Wavelet to predict bacterial ori and ter: a tendency towards a physical balance.
BACKGROUND
Chromosomal DNA replication in bacteria starts at the origin (ori) and the two replicores propagate in opposite directions up to the terminus (ter) region. We hypothesize that the two replicores need to reach ter at the same time to maintain a physical balance; DNA insertion would disrupt such a balance, requiring chromosomal rearrangements to restore the balance. To test this hypothesis, we needed to demonstrate that ori and ter are in a physical balance in bacterial chromosomes. Using wavelet analysis, we documented GC skew, AT skew, purine excess and keto excess on the published bacterial genomic sequences to locate the turning (minimum and maximum) points on the curves. Previously, the minimum point had been supposed to correlate with ori and the maximum to correlate with ter.


RESULTS
We observed a strong tendency of the bacterial chromosomes towards a physical balance, with the minima and maxima corresponding to the known or putative ori and ter and being about half chromosome separated in most of the bacteria studied. A nonparametric method based on wavelet transformation was employed to perform significance tests for the predicted loci.


CONCLUSIONS
The wavelet approach can reliably predict the ori and ter regions and the bacterial chromosomes have a strong tendency towards a physical balance between ori and ter.
Song
Jiuzhou
J
Department of Microbiology, University of Calgary, Calgary, Canada. songj@ucalgary.ca
Ware
Antony
A
Liu
Shu-Lin
SL
D020856:AT Rich Sequence / Q000235:genetics; D001482:Base Composition / Q000235:genetics; D002876:Chromosomes, Bacterial / Q000235:genetics*; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D004269:DNA, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D019453:Escherichia coli O157 / Q000235:genetics; D020862:GC Rich Sequence / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D015233:Models, Statistical; D011237:Predictive Value of Tests; D018741:Replication Origin / Q000235:genetics*; D012486:Salmonella typhimurium / Q000235:genetics; D013045:Species Specificity; D016615:Telomere / Q000235:genetics*
D004269:DNA, Bacterial