Repeating cycles of chemically-driven RNA replication within model protocells

Project Information

RNA-Rep

Grant agreement ID: 839899

DOI

10.3030/839899

Project closed

EC signature date 21 March 2019

Start date 1 April 2019

End date 31 March 2021

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 224 933,76

EU contribution

€ 224 933,76

Coordinated by

UNITED KINGDOM RESEARCH AND INNOVATION
United Kingdom

Periodic Reporting for period 1 - RNA-Rep (Repeating cycles of chemically-driven RNA replication within model protocells)

Reporting period: 2019-04-01 to 2021-03-31

Summary of the context and overall objectives of the project

Deciphering how nucleic acids replicated in the absence of genetically encoded enzymes is critical to understanding the onset of Darwinian evolution. One unsolved difficulty with non-enzymatic RNA replication is that non-enzymatic copying of a template strand results in the formation of an RNA duplex, which must then be denatured in order for subsequent rounds of replication to take place. Although RNA strands can be separated by heating, re-annealing kinetically outcompetes slow non-enzymatic copying, thus inhibiting RNA amplification. The project "RNA-Rep" was designed to develop a primitive cell-based method to favour multiple cycling of non-enzymatic RNA replication by physically separating melted strands of RNA in different compartments, so that re-annealing is not possible.

The ultimate goal of RNA-Rep was to enable multiple cycles of non-enzymatic RNA replication by exploiting efficient activating agents and prebiotic compartmentalisation. The strategy was to use protocells as self-boundary systems with thermally-driven permeability, allowing for the reshuffling of activated substrates after each non-enzymatic RNA replication cycle. The specific objectives of RNA-Rep were:
1. to identify the optimal compartmentalisation model compatible with prebiotic activation and thermal fluctuations;
2. to evaluate the effect of compartmentalisation on thermally-driven multiple cycling of non-enzymatic RNA replication;
3. to evaluate the effect of free or membrane-bound RNA molecules in the efficiency of non-enzymatic RNA replication.

RNA-Rep was a highly original and multidisciplinary project, which combined the strength of organic and supramolecular chemistry with the power of non-enzymatic RNA biochemistry to yield an innovative project that exploited the ER's expertise in protocellular systems and provided the ER with extensive training in organic synthesis, chemical biology and biophysics.
While the development of the challenging concepts upon which RNA-Rep was built took longer than foreseen and experimental work was heavily impacted by the pandemic that affected one year of this fellowship, promising results have been obtained regarding the compatibility of prebiotic activation with protocells and the effect of multiple thermal cycling on compartments.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The work performed has covered several aspects related to the main scope of RNA-Rep, as summarised in the following outcomes.

- Compartmentalisation and prebiotic activation.
Before the beginning of this fellowship, the ER contributed to the development of a so-called "prebiotic activation chemistry" that can be used to simultaneously activate phosphate and carboxylate groups. This activation chemistry was exploited for the synthesis of prebiotic lipids, as well as for the non-enzymatic polymerisation of RNA and peptides. Therefore, after the beginning of this fellowship, the ER exploited the same chemistry to evaluate its compatibility with a library of prebiotic lipid membranes. Results: Only membranes made of phospholipids bearing a cyclic phosphate headgroup were found to be fully stable and inert to the conditions required for the prebiotic activation of nucleotides and amino acids.
- Membrane-bound biological building blocks.
Fatty acids are considered among the most prebiotic class of lipids likely available on early Earth. Therefore, the ER explored the effect of activation chemistry on membranes made of fatty acids. Results: When membranes made of fatty acids were exposed to activation chemistry, monomeric fatty acids were found to be reactive. The activation of fatty acids' headgroups by prebiotic activating agents yields novel species, namely fatty acylated nucleotides and amino acids. Such amphiphilic species can interact with lipid membranes, driving their growth and co-localising relevant biomolecules (such as RNA strands).
- Compartmentalisation and thermal fluctuations.
Evaluating the effect of thermal fluctuations on lipid membranes was of fundamental importance for the further development of RNA-Rep. Results: While phospholipid-based membranes are stable upon exposure to a wide range of temperatures, membranes made of fatty acids were found to undergo a phase transition to oil droplets upon heating. Such phase transition is reversible and tunable and can be exploited to drive the generation of a new cohort of protocells with reshuffled content.
Overall, all the results obtained with this fellowship validate the proposed approach and pave the way for the efficient multiple cycling of non-enzymatic RNA polymerisation within compartments.

Publications (in the context of RNA-Rep):
Liu Z., Wu L., Xu J., Bonfio C., Russell D. A., Sutherland J. D. - Harnessing chemical energy for the activation and joining of prebiotic building blocks. Nature Chemistry (2020), 12, 1023-1028.
Bonfio C.*, Russell D. A., Green N. J., Mariani A., Sutherland J. D. - Activation chemistry drives the emergence of functionalised protocells. Chemical Science (2020), 11, 10688-10697.
Rubio-Sanchez R., Wang A., O’Flaherty D., Coscia F., Di Michele L., Cicuta P., Bonfio C.* – Thermal oscillations enable reshuffling of genetic material in a primitive cell cycle. BioRxiv (2021), DOI: 10.1101/2021.04.01.438038.

Other publications:
Pellegrini L., Bonfio C., Chadwick J., Begum F., Skehel M., Lancaster M. Choroid plexus organoids predict CNS drug permeability and reveal human CSF proteins produced by specialized cell types. Science (2020), 369, eaaz5626.
Bonfio C.* - The curious case of peptide-coordinated iron-sulfur clusters: prebiotic and biomimetic insights. Dalton Transactions (2021), 50, 801-807.

Dissemination (selected conferences):
Jan 2021 Origin of Life - Early Career Network 1st Symposium (Plenary e-lecture)
Jun 2020 Departmental e-Seminar - Earth Life Science Institute (ELSI), Tokyo, JP
Feb 2020 Dalton Emerging Researcher Award Lecture - University of Bristol, UK
Jan 2020 Meeting of Young Chemists of the Països Catalans - Sitges, ES (Plenary lecture)
Oct 2019 Departmental Seminar - Soft Micro Systems, CNRS, Univ. Bordeaux, FR

Communication and outreach activities:
Sep 2019 Speaker (title of the talk: “A recipe for primordial life”) - European Researchers' Night, Cambridge
Jul 2019 Exhibition Designer and Leading Coordinator (title of the exhibition "A recipe for primordial life") - Royal Society Summer Science Exhibition, London, UK
since 2019 Marie Skłodowska Curie Actions (MSCA) Ambassador - delivered seminars on MSCA project writing at IUPAC 2019 (Paris, FR) and at online events organised by the European Young Chemist Network (2020)

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

In terms of scientific impact, the ER explored for the first time the compatibility between primitive membranes and chemical reactions hosted within them. In general, identifying the optimal class of prebiotic compartments to host chemical processes will support all future studies that aim to bridge prebiotic chemistry with modern biology. Moreover, the findings on the thermal stability of lipid membranes will have not only an impact in future projects within the prebiotic chemistry community, but also for potential studies in the areas of soft matter, drug delivery and biophysics.

In terms of impact on the ER's career development, during the course of RNA-Rep, the ER acquired and improved her skills in grant writing, public outreach, management and leadership.

Primitive cell, composed of 3 elements (primordial genome, metabolism and membrane)