%0 Journal Article
%T Close Encounters of the Third Domain: The Emerging Genomic View of Archaeal Diversity and Evolution
%A Anja Spang
%A Joran Martijn
%A Jimmy H. Saw
%A Anders E. Lind
%A Lionel Guy
%A Thijs J. G. Ettema
%J Archaea
%D 2013
%I Hindawi Publishing Corporation
%R 10.1155/2013/202358
%X The Archaea represent the so-called Third Domain of life, which has evolved in parallel with the Bacteria and which is implicated to have played a pivotal role in the emergence of the eukaryotic domain of life. Recent progress in genomic sequencing technologies and cultivation-independent methods has started to unearth a plethora of data of novel, uncultivated archaeal lineages. Here, we review how the availability of such genomic data has revealed several important insights into the diversity, ecological relevance, metabolic capacity, and the origin and evolution of the archaeal domain of life. 1. Introduction The description of the three (cellular) domains of life¡ªEukarya, Bacteria, and Archaea¡ªby Carl Woese and George Fox [1] represents a milestone in the modern era of microbiology. In particular, using phylogenetic reconstructions of the small-subunit (16S or 18S) ribosomal RNA gene, Woese discovered that microscopically indistinguishable prokaryotes are not a homogeneous assemblage but are comprised of two fundamentally different groups of organisms: Eubacteria (later Bacteria) on one side and an additional life form referred to as Archaebacteria (later Archaea) on the other side [1]. Though not immediately accepted by the scientific community, this finding was early on supported by Wolfram Zillig through his studies on DNA-dependent RNA polymerases, as well as by Otto Kandler investigating ¡°bacterial¡± cell walls [2]. Indeed, a subset of prokaryotic organisms subsequently assigned to Archaea was found to harbor DNA-dependent RNA polymerases that bore more similarity to those of eukaryotes, and to contain proteinaceous cell walls that lack peptidoglycan as well as cell membranes composed of L-glycerol ether lipids with isoprenoid chains instead of D-glycerol ester lipids with fatty acid chains [3¨C6]. Since then, further investigation of cellular characteristics of archaea has revealed that this domain of life contains eukaryotic-like information-processing machineries [7¨C14]. These findings were later supported by genome sequences and comparative analyses of genes coding for replication, transcription, and translation machineries as well as by protein crystal structures [15¨C21]. Additionally, some archaeal lineages were shown to contain homologs of eukaryotic cell division and cytoskeleton genes as well as histones and seem to express a chromatin architecture similar to eukaryotes [22¨C28]. In contrast to information-processing and cell division genes, archaeal operational systems (energy metabolism, biosynthesis pathways, and regulation) often
%U http://www.hindawi.com/journals/archaea/2013/202358/