Visualizing RNA polymers produced by hot wet-dry cycling

An irreversible thermodynamic model of pre-biological small circular molecular dissipative structures inside vacuoles on the Archean Ocean surface

A prebiotic model, based in the framework of thermodynamic efficiency loss from small dissipative eukaryote organisms [1-3], is developed to describe the maximum possible concentration of solar power to be dissipated on topological circular molecules structures encapsulated in lipid-walled vacuoles, which floated in the Archean oceans. By considering previously, the analysis of 71 species examined by covering 18 orders of mass magnitude from the Megapteranovaeangliae to Saccharomyces cerevisiae[2], suggest that in molecular structures of smaller masses than any living being known nowadays, the power dissipation must be directly proportional to the power of the photons of solar origin that impinge them to give rise to the formation of more complex self-assembled molecular structures at the prebiotic stage by a quantum mechanics model of resonant photon wavelength excitation. The analysis of 12 circular molecules (encapsulated in lipid-walled vacuoles) relevant to the evolution of life on planet Earth such as the five nucleobases, and some aromatic molecules as pyrimidine, porphyrin, chlorin, coumarin, xanthine, etc., were carried out. Considering one vacuole of each type of molecule per square meter of the ocean's surface of planet Earth ( vacuoles), their dissipative operation would require only times the matter used by the biomass currently existing on Earth. Relevant numbers for the annual dissipative cycles corresponding to high energy photo chemical events, which in principle allow the assembling of more complex polymers, were obtained. The previous figures are compatible with some results obtained by followers (Miller and Lazcano) of the primordial soup theory [4-5], when they, under certain suppositions about the Archean chemical kinetical changes on the precursors of RNA and DNA try to justify the formation rate of RNA and DNA components and the emergence of life within a 10-million-year window, 3.5 billion years ago. The physical foundation perspective and the simplicity of the proposed approach suggests that it can serve as a possible template for both, the development of new kind of experiments, and for prebiotic theories that address self-organization occurring inside such vacuoles. Our model provides a new way to conceptualize the self-production of simple cyclic dissipative molecular structures in the Archean period of planet Earth. © 2017 ElsevierInc.Allrightsreserved.

Perspective: Protocells and the Path to Minimal Life

The path to minimal life involves a series of stages that can be understood in terms of incremental, stepwise additions of complexity ranging from simple solutions of organic compounds to systems of encapsulated polymers capable of capturing nutrients and energy to grow and reproduce. This brief review will describe the initial stages that lead to populations of protocells capable of undergoing selection and evolution. The stages incorporate knowledge of chemical and physical properties of organic compounds, self-assembly of membranous compartments, non-enzymatic polymerization of amino acids and nucleotides followed by encapsulation of polymers to produce protocell populations. The results are based on laboratory simulations related to cyclic hydrothermal conditions on the prebiotic Earth. The final portion of the review looks ahead to what remains to be discovered about this process in order to understand the evolutionary path to minimal life.

Selection in molecular evolution

Evolution requires selection. Molecular/chemical/preDarwinian evolution is no exception. One molecule must be selected over another for molecular evolution to occur and advance. Evolution, however, has no goal. The laws of physics have no utilitarian desire, intent or proficiency. Laws and constraints are blind to "usefulness." How then were potential multi-step processes anticipated, valued and pursued by inanimate nature? Can orchestration of formal systems be physico-chemically spontaneous? The purely physico-dynamic self-ordering of Chaos Theory and irreversible non-equilibrium thermodynamic "engines of disequilibria conversion" achieve neither orchestration nor formal organization. Natural selection is a passive and after-the-fact-of-life selection. Darwinian selection reduces to the differential survival and reproduction of the fittest already-living organisms. In the case of abiogenesis, selection had to be 1) Active, 2) Pre-Function, and 3) Efficacious. Selection had to take place at the molecular level prior to the existence of non-trivial functional processes. It could not have been passive or secondary. What naturalistic mechanisms might have been at play?

