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. 2004 Jul 16;32(13):3781-91.
doi: 10.1093/nar/gkh699. Print 2004.

Where Does Bacterial Replication Start? Rules for Predicting the oriC Region

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Where Does Bacterial Replication Start? Rules for Predicting the oriC Region

Pawel Mackiewicz et al. Nucleic Acids Res. .
Free PMC article

Abstract

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 gamma 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.

Figures

Figure 1
Figure 1
DNA asymmetry, DnaA box distribution and dnaA gene location on bacterial chromosomes. x-axis—chromosome coordinates in base pairs, in (AE and H) beginning and ending in the presumed terminus of replication (according to the DNA asymmetry). The chromosomal coordinates in (F and G) are as in the databases. The grey line and the right y-axis show the DNA walk describing DNA asymmetry (asymmetry for [A–T] in (F); asymmetry for [G–C] for the other chromosomes). Black peaks with diamonds and the left y-axis show the DnaA box distribution expressed by the b value. The short vertical line indicates the dnaA gene location.
Figure 2
Figure 2
DNA asymmetry in [G–C], DnaA box distribution, and dnaA gene location on the H.pylori J99 chromosome. (A) Distribution of DnaA boxes which differ in more than one position from the perfect DnaA box TTATCCACA; (B) distribution of DnaA boxes experimentally proved to be functional in this genome according to Zawilak et al. (26). The x-axis describing the coordinate position on the chromosome in base pairs begins and ends in the presumed (according to DNA asymmetry) terminus of replication. See Figure 1 for further explanation.
Figure 3
Figure 3
DNA asymmetry in [G–C], DnaA box' distribution and dnaA gene location in the oriC region. Example of single cluster of DnaA boxes (A) and a few separated clusters in the region (B). See Figure 1 for further explanation.
Figure 4
Figure 4
Correlation between G + C content of DnaA boxes (derived from the putative origins identified in 76 chromosomes) and genomic G + C content.
Figure 5
Figure 5
The 16S rRNA phylogenetic tree for 112 analysed bacteria and their classification based on concordance of methods of oriC identification: DNA asymmetry, DnaA box distribution and the dnaA gene location. The tree was built with the minimum evolution method (ME) by the MEGA 2.1 program (42) assuming the Tamura–Nei model of nucleotide substitutions (43). Abbreviations of the bacterial names are listed in Supplementary Table 1. Archaeoglobus fulgidus (ar f) was chosen as representative of the Archaea.

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