Archaea

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Taxonomy

The Archaea represent a monophyletic group distinct from both Bacteria and Eukarya.
The Archaea fall into two major phyla: Euryarchaea and Crenarchaea. Phenotypically, cultivated crenarchaea and some euryarchaea are sulfur-metabolizing thermophiles (yellow in the tree above), whereas the euryarchaea also include the methanogens (green) and extreme halophiles (red). Both major phyla are also home to a large number of ssu-rRNA sequences apparently from planktonic marine species; the phenotypes of these organisms are not known. Two potential minor phyla are the Nanoarchaea and Korarchaea; the relationships between these minor phyla and either the Euryarchaea of Crenarchaea remain unclear.

General properties of the Archaea

Although they superficially resemble Bacteria, the Archaea are neither Bacteria nor Eukarya. In some respects, Archaea do resemble Bacteria. Most metabolic proteins are similar to those of Bacteria, as are gene and chromosome structure, the processes of replication, transcription, and translation, and the cytoskeleton. In many other respects, however, the Archaea are more similar to Eukarya. Most of the information-processing machinery (replication, transcription, translation) is eukaryal-like. Archaea also have nucleosomes, nucleolar enzymes, and cell-cycle proteins not present (or at least very different) in Bacteria. And in some ways, Archaea are different that either Bacteria or Eukarya, the most obvious being membrane lipids.

Morphology

Phenotypically, the Archaea are a lot like Bacteria. Most are small (0.5-5 microns) rods, cocci, spirilla, and filaments. Archaea most often reproduce by fission, like most Bacteria and most unicellular Eukarya, and reproduction is asexual.

Methanosarcina
Methanosarcina barkeri : Dr. Jan KeltjensĀ : http://www.microbiology.science.ru.nl/galleries/

Cell envelop

One of the unique features of Archaea are their membrane lipids, which are quite different than those of either Bacteria or Eukarya. They are ether-linked (not ester-linked) glycerol derivatives of 20 or 40 carbon branched (isoprenyl) lipids. Unsaturations in the lipid chain are generally conjugated (those of Bacteria & eukaryotes are unconjugated). 40-carbon lipids are ether-linked to glycerol at both ends, and if these glycerol moieties are on opposite sides of the membrane form lipid monolayers rather than bilayers. These lipids can be used as chemical signatures for the presence of Archaea in a sample.

membrane lipids
Comparison of bacterial and archaeal membrane lipids : David L. Valentine, Nature Reviews Microbiology 5, 316-323 (April 2007)

Archaea have a cytoplasm membrane only; they do not have an outer membrane.

The Archaea have a wide various cell walls, but none contain peptidoglycan, the signature of bacterial cell walls. Protein or glycoprotein S-layers are common, as are cell walls containing pseudomurien, which is chemically related to peptidoglycan in that it is a fabric of linear disaccharide polymer crosslinked with oligopeptides.

Flagella

Although the flagella of Archaea (those that have them) resemble bacterial flagella superficially, they are fundamentally different structures. Like bacterial flagella, archaeal flagella are composed of a motor embedded in the cell envelop, and a long semi-flexible helical filament that is turned by the motor and drives the cell. The similarity ends there. The archaeal flagellar motor proteins and structure are related to type II secretion systems and type IV pili, whereas bacterial flagella are related to type III secretion systems. The archaeal flagellar motor is driven directly by ATP hydrolysis rather than the flow of protons across the cell membrane - it is a chemical motor rather than an electric motor. Archaeal flagellar filaments are much thinner than are those of bacteria, and are not hollow; protein subunits are added to the base to lengthen the filament, rather than the tip as in Bacteria. Clearly these structures are analogous rather than homologous; they evolved from independent origins, and are a classic example of evolutionary convergence.

archaeal flagella
Archaeal flagella : Ken F. Jarrell & Mark J. McBride, Nature Reviews Microbiology 6, 466-476 (June 2008)

Transcription and translation

The transcriptional/translational machinery in Archaea is fundamentally like those of Bacteria and Eukarya, with 70S (bacterial-sized) ribosomes. Genes are arranged in co-transcribed clusters (operons). Ribosomes recognize translational start sites and bind to the mRNAs directly at 'Shine-Dalgarno' (SD) sequences as in Bacteria. Also as in Bacteria, transcription and translation are linked - that is, they occur simultaneously.

However, in many ways transcription and translation in Archaea is like it is in Eukarya. Although each promoter drives the expression of an entire operon, the promoters are very much like eukaryotic RNA polymerase II promoters, and as in eukaryotes, are binding sites for transcription factors rather than the RNA polymerase itself, as in Bacteria. Archaea have a single RNA polymerase (like Bacteria), but this RNA polymerase is essentially a eukaryotic RNA polymerase II, and requires the same general transcription factors for promoter recognition. Translation is initiated with methionine (like Eukarya) rather than formyl-methionine (Bacteria). Translation is inhibited by diphtheria toxin, as are eukaryal ribosomes, but is not inhibited by most bacterial-translation-inhibiting antibiotics. Chimeric archaeal/eukaryal ribosomes are functional; neither bacterial/archaeal nor bacterial/eukaryal are functional.

Genomes

The genomes of Archaea are generally ca. 2-4Mbp, usually in one main circular DNA molecule, as to most Bacteria. However, as in eukaryotes, Archaea have abundant histone-like proteins and the DNA is packaged in the form of nucleosome-like particles. Hyperthermophilic species contain a reverse gyrase that positively supercoils this genomic DNA, rendering it more resistant to thermal denaturation.

Mth genome
A map of the genome of Methanothermobacter thermoautotrophicus : Smith et al 1997 J. Bacteriol 179:7135

In the same way that transcription and translation processes are generally like those of Bacteria although the machinery that carries these out is essentially like those of Eukarya, so too the genome replication process is similar in Archaea and Bacteria, with one (or a small number of) replication origin and a replication terminus, but this process is carried out by replication machinery that closely resembles the eukaryal replisome. In addition, chromosome replication and segregation/mitosis seem to be distinct processes in the cell cycle of Archaea, as in Eukarya.