14 Archaeal, Bacterial, and Eukaryal DNA Replication Machines

Abstract

During the evolution of life, three distinct phylogenetic domains of cellular organisms have emerged, the Bacteria, the Archaea, and the Eukarya. Ten years ago, in the previous edition of this book, Bruce Stillman wrote a chapter comparing and contrasting DNA replication processes in bacteria and eukaryotes. At that time, little was known about the process of replication in the third domain of life, the Archaea. Thankfully, in the intervening 10 years, a large body of bioinformatic, biochemical, and structural data has been accumulated on the archaeal replication system, revealing striking parallels with the eukaryal apparatus. In this chapter, I focus on the archaeal DNA replication apparatus and compare it with the orthologous eukaryotic and the analogous bacterial systems.

ORIGINS AND INITIATORS
The replicon hypothesis of Jacob and colleagues posits the existence of cis-acting replicators that are acted upon by trans-acting initiators (Jacob et al. 1964). This hypothesis is clearly relevant for bacteria, with the presence of a single replicator or origin of replication per bacterial chromosome, termed oriC. The origin is recognized by the conserved bacterial initiator, DnaA. Indeed, the consensus sequence recognized by DnaA, the DnaA box, is highly conserved across a broad phylogenetic range of bacteria (Messer et al. 2001; Messer 2002). Typically, multiple DnaA boxes exist in oriC, with the consequence that multiple molecules of DnaA bind to origins. In many cases, cooperative interactions are detected between DNA-bound DnaA proteins. The net result of these protein–protein interactions, coupled with the DnaA-induced DNA deformation, is the melting...