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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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Cross-catalytic cycle of proto-adapters. (Only the anticodon sequences shown). Templates with complementary anticodons catalyse each other following Watson-Crick pairing (thin black arrows). However, allowing for non-legitimate pairs G-U allows for cross-catalysis of other templates (thin blue arrows). In this way, each pair of replicators catalyse another cycle of replicators (thick black arrows). This pattern allows formation of closed cycles. This figure shows only one of the possible nested cycles that emerge allowing for non-legitimate template replications. In this cycle, all pairs of templates bear amino acids that are Stickland pairs, and all amino acids are readily formed in Miller-type experiments. Other cycles that involve amino acids that are thought to be included at later evolutionary stages can show exceptions to this pattern.
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Figure 7: Cross-catalytic cycle of proto-adapters. (Only the anticodon sequences shown). Templates with complementary anticodons catalyse each other following Watson-Crick pairing (thin black arrows). However, allowing for non-legitimate pairs G-U allows for cross-catalysis of other templates (thin blue arrows). In this way, each pair of replicators catalyse another cycle of replicators (thick black arrows). This pattern allows formation of closed cycles. This figure shows only one of the possible nested cycles that emerge allowing for non-legitimate template replications. In this cycle, all pairs of templates bear amino acids that are Stickland pairs, and all amino acids are readily formed in Miller-type experiments. Other cycles that involve amino acids that are thought to be included at later evolutionary stages can show exceptions to this pattern.

Mentions: When we consider the set of amino acids produced in Miller's revisited experiment [[13], underlined in Table 1], we find that the associations between Stickland pairs and complementary anticodons still hold, and the adapters form a cross-catalytic cycle (Figure 7). The significance of this observation is not about the plausibility of Miller's experiment as a model of the origins. What Miller-Urey synthesis suggests is that the amino acids are easily formed, with a yield that is somewhat inversely proportional to their chemical complexity. Overall, glycine and alanine are formed at a roughly 2:1 ratio, with a yield more than an order of magnitude higher than that of the rest of the amino acids [13], suggesting that alanine and glycine were the ancestral components of the genetic code, followed by valine and aspartic acid [50].


Amino acid fermentation at the origin of the genetic code.

de Vladar HP - Biol. Direct (2012)

Cross-catalytic cycle of proto-adapters. (Only the anticodon sequences shown). Templates with complementary anticodons catalyse each other following Watson-Crick pairing (thin black arrows). However, allowing for non-legitimate pairs G-U allows for cross-catalysis of other templates (thin blue arrows). In this way, each pair of replicators catalyse another cycle of replicators (thick black arrows). This pattern allows formation of closed cycles. This figure shows only one of the possible nested cycles that emerge allowing for non-legitimate template replications. In this cycle, all pairs of templates bear amino acids that are Stickland pairs, and all amino acids are readily formed in Miller-type experiments. Other cycles that involve amino acids that are thought to be included at later evolutionary stages can show exceptions to this pattern.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: Cross-catalytic cycle of proto-adapters. (Only the anticodon sequences shown). Templates with complementary anticodons catalyse each other following Watson-Crick pairing (thin black arrows). However, allowing for non-legitimate pairs G-U allows for cross-catalysis of other templates (thin blue arrows). In this way, each pair of replicators catalyse another cycle of replicators (thick black arrows). This pattern allows formation of closed cycles. This figure shows only one of the possible nested cycles that emerge allowing for non-legitimate template replications. In this cycle, all pairs of templates bear amino acids that are Stickland pairs, and all amino acids are readily formed in Miller-type experiments. Other cycles that involve amino acids that are thought to be included at later evolutionary stages can show exceptions to this pattern.
Mentions: When we consider the set of amino acids produced in Miller's revisited experiment [[13], underlined in Table 1], we find that the associations between Stickland pairs and complementary anticodons still hold, and the adapters form a cross-catalytic cycle (Figure 7). The significance of this observation is not about the plausibility of Miller's experiment as a model of the origins. What Miller-Urey synthesis suggests is that the amino acids are easily formed, with a yield that is somewhat inversely proportional to their chemical complexity. Overall, glycine and alanine are formed at a roughly 2:1 ratio, with a yield more than an order of magnitude higher than that of the rest of the amino acids [13], suggesting that alanine and glycine were the ancestral components of the genetic code, followed by valine and aspartic acid [50].

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