title: ComEA is essential for the transfer of external DNA into the periplasm in naturally transformable Vibrio cholerae cells.
abstract: The DNA uptake of naturally competent bacteria has been attributed to the action of DNA uptake machineries resembling type IV pilus complexes. However, the protein(s) for pulling the DNA across the outer membrane of Gram-negative bacteria remain speculative. Here we show that the competence protein ComEA binds incoming DNA in the periplasm of naturally competent Vibrio cholerae cells thereby promoting DNA uptake, possibly through ratcheting and entropic forces associated with ComEA binding. Using comparative modeling and molecular simulations, we projected the 3D structure and DNA-binding site of ComEA. These in silico predictions, combined with in vivo and in vitro validations of wild-type and site-directed modified variants of ComEA, suggested that ComEA is not solely a DNA receptor protein but plays a direct role in the DNA uptake process. Furthermore, we uncovered that ComEA homologs of other bacteria (both Gram-positive and Gram-negative) efficiently compensated for the absence of ComEA in V. cholerae, suggesting that the contribution of ComEA in the DNA uptake process might be conserved among naturally competent bacteria.
authors.affiliation: Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
authors.forename: Patrick
authors.initials: P
authors.lastname: Seitz
authors.affiliation: Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland ; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
authors.forename: Hassan
authors.initials: H
authors.lastname: Pezeshgi Modarres
authors.affiliation: Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Borgeaud
authors.affiliation: Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
authors.forename: Roman D
authors.initials: RD
authors.lastname: Bulushev
authors.affiliation: Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
authors.forename: Lorenz J
authors.initials: LJ
authors.lastname: Steinbock
authors.affiliation: Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Radenovic
authors.affiliation: Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland ; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
authors.forename: Matteo
authors.initials: M
authors.lastname: Dal Peraro
authors.affiliation: Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
authors.forename: Melanie
authors.initials: M
authors.lastname: Blokesch
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics*; D019897:Periplasm / Q000235:genetics / Q000378:metabolism; D014169:Transformation, Bacterial / Q000235:genetics*; D014734:Vibrio cholerae / Q000235:genetics / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D004247:DNA