title: Evidence for U-tail stabilization of gRNA/mRNA interactions in kinetoplastid RNA editing.
abstract: The most dramatic example of RNA editing is found in the mitochondria of trypanosomes. In these organisms, U-insertions/deletions can create mRNAs that are twice as large as the gene that encodes them. Guide RNAs (gRNAs) that are complementary to short stretches of the mature message direct the precise placements of the U residues. The binding of gRNA to mRNA is a fundamental step in RNA editing and understanding the relative importance of the elements that confer affinity and specificity on this interaction is critical to our understanding of the editing process. In this study, we have analyzed the relative binding affinities of two different gRNA/mRNA pairs. The affinity of gA6-14 for its message (ATPase 6) is high, with an apparent K(D) in the 5-10 nM range. In contrast, gCYb-558 has a low affinity for its cognate mRNA. Deletion of the gRNA U-tail caused a significant reduction in the binding affinity for only the gCYb-558 pair, and was observed only under physiological magnesium conditions. These results indicate that the U-tail contribution can differ substantially between the different gRNA/mRNA pairs. In addition, our results suggest that the efficiency of gRNA/mRNA interaction is highly dependent on thermodynamic parameters determined by the local sequences and their adopted structures surrounding the anchor-binding site.
authors.affiliation: Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA. koslowsk@msu.edu
authors.forename: Donna J
authors.initials: DJ
authors.lastname: Koslowsky
authors.forename: Larissa
authors.initials: L
authors.lastname: Reifur
authors.forename: Laura E
authors.initials: LE
authors.lastname: Yu
authors.forename: Weiqin
authors.initials: W
authors.lastname: Chen
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry; D007700:Kinetics; D016830:Kinetoplastida / Q000378:metabolism*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D017393:RNA Editing; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid; D013816:Thermodynamics; D014346:Trypanosoma brucei brucei / Q000378:metabolism; D014764:Viral Proteins / Q000737:chemistry
chemical_list: D009841:Oligonucleotides; D012333:RNA, Messenger; D014764:Viral Proteins; D012313:RNA; C062210:bacteriophage T7 RNA polymerase; D012321:DNA-Directed RNA Polymerases