Eucarya, Bacteria, and Archea: The Three Domain System

By: Brad J.B. - Truman State U.

Prior to the advent of genetic sequencing, organisms were organized into taxonomic groups based on recognizable physical characteristics. Thus, the first attempts at reconstructing a phylogeny of all species on Earth were based solely on organism morphology. This posed significant problems since most prokaryotic life does not contain observable characteristics necessary for placement into specific taxonomic groups. Today the sequencing of amino acids in proteins, and nucleotides in DNA and RNA, allows the reconstruction of an accurate universal phylogeny known as the three-domain approach. Based on overwhelming genetic data, the three-domain approach appears to best represent the highest level of organization in the living world, rather than the five- or six-kingdom approach.

Constructing a phylogeny of all organisms using genetic analysis first requires the determination of specific genes with sequences found universally among organisms, regardless of how distantly related they may be. In addition, the genes of choice must code for a product that performs an essential function, and is thereby influenced by “strong stabilizing selection.” It is also necessary that the function performed by the genetic product is the same in every organism. Once these genes are located, a universal phylogeny may be reconstructed based on the degrees of genetic similarity between organisms.

One such gene that meets all the criteria listed above is the gene that codes for small-subunit ribosomal RNA. All organisms, from the simplest prokaryotes to humans, contain ribosomes, and all ribosomes have the same basic tertiary structure with small and large subunits. In addition, ribosomes in every organism perform the same vital function of translation. Because translation is absolutely essential to all organisms, the pressure imposed by natural selection to maintain this process has been very strong. As a result, the nucleotide sequence of ribosomal RNA is very similar in all organisms.

By comparing the sequences of small-subunit rRNA, a universal phylogeny was constructed that clearly shows three major domains, rather than five or six kingdoms. In fact, four of the five kingdoms are now incorporated into a single domain: Eucarya. The two other domains, termed Bacteria and Archea, were both formerly included under the kingdom Monera. The Bacteria domain includes the well-known bacteria, such as cyanobacteria and various gram-positive bacteria. Organisms in the Archea domain are much less well known, and tend to live in harsh environments such as hot springs and thermal vents. It has been demonstrated that the Archea, originally classified as bacteria, are actually more closely related to eukaryotes.

The universal phylogeny based on rRNA clearly supports a three-domain approach to the classification of life rather than the classical five- or six-kingdom approach. By sequencing and comparing genetic information, it has been shown that the three kingdoms most commonly studied by evolutionary biologists, Animals, Plants, and Fungi, actually occupy only a relatively small portion of the tree of life. The more obscure Archea and Bacteria, on the other hand, are shown to compose a much larger portion of the tree.

Based on genetic data shared by all organisms, the three-domain approach is simply a more accurate portrayal of the evolutionary relationships that exist between different taxonomic groups. In addition, the three-domain system better reflects the overwhelming number of “simple” unicellular organisms on Earth. As more genes are sequenced and analyzed, it is likely that individual classifications within the domains will be further refined (especially as more is learned about members of the Archea domain); yet the overall structure will continue to be substantiated.