Biology subjects

Attwater, J.

Publications and source records attributed to Attwater, J..

4 recordsLinked to original sources

bioRxiv2025

5' RNA Aminoacylation via Interstrand Acyl-Transfer

The catalytic transformations driving coded protein synthesis revolve around linkage of amino acids to molecules of RNA as 2'/3'-aminoacyl esters. This defining molecular species of life is installed, supervised and utilised by complex catalysts, but its relative hydrolytic lability limits its accumulation and behaviour during the early development of the translation system in a simpler RNA-based biology. Herein, we describe a rapid catalytic transfer reaction inherent to RNA duplexes that establishes a more stable RNA-amino acid linkage. We observe spontaneous aminoacyl transfer from the 2'/3'-hydroxyl of a donor oligonucleotide to the 5'-hydroxyl of an adjacent template-bound acceptor oligonucleotide. In RNA systems dominated by base pairing, this transfer drives selective accumulation of the more stable 5'-aminoacyl RNA in the presence of a prebiotically-plausible aminoacylation reagent. This catalytic context could shape the distribution of aminoacylation amongst prebiotic RNAs and open opportunities for simple forms of RNA-directed peptide synthesis.

biochemistry↗

bioRxiv2024

A polymerase ribozyme that can synthesize both itself and its complementary strand

The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes could constitute such a system, but their large size and structural complexity hinder their self-replication and make their spontaneous emergence improbable. Here we describe QT45: a 45-nucleotide ribozyme, discovered from a random sequence pool, that catalyzes general RNA-templated RNA synthesis using trinucleotide triphosphate substrates. QT45 can synthesize both its complementary strand from a mix of all 64 trinucleotides and a copy of itself using 13 defined trinucleotides and one hexamer as substrates. The discovery of this complex activity in a small ribozyme suggests that polymerase ribozymes may be more abundant in RNA sequence space than anticipated, thereby facilitating the emergence of self-replication.

biochemistry↗

bioRxiv2023

Trinucleotide building blocks enable exponential ribozyme-catalysed RNA replication and open-ended growth of diverse RNA sequence pools

RNA replication is considered a crucial stage in the origins of life. However, both enzymatic and non-enzymatic RNA replication cycles are impeded by the "strand separation problem" (SSP), a form of product inhibition arising from the extraordinary stability of RNA duplexes and their rapid kinetics of reannealing. Here we show that RNA trinucleotide triphosphates (triplets) can overcome the SSP by binding to and kinetically trapping dissociated RNA strands in a single-stranded form, while simultaneously serving as substrates for RNA replication by a triplet polymerase ribozyme (TPR). This enabled exponential replication of both (+) and (-) strands of double-stranded RNAs by the TPR when driven by coupled pH and freeze-thaw cycles. We demonstrate replication of a fragment of the ribozyme itself, and open-ended amplification of random RNA sequence pools over >70 cycles, with emergence of partial, distributive TPR self-replication and triplet codon drift towards a primordial genetic code. One-sentence summaryRNA trinucleotide substrates together with simple physicochemical cycles enable RNA-catalysed replication of double-stranded RNA and partial, distributive self-replication of an RNA polymerase ribozyme.

molecular biology↗

bioRxiv2022

Cryo-EM structure and functional landscape of an RNA polymerase ribozyme

The emergence of an RNA replicase capable of self-replication is considered an important stage in the origin of life. RNA polymerase ribozymes (PR) including a variant that uses trinucleotide triphosphates (triplets) as substrates have been created by in vitro evolution and are the closest functional analogues of the replicase but the structural basis for their function is poorly understood. Here, we leverage single-particle cryo-EM and high-throughput mutation analysis to obtain the structure of a triplet polymerase ribozyme (TPR) apoenzyme and map its functional landscape. The TPR cryo-EM structure at 5-[A] resolution reveals an RNA heterodimer comprising a catalytic and an inactive accessory subunit, where the complex resembles a left hand with thumb and fingers at a 70{degrees} angle. The two subunits are connected by two distinct kissing-loop (KL) interactions that are essential for polymerase function. Our combined structural and functional data suggest a model for templated RNA synthesis by the TPR holoenzyme whereby heterodimer formation and KL interactions preorganize the TPR for optimal template binding and templated RNA synthesis activity. These results provide a foundation for a better understanding RNAs potential for self-replication.

biochemistry↗