Life Initiated from Two Genes, As Deduced from the RNA World Hypothesis and the Characteristics of Life-Like Systems

life Article A Hypothesis: Life Initiated from Two Genes, as Deduced from the RNA World Hypothesis and the Characteristics of Life-Like Systems Kunio Kawamura Department of Human Environmental Studies, Hiroshima Shudo University, 1-1-1, Ozuka-higashi, Asaminami-ku, Hiroshima 731-3195, Japan; [email protected]; Tel.: +81-82-830-1946 Academic Editor: David Deamer Received: 7 June 2016; Accepted: 25 July 2016; Published: 2 August 2016 Abstract: RNA played a central role in the emergence of the first life-like system on primitive Earth since RNA molecules contain both genetic information and catalytic activity. However, there are several drawbacks regarding the RNA world hypothesis. Here, I briefly discuss the feasibility of the RNA world hypothesis to deduce the RNA functions that are essential for forming a life-like system. At the same time, I have conducted a conceptual analysis of the characteristics of biosystems as a useful approach to deduce a realistic life-like system in relation to the definition of life. For instance, an RNA-based life-like system should possess enough stability to resist environmental perturbations, by developing a cell-like compartment, for instance. Here, a conceptual viewpoint is summarized to provide a realistic life-like system that is compatible with the primitive Earth environment and the capabilities of RNA molecules. According to the empirical and conceptual analysis, I propose the hypothesis that the first life-like system could have initiated from only two genes. Keywords: first genes; metabolism; information flow; RNA world; hydrothermal environments; kinetic model; definition of life; Hadean Earth environments 1. Chemical Evolution and Environments 1.1. Introduction: Chemical Evolution Identifying the molecular structures and functions in organisms, especially in relation to biological information, is a major goal of molecular biology. Biological information is preserved by nucleic acids to direct the biological functions of RNA and proteins through their nucleotide and amino acid sequences, respectively. It is said that the information flow is digitized by associations between the genotype and the phenotype molecules [1–4]. Furthermore, functional molecules, such as ribozymes and enzymes, induce the formation and breakdown of other biological molecules, and a single enzyme normally possesses a single function for controlling a single biochemical reaction. This idea is strengthened by the fact that information stored by a DNA sequence (genotype) is indirectly assigned a one-to-one correspondence to other molecules (phenotype) downstream (Figure1) at the molecular level, while there are many quantitative traits affected by many genes. Although the information flow from DNA to peptide sequences of proteins is normally focused on, it should be noted that the formation of other molecules downstream of proteins is also indirectly assigned by DNA sequences. Biological information is transformed from DNA sequences to RNA sequences, peptide sequences and other biomolecules. These functional molecules perform biological reactions, including DNA replication and repair. The cross-links between the information stored in the DNA sequence and the biological functions performed by other biomolecules is a significant characteristic of life-like systems on Earth. The universal machinery for maintaining this sophisticated information flow likely evolved from a common ancestor of our life-like systems, although this is extremely complicated Life 2016, 6, 29; doi:10.3390/life6030029 www.mdpi.com/journal/life Life 2016, 6, 29 2 of 19 Life 2016, 6, 29 2 of 19 evensophisticated in the simplest information organisms. flow Most likely scientists evolved studyingfrom a common the origins ancestor of life of considerour life-like this systems, a key factor in thealthough origin-of-life this is problem.extremely complicat The facted that even this in information the simplest organisms. flow lies in Most the cross-linkedscientists studying relationship the betweenorigins information of life consider and functionthis a key is factor one ofin thethe mostorigin-of-life important problem. characteristics The fact that of this life-like information systems on Earth;flow here, lies the in assignment the cross-linked between relationship genotype between and phenotype information is extended and function to that is betweenone of the information most and functionimportant [4 characteristics,5]. Thus, it is of assumed life-like systems that the on moment Earth; here, when the the assignment cross-linked between assignment genotype betweenand phenotype is extended to that between information and function [4,5]. Thus, it is assumed that the information and function was established is