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Universal Tree of Life Introductory Article Universal Tree of Life Introductory article James R Brown, SmithKline Beecham Pharmaceuticals, Collegeville, Pennsylvania, USA Article Contents . Comparison of Classification Schemes The universal tree of life represents the proposed evolutionary relationships among all . Archaea, Bacteria and Eukarya cellular life forms (thereby excluding viruses). Gene sequence data has moved the focus of . Evidence of Early Basal Split the universal tree away from emphasizing metazoan diversity to encompassing the greater . The Origin of Eukaryotes genetic diversity found in prokaryotes and single-cell eukaryotes. Presently, the conical universal tree includes three main urkingdoms or domains called the Archaea (archaebacteria), Bacteria (eubacteria) and Eukarya (eukaryotes) with the rooting in the Bacteria such that Archaea and Eukarya are sister groups. However, the evolutionary relationships among these three groups, and even the status of the Archaea, are still hotly debated among evolutionary biologists. Comparison of Classification Schemes the methanogens and their relatives ‘archaebacteria’, a Naturalists have striven perpetually to build a meaningful name which reflected their distinctness from the true classification scheme for living things. Long before bacteria or ‘eubacteria’ as well as contemporary precon- Darwin, plants and animals were believed to be the ceptions that these organisms might have thrived in the primary divisions of life. In 1866, Haeckel was the first to environmental conditions of a younger Earth. challenge this dichotomy by suggesting that the Protista In 1990, Woese, Kandler and Wheelis formally proposed should be considered to be a third kingdom equal in stature the replacement of the bipartite view of life with a new to the Plantae and Animalia. The Bacteria or Monera were tripartite scheme based on three urkingdoms or domains; designated as a fourth kingdom by Copeland, in 1938. the Bacteria (formerly eubacteria), Archaea (formerly Whittaker added the fungi in 1959, and his five kingdom archaebacteria) and Eukarya (formerly eukaryotes (Plantae, Animalia, Protista, Fungi and Monera) universal although this term is still more often used) (Figure 1). The tree is still taught as part of basic biology curricula. rationale behind this revision came from a growing body of Over 50 years ago, Chatton, and Stanier and van Niel biochemical, genomic and phylogenetic evidence which, suggested that life could be subdivided into two even more when viewed collectively, suggested that the archaebacter- fundamental cellular categories, prokaryotes and eukar- ia were worthy of a taxonomic status equal to that of yotes. The distinction between the two groups was eukaryotes and eubacteria. While there was wide accep- subsequently refined as studies of cellular biology and tance of this reclassification by most archaebacteriologists, genetics progressed such that prokaryotes became uni- several evolutionary biologists expressed serious dissent versally distinguishable from eukaryotes on the basis of over the elevation of archaebacteria (and hence the missing internal membranes (such as the nuclear mem- eubacteria) to a taxonomic rank comparable to eukar- brane and endoplasmic recticulum), nuclear division by yotes. fission rather than mitosis and the presence of a cell wall. The definition of eukaryotes was broadened to include Margulis’ endosymbiont hypothesis, which describes how Archaea, Bacteria and Eukarya eukaryotes improved their metabolic capacity by engulfing certain prokaryotes and converting them into intracellular At the centre of the controversy surrounding the concept of organelles, principally mitochondria and chloroplasts. the three domains are the Archaea and their degree of In the late 1970s the fundamental belief in the uniqueness from the Bacteria. Although discovered much prokaryote–eukaryote dichotomy was shattered by the more recently than either the Bacteria or Eukarya, the work of Carl Woese and George Fox. By digesting in vivo biochemistry, genetics and evolutionary relationships of labelled 16S rRNA using T1 ribonuclease then accumulat- the Archaea have been intensively studied. In addition, the ing and comparing catalogues of the resultant oligonucleo- complete genomic DNA sequences are now known for tide ‘words’, Woese and Fox were able to derive several archaeal species. Therefore, it is appropriate to dendrograms showing the relationships between different compare briefly the biology of these interesting organisms bacterial species. Analyses involving some unusual metha- with that of bacteria and eukaryotes. nogenic ‘bacteria’ revealed surprising and unique species According to rRNA trees, there are two groups within clusterings among prokaryotes. So