Thermodynamic cost, speed, fluctuations, and error reduction of biological copy machines

Abstract

Due to large fluctuations in cellular environments, transfer of information in biological processes without regulation is inherently error-prone. The mechanistic details of error-reducing mechanisms in biological copying processes have been a subject of active research; however, how error reduction of a process is balanced with its thermodynamic cost and dynamical properties remain largely unexplored. Here, we study the error reducing strategies in light of the recently discovered thermodynamic uncertainty relation (TUR) that sets a physical bound to the cost-precision trade-off relevant in general dissipative processes. We found that the two representative copying processes, DNA replication by the exonuclease-deficient T7 DNA polymerase and mRNA translation by the \textit{E. coli} ribosome, reduce the error rates to biologically acceptable levels while also optimizing the processes close to the physical limit dictated by TUR.

arXiv comment20 pages, 14 figures, 3 Tables

References in corpus (27)

• Thermodynamic uncertainty relation for biomolecular processes
• Dissipation bounds all steady-state current fluctuations
• Proof of the Finite-Time Thermodynamic Uncertainty Relation for Steady-State Currents
• Fluctuation theorem uncertainty relation
• Thermodynamic uncertainty relations from exchange fluctuation theorems
• The free energy cost of accurate biochemical oscillations
• Generic Properties of Stochastic Entropy Production
• Thermodynamic Bounds on Precision in Ballistic Multi-Terminal Transport
• Energetic costs, precision, and efficiency of a biological motor in cargo transport
• Kinetic vs. energetic discrimination in biological copying
• Bounds on current fluctuations in periodically driven systems
• Entropic bounds on currents in Langevin systems
• Thermodynamics of Error Correction
• Physical insight into the thermodynamic uncertainty relation using Brownian motion in tilted periodic potentials
• Metabolic Futile Cycles and Their Functions: A Systems Analysis of Energy and Control
• Nonequilibrium sensing and its analogy to kinetic proofreading
• Effect of a magnetic field on the thermodynamic uncertainty relation
• The case for absolute ligand discrimination : modeling information processing and decision by immune T cells
• The Thermodynamic Uncertainty Relation in Biochemical Oscillations
• Thermodynamics of accuracy in kinetic proofreading: Dissipation and efficiency trade-offs
• Kinetics and thermodynamics of first-order Markov chain copolymerization
• Kinetic Proofreading and the Limits of Thermodynamic Uncertainty
• Modeling the growth of organisms validates a general relation between metabolic costs and natural selection
• Thermodynamic uncertainty relation of interacting oscillators in synchrony
• Protocols for copying and proofreading in template-assisted polymerization
• Kinetics and thermodynamics of DNA polymerases with exonuclease proofreading
• Kinetics and thermodynamics of exonuclease-deficient DNA polymerases

Cited by in corpus (11)

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• Flow of Energy and Information in Molecular Machines
• Variance sum rule: proofs and solvable models
• Thermodynamic inference in partially accessible Markov networks: A unifying perspective from transition-based waiting time distributions
• Fast Functionalization with High Performance in the Autonomous Information Engine
• The origin of loose bound of the thermodynamic uncertainty relation in a dissipative two-level quantum system
• Stochastic paths controlling speed and dissipation
• Violation of the thermodynamic uncertainty relation in quantum collisional models
• Virial-like Thermodynamic Uncertainty Relation in the Tight-Binding Regime
• Physical Constraints on the Rhythmicity of the Biological Clock