title: Unique and Universal Features of Epsilonproteobacterial Origins of Chromosome Replication and DnaA-DnaA Box Interactions.
abstract: In bacteria, chromosome replication is initiated by the interaction of the initiator protein DnaA with a defined region of a chromosome at which DNA replication starts (oriC). While DnaA proteins share significant homology regardless of phylogeny,oriCregions exhibit more variable structures. The general architecture oforiCs is universal, i.e., they are composed of a cluster of DnaA binding sites, a DNA-unwinding element, and sequences that bind regulatory proteins. However, detailed structures oforiCs are shared by related species while being significantly different in unrelated bacteria. In this work, we characterized EpsilonproteobacterialoriCregions.Helicobacter pyloriwas the only species of the class for whichoriCwas characterized. A few unique features were found such as bipartiteoriCstructure, not encountered in any other Gram-negative species, and topology-sensitive DnaA-DNA interactions, which have not been found in any other bacterium. These unusualH. pylori oriCfeatures raised questions of whetheroriCstructure and DnaA-DNA interactions are unique to this bacterium or whether they are common to related species. Byin silicoandin vitroanalyses we identified putativeoriCs in three Epsilonproteobacterial species: pathogenicArcobacter butzleri, symbioticWolinella succinogenes, and free-livingSulfurimonas denitrificans. We propose thatoriCs typically co-localize withruvC-dnaA-dnaNin Epsilonproteobacteria, with the exception of Helicobacteriaceae species. The clusters of DnaA boxes localize upstream (oriC1) and downstream (oriC2) ofdnaA, and they likely constitute bipartite origins. In all cases, DNA unwinding was shown to occur inoriC2. Unlike the DnaA box pattern, which is not conserved in EpsilonproteobacterialoriCs, the consensus DnaA box sequences and the mode of DnaA-DnaA box interactions are common to the class. We propose that the typical Epsilonproteobacterial DnaA box consists of the core nucleotide sequence 5'-TTCAC-3' (4-8 nt), which, together with the significant changes in the DNA-binding motif of corresponding DnaAs, determines the unique molecular mechanism of DnaA-DNA interaction. Our results will facilitate identification oforiCs and subsequent identification of factors which regulate chromosome replication in other Epsilonproteobacteria. Since replication is controlled at the initiation step, it will help to better characterize life cycles of these species, many of which are considered as emerging pathogens.
authors.affiliation: Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wrocław, Poland.
authors.forename: Pawel
authors.initials: P
authors.lastname: Jaworski
authors.affiliation: Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wrocław, Poland.
authors.forename: Rafal
authors.initials: R
authors.lastname: Donczew
authors.affiliation: Max Planck Institute for Molecular Genetics Berlin, Germany.
authors.forename: Thorsten
authors.initials: T
authors.lastname: Mielke
authors.affiliation: Laboratory of Biopolymers Structure, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk Gdańsk, Poland.
authors.forename: Marcel
authors.initials: M
authors.lastname: Thiel
authors.affiliation: Laboratory of Biopolymers Structure, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk Gdańsk, Poland.
authors.forename: Stanislaw
authors.initials: S
authors.lastname: Oldziej
authors.affiliation: Department of Life Science Engineering, Fachbereich 2, HTW Berlin Berlin, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Weigel
authors.affiliation: Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wrocław, Poland.
authors.forename: Anna
authors.initials: A
authors.lastname: Zawilak-Pawlik
keywords: DnaA; DnaA box; Epsilonproteobacteria; initiation of chromosome replication; oriC; orisome