title: topIb, a phylogenetic hallmark gene of Thaumarchaeota encodes a functional eukaryote-like topoisomerase IB.
abstract: Type IB DNA topoisomerases can eliminate torsional stresses produced during replication and transcription. These enzymes are found in all eukaryotes and a short version is present in some bacteria and viruses. Among prokaryotes, the long eukaryotic version is only observed in archaea of the phylum Thaumarchaeota. However, the activities and the roles of these topoisomerases have remained an open question. Here, we demonstrate that all available thaumarchaeal genomes contain a topoisomerase IB gene that defines a monophyletic group closely related to the eukaryotic enzymes. We show that the topIB gene is expressed in the model thaumarchaeon Nitrososphaera viennensis and we purified the recombinant enzyme from the uncultivated thaumarchaeon Candidatus Caldiarchaeum subterraneum. This enzyme is active in vitro at high temperature, making it the first thermophilic topoisomerase IB characterized so far. We have compared this archaeal type IB enzyme to its human mitochondrial and nuclear counterparts. The archaeal enzyme relaxes both negatively and positively supercoiled DNA like the eukaryotic enzymes. However, its pattern of DNA cleavage specificity is different and it is resistant to camptothecins (CPTs) and non-CPT Top1 inhibitors, LMP744 and lamellarin D. This newly described thermostable topoisomerases IB should be a promising new model for evolutionary, mechanistic and structural studies.
authors.affiliation: Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris-Seine (IBPS), Unité Evolution Paris-Seine (UMR 7138), F-75005 Paris, France.
authors.forename: Narimane
authors.initials: N
authors.lastname: Dahmane
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ.Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.
authors.forename: Danièle
authors.initials: D
authors.lastname: Gadelle
authors.affiliation: Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris-Seine (IBPS), Unité Evolution Paris-Seine (UMR 7138), F-75005 Paris, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Delmas
authors.affiliation: Hub Bioinformatique et Biostatistique - C3BI, USR 3756 IP CNRS, Institut Pasteur, 25-28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
authors.forename: Alexis
authors.initials: A
authors.lastname: Criscuolo
authors.affiliation: Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris-Seine (IBPS), Unité Evolution Paris-Seine (UMR 7138), F-75005 Paris, France.
authors.forename: Stephan
authors.initials: S
authors.lastname: Eberhard
authors.affiliation: Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, 25-28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
authors.forename: Nicole
authors.initials: N
authors.lastname: Desnoues
authors.affiliation: Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris-Seine (IBPS), Unité Evolution Paris-Seine (UMR 7138), F-75005 Paris, France.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Collin
authors.affiliation: Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.
authors.forename: Hongliang
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA forterre@pasteur.fr.
authors.forename: Yves
authors.initials: Y
authors.lastname: Pommier
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ.Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, 25-28, rue du Docteur Roux, 75724 Paris Cedex 15, France forterre@pasteur.fr.
authors.forename: Patrick
authors.initials: P
authors.lastname: Forterre
authors.affiliation: Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris-Seine (IBPS), Unité Evolution Paris-Seine (UMR 7138), F-75005 Paris, France forterre@pasteur.fr.
authors.forename: Guennadi
authors.initials: G
authors.lastname: Sezonov
mesh_terms: D000595:Amino Acid Sequence; D001105:Archaea / Q000737:chemistry* / Q000145:classification / Q000201:enzymology; D019843:Archaeal Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D002166:Camptothecin / Q000737:chemistry; D003001:Cloning, Molecular; D003374:Coumarins / Q000737:chemistry; D004264:DNA Topoisomerases, Type I / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004278:DNA, Superhelical / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D006576:Heterocyclic Compounds, 4 or More Rings / Q000737:chemistry; D006358:Hot Temperature; D006801:Humans; D007546:Isoquinolines / Q000737:chemistry; D024101:Mitochondrial Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D055550:Protein Stability; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D059004:Topoisomerase I Inhibitors / Q000737:chemistry
chemical_list: D019843:Archaeal Proteins; D003374:Coumarins; D004278:DNA, Superhelical; D006576:Heterocyclic Compounds, 4 or More Rings; D007546:Isoquinolines; D024101:Mitochondrial Proteins; D011994:Recombinant Proteins; D059004:Topoisomerase I Inhibitors; C455554:lamellarin D; D004264:DNA Topoisomerases, Type I; C528909:TOP1 protein, human; D002166:Camptothecin