A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus

Abstract

We determined the complete mtDNA sequence of the centipede Lithobius forficatus and found that only one of the 22 inferred tRNA genes encodes a fully paired aminoacyl acceptor stem. The other 21 genes encode tRNAs with up to five mismatches in these stems, and some of these overlap extensively with the downstream genes. Because a well-paired acceptor stem is required for proper tRNA functioning, RNA editing in the products of these genes was suspected. We investigated this hypothesis by studying cDNA sequences from eight tRNAs and found the editing of up to 5 nt at their 3 ends. This editing appears to occur by a novel mechanism with the 5 end of the acceptor stem being used as a template for the de novo synthesis of the 3 end, presumably by an RNA-dependent RNA polymerase. In addition, unusual secondary structures for several tRNAs were found, including those lacking a T⌿C (T) or a dihydrouridine (D) arm, and having an unusual number of base pairs in the acceptor or anticodon stems.

Large gene overlaps and tRNA processing in the compact mitochondrial genome of the crustaceanArmadillidium vulgare

“…Two ways to restore base-pairing in the stem are possible. Either the truncated sequence is repaired by a trial and error process involving nucleotides elongation/degradation until the sequence is correct (a tRNA repair process demonstrated in metazoan mitochondria 30 ), or the 5 0 -end of the acceptor stem is used as a template for synthesis of the 3 0 -end by a RNA-dependent RNA polymerase (RdRp) (as suggested in centipede mitochondria 31 ). No tRNA processing intermediates showing mis-incorporated nucleotides were found, thus the action of the second repair process appears to be more likely.…”

The mitochondrial genome of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera)

“…Some tRNAs (most notably tRNA-V, but also tRNA-D, tRNA-M, tRNA-E, tRNA-S(gcu) and the three tRNA-H) have some unusual basepairings in their arms. Substantial post-transcriptional RNA editing has been shown to occur in some metazoan mitochondrial tRNAs, especially when mismatches fall in regions where the tRNA genes overlap with adjacent down-stream genes (Lonergan and Gray, 1993;Lavrov et al, 2000;Masta and Boore 2004), and so could potentially occur here to create a more conforming structure. The presence of unusual TΨC and DHU arms for mitochondrial tRNAs has been observed in some other arthropodan taxa (Masta, 2000;Ogoh and Ohmiya, 2004).…”

Modification of the universally unmodified uridine-33 in a mitochondria-imported edited tRNA and the role of the anticodon arm structure on editing efficiency

“…Nucleoside modifications are a universal feature of tRNAs, necessary for fine-tuning the tRNA structure for translational efficiency and in a few cases modifications even change the tRNA amino acid specificity (Muramatsu et al+, 1988a(Muramatsu et al+, , 1988bWeber et al+, 1990)+ Although in various organisms specific modifications at certain positions in a particular tRNA show phylogenetic conservation, only a few positions and/or modifications are highly conserved (Auffinger & Westhof, 1998)+ These include the 39 CCA, pseudouridine (⌿) at position 55, and the unmodified pyrimidine at position 33 (uridine in 97% of the cases; Sprinzl et al+, 1998a)+ Unlike RNA modification, editing of tRNAs has been observed in several eukaryotes ranging from protists to metazoans (Lonergan & Gray, 1993;Yokobori & Pääbo, 1995Marechal-Drouard et al+, 1996;Antes et al+, 1998;Price & Gray, 1999;Lavrov et al+, 2000)+ RNA editing typically restores base pairing at various positions in the tRNA molecule, regenerating conserved structural motifs important for tRNA processing and function+ In cases where tRNA editing alters the anticodon sequence, enzymatic deamination of adenosine to inosine is the common mechanism and it helps expand the base-pairing ability of the tRNA codonanticodon interaction (Auxilien et al+, 1996;Gerber & Keller, 1999)+ Two instances of cytidine (C)-to-uridine (U) alterations of the anticodon sequences of tRNAs have also been reported+ In marsupials, a single C-to-U editing event in the second position of the anticodon changes the decoding properties of a mitochondriaencoded tRNA Asp (Janke & Pääbo, 1993), and in Leishmania tarentolae, the single nucleus-encoded tRNA Trp is imported into the mitochondrion and undergoes C-to-U editing at the wobble position, thereby allowing decoding of UGA codons as tryptophan (Alfonzo et al+, 1999)+ In many organisms, a set of nucleus-encoded tRNAs is imported into the mitochondria (Schneider & Marechal-Drouard, 2000)+ The number of imported tRNAs varies from a single tRNA in yeast (Kolesnikova et al+, 2000) to all mitochondrial tRNAs in trypanosomatids (Simpson et al+, 1989;Hancock & Hajduk, 1990)+ Little is known about the extent, nature, or function of nucleotide modifications of such imported tRNAs+ Modification of U33 in mitochondrial (mt) tRNA Tyr and C32 in mt tRNA Lys and tRNA Leu in Trypanosoma brucei has been reported, but the nature of these modifications was not established …”