Self-instructed condensation of amino acids into polymers

In contemporary cells biological information is largely stored in nucleic acids. Therefore, a prerequisite in many theories on the origin of cellular life is the pre-existance of self-replicating polynucleotides that had to be formed by abiotic processes on the prebiotic Earth. It is usually assumed that the spontaneous synthesis of a self-replicating polynucleotide could take place readily. However, serious stereochemical obstacles exist which make such a synthesis extremely improbable. Amino acids on the other hand, which are abundantly formed in prebiotic simulation experiments, are relatively easily polymerized to macromolecules (protoproteins) that share with modern proteins many properties: e.g., definable non-random structure, selected amino acid sequences, enzyme-like activities and self-assembly into supramolecular structures. Prebiotic polyamino acids are therefore regarded by some scientists, including the present author, as the first informational macromolecules. The origin of this information is the chemical reactivity of the various prebiotic amino acids and their chemical response to their environment. The first informational polynucleotides were likely formed by a polynucleotide polymerase activity of prebiotic protoproteins. A contemporary model for this process is seen, e.g., in the activity of template-free Qβ-replicase.     

Evolution of anticodons

Anticodons are trinucleotides in transfer RNA (tRNA) molecules. The latter carry amino acids for insertion into the polypeptide sequences of proteins during the translation of messenger RNA (mRNA) molecules. Messenger RNA molecules are transcribed from genes. Evolution of tRNA molecules has resulted in a set of anticodons for the 20 amino acids that are used in protein synthesis. This set of anticodons is slightly different in mitochondrial codes from the set that is used in the nuclear “universal” code. Theories for the evolution of the code include frozen accident, doublet expansion, repeating triplets and coevolutionary distribution. The number of codons has always been fixed at 64 by mathematical rules, but because an anticodon may pair with more than one codon, the number of anticodons is only 54 in the universal code, is smaller in mitochondrial codes, and was probably even smaller in archetypal primitive codes. Evidence of anticodon evolution can be seen by comparing mitochondrial codes with the universal code. Codes used by very primitive organisms that are now extinct might have specified fewer amino acids than are now used.     

Chemical evolution of RNA under hydrothermal conditions and the role of thermal copolymers of amino acids for the prebiotic degradation and formation of RNA.

The roles of thermal copolymers of amino acids (TCAA) were studied for the prebiotic degradation of RNA. A weak catalytic ability of TCAA consisted of Glu, L-Ala, L-Val, L-Glu, L-Asp, and optionally L-His was detected for the cleavage of the ribose phosphodiester bond of a tetranucleotide (5'-dCrCdGdG) in aqueous solution at 80 degees C. The rate constants of the disappearance of 5'-dCrCdGdG were determined in aqueous solutions using different pH buffer and TCAA. The degradation rates were enhanced 1.3-3.0 times in the presence of TCAA at pH 7.5 and 8.0 at 80 degrees C, while the hydrolysis of oligoguanylate (oligo(G)) was accelerated about 1.6 times at pH 8.0. A weak inhibitory activity for the cleavage of oligo(G) was detected in the presence of 0.055 M TCAA-Std. On the other hand, our recent study on the influences of TCAA for the template-directed reaction of oligo(G) on a polycytidylic acid template showed that TCAA has an acceleration activity for the degradation of the activated nucleotide monomer and an acceleration activity for the formation of G5' ppG capped oligo(G). This series of studies suggest that efficient and selective catalytic or inhibitory activities for either the degradation or formation of RNA under hydrothermal conditions could have hardly emerged from the simple thermal condensation products of amino acids. A scenario is going to be deduced on the chemical evolution of enzymatic activities and RNA molecules concerning hydrothermal earth conditions.     

Chemical evolution of primitive solar system bodies.

In this paper we summarize some of the most salient observations made recently on the organic molecules and other compounds of the biogenic elements present in the interstellar medium and in the primitive bodies of the solar system. They include the discovery of the first phosphorus molecular species in dense interstellar clouds, the presence of complex organic ions in the dust and gas phase of Halley's coma, the finding of unusual, probably presolar, deuterium-hydrogen ratios in the amino acids of carbonaceous chondrites, and new developments on the chemical evolution of Titan, the primitive Earth, and early Mars. Some of the outstanding problems concerning the synthesis of organic molecules on different cosmic bodies are also discussed from an exobiological perspective.     

