Table 2.
Escherichia coli | |||||||||
---|---|---|---|---|---|---|---|---|---|
WT E. coli | ΔTrmH E. coli | Difference | |||||||
tdbR Number | tRNA | Modification | Position * | ScoreMean | MethScore | ScoreMean | MethScore | ScoreMean | MethScore |
tdbR00000160 | tRNAIle(k2CAU) | Gm18 | 18 | 0.92 | 0.68 | 0.29 | −0.37 | 0.63 | 1.05 |
tdbR00000332 | tRNAGln(CUG) | Gm18 | 18 | 0.97 | 0.85 | 0.94 | 0.79 | 0.03 | 0.06 |
tdbR00000333 | tRNAGln(U*UG) | Gm18 | 18 | 0.81 | 0.7 | 0.76 | 0.67 | 0.05 | 0.04 |
tdbR00000390 | tRNASer(CGA) | Gm18 | 18 | 0.6 | 0.25 | 0.24 | −0.3 | 0.35 | 0.55 |
tdbR00000392-393 | tRNASer(GGA) | Gm18 | 18 | 0.86 | 0.76 | 0.26 | 0.32 | 0.6 | 0.44 |
tdbR00000394 | tRNASer(cmo5UGA) | Gm18 | 18 | 0.98 | 0.88 | 0.94 | 0.8 | 0.04 | 0.08 |
tdbR00000545-546 | tRNATyr(QUA) | Gm18 | 18 | 0.93 | 0.84 | 0.35 | 0.17 | 0.58 | 0.67 |
tdbR00000220 | tRNALeu(cmnm5UmAA) | Gm18 | 19 | 0.87 | 0.42 | 0.46 | −0.78 | 0.42 | 1.21 |
tdbR00000221 | tRNALeu(CAG) | Gm18 | 19 | 0.97 | 0.89 | 0.35 | −0.02 | 0.62 | 0.9 |
tdbR00000222 | tRNALeu(GAG) | Gm18 | 19 | 0.99 | 0.95 | 0.25 | −0.48 | 0.74 | 1.44 |
tdbR00000276 | tRNAMet(ac4CAU) | Gm18 | 19 | 0.58 | 0.42 | 0.75 | 0.44 | −0.17 | −0.02 |
tdbR00000595 | tRNALeu(CmAA) | Gm18 | 19 | 0.93 | 0.9 | 0.73 | 0.67 | 0.19 | 0.22 |
tdbR00000332 | tRNAGln(CUG) | Um32 | 32 | 0.97 | 0.85 | 0.94 | 0.79 | 0.03 | 0.06 |
tdbR00000333 | tRNAGln(U*UG) | Um32 | 32 | 0.81 | 0.7 | 0.76 | 0.67 | 0.05 | 0.04 |
tdbR00000484 | tRNATrp(CCA) | Cm32 | 33 | 0.99 | 0.92 | 0.99 | 0.91 | 0 | 0.01 |
tdbR00000394 | tRNASer(cmo5UGA) | Cm32 | 34 | 0.98 | 0.88 | 0.94 | 0.8 | 0.04 | 0.08 |
tdbR00000510-511 | tRNAMeti(CAU) | Cm32 | 34 | 0.97 | 0.84 | 0.97 | 0.85 | 0 | −0.02 |
tdbR00000623 | tRNAPro(CGG) | Um32 | 34 | 0.98 | 0.93 | 0.97 | 0.92 | 0 | 0.01 |
tdbR00000595 | tRNALeu(CmAA) | Cm34 | 36 | 1 | 0.94 | 0.99 | 0.88 | 0.01 | 0.05 |
tdbR00000220 | tRNALeu(cmnm5UmAA) | cmnm5Um34 | 36 | 1 | 0.94 | 0.98 | 0.81 | 0.02 | 0.13 |
Saccharomyces cerevisae | |||||||||
WT S. cerevisiae | ΔTRM3 S. cerevisiae | Difference | |||||||
