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Abiogenesis & Evolution: PLoS Genetics: The Evolutionary Value of Recombination Is Constrained by Genome Modularity
Primordial Peptides and Proteins
GADV-protein world hypothesis.: "Based on the fact that RNA has not only a genetic function but also a catalytic function, the RNA world theory on the origin of life was first proposed about 20 years ago. The theory assumes that RNA was amplified by self-replication to increase RNA diversity on the primitive earth. Since then, the theory has been widely accepted as the most likely explanation for the emergence of life. In contrast, we reached another hypothesis, the [GADV]-protein world hypothesis, which is based on pseudo-replication of [GADV]-proteins. We reached this hypothesis during studies on the origins of genes and the genetic code, where [G], [A], [D], and [V] refer to Gly, Ala, Asp, and Val, respectively. In this review, possible steps to the emergence of life are discussed from the standpoint of the [GADV]-protein world hypothesis, comparing it in parallel with the RNA world theory. It is also shown that [GADV]-peptides, which were produced by repeated dry-heating cycles and by solid phase peptide synthesis, have catalytic activities, hydrolyzing peptide bonds in a natural protein, bovine serum albumin. These experimental results support the [GADV]-protein world hypothesis for the origin of life."
Ikehara K. Possible steps to the emergence of life: the [GADV]-protein world hypothesis. Chem Rec. 2005;5(2):107-18.
Catalytic Activities Of [GADV]-Peptides Formation and Establishment of [GADV]-Protein World for the Emergence of Life. : "We have previously postulated a novel hypothesis for the origin of life, assuming that life on the earth originated from '[GADV]-protein world', not from the 'RNA world' (see Ikehara's review, 2002). The [GADV]-protein world is constituted from peptides and proteins with random sequences of four amino acids (glycine [G], alanine [A], aspartic acid [D] and valine [V]), which accumulated by pseudo-replication of the [GADV]-proteins. To obtain evidence for the hypothesis, we produced [GADV]-peptides by repeated heat-drying of the amino acids for 30 cycles ([GADV]-P(30)) and examined whether the peptides have some catalytic activities or not. From the results, it was found that the [GADV]-P(30) can hydrolyze several kinds of chemical bonds in molecules, such as umbelliferyl-beta-D-galactoside, glycine-p-nitroanilide and bovine serum albumin. This suggests that [GADV]-P(30) could play an important role in the accumulation of [GADV]-proteins through pseudo-replication, leading to the emergence of life. We further show that [GADV]-octapaptides with random sequences, but containing no cyclic compounds as diketepiperazines, have catalytic activity, hydrolyzing peptide bonds in a natural protein, bovine serum albumin. The catalytic activity of the octapeptides was much higher than the [GADV]-P(30) produced through repeated heat-drying treatments. These results also support the [GADV]-protein-world hypothesis of the origin of life (see Ikehara's review, 2002). Possible steps for the emergence of life on the primitive earth are presented."
Oba T, Fukushima J, Maruyama M, Iwamoto R, Ikehara K. Catalytic Activities Of [GADV]-Peptides Formation and Establishment of [GADV]-Protein World for the Emergence of Life. Orig Life Evol Biosph. 2005 Oct;35(5):447-60.
Dynamic co-evolution of peptides and chemical energetics, a gateway to the emergence of homochirality and the catalytic activity of peptides. : "We propose a scenario for the dynamic co-evolution of peptides and energy on the primitive Earth. From a multi component system consisting of hydrogen cyanide, several carbonyl compounds, ammonia, alkyl amine, carbonic anhydride, borate and isocyanic acid, we show that the reversibility of this system leads to several intermediate nitriles, that irreversibly evolve to alpha-amino acids and N-carbamoyl amino acids via selective catalytic processes. On the primitive Earth these N-carbamoyl amino acids combined with energetic molecules (NOx) may have been the core of a molecular engine producing peptides permanently and assuring their recycling and evolution. We present this molecular engine, a production example, and its various selectivities. The perspectives for such a dynamic approach to the emergence of peptides are evoked in the conclusion."Commeyras A, Taillades J, Collet H, Boiteau L, Vandenabeele-Trambouze O, Pascal R, Rousset A, Garrel L, Rossi JC, Biron JP, Lagrille O, Plasson R, Souaid E, Danger G, Selsis F, Dobrijevic M, Martin H.Dynamic co-evolution of peptides and chemical energetics, a gateway to the emergence of homochirality and the catalytic activity of peptides. Orig Life Evol Biosph. 2004 Feb;34(1-2):35-55.