Chemical evolution and the origin of life.

During the last three decades major advances have been made in our understanding of the formation of carbon compounds in the universe and of the occurence of processes of chemical evolution. 1) Carbon and other biogenic elements (C,H,N,O,S and P) are some of the most abundant in the universe. 2) The interstellar medium has been found to contain a diversity of molecules of these elements. 3) Some of these molecules have also been found in comets which are considered the most primordial bodies of the solar system. 4) The atmospheres of the outer planets and their satellites, for example, Titan, are actively involved in the formation of organic compounds which are the precursors of biochemical molecules. 5) Some of these biochemical molecules, such as amino acids, purines and pyrimidines, have been found in carbonaceous chondrites. 6) Laboratory experiments have shown that most of the monomers and oligomers necessary for life can be synthesized under hypothesized but plausible primitive Earth conditions from compounds found in the above cosmic bodies. 7) It appears that the primitive Earth had the necessary and sufficient conditions to allow the chemical synthesis of biomacromolecules and to permit the processes required for the emergence of life on our planet. 8) It is unlikely that the emergence of life occurred in any other body of the solar system, although the examination of the Jovian satellite Europa may provide important clues about the constraints of this evolutionary process. Some of the fundamental principles of chemical evolution are briefly discussed.     

Direct interaction between amino acids and nucleotides as a possible physicochemical basis for the origin of the genetic code.

A study of the association of homocodonic amino acids and selected heterocodonic amino acids with selected nucleotides in aqueous solution was undertaken to examine a possible physical basis for the origin of codon assignments. These interactions were studied using 1H nuclear magnetic resonance spectroscopy (NMR). Association constants for the various interactions were determined by fitting the changes in the chemical shifts of the anomeric and ring protons of the nucleoside moieties as a function of amino acid concentration to an isotherm which described the binding interaction. The strongest association of all homocodonic amino acids were with their respective anticodonic nucleotide sequences. The strength of association was seen to increase with increase in the chain length of the anticodonic nucleotide. The association of these amino acids with different phosphate esters of nucleotides suggests that a definite isomeric structure is required for association with a specified amino acid; the 5'-mononucleotides and (3'-5')-linked dinucleotides are the favored geometries for strong associations. Use of heterocodonic amino acids and nonprotein amino acids supports these findings. We conclude that there is at least a physicochemical, anticodonic contribution to the origin of the genetic code.     

The evolution of nucleotides.

There has been much speculation about the types of molecules that were present in the first living forms. Recent discoveries show that RNA is a more versatile molecule than was previously believed, but whether it was ever able, for example, to synthesize its own monomers from available precursors is not yet known. If amino acids coexisted with nucleosides on the prebiotic Earth, then it seems likely that these two classes of molecules would have interacted with each other. We have been studying oligonucleotide-directed peptide bond formation, and during this work we discovered that aminoacylation of the internal 2'-hydroxyl groups of RNA occurred stereoselectively. Investigation of the mechanism of this reaction has been aided by the use of 3'-inosine methyl phosphate (as a simplified model for a dinucleoside monophosphate) and proton nmr spectroscopy of t-butoxycarbonyl-alanyl esters of nucleosides as models for the transition state of the aminoacylation reaction itself.     

Mechano-sensing and mechano-reaction of soft connective tissue cells.

One main function of the connective tissues is to provide cells with a mechanically resistant attachment support required for survival, division and differentiation. All cells contain membrane-anchored attachment proteins able to recognize specific chemical motifs in the extracellular macromolecules forming the supporting scaffold, made of various types of collagen, adhesive glycoproteins, elastin, proteoglycans, etc... These cell-matrix interactions are mainly mediated by receptors of the integrins family, heterodimeric molecules made of an extracellular domain connected through a transmembrane sequence to an intracytoplasmic tail. Upon recognition of the extracellular ligand, the clustering and activation of the integrins result in the recruitment of a complex of proteins and formation of the focal adhesion plaque, containing both cytoskeletal and catalytic signaling molecules. Activation results in polymerization of actin and formation of stress fibers. These structures establish a physical link between the extracellular matrix components and the cytoskeleton through the integrins providing a continuous path acting as a mechanotransducer. This connection is used by the cells to perform their mechanical functions as adhesion, migration and traction. In vitro experimental models using fibroblasts in a collagen gel demonstrate that cells are in mechanical equilibrium with their support which regulates their replicative and biosynthetic phenotype. The present review discusses the molecular structures operating in the transmission of the mechanical messages from the support to the connective tissue cells, and their effect on the cellular machinery. We present arguments for investigating these mechanisms in understanding the perception of reduced gravity and the resulting reaction leading to microgravity induced pathologies.     

