Recent Advances in the Identification of Replication Origins Based on the Z-curve Method

Abstract

Precise DNA replication is critical for the maintenance of genetic integrity in all organisms. In all three domains of life, DNA replication starts at a specialized locus, termed as the replication origin, oriC or ORI, and its identification is vital to understanding the complex replication process. In bacteria and eukaryotes, replication initiates from single and multiple origins, respectively, while archaea can adopt either of the two modes. The Z-curve method has been successfully used to identify replication origins in genomes of various species, including multiple oriCs in some archaea. Based on the Z-curve method and comparative genomics analysis, we have developed a web-based system, Ori-Finder, for finding oriCs in bacterial genomes with high accuracy. Predicted oriC regions in bacterial genomes are organized into an online database, DoriC. Recently, archaeal oriC regions identified by both in vivo and in silico methods have also been included in the database. Here, we summarize the recent advances of in silico prediction of oriCs in bacterial and archaeal genomes using the Z-curve based method.

Keywords: Archaea; Bacteria; Comparative genomics; Origins of replication; Z-curve..

Fig. (1)

RY, MK, AT and GC disparity curves reveal oriC locations in bacterial and archaeal genomes. Z-curves show a single oriC in the genome of the bacterium of Cyanothece sp. PCC 7425 (A) and one, two, three oriCs in genomes of the archaea of Pyrococcus abyssi GE5 (B), Halobacterium sp. NRC-1 (C), and Sulfolobus acidocaldarius DSM 639 (D), respectively. Note that the Z-curves have been drawn for the rotated sequences beginning and ending in the maximum of the GC disparity curves. Short vertical line indicates dnaA or cdc6 gene location, and short up vertical arrow indicates the identified oriC location.

Fig. (2)

Schematic diagram of the replication origins of P. calidifontis JCM 11548. Within the oriC1 (A), there are two 12-mer palindromic sequences (blue) annotated as Orb-1 elements in Pelve et al., 2012. Within the oriC2 (B), oriC3 (C) and oriC4 (D), there is a 13-mer consensus element (yellow) and a tRNA gene (blue).

Fig. (3)

Graphical circular map of the archaeon P. calidifontis JCM 11548. The filled circles indicate the locations of four chromosome replication origins in P. calidifontis JCM 11548, determined by using the high-throughput sequencing-based marker frequency analysis. The lines indicate the locations of the predicted replication origins and some conserved genes related to the origin regions, such as tRNA gene and copG gene.

Fig. (4)

Conserved domain annotation on the protein sequence of Mc-pRIP in M. jannaschii DSM 2661. Shown here is the full view generated by the CD-Search tool, and the default values are used for the BLAST search parameters.