Transcriptional analysis of the jamaicamide gene cluster from the marine cyanobacterium Lyngbya majuscula and identification of possible regulatory proteins

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)
up *jamA*	6626	6630	CTGACTTTCCACGACATGGGACTGATGGGAAATGTATATTTATTTGA
up *jamB*	8464	8591	GTGGGTTGATTTGATCAAGTTTGATGATATAATTTGATTTA
up *jamB*	8501	8591	TTTAATTTACAGGGATACCGCCAATTCGGTAACCTGGAAAA
up *jamC*	9614	9718	AAAACTTGTCAACCTGAACAAGATCCTGAACAAAATATTGTTG
up *jamD*	10433	10463	ACAGTTTGATGGTGCCGCTATTTTGAAGTTGG AAAATTTTTTA
up *jamG*	18145	18222	ATTTGTTGTTTGGGAATCGGGAATTGGTATTAGTAGTGGAA
upjamI	20776	20982	CGGAATTCAAAATTCAAAATTCAAAATGCTTATGGATTATGGAGTAAA
up *jamI*	20989	20982	CCAGGTTGACAAACCATTGATAAAGCTATAGT ATGTATTA
up *jamN*	51787	51811	TGGAGTATAAAAAACAGAGCCTGGTGATAGTTAATTAA
upjamQ	63710^a	63646^a	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].

ISSN: 1471-2180