How were archaea discovered?
Archaea maybe existed on Earth during the early stages of life evolution, but they were classified as bacteria before the 1970s. It was not until 1977 that American biologists Carl Woese and George Fox identified them as the third form of life after analyzing their genetic material.
Throughout the lengthy evolution, nucleic acid sequences mutated constantly and randomly. The rate of mutation remained relatively constant, that is, the number of replaced bases at regular intervals is same for a certain DNA fragment. Because different species diverged from a common ancestor, they share certain homologous nucleotide sequences that scientists study to explore where these species lie on the evolutionary tree and when they split apart. Small-subunit ribosomal RNA was used by Carl Woese and George Fox as a molecular clock to confirm relationships among microorganisms. It is highly conserved because it is a critical component in protein synthesis machinery that drives all life activities.
Carl Woese and George Fox discovered that methanogens, previously categorized as bacteria, represent a third type of life between prokaryotes and eukaryotes. Their cell structure is similar to bacteria, but their genetic information and gene expression are closer to eukaryotes. These organisms are called archaea because their living environments may be similar to early Earth. They form the three-domain system of lives along with bacteria and eukaryotes.
Difference between Archaea and Bacteria, Bacteria vs Archaea
Cell wall: Protein granules
Nearly all bacteria cell wall is built by peptidoglycan (β-1,4-glycosidic bond), especially the Gram-positive bacteria. Archaea lack this component, but a few species, such as methanogens, have a similar component whose sugar linking is different (β-1,3-glycosidic bond) and there is no muramic acid or D-amino acid. Some other species use complex polysaccharides to construct their cell walls. However, the main component of most archaeal cell walls is a 20-40nm protein layer. Protein or glycoprotein granules are embedded one by one on cell membrane, like a scale armour of ancient warriors. It is not surprising that antibiotics and lysozyme against peptidoglycan are ineffective for them.
Cell membrane: Ether bond and saturated branched hydrocarbons
The phospholipid bilayer is the main component of most cell membranes. Unsaturated non-branched fatty acids are linked to glycerol through esterification. However, the archaea cell membrane is an ether lipids formed by etherification of branched saturated hydrocarbons and glycerol. Longer hydrocarbon of at least 20 carbon atoms, and more stable ether bonds help them survive in harsh environments. Some archaea use two hydrocarbons, each around 40 carbons, and two glycerol to synthesize a very long lipid. Cell membranes containing this lipid are single-layered, and held together in the middle by covalent bonds rather than hydrophobic effect. Therefore, its strong integrity is well suited to withstand high temperature.
Metabolic Pathways
Most bacteria and eukaryotes obtained aerobic respiration after Great Oxidation Event. Some corners in our planet still have environment that is like early Earth and suitable for archaea. It is usually anaerobic, reducing and extreme, such as high-temperature hydrothermal vents in deep sea floor, highly saline lakes, acidic or alkaline springs. Therefore, their metabolism differs from bacteria very much.
Many archaea harvest energy from a modified glycolytic pathway rather than glycolysis because they cannot produce fructose-6-phosphate. Glucose is converted into pyruvate, ATP, and NADH in just four steps, but ATP production is decreased by 50%. Methanogens even can’t catabolize glucose for energy. ATP is produced by them from hydrogen gas, carbon dioxide, short-chain fatty alcohols and acids.
Some archaea are phototrophic, but their metabolism for absorbing sunlight is entirely different from plants photosynthesis. Archaea lack chlorophyll, and their cell membranes are rich in carotenoids and rhodopsins. Carotenoids capture and transfer photons and prevent sunlight damage. Rhodopsins absorb light energy and pump protons into the space between cell membrane and cell wall to create a proton gradient. Then, the protons drive ATP synthase to produce ATP. This is the simplest light phosphorylation that relies on conformational change of rhodopsin rather than electron transport chain. The absence of NADPH or NADH means it doesn’t couple with carbon fixation.
ADP + Pi + sunlight → ATP + H₂O
A reverse citric acid cycle, anaerobic acetyl-CoA pathway (in methanogens), or other pathways is use by archaea to fix carbon. However, they are independent of light absorption and are not the Calvin cycle common in plants and bacteria. Therefore, light is not a necessary condition for archaea to convert inorganic carbon sources into organic matter.