Peptides by activation of amino acids with CO on (Ni,Fe)S surfaces: implications for the origin of life. : "In experiments modeling volcanic or hydrothermal settings amino acids were converted into their peptides by use of coprecipitated (Ni,Fe)S and CO in conjunction with H2S (or CH3SH) as a catalyst and condensation agent at 100 degreesC and pH 7 to 10 under anaerobic, aqueous conditions. These results demonstrate that amino acids can be activated under geochemically relevant conditions. They support a thermophilic origin of life and an early appearance of peptides in the evolution of a primordial metabolism."
Huber C, Wachtershauser G. Peptides by activation of amino acids with CO on (Ni,Fe)S surfaces: implications for the origin of life. Science. 1998 Jul 31;281(5377):670-2.
Comment in: Science. 1998 Jul 31;281(5377):627, 629.
A possible primordial peptide cycle. : "alpha-Amino acids can undergo peptide formation by activation with carbon monoxide (CO) under hot aqueous conditions in the presence of freshly coprecipitated colloidal (Fe,Ni)S. We now show that CO-driven peptide formation proceeds concomitantly with CO-driven, N-terminal peptide degradation by racemizing N-terminal hydantoin and urea derivatives to alpha-amino acids. This establishes a peptide cycle with closely related anabolic and catabolic segments. The hydantoin derivative is a purin-related heterocycle. The (Fe,Ni)S-dependent urea hydrolysis could have been the evolutionary precursor of the nickelenzyme urease. The results support the theory of a chemoautotrophic origin of life with a CO-driven, (Fe,Ni)S-dependent primordial metabolism."
Huber C, Eisenreich W, Hecht S, Wachtershauser G. A possible primordial peptide cycle. Science. 2003 Aug 15;301(5635):938-40.
[The simultaneous synthesis of peptides and oligonucleotides on kaolinite with the participation of aminoacyladenylates] "A simultaneous synthesis of peptides (2-5 residues) and oligonucleotides (3-9 residues) has been carried out on caolinite matrix using amino acids and aminoacyladenylates as substrates. The rate of oligomer synthesis on mineral surface is higher than that in solution. The mechanism of synthesis has been described. The data has been discussed in connection with abiogenesis of two major types of biopolymers, proteins and nucleic acids."
[The simultaneous synthesis of peptides and oligonucleotides on kaolinite with the participation of aminoacyladenylates]Egofarova RKh, Vasil'eva NV, Moiseeva LN, Otroshchenko VA, Pavlovskaia TE.Izv Akad Nauk SSSR Biol. 1990 Jan-Feb;(1):136-40.
Comparative study of abiogenesis of cysteine and other amino acids catalyzed by various metal ions. : "The present work pertains to the study of the influence of nickel, cobalt, thorium, vanadium, molybdate, ferrous ions on the formation of cysteine which is synthesized abiogenically together with other amino acids in sterilized aqueous mixtures of ammonium thiocyanate, formaldehyde, potassium dihydrogen phosphate, calcium acetate, and biological minerals after irradiating by artificial light. The effect of these catalysts on cysteine formation was of the order: Fe++ greater than Mo++ greater than Th++++ greater than V++ greater than Co++ greater than Ni."Bahadur K, Sen P.Comparative study of abiogenesis of cysteine and other amino acids catalyzed by various metal ions.Z Allg Mikrobiol. 1975;15(3):143-7.
