Exploration of RNA Sequence Space in the Absence of a Replicase

  • Madhan R. Tirumalai
  • Quyen Tran
  • Maxim Paci
  • Dimple Chavan
  • Anuradha Marathe
  • George E. Fox
Original Article

Abstract

It is generally considered that if an RNA World ever existed that it would be driven by an RNA capable of RNA replication. Whether such a catalytic RNA could emerge in an RNA World or not, there would need to be prior routes to increasing complexity in order to produce it. It is hypothesized here that increasing sequence variety, if not complexity, can in fact readily emerge in response to a dynamic equilibrium between synthesis and degradation. A model system in which T4 RNA ligase catalyzes synthesis and Benzonase catalyzes degradation was constructed. An initial 20-mer served as a seed and was subjected to 180 min of simultaneous ligation and degradation. The seed RNA rapidly disappeared and was replaced by an increasing number and variety of both larger and smaller variants. Variants of 40–80 residues were consistently seen, typically representing 2–4% of the unique sequences. In a second experiment with four individual 9-mers, numerous variants were again produced. These included variants of the individual 9-mers as well as sequences that contained sequence segments from two or more 9-mers. In both cases, the RNA products lack large numbers of point mutations but instead incorporate additions and subtractions of fragments of the original RNAs. The system demonstrates that if such equilibrium were established in a prebiotic world it would result in significant exploration of RNA sequence space and likely increased complexity. It remains to be seen if the variety of products produced is affected by the presence of small peptide oligomers.

Keywords

RNA World Dynamic combinatorial chemistry Sequence space Origin of life Benzonase T4 RNA ligase 

Notes

Acknowledgements

This project/publication was made possible through the support of a Grant from the John Templeton Foundation. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation.

Author Contributions

MRT and QT contributed equally. MRT, AM, DC, and GEF designed experimental work which was carried out by MRT, AM, and DC. QT designed and implemented the data analysis procedures and prepared tables and figures. MP and GEF conceived the project. GEF and MP contributed intellectually and assisted with manuscript preparation and proofreading. All authors reviewed the manuscript.

Compliance with Ethical Standards

Conflict of interest

The authors declare they have no conflict of interest.

Supplementary material

239_2018_9846_MOESM1_ESM.docx (361 kb)
Supplementary material 1 (DOCX 361 KB)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department Biology & BiochemistryUniversity of HoustonHoustonUSA

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