The proteins that archaea, bacteria, and eukaryotes share form a common core of cell function, relating mostly to transcription, translation, and nucleotide metabolism. Other characteristic archaean features are the organization of genes of related function—such as enzymes that catalyze steps in the same metabolic pathway into novel operons, and large differences in tRNA genes and their aminoacyl tRNA synthetases.
Transcription and translation in archaea resemble these processes in eukaryotes more than in bacteria, with the archaean RNA polymerase and ribosomes being very close to their equivalents in eukaryotes. However, other archaean transcription factors are closer to those found in bacteria. Post-transcriptional modification is simpler than in eukaryotes, since most archaean genes lack introns, although there are many introns in their transfer RNA and ribosomal RNA genes, and introns may occur in a few protein-encoding genes.
Privacy Policy. Skip to main content. Microbial Evolution, Phylogeny, and Diversity. Search for:. Archaeal Diversity. Energy Conservation and Autotrophy in Archaea Archaea can use a number of different mechanisms to get nutrients and energy. Learning Objectives Discuss archaea energy sources. Key Takeaways Key Points Lithotrophic archaea use non- organic sources to live. Phototrophic archaea use light in a non-photosynthetic fashion to drive ion pumps needed to survive.
Archaeal energy sources are extremely diverse, including light, metallic ions, and even acidic pH -dependent sources. Key Terms autotroph : Any organism that can synthesize its food from inorganic substances, using heat or light as a source of energy.
Archaeal Gene Regulation Archaea are very different genetically from bacteria and eukaryotes. Learning Objectives Describe the unique features of archaea. Key Takeaways Key Points Like bacteria and eukaryotes, archaea can be infected by viruses.
Many unique proteins are encoded by archaea, many of these proteins have unknown functions. Introns are more rare than eukaryotic species, and additionally unlike eukaryotes the introns usually do not reside in protein coding genes but rather rRNA and tRNA.
This allows oxidation of glucose to two acetates with the production of 2 mol of ATP by substrate-level phosphorylation Fig. Thus, there is no loss of ATP synthesized by substrate-level phosphorylation. Even better, if hydrogen production from reduced ferredoxin is coupled to generation, more ATP can be synthesized.
This is where the multisubunit, Mbh comes into play. Model of energy conservation in Pyrococcus furiosus. All oxidative steps of this modified Embden-Meyerhof-Parnas pathway, the reactions catalyzed by the glyceraldehydephosphate:ferredoxin oxidoreductase GAPOR and the pyruvate:ferredoxin oxidoreductase POR , use ferredoxin as an electron acceptor. Hydrogen gas is produced by the Mbh, coupled to the oxidation of reduced ferredoxin and generation of a proton gradient.
The figure shows the nature of the ions pumped, but the stoichiometries of the reactions are unknown. Hydrogen is evolved by hydrogenases, and the genome of P.
The third hydrogenase, encoded in the genome of P. This exergonic reaction is used to pump ions out of the cell, and the electrochemical ion gradient established is then used to drive ATP synthesis Fig.
In principle, the reaction is similar to the Ech-catalyzed reaction. Measurements of ATP synthesis and hydrogen production in inverted membrane vesicles of P. Although the coupling ion was not addressed in this study, it was hypothesized that protons were translocated.
However, with the finding that the ATP synthase of P. Therefore, it might be possible that the Mbh of P. There is also a striking sequence identity of Mbh to complex I of respiratory chains. Its soluble domain, consisting of modules N and Q, catalyzes NADH oxidation and transfers electrons via a chain of iron—sulfur center to the membrane. The soluble domain is indeed similar to soluble hydrogenases.
In complex I of E. Yes, such an Mrp—Mbh system is also genetically encoded in the genera Thermococcus , Desulfurococcus , Thermosphaera , Ignisphaera , and Staphylothermus Schut et al. It might be possible that such a system of energy conservation is an adaptation of hyperthermophilic archaea to environments with high temperatures. Model of energy conservation in Ignicoccus hospitalis. This archaeon has two membranes, an outer cellular membrane and an inner membrane.
