title: Tertiary network in mammalian mitochondrial tRNAAsp revealed by solution probing and phylogeny.
abstract: Primary and secondary structures of mammalian mitochondrial (mt) tRNAs are divergent from canonical tRNA structures due to highly skewed nucleotide content and large size variability of D- and T-loops. The nonconservation of nucleotides involved in the expected network of tertiary interactions calls into question the rules governing a functional L-shaped three-dimensional (3D) structure. Here, we report the solution structure of human mt-tRNA(Asp) in its native post-transcriptionally modified form and as an in vitro transcript. Probing performed with nuclease S1, ribonuclease V1, dimethylsulfate, diethylpyrocarbonate and lead, revealed several secondary structures for the in vitro transcribed mt-tRNA(Asp) including predominantly the cloverleaf. On the contrary, the native tRNA(Asp) folds into a single cloverleaf structure, highlighting the contribution of the four newly identified post-transcriptional modifications to correct folding. Reactivities of nucleotides and phosphodiester bonds in the native tRNA favor existence of a full set of six classical tertiary interactions between the D-domain and the variable region, forming the core of the 3D structure. Reactivities of D- and T-loop nucleotides support an absence of interactions between these domains. According to multiple sequence alignments and search for conservation of Leontis-Westhof interactions, the tertiary network core building rules apply to all tRNA(Asp) from mammalian mitochondria.
authors.affiliation: Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC 15 rue René Descartes, 67084 Strasbourg, France.
authors.forename: Marie
authors.initials: M
authors.lastname: Messmer
authors.forename: Joern
authors.initials: J
authors.lastname: Pütz
authors.forename: Takeo
authors.initials: T
authors.lastname: Suzuki
authors.forename: Tsutomu
authors.initials: T
authors.lastname: Suzuki
authors.forename: Claude
authors.initials: C
authors.lastname: Sauter
authors.forename: Marie
authors.initials: M
authors.lastname: Sissler
authors.forename: Florentz
authors.initials: F
authors.lastname: Catherine
mesh_terms: D001483:Base Sequence; D030561:Databases, Nucleic Acid; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012313:RNA / Q000737:chemistry* / Q000378:metabolism*; D000077278:RNA, Mitochondrial; D012349:RNA, Transfer, Asp / Q000737:chemistry* / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D000077278:RNA, Mitochondrial; D012349:RNA, Transfer, Asp; D012313:RNA