1. Plant Growth & Development
3 stages
Embryogenesis
Fertilization to seed
2. Vegetative growth
Juvenile stage
Germination to adult
"phase change" marks transition
3. Reproductive development
Make flowers, can
reproduce sexually

2. Light regulation of growth
Plants sense
Light quantity
Light quality (colors)
Light duration
Direction it comes from

3. Light regulation of growth
Measures night! 30" flashes during night stop flowers
LDP plants such as Arabidopsis need long days to flower
SDP flower in fall, LDP flower in spring, neutral flower when ready
Next : color matters! Red light works best for flowering

4. Phytochrome
Next : color matters! Red light (666 nm)works best for flowering & for germination of many seeds!
But, Darwin showed blue works best for phototropism!

5. Phytochrome
But, Darwin showed blue works best for phototropism!
Different photoreceptor!
Red light (666 nm) promotes germination
Far red light (>700 nm) blocks germination

6. Phytochrome
Red light (666 nm) promotes germination
Far red light (>700 nm) blocks germination
After alternate R/FR color of final flash decides outcome
Seeds don't want to germinate in the shade!
Pigment is photoreversible

7. Phytochrome
Red light (666 nm) promotes germination
Far red light (730 nm) blocks germination
After alternate R/FR color of final flash decides outcome
Pigment is photoreversible! -> helped purify it!
Looked for pigment that absorbs first at 666 nm, then 730

8. Phytochrome
Red light (666 nm) promotes germination
Far red light (730 nm) blocks germination
After alternate R/FR color of final flash decides outcome
Pigment is photoreversible! -> helped purify it!
Looked for pigment that absorbs first at 666 nm, then 730

9. Phytochrome
Red light (666 nm) promotes germination
Far red light (730 nm) blocks germination
After alternate R/FR color of final flash decides outcome
Pigment is photoreversible! -> helped purify it!
Looked for pigment that absorbs first at 666 nm, then 730
Made as inactive cytoplasmic Pr that absorbs at 666 nm

10. Phytochrome
Made as inactive cytoplasmic Pr that absorbs at 666 nm or in blue
Converts to active Pfr that absorbs far red (730nm)

11. Phytochrome
Made as inactive cytoplasmic Pr that absorbs at 666 nm or in blue
Converts to active Pfr that absorbs far red (730nm)
97% of Pfr is converted back to Pr by far red light

12. Phytochrome
Made as inactive cytoplasmic Pr that absorbs at 666 nm or in blue
Converts to active Pfr that absorbs far red (730nm)
97% of Pfr is converted back to Pr by far red light
Also slowly reverts in dark

13. Phytochrome
Made as inactive cytoplasmic Pr that absorbs at 666 nm or in blue
Converts to active Pfr that absorbs far red (730nm)
97% of Pfr is converted back to Pr by far red light
Also slowly reverts in dark: how plants sense night length

14. Types of Phytochrome Responses
Two categories based on speed
Rapid biochemical events
Morphological changes

15. Types of Phytochrome Responses
Two categories based on speed
Rapid biochemical events
Morphological changes
Lag time also varies from minutes to weeks

16. Types of Phytochrome Responses
Two categories based on speed
Rapid biochemical events
Morphological changes
Lag time also varies from minutes to weeks: numbers of steps after Pfr vary

17. Types of Phytochrome Responses
Lag time also varies from minutes to weeks: numbers of steps after Pfr vary
"Escape time" until a response can no longer be reversed by FR also varies

18. Types of Phytochrome Responses
Lag time also varies from minutes to weeks: numbers of steps after Pfr vary
"Escape time" until a response can no longer be reversed by FR also varies: time taken for Pfr to do its job
Conclusions: phytochrome acts on many processes in many ways

19. Types of Phytochrome Responses
Two categories based on speed
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2

20. Types of Phytochrome Responses
Two categories based on speed
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2
Changes 0.02% of Pr to Pfr

21. Types of Phytochrome Responses
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2
Changes 0.02% of Pr to Pfr
Are not FR-reversible!

22. Types of Phytochrome Responses
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2
Changes 0.02% of Pr to Pfr
Are not FR-reversible! But action spectrum same as Pr

23. Types of Phytochrome Responses
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2
Changes 0.02% of Pr to Pfr
Are not FR-reversible! But action spectrum same as Pr
Induced by FR!

24. Types of Phytochrome Responses
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2
Changes 0.02% of Pr to Pfr
Are not FR-reversible! But action spectrum same as Pr
Induced by FR!
Obey law of reciprocity:
1 nmol/m-2 x 100 s =
100 nmol/m-2 x 1 sec

25. Types of Phytochrome Responses
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2
Changes 0.02% of Pr to Pfr
Are not FR-reversible! But action spectrum same as Pr
Induced by FR!
Obey law of reciprocity:
1 nmol/m-2 x 100 s =
100 nmol/m-2 x 1 sec
Examples: Cab gene
induction, oat
coleoptile growth

26. Types of Phytochrome Responses
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2
Changes 0.02% of Pr to Pfr
Are not FR-reversible! But action spectrum same as Pr
Induced by FR!
Obey law of reciprocity:
1 nmol/m-2 x 100 s =
100 nmol/m-2 x 1 sec
Examples: Cab gene
induction, oat
coleoptile growth
2. LF: induced by
1 µmol/m-2,
1000 µmol/m-2

27. Types of Phytochrome Responses
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2
2. LF: induced by 1 µmol/m-2, µmol/m-2
Are FR-reversible!

