A DNA structural atlas for Escherichia coli

We have performed a computational analysis of DNA structural features in 18 fully sequenced prokaryotic genomes using models for DNA curvature, DNA fl exibility, and DNA stability. The structural values that are computed for t he Escherichia coli chromosome are significantly different from land genera lly more extreme than that expected from the nucleotide composition. To aid this analysis, we have constructed tools that plot structural measures for ail positions in a long DNA sequence (e.g. an entire chromosome) in the fo rm of color-coded wheels (http:// www.cbs.dtu.dk/services/GenomeAtlas/). We find that these "structural atlases" are useful for the discovery of inter esting features that may then be investigated in more depth using statistic al methods. From investigation of the E. coli structural atlas, we discover ed a genome-wide trend, where an extended region encompassing the terminus displays a high of level curvature, a low level of flexibility, and a low d egree of helix stability. The same situation is found in the distantly rela ted Gram-positive bacterium Bacillus subtilis, suggesting that the phenomen on is biologically relevant. Based on a search for long DNA segments where all the independent structural measures agree, we have found a set of 20 re gions with identical and very extreme structural properties. Due to their s trong inherent curvature, we suggest that these may function as topological domain boundaries by efficiently organizing plectonemically supercoiled DN A. Interestingly, we find that in practically all the investigated eubacter ial and archaeal genomes, there is a trend for promoter DNA being more curv ed, less flexible, and less stable than DNA in coding regions and in interg enic DNA without promoters. This trend is present regardless of the absolut e levels of the structural parameters, and we suggest that this may be rela ted to the requirement for helix unwinding during initiation of transcripti on, or perhaps to the previously observed location of promoters at the apex of plectonemically supercoiled DNA. We have also analyzed the structural s imilarities between groups of genes by clustering all RNA and protein-encod ing genes in E. coli, based on the average structural parameters. We find t hat most ribosomal genes (protein-encoding as well as rRNA genes) cluster t ogether, and we suggest that DNA structure may play a role in the transcrip tion of these highly expressed genes. (C) 2000 Academic Press.