bitter taste genetics: ptc and other stories lynn jorde and steve wooding department of human...
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Bitter Taste Genetics:Bitter Taste Genetics: PTC and Other Stories PTC and Other Stories
Lynn Jorde and Steve WoodingLynn Jorde and Steve WoodingDepartment of Human GeneticsDepartment of Human Genetics
University of Utah School of MedicineUniversity of Utah School of Medicine
OverviewOverview
PTC: evidence for balancing selectionPTC: evidence for balancing selection
PTC in chimps and humansPTC in chimps and humans
The other bitter taste receptor genesThe other bitter taste receptor genes
Michael Bamshad, MD Stephen Wooding, PhD
Molecules involved in taste perceptionMolecules involved in taste perceptionSourSour Ion channelsIon channels
SaltySalty Ion channelsIon channels
SweetSweet TAS1R family of G-TAS1R family of G-protein coupled protein coupled receptorsreceptors
UmamiUmami TAS1R family of G-TAS1R family of G-protein coupled protein coupled receptorsreceptors
BitterBitter TAS2R family (25 TAS2R family (25 functional members)functional members)
Sweet and Umami (T1R)Sweet and Umami (T1R)
T1R1 T1R2 T1R3
11
22 33 High-affinity sugar receptorHigh-affinity sugar receptor
33 High-affinity umami receptorHigh-affinity umami receptor
33 Low-affinity umami receptorLow-affinity umami receptor
Cell types Cell types observed observed in vivoin vivo
The Bitter DraughtAdriaen Brouwer, 1635
Many plants contain toxinsMany plants contain toxins
Ricin
AbrinStrychnine
Digitoxin
Many plant toxins taste bitterMany plant toxins taste bitter
Quinine Nicotine
PapaverineSalicin
Biomedical relevance of bitter tasteBiomedical relevance of bitter taste
Bitter-tasteBitter-taste sensitivity
SmokingSmoking
Body Mass IndexBody Mass Index
Diet ChoiceDiet Choice
CancerCancer
Bitter-taste (TAS2R) ReceptorsBitter-taste (TAS2R) Receptors
Bitter-taste (TAS2R) ReceptorsBitter-taste (TAS2R) Receptors
TAS2R
G
x
Ca+
Ca+Ca+
Ca+
Bitter-taste receptors bind plant toxinsBitter-taste receptors bind plant toxins
TAS2R10TAS2R10 strychninestrychnine
TAS2R14TAS2R14 -thujones-thujones
TAS2R16TAS2R16 salicin, salicin, cyanogenic compoundscyanogenic compounds
Bufe et al., Nat. Gen., 2002; Behrens et al., BBRC, 2004
L’absintheEdgar Degas, 1876
Phenylthiocarbamide (PTC)Phenylthiocarbamide (PTC)
SyntheticSynthetic• Bitter or tastelessBitter or tasteless
Fox 1932Fox 1932• Variable sensitivityVariable sensitivity• Similar in structure to plant compounds Similar in structure to plant compounds
Blakeslee 1932Blakeslee 1932• Taste blindness is Mendelian recessiveTaste blindness is Mendelian recessive
Fisher et al., 1939Fisher et al., 1939• Variable sensitivity in chimpVariable sensitivity in chimp
Thousands of individuals have been typed for Thousands of individuals have been typed for PTC taster statusPTC taster status
PTCPTC Gene Gene
Drayna Drayna et al., et al., 20032003• Genome-wide linkage analysisGenome-wide linkage analysis
• Utah CEPH families• PTC gene localized to chromosome 7 and subsequently
cloned
How have natural selection and population historyaffected the PTC gene?
• PTCPTC Gene ( Gene (TAS2R38TAS2R38))• Haplotypes strongly associated with phenotype• Accounted for ~50-85% of phenotypic variance
PTCPTC resequencing in humans resequencing in humans
Sequenced entire coding region (1,002 bp)Sequenced entire coding region (1,002 bp)
• 174 individuals (348 chromosomes)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
Diversity in Diversity in PTCPTC
6 nucleotide substitutions in humans6 nucleotide substitutions in humans
Diversity in Diversity in PTCPTC
6 nucleotide substitutions6 nucleotide substitutions• 7 haplotypes7 haplotypes
PAV AVI
Diversity in Diversity in PTCPTC
TasterAllele
NontasterAllele
6 nucleotide substitutions6 nucleotide substitutions• 7 haplotypes7 haplotypes
PAV: AVI:
Allele frequenciesAllele frequencies
African Asian EuropeanNative
American
T
t
FST = 0.05
Has selection been acting?Has selection been acting?
