Codon Based Immunity and the Varieties of Genetic Redundancy
  David C. Krakauer
Institute for Advanced Study 
310 Olden Lane, Princeton, 08540 NJ 
krakauer@ias.edu  
 

Within the universal genetic code there are a possible 64 codons, 61 of which encode 20 amino acids. Thus the ratio of codons to amino acids is greater than one. The redundant
mapping of codons to amino acids has been explained as an adaptation to minimize the influence of mutational load.There are however at least a further two forms of redundancy associated with the code: redundancy arising from the ratio of tRNA anticodons to amino acids and redundancy in the number of copies of each unique tRNA. We explore adaptive explanations for the latter two sorts of redundancy based on the genetic code viewed as a primitive immune system. Modifying the set of codons
bound by tRNA anticodons reduces the efficiency of virus and transposon replication
within host cells. This is because increased translational efficiency of the parasite implies a match between the pool of host tRNAs and the parasite codons. In light of the theory we discuss (1) the unique plasticity of tRNA bases, (2) the extreme codon biases observed in parasites, and (3) how selective changes in codon usage might produce deviant codes.

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