Protein complexes for energy conservation are localized in the outer cellular membrane, so far exclusively. For energy conservation, the H2:sulfur oxidoreductase reduces sulfur with H 2 to H 2 S. This reaction is coupled to the generation of an electrochemical ion most likely proton potential by an unknown mechanism. It may involve a proton-motive Q-cycle or equivalent. The figure shows the nature of the ions pumped, but not the stoichiometries of the reaction. Adapted from Huber et al. However, the mechanism of membrane energization is obscure.
If the hydrogenase and sulfur reductase face to the outside, it must involve an active transport of protons from the inside to the outside because there is no net charge generation in the redox reaction. This is consistent with proton-driven ATP synthesis and the presence of a primary proton gradient across the membrane. Nanoarchaeum equitans , the small riding companion of I.
Thus, the working hypothesis is that it gains ATP from its host. Even if this is correct, every living cell requires an energized membrane. In fact, this is not uncommon and observed in many strictly fermenting bacteria.
However, the genome of N. Whether N. Despite all the differences in the ways the electrochemical ion gradient is generated, the common feature of archaea and other life forms is an enzyme that synthesizes ATP, according to Eqn.
In the ATP hydrolysis mode, ATP hydrolyzed by the soluble motor, localized in the cytoplasm of bacteria and archaea, drives rotation of the central stalk that is physically connected to the membrane-embedded, ion-translocating motor.
Rotation of this motor is obligatorily coupled to the translocation of ions, in the hydrolysis mode from the inside to the outside. In the synthesis mode, the electrochemical ion potential drives the influx of ions into the motor, forcing it to rotate.
Ions are translocated from the outside to the inside, and the central stalk starts to rotate. This is consistent with the phylogenetic tree of life that shows a rather late divergence of archaea and eukarya from a common ancestor.
Genes are transferred between the domains of life by horizontal gene transfer. This also holds true for archaea and bacteria Averhoff, This is true for Thermus thermophilus and Enterococcus hirae and may be also true for other bacteria, as evident from genome sequences. As long as these wrong annotations are not taken out of data bases, they will continue due to the use of annotation programs. Subunit a of the yeast V 1 V O ATPase has two isoforms Vph1p complex targeting to the vacuole and Stv1p complex targeting to the Golgi apparatus , which are not mentioned in the figure.
All subunits contain the Walker motifs A and B, which are located at the boundary surface of each subunit. These Walker motifs have conserved amino acids for the binding of nucleotides Boyer, The Walker A motif, also named P-loop Walker et al. The Walker B motif is involved in coordination of the nucleotides and contains a glutamate, which activates a water molecule, which is essential for the cleavage of the phosphoanhydride bond during ATP hydrolysis Abrahams et al.
With this mechanism, three ATPs can be synthesized by one rotation of the membrane-embedded motor Boyer, ; Yoshida et al. ATP synthesis is reversible in vitro , but it is important to note that this is different in vivo.
Moreover, energy conservation in eukaryotes is in mitochondria or chloroplasts and catalyzed by F 1 F O ATP synthases. In contrast, energization of membranes of eukaryal compartments such as the vacuole or the endoplasmic reticulum is by the generation of an ion gradient across the organelle membranes by the action of rotary ATP hydrolases the V 1 V O ATPases.
The number of ion-binding sites in the rotor is determined by the primary structure of the c subunit and the number of c subunits in the ring Fig. In its simplest form, the c subunit contains two transmembrane helices connected by a small, cytoplasmic loop. Noteworthy, only Gln32, Glu65, and Ser66 are sufficiently conserved in evolution and found in all methanogens, Pyrococci, and Thermococci.
Therefore, the switch from a sodium ion P. Most archaea, like Methanosarcina mazei , have a c subunit with one hairpin and one ion-binding site E, glutamate residue. Methanothermobacter thermautotrophicus has a c subunit consisting of two hairpins with two ion-binding sites.
The c subunit of Methanocaldococcus jannaschii has a triplicated hairpin with two ion-binding sites, and the c subunit of Methanopyrus kandleri consists of 13 hairpins with 13 ion-binding sites.
