Table 2. List of confirmed and predicted genes responsible for post-transcriptional modifications in mammalian mt tRNAs.
| Position a | tRNA species | Modification b | Confirmed gene(s) in human or mammals | Predicted gene(s) in human |
|---|---|---|---|---|
| 6 | Asp | m2G | THUMPD3 or THUMPD2 (52,53) | |
| 9 | Ala, Asp, Glu, Phe, Gly, His, Lys, Leu(CUN),Asn, Pro, Arg, Thr, Val, Trp | m1A | TRMT10C and SDR5C1 (54) | |
| Cys, Ile, Leu(UUR), Gln, Tyr | m1G | TRMT10C and SDR5C1 (54) | ||
| 10 | Ala, Phe, Gly, His, Lys, Leu(UUR), Leu(CUN), Asn, Pro, Val, Trp, Tyr | m2G | TRMT11 and TRMT112 (55) | |
| 20 | Leu(UUR), Leu(CUN), Ser(UCN) | D | DUS2 (56) | |
| 26 | Ala, Glu, Leu(UUR) | m2G | TRMT1 | |
| Ile | m22G | TRMT1 (57,58) | ||
| 27a c | Ser(UCN) | Ψ | PUS1 | |
| 27 | Cys, Asp, His, Ile, Leu(UUR), Leu(CUN), Asn, Pro, Val, Met | Ψ | PUS1 (25) | |
| 28 | Ala, Cys, Glu, Lys, Leu(CUN), Asn, Ser(UCN), Tyr | Ψ | PUS1 (25) | |
| 29 | Ser(UCN) | Ψ | PUS1 | |
| 31 | Asp, Leu(CUN) | Ψ | RPUSD1, RPUSD2, RPUSD3 or RPUSD4d | |
| 32 | Cys, Val | Ψ | RPUSD1, RPUSD2, RPUSD3 or RPUSD4d | |
| Ser(UCN), Thr | m3C | METTL2B (59,60) | ||
| 34 | Leu(UUR), Trp, Glu, Lys, Gln, | τm5U | GTPBP3 and MTO1 (61,62) | |
| Glu, Lys, Gln | τm5s2U e | MTU1e (63) and NFS1e (64) | ||
| Met | f5C | Unidentified | ||
| Asp, His, Asn, Tyr | Q | hQTRT1 and hQTRTD1 (65,66) | ||
| 37 | Ile, Lys, Asn, Ser(AGY), Thr | t6A | YRDC and QRI7 (OSGEPL1) (67) | |
| Cys, Phe, Ser(UCN), Trp, Tyr | i6A | TRIT1 (68) | ||
| Phe, Ser(UCN), Trp, Tyr | ms2i6Af | CDK5RAP1f (69) | ||
| Leu(CUN), Pro, Gln | m1G | TRMT5 (70) | ||
| 39 | Ala, Cys, Phe, Gly, His, Leu(UUR), Gln, Arg, Tyr | Ψ | PUS3 (71) | |
| 40 | Glu, Gln | Ψ | PUS3d | |
| 48 | Leu(UUR), Asn, Trp | m5C | NSUN2 (72,73) | |
| 49 | Glu, Ser(AGY) | m5C | NSUN2 (72,73) | |
| 50 | Met | Ψ | Unidentified | |
| 55 | Glu, Gln, Ser(UCN), Tyr | Ψ | TRUB2 (74) | |
| 57 | Ala | Ψ | Unidentified | |
| 58 | Cys, Glu, Ile, Lys, Leu(UUR), Ser(UCN) | m1A | TRMT61B (75) | |
| 67 | Thr | Ψ | PUS1d (76) | |
| 72 | Thr | m5C | Unidentified |
aNumbering system for tRNA comes from the tRNAdb compilation (40).
bSymbols for modifications originate from MODOMICS (http://modomics.genesilico.pl/) (39).
cThis position number is unique to mt tRNASer(UCN) (77).
dThese predictions were altered from our previous prediction (2).
eMTU1 and NFS1 are involved in 2-thiolation of τm5s2U34. MTU1 (Mitochondrial tRNA-specific 2-thiouridylase 1) is known as TRMU which originated from bacterial trmU (tRNA methyltransferase U). However, trmU (renamed as mnmA) was found to be a mis-annotation because it is not a tRNA methyltransferase.
fCDK5RAP1 is required for 2-methylthiolation of ms2i6A37.