Editorial: DNA Replication Origins in Microbial Genomes

In all three domains of life, DNA replication initiates on defined genome sites, termed replication origins. In bacteria, replication typically initiates from a single replication origin (oriC). In eukaryotic genomes, replication initiates from significantly more replication origins, ranging from hundreds in yeast to tens of thousands in human (Gao et al., 2012). Within the archaeal domain, multiple replication origins have been identified in Sulfolobus species, haloarchaea etc. The research on replication origins is important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. Therefore, intensive studies, by in silico analyses as well as in vivo and in vitro experiments, have been carried out in the last two decades. Based on the sequence-derived features, various in silico approaches have been developed to identify microbial replication origins For example, the locations of replication origins sites have been predicted for thousands of bacterial genomes by Ori-Finder, a web-based system for finding oriCs in bacterial genomes (Gao and Zhang, 2007; Gao et al., 2013). A new version of Ori-Finder for archaea, Ori-Finder 2, has been developed to predict oriCs in archaeal genomes automatically (Luo et al.). To confirm the predicted replication origins, it is important to choose a most suitable experimental strategy. Song et al. summarize the main existing experimental methods to determine the replication origin regions and their practical applications (Song et al.). As a study from in silico to in vitro, the experimental supports are provided for the identified replication origins in Cyanothece ATCC 51142 (Gao and Zhang, 2008b), and their interactions with the initiator protein DnaA (Huang et al.). In spite of a great variety of origin sequences across species, all bacterial replication origins contain the information necessary to guide assembly of the DnaA protein complex at oriC, triggering the unwinding of DNA and the beginning of replication. Therefore, oriC-encoded instructions should be interpreted particularly in the context of replication initiation and its regulation (Wolanski et al.). Wolanski et al. show that oriC-encoded instructions allow not only for initiation but also for precise regulation of replication initiation and coordination of chromosomal replication with the cell cycle (also in response to environmental signals; Wolanski et al.). Frimodt-Moller et al. find control regions for chromosome replication are conserved with respect to sequence and location among Escherichia coli strains (Frimodt-Moller et al.). Based on the …