Complete genome sequence of the hyperthermophilic archaeon <i>Thermococcus kodakaraensis</i> KOD1 and comparison with <i>Pyrococcus</i> genomes

TLDR

Thermococcus is a sulfur‑reducing hyperthermophilic archaeal genus in Thermococcales, closely related to Pyrococcus, and is ubiquitous in high‑temperature environments where it plays a key ecological role. The authors sequenced and annotated the complete 2.09‑Mb genome of Thermococcus kodakaraensis KOD1 and compared it with the three available Pyrococcus genomes to gain insight into this genus. The genome contains 2,306 coding sequences, of which 1,165 are annotated, and comparative genomics shows 1,204 shared proteins while 689 unique genes encode functions related to pyruvate oxidation, nucleotide metabolism, metal transport, stress response, and a distinct restriction system, with mobile elements indicating horizontal gene transfer.

Abstract

The genus Thermococcus , comprised of sulfur-reducing hyperthermophilic archaea, belongs to the order Thermococcales in Euryarchaeota along with the closely related genus Pyrococcus . The members of Thermococcus are ubiquitously present in natural high-temperature environments, and are therefore considered to play a major role in the ecology and metabolic activity of microbial consortia within hot-water ecosystems. To obtain insight into this important genus, we have determined and annotated the complete 2,088,737-base genome of Thermococcus kodakaraensis strain KOD1, followed by a comparison with the three complete genomes of Pyrococcus spp. A total of 2306 coding DNA sequences (CDSs) have been identified, among which half (1165 CDSs) are annotatable, whereas the functions of 41% (936 CDSs) cannot be predicted from the primary structures. The genome contains seven genes for probable transposases and four virus-related regions. Several proteins within these genetic elements show high similarities to those in Pyrococcus spp., implying the natural occurrence of horizontal gene transfer of such mobile elements among the order Thermococcales. Comparative genomics clarified that 1204 proteins, including those for information processing and basic metabolisms, are shared among T. kodakaraensis and the three Pyrococcus spp. On the other hand, among the set of 689 proteins unique to T. kodakaraensis , there are several intriguing proteins that might be responsible for the specific trait of the genus Thermococcus , such as proteins involved in additional pyruvate oxidation, nucleotide metabolisms, unique or additional metal ion transporters, improved stress response system, and a distinct restriction system.