dorsal/arxiv
View SchemaA Unified Model of Codon Reassignment in Alternative Genetic Codes
| Authors | Supratim Sengupta, Paul G. Higgs |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0410022 |
| URL | https://arxiv.org/abs/q-bio/0410022 |
| Journal | Genetics 170 (2005) 831-840 |
Abstract
Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a model that unifies four possible mechanisms for reassignment, based on the observation that reassignment involves a gain and a loss. The loss could be the deletion or loss of function of a tRNA or release factor. The gain could be the gain of a new type of tRNA for the reassigned codon, or the gain of function of an existing tRNA due to a mutation or a base modification. In the codon disappearance mechanism, the codon disappears from the genome during the period of reassignment. In the other mechanisms, the codon does not disappear. In the ambiguous intermediate mechanism, the gain precedes the loss; in the unassigned codon mechanism, the loss precedes the gain; and in the compensatory change mechanism, the loss and gain spread through the population simultaneously. We present simulations of the gain-loss model and demonstrate that all four mechanisms are possible. The frequencies of the different mechanisms are influenced by selection strengths, number of codons undergoing reassignment, directional mutation pressure and the possibility of selection for reduced genome size.
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"abstract": "Many modified genetic codes are found in specific genomes in which one or\nmore codons have been reassigned to a different amino acid from that in the\ncanonical code. We present a model that unifies four possible mechanisms for\nreassignment, based on the observation that reassignment involves a gain and a\nloss. The loss could be the deletion or loss of function of a tRNA or release\nfactor. The gain could be the gain of a new type of tRNA for the reassigned\ncodon, or the gain of function of an existing tRNA due to a mutation or a base\nmodification. In the codon disappearance mechanism, the codon disappears from\nthe genome during the period of reassignment. In the other mechanisms, the\ncodon does not disappear. In the ambiguous intermediate mechanism, the gain\nprecedes the loss; in the unassigned codon mechanism, the loss precedes the\ngain; and in the compensatory change mechanism, the loss and gain spread\nthrough the population simultaneously. We present simulations of the gain-loss\nmodel and demonstrate that all four mechanisms are possible. The frequencies of\nthe different mechanisms are influenced by selection strengths, number of\ncodons undergoing reassignment, directional mutation pressure and the\npossibility of selection for reduced genome size.",
"arxiv_id": "q-bio/0410022",
"authors": [
"Supratim Sengupta",
"Paul G. Higgs"
],
"categories": [
"q-bio.PE"
],
"journal_ref": "Genetics 170 (2005) 831-840",
"title": "A Unified Model of Codon Reassignment in Alternative Genetic Codes",
"url": "https://arxiv.org/abs/q-bio/0410022"
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