FIGURE 2.
tRNA abundance scales with biased codon representation in the Kc167 cell proteome. (A) Experimental design for integrated tRNA, transcript, and protein profiling in Drosophila Kc167 cells during the temporal-specific early and late ecdysone responses. Small RNA and mRNA analyses were performed on biological replicates at 0, 3, and 48 h after treatment with ecdysone. Label-free quantitative mass spectrometry was performed at 0 and 48 h on cellular lysates matched to small RNA-seq experiments. (B) Correlation plot for transcriptional codon usage (x-axis) and codon representation in the proteome at 0 h. ρ = 0.982; Spearman's rank correlation, P < 2.2 × 10−16. (C) Biased codon representation in the proteome compared with transcriptomic codon usage frequencies (y-axis) as a function of transcriptomic codon usage (x-axis). (D) Correlation plot for biased proteomic codon representation (y-axis) with tRNA levels (log10 tRNA abundance, as measured by small RNA-seq experiments; x-axis). ρ = 0.639; Spearman's rank correlation, P = 6.9 × 10−6. (E) Box and whisker diagram comparing the abundance for all tRNAs matching underrepresented codons (pCR < tCU, blue) with tRNAs matching overrepresented codons (pCR > tCU, red), comparing the proteome with the transcriptome. (pCR) Proteomic codon representation, (tCU) transcriptomic codon usage. P = 5.9 × 10−4, Wilcoxon rank sum test.