deep was the split in the the Archaea: the kingdoms Crenarchaeota and Euryarch- prokaryotes that Woese and Fox proposed in 1977 to call aeota. The Crenarchaeota are generally hyperthermo- ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net 1 Universal Tree of Life Eukarya Animals Fungi Archaea Plants Entamoeba Euryarchaeota Crenarchaeota Euglena Bacteria Korarchaeota High G + C Gram Kinetoplasta Low G + C Gram positives (e.g. Trypanosoma) positives Parabasalia δ/ε-Purples (e.g. Trichomonas) α -Purples and mitochondria ‘Archezoa’ γ/β-Purples Microsporidia [?] Spirochaetes (e.g. Nosema) Fusobacteria Thermotogales Metamonda Flexibacter/bacteroides (e.g. Giardia) Cyanobacteria and chloroplasts Thermus Aquifex ‘Cenancestor’ Figure 1 Schematic drawing of a universal rRNA tree showing the relative positions of evolutionary pivotal groups in the domains Bacteria, Archaea and Eukarya. The location of the root (the cenancestor) corresponds with that proposed by reciprocally rooted gene phylogenies. The question mark beside the Archezoa group Microsporidia denotes recent suggestions that it might branch higher in the eukaryotic portion of the tree. (Branch lengths have no meaning in this tree.) philes or thermoacidophiles (some genera are Desulfur- isopranyl ether lipids, the absence of acyl ester lipids and ococcus, Pyrodictium, Sulfolobus, Thermofilum and Ther- fatty acid synthetase, specially modified tRNA molecules, moproteus). The Euryarchaeota span a broader ecological a split in one of the RNA polymerase subunits, and a range and include hyperthermophiles (e.g. Pyrococcus and specific range of antibiotic sensitivities. Among the species Thermococcus), methanogens (e.g. Methanosacrina), halo- of Archaea there are a variety of metabolic regimes which philes (e.g. Halobacterium and Haloferax), and even often differ greatly from the better known metabolic thermophilic methanogens (e.g. Methanobacterium, pathways of Bacteria and eukaryotes. Methanococcus and Methanothermus). However, it is Archaea and Bacteria are united in the ‘realm of important to note that microbial species assemblages in prokaryotes’ by generally similar cell sizes, a lack of a extreme environments are not exclusively archaeal as nuclear membrane and organelles, and the presence of a bacteria-specific rRNA signatures can also be amplified large circular chromosome occasionally accompanied by from such sites. In addition, through polymerase chain one or more smaller circular DNA plasmids. Like the reaction (PCR) amplification of rRNA sequences from Bacteria, the Archaea have multiple genes organized into water and sediment samples, a plethora of new archaeal operon transcriptional units and several of these operons species belonging to both kingdoms have been found in have the same gene order as their counterparts in the mesophilic environments such as temperate marine coastal Bacteria. Archaeal and bacterial mRNAs lack 5’ end caps waters, the Antarctic Ocean, and freshwater lakes, even as and often have Shine–Dalgarno ribosome binding sites. marine sponge symbionts. PCR-based surveys of hot However, the locations of putative Shine–Dalgarno springs’ microbiota have also detected novel archaeal sequences relative to the translational initiation codon rRNA sequences that possibly branch deeper than the are more variable in Archaea, and in fact, the upstream Crenarchaeota–Euryarchaeota divergence. These ‘organ- sequences of several highly expressed genes bear little isms’ have been tentatively assigned to a third archaeal resemblance to Shine–Dalgarno motifs. Other features kingdom, the Korarchaeota. shared between the Archaea and Bacteria include type II The Archaea have several unique biochemical charac- restriction enzyme systems, the absence of splicesomal teristics as well as unusual combinations of characteristics introns found in eukaryotes, and the presence of homing once thought to be exclusive to either the Bacteria or the endonucleases typical of group I introns found in Eukarya. Some solely archaeal characteristics include mitochondria and bacteriophages. 2 ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net Universal Tree of Life While cell division in the Archaea might function as in Although Archaea lack eukaryotic splicesomal introns, Bacteria, many components of DNA replication, tran- they do have introns in tRNA genes which are of similar scription and translation are definitely more eukaryote- size and often inserted between the same residues as those like. Hints of genetic homology among Archaea and found in eukaryotes. Excision of tRNA introns in eukaryotes were first found in studies which revealed that eukaryotes involves a site-specific endonuclease compris- archaeal species showed patterns of antibiotic sensitivities ing two duplicated
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