title: Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon.
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.
authors.affiliation: Département de Microbiologie, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, France.
authors.forename: Carole
authors.initials: C
authors.lastname: Jaubert
authors.forename: Chloë
authors.initials: C
authors.lastname: Danioux
authors.forename: Jacques
authors.initials: J
authors.lastname: Oberto
authors.forename: Diego
authors.initials: D
authors.lastname: Cortez
authors.forename: Ariane
authors.initials: A
authors.lastname: Bize
authors.forename: Mart
authors.initials: M
authors.lastname: Krupovic
authors.forename: Qunxin
authors.initials: Q
authors.lastname: She
authors.forename: Patrick
authors.initials: P
authors.lastname: Forterre
authors.forename: David
authors.initials: D
authors.lastname: Prangishvili
authors.forename: Guennadi
authors.initials: G
authors.lastname: Sezonov
mesh_terms: D000992:Antitoxins / Q000378:metabolism; D064112:Clustered Regularly Interspaced Short Palindromic Repeats / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D022761:Gene Transfer, Horizontal; D019766:Genes, Archaeal; D023281:Genomics; D008957:Models, Genetic; D010802:Phylogeny; D012343:RNA, Transfer / Q000235:genetics / Q000378:metabolism; D018741:Replication Origin / Q000235:genetics; D017422:Sequence Analysis, DNA; D016944:Sulfolobus / Q000145:classification / Q000235:genetics*; D014118:Toxins, Biological / Q000378:metabolism
chemical_list: D000992:Antitoxins; D004251:DNA Transposable Elements; D014118:Toxins, Biological; D012343:RNA, Transfer