Aqueous synthesis of Peptide thioesters from amino acids and a thiol using 1,1'-carbonyldiimidazole. : "A new method was developed for the synthesis of peptide thioesters from free amino acids and thiols in water. This one-pot simple method involves two steps: (1) activation in water of an amino acid presumably as its N-carboxyanhydride (NCA) using 1,1'-carbonyldiimidazole (CDI), and (2) subsequent condensation of the activated amino acid-NCA in the presence of a thiol. With this method citrulline peptide thioesters containing up to 10 amino acid residues were prepared in a single reaction. This aqueous synthetic method provides a simple way to prepare peptide thioesters for studies of peptide replication involving ligation of peptide thioesters on peptide templates. The relevance of peptide replication to the origin-of-life process is supported by previous studies showing that amino acid thioesters (peptide thioester precursors) can be synthesized under prebiotic conditions by reaction of small sugars with ammonia and a thiol."
Weber AL. Aqueous synthesis of Peptide thioesters from amino acids and a thiol using 1,1'-carbonyldiimidazole. Orig Life Evol Biosph. 2005 Oct;35(5):421-7.
A model for the role of short self-assembled peptides in the very early stages of the origin of life : "The molecular basis of the origin of life is one of the most fundamental questions in modern biology. While the 'RNA world' hypothesis offers a very sensible model for the evolvement of the current biochemical networks, there is a lack of knowledge about the early steps that led to the formation of the first RNA molecules. This issue is essential as it is practically impossible that complex molecules as functional RNA oligonucleotides had evolved spontaneously. It was recently demonstrated that peptide molecules as simple as dipeptides can self-assemble into well-ordered tubular, fibrilar, and closed-cage structures. Other studies have confirmed the ability of dipeptides to act as catalysts and the capability of other peptides, as short as tripeptides, to serve as a template for nucleotide binding and orientation. Unlike complex RNA molecules, the spontaneous formation of functional short peptides in the primordial earth conditions is very likely. We suggest a novel mechanism for the origin of life that is based on the ability of short peptides to form encapsulated structures, catalyst chemical reaction, and serve as highly ordered template for the assembly of nucleotides. This model may explain the early events that led to the formation of the current biochemical machinery that combines the elaborated and coordinated interaction between nucleic acids and proteins to allow the function of living systems."
Carny O, Gazit E. A model for the role of short self-assembled peptides in the very early stages of the origin of life. FASEB J. 2005 Jul;19(9):1051-5.
N-carbamoyl-alpha-amino acids rather than free alpha-amino acids formation in the primitive hydrosphere: a novel proposal for the emergence of prebiot : "Our previous kinetic and thermodynamic studies upon the reactional system HCHO/HCN/NH3 in aqueous solutions are completed. In the assumed prebiotic conditions of the primitive earth ([HCHO] and [HCN] near 1 g L-1, T = 25 degrees C, pH = 8, [NH3] very low), this system leads to 99.9% of alpha-hydroxyacetonitrile and 0.1% of alpha-aminoacetonitrile (precursor of the alpha-amino acid). The classical base-catalyzed hydration of nitriles, slow and not selective, can not modify significantly this proportion. On the contrary, we found two specific and efficient reactions of alpha-aminonitriles which shift the initial equilibrium in favor of the alpha-aminonitrile pathway. The first reaction catalyzed by formaldehyde generates alpha-aminoamides, precursors of alpha-aminoacids. The second reaction catalyzed by carbon dioxide affords hydantoins, precursors of N-carbamoyl-alpha-aminoacids. In the primitive hydrosphere, where the concentration in carbon dioxide was estimated to be higher than that of formaldehyde, the formation of hydantoins was consequently more efficient. The rates of hydrolysis of the alpha-aminoacetamide and of the hydantoin at pH 8 being very similar, the synthesis of the N-carbamoyl-alpha-amino acid seems then to be the fatal issue of the HCHO/HCN/NH3 system that nature used to perform its evolution. These N-protected alpha-amino acids offer new perspectives in prebiotic chemistry, in particular for the emergence of peptides on the prebiotic earth."
Taillades J, Beuzelin I, Garrel L, Tabacik V, Bied C, Commeyras A.
N-carbamoyl-alpha-amino acids rather than free alpha-amino acids formation in the primitive hydrosphere: a novel proposal for the emergence of prebiotic peptides. Orig Life Evol Biosph. 1998 Feb;28(1):61-77.
Prebiotic transamination : "Biological amino acids and alpha keto acids directly condense with decarboxylation and transamination to yield product amino acids. This process is closely related to unusual amino acid decarboxylase enzymes in certain microorganisms and may represent a primordial mode of amino acid metabolism."
