The Chemical Likelihood of Ribonucleotide-α-Amino acid Copolymers as Players for Early Stages of Evolution

Abstract

How ribosomal translation could have evolved remains an open question in most available scenarios for the early developments of life. Rather than considering RNA and peptides as two independent systems, this work is aimed at assessing the possibility of formation and stability of co-polymers or co-oligomers of α-amino acids and nucleotides from which translation might have evolved. Here we show that the linkages required to build such mixed structures have lifetimes of several weeks to months at neutral pH and 20 °C owing to the mutual protecting effect of both neighboring phosphoramidate and ester functional groups increasing their stability by factors of about 1 and 3 orders of magnitude, respectively. This protecting effect is reversible upon hydrolysis allowing the possibility of subsequent reactions. These copolymer models, for which an abiotic synthesis pathway is supported by experiments, form a basis from which both polymerization and translation could have logically evolved. Low temperatures were identified as a critical parameter for the kinetic stability of the aminoacylated nucleotide facilitating the synthesis of the model. This observation independently supports the views that any process involving RNA aminoacyl esters, outstandingly including the emergence of translation, was more probable at 0 °C or below and might be considered a kinetic marker constraining the environment in which translation has evolved. Electronic supplementary material The online version of this article (10.1007/s00239-019-9887-7) contains supplementary material, which is available to authorized users.

A Potential Role for Aminoacylation in Primordial RNA Copying Chemistry

“…As the gel-based assay does not report on the specific linkage cleaved (ester vs. phosphoramidate), we desalted samples from the cleavage of 2 after 24 hours and analyzed the reaction products by LC-MS. Only products resulting from ester cleavage could be observed ( Figure S4), consistent with the previously reported stability of the phosphoramidate linkage at pH values above 5.0. 9 The proportion of amino acid bridged RNAs within a prebiotic population of polynucleotides would depend on the rates of amino acid activation and aminoacylation of RNA, and the competing rates of aminoacyl ester hydrolysis and phosphoramidate linkage formation. To investigate the rate of primer extension via phosphoramidate formation we measured the rates of primer extension on a template designed to provide a single binding site for C*C imidazolium-bridged dinucleotide (Figure 4, Figure S5).…”

“…On a poly(U) template, 2′(3′)-glycyl adenosine reacted with 5ʹ-imidazole activated AMP to afford a dinucleotide species that was bridged by the glycine residue 8 . Formation of such phosphoramidate linked amino-acid RNA 'co-polymers' dramatically increases the stability of both the aminoacyl ester and phosphoramidate bonds, suggesting a mechanism for enhanced covalent capture of amino acids by early RNA 9 . In parallel, the Orgel laboratory 10,11 and later our own group [12][13][14] demonstrated that nucleotides with either 2ʹ-or 3ʹ-amino groups exhibit a large increase in the rate and yield of non-enzymatic polymerization due to the greater nucleophilicity of the amine substituent relative to a hydroxyl group.…”

How Prebiotic Chemistry and Early Life Chose Phosphate

“…However, in some cases their reactivity could be advantageous as probably in the case of the aminoacylation of the 3′(2′)-end of RNA for which NCA proved to be inefficient [58]. Examples of an advantageous role of mixed anhydrides have been observed from their involvement as intermediates undergoing a fast intramolecular acyl transfer as in the formation of esters with ribonucleotides [50,56,59,60]. Phosphate moieties could indeed act as handles capable of reacting with activated acyl moieties and then to intramolecularly transfer the acyl group to a poor nucleophile thanks to the entropic advantage of intramolecular processes [16,61].…”

“…The facilitated nucleotide polymerization has allowed major studies of the replication process proceeding in the absence of enzymes [31,83,84,85]. It could also be considered as a basis for the formation of mixed structures [60,86] involving both amino acids and nucleotides bound through ester and phosphoramidate linkage with an unexpected lifetime for aminoacyl esters (Figure 6) [60].…”

Templates direct the sequence-specific anchoring of theC-terminus of peptido RNAs

“…Transamidation involving 2′/3′-linked amino acids and 5′-phosphoimidazolides templated by a homopolymer has been studied in the 1970s, 23 and doubly linked amino acids were recently shown to be more stable hydrolytically than their aminoacyl counterparts. 24 More distantly related coupling reactions have been performed with the goal of reading out sequence information of a template, 25 but how RNA templates may have directed the anchoring of the carboxy-terminus of N -terminally linked peptides to the 3′-terminus of oligonucleotides sequence-specifically was unclear.…”