s conserved in Bacteria and Archaea and is different from the linear form of eukaryotic genomes. These features have encouraged us to study archaeal DNA replication, in the hopes of gaining fundamental insights into this molecular mechanism and its machinery from an evolutional perspective. study of bacterial DNA replication at a molecular level started in about 1960, and then eukaryotic studies followed since 1980. Because Archaea was recognized as the third domain of life later, the archaeal DNA replication research became active after 1990. With increasing the available total genome sequences, the progress of research on archaeal DNA replication has been rapid, and the depth of our knowledge of archaeal DNA replication has almost caught up with those of the bacterial and eukaryotic research fields. In this chapter, we will summarize the current knowledge of DNA replication in Archaea.
2. Replication origin
The basic mechanism of DNA replication was predicted as replicon theory by Jacob et al. They proposed that an initiation factor recognizes the replicator, now referred to as a replication origin, to start replication of the chromosomal DNA. Then, the replication origin of E. coli DNA was identified as oriC (origin of chromosome). The archaeal replication origin was identified in the Pyrococcus abyssi in 2001 as the first archaeal replication origin. origin was located just upstream of the gene encoding the Cdc6 and Orc1-like sequence s in the Pyrococcus genome. We discovered a gene encoding an amino acid sequence that bore similarity to those of both eukaryotic Cdc6 and Orc1, which are the eukaryotic initiators. After confirming that this protein actually binds to the oriC region on the chromosomal DNA we named the gene product Cdc6/Orc1 due to its roughly equal homology with regions of eukaryotic Orc1 and Cdc6. The gene consists of an operon with the gene encoding DNA polymerase D (it was originally called Pol II, as the second DNA polymerase from Pyrococcus furiosus ) in the genome. characteristic of the oriC is the conserved 13 bp repeats, as predicted earlier by bioinformatics, and two of the repeats are longer and surround apredicted DUE (DNA unwinding element) with an AT-rich sequence in Pyrococcus genomes (Figure 2). The longer repeated sequence was designated as an ORB (Origin Recognition Box), and it was actually recognized by Cdc6/Orc1 in a Sulfolobus solfataricus study. The 13 base repeat is called a miniORB, as a minimal version of ORB. A whole genome microarray analysis of P. abyssi showed that the Cdc6/Orc1 binds to the oriC region with extremes pecificity, and the specific binding of the highly purified P. furiosus Cdc6/Orc1 to ORB and miniORB was confirmed in vitro . It has to be noted that multiple origins were identified in the Sulfolobus genomes. It is now well recognized that Sulfolobus has three origins and they work at the same time in the cell cycle. of the mechanism of how the multiple origins are utilized for genome re...
