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Amino acid fermentation at the origin of the genetic code.

de Vladar HP - Biol. Direct (2012)

Bottom Line: This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation.In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons.These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors.

View Article: PubMed Central - HTML - PubMed

Affiliation: hpvladar@ist.ac.at

ABSTRACT
There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors.

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Evolution of early codes by selecting on the ATP yield. Evolution of the assignation of amino acids to adapters by selecting on the resulting ATP yield. (A) Employing only the simplest four Miller amino acids (alanine, aspartic acid, glycine and valine) 104 runs with initial random associations converged to optimise the ATP yield, in all cases reaching to the maximum of 2 moles of ATP. (B) 100 runs started from random associations to alanine and glycine and every 7000 generations a new Miller amino acid, randomly selected, was included and assigned to a random adapter. Most runs converged to optimal codes (with the maximum yield of 3 moles of ATP), but three did not.
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Figure 10: Evolution of early codes by selecting on the ATP yield. Evolution of the assignation of amino acids to adapters by selecting on the resulting ATP yield. (A) Employing only the simplest four Miller amino acids (alanine, aspartic acid, glycine and valine) 104 runs with initial random associations converged to optimise the ATP yield, in all cases reaching to the maximum of 2 moles of ATP. (B) 100 runs started from random associations to alanine and glycine and every 7000 generations a new Miller amino acid, randomly selected, was included and assigned to a random adapter. Most runs converged to optimal codes (with the maximum yield of 3 moles of ATP), but three did not.

Mentions: One hundred and four replicas of the process were initiated with the following amino acids drawn with equal probability: alanine, glycine, aspartic acid and valine. All processes converged in between 5,000 and 30,000 generations (Figure 10A), and the resulting codes all produced 2 mol of ATP (the maximum possible according to the stoichiometry). The codes have an overrepresentation of the acceptor amino acids over the donors (Table 2). The latter, were almost invariably assigned to four of the eight codons composed exclusively of U+G, confirming the reasoning above (Table 2).


Amino acid fermentation at the origin of the genetic code.

de Vladar HP - Biol. Direct (2012)

Evolution of early codes by selecting on the ATP yield. Evolution of the assignation of amino acids to adapters by selecting on the resulting ATP yield. (A) Employing only the simplest four Miller amino acids (alanine, aspartic acid, glycine and valine) 104 runs with initial random associations converged to optimise the ATP yield, in all cases reaching to the maximum of 2 moles of ATP. (B) 100 runs started from random associations to alanine and glycine and every 7000 generations a new Miller amino acid, randomly selected, was included and assigned to a random adapter. Most runs converged to optimal codes (with the maximum yield of 3 moles of ATP), but three did not.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3376031&req=5

Figure 10: Evolution of early codes by selecting on the ATP yield. Evolution of the assignation of amino acids to adapters by selecting on the resulting ATP yield. (A) Employing only the simplest four Miller amino acids (alanine, aspartic acid, glycine and valine) 104 runs with initial random associations converged to optimise the ATP yield, in all cases reaching to the maximum of 2 moles of ATP. (B) 100 runs started from random associations to alanine and glycine and every 7000 generations a new Miller amino acid, randomly selected, was included and assigned to a random adapter. Most runs converged to optimal codes (with the maximum yield of 3 moles of ATP), but three did not.
Mentions: One hundred and four replicas of the process were initiated with the following amino acids drawn with equal probability: alanine, glycine, aspartic acid and valine. All processes converged in between 5,000 and 30,000 generations (Figure 10A), and the resulting codes all produced 2 mol of ATP (the maximum possible according to the stoichiometry). The codes have an overrepresentation of the acceptor amino acids over the donors (Table 2). The latter, were almost invariably assigned to four of the eight codons composed exclusively of U+G, confirming the reasoning above (Table 2).

Bottom Line: This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation.In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons.These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors.

View Article: PubMed Central - HTML - PubMed

Affiliation: hpvladar@ist.ac.at

ABSTRACT
There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors.

Show MeSH
Related in: MedlinePlus