Visualizing ribonuclease digestion of RNA-like polymers produced by hot wet-dry cycles

Polymerization of nucleotides under prebiotic conditions simulating the early Earth has been extensively studied. Several independent methods have been used to verify that RNA-like polymers can be produced by hot wet-dry cycling of nucleotides. However, it has not been shown that these RNA-like polymers are similar to biological RNA with 3'-5' phosphodiester bonds. In the results described here, RNA-like polymers were generated from 5'-monophosphate nucleosides AMP and UMP. To confirm that the polymers resemble biological RNA, ribonuclease A should catalyze hydrolysis of the 3'-5' phosphodiester bonds between pyrimidine nucleotides to each other or to purine nucleotides, but not purine-purine nucleotide bonds. Here we show AFM images of specific polymers produced by hot wet-dry cycling of AMP, UMP and AMP/UMP (1:1) solutions on mica surfaces, before and after exposure to ribonuclease A. AMP polymers were unaffected by ribonuclease A but UMP polymers disappeared. This indicates that a major fraction of the bonds in the UMP polymers is indeed 3'-5' phosphodiester bonds. Some of the polymers generated from the AMP/UMP mixture also showed clear signs of cleavage. Because ribonuclease A recognizes the ester bonds in the polymers, we show for the first time that these prebiotically produced polymers are in fact similar to biological RNA but are likely to be linked by a mixture of 3'-5' and 2'-5' phosphodiester bonds.

The Moon-Forming Impact and the Autotrophic Origin of Life

The Moon-forming impact vaporized part of Earth's mantle, and turned the rest into a magma ocean, from which carbon dioxide degassed into the atmosphere, where it stayed until water rained out to form the oceans. The rain dissolved CO2 and made it available to react with transition metal catalysts in the Earth's crust so as to ultimately generate the organic compounds that form the backbone of microbial metabolism. The Moon-forming impact was key in building a planet with the capacity to generate life in that it converted carbon on Earth into a homogeneous and accessible substrate for organic synthesis. Today all ecosystems, without exception, depend upon primary producers, organisms that fix CO2 . According to theories of autotrophic origin, it has always been that way, because autotrophic theories posit that the first forms of life generated all the molecules needed to build a cell from CO2 , forging a direct line of continuity between Earth's initial CO2 -rich atmosphere and the first microorganisms. By modern accounts these were chemolithoautotrophic archaea and bacteria that initially colonized the crust and still inhabit that environment today.

Crystallization as a selection force at the polymerization of nucleotides in a prebiotic context

Accumulation and selection of nucleotides is one of the most challenging problems surrounding the origin of the first RNA molecules on our planet. In the current work we propose that guanosine 3',5' cyclic monophosphate could selectively crystallize upon evaporation of an acidic prebiotic pool containing various other nucleotides. The conditions of the evaporative crystallization are fully compatible with the subsequent acid catalyzed polymerization of this cyclic nucleotide reported in earlier studies and may be relevant in a broad range of possible prebiotic environments. Albeit cytidine 3',5' cyclic monophosphate has the ability to selectively accumulate under the same conditions, its crystal structure is not likely to support polymer formation.

Open Questions about the Roles of DnaA, Related Proteins, and Hyperstructure Dynamics in the Cell Cycle

The DnaA protein has long been considered to play the key role in the initiation of chromosome replication in modern bacteria. Many questions about this role, however, remain unanswered. Here, we raise these questions within a framework based on the dynamics of hyperstructures, alias large assemblies of molecules and macromolecules that perform a function. In these dynamics, hyperstructures can (1) emit and receive signals or (2) fuse and separate from one another. We ask whether the DnaA-based initiation hyperstructure acts as a logic gate receiving information from the membrane, the chromosome, and metabolism to trigger replication; we try to phrase some of these questions in terms of DNA supercoiling, strand opening, glycolytic enzymes, SeqA, ribonucleotide reductase, the macromolecular synthesis operon, post-translational modifications, and metabolic pools. Finally, we ask whether, underpinning the regulation of the cell cycle, there is a physico-chemical clock inherited from the first protocells, and whether this clock emits a single signal that triggers both chromosome replication and cell division.

Template-Directed Replication and Chiral Resolution during Wet-Dry Cycling in Hydrothermal Pools

The commonly supposed template-based format for RNA self-replication requires both duplex assembly and disassembly. This requisite binary provision presents a challenge to the development of a serviceable self-replication model since chemical reactions are thermochemically unidirectional. We submit that a solution to this problem lies in volcanic landmasses that engage in continuous cycles of wetting and drying and thus uniquely provide the twofold state required for self-replication. Moreover, they offer conditions that initiate chain branching, and thus furnish a path to autocatalytic self-replication. The foundations of this dual thermochemical landscape arise from the broad differences in the properties of the bulk water phase on the one hand, and the air/water interfacial regions that emerge in the evaporative stages on the other. With this reaction system as a basis and employing recognized thermochemical and kinetic parameters, we present simulations displaying the spontaneous and autocatalyzed conversion of racemic and unactivated RNA monomers to necessarily homochiral duplex structures over characteristic periods of years.

