title: Unmasking the ancestral activity of integron integrases reveals a smooth evolutionary transition during functional innovation.
abstract: Tyrosine (Y)-recombinases have evolved to deliver mechanistically different reactions on a variety of substrates, but these evolutionary transitions are poorly understood. Among them, integron integrases are hybrid systems recombining single- and double-stranded DNA partners. These reactions are asymmetric and need a replicative resolution pathway, an exception to the canonical second strand exchange model of Y-recombinases. Integron integrases possess a specific domain for this specialized pathway. Here we show that despite this, integrases are still capable of efficiently operating the ancestral second strand exchange in symmetrical reactions between double-stranded substrates. During these reactions, both strands are reactive and Holliday junction resolution can follow either pathway. A novel deep-sequencing approach allows mapping of the crossover point for the second strand exchange. The persistence of the ancestral activity in integrases illustrates their robustness and shows that innovation towards new recombination substrates and resolution pathways was a smooth evolutionary process.
authors.affiliation: Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, 28 Rue du Dr Roux, 75015 Paris, France.|CNRS, UMR3525, 28 Rue du Dr Roux, 75015 Paris, France.
authors.forename: Jose Antonio
authors.identifier: http://orcid.org/0000-0001-8552-2956
authors.initials: JA
authors.lastname: Escudero
authors.affiliation: Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, 28 Rue du Dr Roux, 75015 Paris, France.|CNRS, UMR3525, 28 Rue du Dr Roux, 75015 Paris, France.
authors.forename: Celine
authors.initials: C
authors.lastname: Loot
authors.affiliation: Laboratoire de Microbiologie Fondamentale et Pathogénicité UMR-CNRS 5234. Bat 3A 3ème étage, 146 rue Léo Saignat, 33076 Bordeaux, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Parissi
authors.affiliation: Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, 28 Rue du Dr Roux, 75015 Paris, France.|CNRS, UMR3525, 28 Rue du Dr Roux, 75015 Paris, France.|Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France.
authors.forename: Aleksandra
authors.identifier: http://orcid.org/0000-0002-1802-3724
authors.initials: A
authors.lastname: Nivina
authors.affiliation: Institut Pasteur, Genomic Platform, 28 Rue du Dr Roux, 75015 Paris, France.
authors.forename: Christiane
authors.initials: C
authors.lastname: Bouchier
authors.affiliation: Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, 28 Rue du Dr Roux, 75015 Paris, France.|CNRS, UMR3525, 28 Rue du Dr Roux, 75015 Paris, France.
authors.forename: Didier
authors.initials: D
authors.lastname: Mazel
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D010582:Bacteriophage lambda / Q000235:genetics*; D003198:Computer Simulation; D004247:DNA / Q000378:metabolism*; D045566:DNA, Cruciform; D004277:DNA, Single-Stranded / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics*; D019143:Evolution, Molecular; D066298:In Vitro Techniques; D019426:Integrases / Q000235:genetics*; D032023:Integrons / Q000235:genetics*; D009690:Nucleic Acid Conformation; D017434:Protein Structure, Tertiary; D014734:Vibrio cholerae / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D045566:DNA, Cruciform; D004277:DNA, Single-Stranded; D029968:Escherichia coli Proteins; D004247:DNA; D019426:Integrases