DNA replication is a fundamental phenomenon to maintain and transfer of the genetic information in the living organisms. Elucidation of the molecular mechanism of DNA replication has been one of the main subjects since molecular biology started. Most of the research results in the field were obtained from Escherichia coli and its phages in an early stage. Then, research was expanded to the eukaryotic cells, including yeast and mammalian cells. It is now well recognized that living organisms are divided into three domains. Archaea, the third domain, different from Bacteria and Eukarya, was joined to the field of DNA replication after two other domains and the research has been active since late 1990’s to present. Comparative studies in the three domains of life provide much useful information to understand the evolution of DNA replication machinery. In this mini-review article, we will discuss mainly the molecular evolution of DNA polymerase in the living organisms.
In Archaea, almost all introns in pre-tRNA, pre-rRNA, and pre-mRNA are spliced through two common steps by protein enzymes: cleavage of the precursor with splicing endonuclease, and ligation of the exons with RNA ligase. We found the first examples of archaeal pre-mRNA splicing and cleavage of the pre-mRNA with a novel subclass of archaeal splicing endonuclease. We further solved the novel tertiary structure of the splicing endonuclease, and revealed that the lineage-specific insertion of amino acid residues in the endonuclease expands the recognition of the substrate precursor RNA. We also discuss the possible involvement of tRNA splicing and its machinery in the origin of the tRNA molecule.
Archaea was established according to difference of 16S rRNA nucleotide sequences, and is thought to be the ancestral organism for eukaryote. Now many entire nucleotide sequences of Archaeal genomes are available. By comparing among Archaeal genomic data, information for their evolution can be extracted. In this work, the evolutional features are extracted from genomic information of three Archaeal species, Pyrococcus horikoshii, Aeropyrum pernix and Sulfolobus tokodaii. 1. From the comparison of the overall positioning of the similar genes, it is shown that two Pyrococcus species, P. abyssi and P. horikoshii, conserve their overall gene ordering with a few times grovel genomic recombination, revealing that these two species were separated recently. Conversely, species in genus Sulfolobus did not show any structural similarity of genome, predicting that species in genus Sulfolobus were developed independently. 2. Among Pyrococcus species, the gene ordering within the mannosylglycerate biosynthesis gene cluster is completely retained with high sequence similarity of each gene, revealing that this cluster is thought to be important for genus Pyrococcus. 3. From comparison of gene ordering within the UDP-GlcNAc biosynthesis gene cluster, it is shown that phylogenetic distance between P. horikoshii and A. pernix is closer than that between P. horikoshii and S. tokodaii. 4. When compared the amino acid sequences of the gene family, functionally similar genes are consisting a phylogenetic cluster. But when compared the nucleotide sequences, genes from same species are consisting a phylogenetic cluster. These results indicate that nucleotide sequences were developed with retaining features of the host species, but the translated amino acid sequences were developed under pressure of the function. 5. Other features, like presence or absence of plasmid, transposable elements, duplication and recombination, also provide the important information on evolution. These analyses shown above indicate detail analysis is necessary for recognition of the recent history of genomic evolution.