TY - JOUR

T1 - Decomposing bulk signals to reveal hidden information in processive enzyme reactions: A case study in mRNA translation

AU - Haase, Nadin

AU - Holtkamp, Wolf

AU - Christ, Simon

AU - Heinemann, Dag

AU - Rodnina, Marina V.

AU - Rudorf, Sophia

N1 - This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 437345987 (S.R.). https://www.dfg.de/en N.H. is supported by the Add-on Fellowship of the Joachim Herz Foundation. https://www.joachim-herz-stiftung.de/en/ The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

PY - 2024/3/5

Y1 - 2024/3/5

N2 - Processive enzymes like polymerases or ribosomes are often studied in bulk experiments by monitoring time-dependent signals, such as fluorescence time traces. However, due to biomolecular process stochasticity, ensemble signals may lack the distinct features of single-molecule signals. Here, we demonstrate that, under certain conditions, bulk signals from processive reactions can be decomposed to unveil hidden information about individual reaction steps. Using mRNA translation as a case study, we show that decomposing a noisy ensemble signal generated by the translation of mRNAs with more than a few codons is an ill-posed problem, addressable through Tikhonov regularization. We apply our method to the fluorescence signatures of in-vitro translated LepB mRNA and determine codon-position dependent translation rates and corresponding state-specific fluorescence intensities. We find a significant change in fluorescence intensity after the fourth and the fifth peptide bond formation, and show that both codon position and encoded amino acid have an effect on the elongation rate. This demonstrates that our approach enhances the information content extracted from bulk experiments, thereby expanding the range of these time- and cost-efficient methods.

AB - Processive enzymes like polymerases or ribosomes are often studied in bulk experiments by monitoring time-dependent signals, such as fluorescence time traces. However, due to biomolecular process stochasticity, ensemble signals may lack the distinct features of single-molecule signals. Here, we demonstrate that, under certain conditions, bulk signals from processive reactions can be decomposed to unveil hidden information about individual reaction steps. Using mRNA translation as a case study, we show that decomposing a noisy ensemble signal generated by the translation of mRNAs with more than a few codons is an ill-posed problem, addressable through Tikhonov regularization. We apply our method to the fluorescence signatures of in-vitro translated LepB mRNA and determine codon-position dependent translation rates and corresponding state-specific fluorescence intensities. We find a significant change in fluorescence intensity after the fourth and the fifth peptide bond formation, and show that both codon position and encoded amino acid have an effect on the elongation rate. This demonstrates that our approach enhances the information content extracted from bulk experiments, thereby expanding the range of these time- and cost-efficient methods.

U2 - 10.1101/2023.05.17.541147

DO - 10.1101/2023.05.17.541147

M3 - Article

VL - 20

JO - PLoS Computational Biology

JF - PLoS Computational Biology

SN - 1553-734X

IS - 3

M1 - e1011918

ER -