Based on a hypothetical c ring composed of 24 transmembrane helices, the number of monomers decreases with the temperature from 12 to 1 in the different species. The individual c subunits assemble to a ring that rotates against the stator subunit a. Not only the ion-binding site with its conserved carboxylate, but also a conserved arginine of the membrane-embedded part of subunit a is essential for ion translocation Fig.
The rotational movement of the c ring is coupled to the rotation of the central stalk, which transmits this rotational energy into the soluble domain Fig.
Proposed mechanism of ion translocation in the membrane-embedded domain of the ATP synthase. Individual c subunits assemble to a ring that rotates against the stator subunit a. For example, if the c ring has 12 monomers, with two transmembrane helices each, the c ring has 12 ion-binding sites. One way to change this ratio is to change the number of ion-binding sites in the c ring either by changing the stoichiometry of monomers in the ring or by changing the primary structure of the monomers.
Actually, the c subunit of V 1 V O ATPases arose by gene duplication of an ancestral 8-kDa c subunit gene followed by fusion of the products. However, one ion-binding site was lost during the duplication event. Thus, if the same number of transmembrane helices is compared, the rotor of V 1 V O ATPases has only half the number of ion-binding sites. ATP synthesis is thermodynamically impossible, but the enzyme is a very good ion pump: because it translocates fewer ions, it is able to generate steeper gradients Nelson, ; c.
The evolution of a duplicated c subunit with only half the number of ion-binding sites was seen as the starting point for the evolution of ATPases locked in the hydrolysis mode V 1 V O ATPases.
Later, additional subunits were evolved to reflect the need for the interaction of the enzyme with a complex regulatory network in the eukaryotic cell Wieczorek et al.
With the improvement in DNA sequencing technology, genome sequences from archaea became available. The first insights into the structure of the A 1 A O ATP synthases came from analyses of electron micrographs of enzymes isolated from hyperthermophiles. In general, the A 1 A O ATP synthase has a bipartite structure, consisting of an A 1 domain and A O domain, which form a pair of coupled rotary motors connected with one central and two peripheral stalks Fig.
The soluble A 1 domain has the catalytic activity, and the hydrophobic membrane-embedded A O domain is responsible for ion translocation across the membrane. The A 1 domain, often also described as catalytic head domain, shows pseudofold symmetry and clear asymmetry because of the presence of the central stalk Vonck et al.
Subunit A can be clearly identified in the 3D reconstruction by its spike-like structures, and the gen atpA contains a bp-long intein, which makes atpA from archaea longer than its homologues Bowman et al. The asymmetric head domain is connected to the central stalk, which is composed of subunits C, D, and F. Furthermore, a knob-like structure over subunit C is visible in the 3D reconstruction.
This is subunit F, which has a globular N-terminal domain and an elongated C-terminal part, which extends deep into the A 1 head domain and interacts there with subunit B Gayen et al. Surface representation of the ATP synthase in top view, bottom view, and side view orientation. Main features of this new class of A 1 A O ATP synthases are a collar-like structure subunit a and two peripheral stalks each composed of an EH complex.
The EC domain pink from P. New structural features are a collar-like structure located perpendicular to the c ring and two peripheral stalks Fig. In contrast, the F 1 F O ATP synthases of bacteria, mitochondria, and chloroplasts have only one peripheral stalk and no collar.
This EH dimer is connected to the A 1 domain. Fluorescence correlation spectroscopy showed that subunit E of the EH dimer is binding stronger to subunit B than to the catalytic subunit A Hunke et al.
It might be possible that these four motifs are the connecting sites for the peripheral stalks to subunit a and therefore to the A O domain.
Species of the genera Pyrococcus experimentally proved and Thermococcus deduced from DNA data have a kDa c subunit with four transmembrane helices, but only one ion-binding site Mayer et al. In contrast, the kDa c subunits from the methanogens M. Also M. What are the physiological consequences of the different numbers of ion-binding sites per c ring? Obviously, the ion-to-ATP ratio changes and this is an important, if not the most important, parameter to adapt ATP synthesis to low-energy environments.
