A Survey of the Genome of the Hyperthermophilic Archaeon,Pyrococcus furiosus

Abstract

Pyrococcus furiosus is a marine microorganism with the unusual ability to grow optimally at 100°C. It is classified as a member of the domain Archaea (Archaebacteria). We present studies on the genome of P. furiosus, consisting of a precise determination of the size of the chromosome, 2.05 mb, and an analysis of sequence data from cDNA and genomic libraries. The sequence analysis included a total of 1176 sequences, representing 14.7% of the genome, which were compared with the current databases using the BLAST X algorithm. Expressed sequence tag (EST) analysis is skewed toward the repeated detection of highly expressed genes, for example, ribosomal RNA, in P. furiosus. The relatively small size of the genome implies a high coding density, and randomly chosen genomic sequences provide good performance in gene discovery with relatively fewer identical hits compared with the EST database. The recovery of database matches with P(n) ≤ 1.0e−05 was 30% of the total sequences tested. We estimate that the genome contains approximately 1800 genes, and this study has provided evidence for 309 genes. The average G+C content of the sequences obtained was 41.2%, and no repetitive sequences were detected. Genes from Eukarya and Bacteria are almost equally represented in the matches obtained in this study. The homologs representing central metabolism exhibit preferential similarity to their homologs from bacteria, despite the availability of eukaryotic homologs in the databases. Several characteristically eukaryotic protein homologs were found with functions in transcription, translation, and membrane transport. We propose that the archaeal genome is a mosaic, consisting of ancient gene sequences related to eukaryal homologs and more recently acquired genes, many of which are related to bacterial metabolic functions. Further sequencing and phylogenetic studies are needed to confirm this hypothesis, which predicts that there was extensive lateral genetic transfer among Bacteria, Eukarya, and Archaea during a period when the original gene pool was expanding into the early lineages of life.