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

Autor: Haase N; Leibniz University Hannover, Institute of Cell Biology and Biophysics, Hannover, Germany., Holtkamp W; Max Planck Institute for Multidisciplinary Sciences, Department of Physical Biochemistry, Göttingen, Germany.; Paul-Ehrlich-Institut, Division of Allergology, Langen, Germany., Christ S; Leibniz University Hannover, Institute of Cell Biology and Biophysics, Hannover, Germany., Heinemann D; Leibniz University Hannover, Hannover Centre for Optical Technologies (HOT), Hannover, Germany.; Leibniz University Hannover, Institute of Horticultural Production Systems, Hannover, Germany.; Leibniz University Hannover, PhoenixD Cluster of Excellence, Hannover, Germany., Rodnina MV; Max Planck Institute for Multidisciplinary Sciences, Department of Physical Biochemistry, Göttingen, Germany., Rudorf S; Leibniz University Hannover, Institute of Cell Biology and Biophysics, Hannover, Germany.
Jazyk: angličtina
Zdroj: PLoS computational biology [PLoS Comput Biol] 2024 Mar 05; Vol. 20 (3), pp. e1011918. Date of Electronic Publication: 2024 Mar 05 (Print Publication: 2024).
DOI: 10.1371/journal.pcbi.1011918
Abstrakt: 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.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2024 Haase et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
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