A liquid crystal world for the origins of life

Nucleic acids (NAs) in modern biology accomplish a variety of tasks, and the emergence of primitive nucleic acids is broadly recognized as a crucial step for the emergence of life. While modern NAs have been optimized by evolution to accomplish various biological functions, such as catalysis or transmission of genetic information, primitive NAs could have emerged and been selected based on more rudimental chemical-physical properties, such as their propensity to self-assemble into supramolecular structures. One such supramolecular structure available to primitive NAs are liquid crystal (LC) phases, which are the outcome of the collective behavior of short DNA or RNA oligomers or monomers that self-assemble into linear aggregates by combinations of pairing and stacking. Formation of NA LCs could have provided many essential advantages for a primitive evolving system, including the selection of potential genetic polymers based on structure, protection by compartmentalization, elongation, and recombination by enhanced abiotic ligation. Here, we review recent studies on NA LC assembly, structure, and functions with potential prebiotic relevance. Finally, we discuss environmental or geological conditions on early Earth that could have promoted (or inhibited) primitive NA LC formation and highlight future investigation axes essential to further understanding of how LCs could have contributed to the emergence of life.

Novel Apparatuses for Incorporating Natural Selection Processes into Origins-of-Life Experiments to Produce Adaptively Evolving Chemical Ecosystems

Origins-of-life chemical experiments usually aim to produce specific chemical end-products such as amino acids, nucleic acids or sugars. The resulting chemical systems do not evolve or adapt because they lack natural selection processes. We have modified Miller origins-of-life apparatuses to incorporate several natural, prebiotic physicochemical selection factors that can be tested individually or in tandem: freezing-thawing cycles; drying-wetting cycles; ultraviolet light-dark cycles; and catalytic surfaces such as clays or minerals. Each process is already known to drive important origins-of-life chemical reactions such as the production of peptides and synthesis of nucleic acid bases and each can also destroy various reactants and products, resulting selection within the chemical system. No previous apparatus has permitted all of these selection processes to work together. Continuous synthesis and selection of products can be carried out over many months because the apparatuses can be re-gassed. Thus, long-term chemical evolution of chemical ecosystems under various combinations of natural selection may be explored for the first time. We argue that it is time to begin experimenting with the long-term effects of such prebiotic natural selection processes because they may have aided biotic life to emerge by taming the combinatorial chemical explosion that results from unbounded chemical syntheses.

Origins of Life Research: The Conundrum between Laboratory and Field Simulations of Messy Environments

Most experimental results that guide research related to the origin of life are from laboratory simulations of the early Earth conditions. In the laboratory, emphasis is placed on the purity of reagents and carefully controlled conditions, so there is a natural tendency to reject impurities and lack of control. However, life did not originate in laboratory conditions; therefore, we should take into consideration multiple factors that are likely to have contributed to the environmental complexity of the early Earth. This essay describes eight physical and biophysical factors that spontaneously resolve aqueous dispersions of ionic and organic solutes mixed with mineral particles and thereby promote specific chemical reactions required for life to begin.

Rolling Circles as a Means of Encoding Genes in the RNA World

The rolling circle mechanism found in viroids and some RNA viruses is a likely way that replication could have begun in the RNA World. Here, we consider simulations of populations of protocells, each containing multiple copies of rolling circle RNAs that can replicate non-enzymatically. The mechanism requires the presence of short self-cleaving ribozymes such as hammerheads, which can cleave and re-circularize RNA strands. A rolling circle must encode a hammerhead and the complement of a hammerhead, so that both plus and minus strands can cleave. Thus, the minimal functional length is twice the length of the hammerhead sequence. Selection for speed of replication will tend to reduce circles to this minimum length. However, if sequence errors occur when copying the hammerhead sequence, this prevents cleavage at one point, but still allows cleavage on the next passage around the rolling circle. Thus, there is a natural doubling mechanism that creates strands that are multiple times the length of the minimal sequence. This can provide space for the origin of new genes with beneficial functions. We show that if a beneficial gene appears in this new space, the longer sequence with the beneficial function can be selected, even though it replicates more slowly. This provides a route for the evolution of longer circles encoding multiple genes.