Origins of Life: Emergence of Amino Acids
Robert Pascal* and Laurent Boiteau, UMR5247, CNRS-university of Montpellier 1 and University of Montpellier 2, Montpellier, France
Amino acids can be synthesized from inanimate matter through processes independent of living organisms. An overview of these processes occurring in various environments, including interstellar media, is given with a special emphasis on Strecker synthesis and related processes compatible with primitive Earth conditions. When analyzing their relevance to the origin of life, chemical pathways leading to a-amino acids from activated precursors may be considered independent from further polymerization into peptides promoted by activating agents. Alternatively, both processes may also be connected to each other so that the emergence of amino acids and the prebiotic formation of peptide may have been closely associated. The last possibility is that prebiotic chemistries of amino acids and nucleotides may have been cooperating with each other in a way that led to the emergence of the genetic code and to a rudimentary translation apparatus.
The emergence of life has become a scientific field of interest since Darwinian theory was introduced, presuming the evolution of living organisms. Strong evidence exists that all living beings on Earth have a common ancestor. However, this Last Common Ancestor (LCA) (1) was most probably a living entity involving nucleic acid-based information storage (RNA and probably DNA) and ribosomal translation machinery. It lived probably several hundred millions years, and possibly more than one billion years, after life originated. We have no clues to the evolution pathway that led from the emergence of life to this LCA and on the preceding chemical evolution. These processes are the field of investigation of researchers in prebiotic chemistry and in early evolution; they try to build self-consistent hypotheses for the development of life. Some information can be gained from the analysis of biochemical pathways, keeping in mind that new pathways may have evolved replacing extinct ones. Other indications can be obtained by reproducing the conditions assumed to have occurred on the early Earth (the panspermia hypothesis will not be considered here). Indeed, the first scientists who analyzed the origin of life process (2, 3) proposed that early life forms were dependent on abiotically formed organic molecules as carbon and energy sources for their growth (the heterotrophic hypothesis). These organisms existed as carbon and energy sources for their growth (the heterotrophic hypothesis). The formation of amino acids by electric discharges in reducing mixtures of gases (CH4, NH3, H2O) through the Miller experiment (4) has given experimental support to this hypothesis by demonstrating that some essential building blocks of life can be efficiently formed abiotically. The presence of amino acids in several extraterrestrial samples of matter delivered to the Earth as meteorites is also clearly established. Amino acids, and more generally organic matter, must not be considered rare in the universe, which is also independently supported by the spectroscopic analysis of interstellar molecular clouds. In the following sections, we will describe different processes leading to α-amino acids under potentially prebiotic conditions, as well as analyze their relevance to the origin of life and their connection with the role of amino acids at the early stages of life evolution.
*To receive any correspondance.
α-Amino Acids and the Origin of Life Process
Proteins are one of the main classes of biopolymers found in living organisms. They can adopt a large variety of structural patterns, which makes them essential cell constituents mostly involved in recognition processes. Their molecular recognition ability is remarkable in catalysis because enzymes have evolved to accommodate transition states in their active site to lower the kinetic barriers of most biochemical reactions. This ability is connected to appropriate primary sequences, and it allows the proteins to fold into well-defined three-dimensional structures. However, the accuracy of the primary sequence, which is ensured by the translation of genomic sequences in current-day living organisms, seems out of reach of prebiotic systems. Therefore, the actual role of amino acids at that time is not clearly known. Nevertheless, if we still assume that their prebiotic role was the catalytic ability of polypeptides, another unresolved question lies in the prebiotic pathway of synthesis of these polymers. It is believed that prebiotic peptides have been formed from monomeric α-amino acid through physically or chemically induced processes. This assumption is not supported by strong evidence and alternative processes may have taken place. From a more general point of view, the biochemical route to biopolymers represents one kind of disconnection among the various possible retrosynthetic pathways that can be conceived starting from highly activated simple organic compounds (5). In this view, the stepwise formation of biopolymers by adding monomeric building blocks using condensing (dehydrating) agents in (most probably) diluted aqueous solution seems unlikely compared with a self-assembly that could take place directly from activated simple organic precursors with no need of further activation. As a result, the current discussion of the emergence of α-amino acids also includes the possibility that peptides may have been formed directly from activated precursors through processes bypassing monomeric a-amino acids.
An amino acid and peptide world?
