ScienceDaily (Aug. 31, 2009) — In 1952, Stanley Miller filled two flasks with chemicals assumed to be present on the primitive Earth, connected the flasks with rubber tubes and introduced some electrical sparks as a stand-in for lightning. The now famous experiment showed what amino acids, the building blocks of proteins, could easily be generated from this primordial stew. But despite that seminal experiment, neither he nor others were able to take the next step: that of showing how life’s code could come from such humble beginnings.
Midway Geyser Basin, Yellowstone National Park, Wyoming. The orange color is due to cyanobacteria, one of the earliest forms of life on Earth. A new model shows how primitive life could have evolved from simple amino acids in a "primordial soup." (Credit: iStockphoto/Steve Geer)
By working with the simplest amino acids and elementary RNAs, physicists led by Rockefeller University’s Albert J. Libchaber, head of the Laboratory of Experimental Condensed Matter Physics, have now generated the first theoretical model that shows how a coded genetic system can emerge from an ancestral broth of simple molecules. “All these molecules have different properties and these properties define their interactions,” says first author Jean Lehmann, a postdoctoral fellow in the lab, whose work appears in the June issue of PLoS One. “What are the constraints that allow these molecules to self-organize into a code? We can play with that.”
The genetic code is a triplet code such that every triplet sequence of letters on messenger RNA corresponds to one of the 20 amino acids that make up proteins. Molecular adapters called transfer RNAs (tRNAs) then convert this information into proteins that can achieve some specific tasks in the organism. Let’s say that each triplet sequence on messenger RNA, known as a codon, represents an outlet that can only accept a tRNA with a complementary anticodon. Translation works because each codon-anticodon match corresponds with an amino acid. As each tRNA is plugged in, a chain of amino acids is formed in the same order as the codons until translation is complete.
However, primitive tRNAs were not as finicky as tRNAs are today and could load any amino acid known to exist during the time of prebiotic Earth. Without the ability of tRNAs to discriminate between various amino acids, such a random system might not be able to self-assemble into a highly organized code capable of supporting life.
To find out if it could, Libchaber and Lehmann, together with Michel Cibils at the Swiss Federal Institute of Technology (EPFL) in Lausanne, Switzerland, worked with a simple theoretical system. They took two of the simplest amino acids thought to exist billions of years ago, two primitive tRNAs and an RNA template with two complementary codons, and then developed an algorithm to incrementally change the concentration of each molecule. Their goal was to see which conditions, if any, could coax the system to specifically translate codons in a nonrandom fashion. They found that the properties of the molecules set the concentrations at which the molecules needed to exist for a coded regime to emerge.
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Emergence of a Code in the Polymerization of Amino Acids along RNA Templates
Jean Lehmann1*, Michel Cibils2, Albert Libchaber1
1 Center for Studies in Physics and Biology, The Rockefeller University, New York, New York, United States of America, 2 Section de Mathématiques, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
Abstract Top
The origin of the genetic code in the context of an RNA world is a major problem in the field of biophysical chemistry. In this paper, we describe how the polymerization of amino acids along RNA templates can be affected by the properties of both molecules. Considering a system without enzymes, in which the tRNAs (the translation adaptors) are not loaded selectively with amino acids, we show that an elementary translation governed by a Michaelis-Menten type of kinetics can follow different polymerization regimes: random polymerization, homopolymerization and coded polymerization. The regime under which the system is running is set by the relative concentrations of the amino acids and the kinetic constants involved. We point out that the coding regime can naturally occur under prebiotic conditions. It generates partially coded proteins through a mechanism which is remarkably robust against non-specific interactions (mismatches) between the adaptors and the RNA template. Features of the genetic code support the existence of this early translation system.
Citation: Lehmann J, Cibils M, Libchaber A (2009) Emergence of a Code in the Polymerization of Amino Acids along RNA Templates. PLoS ONE 4(6): e5773. doi:10.1371/journal.pone.0005773
Editor: Jörg Langowski, German Cancer Research Center, Germany
Received: March 10, 2009; Accepted: May 5, 2009; Published: June 3, 2009
Copyright: © 2009 Lehmann et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: The authors have no support or funding to report.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: jlehmann@rockefeller.edu
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