Autopoiesis and the origin of bacteria.

"Autopoiesis" is the explanatory principle for the organization of living systems, a concept directly applicable to the problematic issues surrounding the origins of life. Because it provides criteria by which a system may be judged as living, autopoiesis can be used to characterize a minimal living system. Once these defining characteristics have been established, we can extrapolate the conditions which would have made possible the emergence of earliest life. Because autopoiesis is a principle of organization, it provides a definition of living systems not restricted to specific molecules or structures--that is, to those nucleic-acid/protein/lipid cellular life forms with which we are familiar. Autopoiesis provides the conceptual and systematic framework within which any living system may be identified. In examining living systems, then, autopoiesis gives us a literally "meta-physical" view of life.     

Microtubule self-organisation depends upon gravity.

The molecular processes by which gravity is transduced into biological systems are poorly, if at all, understood. Under equilibrium conditions, chemical and biochemical structures do not depend upon gravity. It has been proposed that biological systems might show a gravity dependence by way of the bifurcation properties of certain types of non-linear chemical reactions that are far-from-equilibrium. We have found that in-vitro preparations of microtubules, an important element of the cellular cytoskeleton, show this type of behaviour. On earth, the solutions show macroscopic self-ordering, and the morphology of the structures that form depend upon the orientation of the sample with respect to gravity at a critical moment at an early stage in the development of the self-organised state. An experiment carried out in a sounding rocket, showed that as predicted by theories of this type, no self-organisation occurs when the microtubules are assembled under low gravity conditions. This is an experimental demonstration of how a very simple biochemical system, containing only two molecules, can be gravity sensitive. At a molecular level this behaviour results from an interaction of gravity with macroscopic concentration and density fluctuations that arise from the processes of microtubule contraction and elongation.     

Amino acids in meteorites.

Carbonaceous chondrites carry a record of chemical evolution that is unparalleled among presently accessible natural materials. Within the complex suite of organic compounds that characterize these meteorites, amino acids occur at a total concentration that may reach 0.6 micromole g-1 meteorite (approximately 60 ppm). Both free amino acids and acid-labile amino acid derivatives have been found in hot-water extracts of a CI1 and seven CM2 chondrites. Although the amino acid composition of all CM2 chondrites is not the same, differences may be largely explicable on the basis of spontaneous and biologically-caused decomposition occurring during their terrestrial residence. The amino acids of the Murchison meteorite (CM2) have been extensively analyzed and 52 amino acids have been positively identified. Thirty three of these amino acids are unknown in natural materials other than carbonaceous chondrites. Thus the Murchison meteorite has recently been the major source of new naturally-occurring amino acids. The Murchison amino acids comprise a mixture of C2 through C8 cyclic and acyclic monoamino alkanoic and alkandioic acids of nearly complete structural diversity. Within the acyclic monoamino alkanoic acid series, primary alpha-amino alpha-branched amino acids are predominant. The concentrations of individual amino acids decline exponentially with increasing carbon number within homologous series. Amino acid enantiomers are found in approximately equal amounts. Eight of the terrestrial protein amino acids have been found.     

Stability of nucleic acid under the effect of UV radiation.

Nucleic acids (combined with protein molecules) are essential constituents of the living systems playing an important role in the early evolution of life as well. A specific feature of these molecules has been found and directly confirmed recently: under the influence of short-wavelength UV radiation bipyrimidine photoproducts (cyclobutane dimers and 6-4 bipyrimidines) are induced and the reversion of them can be provoked by the same photons. However, reversion is preferred by the shorter wavelengths. With increasing ratio of the longer wavelength components of the radiation (using artificial UV sources and solar light on the Earth's surface) the impact of the reversible photoproducts in the harmful biological effect decreases and other photoproducts are dominant. Assuming the photoinduced reactions (dimerisation and reversion) are statistical events, during the irradiation the chance for a number of nucleoprotein molecules to survive the radiation damage can be reality. The theoretical and experimental basis of these assumptions will be discussed in the case of bacteriophage T7 nucleoprotein.     

