A System of Two Polymerases – A Model for the Origin of Life

What was the first living molecule – RNA or protein?This question embodies the major disagreement instudies on the origin of life. The fact that incontemporary cells RNA polymerase is a protein andpeptidyl transferase consists of RNA suggests theexistence of a mutual catalytic dependence betweenthese two kinds of biopolymers. I suggest that thisdependence is a `frozen accident', a remnant from thefirst living system. This system is proposed to be acombination of an RNA molecule capable of catalyzingamino acid polymerization and the resulting proteinfunctioning as an RNA-dependent RNA polymerase. Thespecificity of the protein synthesis is thought to beachieved by the composition of the surrounding mediumand the specificity of the RNA synthesis – by Watson– Crick base pairing. Despite its apparent simplicity,the system possesses a great potential to evolve intoa primitive ribosome and further to life, as it isseen today. This model provides a possible explanationfor the origin of the interaction between nucleicacids and protein. Based on the suggested system, Ipropose a new definition of life as a system ofnucleic acid and protein polymerases with a constantsupply of monomers, energy and protection.     

An Interpretive Review of the Origin of Life Research

Life appears to be a natural property of matter, but the problem of its origin only arose after early scientists refuted continuous spontaneous generation. There is no chance of life arising ‘all at once’, we need the standard scientific incremental explanation with large numbers of small steps, an approach used in both physical and evolutionary sciences. The necessity for considering both theoretical and experimental approaches is emphasized. After describing basic principles that are available (including the Darwin-Eigen cycle), the search for origins is considered under four main themes. These are the RNA-world hypothesis; potential intermediates between an RNA-world and a modern world via the evolution of protein synthesis and then of DNA; possible alternatives to an RNA-world; and finally the earliest stages from the simple prebiotic systems to RNA. The triplicase/proto-ribosome theory for the origin of the ribosome is discussed where triples of nucleotides are added to a replicating RNA, with the origin of a triplet code well-before protein synthesis begins. The length of the code is suggested to arise from the early development of a ratchet mechanism that overcomes the problem of continued processivity of an RNA-based RNA-polymerase. It is probable that there were precursor stages to RNA with simpler sugars, or just two nucleotides, but we do not yet know of any better alternatives to RNA that were likely to arise naturally. For prebiotic stages (before RNA) a flow-reactor model is suggested to solve metabolism, energy gradients, and compartmentation simultaneously – thus the intense interest in some form of flow reactor. If an autocatalytic cycle could arise in such a system we would be major steps ahead. The most likely physical conditions for the origin of life require further clarification and it is still unclear whether the origin of life is more of an entropy (information) problem (and therefore high temperatures would be detrimental), rather than a kinetic problem (where high temperatures may be advantageous).     

菊花花色遗传及花色嵌合体发现

对开黄花菊花和开白花菊花材料分别和开红花菊花材料进行了正反交,结果表明,花色遗传比较复杂, 在以红花材料作为母本组合中表现为比较明显的偏母性遗传特征,而以黄花和白花材料为母本则不表现偏母性特征;除此之外,菊花花色遗传还表现出不完全显性和镶嵌显性的特点。在黄花材料3501和红花材料3509所得到杂种中发现了2个分枝出现花色嵌合体的现象,该嵌合体特征是花一边为红色,而另一边则出现镶嵌显性的现象。染色体分析表明,不同颜色嵌合体花瓣的染色体数目都是36条,因此,实验所得到的花色嵌合体不是由染色体数目变化造成的,而有可能是转座子插入影响色素合成基因造成的。     

Self-Organization and Evolutionin a Simulated Cross Catalyzed Network

Motivated by an alternative to the concept of a prebiotic soup inthe form of interacting crystal growth close to hot vents, we investigatea model system in which the growth rate of a particular entity is modified (enhanced or reduced) by other entities present, thus forming aweb of cross catalysis. Initially random interactions are imposed, butthe entities compete for a common source, and some entities may thusvanish in the competition. New entities, or mutations (error copies),with randomly selected interactions to the web are then introduced,and the concentrations of the entities are followed as solutions to stiffordinary differential equations. Entities with positive growth maycreate new related entities with slightly randomly modified interactions to the web. Extinctions, wild-type survival and replacement,and self-organization to sustain periodic external variations, are studied. It is shown that even systems with mostly cross-inhibition and noinitial autocatalysis may eventually create highly stable self-organizedsystems. We find that an already established cross catalyzed systemoften wins over a selfreplicating invader (or mutant).     