In biology, the catalytic role is mostly played by enzymes. It is tempting to speculate that life may have emerged in a peptide world (6). Short peptides and even isolated a-amino acids are capable of catalyzing prebiotic processes (7). Various physical or chemical pathways are available for the formation of peptides from inactivated or activated monomers. However, with respect to the sequence of peptides derived from common a-amino acids, this kind of chemistry still fails to provide an efficient replication system. For instance, peptide segments (activated as thioesters) can be self-replicated by ligation if selected residues (cysteine) are present at the N-terminus (8, 9), but the replication of a complete peptide sequence from monomers seems unattainable. The only remaining possibility is an early system of information storage based on unnatural amino acids that is capable of base pairing or related molecules such as peptide nucleic acids (PNAs). Although a transfer of information from PNA to RNA is materially feasible (10), it is unclear why this system could have been replaced by nucleic acids rather than being improved by evolution. Moreover, no remnant of this system has been preserved in current-day living organisms.
The role of α-amino acids in the RNA world scenario
The RNA-related nature of most coenzymes and cofactors, the role of RNA in the translation process, and the catalytic abilities of RNA show that RNAs have played a crucial role in early biochemistry and have supported the hypothesis of an RNA world (11). In this scenario, living organisms primarily used RNA for both catalysis and information storage before the advent of coded peptides and of the translation apparatus. But most supporters of this scenario believe that amino acids and peptides may have played a part in catalytic activity, for instance as ribozyme cofactors (12). This provides a rationale for the evolution of the genetic code. In any case, covalent interactions of RNA with amino acids and peptides were probably required early to initiate the development of translation, so that hypotheses considering that polypeptides cooperated with RNAs since the early beginning of the RNA world have been presented (13, 14).
A coevolution process toward the genetic code
Because the translation apparatus is among the oldest components of living beings, it is tempting to consider the emergence of life and of translation to be closely related. In other words, we can make the hypothesis that nucleic acids and translated peptides may not be considered as two independent subsystems but as one subsystem, the RNA-coded peptides (5). Experimentally, reactions starting from α-amino acids activated as N-carboxyanhydrides, and nucleotides have recently demonstrated the possibility of obtaining covalent conjugates (15) under prebiotically relevant conditions. Similarly, reactions of N-phosphoryl α-amino acids can result in both oligopeptides and oligonucleotides (16). The chemistry involved in such systems may have served as a starting point for the evolution toward the translation apparatus. Subsequently we must determine how the current-day set of coded residues has been selected among many possible structures and how they have been allocated a triplet codon to allow the translation of the genetic information into protein sequences. The coevolution theory of the genetic code (17, 18) (that may also be independent of the coevolution process mentioned above) states that codons have initially been selected for a subset of prebiotically synthesized a-amino acids. Then codon allocation was guided by potential biochemical conversions between the amino acids.
Abiotic and Prebiotic Chemistry of Amino Acids
Amino acids have probably formed in different places of the Solar system through processes independent of living organisms as shown by their occurrence in carbonaceous chondrites, a particular class of meteorites. Among these processes, only a particular subset of them can be considered to be truly prebiotic. It is the processes that make amino acids available in environments capable of developing a complex chemistry compatible, or at least presumed to be compatible, with the emergence of life.
Formation on the early earth
Several processes may have been responsible for the local formation of amino acids. In fact, energy release (electrical discharges, ultraviolet light, or impact shocks) into gas mixtures containing elementary carbon sources (CO2, CO, CH4), water, and nitrogen produces organic molecules, including amino acids, but significant yields require a reduced overall redox state. This requirement is fulfilled for electric discharges in a reduced atmosphere containing methane, ammonia, and water, as in the original Miller experiment. It has also been observed for atmospheres based on N2 and CO or CO2 on the condition that H2 or methane is also present in sufficient amounts (19). A neutral atmosphere (based on N2, CO2, and water) would produce much lower yields of organics (by several orders of magnitude). In the absence of other species to be oxidized, the reduction of CO2 requires the concomitant thermodynamically unfavorable conversion of water into O2 (as in photosynthesis). However, even if the atmosphere was neutral when life arose, as usually believed, the Earth was not uniform with respect to redox state simply because the reduced state of the mantle and the high volcanic activity favored the occurrence of locally reduced environments (for instance, in hydrothermal vents in the oceans). Then, a preservation of the hydrogen content of the early atmosphere or the diversity of environments on the early Earth is likely to have made amino acid formation possible, at least at specific places.
