Identification of replication origins in archaeal genomes based on theZ-curve method

Abstract

TheZ-curve is a three-dimensional curve that constitutes a unique representation of a DNA sequence, i.e., both theZ-curve and the given DNA sequence can be uniquely reconstructed from the other. We employedZ-curve analysis to identify one replication origin in theMethanocaldococcus jannaschiigenome, two replication origins in theHalobacteriumspecies NRC-1 genome and one replication origin in theMethanosarcina mazeigenome. One of the predicted replication origins ofHalobacteriumspecies NRC-1 is the same as a replication origin later identified by in vivo experiments. TheZ-curve analysis of theSulfolobus solfataricusP2 genome suggested the existence of three replication origins, which is also consistent with later experimental results. This review aims to summarize applications of theZ-curve in identifying replication origins of archaeal genomes, and to provide clues about the locations of as yet unidentified replication origins of theAeropyrum pernixK1,Methanococcus maripaludisS2,Picrophilus torridusDSM 9790 andPyrobaculum aerophilumstr. IM2 genomes.