Bishop JC, Cross SD, Waddell TG. Prebiotic transamination. Orig Life Evol Biosph. 1997 Aug;27(4):319-24.
Evolution of selenocysteine-containing proteins: significance of identification and functional characterization of selenoproteins. : "In the genetic code, UGA serves as either a signal for termination or a codon for selenocysteine (Sec). Sec rarely occurs in protein and is different from other amino acids in that much of the biosynthetic machinery governing its incorporation into protein is unique to this amino acid. Sec-containing proteins have diverse functions and lack a common amino acid motif or consensus sequence. Sec has previously been considered to be a relic of the primordial genetic code that was counter-selected by the presence of oxygen in the atmosphere. In the present report, it is proposed that Sec was added to the already existing genetic code and its use has accumulated during evolution of eukaryotes culminating in vertebrates. The more recently evolved selenoproteins appear to take advantage of unique redox properties of Sec that are superior to those of Cys for specific biological functions. Further understanding of the evolution of selenoproteins as well as biological properties and biomedical applications of the trace element selenium requires identification and functional characterization of all mammalian selenoproteins."
Gladyshev VN, Kryukov GV. Evolution of selenocysteine-containing proteins: significance of identification and functional characterization of selenoproteins. Biofactors. 2001;14(1-4):87-92.
Theoretical Biology and Medical Modelling Full text Three subsets of sequence complexity and their relevance to biopolymeric information: "In life-origin science, attention usually focuses on a theorized pre-RNA World [52-55]. RNA chemistry is extremely challenging in a prebiotic context. Ribonucleotides are difficult to activate (charge). And even oligoribonucleotides are extremely hard to form, especially without templating. The maximum length of such single strands in solution is usually only eight to ten monomers (mers). As a result, many investigators suspect that some chemical RNA analog must have existed [56,57]. "
Abel DL, Trevors JT. Three subsets of sequence complexity and their relevance to biopolymeric information. Theor Biol Med Model. 2005 Aug 11;2:29. Free Full Text article
Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software. : "BACKGROUND: There is an increasing need for computer-generated models that can be used for explaining the emergence and predicting the behavior of multi-protein dynamic structures in cells. Multi-agent systems (MAS) have been proposed as good candidates to achieve this goal. RESULTS: We have created 3DSpi, a multi-agent based software that we used to explore the generation of multi-protein dynamic structures. Being based on a very restricted set of parameters, it is perfectly suited for exploring the minimal set of rules needed to generate large multi-protein structures. It can therefore be used to test the hypothesis that such structures are formed and maintained by principles of self-organization. We observed that multi-protein structures emerge and that the system behavior is very robust, in terms of the number and size of the structures generated. Furthermore, the generated structures very closely mimic spatial organization of real life multi-protein structures. CONCLUSION: The behavior of 3DSpi confirms the considerable potential of MAS for modeling subcellular structures. It demonstrates that robust multi-protein structures can emerge using a restricted set of parameters and allows the exploration of the dynamics of such structures. A number of easy-to-implement modifications should make 3DSpi the virtual simulator of choice for scientists wishing to explore how topology interacts with time, to regulate the function of interacting proteins in living cells."Soula H, Robardet C, Perrin F, Gripon S, Beslon G, Gandrillon O. Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software. BMC Bioinformatics. 2005 Sep 19;6:228. Free Full Text article
Investigation of the prebiotic synthesis of amino acids and RNA bases from CO2 using FeS/H2S as a reducing agent. : "An autotrophic theory of the origin of metabolism and life has been proposed in which carbon dioxide is reduced by ferrous sulfide and hydrogen sulfide by means of a reversed citric acid cycle, leading to the production of amino acids. Similar processes have been proposed for purine synthesis. Ferrous sulfide is a strong reducing agent in the presence of hydrogen sulfide and can produce hydrogen as well as reduce alkenes, alkynes, and thiols to saturated hydrocarbons and reduce ketones to thiols. However, the reduction of carbon dioxide has not been demonstrated. We show here that no amino acids, purines, or pyrimidines are produced from carbon dioxide with the ferrous sulfide and hydrogen sulfide system. Furthermore, this system does not produce amino acids from carboxylic acids by reductive amination and carboxylation. Thus, the proposed autotrophic theory, using carbon dioxide, ferrous sulfide, and hydrogen sulfide, lacks the robustness needed to be a geological process and is, therefore, unlikely to have played a role in the origin of metabolism or the origin of life."Keefe AD, Miller SL, McDonald G, Bada J. Investigation of the prebiotic synthesis of amino acids and RNA bases from CO2 using FeS/H2S as a reducing agent. Proc Natl Acad Sci U S A. 1995 Dec 5;92(25):11904-6. Free Full Text article | 1 Guide-Glossary
Ikehara K. Possible steps to the emergence of life: the [GADV]-protein world hypothesis. Chem Rec. 2005;5(2):107-18.
