Structure and Evolution of Genomes

Abstract

The existence of many informational proteins that are common to Archaea and Eucarya and absent from Bacteria is not only true for DNA replication, but also for translation, transcription, and RNA and protein processing. Many reviews have summarized insight from newly sequenced archaeal genomes and have usually focused on aspects of comparative genomics. This chapter focuses on the description of archaeal genomes and what can be learned from archaeal genomics about the mechanisms of genome evolution, and the history of the Archaea domain itself. Compared with Bacteria, the number of completely sequenced archaeal genomes is much smaller. The larger genomes are from mesophilic archaea and contain a high proportion of genes recruited from bacteria by horizontal gene transfer (HGT). The chromosome terminus appears to be a hot spot of recombination in archaea, as it is in bacteria. This was clearly shown from a genome comparison of the two closely related species, Pyrococcus abyssi and Pyrococcus horikoshii. Comparative genomics has shown that gene loss, gene duplication, and integration of foreign DNA are major forces shaping genome evolution. The continuous evolution of archaeal genomes by gene loss and acquisition is obvious from the comparative analyses of the proteomes of closely related species. In a recent study using unfolding simulation experiments to determine amino acid composition, the number of charged residues in hyperthermophiles was reported to be much greater than it would need to be for the stabilization. Ongoing metagenomics projects will continue to broaden the understanding of archaeal diversity and evolution.