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Archaeal genetics — the third way

Nature Reviews Genetics volume 6, pages 58–73 (2005)Cite this article

Key Points

  • Archaea comprise the third domain of life, alongside bacteria and eukaryotes. The domain Archaea was proposed in 1977 by Carl Woese, as a result of phylogenetic studies that used ribosomal-RNA sequences as a molecular chronometer.

  • Archaea are renowned as extremophiles, but environmental studies indicate that they thrive in all habitats. However, so far no pathogenic archaea have been found.

  • Bacteria and archaea share a prokaryotic morphology and have comparable pathways for central metabolism and energy conversion. On the other hand, information-processing pathways in archaea and eukaryotes use similar enzymes; although archaeal systems are much simpler.

  • Lateral gene transfer between archaea and bacteria is common and might be responsible for some evolutionary innovations.

  • As much as 50% of the genes found in archaeal genomes might encode novel proteins with no obvious counterparts in bacteria or eukaryotes.

  • Archaeal proteins have proved invaluable to biochemists and structural biologists, but genetic studies of archaea are still comparatively rare.

  • Genetic techniques for archaea are more advanced than is commonly believed. A wide range of archaeal species can be transformed using integrative and shuttle vectors, carrying various selectable markers. Methods for mutagenesis and gene knockout are available, as are reporter genes such as β-galactosidase.

Abstract

For decades, archaea were misclassified as bacteria because of their prokaryotic morphology. Molecular phylogeny eventually revealed that archaea, like bacteria and eukaryotes, are a fundamentally distinct domain of life. Genome analyses have confirmed that archaea share many features with eukaryotes, particularly in information processing, and therefore can serve as streamlined models for understanding eukaryotic biology. Biochemists and structural biologists have embraced the study of archaea but geneticists have been more wary, despite the fact that genetic techniques for archaea are quite sophisticated. It is time for geneticists to start asking fundamental questions about our distant relatives.

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Figure 1: Gene knockout methods that are used in archaeal genetics.
Figure 2: Plasmid vectors.

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Acknowledgements

We thank Steve Bell, John Leigh, Kevin Sowers, Ed Bolt and numerous other colleagues whose comments have improved the manuscript. We are grateful to John Leigh, Bill Metcalf, Kevin Sowers, Tadayuki Imanaka, David Walsh, Steve Bell, James Chong, Alan Majernik, Friedhelm Pfeiffer, Dieter Oesterhelt and Julie Maupin-Furlow for communicating results before publication, and to Malcolm White, Patrick Forterre, Richard Shand, Joel Querellou, Michel Gouillou, Frank Robb and Cold Spring Harbor Laboratory Press for pictures of archaeal habitats. T.A. is supported by a Royal Society University Research Fellowship.

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  1. Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK

    Thorsten Allers

  2. Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel

    Moshe Mevarech

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FURTHER INFORMATION

American Type Culture Collection

Archaeal genomes at National Center for Biotechnology Information

Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Draft archaeal genomes at Oak Ridge National Laboratory

Draft genomes of psychrophilic archaea at University of New South Wales

Draft Haloferax volcanii genome at The Institute for Genomic Research

Genomes OnLine Database (GOLD)

HaloHandbook

Gordon Research Conference (GRC) on Archaea: Ecology, Metabolism & Molecular Biology

Halobacterium salinarum genome at Max Planck Gesellschaft

Halophile genomes at University of Maryland Biotechnology Institute

Japan collection of microorganisms

National Collections of Industrial, Food and Marine Bacteria

Glossary

DOMAIN

The highest level of taxonomic division, comprising Archaea, Bacteria and Eukarya. In declining order, the other levels include: kingdom, phylum, class, order, family, genus and species.

MONOPHYLETIC

A natural taxonomic group consisting of species that share a common ancestor.

CULTIVATION-INDEPENDENT STUDY

Method for determining environmental biodiversity without the need to obtain microbiologically pure cultures. This can be done by using sequences that are retrieved from environmental samples to construct a molecular phylogenetic survey (for example, through environmental genome-shotgun sequencing).

PSYCHROPHILE

An organism that can grow at permanently low temperatures; typically less than 10°C.

EXTREMOPHILE

An organism that requires extreme environments for growth, such as extremes of temperature, salinity or pH, or a combination of these.

HALOPHILE

An organism that requires high concentrations of salt for growth; typically greater than 1M NaCl.

METHANOGEN

An anaerobic organism that generates methane by reduction of carbon dioxide, various one-carbon compounds or acetic acid.

LATERAL GENE TRANSFER

Horizontal transfer of genes between unrelated species, as opposed to vertical inheritance within a species.

ACIDOPHILE

An organism that requires a low pH for growth; typically less than pH 3.

ALKALIPHILE

An organism that requires a high pH for growth; typically greater than pH 10.

ENVIRONMENTAL GENOME-SHOTGUN SEQUENCING

High-throughput sequencing and computational reconstruction of genomic DNA fragments that are extracted from environmental samples to assess microbial diversity in a cultivation-independent manner.

THERMOPHILE

An organism that requires high temperatures for growth; typically greater than 60°C.

HETEROTROPH

An organism that requires complex organic molecules such as amino acids and sugars to build macromolecules and derive energy.

HYPERTHERMOPHILE

An organism that requires extremely high temperatures for growth; typically greater than 80°C.

TRANSFECTION

Infection of a host cell by naked DNA or RNA that is isolated from a virus.

SPHEROPLAST

A cell that is denuded of most of its cell wall or surface layer, usually by chemical or enzymatic treatment. Also known as a protoplast.

TRANSDUCTION

Transfer of host genes between archaeal or bacterial species, using a virus as a vector.

PROTOTROPH

An organism that can grow on minimal media that contain a carbon source and inorganic compounds.

AUXOTROPH

A mutant that requires nutrients that are not needed by wild-type strains for growth on minimal media.

AUTOTROPH

An organism that can synthesize its own macromolecules from simple, inorganic molecules such as carbon dioxide, hydrogen and ammonia.

COUNTER-SELECTABLE MARKER

A marker that if present leads to cell death under selective conditions, usually by conferring sensitivity to an antibiotic or by promoting the synthesis of a toxic product from a non-toxic precursor.

INTEGRATIVE-VECTOR PLASMID

A plasmid vector that is unable to replicate in an archaeal host, which therefore must integrate into the host chromosome by homologous or site-specific recombination.

SHUTTLE-VECTOR PLASMID

A plasmid vector that can replicate in both Escherichia coli and an archaeal host.

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Allers, T., Mevarech, M. Archaeal genetics — the third way. Nat Rev Genet 6, 58–73 (2005). https://doi.org/10.1038/nrg1504

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