Abstract
The 2 465 177 bp genome of Sulfolobus islandicus LAL14/1, host of the model rudivirus SIRV2, was sequenced. Exhaustive comparative genomic analysis of S. islandicus LAL14/1 and the nine other completely sequenced S. islandicus strains isolated from Iceland, Russia and USA revealed a highly syntenic common core genome of approximately 2 Mb and a long hyperplastic region containing most of the strain-specific genes. In LAL14/1, the latter region is enriched in insertion sequences, CRISPR (clustered regularly interspaced short palindromic repeats), glycosyl transferase genes, toxin–antitoxin genes and MITE (miniature inverted-repeat transposable elements). The tRNA genes of LAL14/1 are preferential targets for the integration of mobile elements but clusters of atypical genes (CAG) are also integrated elsewhere in the genome. LAL14/1 carries five CRISPR loci with 10 per cent of spacers matching perfectly or imperfectly the genomes of archaeal viruses and plasmids found in the Icelandic hot springs. Strikingly, the CRISPR_2 region of LAL14/1 carries an unusually long 1.9 kb spacer interspersed between two repeat regions and displays a high similarity to pING1-like conjugative plasmids. Finally, we have developed a genetic system for S. islandicus LAL14/1 and created ΔpyrEF and ΔCRISPR_1 mutants using double cross-over and pop-in/pop-out approaches, respectively. Thus, LAL14/1 is a promising model to study virus–host interactions and the CRISPR/Cas defence mechanism in Archaea.
Highlights
The genus Sulfolobus was first described by Brock et al in 1972 [1] and includes thermoacidophilic Archaea that grow at 70–858C and pH 2–3 under aerobic conditions either chemolithotrophically by oxidizing elementary sulfur/hydrogen sulfide or & 2013 The Authors
The S. islandicus LAL14/1 genome consists of a single circular chromosome of 2 465 177 bp; 85.6 per cent of the genome is coding
The general properties of the S. islandicus LAL14/1 genome composition are summarized in table 1
Summary
The genus Sulfolobus was first described by Brock et al in 1972 [1] and includes thermoacidophilic Archaea that grow at 70–858C and pH 2–3 under aerobic conditions either chemolithotrophically by oxidizing elementary sulfur/hydrogen sulfide or& 2013 The Authors. Sulfolobus strains have been isolated from various acidic thermal habitats (in the USA, Italy, Iceland, Russia and elsewhere) They are maintained under laboratory conditions, making them convenient models to study the molecular organization of the archaeal cell [3]. The sequences of 12 Sulfolobus genomes are currently available They include Sulfolobus solfataricus P2 [4], Sulfolobus tokodaii [5], Sulfolobus acidocaldarius [6] and nine strains of Sulfolobus islandicus: HV10/4 and REY15A [7] (isolated from hot springs in Iceland) [8]; M.14.25, M.16.27 and M.16.4 (from hot springs at the Mutnovsky Volcano, Kamchatka, Russia); Y.N.15.51 and Y.G.57.14 (from hot springs in Yellowstone National Park, USA); and L.D.8.5 and L.S.2.15 (from Lassen National Park, USA) [9]
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