Kingdom Archaea
Clickable Index of Archaea
Cellular Structure

You have learned that living organisms have at least seven unique properties listed in the index above. As Archaea are living organisms, then they must possess these properties as well.

What are Archaea?

We have learned that Biology can be illustrated as a tree of life:

In this tree of life, one of the basal branches evolves into a group of organisms that is part of Domain Prokarya, and is the current extant Kingdom Archaea. Archaebacteria is a synonym used by some authors for the kingdom of the archaea.

Number of Kingdoms

Prior to 1977 the archaea were considered to be just another group of bacteria, so archaea were first part of Kingdom Plantae (green) when there were only two kingdoms. archaea followed the bacteria as fellow prokaryotes into the new kingdom, Monera (yellow) in the 3 to 5 kingdom era. In 1977 Carl Woese and George Fox proposed that archaea are different enough to have their own kingdom. In 1990 16S rRNA and 18S rRNA sequences for the archaea were found different enough from the other bacteria to justify this. By 2003, the genome sequence analysis results confirmed that archaea are really quite different from bacteria. The archaea were therefore split out from Monera in the transition to 6 kingdoms, and the kingdom was named Archaea.

The archaea have ancient origin, just like the bacteria, but they are somewhat more advanced in certain features. A chief example of these features is that the circular DNA molecule is associated with DNA binding proteins. These are not the histones of eukaryotes, but they are somewhat similar. Bacteria as you recall lack DNA binding proteins. So archaea are somewhere between bacteria and eukaryotes in this regard. So as you noticed in the phylogeny above, the archaea branch on the tree of life is between bacteria and eukaryotes. These organisms have had a long time to evolve and diversify into cells with a wide range of forms and functions.

The archaea can be categorized as being extremophiles, meaning that they are found today in some of the most extreme environments on earth. They live in water that is 90°C (nearly boiling), -4°C (nearly freezing) pH 2 (highly acidic), 25M (very salty), or anaerobic conditions...and often in places with a combination of these characteristics! These are tough organisms!

Archaea Have Cellular Structure

Archaea evolved many cell sizes, but all are relatively small. The thermoplasmas are the smallest of the archaea. Most archaea fall into size classes (0.1 to 15 μ diameter and up to 200 μ long) matching bacteria. So they are about the size of a mitochondrion in a eukaryotic cell.

Archaea have also evolved into many cell shapes similar to those of bacteria. There are bacilli, cocci, spirilli, and plate-like forms of archaea.

Also like bacteria, the cells of archaea form various associations within a population of cells. Some species are unicellular, others are colonial, and yet others are filamentous.

Just like bacterial cells, archaea cells come in three basic forms in terms of the cell boundary.

Mycoplasma-like Thermoplasma cells lack a cell wall. They have a cell membrane bilayer, but it is made of phosphoglycohydrocarbons, or sulfo- or glyco-glycerohydrocarbons. What would be a fatty acid in our cells, is a hydrocarbon in archaea, so they are linked by an ether link rather than the ester linkage to the glycerol. This membrane has transport proteins that regulate what goes into and out of the cell. Without any wall, these cells are forced to live isotonic environments rather than in, say, freshwater environments.

Other species of archaea, such as Methanobacterium are Gram positive because they retain the purple dye-iodine complex inside the thick cell wall after the Gram staining process. The differences between these and the Gram positive bacteria include the fact that the wall material is a glycan...not a peptidoglycan. There is no muramic acid no murein. This rigid wall is what allows these archaea to live in a hypotonic environment without bursting.

A third group of archaea, including Thermoproteus, are Gram negative. These cells typically have only a very thin surface layer of glycan wall which may include glycoproteins. So the purple dye-iodine complex inside the cell rinses right out with the alcohol rinse. So these archaea appear pink rather than purple after the Gram staining procedure.

Archaea Have Homeostasis

Just like the bacteria, the archaea have evolved a diverse array of metabolic pathways. As extremophiles, their metabolism shows many adaptations to the extreme environments of their habitat. There are facultative and obligate anaerobes and aerobic organisms in this kingdom.

The diversity of metabolism among archaea can be divided into four nutritional modes...with many variations within each of them! Just as for bacteria, the different modes are characterized by their energy source and carbon sources.

Nutrition Mode Energy Source Carbon Source
Photoautotroph Light CO2
Chemoautotroph Inorganic
Photoheterotroph Light Organic
Chemoheterotroph Organic

Methanococcus and Pyrococcus are example archaea that are photoautotrophic. They use the Calvin Cycle in photosynthesis just like the chloroplast of eukaryotes.

