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Review
. 2014 Apr 29;5:179.
doi: 10.3389/fmicb.2014.00179. eCollection 2014.

DNA Replication Origins in Archaea

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Free PMC article
Review

DNA Replication Origins in Archaea

Zhenfang Wu et al. Front Microbiol. .
Free PMC article

Abstract

DNA replication initiation, which starts at specific chromosomal site (known as replication origins), is the key regulatory stage of chromosome replication. Archaea, the third domain of life, use a single or multiple origin(s) to initiate replication of their circular chromosomes. The basic structure of replication origins is conserved among archaea, typically including an AT-rich unwinding region flanked by several conserved repeats (origin recognition box, ORB) that are located adjacent to a replication initiator gene. Both the ORB sequence and the adjacent initiator gene are considerably diverse among different replication origins, while in silico and genetic analyses have indicated the specificity between the initiator genes and their cognate origins. These replicator-initiator pairings are reminiscent of the oriC-dnaA system in bacteria, and a model for the negative regulation of origin activity by a downstream cluster of ORB elements has been recently proposed in haloarchaea. Moreover, comparative genomic analyses have revealed that the mosaics of replicator-initiator pairings in archaeal chromosomes originated from the integration of extrachromosomal elements. This review summarizes the research progress in understanding of archaeal replication origins with particular focus on the utilization, control and evolution of multiple replication origins in haloarchaea.

Keywords: DNA replication origin; archaea; control; evolution; haloarchaea; origin recognition box.

Figures

FIGURE 1
FIGURE 1
Distribution of DNA replication origins in three well-studied archaeal model systems, Pyrococcus species (A), Sulfolobus species (B) and Haloarcula hispanica(C). Origins are indicated with filled ovals, and arrowheads designate bidirectional replication. Replicator-initiator indicates that each origin is specified by its proximally encoded initiator. Both Pyrococcus species and Sulfolobus species contain a single chromosome; the chromosome of Pyrococcus species is replicated from a single origin (Myllykallio et al., 2000), whereas the chromosome of Sulfolobus species is replicated from three origins in near synchrony (Duggin et al., 2008). The Haloarcula hispanica genome consists of a main chromosome and two extrachromosomal elements with five active replication origins: oriC1-cdc6A and oriC2-cdc6E in the main chromosome I, oriC6-cdc6I and oriC7-cdc6J in the minichromosome II, and oriP-cdc6K in the megaplasmid pHH400 (Wu et al., 2012).
FIGURE 2
FIGURE 2
The conserved oriC1 origin of replication in sequenced haloarchaeal genomes. The oriC1 context region was mapped as shown in the sequenced haloarchaea. The colored boxed arrows represent different genes as follows: GTP-binding protein (gbp, teal), initiator protein (cdc6, red), signal sequence peptidase (sec, yellow) and DNA-directed DNA polymerase (polA, blue). The inverted ORB elements are indicated by small triangles.

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