The phylogenetics project data revealed!

October 4, 2010OEB 192

Geographic Distribution

Pathogen = Salmonella Typhi

Why so little turnover?

Letters indicate antibiotic resistant haplotypes

Selection less effective due to “carriers” with no symptoms!

Codon Usage Bias & Selection

October 4, 2010OEB 192

Degenerate Code

Codon Usage BiasNon-random usage of codons

Rickettsia (bacteria) - Winkler 1988

Percent codon usage in family

Codons for each amino acid

Preferredargininecodon

Unpreferredargininecodon

Why non-random codon usage?

Codons correspond to anticodons on tRNAs

Unequal numbers of tRNAs

There are six leucine codons

So, there are six corresponding tRNAs

tRNA copy number differences

E. Coli - Ikemura 1981

Species differ in codon usage biasWithout considering selection, why might different species have

different codon usage patterns?

Massey 2003

6 LeucineCodons

Different GC content alters codon usage

Mutational Bias

232 Eubacterial genomes - Guchte 2006

Is there selection on codon bias?

Four levels of evidence:1. Genome level2. Species level3. Tissue level4. 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 tissues

Plotkin et al 2004

Red = selectively expressed in human testes

Blue – selectively expressed In human ovaries

Selection on codons4. 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?

Movie of Translation: http://www.youtube.com/watch?v=Jml8CFBWcDs&p=22FC96CD697EBE40

Process of Translation

Translational SpeedFaster, so allows more protein to be made

Translational AccuracyIncorrect translation is a waste of resources

Discuss evidence:

Protein FoldingTranslational Speed

Speed tuned to protein folding pace

Translational AccuracyMistranslation induced misfolding

Translational RobustnessProtein folds even with errors

Discuss evidence:

Selection on synonymous sitesOther general reasons for selection on synonymous sites (not specifically codon bias):

Aberrant splicingmRNA instability secondary structure

Weak selectionIs population size dependent – WHY?

Smaller populations are more stochastic:7 heads and 3 tails in 10 coin flips - possiblevs. 70,000 heads and 30,000 tails in 100,000 coin flips – rare!

Weak selectionIs population size dependent

Other possible types of weak selection:

Do humans and mammals have selection on codons?

Much stronger in microbes!Allow us to study these patterns-ascertain mechanistic basis for selection-determine average effect of mutation

Genome sizeNumber of introns

Urrutia & Hurst 2003

1. Could effect dN/dS (or other measures of selection)

...but, It’s very weak selection that doesn’t effect all genes

2. Useful to detect HGT

3. Helpful to consider when building genetically modified organisms

4. Medical applications

– Coleman et al. 2008

Implications of selection on synonymous sites

Pride et al 2006

How is codon bias measured?

Measure tRNA abundance

CAI (Codon adaptation index): measures codon composition relative to reference set (usually highly expressed genes from same genome)

Fop (frequency of optimal codons): Measures the number of preferred codons over the total number of amino acids with synonymous codons

Akashi’s test: Tests how strong the correlation is between conserved sites and preferred codons

Still more: ENC (Effective number of codons)MCB (Maximum Likelihood codon bias