Flow chart of promoter validation.

Abstract

<p>Genome-wide motif search using MEME and MAST provided 3874 and 14962 predicted σ⁷⁰-promoters at p-value cut-offs of 10⁻⁴ and (10⁻⁴≤p-value<10⁻³), respectively. For validation of the predicted promoters, transcriptionally active regions (TARs) were detected using tiling array data of <i>L. plantarum</i> WCFS1 and for each TAR the transcription start site (TSS) was determined. After filtering the TSSs for low-expressed TARs, 621 TSSs were obtained for validation of predicted σ⁷⁰-promoters. At a low p-value cut-off (p-value<10⁻⁴), 568 σ⁷⁰-promoters were found that co-localized within a distance of 40 nt of TSSs. An additional 120 σ⁷⁰-promoters were found to co-localized within a distance of 40 nt of TSSs after raising the p-value cut-off (10⁻⁴≤p-value<10⁻³). For 94 TSSs, no co-localized σ⁷⁰-promoter (within a distance of 40 nt) was found.</p