Catalytic Activities Of [GADV]-Peptides Formation and Establishment of [GADV]-Protein World for the Emergence of Life. : "We have previously postulated a novel hypothesis for the origin of life, assuming that life on the earth originated from '[GADV]-protein world', not from the 'RNA world' (see Ikehara's review, 2002). The [GADV]-protein world is constituted from peptides and proteins with random sequences of four amino acids (glycine [G], alanine [A], aspartic acid [D] and valine [V]), which accumulated by pseudo-replication of the [GADV]-proteins. To obtain evidence for the hypothesis, we produced [GADV]-peptides by repeated heat-drying of the amino acids for 30 cycles ([GADV]-P(30)) and examined whether the peptides have some catalytic activities or not. From the results, it was found that the [GADV]-P(30) can hydrolyze several kinds of chemical bonds in molecules, such as umbelliferyl-beta-D-galactoside, glycine-p-nitroanilide and bovine serum albumin. This suggests that [GADV]-P(30) could play an important role in the accumulation of [GADV]-proteins through pseudo-replication, leading to the emergence of life. We further show that [GADV]-octapaptides with random sequences, but containing no cyclic compounds as diketepiperazines, have catalytic activity, hydrolyzing peptide bonds in a natural protein, bovine serum albumin. The catalytic activity of the octapeptides was much higher than the [GADV]-P(30) produced through repeated heat-drying treatments. These results also support the [GADV]-protein-world hypothesis of the origin of life (see Ikehara's review, 2002). Possible steps for the emergence of life on the primitive earth are presented."
Oba T, Fukushima J, Maruyama M, Iwamoto R, Ikehara K. Catalytic Activities Of [GADV]-Peptides Formation and Establishment of [GADV]-Protein World for the Emergence of Life. Orig Life Evol Biosph. 2005 Oct;35(5):447-60.
Dynamic co-evolution of peptides and chemical energetics, a gateway to the emergence of homochirality and the catalytic activity of peptides. : "We propose a scenario for the dynamic co-evolution of peptides and energy on the primitive Earth. From a multi component system consisting of hydrogen cyanide, several carbonyl compounds, ammonia, alkyl amine, carbonic anhydride, borate and isocyanic acid, we show that the reversibility of this system leads to several intermediate nitriles, that irreversibly evolve to alpha-amino acids and N-carbamoyl amino acids via selective catalytic processes. On the primitive Earth these N-carbamoyl amino acids combined with energetic molecules (NOx) may have been the core of a molecular engine producing peptides permanently and assuring their recycling and evolution. We present this molecular engine, a production example, and its various selectivities. The perspectives for such a dynamic approach to the emergence of peptides are evoked in the conclusion."Commeyras A, Taillades J, Collet H, Boiteau L, Vandenabeele-Trambouze O, Pascal R, Rousset A, Garrel L, Rossi JC, Biron JP, Lagrille O, Plasson R, Souaid E, Danger G, Selsis F, Dobrijevic M, Martin H.Dynamic co-evolution of peptides and chemical energetics, a gateway to the emergence of homochirality and the catalytic activity of peptides. Orig Life Evol Biosph. 2004 Feb;34(1-2):35-55.
