title: Experimental verification of the secondary structures of guide RNA-pre-mRNA chimaeric molecules in Trypanosoma brucei.
abstract: RNA editing in kinetoplastid organisms is an RNA-processing reaction that adds and deletes U nucleotides at specific sites in mitochondrial pre-mRNAs. The edited sequence is specified by guide RNAs and the processing presumably occurs within a high-molecular-mass ribonucleoprotein complex containing several enzymatic activities. Although the mechanism is not currently known, potential intermediates or by-products of the editing process are chimaeric RNAs where guide (g) RNAs are covalently attached, via their non-encoded U-tail, to their cognate pre-mRNAs. We determined the secondary structures of three different ATPase 6 chimaeras of Trypanosoma brucei using a set of structure-sensitive chemical and enzymatic probes. The experiments revealed a bipartite domain structure consisting of a gRNA/pre-mRNA interaction hairpin and an independently folding mRNA stem/loop in all three RNAs. The connecting U-tail was a determinant for the length of the interaction stems with the oligo(U) nucleotides base pairing to internal gRNA sequences. The probed structures have calculated delta G27o values of -92 kJ/ mol to -134 kJ/mol, somewhat less stable than the predicted minimal free energy structures and support previously proposed models for the interaction between gRNAs and pre-mRNAs. Optical melting studies indicated additional, higher order structural features for all three molecules with four defined melting transition between 10 degrees C and 90 degrees C. A comparison of CD spectra in the absence and presence of mitochondrial protein extracts demonstrated no gross structural changes of the RNA structures induced by the association with polypeptides.
authors.affiliation: Laboratorium für molekulare Biologie - Genzentrum, Universität München am Max-Planck-Institut für Biochemie, Martinsried, Germany.
authors.forename: B
authors.initials: B
authors.lastname: Schmid
authors.forename: L K
authors.initials: LK
authors.lastname: Read
authors.forename: K
authors.initials: K
authors.lastname: Stuart
authors.forename: H U
authors.initials: HU
authors.lastname: Göringer
mesh_terms: D000251:Adenosine Triphosphatases / Q000235:genetics; D000818:Animals; D001483:Base Sequence; D002678:Chimera / Q000235:genetics; D002942:Circular Dichroism; D017931:DNA Primers / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D017393:RNA Editing; D012322:RNA Precursors / Q000737:chemistry* / Q000235:genetics; D017394:RNA, Guide, Kinetoplastida / Q000737:chemistry* / Q000235:genetics; D016053:RNA, Protozoan / Q000737:chemistry* / Q000235:genetics; D013816:Thermodynamics; D014346:Trypanosoma brucei brucei / Q000737:chemistry* / Q000235:genetics
chemical_list: D017931:DNA Primers; D012322:RNA Precursors; D016053:RNA, Protozoan; D000251:Adenosine Triphosphatases; D017394:RNA, Guide, Kinetoplastida