title: Diversity and evolution of multiple orc/cdc6-adjacent replication origins in haloarchaea.
abstract: BACKGROUND
  While multiple replication origins have been observed in archaea, considerably less is known about their evolutionary processes. Here, we performed a comparative analysis of the predicted (proved in part) orc/cdc6-associated replication origins in 15 completely sequenced haloarchaeal genomes to investigate the diversity and evolution of replication origins in halophilic Archaea.
  
  
  RESULTS
  Multiple orc/cdc6-associated replication origins were predicted in all of the analyzed haloarchaeal genomes following the identification of putative ORBs (origin recognition boxes) that are associated with orc/cdc6 genes. Five of these predicted replication origins in Haloarcula hispanica were experimentally confirmed via autonomous replication activities. Strikingly, several predicted replication origins in H. hispanica and Haloarcula marismortui are located in the distinct regions of their highly homologous chromosomes, suggesting that these replication origins might have been introduced as parts of new genomic content. A comparison of the origin-associated Orc/Cdc6 homologs and the corresponding predicted ORB elements revealed that the replication origins in a given haloarchaeon are quite diverse, while different haloarchaea can share a few conserved origins. Phylogenetic and genomic context analyses suggested that there is an original replication origin (oriC1) that was inherited from the ancestor of archaea, and several other origins were likely evolved and/or translocated within the haloarchaeal species.
  
  
  CONCLUSIONS
  This study provides detailed information about the diversity of multiple orc/cdc6-associated replication origins in haloarchaeal genomes, and provides novel insight into the evolution of multiple replication origins in Archaea.
authors.affiliation: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Zhenfang
authors.initials: Z
authors.lastname: Wu
authors.forename: Hailong
authors.initials: H
authors.lastname: Liu
authors.forename: Jingfang
authors.initials: J
authors.lastname: Liu
authors.forename: Xiaoqing
authors.initials: X
authors.lastname: Liu
authors.forename: Hua
authors.initials: H
authors.lastname: Xiang
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics*; D001483:Base Sequence; D005075:Biological Evolution; D019847:Chromosomes, Archaeal; D004261:DNA Replication; D019641:DNA, Archaeal / Q000235:genetics*; D014644:Genetic Variation; D020745:Genome, Archaeal; D008969:Molecular Sequence Data; D051738:Origin Recognition Complex / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D018741:Replication Origin
chemical_list: D019641:DNA, Archaeal; D051738:Origin Recognition Complex