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.

20 pages, 14 figures, 3 Tables

References in corpus (5)

• Thermodynamic uncertainty relation for biomolecular processes
• Proof of the Finite-Time Thermodynamic Uncertainty Relation for Steady-State Currents
• Nonequilibrium sensing and its analogy to kinetic proofreading
• Effect of a magnetic field on the thermodynamic uncertainty relation
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• 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