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Table 3 tRNA modification candidate genes in Arabidopsis.

From: Transfer RNA modifications and genes for modifying enzymes in Arabidopsis thaliana

Modified Nucleosides Homologous genes found in Arabidopsis
D At4g38890(Dus1,Dus2,Dus3), At5g67220(Dus1, Dus2, Dus3), At5g47970(Dus4), At3g49640(Dus1,Dus2,Dus3,Dus4), At3g63510(Dus1,Dus4)
Ψ At1g76120cyto(Pus1,Pus3), At1g20370(Pus1,Pus3), At1g34150nucl(Pus3,Pus1), At3g06950chlo(Pus3,Pus1), At2g30320(Pus1,Pus3), At5g35400(Pus1,Pus3),At5g14460chlo(Pus4), At5g51140cyto(Pus6, Pus8, Pus9), At3g04820(Pus7), At3g52260cyto(Pus9,Pus8,Pus6), At1g76050chlo(Pus8, Pus9,Pus6), At3g19440(Pus9,Pus8,Pus6), At1g56345(Pus9), At1g78910(Pus9,Pus6)
ncm5U At3g19980cyto, At1g50370cyto, At5g55260cyto, At4g26720cyto, At1g69960cyto, At3g58500cyto, At2g42500cyto, At1g10430cyto, At1g59830cyto (Sit4 family), At1g07990, At2g28360, At3g45190, At1g30470cyto(Sap185, Sap190), At2g15910(Kti11), At1g13870nucl(Kti12), At1g27060nucl, At5g63860nucl, At3g55580nucl, At5g16040, At3g53830nucl, At3g26100nucl (Kti13 family), At5g57015, At1g03930, At4g26100cyto, At1g72710 etc.(Kti14 family), At5g13680cyto(Elp1)
m1A At5g14600(Trm61), At2g45730(Trm6)
m5C At2g22400, At4g40000, At5g55920nucl, At4g26600chlo, At3g13180chlo, At1g06560, At5g66180, At5g26180(Trm4)
Cm At5g01230, At4g25730, At5g13830cyto(Trm7)
m7G At5g24840(Trm8), At5g17660chlo(Trm8), At1g03110nucl(Trm82)
m5U At3g21300mito, At2g28450nucl(Trm2)
I At1g48175, At1g68720nucl(Tad2), At5g24670nucl(Tad3)
Um no gene homolog found
m1I At1g01760nucl(Tad1),At3g56120cyto, At4g27340chlo, At4g04670cyto(Trm5)
Gm At4g17610(Trm3), At5g01230, At4g25730, At5g13830cyto(Trm7)
m1G At3g56120cyto, At4g27340chlo, At4g04670cyto(Trm5), At5g47680(Trm10)
m2G At3g26410cyto(Trm11), At1g78190, At1g22270(Trm112)
ac4C At5g12410(TAN1)
m22G At3g02320, At5g15810mito, At3g56330chlo(Trm1)
Am At4g01880chlo(Trm13)
t6A At5g60590chlo(Sua5)
ms2io6A At4g36390chlo, At1g72090cyto(MiaB), At5g20040/ATIPT9, At2g27760/ATIPT2cyto(MOD5)
Y At1g75200(Tyw1), At4g04670cyto(Tyw3+Tyw4c+Tyw2)
  1. tRNA modifying genes from S. cerevisiae or E. coli were used for BLAST search in TAIR database to find homologous genes in Arabidopsis thaliana. Arabidopsis genes for each modified nucleosides detected in this study is listed and gene used in query was shown in bracket. For multiple gene homologs found in Arabidopsis the query gene is shown in bracket next to the last gene. Genes for m2A and m6A modification were not available, TsaA for m6t6A did not give any homologous genes in Arabidopsis. Predicted subcellular localization of gene products was shown when at least two prediction programs gave the same result (Additional file 2).