Diversity and evolution of multiple orc/cdc6-adjacent replication origins in haloarchaea

Zhenfang Wu,Hailong Liu,Xiaoqing Liu,Hua Xiang,Jingfang Liu

doi:10.1186/1471-2164-13-478

Abstract

BackgroundWhile 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.ResultsMultiple 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.ConclusionThis 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.

Highlights

While multiple replication origins have been observed in archaea, considerably less is known about their evolutionary processes
Identification of orc/cdc6-associated replication origins in H. hispanica Research in archaeal model strains indicates that most replication origins share conserved characteristics, such as the presence of inverted ORB elements and being located directly adjacent to orc/cdc6 genes [5,9,10]
These common features provided us a reference standard to predict replication origins in H. hispanica. Only those intergenic regions (IRs) that contain ORB-like elements and are directly adjacent to orc/cdc6 genes were considered to be putative orc/cdc6-associated replication origins. They were not included in the scope of this study, we do not exclude the possibility of replication origins that are not directly adjacent to orc/cdc6 genes or are without classical ORBlike elements

Summary

Introduction

While multiple replication origins have been observed in archaea, considerably less is known about their evolutionary processes. The study of replication origins in archaea has been ongoing for more than a decade, and multiple replication origins have been identified in several archaeal species [4,5,6,7,8,9,10]. It is not yet understood, why archaea adopt multiple origins to initiate replication of their bacterial-like chromosomes or how these multiple replication origins evolved. In H. volcanii, five replication origins were identified, two within the chromosome and one each within the three megaplasmids pHV1, pHV3 and pHV4 [9]

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Results

Conclusion