lecture #5 vertebrate visual pigments 2/7/13. hw #3 there are two things on the assignment page:...
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Lecture #5
Vertebrate visual pigments2/7/13
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HW #3
• There are two things on the assignment page: Assign#3.pdf which has the homework
problemsHumanGreenRedCones.xlsx which is a
spreadsheet you can use for one of the problems
• I think I turned on online submissions but you don’t have to use that
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Today’s topics
• Visual pigments and opsin genes
• Opsin gene classes and diversity in vertebrates
• Primates: di- and trichromacy
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What absorbs light in a visual pigment?
12
3
O11-cis
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Where does it come from?
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Where does it come from?
Your body turns β-carotene into vitamin A
All trans-retinOL
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Where does it come from?
Vitamin A is converted to 11-cis retinal (visual cycle)
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Absorption spectrum of 11-cis retinal
J Biol Chem 1956
George WaldNobel Prize 1967
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Absorption spectrum of 11-cis retinal
378 nm
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11-cis retinal absorption
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11-cis retinal vs human visual pigments - opsin shift
11-cis S M L
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What is a visual pigment?
• Opsin protein surrounding and bound to 11-cis retinal
• Transmembrane proteinContained in the membrane
• G protein coupled receptorTurns on a G protein
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Membrane holds the visual pigment
Rods have discsCones have continuous membrane
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Opsin protein is threaded through the membrane
80% of protein in outer segment is rhodopsin
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Rhodopsin crystal structure
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Visual pigment =opsin + retinal
11-cis retinal
membrane
In rod, visual pigment is called rhodopsin
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Retinal is in binding pocket of opsin protein
Chang et al. 1995
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11-cis bond isomerizes to form all trans
Chang et al. 1995
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Light causes isomerization
11-cis retinal + photon = all trans retinal
12
3
Light
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Absorbing light
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Excited state - stays as metaII
Meta II actually is what can activate the G protein
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Excited state - stays as metaII
Eventually the excited state decays
All trans retinal dissociates, leaving opsin
Opsin recombines with new 11cis retinal
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Electronic energy levels of visual pigment molecule
Ground state
Excited state
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Electronic energy levels of visual pigment molecule
Ground state
Excited state
light
E = hc/λ
Visual pigment absorbs light at wavelengths which can excite electrons to upper excited state
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Opsin interacts with retinal to make ground and excited states closer
together
Ground state
Excited state
light
E = hc/λ
Energy needed to excite electrons goes down
Absorption is at longer wavelength
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Opsin interacts with retinal to make ground and excited states farther
apart
Ground state
Excited state
light
E = hc/λ
Energy needed to excite electrons goes up
Absorption is at shorter wavelength
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Opsin is bound to and surrounds 11-cis retinal
Chang et al. 1995
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How do we get one rod and three cone visual pigments?
Cones: λmax = 420, 535, 565 nm Rod: λmax = 505 nm
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Put a different opsin protein in each cone type
Webvision
Blue cone - blue opsin
Green cone - green opsin
Red cone - red opsin
Rod - rhodopsin
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Blue opsin versus green opsin
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Human rhodopsin sequence
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Human Rh
sequence
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Nathans et al 1986
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Humans have 3 cone opsin genes
Blue opsin - 5 exons
Green and red - 6 exons
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Sequences for human green and red opsin genes are VERY similar
HumanGreen MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM 60HumanRed MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM 60 ************************************************************
HumanGreen IFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFV 120HumanRed IFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISIVNQVSGYFV 120 **** *********************************************:**** ****
HumanGreen LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWA 180HumanRed LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGNVRFDAKLAIVGIAFSWIWS 180 ********************************:**************************:
HumanGreen AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYL 240HumanRed AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCIIPLAIIMLCYL 240 ************************************************* **:**:****
HumanGreen QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFH 300HumanRed QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMIFAYCVCWGPYTFFACFAAANPGYAFH 300 *********************************::*:*.*****:************.**
HumanGreen PLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS 360HumanRed PLMAALPAYFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS 360 ********:***************************************************
HumanGreen VSPA 364HumanRed VSPA 364 ****
Differ by 15 AA
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Why opsins are so cool
• You can grow cells that express ANY opsin protein you want
• You can add 11-cis retinal and purify the protein
+11-cis retinal
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Why opsins are so cool
• You can grow cells that express ANY opsin protein you want
• You can add 11-cis retinal and purify the protein
• You can measure the absorption spectrum for that visual pigment
+11-cis retinal
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You can mutate one amino acid and see how absorption peak
shifts
F261 F261 F261
+11-cis retinal
F261
Y261 Y261 Y261
+11-cis retinal
Y261
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Changing site 261 from F to Y shifts absorption peak by +10
nm
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Human red and green opsins
535 nm
565 nm
A
S
A
A164S=+2 nm
Y
F
T
F261Y=+10 nmA269T=+14 nm
These 3 AA explain most of the shift between red and green opsin genes
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Location of human opsin genes
RhodopsinChr 3
Blue opsinChr 7
Exon
Red and green opsin - X chromosome
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Normal DNA recombination
Switches genes from one chromosome to the other
Leads to new gene combinations
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Mismatched recombination
If chromosomes misalign, recombination leads to gain in genes on one chromosome and loss of genes on the other.
Tandem arrays of genes
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Opsin gene tandem arrays on X chromosome
Humans differ in how many copies they have of green gene.