tdbR Number | tRNA | Modification | Position * | ScoreMean | MethScore | ScoreMean | MethScore | ScoreMean | MethScore |
tdbR00000129 | tRNAGly(GCC) | Cm4 | 5 | 0.89 | 0.63 | 0.93 | 0.76 | −0.04 | −0.13 |
tdbR00000323-4 | tRNAPro(U*GG) | Cm4 | 5 | 0.95 | 0.83 | 0.95 | 0.81 | 0.01 | 0.02 |
tdbR00000145 | tRNAHis(GUG) | Am5 | 6 | 0.98 | 0.89 | 0.96 | 0.85 | 0.01 | 0.03 |
tdbR00000249 | tRNALeu(CAA) | Gm18 | 18 | 0.99 | 0.89 | 0.84 | 0.03 | 0.15 | 0.87 |
tdbR00000250 | tRNALeu(UAG) | Gm18 | 18 | 0.93 | 0.84 | −0.35 | −0.46 | 1.28 | 1.29 |
tdbR00000251 | tRNALeu(UAA) | Gm18 | 18 | 0.93 | 0.86 | −0.16 | −0.14 | 1.10 | 1.01 |
tdbR00000406 | tRNASer(U*GA) | Gm18 | 18 | 0.91 | 0.85 | 0.75 | 0.57 | 0.15 | 0.29 |
tdbR00000407-8 | tRNASer(IGA) | Gm18 | 18 | 0.95 | 0.81 | −0.35 | −0.80 | 1.30 | 1.61 |
tdbR00000494 | tRNATrp(CmCA) | Gm18 | 18 | 0.93 | 0.81 | 0.26 | −0.05 | 0.67 | 0.87 |
tdbR00000145 | tRNAHis(GUG) | Gm18 | 19 | 0.91 | 0.80 | −0.98 | −0.84 | 1.89 | 1.64 |
tdbR00000555 | tRNATyr(GψA) | Gm18 | 19 | 0.96 | 0.92 | 0.09 | 0.13 | 0.87 | 0.79 |
tdbR00000494 | tRNATrp(CmCA) | Cm32 | 32 | 0.99 | 0.86 | 0.99 | 0.88 | 0.00 | −0.02 |
tdbR00000083-4 | tRNAPhe(GmAA) | Cm32 | 33 | 0.98 | 0.79 | 0.98 | 0.81 | 0.00 | −0.03 |
tdbR00000251 | tRNALeu(UAA) | Cm32 | 34 | 0.92 | 0.55 | 0.95 | 0.69 | −0.03 | −0.14 |
tdbR00000494 | tRNATrp(CmCA) | Cm34 | 34 | 0.99 | 0.87 | 0.99 | 0.89 | 0.00 | −0.03 |
tdbR00000083-4 | tRNAPhe(GmAA) | Gm34 | 35 | 0.96 | 0.74 | 0.93 | 0.63 | 0.03 | 0.10 |
tdbR00000193 | tRNALys(cmnm5UmUU) | cmnm5Um34 | 35 | 0.64 | 0.30 | 0.58 | 0.26 | 0.06 | 0.04 |
tdbR00000406 | tRNASer(U*GA) | Um44 | 45 | 0.93 | 0.86 | 0.93 | 0.83 | −0.01 | 0.03 |
tdbR00000407-8 | tRNASer(IGA) | Um44 | 45 | 0.90 | 0.78 | 0.86 | 0.71 | 0.04 | 0.07 |
tdbR identifiers are taken from tRNAdb [66]; when the collapsed sequence is used, both numbers are indicated. * The position corresponds to the real position of the signal in the sequence of tRNA; thus it appears at position +1 to the 2′-O-methylated residue. U*: unknown modified uridine; Q: queuosine; I: inosine; ψ: pseudouridine. Important changes in ScoreMean and MethScore indicating disappearence of Gm18 are bolded.