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On the evolution of codon usage bias

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.

Identiferoai:union.ndltd.org:UTENN/oai:trace.tennessee.edu:utk_graddiss-2135
Date01 May 2011
CreatorsShah, Premal R
PublisherTrace: Tennessee Research and Creative Exchange
Source SetsUniversity of Tennessee Libraries
Detected LanguageEnglish
Typetext
Formatapplication/pdf
SourceDoctoral Dissertations

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