Neutrality Not Rejected, p > 0.06
Has selection been acting?Has selection been acting?
Wooding et al., Am. J. Hum. Genet., 2004
Neutrality rejected
Exceeds 99.5% of D values reported for Exceeds 99.5% of D values reported for >1,600 genes>1,600 genes
How has selection acted?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?What happened in chimps?
TAS2R38 Resequencing in 37 Wild-born Chimpanzees
AGG StartATG Start
Wooding et al., 2006, Wooding et al., 2006, Nature Nature 440: 930-4440: 930-4
Hypothesized PTC Tasting in Chimpanzees
“Taster” “Non-taster”
Wooding et al., 2006, Wooding et al., 2006, Nature Nature 440: 930-4440: 930-4
How does AGG make a nontaster allele?How does AGG make a nontaster allele?
ATG AGG
Full-length Protein: PTC response Truncated Protein: no PTC response
Phenotyping ChimpanzeesPhenotyping Chimpanzees
Is AGG the nontaster allele in chimps?Is AGG the nontaster allele in chimps? Genotype-phenotype association analysisGenotype-phenotype association analysis
- 40 chimpanzee subjects40 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)Fisher’s Exact Test (2x2)
Taster Nontaster
Taster
Nontaster
23 1
7 8
Expected
Observed
Rejected no association (p < 10-3)AGG/AGG “broken start” chimps eat PTC apples
Humans versus ChimpsHumans versus Chimps
HumansHumans ChimpsChimps
T, t allelesT, t alleles
50:50 frequencies50:50 frequencies
3 amino acid changes3 amino acid changes
T, t allelesT, t alleles
50:50 frequencies50:50 frequencies
One start codon changeOne start codon change
Same gene, same phenotype, same alleleSame gene, same phenotype, same allelefrequencies… different mechanism.frequencies… different mechanism.
Fisher’s HypothesisFisher’s Hypothesis
“Taster” “Non-Taster”
Hu Ch Hu Ch
Ancestral Gene
Chimp-HumanDivergence
Human Chimpanzee
T t T t
Ancestral Gene
Resequencing all 25 Resequencing all 25 TAS2RTAS2R genes in 55 humans genes in 55 humans
Do all TAS2Rs have two clusters (i.e., T and t)?Do all TAS2Rs have two clusters (i.e., T and t)?• No – some have very low levels of variation.No – some have very low levels of variation.
Are all TAS2R alleles found at similar frequencies across Are all TAS2R alleles found at similar frequencies across populations?populations?• No – Some have dramatically different frequenciesNo – Some have dramatically different frequencies• On average populations differ more at TAS2Rs than at other genesOn average populations differ more at TAS2Rs than at other genes
TAS2R49
Kim et al., 2005, Kim et al., 2005, Hum. Mutation Hum. Mutation 26: 199-20426: 199-204
FST = 0.33
Population Differentiation Implies Local Population Differentiation Implies Local AdaptationAdaptation
FST
PTC ObservedSimulated
TAS2Rs (p < 0.01)
Kim et al., 2005, Kim et al., 2005, Hum. Mutation Hum. Mutation 26: 199-20426: 199-204
TAS2R genes are involved in the TAS2R genes are involved in the perception of many substancesperception of many substances
AlcoholAlcohol• Subjects with PTC taster haplotype experience more Subjects with PTC taster haplotype experience more
bitterness and have lower alcohol intake bitterness and have lower alcohol intake (Duffy et al., 2004, (Duffy et al., 2004, Alcohol Clin. Exp. Res. Alcohol Clin. Exp. Res. 28: 1629-37)28: 1629-37)
• Variant in Variant in TAS2R16TAS2R16 is strongly associated with risk of is strongly associated with risk of alcohol dependence alcohol dependence (Hinrichs et al., 2006, (Hinrichs et al., 2006, Am. J. Hum. Genet. Am. J. Hum. Genet. 78: 103-11)78: 103-11)
Cigarette smokeCigarette smoke• Some evidence that PTC tasters are aversive to cigarette Some evidence that PTC tasters are aversive to cigarette
smoke and less likely to become smokers smoke and less likely to become smokers (Enoch et al., 2001, (Enoch et al., 2001, Addict. Behav. Addict. Behav. 26: 399-404)26: 399-404)
