Skip to main content
. 2017 Feb 9;7(1):13. doi: 10.3390/biom7010013

Table 2.

Calculated ScoreMean and MethScore for known 2′-O-methylated positions in E. coli and S. cerevisiae tRNAs extracted from WT and the strain lacking tRNA:Gm18-MTase (TrmH or TRM3).

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.