A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans

Abstract

Background: The relationship between the hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans is the only known example of a specific association between two species of Archaea. Little is known about the mechanisms that enable this relationship.

Results: We sequenced the complete genome of I. hospitalis and found it to be the smallest among independent, free-living organisms. A comparative genomic reconstruction suggests that the I. hospitalis lineage has lost most of the genes associated with a heterotrophic metabolism that is characteristic of most of the Crenarchaeota. A streamlined genome is also suggested by a low frequency of paralogs and fragmentation of many operons. However, this process appears to be partially balanced by lateral gene transfer from archaeal and bacterial sources.

Conclusions: A combination of genomic and cellular features suggests highly efficient adaptation to the low energy yield of sulfur-hydrogen respiration and efficient inorganic carbon and nitrogen assimilation. Evidence of lateral gene exchange between N. equitans and I. hospitalis indicates that the relationship has impacted both genomes. This association is the simplest symbiotic system known to date and a unique model for studying mechanisms of interspecific relationships at the genomic and metabolic levels.

Figure 1

Relationship between the genome size and the number of protein-coding genes in 623 complete archaeal and bacterial genomes, based on data in IMG version 2.5 (March 2008). The line points to I. hospitalis having the smallest genome among independently replicating organisms. The genomes of obligate parasites/symbionts are represented by grey circles. The shaded region of genome sizes spans the transition between obligate symbionts/parasites and free-living organisms.

Figure 2

Numbers of arCOGs in different functional categories (COG classification) lost or gained in the I. hospitalis lineage. The sets of lost and gained genes were derived on the basis of a comparison of the I. hospitalis gene compliment with the reconstructed gene set of the last common ancestor of Desulfurococcales [27] (see Additional data files). The numbers of arCOGs in each category that are present in N. equitans but are absent in I. hospitalis are also indicated. The one letter code for COG categories is the following: amino acid transport and metabolism (E); carbohydrate transport and metabolism (G); cell cycle control, cell division, chromosome partitioning (D); cell motility (N); cell wall/membrane/envelope biogenesis (M); coenzyme transport and metabolism (H); defense mechanisms (V); energy production and conversion (C); inorganic ion transport and metabolism (P); intracellular trafficking, secretion, and vesicular transport (U); lipid transport and metabolism (I); nucleotide transport and metabolism (F); posttranslational modification, protein turnover, chaperones (O); replication, recombination and repair (L); secondary metabolites biosynthesis, transport and catabolism (Q); signal transduction mechanisms (T); transcription (K); and translation, ribosomal structure and biogenesis (J).

Figure 3

Paralog distribution in completely sequenced archaeal genomes. (a) The average number of paralogs in arCOGs for completely sequenced archaeal genomes. The arrows point to the vales for N. equitans and I. hospitalis genomes, respectively. (b) Paralog density in completed genomes of species from the order Desulfurococcales and in N. equitans, determined by blastclust using a variable identity threshold over at least 50% of the aligned pairs of sequences.

Figure 4

Lysine and arginine use in archaeal proteomes, relative to genome G+C content. The dotted lines represent the linear fit to the hyperthermophile data and the goodness of fit values. The archaeal classification as hyperthermophiles, thermophiles and mesophiles follows that of the NCBI Genome Project database [100]. The proposed pathways for the biosynthesis of the two amino acids, the genes predicted to be involved and the metabolic costs of the two reactions are shown below the graphs.

Figure 5

Taxonomic classification of I. hospitalis protein-coding genes based on phylogenetic and COG distribution analyses. Genes labeled in green or blue-green are of Crenarchaeota-type or are of unresolved archaeal nature, respectively. Genes that could represent horizontal gene transfers from Euryarchaeota or Bacteria are labeled in purple and yellow, respectively. Genes that have their closest ortholog in N. equitans are labeled red and are described in the table. Genes labeled in gray lack recognizable homologues in other microbial genomes or have unresolved phylogenies preventing confident affiliation to either Archaea or Bacteria.

Figure 6

Maximum likelihood phylogenetic trees (a) of archaeal valyl-tRNA synthetases and (b) of leucyl aminopeptidases representing the three domains of life and including all the known archaeal sequences. Numbers indicate bootstrap support based on 100 replicates. Where the value was <50, the branch was collapsed. The scale bar indicates the inferred number of substitutions per site. The sequence alignments used to generate the trees are provided in the Additional data file 4.

Figure 7

Predicted functional systems and metabolic pathways of the I. hospitalis-N. equitans system. The numbers refer to the corresponding genes in the I. hospitalis and N. equitans genome (green and red, respectively). Some of the biochemical pathways (carbon fixation, amino acid biosynthesis and sugar metabolism) have been experimentally validated [66,69]. Specific subcellular compartments and structures (periplasmic space, vesicles, tubules, pores, fibers) [9,11,62] are indicated and speculative functions are indicated with question marks. Scissors indicate proteases. Stars indicate specific regulatory proteins. Different transporter categories and their individual subunits are indicated by shape symbols and the direction of transport of specific substrates across the membrane is shown by arrows.