A kinetic error filtering mechanism for enzyme-free copying of nucleic acid sequences
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Curated by eLife
Evaluation Summary:
How was it possible for prebiotic RNA or DNA molecules to reliably self-replicate, in the absence of sophisticated enzymes capable of error correction? This paper proposes a novel mechanism for error correction in templated copying, and is therefore of interest for cell and evolutionary biologists, biophysicists and readers in the field of origin-of-life science. The kinetic error filtering proposed here does not require sophisticated machinery but reduces errors significantly while retaining a reasonable yield rate. Crucial to this mechanism is a cyclically varying environment, such as might exist in hydrothermal vents. The plausibility of the mechanism is supported by thoughtful and rigourous calculations rooted in an experimentally-grounded model.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)
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Abstract
Accurate copying of nucleic acid sequences is essential for self-replicating systems. Modern cells achieve error ratios as low as 10 -9 with sophisticated enzymes capable of kinetic proofreading. In contrast, experiments probing enzyme-free copying of RNA and DNA as potential prebiotic replication processes find error ratios on the order of 10%. Given this low intrinsic copying fidelity, plausible scenarios for the spontaneous emergence of molecular evolution require an accuracy-enhancing mechanism. Here, we study a ‘kinetic error filtering’ scenario that dramatically boosts the likelihood of producing exact copies of nucleic acid sequences. The mechanism exploits the observation that initial errors in template-directed polymerization of both DNA and RNA are likely to trigger a cascade of consecutive errors and significantly stall downstream extension. We incorporate these characteristics into a mathematical model with experimentally estimated parameters, and leverage this model to probe to what extent accurate and faulty polymerization products can be kinetically discriminated. While limiting the time window for polymerization prevents completion of erroneous strands, resulting in a pool in which full-length products show an enhanced accuracy, this comes at the price of a concomitant reduction in yield. We show that this fidelity-yield trade-off can be circumvented via repeated copying attempts in cyclically varying environments such as the temperature cycles occurring naturally in the vicinity of hydrothermal systems. This setting could produce exact copies of sequences as long as 50mers within their lifetime, facilitating the emergence and maintenance of catalytically active oligonucleotides.
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Evaluation Summary:
How was it possible for prebiotic RNA or DNA molecules to reliably self-replicate, in the absence of sophisticated enzymes capable of error correction? This paper proposes a novel mechanism for error correction in templated copying, and is therefore of interest for cell and evolutionary biologists, biophysicists and readers in the field of origin-of-life science. The kinetic error filtering proposed here does not require sophisticated machinery but reduces errors significantly while retaining a reasonable yield rate. Crucial to this mechanism is a cyclically varying environment, such as might exist in hydrothermal vents. The plausibility of the mechanism is supported by thoughtful and rigourous calculations rooted in an experimentally-grounded model.
(This preprint has been reviewed by eLife. We include the public …
Evaluation Summary:
How was it possible for prebiotic RNA or DNA molecules to reliably self-replicate, in the absence of sophisticated enzymes capable of error correction? This paper proposes a novel mechanism for error correction in templated copying, and is therefore of interest for cell and evolutionary biologists, biophysicists and readers in the field of origin-of-life science. The kinetic error filtering proposed here does not require sophisticated machinery but reduces errors significantly while retaining a reasonable yield rate. Crucial to this mechanism is a cyclically varying environment, such as might exist in hydrothermal vents. The plausibility of the mechanism is supported by thoughtful and rigourous calculations rooted in an experimentally-grounded model.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)
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Reviewer #1 (Public Review):
The authors propose a mechanism for error-correction in enzyme-free templated copying, one that could have plausibly operated in prebiotic processes. In contrast to an energy-consuming enzymatic process that corrects errors as they occur, as in kinetic proofreading, here a non-equilibrium environment preferentially removes erroneous copies. The two key ingredients are i. that errors slow down polymerisation, and ii. that the environment periodically and selectively `leaks' out smaller fragments, such that in a finite time the only copies produced (and retained) are those with few errors.
As the authors show, these conditions are met by non-enzymatic copying of DNA and RNA in fluctuating environments that, they argue, are plausible prebiotic niches. By a thorough quantitative analysis, the authors establish …
Reviewer #1 (Public Review):
The authors propose a mechanism for error-correction in enzyme-free templated copying, one that could have plausibly operated in prebiotic processes. In contrast to an energy-consuming enzymatic process that corrects errors as they occur, as in kinetic proofreading, here a non-equilibrium environment preferentially removes erroneous copies. The two key ingredients are i. that errors slow down polymerisation, and ii. that the environment periodically and selectively `leaks' out smaller fragments, such that in a finite time the only copies produced (and retained) are those with few errors.
As the authors show, these conditions are met by non-enzymatic copying of DNA and RNA in fluctuating environments that, they argue, are plausible prebiotic niches. By a thorough quantitative analysis, the authors establish bounds on the environmental timescales that allow for faithful copying of nucleic acid polymers of different lengths.
The paper is clearly written and balances an intuitive description of the proposed kinetic filtering mechanism with the experimentally-grounded model of enzyme-free nucleic acid replication. The numerical and analytical results are thorough and lend credence to the plausibility of the mechanism.
