Bitter Taste Genetics: PTC and Other Stories

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Bitter Taste Genetics PTC and Other Stories

• Lynn Jorde and Steve Wooding
• Department of Human Genetics
• University of Utah School of Medicine

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Overview

• PTC evidence for balancing selection
• PTC in chimps and humans
• The other bitter taste receptor genes

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Michael Bamshad, MD
Stephen Wooding, PhD
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Molecules involved in taste perception
Sour Ion channels
Salty Ion channels
Sweet TAS1R family of G-protein coupled receptors
Umami TAS1R family of G-protein coupled receptors
Bitter TAS2R family (25 functional members)
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Sweet and Umami (T1R)
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The Bitter Draught Adriaen Brouwer, 1635
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Many plants contain toxins
Digitoxin
Ricin
Abrin
Strychnine
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Many plant toxins taste bitter
Quinine
Nicotine
Salicin
Papaverine
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Biomedical relevance of bitter taste
Bitter-taste sensitivity
Smoking
Diet Choice
Body Mass Index
Cancer
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Bitter-taste (TAS2R) Receptors
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Bitter-taste (TAS2R) Receptors
TAS2R
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Bitter-taste receptors bind plant toxins
TAS2R10 strychnine TAS2R14 a-thujones TAS2R16
salicin, cyanogenic compounds
Bufe et al., Nat. Gen., 2002 Behrens et al.,
BBRC, 2004
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Phenylthiocarbamide (PTC)

• Synthetic
• Bitter or tasteless
• Fox 1932
• Variable sensitivity
• Similar in structure to plant compounds
• Blakeslee 1932
• Taste blindness is Mendelian recessive
• Fisher et al., 1939
• Variable sensitivity in chimp
• Thousands of individuals have been typed for PTC
  taster status

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PTC Gene

• Drayna et al., 2003
• Genome-wide linkage analysis
• Utah CEPH families
• PTC gene localized to chromosome 7 and
  subsequently cloned

• PTC Gene (TAS2R38)
• Haplotypes strongly associated with phenotype
• Accounted for 50-85 of phenotypic variance

How have natural selection and population
history affected the PTC gene?
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PTC resequencing in humans

• Sequenced entire coding region (1,002 bp)
• 174 individuals (348 chromosomes)
• 40 African
• 69 Asian
• 55 European
• 10 Native American

• Not selected for PTC sensitivity
• Anthropological sampling

Wooding et al., 2004, Am. J. Hum. Genet. 74
637-46
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Diversity in PTC

• 6 nucleotide substitutions in humans

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Diversity in PTC

• 6 nucleotide substitutions
• 7 haplotypes

PAV
AVI
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Diversity in PTC

• 6 nucleotide substitutions
• 7 haplotypes

PAV
AVI
Taster Allele
Nontaster Allele
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Allele frequencies
T
t
Native American
African
Asian
European
FST 0.05
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Has selection been acting?
Neutrality Not Rejected, p gt 0.06
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Has selection been acting?
Neutrality rejected
Exceeds 99.5 of D values reported for gt1,600
genes
Wooding et al., Am. J. Hum. Genet., 2004
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How has selection acted?
Nontaster alleles are not premature stop codons
or frameshifts
HYPOTHESIS Nontaster allele is a functional
receptor that binds ligands other than PTC.
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What happened in chimps?
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TAS2R38 Resequencing in 37 Wild-born Chimpanzees
AGG Start
ATG Start
Wooding et al., 2006, Nature 440 930-4
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Hypothesized PTC Tasting in Chimpanzees
Non-taster
Taster
Wooding et al., 2006, Nature 440 930-4
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How does AGG make a nontaster allele?
ATG
AGG
Full-length Protein PTC response
Truncated Protein no PTC response
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Phenotyping Chimpanzees
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Is AGG the nontaster allele in chimps?

