Table 3.
Post-transcriptional modifications (bold) identified in the L. lactis tRNAs. The anticodon is underlined in the sequence. Copy number denotes the number of genomic tRNAs. Nucleosides in brackets represent modified sequence locations. Dual nucleosides in brackets (e.g., [m6A/A]) represent sites of hypomodification where RNase digestion products were detected both with and without the identified modification. Methylated nucleosides are placed onto sequence locations, using known tRNA modification homology algorithms (Machnicka et al., 2013) as the LC-MS/MS approach cannot directly reveal the ring location of methylation except for 7-methylguanosine [m7G].
| tRNA | Anticodon | Copy number |
Sequence (5’ – 3’) |
|---|---|---|---|
| Ala | UGC | 6 | GGGGCCU[s4U]AGCUCAGC[D]GGGAGAGCGCCUGCUU[mo5U]GC[m6A/A]CGCAGGAGGUCAGCGG[m5U]UCGAUCCCGCUAGGCUCCACCA |
| Arg 1 | ACG | 2 | GCAGGCGUGGCUCAAC[D]GGA[D]AGAGUACCUGACU[I]CG[m2A/A]AUCAGGC[m7G]UUGUAGG[m5U]UCGAAUCCUACCGCUUGCACCA |
| Arg2 | CCG | 1 | GCGUCCG[s4U]AGUGUAA[D]GGA[D]AUCACGUAAGAUUCCGGUUCUUGAAUGGGGG[m5U]UCGAUUCCCUCCGGACGCACCA |
| Arg 3 | CCU | 1 | GGUCUCUUAGUUAAAUUGGA[D]AUAACUACUGCCUCCUAAGCAGUGAUUGCCAG[m5U]UCGAUUCUGGCAGGGGCCACCA |
| Arg 4 | UCU | 1 | GGUCCGAUAGCUCAGC[D]GGA[D]AGAGCAUUCGCCUUCUAAGCGAACG[m7G]UCGAGGG[m5U]UCGAAUCCCCCUCGGAUCACCA |
| Asn | GUU | 2 | UGCGGAU[s4U/U]AGCUCAGU[D]GG[D]AGUAGCGCAUGACUGUU[t6A]AUCAUGAU[m7G]UCGUCAG[m5U]UCGAGUCUGACAUCCGCAGCCA |
| Asp | GUC | 2 | GGUUCUGUAGUGUAGCGG[D][D]AUCACGUCGCCCUGUCACGGCGAAGAUCGCGGG[m5U]UCGAUUCCCGUCAGAACCGCCA |
| Cys | GCA | 1 | GGCGGCG[s4U]AGUGAAGUGG[D][m1A]ACACAUGGCUCUGCA[i6A]AAGCUUAAUCGUCGG[m5U]UCAAAUCCGACCGUCGCCUCCA |
| Gln | UUG | 2 | UGGGGUA[s4U]AGCCAAGCGG[D]AAGGCAAGGGACUUUGACUCCCUCAUGCGUUGG[m5U]UCGAAUCCAGCUACCCCAGCCA |
| Glu | UUC | 1 | GGUCCGUUGGUC[m1A/A]AGGGG[D][D]AAGACACCGCCUUUUCACGGCGGUAACACGGG[m5U]UCGAAUCCCGUACGGACUACCA |
| Gly 1 | GCC | 2 | GCGAACGUAGUUCAGGGG[D]AGAACACAACCUUGCCAUGGUUGGG[m7G]UCGCGAG[m5U]UCGAAUCUCGUCGUUCGCUCCA |
| Gly 2 | UCC | 2 | GCGGAUGUAGUUUAAUGGUAGAACCCCAGCCU[mo5U]CC[m6A/A]AGCUGGCUACGCGAG[m5U]UCGAUUCUCGUCAUCCGCUCCA |
| His | GUG | 1 | GCGGAUGUGGUGAAGUGG[D][D]AACACACCGGCUUGUGGCGCCGGCACUCGCGAG[m5U]UCGAUCCUCGUCAUCCGCCA |
| Ile | GAU | 2 | GGGAGUU[s4U/U]AGCUCAGU[D]GG[D][D]AGAGCACUGUGUUGAU[t6A]ACGCAGGG[m7G]UCCCAGG[m5U]UCGAAUCCUGGAAUUCCCACCA |
| Leu 1 | AAG | 2 | GCGGUGGUGGCGGAAU[D]GGCAGACGCGCAGGAUUAAG[m1G]AUCCUGUCGGGAAUUUUCUUGGUGCGGG[m5U]UCAAGUCCCGCCCACCGCACUACCA |
| Leu 2 | CAG | 1 | GGGGAAGUGGUGGAAUGGCAGACACGCAUGCUUCAGGUGCAUGUGCGAGAAAUCGCGUGAGGG[m5U]UCAAAUCCCUUCUUCCCCACCA |
| Leu 3 | UAG | 2 | GCGGAUGUGGCGGAAU[D]GGCAGACGCACUAGAUUUAG[m1G]AUCUAGCGCUUAACGGCGUGGGGG[m5U]UCAAGUCCCUUCAUCCGCACCA |
