selection on codons oeb 192 11.10.03. degenerate code
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Selection on codons
OEB 192 11.10.03
Degenerate Code
Codon Usage BiasNon-random usage of codons
Rickettsia - Winkler 1988
Percent codon usage in family
Codons for each amino acid
Preferredargininecodon
Unpreferredargininecodon
Different GC content alters codon usage
Mutational Bias
232 Bacterial genomes - Guchte 2006
Species differ in codon usage biasWithout considering selection, why might different species have
different codon usage patterns?
Massey 2003
6 LeucineCodons
Unequal numbers of tRNAs
There are six leucine codons
So, there are six corresponding tRNAs
tRNA copy number differences
E. coli - Ikemura 1981
Is there selection on codon bias?
Three levels of evidence:1. Genome level2. Species level3. Gene level
Evidence:Non-random patterns of codon usage that are difficult to explain without selection
Selection on codons1. Throughout genomes
Same organism, so not explained by differences in tRNA abundance or mutational bias
2. Between speciesWhy does the pattern decrease from E. coli to Human?
Drummond and Wilke 2008
expressionoptim
al c
odon
s
High Expression level genes have high codon bias
Selection on codons3. Within genes
Conserved sites more likely to use preferred codons
Likely tofind Preferred
codon
Likely tofind Unpreferred
codon
Species in alignemnt: Os = Oryza sativa, Pp = Physcomitrella patens, Dd = Dictyostelium discoideum, Hs = Homo sapiens, Dr = Danio reiro, Dm = Drosophila melanogaster, Sc = Saccharomyces cerevisiae, Sp = Schizosaccharomyces pombe, Pf = Plasmodium falciparum Gene = ubiquitin/SUMO-1 like protein
Wang et. al. 2001
Why is there selection on codons?
Why is there selection on codons?
Target of
selection
Impact of codon identity (effect on
protein cost vs. benefit)
Effect of
% rare
codons
Importance of
codon position
Effect of high
expression on
fitness
mRNA
structure /
sequence
1. Inhibits translation initiation
(insufficient benefit)
No general
prediction
5’ end most
sensitive
+
2. Promotes rapid degradation
(insufficient benefit)
No general
prediction
No general
prediction
+
Ribosomal
pausing
during
translation
of rare
codons
(due to
tRNA
limitation)
3. Slows translation & decreases
protein (insufficient benefit) –
No general
prediction
+
4. Sequesters ribosomes
(excess cost) -
Rare codons
good at 5′ end –
5. Promotes accurate protein folding.
Lack of ribosome pause leads to:
(a) Low protein activity or stability
(insufficient benefit)
No general
prediction
Rare codons
preferred at
domain
boundaries
+
(b) Misfolding-induced toxicity
(excess cost) –
6.
Increases translation errors causing:
(a) Low protein activity or stability
(insufficient benefit)
–
Rare codons
bad at
conserved or
active residues
+
(b) Misfolding-induced toxicity
(excess cost) –
–
(Agashe et al., in prep)
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