Table 2.
The five structural groups of mt-tRNAs. The classification is based on the analysis of tRNA sequences deduced from gene sequences and comparison with cytosolic tRNA sequences, in particular for the content of conserved and semi-conserved nucleotides. * The structural distinction within mt-tRNAs in alveolates and amoebas is not well known since sequence data from these phyla are scarce (e.g., few data on Paramecia, Plasmodia, Tetrahymena, Acanthamoeba species); ** Canonical loops: D-loops with G18G19 and size of 8 to 9 nts; T-loops with U54U55C56 (except in initiator tRNAs) and conserved size of 7 nts; *** Atypical loops of variable size: D-loops of 5–9 nts and T-loops of 6–7 nts (due to partial or total non-conservation of G18, G19, U55 and C56 that govern the D/T-loop interaction); **** D-stem can be restricted to 3 bp in some species. VR for Variable region, including putative helical domains in some mt-tRNALeu, tRNASer and tRNATyr species. In Group 5, the size of the acceptor and anticodon helices deviate from the canonical organization (see Figure 4). Abbreviated names of eukaryal organisms: Ath, Arabidopsis thaliana; Asu, Ascaris suum; Cel, Caenorhabditis elegans; Dno, Dasypusnovemcincus; Dya, Drosophila yakuba; Hsa, Homo sapiens; Mpo, Marchantia polymorpha; Pca, Pichia canadensis; Pvi, Phoca vitulina; Pvu, Phaseolus vulgaris; Sce, Saccharomyces cerevisiae; Rcu, Romanomermis culicivorax; Wha, Walchia hayashii.
| tRNA Groups | Group 1 | Group 2 | Group 3 | Group 4 | Group 5 |
|---|---|---|---|---|---|
| Eukaryote groups | Alveolates & Amoebas * Fungi Plants | Alveolates & Amoebas * some Fungi & Plants Metazoans | Metazoans (e.g., nematodes, arachnids & some bryozoan species) | Metazoans (some insect & bryozoan species & mammals) | Metazoans (acaria & some nematodes) |
| Representative tRNAs |
Ath mt-Asp Sce mt-Glu Pca mt-LeuUAA Pvu mt-Phe |
Mpo mt-Ala Hsa mt-Asp Pca mt-Cys Hsa mt-Phe |
Asu mt-Ala Asu mt-Asn Cel mt-Asp Asu mt-Thr |
Dno mt-Cys Bta mt-SerGCU Dya mt-SerGCU Pvi mt-SerGCU |
Wha mt-Ala Rcu mt-Arg Rcu mt-Ile Rcu mt-Thr |
| Acceptor arm | canonical (stem: 7 bp) |
canonical (stem: 7 bp) |
quasi-canonical (stem: 4–7 bp) |
canonical (stem: 7 bp) |
atypical (stem: 4–5 bp) |
| Anticodon arm | canonical (stem: 5 bp & loop: 7 nts) |
canonical (stem: 5 bp & loop: 7 nts) |
canonical (stem: 5 bp & loop: 7 nts) |
canonical (stem: 5 bp & loop: 7 nts) |
atypical (stem: 5–9 bp) |
| D- and T-arms | canonical ** | atypical *** | atypical T-armless (atypical D-loops of 5–7 nts) |
Atypical D-armless (atypical T-loops of 6–7 nts) |
– D-/T-armless |
| T-arm | stem: 5 bp loop: 7 nts |
stem: 4–5 bp loop: 6–7 nts |
– | stem: 4–5 bp | – |
| D-arm | stem: 4 bp loop: 8–9 nts |
stem: 4 bp **** | stem: 4 bp | – | – |
| L1 connector (size & characteristics) |
19–20 nts (with D-arm) |
16–20 nts (with D-arm) |
16–18 nts (with D-arm) |
5–12 nts | 3–11 nts |
| L2 connector (size & characteristics) |
21–30 nts (with VR & T-arm) |
19–22 nts (with VR & T-arm) |
6–7 nts | 20–21 nts | 5–14 nts |
| core organization in stacked base layers | 7 layers (canonical) | 7 layers (quasi-canonical) | 7 layers (atypical) | 6 layers (atypical) | 1 layer (atypical) |