外源基因在一个转基因水稻四倍体变异株系中的遗传行为

在基因枪介导转化的转基因水稻植株中发现1个四倍体变异株系XIP-4N．该变异株系T₀代植株中转基因的整合模式与二倍体转基因株系XIP-2N相同,并且二者来自同一转化体系,推测XIP-4N株系是转化后的水稻愈伤组织在细胞有丝分裂过程中发生染色体加倍产生的．对外源筛选标记基因bar和非筛选基因cecropinB在转基因株系XIP-4N和XIP-2N中的遗传行为进行了比较研究．在二倍体转基因株系XIP-2N中,bar和cecropinB基因的Southern整合模式从T₀到T₂代遗传稳定,单位点整合的bar基因按孟德尔单基因显性方式向后代传递．四倍体转基因株系XIP-4N中外源基因遗传行为复杂,单位点整合的bar基因（Basta抗性）T₁代按15∶1分离,T₂和T₃代中分离行为复杂,而且bar和cecropinB基因的整合模式遗传不稳定．同源四倍体水稻植株减数分裂过程中染色体结构变异、转基因相关位点DNA片段的遗传重组与修饰,以及由此导致配子的育性降低,可能是导致外源基因遗传行为复杂的主要原因．转基因四倍体水稻变异株系XIP-4N携带易于检测的bar基因,为研究同源四倍体水稻的遗传和生殖机理提供了好材料．     

Formation of Peptide Bonds from Metastable versus Crystalline Phase: Implications for the Origin of Life

Formation of peptide bonds was attempted bythermal activation of dry amino acids from aqueous solutionthat simulated prebiotic evaporative environments. Theevaporation trend of amino acids solutions shows abifurcation and can lead to either a crystalline phase(near equilibrium) or a metastable non-crystalline phase(far from equilibrium). Only amino acids in this metastablephase are able to form peptide bonds by thermal activationat temperatures that are generated by solar radiationtoday. We suggest that this metastable phase is the idealinitial material to trigger amino acid assemblage withprotein-like structure because provide the driving force(supersaturation) for an intense interaction betweenmonomers of different amino acids and allows activation ofthese monomers in plausible prebiotic conditions.     

嫁接杂交与果树遗传的特殊性

在介绍近年来植物嫁接杂交研究新进展的基础上,着重阐述了嫁接杂交与果树遗传特殊性的关系。砧木中的遗传物质转移并整合到接穗生殖细胞和胚胎细胞的染色体组中,是杂种后代出现大量野生植株和果树遗传不遵守孟德尔定律的主要原因。还讨论了嫁接杂交在果树育种中的重要意义。 Abstract：Emphatically discusses the relationship between graft hybridization and the specificity of heredity in fruit trees on the basis of introducing the recent achievements in plant graft hybridization. We propose that genetic materials in rootstock being translocated and integrated into the genome of the germ cells and embryonic cells in scion are the main reasons why the majority of the hybrid seedlings have wild properties and the heredity of fruit trees violate Mendel’s laws of heredity. The potential of graft hybridization in fruit breeding are also discussed.     

The concept of correlated progression as the basis of a model for the evolutionary origin of major new taxa

Understanding the evolutionary processes responsible for the long treks through morphospace associated with the origin of new higher taxa is hampered by the lack of a realistic and usable model that accounts for long-term phenotypic evolvability. The systems-related concept of correlated progression, in which all the traits are functionally linked and so constrained to evolve by small increments at a time in parallel with each other, provides the basis for such a model. Implications for the process of evolution at high taxonomic level are that: the evolving traits must be considered together as a system, and the exact sequence of incremental changes in characters is indeterminable; there are no identifiable key innovations; selection acts on the phenotype as a whole rather than on individual traits; and the selection force is therefore multidimensional. Application of the model to the pattern of evolution of traits and trait states as revealed by the fossil record of the stem groups of such taxa as mammals, turtles and tetrapods generates realistic testable hypotheses about how such groups evolved.     

