Complete Genome Sequence of the Thermoacidophilic Crenarchaeon Thermoproteus uzoniensis 768-20

Abstract

Thermoproteus uzoniensis 768-20 is a thermoacidophilic anaerobic crenarchaeon isolated from a solfataric field in Kamchatka, Russia. The complete genome sequence reveals genes for protein and carbohydrate-active enzymes, beta-oxidation of fatty acids, the Embden-Meyerhof and Entner-Doudoroff pathways for glucose metabolism, the tricarboxylic acid cycle, the dicarboxylate/4-hydroxybutyrate cycle, hydrogenase, and sulfur reductase.

TEXT

Members of the genus Thermoproteus within the crenarchaeal order Thermoproteales were the first hyperthermophilic archaea described (11). Three Thermoproteus species are known, T. tenax (11), T. neutrophilus (3), and T. uzoniensis (1), although T. neutrophilus is phylogenetically affiliated with Pyrobaculum and should be reclassified within this genus (7). The type species, T. tenax, has become a crenarchaeal model organism (5) extensively used to study the central carbohydrate metabolism (9). However, the lack of a publicly available complete genome sequence of this archaeon limits the analysis of its entire metabolic potential.

The type strain Z-605 of T. uzoniensis was isolated from a hot spring in the Uzon Caldera in Kamchatka, Russia (1). Recently, another strain, 768-20, was isolated from the solfataric field close to Moutnovsky volcano in Kamchatka. The 16S rRNA sequences of these strains are 99.7% identical, suggesting that they belong to the same species, T. uzoniensis. The new strain is an obligately anaerobic acidophile growing optimally at pH 5.5 and 85°C on proteinaceous substrates and some sugars, reducing elemental sulfur to H₂S. Unlike T. tenax, both strains of T. uzoniensis can grow in the absence of elemental sulfur. To understand the metabolic potential of T. uzoniensis, a complete genome sequence was determined.

The genome of T. uzoniensis 768-20 was sequenced using a Roche 454 GS FLX pyrosequencing platform. We obtained two libraries of 148,709 single-strand reads and 61,336 paired-end reads containing 3-kb inserts. The reads were assembled into a single scaffold (19 contigs) by the Newbler Assembler 1.1 (454 Life Sciences, Branford, CT). The genome was finished by filling gaps with sequencing and primer walking of PCR products with an ABI3730 capillary sequencer (Applied Biosystems, CA).

The complete genome of T. uzoniensis 768-20 consists of 1,936,063 bp in a single circular chromosome with an average G+C content of 59.7%. Unlike almost all hyperthermophilic archaea, the genome contains no clustered regularly interspaced short palindromic repeat (CRISPR) loci. A total of 2,188 protein-coding genes was predicted by Glimmer (2), covering 91% of the chromosome. Whole-genome annotation and analysis were performed with the AutoFACT tool (6), followed by a round of manual curation. Metabolic pathway analysis revealed that utilization of polysaccharides and proteins involves the function of numerous encoded hydrolytic enzymes, while fatty acids may be metabolized via the beta-oxidation pathway. Similarly to T. tenax (8, 10), glucose oxidation proceeds in both the modified Embden-Meyerhof and Entner-Doudoroff pathways followed by the tricarboxylic acid cycle (TCA), enabling the complete oxidation of organic substrates to CO₂ with the formation of H₂S. The autotrophic carbon dioxide fixation is feasible via the encoded reductive TCA and via the recently discovered (4) dicarboxylate/4-hydroxybutyrate cycle. The presence of membrane-bound hydrogenase and sulfur reductase suggests the possibility of chemolithoautotrophic growth. Making the genome sequence of T. uzoniensis 768-20 available will allow comprehensive comparison with T. tenax and stimulate further investigation into the metabolic capabilities of the Thermoproteales.

Nucleotide sequence accession number.

The complete genome sequence of T. uzoniensis 768-20 was deposited in GenBank under accession number CP002590.