Peptides by activation of amino acids with CO on (Ni,Fe)S surfaces: implications for the origin of life. : "In experiments modeling volcanic or hydrothermal settings amino acids were converted into their peptides by use of coprecipitated (Ni,Fe)S and CO in conjunction with H2S (or CH3SH) as a catalyst and condensation agent at 100 degreesC and pH 7 to 10 under anaerobic, aqueous conditions. These results demonstrate that amino acids can be activated under geochemically relevant conditions. They support a thermophilic origin of life and an early appearance of peptides in the evolution of a primordial metabolism."
Huber C, Wachtershauser G. Peptides by activation of amino acids with CO on (Ni,Fe)S surfaces: implications for the origin of life. Science. 1998 Jul 31;281(5377):670-2.
Comment in: Science. 1998 Jul 31;281(5377):627, 629.
A possible primordial peptide cycle. : "alpha-Amino acids can undergo peptide formation by activation with carbon monoxide (CO) under hot aqueous conditions in the presence of freshly coprecipitated colloidal (Fe,Ni)S. We now show that CO-driven peptide formation proceeds concomitantly with CO-driven, N-terminal peptide degradation by racemizing N-terminal hydantoin and urea derivatives to alpha-amino acids. This establishes a peptide cycle with closely related anabolic and catabolic segments. The hydantoin derivative is a purin-related heterocycle. The (Fe,Ni)S-dependent urea hydrolysis could have been the evolutionary precursor of the nickelenzyme urease. The results support the theory of a chemoautotrophic origin of life with a CO-driven, (Fe,Ni)S-dependent primordial metabolism."
Huber C, Eisenreich W, Hecht S, Wachtershauser G. A possible primordial peptide cycle. Science. 2003 Aug 15;301(5635):938-40.
[The simultaneous synthesis of peptides and oligonucleotides on kaolinite with the participation of aminoacyladenylates] "A simultaneous synthesis of peptides (2-5 residues) and oligonucleotides (3-9 residues) has been carried out on caolinite matrix using amino acids and aminoacyladenylates as substrates. The rate of oligomer synthesis on mineral surface is higher than that in solution. The mechanism of synthesis has been described. The data has been discussed in connection with abiogenesis of two major types of biopolymers, proteins and nucleic acids."
[The simultaneous synthesis of peptides and oligonucleotides on kaolinite with the participation of aminoacyladenylates]Egofarova RKh, Vasil'eva NV, Moiseeva LN, Otroshchenko VA, Pavlovskaia TE.Izv Akad Nauk SSSR Biol. 1990 Jan-Feb;(1):136-40.
Comparative study of abiogenesis of cysteine and other amino acids catalyzed by various metal ions. : "The present work pertains to the study of the influence of nickel, cobalt, thorium, vanadium, molybdate, ferrous ions on the formation of cysteine which is synthesized abiogenically together with other amino acids in sterilized aqueous mixtures of ammonium thiocyanate, formaldehyde, potassium dihydrogen phosphate, calcium acetate, and biological minerals after irradiating by artificial light. The effect of these catalysts on cysteine formation was of the order: Fe++ greater than Mo++ greater than Th++++ greater than V++ greater than Co++ greater than Ni."Bahadur K, Sen P.Comparative study of abiogenesis of cysteine and other amino acids catalyzed by various metal ions.Z Allg Mikrobiol. 1975;15(3):143-7.
Aqueous synthesis of Peptide thioesters from amino acids and a thiol using 1,1'-carbonyldiimidazole. : "A new method was developed for the synthesis of peptide thioesters from free amino acids and thiols in water. This one-pot simple method involves two steps: (1) activation in water of an amino acid presumably as its N-carboxyanhydride (NCA) using 1,1'-carbonyldiimidazole (CDI), and (2) subsequent condensation of the activated amino acid-NCA in the presence of a thiol. With this method citrulline peptide thioesters containing up to 10 amino acid residues were prepared in a single reaction. This aqueous synthetic method provides a simple way to prepare peptide thioesters for studies of peptide replication involving ligation of peptide thioesters on peptide templates. The relevance of peptide replication to the origin-of-life process is supported by previous studies showing that amino acid thioesters (peptide thioester precursors) can be synthesized under prebiotic conditions by reaction of small sugars with ammonia and a thiol."
Weber AL. Aqueous synthesis of Peptide thioesters from amino acids and a thiol using 1,1'-carbonyldiimidazole. Orig Life Evol Biosph. 2005 Oct;35(5):421-7.