On the Emergence of Biological Complexity: Life as a Kinetic State of Matter

A kinetic model that attempts to further clarify the nature of biological complexification is presented. Its essence: reactions of replicating systems and those of regular chemical systems follow different selection rules leading to different patterns of chemical behavior. For regular chemical systems selection is fundamentally thermodynamic, whereas for replicating chemical systems selection is effectively kinetic. Building on an extension of the kinetic stability concept it is shown that complex replicators tend to be kinetically more stable than simple ones, leading to an on-going process of kinetically-directed complexification. The high kinetic stability of simple replicating assemblies such as phages, compared to the low kinetic stability of the assembly components, illustrates the complexification principle. The analysis suggests that living systems constitute a kinetic state of matter, as opposed to the traditional thermodynamic states that dominate the inanimate world, and reaffirms our view that life is a particular manifestation of replicative chemistry.     

Astronomical Sources of Circularly Polarized Light and the Origin of Homochirality

Possible astronomical sources of ultraviolet circularly polarized light(UVCPL) which might be responsible for enantiomeric selection in interstellarorganic molecules are considered, Synchrotron radiation from magnetic neutronstars has been suggested as a possible source of UVCPL. However, synchrotronradiation in these situations is not predicted to be strongly circularlypolarized. Very few such sources show optical synchrotron radiation and in thefew that do circular polarization has not been observed. Magnetic white dwarfsand white dwarf binaries (Polars) can be highly circularly polarized but anyeffect on molecular clouds and star formation regions must rely on rare chance encounters. Recent observations show that substantial levels of circularpolarization are present in reflection nebulae in star formation regions. Thismechanism produces polarized light exactly when and where it is needed inregions where star formation is occurring and organic molecules are known to be present.     

Enantiomeric Crystallization from DL-Aspartic and DL-Glutamic Acids: Implications for Biomolecular Chirality in the Origin of Life

Amino acids in living systems consist almost exclusively of the L-enantiomer. How and when this homochiral characteristic of life came to be has been a matter of intense investigation for many years. Among the hypotheses proposed to explain theappearance of chiral homogeneity, the spontaneous resolution of conglomerates seems one of the most plausible. Racemic solids may crystallize from solution either as racemic compounds(both enantiomeric molecules in the same crystal), or lesscommonly as conglomerates (each enantiomer molecule separate indifferent enantiomeric crystals). Only conglomerates can developa spontaneous resolution (one of the enantiomeric molecule crystallizes preferentially, the other one remains in solution).Most of natural amino acids are racemic compounds at moderatetemperatures. How can we expect a hypothetical spontaneous resolution of these amino acids if they are not conglomerates?In this paper we show how DL-aspartic and DL-glutamic amino acids(racemic compounds), crystallize at ambient conditions as trueconglomerates. The experimental conditions here described,that allows this `anomalous' behaviour, could be also found innatural sedimentary environments. We suggest that these experimental procedures and its natural equivalents, have apotential interest for the investigation of the spontaneous resolution of racemic compounds comprising molecules associatedwith the origin of life.     

河豚毒素的起源及其研究进展

河豚毒素(tetrodotoxin,TTX)是一种毒性很强、相对分子质量小的非蛋白毒素,最初从豚科鱼中发现,故被命名为河豚毒素。1985年有人提出了河豚鱼TTX的体外起源因素,认为所有能产生TTX的生物都与其体内能分泌TTX的微生物有着密切联系,但有部分研究人员证实东方在孵化期间能自行产生TTX。TTX为典型的Na 通道阻断剂,中毒者往往肢体麻木、瘫痪、甚至死亡;但另一方面,TTX具有镇痛、镇静、降压等功效,在临床上的应用十分广泛。本文简要介绍TTX的起源、毒性作用机制、毒性控制、临床及药理学上的应用,及其存在的问题和应用前景。     

Thermal Energy and the Origin of Life

Life has evolved on Earth with electromagnetic radiation (light), fermentable organic molecules, and oxidizable chemicals as sources of energy. Biological use of thermal energy has not been observed although heat, and the thermal gradients required to convert it into free energy, are ubiquitous and were even more abundant at the time of the origin of life on Earth. Nevertheless, Earth-organisms sense thermal energy, and in suitable environments may have gained the capability to use it as energy source. It has been proposed that the first organisms obtained their energy by a first protein named pF₁ that worked on a thermal variation of the binding change mechanism of today's ATP sythase enzyme. Organisms using thermosynthesis may still live where light or chemical energy sources are not available. Possible suitable examples are subsurface environments on Earth and in the outer Solar System, in particular the subsurface oceans of the icy satellites of Jupiter and Saturn.     