Photosynthesis with water: CO2 + H2O light
O2 + CH2O

Chemoautotrophic archaea can reverse the Krebs cycle to fix carbon dioxide from the atmosphere.

Chemoheterotrophic archaea use the Krebs cycle, some do fermentation, and some even use sulfur transporters to drive their ATP synthesis rather than H+. To help you understand this a bit more, notice how the overall respiration diagram has multiple arrows. It is NOT a single-step reaction.

Respiration: CH2O + O2 →→→→→ CO2 + H2O + ATP!

The first about 20 steps are what we would call glycolysis if carbohydrate is a food...occurring in the archaean cytosol.

Glycolysis: sugar + water →→→→→ pyruvate + ATP

The next about 20 steps are what we would call the Krebs, TriCarboxylicAcid (TCA) or Citric Acid cycle....also occurring in the archaean cytosol.

TCA Cycle: pyruvate + water →→→→→ CO2 + NADH

The last part of respiration is Electron Transport and Oxidative Phosphorylation. These about 20 steps are coupled together and occur in association with the archaean cell membrane.

ET + OxPhos: NADH + O2 →→→→→ H2O + ATP!!

Of course not all chemoheterotrophs live in aerobic (oxygen containing) environments. So anaerobic archaeans use glycolysis to convert sugar to pyruvate but then, in just a few steps, convert the pyruvate to either ethyl alcohol and carbon dioxide, or lactic acid. These concluding steps for glycolysis are generically called fermentation. In laboratory you will test the ability of an archaean to ferment a few different sugars. You can see that fermentation can release gas (CO2) or acid (lactic or several others are possible).

But for the archaeans, we might wonder how their metabolism, their respiration or fermentation enzymes and other proteins can tolerate the extremes of their environment. It turns out that study of archaean enzymes shows that they are stabilized by more ionic bridges between amnino acid R-groups and have more hydrophobic core amino acids in their sequence. This means that the proteins fold tightly and strongly to avoid denaturation in heat or salinity.

In addition archaeans have special heat shock proteins, chaperonins, that refold denatured proteins back to their normal conformation and restoring their activity. The archaean, Pyrococcus, can withstand 121°C for 1 hour and survive it! These chaperonins restore damaged proteins.

Some archaeans accumulate 2,3-diphosphoglycerate which reduces the depurination of DNA (removing the bases Adenine and Guanine). For others, the DNA is supercoiled by the action of an enzyme called gyrase; this supercoiling of the DNA can stabilize it. The histone-like DNA binding proteins of archaeans stabilize their DNA as well (compared to unbound bacterial DNA). Sulfolobus has Sac7d, a protein, that stabilizes the DNA double-helix so well that it raises its DNA melting temperature by 40°C!

Finally, the cell membrane structure of archaeans can make them heat-resistant by preventing delamination of the bilayer. Rather than simple phospholipids, the archaean membranes are made of di-bi-phytanyl diether lipids that make the membrane at least a partial monolayer!

The basic unit of the membrane is a diglyceride (rather than a tri-glyceride). The third position is occupied by either a phosphate, a sulfate or a sugar. The two attachments to the glycerol are long-chain branched hydrocarbons rather than fatty acids. So the linkage is an ether rather than an ester link (greenish below). If the membrane unit is made of C20 hydrocarbons, that portion of the membrane will be a bilayer. If the membrane unit is made of C40 hydrocarbons, then the two faces of the membrane are attached...that region of the membrane is a monolayer. In many archaea, the membrane is a mixture of these, making the membrane a mixed mono- and bi-layer...and very heat resistant.

Archaea Grow

As you recall, growth, defined as an irreversible change in size, can be a function of both increases in cell size and cell number. After cell division, the growth of archaeans is like that of bacteria. The cells can double in volume in the 20 minutes between cell divisions. Since the division cycles for archaeans can be 20 minutes apart in ideal conditions, they could take over the earth quickly if conditions would remain ideal. For archaeans, the ideal conditions are pretty extreme, so obviously they are no threat to the other species on our planet. These are ancient organisms, however, so their continued growth has been sustained in extreme environments for billions of years.

Archaea Move

The motor system we learned about for bacteria is virtually identical for the flagella of archaea. The motile archaea often have multiple flagella in a tuft at one place on the cell surface. Would that be lophotrichous, amphitrichous, or peritrichous?

Not surprisingly perhaps, in addition to phototaxis and chemotaxis, these archaea have evolved thermotaxis...movement toward extreme temperatures! If you are competitive in extreme environments, evolution will favor those that can keep themselves in those environments.

Inside archaea cells, materials are in motion as well. So these organisms have cyclosis just as all other cells in spite of their extreme environmental conditions.