Organics produced by ion irradiation of ices: some recent results.

Some results, recently obtained from laboratory experiments of ion irradiation of ice mixtures containing H, C, N, and O, are here summarized. They are relevant to the formation and evolution of complex organics on interstellar dust, comets and other small bodies in the external Solar System. In particular the formation of CN-bearing species is discussed. Interstellar dust incorporated into primitive Solar System bodies and subsequently delivered to the early Earth, may have contributed to the origin of life. The delivery of CN-bearing species seems to have been necessary because molecules containing the cyanogen bond are difficult to be produced in an environment that is not strongly reducing as that of the early Earth probably was. Moreover we report on an ongoing research program concerning the interaction between refractory materials produced by ion irradiation of simple ices and biological materials (amino acids, proteins, cells).     

Pre-biotic stage of life origin under non-photosynthetic conditions.

Spontaneous assembling of a simplest bacterial cell even if all necessary molecules are present in a solution seems to be extremely rare event and from the scientific standpoint has to be considered as impossible. Therefore, a predecessor of a living cell has to be very simple for providing its self-assembling and at the same time it should be able of progressive increase in complexity. Now phase-separated particles, first of all micelles, are put forward as possible predecessors of living cell. According to the offered working concept only phase-separated particles possessing autocatalytic properties can be considered as predecessors of living cells. The first stage of evolution of these phase-separated autocatalytic systems is the appearance of pre-biotic metabolism providing synthesis of amphiphiles for formation of capsules of these systems. This synthesis is maintained by the energy of a base reaction being a component of a planet-chemical cycle. Catalytic system providing functioning of pre-biotic metabolism is based on multivariate oligomeric autocatalyst, which reproduces itself from monomers, penetrating the particles from the outside. Since the autocatalyst realizes random polymerization then a collection of other oligomers possessing different catalytic functions is produced. In the paper the functioning of multivariate oligomeric autocatalyst in flow reactor is analyzed.     

Possible complex organic compounds on Mars.

It is suggested that primitive Mars had somehow similar environments as primitive Earth. If life was born on the primitive earth using organic compounds which were produced from the early Earth environment, the same types of organic compounds were also formed on primitive Mars. Such organic compounds might have been preserved on Mars still now. We are studying possible organic formation on primitive and present Mars. A gaseous mixture of CO2, CO, N2 and H2O with various mixing ratios were irradiated with high energy protons (major components of cosmic rays). Hydrogen cyanide and formaldehyde were detected among volatile products, and yellow-brown-colored water-soluble non-volatile substances were produced, which gave amino acids after acid-hydrolysis. Major part of "amino acid precursors" were not simple molecules like aminonitriles, but complex compounds which eluted earlier than free amino acids in cation-exchange HPLC. These organic compounds should be major targets in the future Mars mission. Strategy for the detection of the complex organics on Mars will be discussed.     

Characterization of complex organic compounds formed in simulated planetary atmospheres by the action of high energy particles.

A wide variety of organic compounds, which are not simple organics but also complex organics, have been found in planets and comets. We reported that complex organics was formed in simulated planetary atmospheres by the action of high energy particles. Here we characterized the experimental products by using chromatographic and mass spectrometric techniques. A gaseous mixture of CO, N2 and H2O was irradiated with high energy protons (major components of cosmic rays). Water-soluble non-volatile substances, which gave amino acids after acid-hydrolysis, were characterized by HPLC and mass spectrometry. Major part of the products were complex compounds with molecular weight of several hundreds. Amino acid precursors were produced even when no water was incorporated with the starting materials. It was suggested that complex molecules including amino acid precursors were formed not in solution from simple molecules like HCN, but directly in gaseous phase.     

Formation of amino acid precursors in cometary ice environments by cosmic radiation.