The strecker synthesis and related processes
The formation of α-aminonitriles: a set of equilibrated reactions
A strong argument in favor of the involvement of Strecker synthesis is that aldehydes and HCN are among the initial species formed in electric discharge experiments leading to α-amino acid formation. Mechanistic and thermodynamic studies (20) of systems derived from aqueous mixtures containing an aldehyde, ammonia, and hydrogen cyanide have disclosed the network of equilibrated reactions involved in these systems (Fig. 1). In the first stage, cyanide is rapidly added to the carbonyl compound and cyanohydrin 2 is produced. Then, the α-aminonitrile 5 is formed more slowly through cyanide attack on an iminium ion intermediate 4. The composition of the equilibrium mixture formed from equimolecular concentrations of aldehyde and cyanide is strongly dependent on the pH and of the initial concentration of ammonia. Then, under conditions simulating a presumed prebiotic aqueous environment (with low concentrations of organic precursors and ammonia and in a 5-7 pH range brought about by a CO2-rich early Earth atmosphere), α-aminonitriles are formed in very low equilibrium yield (21). However, since hydrolysis pathways (Fig. 1) are likely to proceed at different rates, there is no reason for the final hydroxy acid/amino acid ratio to match the large predominance of cyanohydrin over α-aminonitrile at equilibrium. Actually, an important, often overlooked, feature of the Strecker synthesis is that, under neutral or mild alkaline conditions, α-aminonitrile hydrolysis (or conversion into stable derivatives) proceeds through efficient pathways involving the specific participation of the neighboring amino group, which offsets their low thermodynamic stability.
Figure 1. Strecker and related systems: complex network of equilibrium reactions from aqueous solutions of cyanide, ammonia, and aldehyde, 1. Pathways for exiting the equilibrated network correspond to (a) cyanohydrin hydrolysis, (b) aminonitrile hydrolysis, and (c) Bucherer-Bergs reaction. Adducts 6 and 7 and other hydrolysis products can be formed at high concentrations of reactants.
Catalytic conversion of α-aminonitriles: the determining process
It turned out that a-aminonitrile hydration is subject to efficient catalysis by aldehydes (22), which are already reactants of the Strecker reaction (Fig. 2). This catalytic pathway is still prevailing at 20-μM formaldehyde concentrations (21) and half-lives shorter than a year are expected in the presence of 10-mM formaldehyde at pH 7 and 25° C. It proceeds through the addition of the aldehyde at the amino group and the subsequent intramolecular reaction of carbinolamine adduct 13.
Figure 2. The detailed mechanisms for irreversible transformations of α-aminonitriles 5. (a) Aldehyde-catalyzed pathway of hydration predominant in neutral and alkaline aqueous solutions. (b) Bucherer-Bergs conversion of α-aminonitriles into hydantoins.
This reaction (Fig. 2) is closely related to the above described catalytic pathway for α-aminonitrile hydration, but it involves CO2 instead of an aldehyde (23). The main difference lies in the fate of isocyanate 19 (formed instead of imine 15), which easily undergoes the cyclization into hydantoin derivative 12 (instead of hydrolysis to α-aminoamide 16). Considering the kinetic stability of 12, CO2 is a coreactant instead of a catalyst for the Bucherer-Bergs reaction; nevertheless, this pathway is an additional, very efficient process for selecting α-amino acid derivatives rather than those of α-hydroxy acids. Moreover, despite the very sluggish reactions of its products, the Bucherer-Bergs reaction must not be considered as a dead-end since the N-carbamoylamino acid 20 can be converted into the α-amino acid N-carboxyanhydride 21 (Fig. 3), readily under the effect of nitrogen oxides (24), but also slowly through a spontaneous pathway (25, 26).
Figure 3. Plausible prebiotic pathways for the formation of α-amino acid N-carboxyanhydrides 21 from free amino acids, N-carbamoylamino acids 20, or activated α-amino acid derivatives 22.
The synthesis of amino acids in aqueous media is energetically feasible in reducing fluids and temperatures found in hydrothermal systems (27). Amino acids have indeed been produced, although in micromolar concentrations, by heating a mixture of methane and nitrogen in simulated hydrothermal fluids (28). A likely process for their production could be a Strecker reaction. Plausible chemical pathways have been thermodynamically analyzed (29), and a process involving reductive amination of keto acids (30) has also been proposed. On the other hand, high temperatures are also likely to damage organic molecules.
Formation in interstellar media
Another potential source of organic compounds on early Earth is extraterrestrial bodies (31-33). This possibility is attested by the presence of a-amino acids in meteorites. The synthesis of organic compounds occurred in the presolar molecular cloud or in the protoplanetary disk that preceded the formation of planets (34). It is likely to have resulted from UV-irradiation of interstellar ices (35) with the formation of radicals and/or other highly activated species, which then randomly combined into more complex organic compounds at the low temperature of the molecular cloud. Then these ice particles were involved in the accretion of meteorite parent bodies, where organic matter could be preserved from the heat released by the process in small accreting bodies. Subsequently, reactions like those involved in Miller’s experiment may have occurred on meteorite parent bodies early in the history of the solar system. Then, these organic molecules could have been delivered to the Earth through impacts of meteorites, micrometeorites, and comets.
