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Real ribozymes suggest a relaxed error threshold

Abstract

The error threshold for replication, the critical copying fidelity below which the fittest genotype deterministically disappears, limits the length of the genome that can be maintained by selection. Primordial replication must have been error-prone, and so early replicators are thought to have been necessarily short1. The error threshold also depends on the fitness landscape. In an RNA world2, many neutral and compensatory mutations can raise the threshold, below which the functional phenotype3, rather than a particular sequence, is still present4,5. Here we show, on the basis of comparative analysis of two extensively mutagenized ribozymes, that with a copying fidelity of 0.999 per digit per replication the phenotypic error threshold rises well above 7,000 nucleotides, which permits the selective maintenance of a functionally rich riboorganism6 with a genome of more than 100 different genes, the size of a tRNA. This requires an order of magnitude of improvement in the accuracy of in vitro–generated polymerase ribozymes7,8. Incidentally, this genome size coincides with that estimated for a minimal cell achieved by top-down analysis9, omitting the genes dealing with translation.

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Figure 1: Mutagenized ribozymes.
Figure 2: Time to extinction in generations as a function of the per digit effective mutation rate (μ*) in a population of constant size with N = 10,000 molecules for the Neurospora VS ribozyme (a,c,e,g) and the hairpin ribozyme (b,d,f,h).
Figure 3: Fraction of mutants with full activity (filled circles) or any activity (open squares), as a function of the number of point mutations.
Figure 4: Relationship between the per digit replication accuracy (q) and the permissible genome size (L) estimated from equation 2 with λ = 0.22 and s = 351.

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Acknowledgements

We thank I. Hofacker for his help with the Vienna RNA package, P. Mezey for allowing us to use the computer facilities at MUN (Canada) and F. Kondrashov for comments on an earlier version of the manuscript. Computer facilities were provided by Microdigit. This work was supported by grant and postdoctoral fellowship from the Hungarian National Research Fund (OTKA) to Á.K. M.S. is partially supported by Fundación Ramón Areces (Spain). This work was also supported by the COST D27 action (Prebiotic chemistry and early evolution).

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Correspondence to Eörs Szathmáry.

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Supplementary information

Supplementary Table 1

Mutations of the Neurospora VS ribozyme. (PDF 35 kb)

Supplementary Table 2

Mutations of the Hairpin ribozyme. (PDF 32 kb)

Supplementary Note

Construction of the empirically-supported fitness landscape for the Neurospora VS and the hairpin ribozyme. (PDF 58 kb)

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Kun, Á., Santos, M. & Szathmáry, E. Real ribozymes suggest a relaxed error threshold. Nat Genet 37, 1008–1011 (2005). https://doi.org/10.1038/ng1621

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