While there has been some recent work on kinetic aspects of proofreading (for instance, Sartori and Pigolotti, PRL 2013 and J Stat Phys 2016), the proposed mechanism is, as far as I can tell, truly distinct. Nonetheless, while the authors focus on its implementation in enzyme-free nucleic acid copying in a prebiotic context, it seems sufficiently generalisable that it could potentially be at play in other situations.
Overall, the strengths of this paper are a. a demonstration of how non-equilibrium environments can circumvent the error problem in non-enzymatic copying, and b. a novel mechanism of error-correction that is conceptually distinct from kinetic proofreading.
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Reviewer #2 (Public Review):
The paper proposes a mechanism that reduces the replication errors of prebiotic polymerization. The paper assumes a PCR-like situation, that is, template strands, primers, thermal cycles, and copying machines are ready. The authors demonstrated by simulation and theory that a simple kinetic mechanism reduces replication errors while keeping the yield reasonable. The paper uses the following experimental facts and the quantities obtained by experiments:
- The misincorporation of wrong nucleotides slows down the extension.
- The misincorporation triggers successive incorporation of errors, generating error clusters, which result in a significant stalling of the extension.
Hence, the errors can be kinetically discriminated by limiting the polymerization time. They found a time scale where errors are …
Reviewer #2 (Public Review):
The paper proposes a mechanism that reduces the replication errors of prebiotic polymerization. The paper assumes a PCR-like situation, that is, template strands, primers, thermal cycles, and copying machines are ready. The authors demonstrated by simulation and theory that a simple kinetic mechanism reduces replication errors while keeping the yield reasonable. The paper uses the following experimental facts and the quantities obtained by experiments:
- The misincorporation of wrong nucleotides slows down the extension.
- The misincorporation triggers successive incorporation of errors, generating error clusters, which result in a significant stalling of the extension.
Hence, the errors can be kinetically discriminated by limiting the polymerization time. They found a time scale where errors are significantly suppressed while a reasonable yield is obtained. Based on this observation, they tried to filter errors out by repeating temperature cycles with tuned cycle duration. A high temperature resets the extension by dissociating the perfect and partial products from the templates. They found that there is a time-scale range where the replication does not suffer the fidelity-speed trade-off.
Strengths:
- The replication with fidelity is indispensable for stable autocatalytic systems to emerge in the prebiotic environment. However, the replication is erroneous without sophisticated error-suppression machinery used in modern biology. The hypercycle proposed by Eigen and Schuster in the 1970s is one of the mechanisms to suppress errors without such modern machinery. However, the hypercycle requires the formation of a complex autocatalytic network and is not expected to emerge spontaneously. As well, the hypercycle is not very stable due to multiple problems. The kinetic error filtering proposed in this paper provides a promising mechanism to reduce errors because it does not require complex systems. In addition, the simulations are based on the parameters obtained by experiments.
Weaknesses:
- The maximum length that can be copied without errors is 50nt for DNA and 25nt for RNA. It is not clear if sequences with such a short length can have sufficient polymerization activity. We would need more mechanisms to solve the information-keeping problems. However, the kinetic error filtering is simple and could be combined with other mechanisms. Or, some nucleotide analogs may have better parameters generating longer strands. It would be true that the kinetic filtering lowers the hurdle for the emergence of autocatalytic systems in the prebiotic soup.
- Other things to be considered include the effect of the product-template rebinding. The template concentration is assumed to be very small so that the product does not rebind to the template. However, it would be necessary to consider the effect in more realistic situations. The product-template rebinding is one of the significant issues in the prebiotic autocatalytic system. In the present scenario, if the products with incomplete copying bind to the template, they quickly finish copying during the limited cycle duration. This may weaken the kinetic filtering.
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Reviewer #3 (Public Review):
This manuscript proposes a kinetic error-correction mechanism that does not require enzymes. The authors argue that this mechanism could have played a relevant role in prebiotic environments. The enzyme-free kinetic mechanism proposed in this manuscript is conceptually different from kinetic proofreading, which is a non-equilibrium error-correction mechanism characterizing accurate polymerization assisted by enzymes.
Strengths:
The results presented in this manuscript are convincing. The authors make a case that the kinetic error filtering mechanism is a plausible scenario for the emergence of low error rates in prebiotic copying of DNA and RNA. I feel that the manuscript is an interesting, timely, and important contribution to the debate on the origin of life and is likely to stimulate experimental efforts …
Reviewer #3 (Public Review):
This manuscript proposes a kinetic error-correction mechanism that does not require enzymes. The authors argue that this mechanism could have played a relevant role in prebiotic environments. The enzyme-free kinetic mechanism proposed in this manuscript is conceptually different from kinetic proofreading, which is a non-equilibrium error-correction mechanism characterizing accurate polymerization assisted by enzymes.
Strengths:
The results presented in this manuscript are convincing. The authors make a case that the kinetic error filtering mechanism is a plausible scenario for the emergence of low error rates in prebiotic copying of DNA and RNA. I feel that the manuscript is an interesting, timely, and important contribution to the debate on the origin of life and is likely to stimulate experimental efforts to test the proposed hypothesis.
Weaknesses:
I feel that the results are compelling, but the modeling choice and the comparison with previous models in the literature should be clarified. I feel that this clarification is important both to understand the relevance of modeling details and for the impact of this paper on the theoretical research on error correction in biology.
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