• Genotype-phenotype association analysis
• 40 chimpanzee subjects
• Genotyped
• Phenotyped
• Apples soaked in H2O or 4.0 mM PTC
• Response on a 1-5 scale (1 Readily Accepted 5
  Strongly Rejected)
• Fishers Exact Test (2x2)

Expected
Taster
Nontaster
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1
Taster
Observed
7
8
Nontaster
Rejected no association (p lt 10-3) AGG/AGG
broken start chimps eat PTC apples
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Humans versus Chimps
Humans
Chimps
T, t alleles
T, t alleles
5050 frequencies
5050 frequencies
3 amino acid changes
One start codon change
Same gene, same phenotype, same
allele frequencies different mechanism.
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Fishers Hypothesis
Taster
Human
Non-Taster
Chimpanzee
Ch
Hu
Ch
t
T
t
Hu
T
Chimp-Human Divergence
Ancestral Gene
Ancestral Gene
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Resequencing all 25 TAS2R genes in 55 humans

• Do all TAS2Rs have two clusters (i.e., T and t)?
• No some have very low levels of variation.
• Are all TAS2R alleles found at similar
  frequencies across populations?
• No Some have dramatically different frequencies
• On average populations differ more at TAS2Rs than
  at other genes

TAS2R49
FST 0.33
Kim et al., 2005, Hum. Mutation 26 199-204
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Population Differentiation Implies Local
Adaptation
PTC
Observed Simulated
FST
TAS2Rs (p lt 0.01)
Kim et al., 2005, Hum. Mutation 26 199-204
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TAS2R genes are involved in the perception of
many substances

• Alcohol
• Subjects with PTC taster haplotype experience
  more bitterness and have lower alcohol intake
• (Duffy et al., 2004, Alcohol Clin. Exp. Res. 28
  1629-37)
• Variant in TAS2R16 is strongly associated with
  risk of alcohol dependence (Hinrichs et al.,
  2006, Am. J. Hum. Genet. 78 103-11)
• Cigarette smoke
• Some evidence that PTC tasters are aversive to
  cigarette smoke and less likely to become smokers
  
• (Enoch et al., 2001, Addict. Behav. 26 399-404)
• Saccharin and acesulfame K
• Activate TAS2R43 and TAS2R44 bitter taste
  receptors
• (Kuhn et al., 2004, J. Neurosci. 10 10260-5)

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Summary

• Polymorphism in the human PTC gene is maintained
  by balancing natural selection
• Humans and chimps both have taster and non-taster
  alleles, but these alleles arose independently
• Substantial inter-population differentiation of
  TAS2R genes exists, consistent with local
  adaptation to environmental toxins

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Acknowledgments
University of Utah Mike Bamshad, Steve Wooding,
Diane Dunn, Bob Weiss, Mike Howard NIH Dennis
Drayna, U. Kim Potsdam Bernd Bufe, Wolfgang
Meyerhof University of Arizona Anne Stone
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(No Transcript)
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How has selection acted?
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How does AGG make a nontaster allele?
ATG
AGG
DNA
TCC
TAC
Transcription
AUG
AGG
RNA
Translation
Met
Met
Met
Protein
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Has selection been acting?

• Tajimas D statistic
• Compares S

S Number of nucleotide substitutions
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Has selection been acting?

• Tajimas D statistic
• Compares S and P

P Mean pairwise nucleotide difference
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Has selection been acting?

• Tajimas D statistic
• Compares S and P
• Affected by shape of haplotype network

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Has selection been acting?

• Tajimas D statistic
• Compares S and P
• Affected by shape of haplotype network

S 6
S 6
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Has selection been acting?

• Tajimas D statistic
• Compares S and P
• Affected by shape of haplotype network

S 6
S 6
P 0.1
P 3.0
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Has selection been acting?

• Tajimas D statistic
• Compares S and P
• Affected by shape of haplotype network

S 6
S 6
P 0.1
P 3.0
D -2.0
D 3.6
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Has selection been acting?

• Tajimas D statistic
• Compares S and P
• Affected by shape of haplotype network

Balancing selection or Local adaptation
Positive selection
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Human Variation
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Habitats
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Genes and diet
Gene Phenotype
Hemochromatosis Iron absorption

Angiotensinogen Sodium retention
Lactase Lactose tolerance

Alcohol dehydrogenase Ethanol metabolism

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Environmentally Responsive Genes
Genes controlling the active interface
between the human body and its environment
Genes involved in Sensory perception Immune
system Toxin metabolism
Bitter-taste sensitivity