According to Eqn. In this example, the loss of one ion-binding site in every second hairpin of the rotor would lower the number of ions by half. Apparently, the ATP synthase of P. But how can this apparent contradiction be solved? The answer is rather simple: by adding more c subunits and thus more ion-binding sites to the c ring.
Indeed, the c ring of P. The ratio is not unusual and, for example, also predicted for yeast ATP synthase Petersen et al. The deduction of the number of ion-binding sites is not unambiguous for the other species. For example, M. If we take four subunits to make the c ring, we have 12 transmembrane helices with eight ion-binding sites; if we take 5, we will have 15 transmembrane helices and 10 ion-binding sites; six gives 18; and seven gives 21 with 12 or 14 ion-binding sites.
These values are all within the physiological range. Clearly, the variation in c subunits of archaeal A 1 A O ATP synthases has to be of evolutionary advantage and may reflect an adaptation to the environment these archaea live in. How proteins adapt to high temperature has been the subject of many excellent reviews Somero, ; Macario et al. Among the membrane protein complexes, the ATP synthases are special because they work by a rotational mechanism.
Because a number of archaea live at the thermodynamic limit of life, the coupling mechanism has to be very tight, and any leakage of the coupling ion through the motor has to be avoided. Some of these features were apparently evolved very early in the evolution, but then kept also by mesophiles.
Ion transport drives rotation of the central stalk within the static A 3 B 3 subassembly. The A 1 domain is placed asymmetrically on the central stalk, which causes a wobbling of the head domain during rotation of the central stalk. The most important difference to other ATP synthases is the length of the c subunits.
Most mesophilic archaea have a 8-kDa c subunit with two transmembrane helices, and the copy number in the ring is not known, but in F 1 F O ATP synthases, this varies from 8 to 15 Mitome et al.
Let us assume that the rotor of the ATP synthases consists of 8—15 noncovalently bound c subunits that form a ring that rotates against the a subunit that is coupled to ion translocation, one ion per two transmembrane helices. It is easily conceivable that thermal fluctuations will result in less-stable interactions of c subunits in the ring. One way to circumvent the problem is to covalently link individual c subunits in the ring, and the more the covalent bonds, the higher is its stability Fig.
Indeed, while most mesophiles have a c subunit with two transmembrane helices, Methanothermobacter and Methanosphaera as well as Pyrococcus and Thermococcus species have a c subunit with four transmembrane helices, and Methanocaldococcus species have a c subunit with six transmembrane helices.
Not only the size of the c subunits, but also the coupling ion used may be seen as an adaptation to high temperatures and for low-energy environments. Any loss of ions back into the cell by leakage would be detrimental. Biological membranes are leakier for protons than for sodium ions, and this effect is even bigger at high temperatures van de Vossenberg et al. Thus, a sodium bioenergetics is advantageous and is seen as the primary event in the evolution of bioenergetics Mulkidjanian et al.
Indeed, cytochrome-free methanogens rely on sodium bioenergetics Thauer et al. This is obviously the case McMillan et al. The ATP synthase of P.
The same bioenergetic scenario may be present in the close relative T. A 1 A O ATP synthases have undergone multiple variations as adaptation to their environment, but the biggest change may be encountered in N. A search of the genome sequence revealed only genes encoding subunits A, B, D, a , and c.
Although this has to be interpreted with caution, this may also be seen as an adaptation to the energy metabolism of N. Unfortunately, the cells are hard to grow, and purification and biochemical analysis of the enzyme have not been possible yet due to a lack of biomass.
This type of reaction is catalyzed by the Ech hydrogenase and the much more complex Mbhs of Pyrococcus or Thermococcus. A similar type of reaction is catalyzed by the Rnf complex that is found in some archaea, but very widespread in bacteria Biegel et al. Thus, the common principle is the use of a ferredoxin-fueled electron transport chain inherent to one or more protein complexes. A sodium ion-based bioenergetics was expected to be present in organisms that live at high NaCl concentrations, but astonishingly, none of the known halophilic or moderately halophilic archaea and bacteria has a sodium ion-based primary bioenergetics.