considered as a great event for the emergence of life-life moment when the cross-linked assignment between information and function was established is systemsconsidered on Earth. as a great event for the emergence of life-life systems on Earth. FigureFigure 1. Assignment 1. Assignment flow flow of biologicalof biological information information to functional biomolecules biomolecules downstream. downstream. Extended Extended informationinformation flow flow is illustrated is illustrated beyond beyond the the central central dogma.dogma. RNA RNA and and proteins proteins are are phenotype phenotype molecules, molecules, but also possess roles for assigning other biomolecules downstream. From this viewpoint, DNA but also possess roles for assigning other biomolecules downstream. From this viewpoint, DNA molecules are also regarded as phenotypes, which would possess only a function for replication. molecules are also regarded as phenotypes, which would possess only a function for replication. This information flow likely formed slowly, step-by-step, with a number of important chemical Thisevolutionary information events, flow rather likely than formed the necessary slowly, even step-by-step,ts happening with all at a numberonce. Furthermore, of important it is chemicalwell evolutionaryestablished events, that the rather relationship than the between necessary informatio eventsn and happening function is all regarded at once. as Furthermore,the chicken and itegg is well establishedparadox. that The the RNA relationship world hypothesis between is informationproposed as a and hypothesis function that is regardedwould solve as thethis chickenparadox and[6], egg while the idea that RNA would have played the roles of both DNA and proteins was anticipated prior paradox. The RNA world hypothesis is proposed as a hypothesis that would solve this paradox [6], to the appearance of the term “the RNA world hypothesis” [7,8]. The RNA world hypothesis seems to while the idea that RNA would have played the roles of both DNA and proteins was anticipated prior be the most attractive hypothesis for the origin of life; therefore, the validity of the RNA world to thehypothesis appearance has ofbeen the extensively term “the RNAevaluated world by hypothesis”experimentally [7 simulating,8]. The RNA the chemical world hypothesis evolution of seems to beRNA the most and in attractive vitro selection hypothesis techniques for of the functi originonal of RNA life; molecules. therefore, Nevertheless, the validity the of theRNA RNA world world hypothesishypothesis has still been possesses extensively discrepancies evaluated from by the experimentally following viewpoints: simulating the chemical evolution of RNA and in vitro selection techniques of functional RNA molecules. Nevertheless, the RNA world An insufficient number of simulation experiments have been conducted to render the RNA world hypothesishypothesis still possesses compatible discrepancies with extreme from primitive the following Earth environments viewpoints: (Figure 2). Especially, the RNA world hypothesis has not been sufficiently evaluated from the viewpoint of the ‚ An insufficient number of simulation experiments have been conducted to render the RNA world hydrothermal origin of life. This was extensively investigated to verify conditions likely for hypothesischemical compatible evolution withof RNA extreme and related primitive molecules Earth environments by using hydrothermal (Figure2). flow Especially, reactors the by RNA worldresearchers, hypothesis including has not our been group. sufficiently evaluated from the viewpoint of the hydrothermal origin There of life. are Thisstill unknown was extensively pathways investigated for the formatio to verifyn of functional conditions RNA likely molecules, for chemical such as evolution the of RNAformation and related of ribose molecules and the prebiotic by using replication hydrothermal process. flow reactors by researchers, including our group.A realistic RNA-based life-like system has not been well described. It is unknown whether the ‚ Therefirst are RNA-based still unknown life-like pathways systems for may the formationinclude a ofquasi-species-type functional RNA RNA molecules, system such or asa the capsulated-type system consisting of several functional RNA molecules. formation of ribose and the prebiotic replication process. ‚ A realistic RNA-based life-like system has not been well described. It is unknown whether the first RNA-based life-like systems may include a quasi-species-type RNA system or a capsulated-type system consisting of several functional RNA molecules. Life 2016, 6, 29 3 of 19 Life 2016, 6, 29 3 of 19 ‚ It has not been determined how a simple population of functional RNA molecules became a life-likeIt has systemnot been that determined

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