Genetic Code - Origin

Origin

If amino acids were randomly assigned to triplet codons, then there would be 1.5 x 1084 possible genetic codes to choose from. However, the genetic code used by all known forms of life is nearly universal with few minor variations. This suggests that a single evolutionary history underlies the origin of the genetic code. Many hypotheses on the evolutionary origins of the universal genetic code have been proposed.

Four themes run through the many hypotheses about the evolution of the genetic code:

• Chemical principles govern specific RNA interaction with amino acids. Experiments with aptamers showed that some amino acids have a selective chemical affinity for the base triplets that code for them. Recent experiments show that of the 8 amino acids tested, 6 show some RNA triplet-amino acid association.

• Biosynthetic expansion. The standard modern genetic code grew from a simpler earlier code through a process of "biosynthetic expansion". Here the idea is that primordial life "discovered" new amino acids (for example, as by-products of metabolism) and later incorporated some of these into the machinery of genetic coding. Although much circumstantial evidence has been found to suggest that fewer different amino acids were used in the past than today, precise and detailed hypotheses about which amino acids entered the code in what order have proved far more controversial.
• Natural selection has led to codon assignments of the genetic code that minimize the effects of mutations. A recent hypothesis suggests that the triplet code was derived from codes that used longer than triplet codons (such as quadruplet codons). Longer than triplet decoding would have higher degree of codon redundancy and would be more error resistant than the triplet decoding. This feature could allow accurate decoding in the absence of highly complex translational machinery such as the ribosome and prior to the time when cells began making ribosomes.
• Information channels: Information-theoretic approaches see the genetic code as an error-prone information channel. The inherent noise (that is, the error) in the channel poses the organism with a fundamental question: how can a genetic code be constructed to withstand the impact of noise while accurately and efficiently translating information? These “rate-distortion” models suggest that the genetic code originated as a result of the interplay of the three conflicting evolutionary forces: the needs for diverse amino-acids, for error-tolerance and for minimal cost of resources. The code emerges at a coding transition when the mapping of codons to amino-acids becomes nonrandom. The emergence of the code is governed by the topology defined by the probable errors and is related to the map coloring problem.

Transfer RNA molecules appear to have evolved prior to modern aminoacyl-tRNA synthetases, so the latter cannot be part of the explanation of its patterns.

There are enough data to refute the possibility that the genetic code was randomly constructed ("a frozen accident"). For example, the genetic code clusters certain amino acid assignments. Amino acids that share the same biosynthetic pathway tend to have the same first base in their codons. Amino acids with similar physical properties tend to have similar codons. A robust hypothesis for the origin of genetic code should also address or predict the following gross features of the codon table:

1. absence of codons for D-amino acids
2. secondary codon patterns for some amino acids
3. confinement of synonymous positions to third position
4. limitation to 20 amino acids instead of a number closer to 64
5. relation of stop codon patterns to amino acid coding patterns