Variation of the virus-related elements within syntenic genomes of the hyperthermophilic Archaeon Aeropyrum.

The increasing number of genome sequences of archaea and bacteria show their adaptation to different environmental conditions at the genomic level. Aeropyrum spp. are aerobic and hyperthermophilic archaea. Aeropyrum camini was isolated from a deep-sea hydrothermal vent, and Aeropyrum pernix was isolated from a coastal solfataric vent. To investigate the adaptation strategy in each habitat, we compared the genomes of the two species. Shared genome features were a small genome size, a high GC content, and a large portion of orthologous genes (86 to 88%). The genomes also showed high synteny. These shared features may have been derived from the small number of mobile genetic elements and the lack of a RecBCD system, a recombinational enzyme complex. In addition, the specialized physiology (aerobic and hyperthermophilic) of Aeropyrum spp. may also contribute to the entire-genome similarity. Despite having stable genomes, interference of synteny occurred with two proviruses, A. pernix spindle-shaped virus 1 (APSV1) and A. pernix ovoid virus 1 (APOV1), and clustered regularly interspaced short palindromic repeat (CRISPR) elements. Spacer sequences derived from the A. camini CRISPR showed significant matches with protospacers of the two proviruses infecting A. pernix, indicating that A. camini interacted with viruses closely related to APSV1 and APOV1. Furthermore, a significant fraction of the nonorthologous genes (41 to 45%) were proviral genes or ORFans probably originating from viruses. Although the genomes of A. camini and A. pernix were conserved, we observed nonsynteny that was attributed primarily to virus-related elements. Our findings indicated that the genomic diversification of Aeropyrum spp. is substantially caused by viruses.

Purification and characterization of the oxygen-thermostable hydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum camini.

Aeropyrum camini that was isolated from a deep-sea hydrothermal vent chimney, possessed two hydrogenases (161 and 85 kDa) in its soluble fraction. The 85-kDa hydrogenase was purified to homogeneity using several chromatography columns. The specific activities of the purified hydrogenase were: 14.8 micromol methyl viologen(ox)/mg/min for hydrogen oxidation, and 14.6 micromol methyl viologen(red)/mg/min for proton reduction. The oxygen stabilities of hydrogenases that were purified from A. camini and the hydrogen thermophilic bacterium Persephonella hydrogeniphila, were compared. The hydrogenase purified from P. hydrogeniphila completely lost its activity following a 96-h exposure to atmosphere; however, the A. camini hydrogenase maintained 75% of its initial activity, even after a 168 h of atmospheric exposure. A. camini hydrogenase showed a half-life of 48 h at 90 degrees C, while P. hydrogeniphila hydrogenase showed complete denaturation after a 30 min incubation at the same temperature. Nine residues of the N-terminal amino acid sequence of A. camini hydrogenases (MARLLMIPGT) correspond to the protein sequence encoded by the hypothetical soluble hydrogenase subunit gene (APE2423) from A. pernix strain K1. A. camini hydrogenase has a high thermostability and is very tolerant to oxygen; therefore, it may be used for actual H(2) production.

Aeropyrum camini sp. nov., a strictly aerobic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney.

A novel hyperthermophilic archaeon, designated strain SY1(T), was isolated from a deep-sea hydrothermal vent chimney sample collected from the Suiyo Seamount in the Izu-Bonin Arc, Japan, at a depth of 1385 m. The cells were irregular cocci (1.2 to 2.1 micro m in diameter), occurring singly or in pairs, and stained Gram-negative. Growth was observed between 70 and 97 degrees C (optimum, 85 degrees C; 220 min doubling time), pH 6.5 and 8.8 (optimum, pH 8.0), and salinity of 2.2 and 5.3 % (optimum, 3.5 %). It was a strictly aerobic heterotroph capable of growing on complex proteinaceous substrates such as yeast extract and tryptone. The G+C content of the genomic DNA was 54.4 mol%. Phylogenetic analysis based on the 16S rDNA sequence of the isolate indicated that the isolate was closely related to Aeropyrum pernix strain K1(T). However, no significant genetic relatedness was observed between them by DNA-DNA hybridization. On the basis of the molecular and physiological traits of the new isolate, the name Aeropyrum camini sp. nov. is proposed, with the type strain SY1(T) (=JCM 12091(T)=ATCC BAA-758(T)).