Cometary ices are believed to contain water, carbon monoxide, methane and ammonia, and are possible sites for the formation and preservation of organic compounds relating to the origin of life. Cosmic rays, together with ultraviolet light, are among the most effective energy sources for the formation of organic compounds in space. In order to study the possibility of the formation of amino acids in comets or their precursory bodies (interstellar dust grains), several types of ice mixtures made in a cryostat at 10 K ("simulated cometary ices") were irradiated with high energy protons. After irradiation, the volatile products were analyzed with a quadrupole mass spectrometer, while temperature of the cryostat was raised to room temperature. The non-volatile products remaining in the cryostat at room temperature were collected with water. They were acid-hydrolyzed, and analyzed by ion-exchange chromatography. When an ice mixture of carbon monoxide (or methane), ammonia and water was irradiated, some hydrocarbons were formed, and amino acids such as glycine and alanine were detected in the hydrolyzate. These results suggest the possible formation of "amino acid precursors" (compounds yielding amino acids after hydrolysis) in interstellar dust grains by cosmic radiation. We previously reported that amino acid precursors were formed when simulated primitive planetary atmospheres were irradiated with cosmic ray particles. It will be of great interest to compare the amount of bioorganic compounds that were formed in the primitive earth and that brought by comets to the earth.     

Chemical evolution in space--a source of prebiotic molecules.

In Laboratory Astrophysics at Leiden University a laboratory analog for following the chemical evolution of interstellar dust in space shows that the dust contains the bulk of organic material in the universe. We follow the photoprocessing of low temperature (10 K) mixtures of ices subjected to vacuum ultraviolet radiation in simulation of interstellar conditions. The most important, but necessary, difference is in the time scales for photo-processing. One hour in the laboratory is equivalent to one thousand years in low density regions of space and as much as, or greater than, ten thousand to one million years in the depths of dense molecular clouds. The ultimate product of photoprocessing of grain material in the laboratory is a complex nonvolatile residue which is yellow in color and soluble in water and methanol. The molecular weight is greater than the mid-hundreds. The infrared absorption spectra indicate the presence of carboxylic acid and amino groups resembling those of other molecules of presumably prebiological significance produced by more classical methods. One of our residues, when subjected to high resolution mass spectroscopy gave a mass of 82 corresponding to C4H6H2 after release of CO2 and trace ammounts of urea suggesting amino pyroline rings. The deposit of prebiotic dust molecules occurred as many as 5 times in the first 500-700 million years on a primitive Earth by accretion during the passage of the solar system through a dense interstellar cloud. The deposition rate during each passage is estimated to be between 10(9) and 10(10) g per year during the million or so years of each passage; i.e., a total deposition of 1O(9)-10(10) metric tons of complex organic material per passage.     

Dictyostelium discoideum, a lower eukaryote model for the study of DNA repair: implications for the role of DNA-damaging chemicals in the evolution of repair proficient cells.

The evolution of the ability of living cells to cope with stress is crucial for the maintenance of their genetic integrity. Yet low levels of mutation must remain to allow adaptation to environmental changes. The cellular slime mold D. discoideum is a good system for studying molecular aspects of the repair of lethal and mutagenic damage to DNA by radiation and chemicals. The wild-type strains of this soil microorganism are extremely resistant to DNA damaging agents. In nature the amoeboid cells in their replicative stage feed on soil bacteria and are exposed to numerous DNA-damaging chemicals produced by various soil microorganisms. It is probable that the evolution of repair systems in this organism and perhaps in others is a consequence of the necessity to cope with chemical damage which also confers resistance to radiation.     

The cometary contribution to prebiotic chemistry.

Different estimates based on dynamical considerations, lunar cratering rates, Solar System chemical abundances, and the single-impact theory on the origin of the Earth-Moon system suggest that comets and other related small, volatile-rich primitive minor bodies captured by the Earth during the early Archean must have been a major source of volatiles on our planet. It is likely that a substantial fraction of the organic molecules present in the colliding cometary nuclei, which may have included nitrogen bases and the precursors of amino acids, were destroyed due to the high temperatures and shock wave energy associated with the collision. However, the presence of H2O, CN, CH, CO, CO2 and other carbon-bearing molecules and radicals in the atmosphere of the Sun and in circumstellar shells around carbon-rich stars suggests that at least simple carbon species could have survived the cometary collisions. Under the anoxic conditions thought to prevail in the prebiotic terrestrial paleoatmosphere, the post-collisional formation of a large number of excited molecules and radicals, and the rapid quenching of the expanding gaseous ball may have led, upon rapid cooling, to the formation of molecules of biogenic elements and to their eventual deposition in localized environments where complex organic compounds of biochemical significance may have been produced and accumulated.