Self-replicating Molecules Research Articles

Noisy clues to the origin of life.

The origin of stable self-replicating molecules represents a fundamental obstacle to the origin of life. The low fidelity of primordial replicators places restrictions on the quantity of information encoded in a primitive nucleic acid alphabet. Further difficulties for the origin of life are the role of drift in small primordial populations, reducing the rate of fixation of superior replicators, and the hostile conditions increasing developmental noise. Thus, mutation, noise and drift are three different stochastic effects that are assumed to make the evolution of life improbable. Here we show, to the contrary, how noise present in hostile early environments can increase the probability of faithful replication, by amplifying selection in finite populations. Noise has negative consequences in infinite populations, whereas in finite populations, we observe a synergistic interaction among noise sources. Hence, two factors formerly considered inimical to the origin of life-developmental noise and drift in small populations-can in combination give rise to conditions favourable to robust replication.

The reactions of nitrogen heterocycles with acrolein: scope and prebiotic significance.

It has been suggested that life began with a self-replicating RNA molecule. However, after much research into the prebiotic synthesis of RNA, the difficulties encountered have lead some to hypothesize that RNA was preceded by a simpler molecule, one more easily synthesized prebiotically. Many of the proposed alternative molecules are based on acrolein, since it reacts readily with nucleophiles, such as the nucleobases, via Michael addition and is readily synthesized from formaldehyde and acetaldehyde. Reports regarding the reactions of nucleobases with concentrated acrolein solutions suggest that this is a plausible reaction mechanism, though there are also reports that the "incorrect" isomers are obtained. The scope and kinetics of the reaction of acrolein with various nitrogen heterocycles are reported here. Reactions of pyrimidines often give N(1) adducts as the major products. Reactions of purines often give N(9) adducts in good yield. The reactions are rapid under neutral to slightly alkaline conditions, and proceed at low temperatures and dilutions. The implications of these findings for the origin of life are discussed.

Evolvable self-replicating molecules in an artificial chemistry.

This paper gives details of Squirm3, a new artificial environment based on a simple physics and chemistry that supports self-replicating molecules somewhat similar to DNA. The self-replicators emerge spontaneously from a random soup given the right conditions. Interactions between the replicators can result in mutated versions that can outperform their parents. We show how artificial chemistries such as this one can be implemented as a cellular automaton. We concur with Dittrich, Ziegler, and Banzhaf that artificial chemistries are a good medium in which to study early evolution.

A self-replicating ligase ribozyme.

A self-replicating molecule directs the covalent assembly of component molecules to form a product that is of identical composition to the parent. When the newly formed product also is able to direct the assembly of product molecules, the self-replicating system can be termed autocatalytic. A self-replicating system was developed based on a ribozyme that catalyzes the assembly of additional copies of itself through an RNA-catalyzed RNA ligation reaction. The R3C ligase ribozyme was redesigned so that it would ligate two substrates to generate an exact copy of itself, which then would behave in a similar manner. This self-replicating system depends on the catalytic nature of the RNA for the generation of copies. A linear dependence was observed between the initial rate of formation of new copies and the starting concentration of ribozyme, consistent with exponential growth. The autocatalytic rate constant was 0.011 min(-1), whereas the initial rate of reaction in the absence of pre-existing ribozyme was only 3.3 x 10(-11) M.min(-1). Exponential growth was limited, however, because newly formed ribozyme molecules had greater difficulty forming a productive complex with the two substrates. Further optimization of the system may lead to the sustained exponential growth of ribozymes that undergo self-replication.

The unlimited complexity of biological systems and astonishing diversity of living organisms will remain the driving force of the physicochemical biology in the first third of the XXI century

What kind of thoughts and feelings is aroused today, on the eve of the XXI century, by the short prognostic article written by Francis Crick? First of all, it is a deep respect to the outstanding personality of the author-one of the most romantic creators of molecular biology. Perhaps we could not find in our memory a better scientific prophet--his adaptor hypothesis, set forth in 1955 (see [ 1 ]), was probably the most outstanding heuristic achievement of the outgoing century. For comparison, here is an example of a similar kind of the heuristic opportunity having been missed--what I have in mind is the RNA world concept [2, 3]. This is also very fruitful and widely accepted these days, but we must realize that this "second RNA hypothesis" was formulated only after the main experimental data concerning this topic (before all, the enzymatic function of RNA) had become available [4, 5]. Can we honestly say that knowledge of RNA's chemical nature and the mechanisms of its biosynthesis (in comparison with that for DNA and proteins) was not enough for understanding that RNA, and only RNA, could be the first self-replicating molecule on our planet?

