Fig. 4: Cytosolic tRNA structure and interaction in response to arsenite stress.

The parameters used here are: ΔDMS signal = DMS signal^{in vivo_AsO2} – DMS signal^{in vivo_control}. a Heatmap of the positional ΔDMS signal on tRNA_i^Met, red: higher, blue: lower DMS signal with arsenite. Native modifications³⁰ that are incompletely removed by demethylases are marked with “X”. The blue line and residue numbers indicate the residues that show a large DMS profile change under arsenite stress. The orange line indicates the anticodon nucleotides. b Heatmap of the positional ΔDMS signal of the most abundant isodecoder in each anticodon family, red: higher, blue: lower DMS signal with arsenite. Native modifications³⁰ that are incompletely removed by demethylases are marked with “X”. tRNA positions are according to the standard tRNA nomenclature, residues missing in specific tRNAs are marked in gray. c Anticodon loop (excluding position 37) average ΔDMS signals in tRNA groups with different modification status at position 37. Only the most abundant isodecoders from each isoacceptor family are included. tRNAs are grouped as follows: A37 (n = 14): Asp, GluCTC, GluTTC, GlyCCC, GlyGCC, GlyTCC, GlnCTC, GlnTTC, ThrAGT, ThrCGT, ThrTGT, ValAAC, ValCAC, ValTAC; t6/i6A37 (n = 12): IleAAT, IleTAT, LysCTT, LysTTT, Met, iMet, Asn, SerAGA, SerCGA, SerGCT, SerTGA, ArgCCT, ArgTCT; m1G/m1I/W37 (n = 19): AlaAGC, AlaCGC, AlaTGC, ArgACG, ArgCCG, ArgTCG, Cys, His, LeuAAG, LeuCAG, LeuTAG, LeuCAA, LeuTAA, Phe, ProAGG, ProCGG, ProTGG, Trp, Tyr. P-values are calculated with two-sided Wilcoxon signed-rank test. In each box whisker plot, the maxima represent the first quantiles, the middle lines represent the medians, the minima represent the 75th quantiles, the crosses in the center represent the means, and the whiskers represent the standard deviation. d Box-whisker plot of DMS signal differences for each A and C residues in every tRNA in D, T, anticodon, variable loops, and the 3’ unpaired CCA regions. Depleted (=1) or enriched (=2): tRNAs that are significantly decreased or increased in the polysomes with arsenite, respectively. Average n = 42 for the depleted group and n = 14 for the enriched group for each region. P-values are calculated with a standard two-sided Wilcox rank-sum test; n.s.: not significant, **: p < 10^-2. The exact P-values for each box-whisker plot are as follows: D loop p = 0.15, Anticodon loop p = 0.0046, Variable loop p = 0.67, T loop p = 0.31, CCA p = 0.018. In each box whisker plot, the maxima represent the first quantiles, the middle lines represent the medians, the minima represent the 75th quantiles, the crosses in the center represent the means, and the whiskers represent the standard deviation.