1. Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon
- Author
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Carole Jaubert, Jacques Oberto, Guennadi Sezonov, Diego Cortez, Mart Krupovic, Chloé Danioux, Qunxin She, Patrick Forterre, Ariane Bize, David Prangishvili, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Hydrosystèmes et Bioprocédés (UR HBAN), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Danish Archaea Centre, Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), This work was supported by PhD fellowships from the ‘Ministère de l'enseignement supérieur et de la recherche’ (C.J. and C.D.) and by Pasteur-Weizmann (C.J.) allocations., We thank Nuno Peixeiro and Sophie Schbath for helpful discussions., Institut Pasteur [Paris] (IP), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], and University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)
- Subjects
MESH: Sequence Analysis, DNA ,Genome ,Genes, Archaeal ,MESH: RNA, Transfer/metabolism ,Plasmid ,RNA, Transfer ,CRISPR ,Clustered Regularly Interspaced Short Palindromic Repeats ,genetics ,MESH: Models, Genetic ,Insertion sequence ,MESH: Sulfolobus/genetics ,crispr ,MESH: Phylogeny ,lcsh:QH301-705.5 ,Phylogeny ,genome analysis ,Genetics ,0303 health sciences ,biology ,General Neuroscience ,MESH: Genomics ,Genomics ,MESH: Toxins, Biological/metabolism ,Sulfolobus ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,MESH: RNA, Transfer/genetics ,MESH: Genes, Archaeal ,Research Article ,Gene Transfer, Horizontal ,archaea ,Immunology ,Replication Origin ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,MESH: DNA Transposable Elements/genetics ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,sulfolobus islandicus lal14/1 ,MESH: Replication Origin/genetics ,Toxins, Biological ,030304 developmental biology ,Models, Genetic ,030306 microbiology ,Research ,MESH: Antitoxins/metabolism ,MESH: Clustered Regularly Interspaced Short Palindromic Repeats/genetics ,Sequence Analysis, DNA ,biology.organism_classification ,MESH: Gene Transfer, Horizontal ,SULFOLOBUS ISLANDICUS ,lcsh:Biology (General) ,MESH: Sulfolobus/classification ,DNA Transposable Elements ,CRISPR Loci ,Antitoxins ,Mobile genetic elements ,Rudivirus - Abstract
The 2 465 177 bp genome ofSulfolobus islandicusLAL14/1, host of the model rudivirus SIRV2, was sequenced. Exhaustive comparative genomic analysis ofS. islandicusLAL14/1 and the nine other completely sequencedS. islandicusstrains 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 forS. islandicusLAL14/1 and createdΔpyrEFandΔCRISPR_1mutants 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.
- Published
- 2013
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