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RNA teams up to beat selfish rivals | Chemistry World

 

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A network of ribozymes that catalyse each other’s bonding can out-compete other autocatalytic molecules © NPG

RNA molecules can team up to dominate more selfish rivals, in a way that might have allowed genetic information to survive in an early ‘RNA world’. Niles Lehman from Portland State University and his team have shown that cooperative ribozymes – RNA enzymes – outdo ‘selfish’ autocatalytic competitors for the same building blocks.1 ‘That says cooperation is an intrinsic facet to the origin of life and was a key step in going from chemistry to biology,’ Lehman tells Chemistry World.

 

The RNA world theory says that RNA both stored and catalysed reactions that reproduced genetic information in early evolution. But mutations or reactions that aren’t self-replication could easily halt individual molecules’ evolution. To avoid this, scientists proposed in the 1970s that RNA strands could work together, catalysing and reinforcing each other’s formation in a hypercycle network.2

In 2006 Lehman’s team broke a ribozyme from the proteobacteria Azoarcus into four fragments that could catalyse their own self-assembly.3 Having realised that their ribozyme could become part of a cooperative cycle, the chemists set out to produce a simple network comprising three different versions of it. Each version could only be correctly assembled from a specific pair of RNA fragments, but catalyses phosphodiester bond formation between a different pair.

The researchers controlled pairing through recognition sequences three bases long. The ribozyme’s 3’ ‘back’ fragment contained one recognition sequence and a catalytic core. The 5’ or ‘front’ fragment had one recognition sequence at each end, one of which recognised its 3’ partner. The other recognised the binding site in the catalytic core. Compared separately with a system of three autocatalytic, or selfish, ribozymes using the same type of back fragments, the cooperative networks yielded less ribozyme. But when selfish and cooperative systems were combined in the same tube, so that they would compete for the catalytic core, the cooperative system yielded more.

‘Essence of life’

For more complex networks, Lehman’s team produced front fragments with all four possible RNA bases in the middle position of each of the recognition sequences. Incubating all these randomised fragments with three ‘back’ partners provided 48 ribozyme combinations. After eight hours, the most abundant ribozymes in the mixture formed cooperatively, though selfish combinations persisted.

Lehman and his colleagues then used the same randomised combination, but extracted 10% of the mixture and introduced it to a new stock of starting fragments every hour. After one hour, 33% of the ribozymes were autocatalytic, but by 8 hours that had fallen to just 25%. Lehman notes that in both of the more complex network experiments, those changes are telling. ‘You can not only form networks, but the network structure, dynamics and interactions are evolving,’ he says. ‘These are chemical dynamics that are starting to manifest informational characteristics. We’re looking at interactions that change over time, which start to capture the essence of life.’

Phil Holliger from the MRC Laboratory of Molecular Biology in Cambridge, UK, who has worked on non-DNA polymer evolution disagrees that these dynamics evolve. ‘But they clearly develop over time and that raises interesting questions,’ he says. ‘Is more interconnection better than less interconnection? This area of RNA systems chemistry is going to be very interesting to follow up.’

Gerald Joyce from the Scripps Research Institute in La Jolla, California, who has studied ribozymes’ role in the RNA world, calls the work ‘fascinating’. ‘This is the first paper to dig into what I would call the birth of molecular ecology, how these catalytic entities play off of each other,’ he says. ‘Do they fight tooth and claw? Or do they cooperate? They’ve shown, with real molecules, that they cooperate.’

 

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Iron and RNA catalysis

Chemical substitution: On early Earth, iron may have performed magnesium’s RNA folding job

Chemical substitution: On early Earth, iron may have performed magnesium’s #RNA folding job:… #scidaily @MyEN

Jun 1  – Sciencedaily (Reply uRemove Tweet hRetweet òMore

RNA Folding and Catalysis Mediated by Iron (II)

Abstract

Mg2+ shares a distinctive relationship with RNA, playing important and specific roles in the folding and function of essentially all large RNAs. Here we use theory and experiment to evaluate Fe2+ in the absence of free oxygen as a replacement for Mg2+ in RNA folding and catalysis. We describe both quantum mechanical calculations and experiments that suggest that the roles of Mg2+ in RNA folding and function can indeed be served by Fe2+. The results of quantum mechanical calculations show that the geometry of coordination of Fe2+ by RNA phosphates is similar to that of Mg2+. Chemical footprinting experiments suggest that the conformation of the Tetrahymena thermophila Group I intron P4P6 domain RNA is conserved between complexes with Fe2+ or Mg2+. The catalytic activities of both the L1 ribozyme ligase, obtained previously by in vitro selection in the presence of Mg2+, and the hammerhead ribozyme are enhanced in the presence of Fe2+ compared to Mg2+. All chemical footprinting and ribozyme assays in the presence of Fe2+ were performed under anaerobic conditions. The primary motivation of this work is to understand RNA in plausible early earth conditions. Life originated during the early Archean Eon, characterized by a non-oxidative atmosphere and abundant soluble Fe2+. The combined biochemical and paleogeological data are consistent with a role for Fe2+ in an RNA World. RNA and Fe2+ could, in principle, support an array of RNA structures and catalytic functions more diverse than RNA with Mg2+ alone.

RNA in evolution

Overview

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RNA in evolution

  1. Niles Lehman

Article first published online: 16 JUL 2010

DOI: 10.1002/wrna.37

Copyright © 2010 John Wiley & Sons, Ltd.

Issue

Wiley Interdisciplinary Reviews: RNA

Wiley Interdisciplinary Reviews: RNA

Volume 1, Issue 2, pages 202–213, September/October 2010

RNA has played a variety of roles in the evolutionary history of life on the Earth. While this molecule was once considered a poor cousin of the more influential polymers in the cell, namely DNA and proteins, a string of important discoveries over the last 50 years has revealed that RNA may in fact be the cornerstone of biological function. In particular, the finding that RNA can be catalytic, and thus possess both a genotype and a phenotype, has forced us to consider the possibility that life’s origins began with RNA, and that the subsequent diversification of life is aptly described as a string of innovations by RNA to adapt to a changing environment. Some of these adaptations include riboswitches, ribonucleoproteins (RNPs), RNA editing, and RNA interference (RNAi). Although many of these functions may seem at first glance to be recent evolutionary developments, it may be the case that all of their catalytic activities trace their roots back to a primordial ‘RNA World’ some four billion years ago, and that RNA’s diversity has a continuous thread that pervades life from its very origins. Copyright © 2010 John Wiley & Sons, Ltd.

 

A World Apart: From the RNA World to the Real World

“More than a half-dozen biotechnology companies have been launched to develop and commercialize ribozyme-based diagnostics and therapeutics. The pioneer was Ribozyme Pharmaceuticals, Inc. (RPI), of Boulder, Colorado. Founded in 1992 by current HHMI President Thomas R. Cech, the company was organized to pursue the discovery from Cech’s laboratory that some types of RNA, called ribozymes, can cleave other RNA molecules. RPI is developing therapeutic ribozymes to target the messenger RNA (mRNA) of proteins implicated in specific diseases. Like all proteins, disease-related proteins are encoded by genes, whose instructions are carried to the ribosome by mRNA. By synthesizing ribozymes that bind and cleave these mRNAs, RPI scientists are trying to prevent undesirable proteins from being produced.

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Hhmi_bulletin-a_world_apart_20100922

(download)

Illustration: J.W. Stewart

source: the HHMI Bulletin,
June 2002, pages 14-19.
©2002 Howard Hughes Medical Institute

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