Saccharin and acesulfame KSaccharin and acesulfame K• Activate TAS2R43 and TAS2R44 bitter taste receptorsActivate TAS2R43 and TAS2R44 bitter taste receptors
(Kuhn et al., 2004, (Kuhn et al., 2004, J. Neurosci.J. Neurosci. 10: 10260-5) 10: 10260-5)
SummarySummary
Polymorphism in the human Polymorphism in the human PTCPTC gene is gene is maintained by balancing natural selectionmaintained by balancing natural selection
Humans and chimps both have taster and Humans and chimps both have taster and non-taster alleles, but these alleles arose non-taster alleles, but these alleles arose independentlyindependently
Substantial inter-population differentiation Substantial inter-population differentiation of of TAS2RTAS2R genes exists, consistent with genes exists, consistent with local adaptation to environmental toxinslocal adaptation to environmental toxins
University of Utah: Mike Bamshad, Steve Wooding, Mike Bamshad, Steve Wooding, Diane Dunn, Bob Weiss, Mike Howard Diane Dunn, Bob Weiss, Mike Howard
NIH: Dennis Drayna, U. KimDennis Drayna, U. Kim
Potsdam: Bernd Bufe, Wolfgang Meyerhof Bernd Bufe, Wolfgang Meyerhof
University of Arizona: Anne StoneAnne Stone
University of Utah: Mike Bamshad, Steve Wooding, Mike Bamshad, Steve Wooding, Diane Dunn, Bob Weiss, Mike Howard Diane Dunn, Bob Weiss, Mike Howard
NIH: Dennis Drayna, U. KimDennis Drayna, U. Kim
Potsdam: Bernd Bufe, Wolfgang Meyerhof Bernd Bufe, Wolfgang Meyerhof
University of Arizona: Anne StoneAnne Stone
AcknowledgmentsAcknowledgments
How has selection acted?How has selection acted?
How does AGG make a nontaster allele?How does AGG make a nontaster allele?
ATG AGG
AUG AGG
Met Met Met
Transcription
Translation
TAC TCC
DNA
RNA
Protein
Has selection been acting?Has selection been acting?
Tajima’s D statisticTajima’s D statistic• Compares SCompares S
S = Number of nucleotide substitutions
Has selection been acting?Has selection been acting?
Tajima’s D statisticTajima’s D statistic• Compares S and Compares S and
= Mean pairwise nucleotide difference
Has selection been acting?Has selection been acting?
Tajima’s D statisticTajima’s D statistic• Compares S and Compares S and • Affected by “shape” of haplotype networkAffected by “shape” of haplotype network
Has selection been acting?Has selection been acting?
Tajima’s D statisticTajima’s D statistic• Compares S and Compares S and • Affected by “shape” of haplotype networkAffected by “shape” of haplotype network
S = 6 S = 6
Has selection been acting?Has selection been acting?
Tajima’s D statisticTajima’s D statistic• Compares S and Compares S and • Affected by “shape” of haplotype networkAffected by “shape” of haplotype network
S = 6 S = 6 = 0.1 = 3.0
Has selection been acting?Has selection been acting?
Tajima’s D statisticTajima’s D statistic• Compares S and Compares S and • Affected by “shape” of haplotype networkAffected by “shape” of haplotype network
S = 6 S = 6 = 0.1 = 3.0
D = -2.0 D = 3.6
Has selection been acting?Has selection been acting?
Tajima’s D statisticTajima’s D statistic• Compares S and Compares S and • Affected by “shape” of haplotype networkAffected by “shape” of haplotype network
Positive selection Balancing selectionor
Local adaptation
Human Variation
Habitats
Genes and dietGenes and diet
GeneGene PhenotypePhenotype
HemochromatosisHemochromatosis Iron absorptionIron absorption
AngiotensinogenAngiotensinogen Sodium retentionSodium retention
LactaseLactase Lactose toleranceLactose tolerance
Alcohol dehydrogenaseAlcohol dehydrogenase Ethanol metabolismEthanol metabolism
Environmentally Responsive GenesEnvironmentally Responsive Genes
Genes controlling the active interface betweenthe human body and its environment
Genes involved in:
Sensory perception
Immune system
Toxin metabolism
Bitter-taste sensitivity