Genome variation in the hyperthermophilic archaeon Aeropyrum

Abstract

Aeropyrum spp are aerobic, heterotrophic, and hyperthermophilic marine archaea. There are two closely related Aeropyrum species, Aeropyrum camini and Aeropyrum pernix, which are isolated from geographically distinct locations. Recently, we compared their genome sequences to determine their genomic variation. They possess highly conserved small genomes, reflecting their close relationship. The entire genome similarity may result from their survival strategies in adapting to extreme environmental conditions. Meanwhile, synteny disruptions were observed in some regions including clustered regularly interspaced short palindromic repeats elements. Further, the largest portion of their non-orthologous genes were genes in the two proviral regions of A. pernix (Aeropyrum pernix spindle-shaped virus 1 and Aeropyrum pernix ovoid virus 1) or ORFans considered to be derived from viruses. Our data shows that genomic diversification of Aeropyrum spp may be substantially induced by viruses. This suggests that Aeropyrum spp may have a large pan-genome that can be extended by viruses, while each of the species shares a highly conserved small genome specializing for extreme environments.

The members of the genus Aeropyrum are heterotrophic, aerobic, and hyperthermophilic crenarchaea.^1,2 The genus is composed of two closely related species, Aeropyrum camini and Aeropyrum pernix. The type strains are A. camini SY1 and A. pernix K1. A. camini SY1 was isolated from the surface of a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc, Japan, at a depth of 1385 m;¹ and A. pernix K1 was isolated from a coastal solfataric thermal vent in Kodakara-Jima Island in southwestern Japan.²

Comparative genome analysis between closely related organisms shows relevant physiological differences depending on their habitat, which are reflected in genome divergence.^3,4 We recently determined the complete genome sequence of A. camini and compared it with the A. pernix genome⁵ to determine the genetic differences between close relatives in distinct habitats.⁶

The general genome features were similar between A. camini and A. pernix: small genome size (1.60 to 1.67 Mbp), G+C content (56.3 to 56.7%), and number of open reading frames (ORFs) (1645 to 1700). The genomic similarity score, which is calculated using the bit scores of shared orthologous genes,⁷ was 0.87 and nucleotide identity between the two chromosomes was 73.2 to 76.6% over a wide range of the chromosomes (86.2 to 90.2%), indicating their close relationship. The genomes also showed high synteny. Within other closely related archaea and bacteria, comparative genomics shows extensive rearrangements in the nucleotide alignment and poorly conserved gene order.⁸

One of the factors promoting genomic synteny is possibly the lack of the RecBCD system, a well-characterized recombinational enzyme complex in bacteria, or the restricted number of mobile elements like insertion sequences and miniature inverted-repeat transposable elements that can be the target sequences for homologous recombination. In addition, we speculate Aeropyrum spp are specialized in their extreme and narrow-range habitat at the genomic level and their specialized genome may contribute to their genomic integrity, because disruptions in synteny can lead to alteration in gene regulation associated with lower fitness for their habitat. This was supported by the estimate that 82 to 84% of the horizontally acquired genes identified in the Aeropyrum genomes were derived from thermophiles.

We observed some genomic variations, although the two genomes were highly conserved. Remarkable synteny disruptions were identified in the virus-related elements. In general, integrative genetic elements are often found at the tRNA loci,⁹ where the A. pernix genome included two proviral regions (Fig. 1). The replication of these proviruses is induced under oxygen-limiting conditions. They are named Aeropyrum pernix spindle-shaped virus 1 (APSV1) and Aeropyrum pernix ovoid virus 1 (APOV1).¹⁰ Conversely, the two proviral sequences were absent in the A. camini genome despite the synteny of neighboring regions. Instead, A. camini encoded two non-orthologous genes, ORF575 (COG1111, ERCC4-like helicase) and ORF576 (hypothetical protein), next to tRNA21-Val (Fig. 1). The genome synteny was also broken at the clustered regularly interspaced short palindromic repeats (CRISPR) elements. The CRISPR element is an acquired immune system in archaea and bacteria against viruses and plasmids via incorporation of short sequences, called spacers, derived from foreign genetic elements.¹¹ In other words, CRISPR spacers represent signatures of invading genetic elements. The composition of CRISPR spacers was different between A. camini and A. pernix. When all 144 spacer sequences collected from both genomes were compared against the NCBI nr nucleotide database using BLASTN,¹² three spacers (two spacers in A. camini and a spacer in A. pernix) and a spacer in A. camini significantly matched the genomes of APSV1 and APOV1, respectively, indicating that A. camini interacted with viruses closely related to them in the past, and if the CRISPR is functional, A. camini may escape viral infection. The other 140 spacers did not show similarity to any other nucleotide sequence in the database. This implies that Aeropyrum spp are challenged by diverse and uncharacterized foreign genetic elements in addition to known viruses infecting A. pernix.^13,14

Figure 1. Two proviral regions (APOV1 and APSV1) were present in A. pernix and absent in A. camini. Proviral regions, tRNAs, and open reading frames (ORFs) are shown as red boxes, green vertical lines, and arrows, respectively. Orthologous genes are shown in navy blue highlighted by orange.

A detailed analysis of the non-orthologous genes in Aeropyrum spp supports our supposition that viruses may be involved in their genome variations. Among the non-orthologous genes, the major portion of them (41 to 45%) were classified into ORFans, which did not show similarity to any other available protein sequence and are potentially derived from viruses, and proviral genes. We conclude that Aeropyrum spp interact with diverse viruses and their genomic diversification may be substantially due to viruses, notwithstanding their conserved genomes specializing in extreme environment.

The variable gene component is responsible for expanding physiological and ecological capabilities of microorganisms,¹⁵ most notably antibiotic resistance among bacterial pathogens.¹⁶ Although the variable genes in Aeropyrum were mostly derived from viruses with unknown functions, they are potentially responsible for the acquisition of new functions. If every unique microbial strain contains a different set of variable genes, the size of the pan-genome (the total set of genes found in all strains¹⁷) becomes vast in a large microbial population. Each Aeropyrum strain appears to share conserved small genomes encoding genes required for cell maintenance and, at the same time the Aeropyrum population’s pan-genome may be extended by viruses to give a significant genetic reservoir exploited for adaptive purposes, resulting in the increased fitness of the population in changeable extreme environments.

Glossary

Abbreviations:

ORF

open reading frame

APSV1

Aeropyrum pernix spindle-shaped virus 1

APOV1

Aeropyrum pernix ovoid virus 1

CRISPR

clustered regularly interspaced short palindromic repeats

Citation: Daifuku T, Yoshida T, Sako Y. Genome variation in the hyperthermophilic archaeon Aeropyrum. Mobile Genetic Elements 2013; 3:e26833; 10.4161/mge.26833

Daifuku T, Yoshida T, Kitamura T, Kawaichi S, Inoue T, Nomura K, Yoshida Y, Kuno S, Sako Y. Variation of the virus-related elements within syntenic genomes of the hyperthermophilic Archaeon Aeropyrum. Appl Environ Microbiol. 2013;79:5891–8. doi: 10.1128/AEM.01089-13.

Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.