Table 1.
Predicted -35 and -10 promoter regions (bold) and transcription start sites (TSS; nucleotides in bold italics at the end of each sequence) for intergenic regions in the jamaicamide gene cluster (accession #AY522504).
| Upstream region of gene | Predicted TSS location (bp) | ORF start (bp) | |||
|---|---|---|---|---|---|
| upjamA | 6626 | 6630 | CTGACTTTCCACGACATGGGACTGATGGGAAATGTATATTTATTTGA | ||
| upjamB | 8464 | 8591 | GTGGGTTGATTTGATCAAGTTTGATGATATAATTTGATTTA | ||
| upjamB | 8501 | 8591 | TTTAATTTACAGGGATACCGCCAATTCGGTAACCTGGAAAA | ||
| upjamC | 9614 | 9718 | AAAACTTGTCAACCTGAACAAGATCCTGAACAAAATATTGTTG | ||
| upjamD | 10433 | 10463 | ACAGTTTGATGGTGCCGCTATTTTGAAGTTGGAAAATTTTTTA | ||
| upjamG | 18145 | 18222 | ATTTGTTGTTTGGGAATCGGGAATTGGTATTAGTAGTGGAA | ||
| upjamI | 20776 | 20982 | CGGAATTCAAAATTCAAAATTCAAAATGCTTATGGATTATGGAGTAAA | ||
| upjamI | 20989 | 20982 | CCAGGTTGACAAACCATTGATAAAGCTATAGTATGTATTA | ||
| upjamN | 51787 | 51811 | TGGAGTATAAAAAACAGAGCCTGGTGATAGTTAATTAA | ||
| upjamQ | 63710a | 63646a | GAACTTTGAATCCTCTATTTTGATTAAATTTGGAGA | ||
a: Numbers correspond to bp in complementary 3' - 5' direction.
Bold -35 and -10 binding regions were predicted using BPROM (softberry.com) in comparison to the E. coli σ70 consensus -35 (TTGACA) and -10 (TATAAT) promoter regions. If upstream regions had more than one predicted promoter region, the region receiving the highest predicted score is provided (with the exception of upjamB, which had two high scoring regions, and upjamI, in which both predicted promoters were tested in the β-galactosidase assay). Each upstream region listed in the first column had activity in the reporter assay, except those not shown in bold text. The italic ATG in the second upjamI predicted promoter region indicates the jamI start codon. TSS nucleotides were predicted to be A or G based on comparisons to the most common TSS nucleotides in E. coli[29].