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Pyrococcus yayanosii CH1 is the first obligate piezophilic hyperthermophilic archaeon isolated from the deep-sea hydrothermal site Ashadze on the mid-Atlantic ridge at a depth of 4,100 m. This organism grows within a temperature range of 80 to 108°C and a hydrostatic pressure range of 20 to 120 MPa, with optima at 98°C and 52 MPa, respectively. Here, we report the complete genome sequence (1,716,817 bp, with a G+C content of 51.6%) of the type strain P. yayanosii CH1T (= JCM 16557). This genomic information reveals a systematic view of the piezoadaptation strategy and evolution scenario of metabolic pathways in Thermococcales.
Pyrococcus yayanosii CH1 is the first obligate piezophilic hyperthermophilic archaeon isolated from the deep-sea hydrothermal site named Ashadze located on the mid-Atlantic ridge at a depth of 4,100 m. P. yayanosii CH1 was cultivated in TRM medium (2, 7) under optimal growth conditions (98°C and 52 MPa) for 2 days. Cells were collected by centrifugation, and then the genomic DNA was prepared by the alkaline lysis method. The genome of CH1 has been sequenced by both Solexa at the Beijing Genomics Institute and 454 pyrosequencing at the Chinese National Human Genome Center in Shanghai to ensure good accuracy.
Solexa sequencing revealed 11 scaffolds ranging from 5.3 kb to 458 kb to give ~374-fold coverage of the genome. In the case of 454 pyrosequencing, 17 contigs were generated (size range of 6.5 kb to 336 kb) to give ~68.5-fold coverage of the genome. These sequencing data were combined, and gaps were closed by PCR sequencing.
The genome consists of a circular DNA molecule of 1,716,817 bp with a G+C% content of 51.6%, which is higher than that of other related Pyrococcus species like P. abyssi, P. horikoshii, and P. furiosus (3, 5, 6).
A total of 1,926 coding sequences (CDSs) were predicted by Glimmer 3.02 and tRNAscan-SE 1.21. The average gene size is 816 bp, comprising CDSs ranging from 37 to 1,405 amino acids. There are two predicted copies of the 5S rRNA gene, one of the 16S rRNA gene, and one of the 23S rRNA gene and 46 predicted tRNAs. The genome sequence was annotated by integrated BLAST analysis against the KEGG, UniProt, and Clusters of Orthologous Groups databases.
The genome was categorized into 168 subsystems by authorized annotation using the RAST (rapid annotation using subsystem technology) server (1). The reconstructed metabolic network includes a modified Embden-Meyerhof pathway, a partial pentose phosphate (Entner-Doudoroff) pathway, and reverse tricarboxylic acid cycles.
The amino acid composition and codon usage bias of all of the predicted P. yayanosii CH1 open reading frames were analyzed using the Acua version 1.0 software. Observations of the asymmetries in the amino acid substitutions in 200 pairs of orthologous proteins from P. furiosus and P. yayanosii CH1 were made. Piezophily in the physicochemical properties of amino acids and in the genetic code could be ranked by PAI (pressure asymmetry index) after comparison of proteins from P. furiosus and P. abyssi as assumed by Massimo Di Giulio (4). Our data show that both alanine and arginine have higher PAI values and the ratio of appearances in the genome of P. yayanosii CH1 is higher than that in other Pyrococcus species. This result suggests that piezophilic amino acids are prone to be low in molecular weight and higher in polarity.
Taking together the results from genome annotation, physiological and genetic characterization, and high-throughput transcriptomic, proteomic, and metabolomic comparisons, a systematic view of the piezoadaptation strategy and evolution scenario of metabolic pathways in P. yayanosii CH1 could be reached.
The final annotated genome of P. yayanosii strain CH1 reported in this paper is now accessible in GenBank under accession number CP002779.
This work was supported by grants from the National Natural Science Foundation of China to X.X. (NSFC 40625016, NSFC 40830213) and the Science and Technology Commission of Shanghai Municipality (10JC1406700). This work was also supported in part by the Agence Nationale de la Recherche (ANR 10 BLAN 1725 01-Living Deep) and a Partenariat Hubert Curien PFCC collaboration grant (20970WC) from Egide to M.J.
We thank Daniel Prieur and Jean Louis Birrien for helpful discussions and support.
Published ahead of print on 24 June 2011.