A model for the role of short self-assembled peptides in the very early stages of the origin of life : "The molecular basis of the origin of life is one of the most fundamental questions in modern biology. While the 'RNA world' hypothesis offers a very sensible model for the evolvement of the current biochemical networks, there is a lack of knowledge about the early steps that led to the formation of the first RNA molecules. This issue is essential as it is practically impossible that complex molecules as functional RNA oligonucleotides had evolved spontaneously. It was recently demonstrated that peptide molecules as simple as dipeptides can self-assemble into well-ordered tubular, fibrilar, and closed-cage structures. Other studies have confirmed the ability of dipeptides to act as catalysts and the capability of other peptides, as short as tripeptides, to serve as a template for nucleotide binding and orientation. Unlike complex RNA molecules, the spontaneous formation of functional short peptides in the primordial earth conditions is very likely. We suggest a novel mechanism for the origin of life that is based on the ability of short peptides to form encapsulated structures, catalyst chemical reaction, and serve as highly ordered template for the assembly of nucleotides. This model may explain the early events that led to the formation of the current biochemical machinery that combines the elaborated and coordinated interaction between nucleic acids and proteins to allow the function of living systems."
Carny O, Gazit E. A model for the role of short self-assembled peptides in the very early stages of the origin of life. FASEB J. 2005 Jul;19(9):1051-5.
N-carbamoyl-alpha-amino acids rather than free alpha-amino acids formation in the primitive hydrosphere: a novel proposal for the emergence of prebiot : "Our previous kinetic and thermodynamic studies upon the reactional system HCHO/HCN/NH3 in aqueous solutions are completed. In the assumed prebiotic conditions of the primitive earth ([HCHO] and [HCN] near 1 g L-1, T = 25 degrees C, pH = 8, [NH3] very low), this system leads to 99.9% of alpha-hydroxyacetonitrile and 0.1% of alpha-aminoacetonitrile (precursor of the alpha-amino acid). The classical base-catalyzed hydration of nitriles, slow and not selective, can not modify significantly this proportion. On the contrary, we found two specific and efficient reactions of alpha-aminonitriles which shift the initial equilibrium in favor of the alpha-aminonitrile pathway. The first reaction catalyzed by formaldehyde generates alpha-aminoamides, precursors of alpha-aminoacids. The second reaction catalyzed by carbon dioxide affords hydantoins, precursors of N-carbamoyl-alpha-aminoacids. In the primitive hydrosphere, where the concentration in carbon dioxide was estimated to be higher than that of formaldehyde, the formation of hydantoins was consequently more efficient. The rates of hydrolysis of the alpha-aminoacetamide and of the hydantoin at pH 8 being very similar, the synthesis of the N-carbamoyl-alpha-amino acid seems then to be the fatal issue of the HCHO/HCN/NH3 system that nature used to perform its evolution. These N-protected alpha-amino acids offer new perspectives in prebiotic chemistry, in particular for the emergence of peptides on the prebiotic earth."
Taillades J, Beuzelin I, Garrel L, Tabacik V, Bied C, Commeyras A.
N-carbamoyl-alpha-amino acids rather than free alpha-amino acids formation in the primitive hydrosphere: a novel proposal for the emergence of prebiotic peptides. Orig Life Evol Biosph. 1998 Feb;28(1):61-77.
Prebiotic transamination : "Biological amino acids and alpha keto acids directly condense with decarboxylation and transamination to yield product amino acids. This process is closely related to unusual amino acid decarboxylase enzymes in certain microorganisms and may represent a primordial mode of amino acid metabolism."
Bishop JC, Cross SD, Waddell TG. Prebiotic transamination. Orig Life Evol Biosph. 1997 Aug;27(4):319-24.
