Protein-free ribosomal RNA scaffolds can assemble poly-lysine oligos from charged tRNA fragments

Abstract

Ribosomal protein synthesis is a central process of the modern biological world. Because the ribosome contains proteins itself, it is very important to understand its precursor and evolution. Small ribozymes have demonstrated the principle of “RNA world” hypothesis, but protein free peptide ligase remains elusive. In this report, we have identified two fragments in the peptidyl transfer center that can synthesize a 9-mer poly-lysine in a solution contains Mg 2+ . This result is deduced from isotope-shifting in high resolution MS. To our best knowledge, this is the longest peptide oligo that can be synthesized by a pure ribozyme. Via single molecule FRET experiments, we have demonstrated the ligase mechanism was probably by substrate proximity via dimerization. We prospect that these RNA fragments can be useful to synthesize template free natural and non-natural peptides, to be model system for peptidyl transfer reaction mechanism and can shed light to the evolution of ribosome.

Origin of Life: Chiral Short RNA Chains Capable of Non‐Enzymatic Peptide Bond Formation

“…[28] Additionally, a very recent report indicated that even Mg dependent RNA dimers, of a sequence of ribosomal RNA chains that includes the protoribosome and a part of its immediate neighborhood, were found suitable for allowing the synthesis of a 9-mer oligo-lysine. [29] Here we suggest that individual RNA chains can self-fold and iteract with each other to form dimeric apparatuses that could have evolved into the protoribosome. As only the structure of the backbone of the symmetrical region obeys the pseudo two-fold symmetry, with no sequence symmetry, we investigated the terms under which several sequences of this apparatus, found in various existing ribosomes, can produce RNA dimers capable of facilitating peptide bond formation by virtue of the amino acids positioning.…”

Origin of life: protoribosome forms peptide bonds and links RNA and protein dominated worlds

“…( 34 ) generated a minimal construct that comprises much of the 23S rRNA peptidyl transferase center, including the central loop and the A- and P-loops but their minimal rRNA domain was inactive for peptide bond formation under all tested conditions. In addition, while working on this manuscript a study ( 58 ), which is based on our suggestions ( 12 , 21 , 25 , 59–66 ), indicating that a 9 lysines oligomer could be produced by a larger RNA construct encapsulating the ribosomal PTC, was published. However, their constructs include additional extensions to the minimal protoribosome and are 2x110-mer long.…”

Prebiotic Assembly of Cloverleaf tRNA, Its Aminoacylation and the Origin of Coding, Inferred from Acceptor Stem Coding-Triplets

“…Additionally, a model for the autonomous formation of a non-coding proto-ribosome, derived from the symmetrical region enclosing the PTC of the contemporary large ribosomal subunit [ 35 ], which materialized via the dimerization of two L-shaped RNA entities, was suggested [ 36 , 37 ]. Recently such dimeric proto-ribosomes were experimentally demonstrated to assemble spontaneously, catalyzing peptide bond formation and yielding short peptides [ 38 , 39 ].…”