Decomposing bulk signals to reveal hidden information in processive enzyme reactions: A case study in mRNA translation
Creators: name: Haase, Nadin
name: Holtkamp, Wolf
name: Christ, Simon
name: Heinemann, Dag
name: Rodnina, Marina V.
name: Rudorf, Sophia
Publisher: name: San Francisco, Calif. : Public Library of Science
Year: 2024
Subjects: subject: Codon
subject: Fluorescence
subject: Protein Biosynthesis
subject: Ribosomes
subject: RNA, Messenger
subject: Enzymes
subject: Signal processing
subject: amino acid
subject: guanosine triphosphatase
subject: messenger RNA
subject: transfer RNA
subject: Biomolecular process
subject: Case-studies
subject: Enzyme reaction
subject: Fluorescence intensities
subject: Hidden information
subject: Monitoring time
subject: Single molecule
subject: Stochasticity
subject: Time trace
subject: Time-dependent signals
subject: Article
subject: biochemical analysis
subject: biochemical reaction
subject: biomolecular process stochasticity
subject: chromophore assisted light inactivation
subject: codon position
subject: codon usage
subject: cost effectiveness analysis
subject: decomposing bulk signal
subject: elongation rate
subject: ensemble fluorescence signature
subject: enzyme mechanism
subject: Escherichia coli
subject: feasibility study
subject: fluorescence analysis
subject: fluorescence intensity
subject: fluorescence signature
subject: fluorescence signature decomposition
subject: growth
subject: hidden information
subject: hydrolysis
subject: kinetics
subject: least square analysis
subject: magnitude estimation method
subject: Markov chain
subject: model parameterization
subject: molecular biology
subject: noise
subject: probability
subject: regularization parameters
subject: thermal fluctuation
subject: time dependent signal
subject: transition rate
subject: translation dynamics
subject: translation elongation cycle
subject: codon
subject: fluorescence
subject: genetics
subject: metabolism
subject: protein synthesis
subject: ribosome
subject: 570
subject: 004
subject: 610

description: 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.