Once upon a time

How did life begin? One way to find out is to make it happen again in the laboratory. Scientists have yet to generate life from scratch. The best they have managed is to simulate the Earth's primordial soup with educated guesses at what chemicals must have been present four billion years ago; they have then coaxed from it some basic biological building blocks such as amino acids. But this is just child's play. In the coming century, Harvard geneticist Jack Szostak predicts that researchers will reproduce in the lab likely candidates for the Earth's original self-replicating molecules. They may even recreate the first cells.

Bacterial plasmids: replication of extrachromosomal genetic elements encoding resistance to antimicrobial compounds.

Plasmids are self-replicating extrachromosomal DNA molecules found in Gram-negative and Gram-positive bacteria as well as in some yeast and other fungi. Although most of them are covalently closed circular double-stranded DNA molecules, recently linear plasmids have been isolated from different bacteria. In general, plasmids are not essential for the survival of bacteria, but they may nevertheless encode a wide variety of genetic determinants, which permit their bacterial hosts to survive better in an adverse environment or to compete better with other microorganisms occupying the same ecological niche. The medical importance of plasmids that encode for antibiotic resistance, as well as specific virulence traits has been well documented and demonstrated the important role these bacterial genetic elements play in nature. Although they encode specific molecules required for initiation of their replication, plasmids rely on host-encoded factors for their replication. Plasmid replication initiates in a predetermined cis-site called ori and can proceed either by a rolling circle or a theta replication mechanism. Some of the plasmid-encoded elements required for their replication, such antisense RNA molecules and DNA repeated sequences located close to ori, determine plasmid attributes like copy number and incompatibility.

The forces driving molecular evolution.

Competitive replication among RNA or DNA molecules at linear and non-linear rates of propagation has been reviewed from the perspective of a recent physicochemical model of molecular evolution and the findings are applied to pre-replication, prebiotic and biological evolution. A system of competitively replicating molecules was seen to follow a path of least action on both its thermodynamic and kinetic branch, in evolving toward steady state kinetics and equilibrium for the nucleotide condensation reaction. Stable and unstable states of coexistence, between competing molecular species, arise at nonlinear rates of propagation, and they derive from an equilibrium between kinetic forces. The de novo formation of self-replicating RNA molecules involves damping of these scalar forces, error tolerance and RNA driven strand separation. Increases in sequence complexity in the transition to self-replication does not exceed the free energy dissipated in RNA synthesis. Retrodiction of metabolic pathways and phylogenetic evidence point to the occurrence of three pre-replication metabolic systems, driven by autocatalytic C-fixation cycles. Thermodynamic and kinetic factors led to the replication take over. Biological evolution was found to involve resource capture, in addition to competition for a shared resource.

On the Appearance of Function and Organisation in the Origin of Life

Models for the steps of organisation in the origin of life are discussed with an emphasis on stability, and the possibilities of acquiring a diversity of function. In particular, two basic models are described: that of simple self-replicating molecules, and that of autocatalytic self-reproduction, which is accomplished by a hypercyclic organisation. The latter may be exemplified by the RNA world. The view of a step-wise development with new functions successively incorporated and a high accuracy of the reproduction from the onset is criticised. Instead, we suggest that no clear systematic information is continued to the first cell before the start of protein synthesis. A non-selective manifold of self-replicating molecules and unsystematic protein production from the beginning could have caused a very large diversity from which functions that could stabilise the system by feedback loops could be selected. The only way to stabilise the protein synthesis and the genetic code would be to have feedback mechanisms so that the code actually produced the proteins that supported that very code. The code would then become frozen. As DNA would require control functions, it would not be used as a single information-carrier until protein synthesis had been established and the functions were available.

Ribozymes: aiming at RNA replication and protein synthesis

The RNA world hypothesis is founded on the idea of an RNA replicase, or self-replicating RNA molecule, and presupposes the later emergence of ribozymes capable of catalyzing the synthesis of peptides. The recent demonstrations of ribozyme-catalyzed template-directed primer extension, and of ribozyme-catalyzed amide bond synthesis, confirm the plausibility of the RNA world, and highlight the steps that remain to be demonstrated in the laboratory.

