Replication of Genomes in Eukaryotes: Analyses of the Structure and Functions of the Replicative ε Polymerases from Yeasts, Plants and Animals

In all living organisms, genome replication is an indispensable activity in their life cycle. As compared to prokaryotes, genome replication in eukaryotes is much more complex. In eukaryotes, the genome replication is accomplished by a more specialized, multi-protein complex known as replisome. Therefore, for a complete understanding of the replication process in eukaryotes, the structure-function relationship of their replisome complex is important. The eukaryotic replisome complex is mainly composed of 3 replicative polymerases (pols), viz. α, ε and δ. The initiation of genome replication starts with the synthesis of primers by the α pol (a primase), which is followed by the synthesis of leading- and lagging-strands by the next two replicative pols, viz. ε and δ, respectively. Among them, the pol ε is an essential enzyme that links the DNA replication machinery to S-phase checkpoint-control in eukaryotes. The active sites of pol and proofreading (PR) domains of α and δ were analyzed from yeasts, animal and plant sources and reported by this author already [1, 2]. The third replicative enzyme, viz. the pol ε is analyzed and reported here. Interestingly, the yeast, animal and plant ε pols possess almost identical pol, PR and carboxyl terminal domains (CTD) with the same active site amino acids. Their catalytic cores use the same template-binding pair (–YG-), the catalytic amino acid (K), the nucleotide selection amino acid (Q) and similar catalytic metal-binding motifs in the pol domain as reported for the other replicative pols. However, they exhibit poor identities among themselves, e.g., the human pol ε showed only 46.69% and 43.19% identities to the plant (Arabidopsis thaliana) and yeast (Saccharomyces cerevisiae) pol ε sequences, respectively. Furthermore, these eukaryotic ε pols use the same active site amino acids in the PR exonuclease domain, and belong to the DEDD(Y)-superfamily of PR exonucleases. Moreover, similar to the other two replicative enzymes, the ε pols also use similar regulatory Zn2+-binding motifs (ZBMs) in their CTD. In addition, it harbours a unique ZBM in their pol domain. Interestingly, the two invariant motifs, viz –SLYPS- and -YGDTD- which are the characteristic motifs found in the other replicative α and δ pols and B-family of DNA pols, are not found in ε pols. Many specialized, conserved sequence motifs are also identified in the ε pols and discussed.