Wavelet to predict bacterial ori and ter: a tendency towards a physical balance

Abstract

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.

Figure 1

Wavelet transformation analysis exemplified by the chromosome of S. typhimurium LT2 for GC and AT skews.

Figure 2

Wavelet transformation analysis exemplified by the chromosome of S. typhimurium LT2 for keto and purine excesses.

Figure 3

The spectrum of wavelet analysis for the chromosome of S. typhimurum LT2.

Figure 4

The positions of maxima estimated by Monte-Carlo simulation for 1000 signals and 1000 runs.

Figure 5

Wavelet analysis of keto excess and purine excess for E. coli K12; both are strong.

Figure 6

Wavelet analysis of keto excess and purine excess for Borrelia burgdorferi; keto is strong but purine is weak).

Figure 7

Wavelet analysis of keto excess and purine excess for Lactococcus lactis; purine is strong but keto is weak.

Figure 8

Magnifications of the minimum region of the purine excess curve for E. coli K12; the position of the reported oriC is still almost co-residing with the minimum point.

Figure 9

Further magnification of the minimum region of the purine excess curve for E. coli K12 for resolution at the single base level shows the exact physical relationship of the reported oriC and the minimum point.

Figure 10

The purine excess of E. coli O157:H7 EDL933 and E. coli O157:H7 Sakai-VT2, showing deviation of the reported ter region from the maximum point of the purine excess.