Download Bitter taste genetics

Bitter Taste Genetics:
PTC and Other Stories
Lynn Jorde and Steve Wooding
Department of Human Genetics
University of Utah School of Medicine
Overview
 PTC: evidence for balancing selection
 PTC in chimps and humans
 The other bitter taste receptor genes
Michael Bamshad, MD
Stephen Wooding, PhD
Molecules involved in taste perception
Sour
Ion channels
Salty
Ion channels
Sweet
TAS1R family of Gprotein coupled
receptors
TAS1R family of Gprotein coupled
receptors
TAS2R family (25
functional members)
Umami
Bitter
Sweet and Umami (T1R)
T1R1
Cell types
observed in vivo
T1R2
T1R3
1 3
High-affinity umami receptor
2 3
High-affinity sugar receptor
3
Low-affinity umami receptor
The Bitter Draught
Adriaen Brouwer, 1635
Many plants contain toxins
Ricin
Strychnine
Digitoxin
Abrin
Many plant toxins taste bitter
Quinine
Salicin
Nicotine
Papaverine
Biomedical relevance of bitter taste
Bitter-taste sensitivity
Smoking
Diet Choice
Cancer
Body Mass Index
Bitter-taste (TAS2R) Receptors
Bitter-taste (TAS2R) Receptors
x
TAS2R
Ga
Ca+
Ca+
Ca+
Ca+
Bitter-taste receptors bind plant toxins
TAS2R10
strychnine
TAS2R14
a-thujones
TAS2R16
salicin,
cyanogenic compounds
L’absinthe
Edgar Degas, 1876
Bufe et al., Nat. Gen., 2002; Behrens et al., BBRC, 2004
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
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?
PTC resequencing in humans
 Sequenced entire coding region (1,002 bp)
• 174 individuals (348 chromosomes)
•
•
•
•
40 African
- Not selected for PTC sensitivity
69 Asian
- “Anthropological” sampling
55 European
10 Native American
Wooding et al., 2004, Am. J. Hum. Genet. 74: 637-46
Diversity in PTC
 6 nucleotide substitutions in humans
Diversity in PTC
 6 nucleotide substitutions
• 7 haplotypes
PAV
AVI
Diversity in PTC
 6 nucleotide substitutions
• 7 haplotypes
PAV:
AVI:
Taster
Allele
Nontaster
Allele
Allele frequencies
T
t
African
Asian
European
FST = 0.05
Native
American
Has selection been acting?
Neutrality Not Rejected, p > 0.06
Has selection been acting?
Neutrality rejected
Exceeds 99.5% of D values reported for
>1,600 genes
Wooding et al., Am. J. Hum. Genet., 2004
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.
Tt
+
What happened in chimps?
TAS2R38 Resequencing in
37 Wild-born Chimpanzees
ATG Start
AGG Start
Wooding et al., 2006, Nature 440: 930-4
Hypothesized PTC Tasting in Chimpanzees
“Taster”
“Non-taster”
Wooding et al., 2006, Nature 440: 930-4
How does AGG make a nontaster allele?
ATG
Full-length Protein: PTC response
AGG
Truncated Protein: no PTC response
Phenotyping Chimpanzees
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)
- Fisher’s Exact Test (2x2)
Expected
Taster Nontaster
Observed
Taster
Nontaster
23
1
7
8
Rejected no association (p < 10-3)
AGG/AGG “broken start” chimps eat
PTC apples
Humans versus Chimps
Humans
Chimps
T, t alleles
T, t alleles
50:50 frequencies
50:50 frequencies
3 amino acid changes
One start codon change
Same gene, same phenotype, same allele
frequencies… different mechanism.
Fisher’s Hypothesis
“Taster”
Hu
Ch
“Non-Taster”
Hu
Human
Ch
T
t
Chimpanzee
T
t
Chimp-Human
Divergence
Ancestral Gene
Ancestral Gene
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
Population Differentiation Implies Local
Adaptation
PTC
Observed
Simulated
FST
TAS2Rs (p < 0.01)
Kim et al., 2005, Hum. Mutation 26: 199-204
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)
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
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
How has selection acted?
How does AGG make a nontaster allele?
ATG
AGG
TAC
TCC
DNA
Transcription
RNA
AUG
AGG
Translation
Protein
Met
Met Met
Has selection been acting?
 Tajima’s D statistic
• Compares S
S = Number of nucleotide substitutions
Has selection been acting?
 Tajima’s D statistic
• Compares S and P
P = Mean pairwise nucleotide difference
Has selection been acting?
 Tajima’s D statistic
• Compares S and P
• Affected by “shape” of haplotype network
Has selection been acting?
 Tajima’s D statistic
• Compares S and P
• Affected by “shape” of haplotype network
S=6
S=6
Has selection been acting?
 Tajima’s D statistic
• Compares S and P
• Affected by “shape” of haplotype network
S=6
P = 0.1
S=6
P = 3.0
Has selection been acting?
 Tajima’s D statistic
• Compares S and P
• Affected by “shape” of haplotype network
S=6
P = 0.1
S=6
P = 3.0
D = -2.0
D = 3.6
Has selection been acting?
 Tajima’s D statistic
• Compares S and P
• Affected by “shape” of haplotype network
Positive selection
Balancing selection
or
Local adaptation
Human Variation
Habitats
Genes and diet
Gene
Phenotype
Hemochromatosis
Iron absorption
Angiotensinogen
Sodium retention
Lactase
Lactose tolerance
Alcohol dehydrogenase
Ethanol metabolism
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