Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A)

Abstract

Pyrolobus fumarii Blöchl et al. 1997 is the type species of the genus Pyrolobus, which belongs to the crenarchaeal family Pyrodictiaceae. The species is a facultatively microaerophilic non-motile crenarchaeon. It is of interest because of its isolated phylogenetic location in the tree of life and because it is a hyperthermophilic chemolithoautotroph known as the primary producer of organic matter at deep-sea hydrothermal vents. P. fumarii exhibits currently the highest optimal growth temperature of all life forms on earth (106°C). This is the first completed genome sequence of a member of the genus Pyrolobus to be published and only the second genome sequence from a member of the family Pyrodictiaceae. Although Diversa Corporation announced the completion of sequencing of the P. fumarii genome on September 25, 2001, this sequence was never released to the public. The 1,843,267 bp long genome with its 1,986 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords: GEBA; Pyrodictiaceae; black smoker; chemolithoautotroph; facultative microaerophilic; hydrothermal solfataric vents; hyperthermophile; non-motile.

Figure 1

Phylogenetic tree highlighting the position of P. fumarii relative to the type strains of the other species within the order Desulfurococcales. The tree was inferred from 1,333 aligned characters [8,9] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [10]. Rooting was done initially using the midpoint method [11] and then checked for its agreement with the current classification (Table 1). The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 1,000 ML bootstrap replicates [12] (left) and from 1,000 maximum parsimony bootstrap replicates [13] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [14] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks (see [15-21], and CP002051 for Staphylothermus hellenicus).

Figure 2

Scanning electron micrograph of P. fumarii 1A^T

Figure 3

Graphical circular map of the genome. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Figure 4

GGDC NJ tree inferred from the type strain genomes within the order Desulfurococcales.

Figure 5

Venn diagram depicting the intersections of protein sets (total numbers in parentheses) of P. fumarii, I. aggregans and H. butylicus.