UNEVEN DISTRIBUTION OF GATC MOTIFS IN THE ESCHERICHIA-COLI CHROMOSOME, ITS PLASMIDS AND ITS PHAGES

This work reconsiders the GATC motif distribution in a 1.6 Mb segment of the Escherichia coli genome, compared to its distribution in phages and plasmids. At first sight the distribution of GATC words looks ran dom. But when a realistic model of the chromosome (made of average gen es having the same codon usage as in the real chromosome), is used as a theoretical reference, strong biases are observed. GATC pairs such a s GATCNNGATC are under-represented while there is a strong positive se lection for motifs separated by 10, 19, 70 and 1100 bp. The last class is the only one present in E. coli parasites. It can be ascribed to t he triggering sequences of the long-patch mismatch repair system. The 6 bp class overlaps with the consensus of CAP (catabolite activator pr otein) and FNR (fumarate/nitrate regulator) binding sites, thus accoun ting for counter-selection. The other classes, which could be targets for a nucleic acid binding protein, are almost always present inside p rotein coding sequences, and are members of clusters of GATC motifs. A nalysis of the genes containing these motifs suggests that they corres pond to a regulatory process monitoring the shift from anaerobic to ae robic growth conditions. In particular this regulation, closing down t ranscription of a large number of genes involved in intermediary metab olism would be well suited for the cold and oxygen shift from the mamm al's gut tot he standard environmental conditions. In this process the methylation status of GATC clusters would be very important for tunin g transcription, and a DNA binding protein, probably a member of the c old-shock proteins family would be needed or alleviating the effects m ediated by slackening of the pace of methylation during the shift. (C) 1996 Academic Press Limited