FIG. 3.

Determination of the transcription start sites of the ligK and ligJ operons. (A and B) Primer extension analyses of the ligK operon transcript using PEligK43 (A) or the ligJ operon transcript using PEligJ173 (B). Fluorescent primer extensions were performed with the D4-labeled primer, and total RNA was isolated from SYK-6 harboring pVA01, which carries ligK-orf1-ligI-lsdA, ligJABC, and ligR, grown in the presence (left) or absence (right) of PCA. Primer extension products were combined with DNA size standards and analyzed with the CEQ 2000XL fragment analysis system. (C) Alignment of sequences upstream from the transcription start sites of the ligK and ligJ operons. Vertical lines indicate conserved residues. Transcription start sites are indicated (+1). Putative −35 and −10 regions are underlined. Putative LigR binding sequences are boxed. The start codons of ligK, ligJ, and ligR are shown by arrows. The stop codon of ligR is indicated with a double underline. The residues indicated by dots were substituted nucleotides.