Abstract:More than 130 mutations in human mitochondrial tRNA (mt-tRNA) genes have been correlated with a variety of neurodegenerative and neuromuscular disorders. Their molecular impacts are of mosaic type, affecting various stages of tRNA biogenesis, structure, and/or functions in mt-translation. Knowledge of mammalian mt-tRNA structures per se remains scarce however. Primary and secondary structures deviate from classical tRNAs, while rules for three-dimensional (3D) folding are almost unknown. Here, we take advantag… Show more
“…Reactivities of residues within the variable domain and of residue 26 are compatible with the following triples: G10–C25/A45, A13–U12/A46 and A26–A44. The existence of triple 9/12–23 has been previously supported experimentally, combining a structural and functional mutagenic approach ( 33 ). Only interaction between residues 15 and 48 could not be tested (reactivity of residue 15 is poisoned by a systematic degradation of the 15–16 phosphodiester bond and U48 is not sensitive to the probes used herein).…”
Section: Discussionmentioning
confidence: 88%
“…By analogy to classical tRNAs, only four potential tertiary interactions in the core of the 3D structure would be conserved when the full set of available mammalian mitochondria sequences of tRNA Asp are considered (7,32) (Figure 1B). Among them, the existence of the triple interaction A9/A12-U23 has recently been experimentally confirmed while investigating the effects of myopathy-related mutation A7526G (A9G) on structure and aminoacylation properties of mt-tRNA Asp (33). Figure 1.Tertiary interaction networks in tRNAs.…”
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-tRNAAsp 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-tRNAAsp including predominantly the cloverleaf. On the contrary, the native tRNAAsp 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 tRNAAsp from mammalian mitochondria.
“…Reactivities of residues within the variable domain and of residue 26 are compatible with the following triples: G10–C25/A45, A13–U12/A46 and A26–A44. The existence of triple 9/12–23 has been previously supported experimentally, combining a structural and functional mutagenic approach ( 33 ). Only interaction between residues 15 and 48 could not be tested (reactivity of residue 15 is poisoned by a systematic degradation of the 15–16 phosphodiester bond and U48 is not sensitive to the probes used herein).…”
Section: Discussionmentioning
confidence: 88%
“…By analogy to classical tRNAs, only four potential tertiary interactions in the core of the 3D structure would be conserved when the full set of available mammalian mitochondria sequences of tRNA Asp are considered (7,32) (Figure 1B). Among them, the existence of the triple interaction A9/A12-U23 has recently been experimentally confirmed while investigating the effects of myopathy-related mutation A7526G (A9G) on structure and aminoacylation properties of mt-tRNA Asp (33). Figure 1.Tertiary interaction networks in tRNAs.…”
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-tRNAAsp 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-tRNAAsp including predominantly the cloverleaf. On the contrary, the native tRNAAsp 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 tRNAAsp from mammalian mitochondria.
“…It is suggested that the natural occurring modification m 1 A9, m 2 G10 and Ψ27 are important for correct folding. Queuosine at position 34 in the anticodon loop does likely not contribute to the secondary structure [ 55 ]. ( A , B ) adapted with permission from Motorin and Helm [ 40 ].…”
Transfer RNAs (tRNAs) are central players in translation, functioning as adapter molecules between the informational level of nucleic acids and the functional level of proteins. They show a highly conserved secondary and tertiary structure and the highest density of post-transcriptional modifications among all RNAs. These modifications concentrate in two hotspots—the anticodon loop and the tRNA core region, where the D- and T-loop interact with each other, stabilizing the overall structure of the molecule. These modifications can cause large rearrangements as well as local fine-tuning in the 3D structure of a tRNA. The highly conserved tRNA shape is crucial for the interaction with a variety of proteins and other RNA molecules, but also needs a certain flexibility for a correct interplay. In this context, it was shown that tRNA modifications are important for temperature adaptation in thermophilic as well as psychrophilic organisms, as they modulate rigidity and flexibility of the transcripts, respectively. Here, we give an overview on the impact of modifications on tRNA structure and their importance in thermal adaptation.
“…For the latter, a noncloverleaf conformation with a strong resemblance to the aforementioned extended hairpin of tRNA Lys has been proposed (Figure B). Aminoacylation studies in vitro show that transcripts of animal mitochondrial tRNAs are altogether worse substrates than transcripts of canonical tRNAs in the cytosol ,,− . These findings imply that such plasticity is a common characteristic of animal mitochondrial tRNAs and that despite a general conservation of the base pairing in stem regions , , the minimal structural characteristics of the cloverleaf may frequently be reached only after certain modification steps.…”
Section: Nanoscale Rearrangements Of Trna As An Effect Of Nucleotide ...mentioning
Post-transcriptional ribonucleotide modification is a phenomenon best studied in tRNA, where it occurs most frequently and in great chemical diversity. This paper reviews the intrinsic network of modifications in the structural core of the tRNA, which governs structural flexibility and rigidity to fine-tune the molecule to peak performance and to regulate its steady-state level. Structural effects of RNA modifications range from nanometer-scale rearrangements to subtle restrictions of conformational space on the angstrom scale. Structural stabilization resulting from nucleotide modification results in increased thermal stability and translates into protection against unspecific degradation by bases and nucleases. Several mechanisms of specific degradation of hypomodified tRNA, which were only recently discovered, provide a link between structural and metabolic stability.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
