The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C

Abstract

Hyperthermus butylicus, a hyperthermophilic neutrophile and anaerobe, is a member of the archaeal kingdom Crenarchaeota. Its genome consists of a single circular chromosome of 1,667,163 bp with a 53.7% G+C content. A total of 1672 genes were annotated, of which 1602 are protein-coding, and up to a third are specific to H. butylicus. In contrast to some other crenarchaeal genomes, a high level of GUG and UUG start codons are predicted. Two cdc6 genes are present, but neither could be linked unambiguously to an origin of replication. Many of the predicted metabolic gene products are associated with the fermentation of peptide mixtures including several peptidases with diverse specificities, and there are many encoded transporters. Most of the sulfur-reducing enzymes, hydrogenases and electron-transfer proteins were identified which are associated with energy production by reducing sulfur to H(2)S. Two large clusters of regularly interspaced repeats (CRISPRs) are present, one of which is associated with a crenarchaeal-type cas gene superoperon; none of the spacer sequences yielded good sequence matches with known archaeal chromosomal elements. The genome carries no detectable transposable or integrated elements, no inteins, and introns are exclusive to tRNA genes. This suggests that the genome structure is quite stable, possibly reflecting a constant, and relatively uncompetitive, natural environment.

Figure 1.

Homologous protein genes of H. butylicus and other hyperthermophiles. The overlapping circle plot shows the number of homologs shared between the genomes of A. H. butylicus, A. pernix and P. aerophilum, chosen as representatives of the three major crenarchaeal neutrophile families for which genome sequences are available, and B. H. butylicus, M. jannaschii and A. aeolicus representing hyperthermophilic crenarchaea, euryarchaea and bacteria, respectively. Blue, red and green numbers each show the number of genes of one genome which are specific to that genome or which are shared (homologous) with one, or both, of the other two genomes.

Figure 2.

A GC-skew analysis of the H. butylicus genome showing the major peaks where nucleotide compositional deviations occur. Shown below are some of the main features of the genome including the two cdc6 genes, rRNA genes and large repeat clusters (CRISPR). The ordinate scale is arbitrary, showing positive and negative G/C deviations. The abscissa corresponds to the genome sequence length where the numbering starts just upstream from the 16S + 23S rRNA operon.

Figure 3.

Phylogenetic tree based on 16S rRNA sequences generated with MEGA3 (Kumar et al. 2004) showing representatives of the three major crenarchaeal orders, Desulfurococcales (families Desulfurococcaceae and Pyrodictiaceae), Thermoproteales and Sulfolobales, for which completely sequenced genomes are available (blue) or for which genome sequences are incomplete and/or unpublished (red).