Archaea Reproduce

As discussed previously, archaea can divide rapidly to produce more cells. This is a kind of reproduction that does not involve sex; we call it asexual reproduction. As with bacteria, cell division in archaea is not mitosis...anything you know about mitosis such as prophase, metaphase, anaphase, or telophase is irrelevant! The process of cell division in archaea is completely different and called binary fission instead. Remember there is no nucleus in a prokaryotic cell!

The genome of the archaea is mostly held in a single circular DNA molecule. This DNA is not associated with histone proteins, but does have unique DNA binding proteins, so the word chromosome can be used for archaea. The DNA-protein complex can take up artificial dyes to show up as a colored body. The genomic chromosome is attached to the cell membrane at one point just as in bacteria. However, this genome is smaller than typical bacteria, it has gene sequences closer to similar genes in eukaryotes rather than those of bacteria. Some of the genes are expressed in operons, like those of bacteria. But the genes for rRNA and tRNA have introns...non-coding sequences...found inside eukaryotic genes, but not found in bacterial genes. The archaea also show insertion sites in their gene sequences for transposable elements (transposons). This is a feature of eukaryotic organisms, rather than bacteria too. The transcription of genes in archaea is accomplished by an RNA polymerase that is very, very similar to that of RNA polymerase II of eukaryotic cells rather than bacterial RNA polymerase. Moreover, it binds at TATA sequences, just like RNA polymerase II of eukaryotes.

Binary fission starts with the replication of the genome by the action of a range of proteins including DNA polymerase. The genome and the copy are identical. They are separated by movement of the proteins that attach them in the fluid mosaic of the cell membrane. By some as yet undetermined mechanism, the genome and its copy end up at opposite ends of the cell. The cell divides into two by the process of furrowing, a kind of pinching apart of one cell into two cells.

The archaea differ from bacteria in having, in addition to the genomic chromosome, some additional small circular DNAs. These replicons have additional genes that are essential to the life of the archaean. Precisely how two cells resulting from binary fission obtain exactly the one genomic chromosome and one and only one copy of each essential replicon is not known. Obviously this must be coordinated in some way parallel to what happens in eukaryotic mitosis, but the details remain to be told. The synthesis of a copy of each genetic unit must be virtually simulataneous. Then, the movement of the genetic units to opposite ends of the cells prior to furrowing must also be properly coordinated.

In binary fission, there is no synapsis of homologous chromosomes, because archaea are fundamentally haploid (they have only the one set of chromosomes). During this process there is no genetic recombination (there is no exchange of DNA between one molecule and another). So, except for chance mutation, there is little chance for anything but clonal reproduction here.

Since there is no synapsis to diploidy, there is no meiosis either! So, there is no sexual reproduction of any kind in archaea. However, just like bacteria, archaea do have parasexual recombination. Archaea produce pili for conjugation.

Archaea Respond

Throughout the material above, you have read about archaea responding to the environment, to the presence of chemicals, light, or other organisms. I don't think we need to amplify this too much right here. But in your course on genetics, you will learn a bit more about how those genes are turned on that result in responses!

Bacteria Evolve

All of the structural and functional features allow the 1,000 or so species of Kingdom Archaea to be related into a cladogram.

Kingdom Archaea can be divided into two major phyla. The Euarchaeota phylum contains those archaea that are halophilic (Halobacteriales) meaning that they live in very concentrated salt solutions...brine. When our biology students visit the Bahamas this spring, they will canoe on and snorkel in some of the hypersaline lakes on the interior of San Salvador Island. These lakes are often streaked with orange, red, and purple colors by the halophilic archaea that live there. These are chemoheterotrophs that respire with oxygen, and chemoautotrophs that may use bacteriorhodopsin to harvest light energy to make ATP.

Phylum Euarchaeota also includes methanogens (Methanogenales). These anaerobic archaea convert carbon dioxide and hydrogen to methane (CH4), known as swamp gas or natural gas. Some of these organisms use a fluorescent pigment for energy to drive this reaction. Some of these species indeed live in swamps, marshes, and landfills. Others live in the gut of ruminant animals who then belch quantities of methane into the atmosphere.

Phylum Euarcheota as well includes thermophiles (Thermoplasmales, Thermococcales, and Archaeoglobales). These organisms live in hot water in geothermal features (geysers, paint pots, hot springs, mud pots, etc.). Some of these are chemoheterotrophs that use inorganic chemicals for energy (converting sulfur to hydrogen sulfide gas Phew!) to convert larger organic molecules to carbon dioxide. Other species in this group are autotrophic, converting sulfates in the geothermal features to hydrogen sulfide gas (again, Phew!) Some of archaea in these groups live near hydrothermal vents...and convert methane gas backwards into lactate, and then from there to hydrogen gas and carbon dioxide.

