Structural heterogeneity of attC integron recombination sites revealed by optical tweezers

Autor: Mukhortava, Ann, Pöge, Matthias, Grieb, Maj Svea, Nivina, Aleksandra, Loot, Céline, Mazel, Didier, Schlierf, Michael
Přispěvatelé: B CUBE - Center for Molecular Bioengineering [TU Dresden, Germany], Center for Molecular and Cellular Bioengineering [TU Dresden, Germany] (CMCB), Technische Universität Dresden = Dresden University of Technology (TU Dresden)-Technische Universität Dresden = Dresden University of Technology (TU Dresden), Université Paris Descartes - Paris 5 (UPD5), Plasticité du Génome Bactérien - Bacterial Genome Plasticity (PGB), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), German Federal ministry of Education and Research [BMBF 03Z2EN11 to M.S.], Franco-German PROCOPE program of the German Academic exchange service [DAAD 55931827 to M.S.], French Ministry of Foreign Affairs [PHC N° 28351PC to D.M.], Institut Pasteur, the Centre National de la Recherche Scientifique, the Fondation pour la Recherche Médicale [FDT20150532465 to A.N.], Doctoral School ‘Frontières du Vivant’ funded by the University Paris Descartes. Funding for open access charge: SLUB/TU Dresden., We thank all members of the Schlierf and Mazel group for discussions., Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Technische Universität Dresden (TUD)-Technische Universität Dresden (TUD), Plasticité du Génome Bactérien
Rok vydání: 2018
Předmět:
Zdroj: Nucleic Acids Research
Nucleic Acids Research, Oxford University Press, 2019, 47 (4), pp.1861-1870. ⟨10.1093/nar/gky1258⟩
NUCLEIC ACIDS RESEARCH
Nucleic Acids Research, 2019, 47 (4), pp.1861-1870. ⟨10.1093/nar/gky1258⟩
ISSN: 1362-4962
0305-1048
DOI: 10.1093/nar/gky1258⟩
Popis: A predominant tool for adaptation in Gram-negative bacteria is the functional genetic platform called integron. Integrons capture and rearrange promoterless gene cassettes in a unique recombination process involving the recognition of folded single-stranded DNA hairpins—so-called attC sites—with a strong preference for the attC bottom strand. While structural elements have been identified to promote this preference, their mechanistic action remains incomplete. Here, we used high-resolution single-molecule optical tweezers (OT) to characterize secondary structures formed by the attC bottom (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${{att}}{{{C}}_{{\rm{bs}}}}$\end{document}) and top (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${{att}}{{{C}}_{{\rm{ts}}}}$\end{document}) strands of the paradigmatic attCaadA7 site. We found for both sequences two structures—a straight, canonical hairpin and a kinked hairpin. Remarkably, the recombination-preferred \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${{att}}{{{C}}_{{\rm{bs}}}}$\end{document} predominantly formed the straight hairpin, while the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${{att}}{{{C}}_{{\rm{ts}}}}$\end{document} preferentially adopted the kinked structure, which exposes only one complete recombinase binding box. By a mutational analysis, we identified three bases in the unpaired central spacer, which could invert the preferred conformations and increase the recombination frequency of the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${{att}}{{{C}}_{{\rm{ts}}}}$\end{document}in vivo. A bioinformatics screen revealed structural bias toward a straight, canonical hairpin conformation in the bottom strand of many antibiotic resistance cassettes attC sites. Thus, we anticipate that structural fine tuning could be a mechanism in many biologically active DNA hairpins.
Databáze: OpenAIRE
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