3R, 5′-IGC ITG ITG ATC III GTG ICG CTG IAG-3′ | 429 (549) | FJ590423 |
| nidA-F, -R | nidA | 29 | nidA-F, 5′-GGACTACCTCGGCGATATGA-3′; nidA-R, 5′-TGTGGACGTGCTCTCCATAG-3′ | 310a (233) | FJ590424 |
| PAH-RHD-GP F, R | (Naphthalene inducible dioxygenase) | 5 | PAH-RHD-GP F, 5′-CGGCGCCGACAAYTTYGTNGG-3′; PAH-RHD-GP R, 5′-GGGAACACGGTGCCRTGDATRAA-3′ | 292 | |
| R. aetherivorans | |||||
| alk-H1F, alk-H3R | alkB (alkane hydroxylase) | 8 | alk-H1F, 5′-CIG IIC ACG AII TIG GIC ACA AGA AGG-3′; alk-H3R, 5′-IGC ITG ITG ATC III GTG ICG CTG IAG-3′ | 309 (549) | FJ590422 |
| ethB-F2, -R2 | ethB (cytochrome P450) | 6 | ethB-F2, 5′-CACGCGCTCGGCGACTGGCAGACGTTCAGT-3′; ethB-R2, 5′-TCCGACGCACATGTGCGGGCCGTACCCGAA-3′ | 698 (881) | FJ607040 |
a
Complete DNA sequence determined and assembled from the nidA and PAH overlapping PCR fragments.