title: Molecular crowding inhibits U-insertion/deletion RNA editing in vitro: consequences for the in vivo reaction.
abstract: Mitochondrial pre-mRNAs in African trypanosomes are edited to generate functional transcripts. The reaction is typified by the insertion and deletion of U nucleotides and is catalyzed by a macromolecular complex, the editosome. Editosomes bind pre-edited mRNA/gRNA pairs and the reaction can be recapitulated in vitro by using pre-mRNA- and gRNA-mimicking oligoribonucleotides together with enriched editosome preparations. Although the in vitro assay has been instrumental in unraveling the basic steps of the editing cycle it is performed at dilute solvent conditions. This ignores the fact that editing takes place inside the highly crowded mitochondria. Here we investigate the effects of molecular crowding on RNA editing. By using neutral, macromolecular cosolutes we generate defined dilute, semidilute and crowded solvent properties and we demonstrate different thermodynamic stabilities of the pre-mRNA/gRNA hybrid RNAs at these conditions. Crowded conditions stabilize the RNAs by -30 kJ/mol. Furthermore, we show that the rate constants for the association and dissociation (kass/kdiss) of substrate RNAs to editosomes decrease, ultimately inhibiting the in vitro reaction. The data demonstrate that the current RNA editing in vitro system is sensitive to molecular crowding, which suggests that the in vivo reaction cannot rely on a diffusion-controlled, collision-based mechanism. Possible non-diffusional reaction pathways are discussed.
authors.affiliation: Department of Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany.
authors.forename: Venkata Subbaraju
authors.initials: VS
authors.lastname: Katari
authors.affiliation: Department of Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany.
authors.forename: Lea
authors.initials: L
authors.lastname: van Esdonk
authors.affiliation: Department of Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany.
authors.forename: H Ulrich
authors.initials: HU
authors.lastname: Göringer
mesh_terms: D001483:Base Sequence; D054643:INDEL Mutation; D007700:Kinetics; D046911:Macromolecular Substances / Q000378:metabolism*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D017393:RNA Editing; D012322:RNA Precursors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D020871:RNA Stability; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D000077278:RNA, Mitochondrial; D016053:RNA, Protozoan / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D013816:Thermodynamics; D014346:Trypanosoma brucei brucei / Q000166:cytology / Q000235:genetics / Q000378:metabolism
chemical_list: D046911:Macromolecular Substances; D012322:RNA Precursors; D012333:RNA, Messenger; D000077278:RNA, Mitochondrial; D016053:RNA, Protozoan; C029305:mitochondrial messenger RNA