Non-random distribution of GATC sequences in regions of promoters stimulated by the SeqA protein of Escherichia coli.

The SeqA protein of Escherichia coli is not only the main negative regulator of DNA replication initiation but also a specific transcription factor. It binds to hemimethylated GATC sequences and, with somewhat different specificity, to fully methylated GATC regions. Recently, a microarray analysis was reported, in which transcriptomes of wild-type and ΔseqA strains were compared. Although in the seqA mutant the levels of some transcripts were significantly decreased while certain transcripts were evidently more abundant relative to wild-type bacteria, no correlation between the presence of GATC motifs in promoter sequences and transcription activity was found. However, here we show that when larger DNA fragments, encompassing positions from -250 to +250 relative to the transcription start site, are analyzed, some common features of GATC distribution near the promoters activated by SeqA can be demonstrated. Nevertheless, it seems that the GATC pattern is not the only determinant of SeqA-dependence of promoter activity.