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.

Noise‐reduction filtering for accurate detection of replication termini in bacterial genomes

“…Finally, ori and ter of E. coli were predicted using GC skew, keto and purine excesses, low‐pass filtering by FFT, and elimination of subgenomic regions. The predicted results were compared with experimentally confirmed loci [35] and with the prediction by Song et al [19], which has the best accuracy among methods that utilize compositional information with wavelet transform (Table 1 ). Elimination of statistically high/low GC regions, intergenic regions, predicted HGT regions, and genes documented in HGT‐DB, used as a control in comparison with noise reduction by FFT, had either very little (for ter ) or no (for ori ) effect.…”

“…Compositional skews may be disrupted by genomic insertions and by lateral gene‐transfer events [19]. To take into account the effects of these events as the control for comparison of noise reduction by FFT, we also predicted ori and ter after masking four types of subgenomic regions, namely, (1) intergenic regions; (2) low/high GC regions; (3) predicted regions of horizontal gene transfer (HGT) based on codon usage; and (4) horizontally transferred genes listed in the horizontal gene transfer database (HGT‐DB) [33].…”

“…The use of characteristic short oligomers that are highly skewed has also been proposed for higher precision [16]. These methods are implemented by computational software such as Oriloc [17], and although they have been utilized successfully in many genome projects to predict putative ori and ter sites, the predicted loci are not always precise [18], especially in the case of the ter region [19].…”

The Genome of Salmonella enterica Serovar Gallinarum: Distinct Insertions/Deletions and Rare Rearrangements

“…Previous studies have explored the reasons why some bacteria undergo frequent recombination events but many of their close relatives do not, such as in the case of serovar Typhi versus serovar Typhimurium (26,28,30). Previously, it was demonstrated that bacterial genomes have a tendency to obtain a physical balance (44). Based on this and other evidence, it was hypothesized that recombination may help the bacteria to rebalance the genome following major genomic insertions or deletions, which may have disrupted the genomic balance (19,30,31), although this hypothesis needs to be tested further as exceptions awaiting explanation also exist.…”

γBOriS: Identification of Origins of Replication in Gammaproteobacteria using Motif-based Machine Learning

“…All currently available computational methods for the identification of oriC sequences in bacterial chromosomes rely on nucleotide disparities on the leading and lagging strand of the DNA double helix (13)(14)(15)(16)(17). As replication usually extends from oriC bidirectionally, it is one of two chromosomal sites where the leading and lagging strand switch places.…”