A theory of evolution that includes prebiotic self-organization and episodic species formation.

A theory has been proposed that encompasses pre-replication changes in RNA synthesis and non-gradual variant formation, in addition to competitive replication. Using a fundamental theorem of natural selection and maximum principle scaled to nucleotide condensation, evolution in vitro was demonstrated to maximally damp both kinetic and thermodynamic forces driving this reaction, from its pre-replication stage. This led to the finding that evolution follows a path of least action. These principles form the framework for a general theory of evolution, whose scope extends beyond evolution modeled by synthesis of non-interacting RNA molecules. It applies, in particular, to standard processes, such as competitive crystallization. In calculations simulating de novo formation of self-replicating RNA molecules in the Qbeta replicase system, spontaneous changes in strand secondary structure promoted the transition from random copolymerization to template-directed polymerization. This finding indicates selection preceded genome self-propagation. Non-gradual species formation was attributed to the presence of heterogeneous thermodynamic forces. Growth unconstrained by competition follows mutation to a variant able to utilize a free energy source alien to its progenitors. Evolution in a heterogeneous system can, therefore, exhibit discontinuous rates of species formation and spawn new species populations. Natural selection among competing self-propagators thus gives way to a principle of wider scope stating that evolution optimally damps the physicochemical forces causing change within an evolving system.

A theory of evolution that includes prebiotic self-organization and episodic species formation

A theory has been proposed that encompasses pre-replication changes in RNA synthesis and non-gradual variant formation, in addition to competitive replication. Using a fundamental theorem of natural selection and maximum principle scaled to nucleotide condensation, evolution in vitro was demonstrated to maximally damp both kinetic and thermodynamic forces driving this reaction, from its pre-replication stage. This led to the finding that evolution follows a path of least action. These principles form the framework for a general theory of evolution, whose scope extends beyond evolution modeled by synthesis of non interacting RNA molecules. It applies, in particular, to standard processes, such as competitive crystallization. In calculations simulating de novo formation of self-replicating RNA molecules in the Qβ replicase system, spontaneous changes in strand secondary structure promoted the transition from random copolymerization to template-directed polymerization. This finding indicates selection preceded genome self-propagation. Non-gradual species formation was attributed to the presence of heterogeneous thermodynamic forces. Growth unconstrained by competition follows mutation to a variant able to utilize a free energy source alien to its progenitors. Evolution in a heterogeneous system can, therefore, exhibit discontinuous rates of species formation and spawn new species populations. Natural selection among competing self-propagators thus gives way to a principle of wider scope stating that evolution optimally damps the physicochemical forces causing change within an evolving system.

Significance of strand configuration in self-replicating RNA molecules.

The kinetic theory of replication has been extended to include dual mechanisms for conversion of self-annealed single-strand RNA to double-strand molecules, which do not replicate. An analysis of experimental results established that the replicate-template annealing reaction during transcription significantly retarded replication in vitro among three RNA variants copied by Q beta replicase. Annealing between complementary RNA strands free in solution had far less significance. The finding that an RNA variant can be replicated in a multiple hairpin configuration, but not as its single, long hairpin conformer, the correlation between stability of strand secondary structure and replicative fitness, and a lack of homology in the internal sequence of RNA variants copied by Q beta replicase support the conclusion that template competence depends on strand configuration, independent of most of the underlying base sequence. Occurrence of self-annealed strands in the Q beta replicase system was attributed to its reliance on RNA-driven strand separation, in the absence of enzyme catalysed strand unwinding. A 'configuration before sequence' path to self-replication exhibited a substantially lower combinatorial barrier than standard sequence-dependent evolution. RNA-dependent RNA synthesis in the Q beta system thus displays features of an RNA World and, interestingly, they reveal a rapid path for evolution of the first self-replicating molecule on Earth.

