Figure 1.
Correlation of Protein Abundance and Different Translation Rates
Shows Spearman rank correlation (rs) of TA versus reference protein abundance; error bars indicate ± one standard deviation based on random subsamples. TA1 = mRNA × ribocc × ribden; TA2 = TA1 × CAI; TA3 assumes Michaelis–Menten kinetics for the TA (Equation 3). The tRNA–AIs were calculated as described in Methods; tRNA–AI_p indicates the codon–tRNA assignment according to [42] and tRNA–AI _c the assignment according to Crick's wobble rules [43]. All correlations are based on 4,123 ORFs. Accounting for tRNA–AI_p slightly improves correlations compared with TA1 alone. However, TA2 (with CAI) performs better. Overall, considering saturation, (TA3) gave the best results.
Table 1.
Contribution of Each Factor to the Translational Activity
Figure 2.
Saturation of the Transactional Activity
Shows Spearman rank correlation (rs) of different models for TA prediction as a function of the Michaelis constant, Km. All four factors (F) contributing to TA (mRNA, ribocc, ribden, CAI) were tested for saturation individually and in combination. The different colors indicate the models for TA prediction:
The product of mRNA × ribocc × ribden in the saturation term (i.e., TA3) yielded the best correlation with reference protein concentrations. The value without any saturation (rs = 0.68) is approached for Km → ∞.
Table 2.
Comparison of Different Saturation Models (Cross-Validation)
Figure 3.
Change of Translation Rate and Protein Change in Response to Different Stimuli
Median protein and translation rate ratios are shown for the conditions ± galactose (A), ethanol/galactose (B), minimal medium/normal medium (C), ± mating pheromone (D). Translation rates were calculated according to Equation 3, assuming constant ribden and ribocc (because those changes were unavailable for all but one condition). Proteins were functionally grouped based on MIPS annotation.
AR, protein activity regulation; BG, biogenesis; CC, cell cycle/DNA processing; CF, cell fate; CR, cell rescue/defense/virulence; DF, differentiation; IE, interaction with cellular environment; MB, metabolism; PB, protein with binding function; PF, protein fate; ST, cellular communication/signal transduction; TC, transcription; TP, cellular transport.
Table 3.
Selected Examples of Proteins with Clear Patterns of Specific Stress Response (First Seven Rows) or Generic Stress Response (Last Eight Rows) after Accounting for Saturation of the Translational Activitya