title: The pathway for DNA recognition and RNA integration by a group II intron retrotransposon.
abstract: Group II intron RNPs are mobile genetic elements that attack and invade duplex DNA. In this work, we monitor the invasion reaction in vitro and establish a quantitative kinetic framework for the steps of this complex cascade. We find that target site specificity is achieved after DNA binding, which occurs nonspecifically. RNP searches the bound DNA before undergoing a conformational change that is associated with identification of its specific binding site. The study reveals a facile equilibrium between intron invasion and splicing, indicating that RNP invasion of top strand DNA is a relatively unfavorable event. Group II mobility must therefore depend on the trapping of invasion products, potentially through interaction of the intron-encoded protein with the DNA target and/or initiation of reverse transcription.
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
authors.forename: Yasunori
authors.initials: Y
authors.lastname: Aizawa
authors.forename: Qing
authors.initials: Q
authors.lastname: Xiang
authors.forename: Alan M
authors.initials: AM
authors.lastname: Lambowitz
authors.forename: Anna Marie
authors.initials: AM
authors.lastname: Pyle
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000378:metabolism* / Q000494:pharmacology; D004305:Dose-Response Relationship, Drug; D007438:Introns; D007700:Kinetics; D008954:Models, Biological; D008969:Molecular Sequence Data; D009841:Oligonucleotides / Q000494:pharmacology; D012313:RNA / Q000378:metabolism*; D012194:RNA-Directed DNA Polymerase; D018626:Retroelements; D013997:Time Factors
chemical_list: D001426:Bacterial Proteins; D009841:Oligonucleotides; D018626:Retroelements; D012313:RNA; D004247:DNA; C099785:LtrA protein, Lactococcus lactis; D012194:RNA-Directed DNA Polymerase