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...
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ndltd-UTENN-oai-trace.tennessee.edu-utk_graddiss-21352011-12-13T16:06:06Z On the evolution of codon usage bias Shah, Premal R 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. 2011-05-01 text application/pdf http://trace.tennessee.edu/utk_graddiss/1024 Doctoral Dissertations Trace: Tennessee Research and Creative Exchange codon usage bias population genetics translation efficiency translation errors RNA thermometer Evolution |
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codon usage bias population genetics translation efficiency translation errors RNA thermometer Evolution |
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codon usage bias population genetics translation efficiency translation errors RNA thermometer Evolution Shah, Premal R On the evolution of codon usage bias |
description |
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. |
author |
Shah, Premal R |
author_facet |
Shah, Premal R |
author_sort |
Shah, Premal R |
title |
On the evolution of codon usage bias |
title_short |
On the evolution of codon usage bias |
title_full |
On the evolution of codon usage bias |
title_fullStr |
On the evolution of codon usage bias |
title_full_unstemmed |
On the evolution of codon usage bias |
title_sort |
on the evolution of codon usage bias |
publisher |
Trace: Tennessee Research and Creative Exchange |
publishDate |
2011 |
url |
http://trace.tennessee.edu/utk_graddiss/1024 |
work_keys_str_mv |
AT shahpremalr ontheevolutionofcodonusagebias |
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