On the Chemical Nature and Origin of Teleonomy

The physico-chemical characterization of a teleonomic event and the nature of the physico-chemical process by which teleonomic systems could emerge from non-teleonomic systems are addressed in this paper. It is proposed that teleonomic events are those whose primary directive is discerned to be non-thermodynamic, while regular (non-teleonomic) events are those whose primary directive is the traditional thermodynamic one. For the archetypal teleonomic event, cell multiplication, the non-thermodynamic directive can be identified as being a kinetic directive. It is concluded, therefore, that the process of emergence, whereby non-teleonomic replicating chemical systems were transformed into teleonomic ones, involved a switch in the primacy of thermodynamic and kinetic directives. It is proposed that the step where that transformation took place was the one in which some pre-metabolic replicating system acquired an energy-gathering capability, thereby becoming metabolic. Such a transformation was itself kinetically directed given that metabolic replicators tend to be kinetically more stable than non-metabolic ones. The analysis builds on our previous work that considers living systems to be a kinetic state of matteras opposed to the traditional thermodynamic states that dominate the inanimate world     

Origins of gene, genetic code, protein and life: comprehensive view of life systems from a GNC-SNS primitive genetic code hypothesis

We have investigated the origin of genes, the genetic code, proteins and life using six indices (hydropathy, α-helix, β-sheet and β-turn formabilities, acidic amino acid content and basic amino acid content) necessary for appropriate three-dimensional structure formation of globular proteins. From the analysis of microbial genes, we have concluded that newly-born genes are products of nonstop frames (NSF) on antisense strands of microbial GC-rich genes [GC-NSF(a)] and from SNS repeating sequences [(SNS)_n] similar to the GC-NSF(a) (S and N mean G or C and either of four bases, respectively). We have also proposed that the universal genetic code used by most organisms on the earth presently could be derived from a GNC-SNS primitive genetic code. We have further presented the [GADV]-protein world hypothesis of the origin of life as well as a hypothesis of protein production, suggesting that proteins were originally produced by random peptide formation of amino acids restricted in specific amino acid compositions termed as GNC-, SNS and GC-NSF(a)-0th order structures of proteins. The [GADV]-protein world hypothesis is primarily derived from the GNC-primitive genetic code hypothesis. It is also expected that basic properties of extant genes and proteins could be revealed by considerations based on the scenario with four stages This review is a modified English version of the paper, which was written in Japanese and published inViva Origino 2001 29 66–85.     

Origin and early evolution of photosynthesis

Photosynthesis was well-established on the earth at least 3.5 thousand million years ago, and it is widely believed that these ancient organisms had similar metabolic capabilities to modern cyanobacteria. This requires that development of two photosystems and the oxygen evolution capability occurred very early in the earth's history, and that a presumed phase of evolution involving non-oxygen evolving photosynthetic organisms took place even earlier. The evolutionary relationships of the reaction center complexes found in all the classes of currently existing organisms have been analyzed using sequence analysis and biophysical measurements. The results indicate that all reaction centers fall into two basic groups, those with pheophytin and a pair of quinones as early acceptors, and those with iron sulfur clusters as early acceptors. No simple linear branching evolutionary scheme can account for the distribution patterns of reaction centers in existing photosynthetic organisms, and lateral transfer of genetic information is considered as a likely possibility. Possible scenarios for the development of primitive reaction centers into the heterodimeric protein structures found in existing reaction centers and for the development of organisms with two linked photosystems are presented.Abbreviation Gyr gigayears     

On the Origin of Metabolic Pathways

The heterotrophic theory of the origin of life is the only proposal available with experimental support. This comes from the ease of prebiotic synthesis under strongly reducing conditions. The prebiotic synthesis of organic compounds by reduction of CO₂ to monomers used by the first organisms would also be considered an heterotrophic origin. Autotrophy means that the first organisms biosynthesized their cell constituents as well as assembling them. Prebiotic synthetic pathways are all different from the biosynthetic pathways of the last common ancestor (LCA). The steps leading to the origin of the metabolic pathways are closer to prebiotic chemistry than to those in the LCA. There may have been different biosynthetic routes between the prebiotic and the LCAs that played an early role in metabolism but have disappeared from extant organisms. The semienzymatic theory of the origin of metabolism proposed here is similar to the Horowitz hypothesis but includes the use of compounds leaking from preexisting pathways as well as prebiotic compounds from the environment.     

