Catalyzed and Spontaneous Reactions on Ribozyme Ribose

Abstract

The RNA world hypothesis requires that early translation be catalyzed by RNA enzymes. Here we show that a five-nucleotide RNA enzyme, reacting with a tetranucleotide substrate and elevated PheAMP, forms aminoacyl- and peptidyl-RNAs RNA-Phe through RNA-Phe(5). A second series of products is formed from RNA-Phe diesters, after trans migration of phenylalanine from the 2'- to the 3'-hydroxyl group of the substrate RNA, followed by reaminoacylation of the 2'-OH. While the ribozyme is required for initial attachment of phenylalanine to an RNA substrate, as well as reacylation (and thus for formation of all products), further extension into RNA-peptides appears to be an uncatalyzed, but RNA-stimulated reaction. The ribozyme readily turns over at high PheAMP and GCCU concentrations. Thus, GUGGC/GCCU comprises a true RNA enzyme. We define Michaelis-Menten parameters plus and minus divalent magnesium and characterize ca. 20 molecular species of aminoacyl-, peptidyl-, dipeptidyl-, and mixed peptidyl/aminoacyl-RNAs.

An Exit Cavity Was Crucial to the Polymerase Activity of the Early Ribosome

“…The recently described aminoacylated RNAs and the extremely small ribozymes that produce them (Turk et al, 2011) are highly consistent with the RNA World. The pocket-like protoribosome proposed previously (Davidovich et al, 2009;Krupkin et al, 2011) is as small as 120-180 nucleotides and might actually be constructed by hybridization of several smaller pieces as well as by ligation or duplication of RNA chains.…”

“…1. This, coupled with a recent breakthrough discovery that a fourbase RNA can be readily aminoacylated by a five-residue ribozyme (Turk et al, 2011), has led us to hypothesize that an exit cavity was a key feature of the prebiotic bonding machine that led to the eventual development of the modern ribosome.…”

“…Although we expect that the presumed protoribosome will ultimately be shown to have catalytic ability, the argument described above is not changed if a larger portion of the modern RNA is required for its catalytic activity as long as a portion of the exit cavity is present. Likewise, no change is necessary for cases when the carriers/ activators are short RNAs if one of them is carrying a di-or tripeptide (Turk et al, 2011), as the preexisting small peptide could enter the tunnel cavity prior to the first synthesis step.…”

The meaning of a minuscule ribozyme

“…It is -only slightly dependent on divalents, functional with dilute monovalents; -still yields highly regiospecific initial aminoacylation at U 2 0 -OH; -faster at higher pH, suggesting that attack by 2 0 -OH is probably rate-limiting; and -undiscriminating with regard to the aminoacyl group and activating nucleotide 8. KINETIC ANALYSIS Moreover, the kinetics of GUGGC/GCCU are describable as those of an ordered bisubstrate enzyme [11]. The chemistry seems necessarily ordered, because the substrate GCCU must assemble with ribozymic GUGGC before the active site for PheAMP binding exists.…”

The evolutionary history of the ribosome and its relevance to the search for life elsewhere in the universe

“…The formation of extremely small RNAs carrying amino acids has recently been shown to be compatible with an RNA world. 16 If such a system is shown to be capable of synthesizing peptides then this may require some rethinking of the RNA World hypothesis. The usual belief is that a RNA capable of self replication could evolve.…”