title: DNA topoisomerase VIII: a novel subfamily of type IIB topoisomerases encoded by free or integrated plasmids in Archaea and Bacteria.
abstract: Type II DNA topoisomerases are divided into two families, IIA and IIB. Types IIA and IIB enzymes share homologous B subunits encompassing the ATP-binding site, but have non-homologous A subunits catalyzing DNA cleavage. Type IIA topoisomerases are ubiquitous in Bacteria and Eukarya, whereas members of the IIB family are mostly present in Archaea and plants. Here, we report the detection of genes encoding type IIB enzymes in which the A and B subunits are fused into a single polypeptide. These proteins are encoded in several bacterial genomes, two bacterial plasmids and one archaeal plasmid. They form a monophyletic group that is very divergent from archaeal and eukaryotic type IIB enzymes (DNA topoisomerase VI). We propose to classify them into a new subfamily, denoted DNA topoisomerase VIII. Bacterial genes encoding a topoisomerase VIII are present within integrated mobile elements, most likely derived from conjugative plasmids. Purified topoisomerase VIII encoded by the plasmid pPPM1a from Paenibacillus polymyxa M1 had ATP-dependent relaxation and decatenation activities. In contrast, the enzyme encoded by mobile elements integrated into the genome of Ammonifex degensii exhibited DNA cleavage activity producing a full-length linear plasmid and that from Microscilla marina exhibited ATP-independent relaxation activity. Topoisomerases VIII, the smallest known type IIB enzymes, could be new promising models for structural and mechanistic studies.
authors.affiliation: Université Paris-Sud, CNRS UMR8621, Institut de Génétique Microbiologie, 91405 Orsay Cedex, France.
authors.forename: Danièle
authors.initials: D
authors.lastname: Gadelle
authors.affiliation: Institut Pasteur, Unité de Biologie moléculaire du gène chez les extrêmophiles, Département de Microbiologie, F-75015 Paris, France.
authors.forename: Mart
authors.initials: M
authors.lastname: Krupovic
authors.affiliation: Institut Pasteur, Unité de Biologie moléculaire du gène chez les extrêmophiles, Département de Microbiologie, F-75015 Paris, France.
authors.forename: Kasie
authors.initials: K
authors.lastname: Raymann
authors.affiliation: Institut Pasteur, Unité de Microbiologie structurale, Département de Biologie structurale et Chimie, F-75015 Paris, France CNRS, UMR3528, F-75015 Paris, France Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, rue du Dr Roux 75015 Paris, France.
authors.forename: Claudine
authors.initials: C
authors.lastname: Mayer
authors.affiliation: Université Paris-Sud, CNRS UMR8621, Institut de Génétique Microbiologie, 91405 Orsay Cedex, France Institut Pasteur, Unité de Biologie moléculaire du gène chez les extrêmophiles, Département de Microbiologie, F-75015 Paris, France patrick.forterre@pasteur.fr.
authors.forename: Patrick
authors.initials: P
authors.lastname: Forterre
mesh_terms: D000595:Amino Acid Sequence; D001105:Archaea / Q000201:enzymology* / Q000235:genetics; D019843:Archaeal Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics / Q000378:metabolism; D001419:Bacteria / Q000201:enzymology*; D001426:Bacterial Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics / Q000378:metabolism; D017124:Conserved Sequence; D026942:DNA Topoisomerases / Q000737:chemistry / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D016680:Genome, Bacterial; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D026942:DNA Topoisomerases