An official website of the United States government
Many biological processes discriminate between correct and incorrect substrates through the kinetic proofreading mechanism that enables lower error at the cost of higher energy dissipation. Elucidating physico-chemical constraints for global minimization of dissipation and error is important for understanding enzyme evolution. Here, we identify theoretically a fundamental error–cost bound that tightly constrains the performance of proofreading networks under any parameter variations preserving the rate discrimination between substrates. The bound is kinetically controlled, i.e. completely determined by the difference between the transition state energies on the underlying free energy landscape. The importance of the bound is analysed for three biological processes. DNA replication by T7 DNA polymerase is shown to be nearly optimized, i.e. its kinetic parameters place it in the immediate proximity of the error–cost bound. The isoleucyl-tRNA synthetase (IleRS) of E. coli also operates close to the bound, but further optimization is prevented by the need for reaction speed. In contrast, E. coli ribosome operates in a high-dissipation regime, potentially in order to speed up protein production. Together, these findings establish a fundamental error–dissipation relation in biological proofreading networks and provide a theoretical framework for studying error–dissipation trade-off in other systems with biological discrimination.
more »
« less
This content will become publicly available on February 19, 2027
Evolution of error correction through a need for speed
Kinetic proofreading is a class of error-correcting mechanisms in biology that expend energy to avoid mistakes during replication, transcription, and translation. Proofreading is typically assumed to evolve when selection for fidelity outweighs costs in energy and the speed of replication. We show that when stalling after misincorporations is accounted for, proofreading can instead speed up replication. Consistent with data on polymerase mutagenesis, our results suggest that proofreading can evolve under selection for speed alone. We generalize to multicomponent self-assembly and show that analogous error-correcting processes, such as dynamic instability, can likewise emerge purely from selection for rapid assembly. Thus, nonequilibrium error correction can evolve from selection for speed, even without direct fidelity advantages. We discuss implications for mutation-rate evolution, molecular assembly processes, and models of early life.
more »
« less
- PAR ID:
- 10688596
- Publisher / Repository:
- American Association for the Advancement of Science
- Date Published:
- Journal Name:
- Science
- Volume:
- 391
- Issue:
- 6787
- ISSN:
- 0036-8075
- Page Range / eLocation ID:
- 818 to 824
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
To reliably transmit information, cells exploit nonequilibrium drives to reduce errors. Kinetic proofreading is a classic mechanism that sharpens ligand discrimination by T lymphocytes, yet it remains unclear whether adaptive immunity relies on kinetic proofreading alone to achieve high fidelity. Here, we propose an alternative: an enhanced form of mechanical proofreading (MPR), in which adaptive force generation during dynamic cell-cell contact enables faithful selection of high-affinity B lymphocytes. Using a coarse-grained model validated by experiments, we show that adaptive MPR, characterized by mechanical feedback between force exertion and contact formation, supports robust discrimination of receptor quality regardless of ligand quantity. While MPR generally balances tradeoffs between speed and fidelity, a negative scaling of contact duration with ligand abundance reveals the presence of feedback. By modulating interactions among distinct ligands that share mechanical load at membrane contacts, adaptive MPR may help mitigate autoimmunity or enhance multivalent vaccines. Overall, this work generalizes proofreading to include cellular designs that operate across scales to reconcile competing functional demands at the systems level.more » « less
-
Transcription fidelity is inherently coupled to its strength, and highly expressed genes often exhibit elevated error rates. Epigenetic and structural factors, including histone modifications, DNA methylation, and nucleoid-associated proteins, modulate transcriptional output and, consequently, fidelity. However, the mechanistic origin of this fidelity-strength relationship remains poorly understood. Here, we propose that repulsive interactions among cotranscribing RNA polymerases (RNAPs) might explain these couplings. We develop a stochastic kinetic model of transcription elongation that incorporates both kinetic proofreading and repulsive forces generated through collisions between the neighboring RNAPs. In this framework, it is found that the collision forces accelerate leading RNAPs' elongation speed and impede their kinetic proofreading; the opposite trends occur for the trailing enzymes. As a result, interactions among multiple RNAPs at high initiation rates substantially elevate transcriptional error relative to isolated enzymes, with the magnitude of this increase determined by the intrinsic proofreading rate. In contrast, the mechanical partitioning of force between forward translocation and backtracking pathways primarily modulates elongation speed without altering fidelity. Together, our study provides a quantitative and mechanistic framework that links the collective dynamics of RNAPs to transcriptional errors, offering new physical insights into how transcriptional strength intrinsically compromises fidelity.more » « less
-
Nonequilibrium error-correction mechanisms, such as kinetic proofreading, enable biological systems to amplify the discrimination among cognate and non-cognate substrates beyond what is possible at equilibrium. However, it remains unclear how such discrimination should be distributed over the underlying network to achieve the full nonequilibrium advantage of error reduction. Using a discrete-state stochastic framework, we first show that the Hopfield network, the seminal model of proofreading, with discrimination concentrated in two dissociation steps, displays distinct regimes of error reduction depending on the relative magnitudes of the rate constants of various steps. One such regime is actually anti-proofreading, showing no improvement in accuracy with increasing discrimination. In contrast, a biologically realistic model of the tRNA selection network in protein translation by the E. coli ribosome exhibits distributed discrimination. We demonstrate that the spread of discrimination across the entire network enables the system to achieve the full nonequilibrium advantage, even in the kinetic regime where the Hopfield network lies in the anti-proofreading zone at low discrimination strength. Our results further indicate that excessively strong discrimination adversely affects the system, eliminating the nonequilibrium advantage of error reduction without providing any additional gain in the speed of translation.more » « less
-
Polymerization and editing modes of a high-fidelity DNA polymerase are linked by a well-defined pathnull (Ed.)Abstract Proofreading by replicative DNA polymerases is a fundamental mechanism ensuring DNA replication fidelity. In proofreading, mis-incorporated nucleotides are excised through the 3′-5′ exonuclease activity of the DNA polymerase holoenzyme. The exonuclease site is distal from the polymerization site, imposing stringent structural and kinetic requirements for efficient primer strand transfer. Yet, the molecular mechanism of this transfer is not known. Here we employ molecular simulations using recent cryo-EM structures and biochemical analyses to delineate an optimal free energy path connecting the polymerization and exonuclease states of E. coli replicative DNA polymerase Pol III. We identify structures for all intermediates, in which the transitioning primer strand is stabilized by conserved Pol III residues along the fingers, thumb and exonuclease domains. We demonstrate switching kinetics on a tens of milliseconds timescale and unveil a complete pol-to-exo switching mechanism, validated by targeted mutational experiments.more » « less
