The genetic code is redundant, with most amino acids coded by multiple codons. In many organisms, codon usage is biased towards particular codons. A variety of adaptive and non-adaptive explanations have been proposed to explain these patterns of codon usage bias. Using mechanistic models of protein translation and population genetics, I explore the relative importance of various evolutionary forces in shaping these patterns. This work challenges one of the fundamental assumptions made in over 30 years of research: codons with higher tRNA abundances leads to lower error rates. I show that observed patterns of codon usage are inconsistent with selection for translation accuracy. I also show that almost all the variation in patterns of codon usage in S. cerevisiae can be explained by a model taking into account the effects of mutational biases and selection for efficient ribosome usage. In addition, by sampling suboptimal mRNA secondary structures at various temperatures, I show that melting of ribosomal binding sites in a special class of mRNAs known as RNA thermometers is a more general phenomenon.
| Identifer | oai:union.ndltd.org:UTENN/oai:trace.tennessee.edu:utk_graddiss-2135 |
| Date | 01 May 2011 |
| Creators | Shah, Premal R |
| Publisher | Trace: Tennessee Research and Creative Exchange |
| Source Sets | University of Tennessee Libraries |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | Doctoral Dissertations |
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