Evolution of selenocysteine-containing proteins: significance of identification and functional characterization of selenoproteins. : "In the genetic code, UGA serves as either a signal for termination or a codon for selenocysteine (Sec). Sec rarely occurs in protein and is different from other amino acids in that much of the biosynthetic machinery governing its incorporation into protein is unique to this amino acid. Sec-containing proteins have diverse functions and lack a common amino acid motif or consensus sequence. Sec has previously been considered to be a relic of the primordial genetic code that was counter-selected by the presence of oxygen in the atmosphere. In the present report, it is proposed that Sec was added to the already existing genetic code and its use has accumulated during evolution of eukaryotes culminating in vertebrates. The more recently evolved selenoproteins appear to take advantage of unique redox properties of Sec that are superior to those of Cys for specific biological functions. Further understanding of the evolution of selenoproteins as well as biological properties and biomedical applications of the trace element selenium requires identification and functional characterization of all mammalian selenoproteins."
Gladyshev VN, Kryukov GV. Evolution of selenocysteine-containing proteins: significance of identification and functional characterization of selenoproteins. Biofactors. 2001;14(1-4):87-92.
Theoretical Biology and Medical Modelling Full text Three subsets of sequence complexity and their relevance to biopolymeric information: "In life-origin science, attention usually focuses on a theorized pre-RNA World [52-55]. RNA chemistry is extremely challenging in a prebiotic context. Ribonucleotides are difficult to activate (charge). And even oligoribonucleotides are extremely hard to form, especially without templating. The maximum length of such single strands in solution is usually only eight to ten monomers (mers). As a result, many investigators suspect that some chemical RNA analog must have existed [56,57]. "
Abel DL, Trevors JT. Three subsets of sequence complexity and their relevance to biopolymeric information. Theor Biol Med Model. 2005 Aug 11;2:29. Free Full Text article
Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software. : "BACKGROUND: There is an increasing need for computer-generated models that can be used for explaining the emergence and predicting the behavior of multi-protein dynamic structures in cells. Multi-agent systems (MAS) have been proposed as good candidates to achieve this goal. RESULTS: We have created 3DSpi, a multi-agent based software that we used to explore the generation of multi-protein dynamic structures. Being based on a very restricted set of parameters, it is perfectly suited for exploring the minimal set of rules needed to generate large multi-protein structures. It can therefore be used to test the hypothesis that such structures are formed and maintained by principles of self-organization. We observed that multi-protein structures emerge and that the system behavior is very robust, in terms of the number and size of the structures generated. Furthermore, the generated structures very closely mimic spatial organization of real life multi-protein structures. CONCLUSION: The behavior of 3DSpi confirms the considerable potential of MAS for modeling subcellular structures. It demonstrates that robust multi-protein structures can emerge using a restricted set of parameters and allows the exploration of the dynamics of such structures. A number of easy-to-implement modifications should make 3DSpi the virtual simulator of choice for scientists wishing to explore how topology interacts with time, to regulate the function of interacting proteins in living cells."Soula H, Robardet C, Perrin F, Gripon S, Beslon G, Gandrillon O. Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software. BMC Bioinformatics. 2005 Sep 19;6:228. Free Full Text article
Investigation of the prebiotic synthesis of amino acids and RNA bases from CO2 using FeS/H2S as a reducing agent. : "An autotrophic theory of the origin of metabolism and life has been proposed in which carbon dioxide is reduced by ferrous sulfide and hydrogen sulfide by means of a reversed citric acid cycle, leading to the production of amino acids. Similar processes have been proposed for purine synthesis. Ferrous sulfide is a strong reducing agent in the presence of hydrogen sulfide and can produce hydrogen as well as reduce alkenes, alkynes, and thiols to saturated hydrocarbons and reduce ketones to thiols. However, the reduction of carbon dioxide has not been demonstrated. We show here that no amino acids, purines, or pyrimidines are produced from carbon dioxide with the ferrous sulfide and hydrogen sulfide system. Furthermore, this system does not produce amino acids from carboxylic acids by reductive amination and carboxylation. Thus, the proposed autotrophic theory, using carbon dioxide, ferrous sulfide, and hydrogen sulfide, lacks the robustness needed to be a geological process and is, therefore, unlikely to have played a role in the origin of metabolism or the origin of life."Keefe AD, Miller SL, McDonald G, Bada J. Investigation of the prebiotic synthesis of amino acids and RNA bases from CO2 using FeS/H2S as a reducing agent. Proc Natl Acad Sci U S A. 1995 Dec 5;92(25):11904-6. Free Full Text article | 1 Guide-Glossary