By:Eugene V. Koonin, Ph.D.(National Center for Biotechnology Information, National Institutes of Health)©2010nadechworld.com Education
Citation:Koonin,E.V.(2010)The Two Empires and Three Domains of Life in the Postgenomic Age.nadechworld.com Education3(9):27
How do scientists study and classify life-forms? How can we understand the complex evolutionary connections between living organisms?
Comparative genomics, which involves analysis of the nucleotidesequences of genomes, shows that the known life-forms comprise two majordivisions: the cellular and the viral “empires.” The cellular empire consistsof three domains: Bacteria, Archaea, and Eukarya. What are the evolutionaryrelationships between the two empires and the three domains? Comparativegenomics sheds light on this key question by showing that the previousconception of the Tree of Life should be replaced by a complex network of treelikeand netlike routes of evolution to depict the history of life. Even under thisnew perspective on evolution, the two empires and the three cellular domainsremain distinct. Furthermore, comparative genomics suggests that eukaryotes arearchaebacterial chimeras, which evolved as a result of, or at least under astrong influence of, an endosymbiotic event that gave rise to mitochondria.
Cells, Viruses, and the Classification of Organisms
All living organisms consist of elementary units calledcells. Cells are membrane-enclosed compartments that contain genomic DNA(chromosomes), molecular machinery for genome replication and expression, atranslation system that makes proteins, metabolic and transport systems thatsupply monomers for these processes, and various regulatory systems. Scientistshave performed careful microscopic observations and other experiments to showthat all cells reproduce by different forms of division. Cell division is anelaborate process that ensures faithful segregation of copies of the replicatedgenome into daughter cells. The best-characterized cells are the relativelylarge cells of animals, plants, fungi, and diverse unicellular organisms knownas protists, such as amoebae or paramecia. These cells possess an internalcytoskeleton and a complex system of intracellular membrane partitions,including the nucleus, a compartment that encloses the chromosomes. Theseorganisms are known as eukaryotes because they possess a true nucleus (karyon in Greek). In contrast, the muchsmaller cells of bacteria have no nucleus and are named prokaryotes.
In the twentieth century, scientists devised new imaging methodslike electron microscopy, which can be used to view tiny particles that aremuch smaller than cells, to detect a second fundamental form of biological organization:the viruses. Viruses are obligate intracellular parasites. These selfishgenetic elements typically encode some proteins essential for viral replication,but they never contain the full complement of genes for the proteins and RNAsrequired for translation, membrane function, or metabolism. Therefore, virusesexploit cells to produce their components.
Classifying organisms (known as systematics or taxonomy) isone of the oldest occupations of biologists. Carolus Linnaeus constructed hisnow famous taxonomic system — certainly one of the foundations of scientificbiology — in the middle of the eighteenth century. How did he classifyorganisms? Since Linnaeus was not an evolutionist, his classifications strivedto reflect only similarities between species that were considered immutable.The goals of systematics changed after Charles Darwin introduced the concept ofthe Tree of Life (hereafter, TOL). At least in principle, the TOL was perceivedas an accurate depiction of the evolutionary relationships between alllife-forms. After Darwin,evolutionary biologists attempted to delineate monophyletic taxa, which aregroups of organisms that share a common ancestry and thus form a distinctbranch in the TOL. Until the last quarter of the twentieth century, however, taxonomistsworked with phenotypic similarities between organisms, so monophyly remained ahypothesis based on the hierarchy of similar features. Accordingly, biologistscould boast substantial advances in the classification of animals and plants,and to a lesser extent, simpler multicellular life-forms, such as fungi andalgae. However, taxonomy was nearly helpless when it came to unicellularorganisms, particularly bacteria, which have few easily observed features tocompare. As a result, microbiologists were skeptical about whether it waspossible to establish the evolutionary relationships between microbes. Howcould they compare these tiny organisms?
A revolution occurred in 1977 when Carl Woese and his co-workersperformed pioneering studies to compare the nucleotide sequences of a moleculethat is conserved in all cellular life-forms: the small subunit of ribosomalRNA (known as 16S rRNA). By comparing the nucleotide sequences of the 16S rRNA,they were able to derive a global phylogeny of cellular organisms for the firsttime. This phylogeny overturned the eukaryote-prokaryote dichotomy by showingthat the 16S rRNA tree neatly divided into three major branches, which becameknown as the three domains of (cellular) life: Bacteria, Archaea and Eukarya (Woese et al.1990). This discovery was enormously surprising, given thatsuperficially the members of the new Archaea domain did not appear particularlydifferent from bacteria. Since archaea and bacteria looked alike, how differentcould they be?