title: A stepwise 2'-hydroxyl activation mechanism for the bacterial transcription termination factor Rho helicase.
abstract: The bacterial Rho factor is a ring-shaped ATP-dependent helicase that tracks along RNA transcripts and disrupts RNA-DNA duplexes and transcription complexes in its path. Using combinatorial nucleotide analog interference mapping (NAIM), we explore the topology and dynamics of functional Rho-RNA complexes and reveal the RNA-dependent stepping mechanism of Rho helicase. Periodic Gaussian distributions of NAIM signals show that Rho forms uneven productive interactions with the track nucleotides and disrupts RNA-DNA duplexes in a succession of large ( approximately 7-nucleotide-long) discrete steps triggered by 2'-hydroxyl activation events. This periodic 2'-OH-dependent activation does not depend on the RNA-DNA pairing energy but is finely tuned by sequence-dependent interactions with the RNA track. These features explain the strict RNA specificity and contextual efficiency of the enzyme and provide a new paradigm for conditional tracking by a helicase ring.
authors.affiliation: Centre Nationale de la Recherche Scientifique (CNRS) UPR4301, Centre de Biophysique Moléculaire, Orléans, France.
authors.forename: Annie
authors.initials: A
authors.lastname: Schwartz
authors.forename: Makhlouf
authors.initials: M
authors.lastname: Rabhi
authors.forename: Frédérique
authors.initials: F
authors.lastname: Jacquinot
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Margeat
authors.forename: A Rachid
authors.initials: AR
authors.lastname: Rahmouni
authors.forename: Marc
authors.initials: M
authors.lastname: Boudvillain
mesh_terms: D001483:Base Sequence; D004269:DNA, Bacterial / Q000378:metabolism*; D008954:Models, Biological; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D011485:Protein Binding; D020365:RNA Helicases / Q000235:genetics / Q000378:metabolism*; D012329:RNA, Bacterial / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism*; D012234:Rho Factor / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic / Q000502:physiology*
chemical_list: D004269:DNA, Bacterial; D012329:RNA, Bacterial; D012333:RNA, Messenger; D012234:Rho Factor; D020365:RNA Helicases