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New Findings Challenge Assumptions about the Origins of Life | SciTech Daily

 

New Findings Challenge Assumptions about the Origins of Life | SciTech Daily.

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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.’

 

Synthetic Biology Explained – YouTube

Martin Hanczyc: The line between life and not-life – YouTube

How to Make Life from the Primordial Soup on Vimeo

NASA – NASA Researchers: DNA Building Blocks Can Be Made in Space

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Ribozyme-Catalyzed Transcription of an Active Ribozyme

Abstract

A critical event in the origin of life is thought to have been the emergence of an RNA molecule capable of replicating a primordial RNA “genome.” Here we describe the evolution and engineering of an RNA polymerase ribozyme capable of synthesizing RNAs of up to 95 nucleotides in length. To overcome its sequence dependence, we recombined traits evolved separately in different ribozyme lineages. This yielded a more general polymerase ribozyme that was able to synthesize a wider spectrum of RNA sequences, as we demonstrate by the accurate synthesis of an enzymatically active RNA, a hammerhead endonuclease ribozyme. This recapitulates a central aspect of an RNA-based genetic system: the RNA-catalyzed synthesis of an active ribozyme from an RNA template.

via sciencemag.org

 

 

Ribozyme-catalyzed transcription of an active ribozyme.

Summary

A critical event in the origin of life is thought to have been the emergence of an RNA molecule capable of replicating a primordial RNA “genome.” Here we describe the evolution and engineering of an RNA polymerase ribozyme capable of synthesizing RNAs of up to 95 nucleotides in length. To overcome its sequence dependence, we recombined traits evolved separately in different ribozyme lineages. This yielded a more general polymerase ribozyme that was able to synthesize a wider spectrum of RNA sequences, as we demonstrate by the accurate synthesis of an enzymatically active RNA, a hammerhead endonuclease ribozyme. This recapitulates a central aspect of an RNA-based genetic system: the RNA-catalyzed synthesis of an active ribozyme from an RNA template.

Affiliation

Medical Research Council (MRC) Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.

Journal Details

Name: Science (New York, N.Y.)
ISSN: 1095-9203
Pages: 209-12

Links

 PubMed Articles

 

Glimpses of the Fourth Domain? | The Loom | Discover Magazine

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Wu et al., Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees, 2011. 

A preview of Principles of Life | NCSE

NCSE is pleased to offer a free preview (PDF) of David M. Hillis, David Sadava, H. Craig Heller, and Mary V. Price’s new textbook Principles of Life (Sinauer Associates and W. H. Freeman, 2010). The excerpt constitutes the whole of chapter 15, “Mechanisms of Evolution,” and offers as seven “key concepts” the principles that evolution is both factual and the basis of broader theory; that mutation, selection, gene flow, genetic drift, and nonrandom mating result in evolution; that evolution can be measured by changes in allele frequencies; that selection can be stabilizing, directional, or disruptive; that genomes reveal both neutral and selective processes of evolution; that recombination, lateral gene transfer, and gene duplication can result in new features; and that evolutionary theory has practical applications.

The publishers proclaim, “Numerous recent studies … confirm what a growing number of educators already know: the typical majors biology textbook has become too long, too detailed, and too expensive. … Written in the spirit of the reform movement that is reinvigorating the introductory majors course, Principles of Life cuts through the thicket of excessive detail and factual minutiae to focus on what matters most in the study of biology today. Students explore the most essential biological ideas and information in the context of the field’s defining experiments, and are actively engaged in analyzing research data. The result is a textbook that is hundreds of pages shorter (and significantly less expensive) than the current majors introductory books.”

 

 

Abiogenesis – origin of life

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