title: The juxtaposition of ribose hydroxyl groups: the root of biological catalysis and the RNA world?
abstract: We normally think of enzymes as being proteins; however, the RNA world hypothesis suggests that the earliest biological catalysts may have been composed of RNA. One of the oldest surviving RNA enzymes we are aware of is the peptidyl transferase centre (PTC) of the large ribosomal RNA, which joins amino acids together to form proteins. Recent evidence indicates that the enzymatic activity of the PTC is principally due to ribose 2'-OHs. Many other reactions catalyzed by RNA and/or in which RNA is a substrate similarly utilize ribose 2'-OHs, including phosphoryl transfer reactions that involve the cleavage and/or ligation of the ribose-phosphate backbone. It has recently been proposed by Yakhnin (2013) that phosphoryl transfer reactions were important in the prebiotic chemical evolution of RNA, by enabling macromolecules composed of polyols joined by phosphodiester linkages to undergo recombination reactions, with the reaction energy supplied by the phosphodiester bond itself. The almost unique juxtaposition of the ribose 2'-hydroxyl and 3'-oxygen in ribose-containing polymers such as RNA, which gives ribose the ability to catalyze such reactions, may have been an important factor in the selection of ribose as a component of the first biopolymer. In addition, the juxtaposition of hydroxyl groups in free ribose: (i) allows coordination of borate ions, which could have provided significant and preferential stabilization of ribose in a prebiotic environment; and (ii) enhances the rate of permeation by ribose into a variety of lipid membrane systems, possibly favouring its incorporation into early metabolic pathways and an ancestral ribose-phosphate polymer. Somewhat more speculatively, hydrogen bonds formed by juxtaposed ribose hydroxyl groups may have stabilized an ancestral ribose-phosphate polymer against degradation (Bernhardt and Sandwick 2014). I propose that the almost unique juxtaposition of ribose hydroxyl groups constitutes the root of both biological catalysis and the RNA world.
authors.affiliation: Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand, harold.bernhardt@otago.ac.nz.
authors.forename: Harold S
authors.initials: HS
authors.lastname: Bernhardt
mesh_terms: D055162:Biocatalysis; D019418:Evolution, Chemical; D017665:Hydroxyl Radical / Q000737:chemistry*; D010710:Phosphates / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D012266:Ribose / Q000737:chemistry*
chemical_list: D010710:Phosphates; D017665:Hydroxyl Radical; D012313:RNA; D012266:Ribose