Peptides in Prebiotic Chemistry
I. Localizing RNA to Membranes
In primitive cells, membranes may have played a catalytic role by co-localizing reactants on their surface. For example, the localization of RNAs to membranes could promote ribozyme assembly and facilitate ribozyme catalysis. Such a scenario relies upon a simple mechanism to anchor the RNA onto the protocell membrane. Our studies showed that short, cationic, amphipathic peptides can drive RNA binding to both zwitterionic phospholipid and anionic fatty acid membranes. The association of these cationic peptides with phospholipid vesicles can enhance the local positive charge on a membrane and attract RNA polynucleotides. This discovery opens the door to studying membrane-localized prebiotic reactions with RNA catalysts or substrates.
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Kamat, N.P., Tobé, S., Hill, I.T., Szostak, J.W.*, 2015. Electrostatic Localization of RNA to Protocell Membranes by Cationic Hydrophobic Peptides. Angew Chem Int Ed 54, 11735–11739. PDF
II. Aminoacylation
(A) Schematic secondary structure of the overall chimeric dumbbell RNA crystallization construct. (B) Overall arrangement of the ligated loop construct and Fab BL3-6 in the crystal structure, with the ligated loop in green, glycine linker in cyan, sulphate ions as spheres. (C) Tertiary structure of the ligated loop construct. (D) Secondary structure of the ligated loop; interactions are denoted using the Leontis–Westhof nomenclature.
(A) RNA stems with overhangs become aminoacylated either chemically or enzymatically followed by loop-closing ligation mediated by the amino acid to yield covalently linked chimeric hairpin loops. Ligation of appropriate stem-loops leads to a chimeric aminoacyl-RNA synthetase ribozyme. (B) The proposed autocatalytic assembly cycle using an engineered, chimeric aminoacyl-RNA synthetase ribozyme – the Flexizyme. Glycylation of the cyan overhang followed by loop-closing ligation generates the chimeric ribozyme, which accelerates the initial glycylation leading to autocatalytic self-assembly. The light pink circle represents the weak active site of the non-covalently assembled Flexizyme fragments, while the dark pink circle represents the strong active site of the covalently-assembled Flexizyme.
Understanding how the ribosome and the genetic code became entrenched as the central axis of life is a key question in the field of origins of life. Before the ribosome could evolve, its substrates – aminoacylated RNAs – must have been readily synthesized by early life. However, chemical synthesis results in low steady-state levels of aminoacylated RNA and ribozymatic synthesis presupposes an existing aminoacyl-RNA synthetase ribozyme. How such a ribozyme could emerge is not clear. Resolving this conundrum, we have identified a small RNA motif resembling the T-loop, a universally conserved structure in all tRNAs, that facilitates efficient aminoacylation of a 2’-hydroxyl in its core. We have additionally found that aminoacylated RNA undergoes rapid nonenzymatic ligation with chemically activated RNA in both templated and loop-assisted formats. Combining these two reactions in the same pot, we have assembled a chimeric aminoacyl-RNA synthetase ribozyme that facilitates efficient and general RNA aminoacylation while assembling itself autocatalytically. Our findings help explain how the initial RNA aminoacylation could have occurred and facilitate further study of the evolution of coded ribosomal peptide synthesis.
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Radakovic, A., Wright, T.H., Lelyveld, V.S., Szostak, J.W.*, 2021. A Potential Role for Aminoacylation in Primordial RNA Copying Chemistry. Biochemistry 60, 477–488. PDF
Radakovic, A., DasGupta, S., Wright, T.H., Aitken, H.R.M., Szostak, J.W., 2022. Nonenzymatic assembly of active chimeric ribozymes from aminoacylated RNA oligonucleotides. Proc. Natl. Acad. Sci. U.S.A. 119, e2116840119. PDF
Radakovic, A., Lewicka, A., Todisco, M., Aitken, H.R.M., Weiss, Z., Kim, S., Bannan, A., Piccirilli, J.A., Szostak, J.W.*, 2024. A potential role for RNA aminoacylation prior to its role in peptide synthesis. Proc. Natl. Acad. Sci. U.S.A. 121, e2410206121. PDF