Ribozyme Catalysis of Metabolism in the RNA World

  title={Ribozyme Catalysis of Metabolism in the RNA World},
  author={Xi Chen and Na Li and Andrew D. Ellington},
  journal={Chemistry \& Biodiversity},
In vitro selection has proven to be a useful means of explore the molecules and catalysts that may have existed in a primoridal ‘RNA world’. By selecting binding species (aptamers) and catalysts (ribozymes) from random sequence pools, the relationship between biopolymer complexity and function can be better understood, and potential evolutionary transitions between functional molecules can be charted. In this review, we have focused on several critical events or transitions in the putative RNA… 

RNA Synthesis by in Vitro Selected Ribozymes for Recreating an RNA World

This review focuses on three types of ribozymes that could have been involved in the synthesis of RNA, the core activity in the self-replication of RNA world organisms.

Imaginary Ribozymes.

Some of the most striking observations made from examinations of natural riboswitches are highlighted and used as a basis to imagine the characteristics and functions of long-extinct ribozymes from the RNA World.

The potential versatility of RNA catalysis

How RNA might catalyze a wider variety of chemistries, and particularly how information gleaned from riboswitches could suggest how ribozymes might recruit coenzymes to expand their chemical range is discussed.

Ribozymes and riboswitches: modulation of RNA function by small molecules

Mutational, kinetic and structural analyses reveal that an active‐site guanosine and GlcN6P mutually modulate the ability of each other to function as general acid‐base catalysts.

Arginine Cofactors on the Polymerase Ribozyme

Results suggest that the existing polymerase ribozyme is not well suited to using an arginine cofactor, because this is the amino acid most adept to interact with RNA.

The case of the missing allosteric ribozymes

This Perspective summarizes the known types of ligand-controlled ribozymes and riboswitches and discusses the reasons why allosteric riboz enzymes formed by fusion of RNA enzymes and RNA aptamers are rare in today’s biological systems.

Evolutionary origins and directed evolution of RNA.

Structure and mechanism of a methyltransferase ribozyme

The authors present the crystal structure of the MTR1 ribozyme that transfers the methyl group from O 6 -methylguanine to an adenine N1 in the target RNA and propose a catalytic mechanism based upon proximity, orientation and general acid catalysis.

Model systems for primordial enzymes

Amino-acid and peptidic catalysts, along with artificial proteins constructed from reduced amino acid alphabets demonstrate that simplified building block repertoires suffice to assemble functional enzymes.

Studies towards the prebiotic synthesis and phosphorylation of ribonucleotides

The discovery of a generational node in the network of prebiotic chemistry that links the syntheses of amino acids with nucleotides 5'-phosphates suggests that these different groups of metabolites need not have arisen from separate chemistries, helping to get a better understanding of the processes governing the chemical evolution of life.



In vitro evolution of a self-alkylatlng ribozyme

RNA enzymes are postulated to have catalysed all chemical reactions in the earliest living cells, and selection for self-biotinylation yields a transfer RNA-like ribozyme that efficiently catalyses carbon–nitrogen bond formation.

Ribozyme-catalysed amino-acid transfer reactions

In vitro selection and evolution is used to isolate ribozymes with acyl transferase activity from a pool of random RNA sequences and one of them transfers an amino acid to itself in a reaction that is analogous to peptidyl transfer on the ribosome.

New ligase-derived RNA polymerase ribozymes.

Eight ligase-derived polymerase ribozymes isolated from a pool of variants of an existing RNA ligase ribozyme are reported, each a new potential starting point for further in vitro evolution and engineering and together substantially enrich the set of candidates from which an RNA replicaseribozyme might eventually emerge.

Peptide bond formation by in vitro selected ribozymes

This work demonstrates the in vitro selection of ribozymes (196 nucleotides) that perform the same peptidyl transferase reaction as the ribosome: that is, they can join amino acids by a peptide bond.

Isolation of new ribozymes from a large pool of random sequences [see comment].

An iterative in vitro selection procedure was used to isolate a new class of catalytic RNAs (ribozymes) from a large pool of random-sequence RNA molecules, leading to improvement of the average ligation activity and the emergence of ribozymes with reaction rates 7 million times faster than the uncatalyzed reaction rate.

RNA, the first macromolecular catalyst: the ribosome is a ribozyme.

Selection of RNA amide synthases.