The Oxidative Chlorination of Pyrimidine and Purine Bases,and Nucleosides Using Acyl Chloride-Dimethyl-Formamide-m-Chloroperbenzoic Acid System1

Abstract

Pyrimidine and purine bases, and nucleosides were chlorinated by the reaction of acyl chloride in DMF with MCPBA under mild conditions in moderate yields.     

Montmorillonite,Oligonucleotides, RNA and Origin of Life

Na-montmorillonite prepared from Volclay by the titration method facilitates the self-condensation of ImpA, the 5'-phosphorimidazolide derivative of adenosine. As was shown by AE-HPLC analysis and selective enzymatic hydrolysis of products, oligo(A)s formed in this reaction are 10 monomer units long and contain 67% 3',5'-phosphodiester bonds (Ferris and Ertem, 1992a). Under the same reaction conditions, 5'-phosphorimidazolide derivatives of cytidine, uridine and guanosine also undergo self-condensation producing oligomers containing up to 12-14 monomer units for oligo(C)s to 6 monomer units for oligo(G)s. In oligo(C)s and oligo(U)s, 75-80% of the monomers are linked by 2',5'-phosphodiester bonds. Hexamer and higher oligomers isolated from synthetic oligo(C)s formed by montmorillonite catalysis, which contain both 3',5'- and 2',5'-linkages, serve as catalysts for the non-enzymatic template directed synthesis of oligo(G)s from activated monomer 2-MeImpG, guanosine 5'-phospho-2-methylimidazolide (Ertem and Ferris, 1996). Pentamer and higher oligomers containing exclusively 2',5'-linkages, which were isolated from the synthetic oligo(C)s, also serve as templates and produce oligo(G)s with both 2',5'- and 3',5'-phosphodiester bonds. Kinetic studies on montmorillonite catalyzed elongation rates of oligomers using the computer program SIMFIT demonstrated that the rate constants for the formation of oligo(A)s increased in the order of 2-mer < 3-mer < 4-mer ... < 7-mer (Kawamura and Ferris, 1994). A decameric primer, dA(pdA)8pA bound to montmorillonite was elongated to contain up to 50 monomer units by daily addition of activated monomer ImpA to the reaction mixture (Ferris, Hill and Orgel, 1996). Analysis of dimer fractions formed in the montmorillonite catalyzed reaction of binary and quaternary mixtures of ImpA, ImpC, 2-MeImpG and ImpU suggested that only a limited number of oligomers could have formed on the primitive Earth rather than equal amounts of all possible isomers (Ertem and Ferris, 2000). Formation of phosphodiester bonds between mononucleotides by montmorillonite catalysis is a fascinating discovery, and a significant step forward in efforts to find out how the first RNA-like oligomers might have formed in the course of chemical evolution. However, as has been pointed out in several publications, these systems should be regarded as models rather than a literal representation of prebiotic chemistry (Orgel, 1998; Joyce and Orgel, 1999; Schwartz, 1999).     

The Sugar Model: Catalytic Flow Reactor Dynamics of Pyruvaldehyde Synthesis from Triose Catalyzed by Poly-L-Lysine Contained in a Dialyzer

The formation of pyruvaldehyde from triose sugars was catalyzedby poly-L-lysine contained in a small dialyzer with a 100molecular weight cut off (100 MWCO) suspended in a much largertriose substrate reservoir at pH 5.5 and 40 °C. Thepolylysine confined in the dialyzer functioned as a catalyticflow reactor that constantly brought in triose from thesubstrate reservoir by diffusion to offset the drop in trioseconcentration within the reactor caused by its conversion topyruvaldehyde. The catalytic polylysine solution (400 mM, 0.35mL) within the dialyzer generated pyruvaldehyde with a syntheticintensity (rate/volume) that was 3400 times greater than that ofthe triose substrate solution (12 mM, 120 mL) outside thedialyzer. Under the given conditions the final yield ofpyruvaldehyde was greater than twice the weight of thepolylysine catalyst. During the reaction the polylysine catalystwas poisoned presumably by reaction of its amino groups withaldehyde reactants and products. Similar results were obtainedusing a dialyzer with a 500 MWCO. The dialyzer method ofcatalyst containment was selected because it provides a simpleand easily manipulated experimental system forstudying the dynamics and evolutionary development of confinedautocatalytic processes related to the origin of life underanaerobic conditions.