| Leu 4 | CAA | 1 | GCCGAAGUGGCGGAAUAGGCAGACGCGCCAGACU[Cm]AA[i6A]UCUGGUUCCUUCACGGGAGUGCCGG[m5U]UCGACCCCGGCCUUCGGCACCA |
| Leu 5 | UAA | 1 | CCCGGGGUGGCGGAAC[D/U]GGCAGACGCACAGGACU[cmnm5s2U]AA[i6A]AUCCUGCGAGGGGUAACCUUCGUACCGG[m5U]UCGAAACCGGUCCUCGGGACCA |
| Leu 6 | UAA2 | 1 | GCUCGAAUGGCGGAAU[D]GGCAGACGCUGCGGACUUAAAAUCCGUUGGUUAUUAAACCGUGAGGG[m5U]UCAAGUCCCUCUUUGAGCACCA |
| Lys 1 | CUU | 1 | GGCCCGGUAGCUCAGU[D]GG[D]AGAGCAGUAGACUCUU[t5A]AUCUAUGG[m7G]UCCAGGG[m5U]UCGAGCCCCUGCCGAGCCACCA |
| Lys 2 | UUU | 1 | GACUCGUUAGCUCAGU[D]GG[D]AGAGCAUUUGACU[cmnm5s2U]UU[t6A]AUCAAAGG[m7G]UCGCUGG[m5U]UCGAGCCCAGCACGGGUCACUACCA |
| Lys 3 | UUU2 | 2 | GACUCGUUAGCUCAGU[D]GG[D]AGAGCAUUUGACU[cmnm5s2U]UU[t6A]AUCAAAGG[m7G]UCGCUGG[m5U]UCGAGCCCAGCACGGGUCACCA |
| Met 1 | CAU | 1 | GGAUCUUUAGCUCAGU[D]GG[D][D]AGAGCUAUCGGCUCAU[m6A/A]ACCGAUCG[m7G]UCGCUGG[m5U]UCGAAUCCAGCAAGAUCCACCA |
| Met 2 | CAU | 1 | GGCGGUGUAGCUCAGCUGGCUAGAGCGUUCGGUU[ac4C]AU[m6A]CCCGAGAGGUCGGGGG[m5U]UCGAUCCCCUUCGCCGCUACCA |
| Met 3 | CAU | 1 | CGCGGGA[s4U]GGAGCAGCUAGG[D]AGCUCGUCGGGCUCAUAACCCGAAG[m7G]UCAUAGG[m5U]UCAAAUCCUAUUCCCGCAACCA |
| Met 4 | CAU | 1 | AGUUCUUUAGCUUAGU[D]GG[D][D]AAAGUCCCCCGCUCAUAACGGGGUAAGCGCUGGUUUGAGUCCAGCAAGAACCA |
| Phe | GAA | 2 | GGCUCGG[s4U]AGCUCAGU[D]GG[D]AGAGCAAUGGAUUGAA[m1G]CUCCAUGU[m7G]UCGGCGG[m5U]UCGAUUCCGUCUCGCGCCACCA |
| Pro | UGG | 2 | CGGGAAGUAGCUCAGCUUGG[D]AGAGUACUUGGUU[mo5U]GG[m1G]ACCAAGGU[m7G]UCGCAGG[m5U]UCGAAUCCUGUCUUCCCGACCA |
| Ser 1 | GGA | 1 | GGAGAAGUGUCCGAG[D]GGCCGAAGGAGCACGCCUGGAAAGUGUGUAUACGUCACAAGCGUAUCGGGGG[m5U]UCGAAUCCCCUCUUCUCCUCCA |
| Ser 2 | CGA | 1 | GGAGCCAUGGCAGAGUGGUAAUGCAGCGGACUCGAAAUCCGUCGAACCGUGUAAAGCGGCGCAGGGG[m5U]UCAAAUCCCCUUGACUCCUCCA |
| Ser 3 | UGA | 1 | GGAGGAUUACCCAAGCCUGGCUGAAGGGAACGGUCU[mo5U]GA[i6A]AACCGUCAGGCAUGUAAAGGCGUGCGUGGG[m5U]UCGAAUCCCACAUCCUCCUCCA |
| Ser 4 | UGA2 | 1 | GGAGGAUUACCCAAGUCCGGCUGAAGGGAACGGUCU[mo5U]GA[i6A]AACCGUCAGGCGUGUAAAAGCGUGCGUGGG[m5U]UCGAAUCCCACAUCCUCCUCCA |
| Ser 5 | GCU | 1 | GGGGGGUUACUCAAGAGGCUGAAGAGGACGGUUUGCUAAAUCGUUAGGUCGGGAAACCGGCGCGAGGG[m5U]UCGAAUCCCUUACCCCCCUCCA |
| Thr 1 | GGU | 1 | GCCGUUGUAGCUCAGUCGGUAGAGCAGCACCAUGGUAAGGUGAAG[m7G]UCGACAG[m5U]UCGAUUCUGUUCAAUGGCACCA |
| Thr 2 | CGU | 1 | GCCGAGUUAGCUCAGUCGGUAGAGCACUUCACUCGUAACGAAGGG[m7G]UCACAGG[m5U]UCGAUUCCUGCACUCGGCACCA |
| Thr 3 | UGU | 2 | GCCGACU[s4U/U]AGCUCAGU[D]GG[D]AGAGCAUCUGAUU[mo5U]GU[t6A]AUCAGAGG[m7G]UCGCGUG[m5U]UCGAAUCAUGUAGUCGGCACCA |
| Trp | CCA | 1 | ACGGGCAUCGUAUAAAGGUAGUACAAAGGUCUCCA[i6A]AACCUUUAGUGUGGG[m5U]UCAAUUCCUGCUGCCCGUGCCA |
| Tyr | GUA | 1 | GGAAGGGUAGCGAAGAGGC[D]AA[m1A]CGCGGCGGACUGUA[i6A]AUCCGCUCCUUCGGG[m5U]UCGGGGGUUCGAAUCCCUCCCCUUCCACCA |
| Val | UAC | 3 | GGGAGUU[s4U/U]AGCUCAGC[D]GGGAGAGCAUCUGCCU[mo5U]AC[m1A]AGCAGAGG[m7G]UCAGCGG[m5U]UCGAUCCCGUUAACUCCCACCA |