Only first 2 genes are expressed so it doesn’t matter if there are more green genes. They are just along for ride.
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Misaligned recombination
If recombination happens within gene, get chimeraIntermediate phenotype which results in color blindness
Opsin genes on X chromosome
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Human red and green opsins
535 nm
565 nm
A
S
A
A164S=+2 nm
Y
F
T
F261Y=+10 nmA269T=+14 nm
554 nm
Chimera has intermediate peak wavelengthA YT
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Protanope - no red cones1% males 0.01% females
λmax = 420, 535nm
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Deuteranope - no green cones1% males 0.01% females
λmax = 420, 565 nm
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Protanomoly - red pigment shifted towards green
λmax = 420, 535, 550 nm
1% male 0.01% female
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Deuteranomoly - green pigment shifted towards red
λmax = 420, 554, 565 nm
5% male 0.04% female
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Mutations in human opsin genes
Protanope
Deuteranope
Protanomalous
Deuteranomalous
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Color “blindness”
Deficiency Males Females
Protanopia 1% 0.01%
Deuteranopia 1% 0.01%
Protanomoly 1% 0.01%
Deuteranomoly 5% 0.4%
Total (red-green) 8% 0.5%
Tritanopia 0.008% 0.008%
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Phylogenetics
• Compare sequences and determine the relatedness of things- Calculate % similarity of DNA or AA
sequences
• Draw relatedness as a treeHuman
Mouse
Bird
Human
Mouse
Bird
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Vertebrates
• Placental mammals Amphibians• Marsupials Birds• Reptiles Cartilagenous
fish• Bony fish Jawless fish
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Vertebrate relationships and divergence times
Kumar and Hedges 1998
Mammals, 100 MY
Fish, 450 MY
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Trees can also tell you about genes
• What organisms have the gene?• Where did the gene come from?• What happens to the gene once
it’s there?Duplicate - tandem
- mRNA can be insertedLost
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Line lengths are proportional to how different sequences are
Human
Chimp
Dog
Humans and chimps had a common ancestor 5-6 MYa so genes will be very similar
Dogs and other mammals are about 100 MY apart so genes will be 20x more different from human as compared to human-chimp
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Default expectation - if gene arose early in vertebrates, all species will have a copy and gene will be related in same
way as organisms
Dog Gene A
Opossum Gene AChicken Gene A
Frog Gene A
Zebrafish Gene A
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Examine whether a gene exists in all organisms
Dog Gene A
Opossum Gene AChicken Gene A
Frog Gene A
Zebrafish No A
Gained
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Examine whether a gene exists in all organisms
Mouse
Platypus
Chicken
Frog
Pufferfish
lost
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What is happening?
• Gene duplication
Human Gene A
Chicken Gene A
Frog Gene A
Zebrafish Gene A1
Dog Gene A
Zebrafish Gene A2
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Human
Chicken
Frog
Zebrafish
Dog
Human
Chicken
Frog
Zebrafish
Dog
Lamprey
Gene duplication
GeneA2
GeneA1
Gene A
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Human
Frog
Dog
Chicken
Frog
Zebrafish
Lamprey
GeneA2
GeneA1
Gene A
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Human
Chicken
Frog
Zebrafish
Dog
Human
Chicken
Frog
Zebrafish
Dog
Gene duplication and then losses
Lamprey
Gene A2
Gene A1
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Opsin genes
• Opsin genes can duplicateTandem duplicationChromosomal duplicationWhole genome duplication
• Opsin genes can be lost
• Can reinsert from mRNANo introns
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Opsin genes from:
• Lamprey (jawless vertebrate)• Zebrafish• Anole (reptile)• Chicken (bird)• Mouse• Human
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LWS
RH2
SWS2
SWS1
RH1
What does this tree tell us?
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Conclusions from opsin tree #1
• 5 opsin classes arose very early in vertebratesSWS1 - very short wavelength sensitiveSWS2 - short wavelength sensitiveRH2 - like rhopopsin but in conesLWS - long wavelength sensitiveRH1 - rhodopsin
rods
cones
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Range of cone visual pigment λmax
SWS1SWS2
RH2LWS
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Conclusion #2
• Rod opsins evolved from cone opsins
LWS
SWS1
SWS2
RH2
RH1
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LWS
RH2
SWS2
SWS1
RH1
Mammalian genes
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Conclusion #3
• Mammals lost two of the opsin classesMammals have LWS, SWS1 and RH1
Only 2 cone opsins (dichromat)Dogs, cats, mice, rats, horses, goats, pigs …
• Mammals went through “nocturnal period” during reign of dinosaurs
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“Rugrats”
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“Spike’s view”
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Spike’s view?
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LWS
RH2
SWS2
SWS1
RH1
Human genes
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Conclusion #4
• Primates had a duplication of the LWS gene
• Went from dichromatic to trichromatic
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Human green and red opsins are part of LWS class = M/LWS
λmax = 535, 565 nm
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M/LWS opsin duplication on X chromosome
RhodopsinChr 3
Blue opsinChr 7
Red and green opsin - X chromosome
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New world vs Old world primates
X
X
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Why trichromacy? Why two ‘LWS’ cone types? Dichromacy with a single LWS and an SWS1 cone type gives no red-green discrimination.
Jim Bowmaker
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Trichromacy with two ‘LWS’ cone types and an SWS1 cone gives red-green discrimination.
Ripe fruit and young, more reddish leaves can be detected against the dappled green foliage.
Jim Bowmaker