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.
  • calvin cycle: A series of biochemical reactions that take place in the stroma of chloroplasts in photosynthetic organisms.

Archaea exhibit a variety of chemical reactions in their metabolism and use many sources of energy. These reactions are classified into nutritional groups, depending on energy and carbon sources. Some archaea, called lithotrophs, obtain energy from inorganic compounds such as sulfur or ammonia. Other examples include nitrifiers, methanogens, and anaerobic methane oxidizers. In these reactions one compound passes electrons to another in a redox reaction, releasing energy to fuel the cell’s activities. One compound acts as an electron donor and one as an electron acceptor. The energy released generates adenosine triphosphate ( ATP ) through chemiosmosis in the same basic process that happens in the mitochondrion of eukaryotic cells.

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Archaea in an Extreme Environment: Archaea can live in extreme environments and live off autotrophic sources. Here archaea were found living under highly acidic conditions, in the runoff from an iron mine.

Many basic metabolic pathways are shared between all forms of life. For example, archaea use a modified form of glycolysis (the Entner–Doudoroff pathway) and either a complete or partial citric acid cycle. These similarities to other organisms probably reflect both early origins in the history of life and their high level of efficiency.

Some Euryarchaeota are methanogens living in anaerobic environments such as swamps. This form of metabolism evolved early, and it is possible that the first free-living organism was a methanogen. A common reaction in methanogens involves the use of carbon dioxide as an electron acceptor to oxidize hydrogen. Methanogenesis uses a range of coenzymes that are unique to these archaea, such as coenzyme M and methanofuran. Other organic compounds such as alcohols, acetic acid, or formic acid are used as alternative electron acceptors by methanogens. These reactions are common in gut-dwelling archaea. Acetotrophic archaea also break down acetic acid into methane and carbon dioxide directly. These acetotrophs are archaea in the order Methanosarcinales, and are a major part of the communities of microorganisms that produce biogas.

Other archaea, called autotrophs, use CO2 in the atmosphere as a source of carbon, in a process called carbon fixation. This process involves either a highly modified form of the Calvin cycle or a recently discovered metabolic pathway called the 3-hydroxypropionate/4-hydroxybutyrate cycle. In addition, the Crenarchaeota use the reverse Krebs cycle while the Euryarchaeota use the reductive acetyl-CoA pathway. Carbon–fixation is powered by inorganic energy sources.

Phototrophic archaea use sunlight as a source of energy; however, oxygen–generating photosynthesis does not occur in any archaea. Instead, in archaea such as the Halobacteria, light-activated ion pumps generate ion gradients by pumping ions out of the cell across the plasma membrane. The energy stored in these electrochemical gradients is then converted into ATP by ATP synthase. This process is a form of photophosphorylation. The ability of these light-driven pumps to move ions across membranes depends on light-driven changes in the structure of a retinol cofactor buried in the center of the protein.

Besides these, archaeal energy sources are extremely diverse, and range from the oxidation of ammonia by the Nitrosopumilales to the oxidation of hydrogen sulfide or elemental sulfur by species of Sulfolobus, using either oxygen or metal ions as electron acceptors.

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.

Key Terms

  • intron: A portion of a split gene that is included in pre-RNA transcripts but is removed during RNA processing and rapidly degraded.
  • ribosome: Small organelles found in all cells; involved in the production of proteins by translating messenger RNA.
  • polymerase: Any of various enzymes that catalyze the formation of polymers of DNA or RNA using an existing strand of DNA or RNA as a template.

Archaea usually have a single circular chromosome, the size of which may be as great as 5,751,492 base pairs in Methanosarcina acetivorans, the largest known archaean genome. One-tenth of this size is the tiny 490,885 base-pair genome of Nanoarchaeum equitans, the smallest archaean genome known. It is estimated to contain only 537 protein-encoding genes. Smaller independent pieces of DNA, called plasmids, are also found in archaea. Plasmids may be transferred between cells by physical contact, in a process that may be similar to bacterial conjugation.

Archaea can be infected by double-stranded DNA viruses that are unrelated to any other form of virus and have a variety of unusual shapes, including bottles, hooked rods, or teardrops. These viruses have been studied in most detail in thermophilics, particularly the orders Sulfolobales and Thermoproteales. Two groups of single-stranded DNA viruses that infect archaea have been recently isolated. One group is exemplified by the Halorubrum pleomorphic virus 1 (“Pleolipoviridae”) infecting halophilic archaea and the other one by the Aeropyrum coil-shaped virus (“Spiraviridae”) infecting a hyperthermophilic (optimal growth at 90-95°C) host. Notably, the latter virus has the largest currently reported ssDNA genome. Defenses against these viruses may involve RNA interference from repetitive DNA sequences that are related to the genes of the viruses.

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Archaeal viral infection: Cell of Sulfolobus infected by virus STSV1 observed under microscopy. Two spindle-shaped viruses were being released from the host cell. The strain of Sulfolobus and STSV1 (Sulfolobus tengchongensis Spindle-shaped Virus 1) were isolated by Xiaoyu Xiang and his colleagues in an acidic hot spring in Yunnan Province, China. At present, STSV1 is the largest archaeal virus to have been isolated and studied. Its genome sequence has been sequenced.

Archaea are genetically distinct from bacteria and eukaryotes, with up to 15% of the proteins encoded by any one archaeal genome being unique to the domain, although most of these unique genes have no known function. Of the remainder of the unique proteins that have an identified function, most belong to the Euryarchaea and are involved in methanogenesis. 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. Although archaea only have one type of RNA polymerase, its structure and function in transcription seems to be close to that of the eukaryotic RNA polymerase II, with similar protein assemblies (the general transcription factors) directing the binding of the RNA polymerase to a gene’s promoter. 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.