Published online 16 July 2004
Nucleic Acids Research, Vol. 32 No. 13 © Oxford University Press 2004; all rights reserved
Where does bacterial replication start? Rules for predicting the oriC region
Mackiewicz
ska1,*aw R. Dudek2aw Cebrat
Department of Genomics, Institute of Genetics and Microbiology, University of Wrocaw, Przybyszewskiego 63/77, 51-148 Wrocaw, Poland, 1 Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Weigla 12, 53-114 Wrocaw, Poland and 2 Institute of Physics, University of Zielona Góra, Szafrana 4A, 65-516 Zielona Góra, Poland
* To whom correspondence should be addressed. Tel: +48 71 337 11 72; Fax: +48 71 337 13 82; Email: zakrzew{at}iitd.pan.wroc.pl
Received May 5, 2004; Revised June 11, 2004; Accepted June 22, 2004
Three methods, based on DNA asymmetry, the distribution of DnaA boxes and dnaA gene location, were applied to identify the putative replication origins in 120 chromosomes. The chromosomes were classified according to the agreement of these methods and the applicability of these methods was evaluated. DNA asymmetry is the most universal method of putative oriC identification in bacterial chromosomes, but it should be applied together with other methods to achieve better prediction. The three methods identify the same region as a putative origin in all Bacilli and Clostridia, many Actinobacteria and 
Proteobacteria. The organization of clusters of DnaA boxes was analysed in detail. For 76 chromosomes, a DNA fragment containing multiple DnaA boxes was identified as a putative origin region. Most bacterial chromosomes exhibit an overrepresentation of DnaA boxes; many of them contain at least two clusters of DnaA boxes in the vicinity of the oriC region. The additional clusters of DnaA boxes are probably involved in controlling replication initiation. Surprisingly, the characteristic features of the initiation of replication, i.e. a cluster of DnaA boxes, a dnaA gene and a switch in asymmetry, were not found in some of the analysed chromosomes, particularly those of obligatory intracellular parasites or endosymbionts. This is presumably connected with many mechanisms disturbing DNA asymmetry, translocation or disappearance of the dnaA gene and decay of the Escherichia coli perfect DnaA box pattern.
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