Published online 15 July 2005
Article |
A-tract clusters may facilitate DNA packaging in bacterial nucleoid
1Laboratory of Experimental and Computational Biology, National Cancer Institute Bethesda, MD 20892, USA 2Laboratory of Molecular Biology, National Cancer Institute Bethesda, MD 20892, USA 3Department of Biological and Medical Physics, V. Karazin Kharkov National University Kharkov, 61077, Ukraine
*To whom correspondence should be addressed. Tel: +1 301 496 8913; Fax: +1 301 402 4724; Email: zhurkin{at}nih.gov
Received January 25, 2005. Revised June 22, 2005. Accepted June 22, 2005.
Molecular mechanisms of bacterial chromosome packaging are still unclear, as bacteria lack nucleosomes or other apparent basic elements of DNA compaction. Among the factors facilitating DNA condensation may be a propensity of the DNA molecule for folding due to its intrinsic curvature. As suggested previously, the sequence correlations in genome reflect such a propensity [Trifonov and Sussman (1980) Proc. Natl Acad. Sci. USA, 77, 3816–3820]. To further elaborate this concept, we analyzed positioning of A-tracts (the sequence motifs introducing the most pronounced DNA curvature) in the Escherichia coli genome. First, we observed that the A-tracts are over-represented and distributed ‘quasi-regularly’ throughout the genome, including both the coding and intergenic sequences. Second, there is a 10–12 bp periodicity in the A-tract positioning indicating that the A-tracts are phased with respect to the DNA helical repeat. Third, the phased A-tracts are organized in 
100 bp long clusters. The latter feature was revealed with the help of a novel approach based on the Fourier series expansion of the A-tract distance autocorrelation function. Since the A-tracts introduce local bends of the DNA duplex and these bends accumulate when properly phased, the observed clusters would facilitate DNA looping. Also, such clusters may serve as binding sites for the nucleoid-associated proteins that have affinities for curved DNA (such as HU, H-NS, Hfq and CbpA). Therefore, we suggest that the 100 bp long clusters of the phased A-tracts constitute the ‘structural code’ for DNA compaction by providing the long-range intrinsic curvature and increasing stability of the DNA complexes with architectural proteins.
Correspondence may also be addressed to Michael Y. Tolstorukov. Tel: +38 057 707 5576; Fax: +1 831 308 7657; Email: tolstorukov{at}gmail.com
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