Phylum Deinococci (Deinococcus/Thermus)

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Taxonomy

  • Phylum Deinococcus/Thermus
    • Class Deinococci
      • Order Deinococcales
        • Family Deinococcaceae
          • Genus Deinococcus
        • Family Trueperaceae
          • Genus Truepera
        • Order Thermales
          • Family Thermaceae
            • Genus Thermus
            • Genus Marinothermus
            • Genus Meiothermus
            • Genus Oceanothermus
            • Genus Vulcanothermus

About this phylum

This phylum contains only two well-known genera: Deinococcus and Thermus. These organisms are quite different phenotypically and phylogenetically, and each represent a small collection of closely-related, very similar species.

Deinococcus & relatives

Diversity

Deinococcus, the only genus in the Family Deincoccales, consists of 18 closely-related species and a collection of other partially characterized isolates. A second genus, Deinobacter, was previously represented by a single specie, D. grandis, which has been reclassified as a member of the genus Deinococcus. The only exception is an additional single specie, Truepera radiovictrix, which is more distantly-related to Deinococcus and shares both the thermophilic phenotype of Thermus and the radiation-resistant phenotype of Deinococcus.

Metabolism

The Deinococci are aerobic heterotrophs, and most are mesophilic. The most striking feature of these organisms is their extreme resistance to ionizing (gamma) radiation, but they are also extremely resistant to UV radiation, dessication, oxidizing agents and mutagens. The common thread is that these all cause damage to DNA, and in the most extreme cases double-stranded breaks. Deinococcus has very active DNA repair systems, and by keeping between 4 and 10 copies of the genome in each cell, homologous recombination can even be used to to reassemble the DNA after wholesale fragmentation by high-energy gamma-irradiation.

Deinococcus UV kill curve
Gamma radiation kill curve of D.radiodurans vs E. coli. From The Prokaryotes, pp3740

Morphology

The Deinococci are non-motile cocci, except for the rod-shaped D. grandis. Although they have a Gram-negative -type envelop, the peptidoglycan layer is very thick, and the outer membrane is covered in an S-layer, resulting in them typically staining Gram-positive. As a result of this and the fact that they are commonly pigmented (pink or red to purple or even black), they can easily be mistaken for Micrococcus. Cell division is unusual in Deinococci - instead of the cells pinching-off into 2 daughter cells, cells divide by forming a ‘septal curtain', which closes inward like the shutter on a camera, without changing the shape of the original cell. The division plane alternates by ca. 90° in the X and Y (but not Z) axes, resulting in tetrads or larger arrangements of cells in some species.

Habitat

Most species were isolated from irradiated samples, including foods supposedly sterilized by irradiation, cleanrooms (which us UV lights for ‘sterilization’), and nuclear reactor cooling pools, but the natural environment of these organisms is not known. They have be isolated sporadically from soils, sediments, sewage, and many dust-covered surfaces. This suggests that their resistance to radiation might be a by-product of their evolved resistance to desiccation, which also induces double-stranded breaks in DNA. It has ben suggested that the natural habitat of this organism might be the water droplets that make up clouds!

Example : Deinococcus radiodurans

Deinococcus
Deinococcus radiodurans : M. J. Daly's lab

D. radiodurans is by far the best studied specie of this Family. It was originally isolated over 50 years ago from cans of meat treated with large doses of gamma-irradiation during the development of this preservation process. Some cans nevertheless spoiled, and the organism responsible was isolated. Irradiation is now a common method for packaged food preservation, and the dosage used is based on the need to kill this organism, just as autoclaving time and temperature is based on the need to kill endospores. Although involved in food spoilage, D. radiodurans is not pathogenic or itself harmful. D. radiodurans has been a model system for the study of the biochemistry of DNA repair. D. radiodurans cells contain several copies of each of the two chromosomes in a torroidal nucleoid

Thermus & relatives

Diversity

This group is more diverse than are the Deinococci, with 17 species in 4 genera. There are also a large number of partially-characterized isolated. T. aquaticus is by far the best known member of this group, and T. thermophilus, because of its very high growth temperature (up to 85°C as compared with 79°C for T. aquaticus), has also been well-studied.

Metabolism

Thermales are all thermophilic heterotrophs, capable of utilizing a wide range of carbon and energy sources but growing best in media with low concentrations of these organic substrates. These organisms are either obligate aerobes or facultative anaerobes, growing anaerobic by nitrate reduction.

Enzymes

Enzymes from these organisms have proven very useful because of their thermostability. This was demonstrated dramatically in the development of the use of T. aquaticus DNA (Taq) polymerase in automated polymerase chain reaction (PCR). Before this, PCR required the user to manually add DNA polymerase (typically from E. coli) to each sample during each cycle of the reaction, and so PCR remained a tedious and obscure method. The use Taq polymerase, because it is not inactivated during the heat DNA denaturation step in each cycle, allowed the automated cycling of PCR reactions, and now PCR is now the mainstay of molecular biology. The DNA polymease from T. thermophilus is also now widely used, because of its greater thermostability and reverse transcriptase activity. These enzymes have largely been replaced in PCR by DNA polymerases from thermophilic Archaea, which are more processive and accurate (because of their 3´-5´ exonuclease ‘proofreading’ activity), and more thermostable.

These organisms are also the sources of other important thermostable enzymes used in biotechnology and industry. Industrially important enzymes are primarily carbohydrate hydrolases, and are useful because their long lifespan (stability) makes them useful in immobilized enzyme systems.

Enzymes from Thermus have been studied extensively by structural biochemists, because their thermostability (and therefore rigidity at moderate temperatures) often results in the ability to easily grow very uniform crystals for X-ray diffraction analysis and determination of three-dimensional structure. In addition, these enzymes are generally readily over-expressed in E.coli, and easily purified from E. coli extracts; a quick heat-treatment curdles all but the smallest of E. coli proteins, leaving the protein of interest the predominant remainder in solution.

Morphology

Most are filamentous in nature and initially upon isolation, but upon domestication become pleomorphic rods and short filaments. The outer membrane of their Gram-negative-type envelop is loosely attached to the cell wall, appearing corrugated by electron microscopy. In captivity, some cells produce vesicular ‘blebs’ and ‘rotund bodies’, aggregates of cell bound inside a common outer membrane. T. filiformis is a filamentous sheathed specie. Most species produce carotinoid pigments, and so form yellow, orange or red/pink colonies.

Habitat

Octopus Spring
Octopus Spring, Yellowstone National Park : James W. Brown

Thermus and the related genera are readily isolated from neutral pH to slightly alkaline hot springs, at temperatures between 55°-80°C. Halophilic species have been isolated from submarine vents. Hot artificial environments can also harbor Thermus, including thermally polluted water outflows, soil heated by steam pipes, and household hot water heaters.

Example : Thermus aquaticus

Thermus
Thermus aquaticus : Brock & Edwards (1970) J. Bacteriol. 104, 509-517.

The original isolates of T. aquaticus were from Mushroom Spring, Octopus Spring, and other alkaline hot springs in the White Creek area of Yellowstone National Park, in attempt to cultivate the pink filamentous growth that is common in these springs (Thermocrinus ruber). It forms pale yellow colonies, growing between 40°C and 79°C, optimally at 70°C. T. aquaticus is an obligate aerobe; it cannot reduce nitrate.