Thermococcus kodakaraensis Genome Project

Imanaka Laboratory, Graduate School of Engineering, Kyoto University, Japan

since 17/Feb/2005

Complete Genome Sequence of the Hyperthermophilic Archaeon
 Thermococcus kodakaraensis KOD1 and Comparison with Pyrococcus Genomes
 Toshiaki Fukui, Haruyuki Atomi, Tamotsu Kanai, Rie Matsumi, Shinsuke Fujiwara,
and Tadayuki Imanaka
Genome Res.,15: 352-363 (2005) [PubMed]
 

Project Information

Background
    Among the living organisms, hyperthermophiles belonging to the third domain of life, Archaea, are attractive subjects of research from various aspects. Many efforts to understand the strategies for adaptation to extremely high temperature environments have revealed numerous physiologically intriguing and unique properties of hyperthermophilic archaea. They have also attracted attention from an industrial point of view as potential resources for highly thermostable enzymes.
    The euryarchaeal order Thermococcales, composed of two major genera Thermococcus and Pyrococcus may be the best-studied hyperthermophiles. They are strictly anaerobic obligate heterotrophs growing on complex proteinaceous substrates, and their growth is strongly associated with the reduction of elemental sulfur. Alternatively, with a few exceptions, they are capable of gaining energy by fermentation of peptides, amino acids and sugars, forming acids, CO2, and H2 in the absence of elemental sulfur.
    The genus Pyrococcus, with a higher optimum growth temperature (95-103 C) than Thermococcus (75-93 C), has fascinated many microbiological researchers and has often been used as the source organism for both fundamental and application-based aspects of research. Therefore, although within the same genus, the complete genome analyses of three species, P. horikoshii (BA000001), P. furiosus (AE009950), and P. abyssi (AL096836), have been performed. In contrast to Pyrococcus, the genus Thermococcus contains the highest number of characterized isolates. Recent culture-dependent and culture-independent studies have indicated that the members of Thermococcus are more ubiquitously present in various deep-sea hydrothermal vent systems than those of Pyrococcus. Consequently, Thermococcus strains, with their larger population, are considered to play a major role in the ecology and metabolic activity of microbial consortia within marine hot-water ecosystems. However, despite the importance of this genus, no complete genome sequence has been determined for Thermococcus. The Thermococcus genome can be expected to encode genes responsible for various cellular functions that provide an advantage for these strains in natural high temperature habitats.

Features of Thermococcus kodakaraensis strain KOD1

• Isolated from a solfatara on the shore of Kodakara Island, Kagoshima, Japan as Pyrococcus sp. strain KOD1 (Morikawa et al. 1994)
• Re-classified as Thermococcus kodakaraensis strain KOD1 based on phylogenetic and DNA-DNA hybridization analyses (Atomi et al. 2004)
  
• Taxonomoic description
  
• Irregular cocci of 1-2µm diameter with several flagella.
• Growth conditions: Temp. 60-100 C (opt. 85 C); pH 5-9 (opt. 6.5); Salt conc. 1-5% (opt. 3%); strict anaerobic
• Growth properties: Obligate heterotrophic
  

  Carbon and energy sources	Sugar metabolism	Electron acceptor	Evolved gas
  Amino acids, peptides	Gluconeogenesis	S0	H2S
  Pyruvate	Gluconeogenesis	H+	H2
  Starch	Glycolysis	H+	H2

• An abundant number of genes and their protein products from this archaeon have been examined (Imanaka and Atomi 2002), such as DNA polymerase (Hashimoto et al. 2001), commercially available as an excellent enzyme for PCR amplification from Toyobo (in Japan), Novagen, and Invitrogen.
• Useful gene disruption system, the first for a hyperthermophile, has been developed (Sato et al. 2003).