Cooperation in an All-RNA Network

  • Nilesh Vaidya
  • Jessica Mellor
  • Niles Lehman
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6937)


The discovery of catalytic RNA molecules (ribozymes) capable of catalyzing a significant number of diverse chemical reactions suggests that an RNA world preceded the DNA-RNA-Protein world we know today. The self-replication of RNA molecules would be the central process of the RNA world.However, a single selfreplicating RNA would not sustain information on its own if it surpassed the “error threshold” leadingto an error catastrophe (1). On the other hand, a cooperative network of RNA replicators would be able to accumulate, preserve and process information.In the current work, we used a collection of RNA fragments that covalently assemble into an Azoarcus group I ribozyme (2) to explore the ability of RNA replicators to form a cooperative catalytic network. Three different constructs of the Azoarcus ribozyme with different internal guide sequences (IGS) – GUG (canonical), GAG, and GCG – were designed that are capable of a minimal amount of self-assembly when broken into two fragments. Here, self-assembly depends on a mismatch with non-complementary sequences, CGU, CAU and CUU, respectively, to be recognized by IGS via autocatalysis. Yet when all three constructs are present in the same reaction vessel, concomitant assembly of all three covalent ribozymes is enhanced through an interdependent reaction network. Analysis of these reactions indicates that each system is capable of guiding its own reproduction weakly, along with providing enhanced catalytic support for the reproduction of other constructs through matched and mismatched IGS-tag interactions. The resulting RNA population was observed to evolve over time based on genotyping of more than 50 individual RNAs for various time-points. The unequal catalytic rates of various assembly reactions favor the assembly of one construct over the others. However, the cooperation among all three constructs help all constructs to assemble demonstrating that this RNA networkmeets many of the requirements of an all RNA hypercycle as envisioned by Eigen (1). Also, when co-incubated with non-interacting (i.e., selfish) yet efficient self-assembly systems, the cooperative assembly outcompetes the selfish self-assembly systems, demonstrating the ability of a cooperative organization to possess an evolutionary advantage (3).


Error Threshold Cooperative Network Assembly Reaction Cooperative Organization Catalytic Support 
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  1. 1.
    Eigen, M., Schuster, P.: The Hypercycle: A principle of natural self-organization. Die Naturwissenschaften 64, 541–565 (1977)CrossRefGoogle Scholar
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    Hayden, et al.: Systems chemistry on ribozyme self-construction: Evidence for anabolic autocatalysis in a recombination network. Angew. Chem. Int. Ed. 47, 8424–8428 (2008)CrossRefGoogle Scholar
  3. 3.
    Nowak, M., Highfield, R.: SuperCooperators: Altruism, Evolution, and Why We Need Each Other to Succeed. Free Press (2011)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Nilesh Vaidya
    • 1
  • Jessica Mellor
    • 1
  • Niles Lehman
    • 1
  1. 1.Department of ChemistryPortland State UniversityPortlandUSA

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