This was always discussed as an adaptation to the marine environment, but in addition these environments are somewhat energy-limited because the pH in these ecosystems is well above 8. How ATP is synthesized by this low is still a mystery Meier et al. Apparently, the only primary sodium bioenergetics is found in anaerobes, bacteria, and archaea, the latter have been described here.
Why is this? To answer this question, we have to have a look at the ecosystem: anaerobic environments often have high concentrations of organic acids such as acetate, propionate, or butyrate. These act as protonophores that enter the cell in the protonated form by diffusion and dissociate inside the cells, due to a higher pH in the cytoplasm.
The ion pumped out sneaks back in through the back door and cannot be used for ATP synthesis. If you live on a diet, you better watch out that your food does not diffuse away. But, it can get worse. This difference increases at high temperature. The third principle is that the ATP synthases are adapted to life under extreme energy limitation.
If the primary gradient is a sodium ion gradient, then the ATP synthase should be driven by. That is indeed observed. Only a few three subtile changes in amino acids are required to change the ion specificity. Why and how can this be of physiological importance? This will bring us to the fourth principle. Data are not available, but in one case Jetten et al.
Describing the basis for life at thermodynamic equilibrium is a challenge for further studies. Be it Thermococcus or anaerobic methane oxidizers that both live at around equilibrium Kim et al. In the last decades, the basis of energy conservation in bacterial and mitochondrial electron transport chains has been deciphered down to the atomistic level.
The principles are well understood. Now, it is the time to discover the beauty of diversity in microbial bioenergetics in unusual organisms such as the archaea.
Much can be learned, also about the origin of bioenergetics. Nature : — Google Scholar. Biochemistry 41 : — J Microbiol Biotechnol 16 : — J Mol Biol : — Biochim Biophys Acta : — J Clin Microbiol 28 : — Structure 12 : — Cell Mol Life Sci 68 : — Biochim Biophys Acta : 19 — J Bioenerg Biomembr 24 : — Extremophiles 1 : 14 — Analysis of vma-1 encoding the 67 kDa subunit reveals homology to other ATPases.
J Biol Chem : — Annu Rev Biochem 66 : — Crenarchaeota is a class of Archaea that is extremely diverse, containing genera and species that differ vastly in their morphology and requirements for growth. All Crenarchaeota are aquatic organisms, and they are thought to be the most abundant microorganisms in the oceans. Figure 1. Sulfolobus , an archaeon of the class Crenarchaeota, oxidizes sulfur and stores sulfuric acid in its granules.
In the presence of oxygen, Sulfolobus spp. In anaerobic environments, they oxidize sulfur to produce sulfuric acid, which is stored in granules. Sulfolobus spp. They have flagella and, therefore, are motile. Thermoproteus has a cellular membrane in which lipids form a monolayer rather than a bilayer, which is typical for archaea. Its metabolism is autotrophic. To synthesize ATP, Thermoproteus spp.
The phylum Euryarchaeota includes several distinct classes. Species in the classes Methanobacteria, Methanococci, and Methanomicrobia represent Archaea that can be generally described as methanogens. Methanogens are unique in that they can reduce carbon dioxide in the presence of hydrogen, producing methane.
They can live in the most extreme environments and can reproduce at temperatures varying from below freezing to boiling. Methanogens have been found in hot springs as well as deep under ice in Greenland. Some scientists have even hypothesized that methanogens may inhabit the planet Mars because the mixture of gases produced by methanogens resembles the makeup of the Martian atmosphere.
Some genera of methanogens, notably Methanosarcina , can grow and produce methane in the presence of oxygen, although the vast majority are strict anaerobes.
Halobacteria require a very high concentrations of sodium chloride in their aquatic environment. One remarkable feature of these organisms is that they perform photosynthesis using the protein bacteriorhodopsin , which gives them, and the bodies of water they inhabit, a beautiful purple color Figure 2. Figure 2. Halobacteria growing in these salt ponds gives them a distinct purple color.
Notable species of Halobacteria include Halobacterium salinarum , which may be the oldest living organism on earth; scientists have isolated its DNA from fossils that are million years old. Archaea are not known to cause any disease in humans, animals, plants, bacteria, or in other archaea. Although this makes sense for the extremophiles, not all archaea live in extreme environments.
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