Many processes have been proposed for the formation of prebiotic peptides. Peptide bond formation from free amino acids can become thermodynamically favorable using physical or chemical means for dehydration (6, 36). Alternatively, activated amino acid derivatives are capable of polymerizing into oligopeptides in aqueous solution. A pathway for the formation of α-amino acid thioesters starting from sugar precursors has been discussed (37). α-Amino acid N-carboxyanhydrides (NCAs) correspond to the most activated form of amino acids reachable in a prebiotic environment with a high content in CO2 or bicarbonate (38), since carboxyl-activated derivatives 22 are easily converted into NCAs through a very efficient CO2-promoted process (39) (Fig. 3). The length of peptide chains formed by polymerization of NCAs is often limited by precipitation, but longer peptides (up to 55-mers) have been obtained in the presence of illite and hydroxylapatite (40). NCAs can also be formed through prebiotically relevant pathways starting from N-carbamoylamino acids (24-26) or through the activation of amino acids with carbonyl sulfide (41).
Amino acids and the emergence of homochirality
The configuration of natural amino acids has led to studies on the possibility that homochirality emerged at a prebiotic stage, which may be supported by the presence of amino acids as non-racemic mixtures in meteorites (32). This enantiomeric excess may have resulted from the exposition of extraterrestrial matter to circularly polarized light (42). Whatever the origin of this enantiomeric excess, it may have initiated stereoselective processes through different catalytic pathways (7). Symmetry breaking may also have resulted from reactivity in connection with other processes such as crystallization or interfacial chemistry (43, 44) and polymerization of amino acids (45).
Relevance of Abiotic Processes to the Emergence of Life
The presence of amino acids in meteorites (chondrites) and their delivery on the surface of the Earth may have triggered prebiotic pathways starting from these building blocks. On the other hand, their occurrence of meteorite parent bodies may simply be considered as a manifestation of their easy synthesis through various abiotic pathways, and of their abundance in the universe and consequently on the early Earth. The answer to this alternative idea mainly depends on the rate of evolution of the atmosphere and on the development of conditions favorable to life on the planet. Most scientists consider that the atmosphere of the Earth was initially based on a mixture of N2 and CO2 with a significant content in H2 and CH4 (favorable to the production of organic molecules). Then, it evolved from this reduced state to a more neutral state (N2, CO2) as hydrogen escaped to outer space (46). The rate of this evolution depends on both the input of H2 from the volcanic activity and its loss to outer space (47). Another problem is the presence of conditions that allow the growth of living beings. Studies on the origin of life processes are strongly dependent on the knowledge gained by other fields of science such as astrophysics, geology, and other planetary sciences. Since liquid water was already present on the Earth a few hundred million years after its accretion leading to the early formation of oceans, a major problem encountered by early forms of life would have been that of impact of asteroids or comets capable of vaporizing the oceans (at least in part) and thus of sterilizing the planet. Both issues are still debated, and many hypotheses are acceptable. Life may have emerged early on Earth in a globally reduced environment and may have survived impacts by asteroids or comets. Alternatively, synthetic processes occurring on early Earth with a reduced atmosphere may have no connection with a later emergence of the ancestors of all living beings that we currently know. Instead, it may have resulted from the delivery of organics or their synthesis in locally reduced environments. It is still possible to speculate that life emerged several times and then was annihilated by impacts.
Future Research Directions
More than 175 years after urea was synthesized from mineral precursors, abiotic processes seem to be capable of having made a-amino acids and various organic molecules available in many places of the solar system. The easy abiotic synthesis of α-amino acids may also be the consequence of their composition based on the most abundant reactive elements in the universe (H, C, N, O). Determining the actual pathway through which life emerged is currently unfeasible considering the absence of remnants, and we have no indication that this situation may change. However, the study of nonlinear processes of complexification, involving biomolecules (including amino acids) and other prebiotic organic or inorganic derivatives, remains an important field of interest for chemical biology. The discovery of processes working under kinetic control and capable of connecting replication, adaptation and self-maintenance, which is one of the biggest problems in modern science, needs additional analysis of simple and robust pathways. Amino acid prebiotic chemistry, starting from activated species and/or energy sources and potentially capable of delivering energy to such systems, has brought about important pieces of information in this direction and will surely be helpful in the achievement of this goal.
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Amino Acids, Chemistry of
Proteins, Chemistry and Chemical Reactivity of
Proteins: Structure, Function and Stability
Homochirality, Spontaneous Generation of
Origin of Life, Chemical Basis for