Where does bacterial replication start? Rules for predicting the oriC region

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.

Genomic Insights into Xylella fastidiosa Interactions with Plant and Insect Hosts

“…The location of the origin of replication can be confidently predicted from three different lines of genomic evidence: the location of the dnaA gene, a cluster of DnaA boxes, and inversion of the G/C and A/T skews (Mackiewicz et al 2004;Simpson et al 2000). The terminus can be identified by similar methods: Both the predicted dif sequence and oligonucleotide asymmetry analysis point to the same region of each sequenced chromosome (Yen et al 2002;Kono et al 2011).…”

Identification of the oriC region and its influence on heterocyst development in the filamentous cyanobacterium Anabaena sp. strain PCC 7120

“…In Bacillus subtilis, the sda gene is a checkpoint factor preventing sporulation at the onset of DNA replication, and upregulation of sda gene expression is dependent on the active form of DnaA (Veening et al, 2009). (Mackiewicz et al, 2004). In bacterial chromosomes, the leading strand has more G or T, while the lagging strand is enriched in amino bases (A or C) (Rocha et al, 1999).…”

Reply to Zhang et al. : Identification of origins of replication in the Cyanothece 51142 genome

“…According to ref. 3, AT skew exhibited a stronger signal than GC skew in strains closely related to Cyanothece 51142 and thus could be more informative than GC skew. Additionally, multiple peaks suggested the possibility of multiple origins of replication (3).…”

“…Origins of replication have been difficult to determine using similar algorithms in numerous cyanobacterial strains lacking distinct patterns of strand asymmetry (3,4). According to ref.…”