157. The Genome Sequence of a Hyperthermophilic Archaeon: Pyrococcus furiosus 

Robert B. Weiss¹, Diane Dunn¹, Mark Stump¹, Raymond Yeh¹, Joshua Cherry¹, and Frank T. Robb^2 
1Dept. of Human Genetics, University of Utah, Salt Lake City, Utah and ²Center of Marine Biotechnology, University of Maryland, Baltimore, Maryland 
bob.weiss@genetics.utah.edu 

Pyrococcus furiosus is a strictly anaerobic archaeon that grows optimally at 100C by a fermentative-type metabolism in which complex peptide mixtures such as yeast extract and Tryptone, and also certain sugars, are oxidized to organic acids, H₂ and CO₂. The organism was isolated from geothermal marine sediment in shallow waters off Vulcano Island, Italy. We have determined the complete sequence of this organism's genome. It is 1,908,253 base pairs in length, with a GC-content of 40.8%. Recently, the complete sequence of a distantly-related species, Pyrococcus horikoshii, has been determined by a group in Japan (www.bio.nite.go.jp). This species was isolated from a hydrothermal vent at a depth of 1395 meters in the Sea of Japan. Comparative analysis is revealing complex gene re-arrangements and changes in gene content between these two Pyrococcus species. 

The genome content and organization reveals many potential operons, one rRNA operon, 46 tRNAs, 22 insertion elements, 7 SR elements, and 14 inteins. 50% of the ORFs are of unknown function, and of this class 19% are in common between the two Pyrococcus species. The 22 putative insertion elements in the genome of P. furiosus are not found in the P. horikoshii genome. 

The genome of P. furiosus is 170 kb larger than P. horikosihii, with about 70% DNA identity conserved within open reading frames. Genome to genome dot plot alignment reveals the remnant of a conserved diagonal. The longest co-linear segment between the two genomes is 70 kb, and much of the remnant diagonal is interspersed with inversions, deletions and insertions. The list of major gene clusters present in P. furiosus but not in P. horikoshii include: maltose/trehalose transport, phosphate uptake system, major parts of the urea and TCA cycle, and amino acid metabolism of tryptophan, aromatics, arginine, and isoleucine/valine. The maltose/trehalose transport operon is within a 17 kb segment flanked by putative insertion elements. This segment is also found in Thermococcus litoralis, another isolate from a Mediterrean marine geothermal location. The high identity (>99%) between these two segments suggests a recent lateral transfer event between T. litoralis and P. furiosus.