Genomic analysis of Acidianus hospitalis W1 a host for studying crenarchaeal virus and plasmid life cycles

Abstract

The Acidianus hospitalis W1 genome consists of a minimally sized chromosome of about 2.13 Mb and a conjugative plasmid pAH1 and it is a host for the model filamentous lipothrixvirus AFV1. The chromosome carries three putative replication origins in conserved genomic regions and two large regions where non-essential genes are clustered. Within these variable regions, a few orphan orfB and other elements of the IS200/607/605 family are concentrated with a novel class of MITE-like repeat elements. There are also 26 highly diverse vapBC antitoxin-toxin gene pairs proposed to facilitate maintenance of local chromosomal regions and to minimise the impact of environmental stress. Complex and partially defective CRISPR/Cas/Cmr immune systems are present and interspersed with five vapBC gene pairs. Remnants of integrated viral genomes and plasmids are located at five intron-less tRNA genes and several non-coding RNA genes are predicted that are conserved in other Sulfolobus genomes. The putative metabolic pathways for sulphur metabolism show some significant differences from those proposed for other Acidianus and Sulfolobus species. The small and relatively stable genome of A. hospitalis W1 renders it a promising candidate for developing the first Acidianus genetic systems.

Fig. 1

The Y component of a Z curve plot for the A. hospitalis chromosome showing the three putative replication origins. The positions of the cdc6-3 gene (origin 2), cdc6-1 gene (origin 3) and the whiP/cdt1 gene (origin 1) are indicated as well as locations of the ribosomal RNA genes, the CRISPR-based systems, transposable elements of the IS200/605/607 family, and vapBC antitoxin–toxin gene pairs

Fig. 2

Model of pathways for oxidation and reduction of sulphur in A. hospitalis indicating the predicted functions of genes in the A. hospitalis genome and corresponding gene numbers are given for each step. The following abbreviations are used: OM outer membrane, IM inner membrane, SQR sulphide:quinone oxidoreductase, Fcc flavocytochrome c sulphide dehydrogenase, SOR sulphur oxygenase-reductase, TetH tetrathionate hydrolase, TQO thiosulphate–quinone oxidoreductase; SulP sulphate transporter permease, QH ₂ quinol pool

Fig. 3

Alignment of 10 MITE-like repeat elements present in the genome of A. hospitalis. The shaded area denotes to a small open reading frame corresponding to the downstream part of the OrfB found within transposable orfB elements

Fig. 4

VapBC trees. Phylogenetic trees for a VapB antitoxins and b VapC toxins. They demonstrate that VapBs, despite their high sequence diversity, can be classified into three main families AbrB, CcdA/CopG and DUF217, whereas the VapCs are highly diverse in their sequences but cannot be classified into major subgroups. The Ahos gene numbers are given for each protein. Moreover, the class of the VapB corresponding to each VapC is given in b. The degree of conservation of the VapC proteins in the available 13 Sulfolobus genomes is indicated in b where 0 indicates it is absent from all the genomes whilst 13 indicates that it is present in all. The antitoxin corresponding to VapC-0183 is not annotated in the genome because it lacks a start codon but it is included in the figure. The VapC-like protein (Ahos0712) is part of the operon with a translation-related protein and lacks a VapB. The Ahos1664/1663 pair are variant ORFs where both VapB and VapC are longer than usual and the VapB does not cluster with the families in a

Fig. 5

Schematic representations of the CRISPR loci of A. hospitalis. a Family II CRISPR module carrying three CRISPR loci and Cmr and Cas family gene cassettes which are both interrupted by, or bordered by, four vapBC gene pairs (orange). b Paired family I CRISPR/Cas system flanked by one vapBC gene pair, and c. an unclassified CRISPR locus lacking a leader region and adjacent cas genes. csm1 is a homolog of cmr2, csm2 is a homolog of cmr5 and csm3 is a homolog of cmr4. The light blue genes each carry two short RAMP motifs. a–c Structures of the individual CRISPR loci are shown together with the leader region (L) where each triangle represents a spacer-repeat unit. Significant spacer matches to sequenced viruses and plasmids are colour coded: red rudivirus, orange lipothrixvirus, yellow fusellovirus, green bicaudavirus, turquoise turreted icosahedral virus, blue conjugative plasmid and violet cryptic plasmid