Comments on “Let there be Life”; Thermodynamic Reflections on Biogenesis and Evolution” by Avshalom C. Elitzur

This comment is in response to a paper previously published in the Journalentitled “Let there be life”, by A. C. Elitzur. Elitzur ascribes to Eigen the proposal that life began with the appearance of an autocatalytic (self-replicating) molecule. This was discussed by biologists and philosophers in the nineteenth century. Eigen's proposal is moot: there never was a primeval soup. The absence of evidence is evidence of absence. Elitzur also confuses thermodynamics with statistical mechanics. The statistical equation of Boltzmann and Planck for entropy appears in discussions of statistical mechanics, not in discussions of classical thermodynamics. Elitzur calls the Second Law of Thermodynamics an explanation of evolution. On the contrary, his mentor Eigen wrote: “In physics we know of principles which cannot be reduced to any more fundamental laws. As axioms, they are abstracted from experience, their predictions being consistent with the consequences that can be subjected to experimental test. “Typical examples are the first and second law of thermodynamics. Darwin's principle of natural selection does not fall into the category of first principles.” The reader is invited to compare the material in Elitzur's paper with the discussion in Yockey's (1992) book, Information Theory and Molecular Biology, Cambridge, Cambridge University Press.

A short introduction to the origin and molecular evolution of viruses.

The present review deals with conceptual and experimental approaches to two aspects of the origin and molecular evolution of viruses. In the section "Role of Retrons, Retroelements, and Reverse Transcriptase in the Evolution of Retroviruses and in Eukaryotic Genome Plasticity", Temin's concept that retrons are an ancient genetic element that during evolution of the species gave rise to retroviruses is presented. An opposing view of Xiong and Eickbush that the most probable ancestor of current retroelements is a retrotransposable element with gag- and pol-like genes is presented. Minus-strand RNA viruses are also discussed. The second aspect of this review is the molecular evolution of viruses at the level of the virus genome. Spiegelman's experiment on the evolution of self-replicating nucleic acid molecules outside living cells and Eigen's experimental and conceptual approaches to this subject are presented, along with studies on the evolutionary rates of base substitutions in viral RNA and defective molecules generated during replication.

Synthetic Self-Replicating Molecules

Synthetic Self-Replicating Molecules

Let There Be Life: Thermodynamic Reflections on Biogenesis and Evolution

The question of how life emerged from inanimate matter is closely related to the more fundamental question, namely: What is life? Both issues yield novel insights when discussed in the light of thermodynamics. The model proposed here is based on a simple assumption, namely, that life began with the accidental assembly of a self-replicating molecule. From this assumption the emergence of life naturally follows, enabling a new understanding of evolution as a whole. The evolution of any type of self-replicating systems, even the simplest ones, is shown to be highly efficient in extracting, recording and processing information about the environment. A variety of related issues yield some surprising conclusions when discussed in the thermodynamic context. New processes of order-increase are pointed out, a novel measure of information is proposed, and Lamarckianism is proved to be inconsistent with thermodynamics. Recent works on biogenesis and evolution are critically reviewed.

Images of evolution: origin of spontaneous RNA replication waves.

Self-replicating molecules set up traveling concentration waves that propagate in an aqueous enzyme solution. The velocity of each wave provides an accurate (+/- 0.1%) noninvasive measure of fitness for the RNA species currently growing in its front. Evolution may be followed from changes in the front velocity, and these differ from wave to wave. Thousands of controlled evolution reactions in traveling waves have been monitored in parallel to obtain quantitative images of the stochastic process of natural selection. An RNA polymerase (RNA-dependent RNA nucleotidyltransferase, EC 2.7.7.6), extracted from bacteria infected by the Q beta RNA virus, catalyzes the replication. The traveling waves that arise spontaneously without added RNA provide a model system for major evolutionary change.

Molecular recognition and self-replication.

Self-replicating molecules stand at the very boundary of chemistry with biology. This review describes the development of synthetic structures capable of self-replication from studies in molecular recognition. The weak intermolecular forces--hydrogen bonds and aromatic stacking interactions--that characterize interactions of nucleic acid components were designed into synthetic receptors for adenine. Covalent conjugates of these receptors with adenines gave self-complementary structures capable of replication. The new systems feature autocatalysis, sigmoidal product growth and even mutation. General rules for the design of replicating systems are described and these suggest that the evolution of replicating molecules was an inevitable event.

Crossover reactions between synthetic replicators yield active and inactive recombinants.

Self-replicating molecules can be synthesized through the covalent linkage of two complementary subunits to give a self-complementary structure. Complementarity refers to sizes, shapes, and the weak intermolecular forces involved in molecular recognition between the two subunits. In order to provide a model system for evolution at the molecular level, "crossover" or recombination experiments were staged with synthetic replicators. These reactions gave rise to new structural types. The ability (or inability) of the new recombinants to catalyze their own formation is shown to be a consequence of their molecular shapes.