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

Jiuzhou Song; Ware, Antony; Shu-Lin Liu
January 2003
BMC Genomics;2003, Vol. 4, p1
Academic Journal
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.


Related Articles

  • Metabolism, cell growth and the bacterial cell cycle. Wang, Jue D.; Levin, Petra A. // Nature Reviews Microbiology;Nov2009, Vol. 7 Issue 11, p822 

    Adaptation to fluctuations in nutrient availability is a fact of life for single-celled organisms in the 'wild'. A decade ago our understanding of how bacteria adjust cell cycle parameters to accommodate changes in nutrient availability stemmed almost entirely from elegant physiological studies...

  • Helical proteins initiate replication of DNA helices. O'Donnell, Mike; Jeruzalmi, David // Nature Structural & Molecular Biology;Aug2006, Vol. 13 Issue 8, p665 

    The article focuses on studies regarding the initiation of chromosome replication in both bacteria and eukaryotes to form protein helical filaments. Studies have found that wrapping of origin DNA around the protein helical filaments may advance DNA unwinding and succeeding assembly of...

  • Coordination of DNA Ends During Double-Strand-Break Repair in Bacteriophage T4. Stohr, Bradley A.; Kreuzer, Kenneth N. // Genetics;Nov2002, Vol. 162 Issue 3, p1019 

    The extensive chromosome replication (ECR) model of double-strand-break repair (DSBR) proposes that each end of a double-strand break (DSB) is repaired independently by initiating extensive semiconservative DNA replication after strand invasion into homologous template DNA. In contrast, several...

  • Genome instability: A U-turn for mutagenesis? Burgess, Darren J. // Nature Reviews Genetics;Jan2013, Vol. 14 Issue 1, p7 

    The article presents a study that investigates the replication restart of yeast and instances when it made a U-turn in the U.S.

  • Computational Prediction of DNA-Protein Interactions: A Review. Xue-Mei Ding; Xiao-Yong Pan; Chen Xu; Hong-Bin Shen // Current Computer-Aided Drug Design;Sep2010, Vol. 6 Issue 3, p197 

    The interaction between DNA and proteins comprises a pivotal role in almost every cellular process, including gene regulation and DNA replication. Given a protein, it is very important to know whether it is a DNA-binding protein or not and where the binding sites are. Over the last three...

  • Functional cooperation between FACT and MCM helicase facilitates initiation of chromatin DNA replication. Tan, Bertrand Chin-Ming; Chien, Cheng-Ting; Hirose, Susumu; Lee, Sheng-Chung // EMBO Journal;9/13/2006, Vol. 25 Issue 17, p3975 

    Chromatin is suppressive in nature to cellular enzymes that metabolize DNA, mainly due to the inherent inaccessibility of the DNA template. Despite extensive understanding of the involvement of chromatin-modifying factors in transcription, roles of related activities in DNA replication remain...

  • The chromosome cycle: coordinating replication and segregation. Blow, J. Julian; Tanaka, Tomoyuki U. // EMBO Reports;Nov2005, Vol. 6 Issue 11, p1028 

    During the cell-division cycle, chromosomal DNA must initially be precisely duplicated and then correctly segregated to daughter cells. The accuracy of these two events is maintained by two interlinked cycles: the replication licensing cycle, which ensures precise duplication of DNA, and the...

  • Proliferating Cell Nuclear Antigen and ASF1 Modulate Silent Chromatin in Saccharomyces cerevisiae via Lysine 56 on Histone H3. Miller, Andrew; Yang, Bo; Foster, Tiaunn; Kirchmaier, Ann L. // Genetics;Jun2008, Vol. 179 Issue 2, p793 

    The formation and stability of epigenetically regulated chromatin is influenced by DNA replication and factors that modulate post-translational modifications on histones. Here we describe evidence that PCNA can affect silencing in Saccharomyces cerevisiae by facilitating deposition of H3 K56ac...

  • Replication and transcription: Shaping the landscape of the genome. Chakalova, Lyubomira; Debrand, Emmanuel; Mitchell, Jennifer A.; Osborne, Cameron S.; Fraser, Peter // Nature Reviews Genetics;Sep2005, Vol. 6 Issue 9, p669 

    As the relationship between nuclear structure and function begins to unfold, a picture is emerging of a dynamic landscape that is centred on the two main processes that execute the regulated use and propagation of the genome. Rather than being subservient enzymatic activities, the replication...


Other Topics