The second phylum of Kingdom Archaea is Crenarchaeota. Most of the organisms in this phylum are also thermophilic, but also most are acidophilic. So they live in very acidic hot water environments. This would be corrosive conditions. Some are autotrophic and use carbon dioxide. Others convert sulfur and hydrogen to hydrogen sulfide gas and more acid! In the absence of oxygen, heterotrophic crenarchaeotes use organic molecules and sulfur to make carbon dioxide and hydrogen sulfide gas. More stinkers! These same crenarchaeotes in the presence of oxygen will process organic molecules by running the TCA cycle backwards to convert sulfur and oxygen into sulfuric acid (H2SO4), otherwise known as battery acid. Obviously these are some organisms that can live in and help maintain some extreme environments.

Example Archaea

To appreciate some of the archaeans that live in conditions that we can only observe from afar, I decided to give you three thumbnail sketches of organisms in Kingdom Archaea.
Sulfolobus acidocaldarius is a strictly aerobic organism. It grows best in the water of a caldera (a lake in a volcanic depression) at about 75°C and at a pH range of 1 to 6. So it likes hot acidic water. Sulfolobus oxidizes sulfur to sulfuric acid or can use Fe2+ or MnO42- as electron acceptors while using glycolysis and the TCA cycle. This organism can produce a pilus to transfer plasmids from one to another, but the plasmids are not similar to the ones found in bacteria.

So given the information that it uses organic chemicals for energy and carbon, is Sulfolobus photoautotrophic, photoheterotrophic, chemoautotrophic, or chemoheterotrophic?
Our second example is Methanococcus jannischii. This organism was isolated from a "white smoker" hydrothermal vent some 2600m deep on the bottom of the Pacific a place called the East Pacific Rise. This organism is obviously a methanogen. It is an obligate anaerobe using Hydrogen gas as an energy source, carbon dioxide as a carbon source, and produces methane (CH4). The water at this location is 50 to 86°C but is also at extreme pressure!

Based upon the scanning electron micrograph, what is the cell shape? Is this cell motile? Based upon the information above, what is the nutritional mode of this archaean: photoautotrophic, photoheterotrophic, chemoautotrophic, or chemoheterotrophic?
Our third example is Halobacterium salinarium. This archaean has three chromosomes: a genomic chromosome of 2,015kb size, a 366kb replicon and a 191kb replicon. Its replicons have genes for DNA polymerase, transcription factors, mineral (K and PO4) uptake, and cell division. The genomic chromosome has many transposon insertion sites. Halobacterium salinarium carries out aerobic respiration but in water up to 5M (25%!) NaCl (salt). It can be found in the Great Salt Lake in Utah and the Red Sea in Asia Minor. So under normal circumstances, this organism has which nutritional mode... photoautotrophic, photoheterotrophic, chemoautotrophic, or chemoheterotrophic?
Halobacterium salinarium supplements its lifestyle with light energy to drive phosphorylation to make ATP without using photosynthesis. Rather than using chlorophyll, this archaean uses bacteriorhodopsin. This is a pigment made of protein and an organic molecule called retinal (a vitamin A relative). This pigment has its maximum absorption at 280nm (in the UV range), but in the visible range it absorbs maximally at 570nm (green).
Given that this absorption spectrum for bacteriorhodopsin has a peak at 570nm (green), and remembering that a pigment reflects any light it does not absorb, what color is bacteriorhodopsin?

Not all extremophiles are Archaeons

As a different example we look at Thermus aquaticus. This is a Gram negative thermophile isolated from Yellowstone National Park in the USA. It was found in a hot spring and grows best in water at 85°C...nearly boiling water. Its macromolecules are exceptionally stable to heat and its enzymes have been harvested for research and commercial use. This bacterium lives near thermophilic cyanobacteria that do photosynthesis to make food to feed Thermus. If you have heard of the polymerase chain reaction (PCR) to clone DNA, that process depends upon the thermal properties of DNA polymerase from this bacterium. If in a biotechnology lab you set up a PCR reaction with "Taq polymerase" you might remember that "Taq" stands for Thermus aquaticus.

Based upon the scanning electron micrograph, is Thermus aquaticus a coccus, bacillus, spirillium, or a vibrio? Based upon its use of organic food from cyanobacteria to do standard respiration, is its nutritional mode photoautotrophic, photoheterotrophic, chemoautotrophic, or chemoheterotrophic? It is worthy to note that in spite of the fact that it is an extremophile, it is not an archaeon; it is a thermophilic bacterium.






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