A stepwise 2'-hydroxyl activation mechanism for the bacterial transcription termination factor Rho helicase.
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.
Schwartz
Annie
A
Centre Nationale de la Recherche Scientifique (CNRS) UPR4301, Centre de Biophysique Moléculaire, Orléans, France.
Rabhi
Makhlouf
M
Jacquinot
Frédérique
F
Margeat
Emmanuel
E
Rahmouni
A Rachid
AR
Boudvillain
Marc
M
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*
D004269:DNA, Bacterial; D012329:RNA, Bacterial; D012333:RNA, Messenger; D012234:Rho Factor; D020365:RNA Helicases