28. Types of Phytochrome Responses
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2
2. LF: induced by 1 µmol/m-2, µmol/m-2
Are FR-reversible! Need > 3% Pfr

29. Types of Phytochrome Responses
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2
2. LF: induced by 1 µmol/m-2, µmol/m-2
Are FR-reversible! Need > 3% Pfr
Obey law of reciprocity

30. Types of Phytochrome Responses
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2
2. LF: induced by 1 µmol/m-2, µmol/m-2
Are FR-reversible! Need > 3% Pfr
Obey law of reciprocity
Examples : Lettuce seed
Germination, mustard
photomorphogenesis,
inhibits flowering in SDP

31. Types of Phytochrome Responses
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2
2. LF: induced by 1 µmol/m-2, µmol/m-2
Are FR-reversible! Need > 3% Pfr
Obey law of reciprocity
Examples : Lettuce seed
Germination, mustard
photomorphogenesis,
inhibits flowering in SDP
3. HIR: require prolonged
exposure to higher fluence

32. Types of Phytochrome Responses
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2
2. LF: induced by 1 µmol/m-2, µmol/m-2
3. HIR: require prolonged exposure to higher fluence
Effect is proportional to
Fluence

33. Types of Phytochrome Responses
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2
2. LF: induced by 1 µmol/m-2, µmol/m-2
3. HIR: require prolonged exposure to higher fluence
Effect is proportional to
Fluence
Disobey law of reciprocity
Are not FR-reversible!

34. Types of Phytochrome Responses
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2
2. LF: induced by 1 µmol/m-2, µmol/m-2
3. HIR: require prolonged exposure to higher fluence
Effect is proportional to fluence
Disobey law of reciprocity
Are not FR-reversible!
Some are induced by FR!

35. Types of Phytochrome Responses
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2
2. LF: induced by 1 µmol/m-2, µmol/m-2
3. HIR: require prolonged exposure to higher fluence
Effect is proportional to fluence
Disobey law of reciprocity
Are not FR-reversible!
Some are induced by FR!
Examples: inhibition of
hypocotyl elongation in
many seedlings,
Anthocyanin synthesis

36. Types of Phytochrome Responses
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2
2. LF: induced by 1 µmol/m-2, µmol/m-2
3. HIR: require prolonged exposure to higher fluence
Effect is proportional to fluence
Disobey law of reciprocity
Are not FR-reversible!
Some are induced by FR!
Examples: inhibition of
hypocotyl elongation in
many seedlings,
Anthocyanin synthesis
Different responses =
Different phytochromes

37. Types of Phytochrome Responses
3 classes based on fluence (amount of light needed)
VLF:induced by 0.1 nmol/m-2 , 50nmol/m-2
2. LF: induced by 1 µmol/m-2, µmol/m-2
3. HIR: require prolonged exposure to higher fluence
Different responses = Different phytochromes:
3 in rice, 5 in Arabidopsis

38. Types of Phytochrome Responses
Different responses = Different phytochromes:
3 in rice, 5 in Arabidopsis
PHYA mediates VLF and HIR due to FR

39. Types of Phytochrome Responses
Different responses = Different phytochromes:
3 in rice, 5 in Arabidopsis
PHYA mediates VLF and HIR due to FR
Very labile in light

40. Types of Phytochrome Responses
Different responses = Different phytochromes:
3 in rice, 5 in Arabidopsis
PHYA mediates VLF and HIR due to FR
Very labile in light
2. PHYB mediates LF and HIR due to R
Stable in light

41. Types of Phytochrome Responses
PHYA mediates VLF and HIR due to FR
Very labile in light
2. PHYB mediates LF and HIR due to R
Stable in light
3. Roles of PHYs C, D & E not so clear

42. Types of Phytochrome Responses
PHYA mediates VLF and HIR due to FR
Very labile in light
2. PHYB mediates LF and HIR due to R
Stable in light
3. Roles of PHYs C, D & E not so clear
PHYA & PHYB are often antagonistic.

43. Types of Phytochrome Responses
PHYA & PHYB are often antagonistic.
In sunlight PHYB mainly controls development

44. Types of Phytochrome Responses
PHYA & PHYB are often antagonistic.
In sunlight PHYB mainly controls development
In shade PHYA 1st controls development, since FR is high

45. Types of Phytochrome Responses
PHYA & PHYB are often antagonistic.
In sunlight PHYB mainly controls development
In shade PHYA 1st controls development, since FR is high
But PHYA is light-labile; PHYB takes over & stem grows
"shade-avoidance"

46. Phytochrome
Pr has cis-chromophore

47. Phytochrome
Pr has cis-chromophore
Red converts it to trans = active shape

48. Phytochrome
Pr has cis-chromophore
Red converts it to trans = active shape
Far-red reverts it to cis

49. Phytochrome
Pfr is a protein kinase: acts by kinasing key proteins
some stays in cytoplasm & activates ion pumps

50. Phytochrome
Pfr is a protein kinase: acts by kinasing key proteins
some stays in cytoplasm & activates ion pumps
Rapid responses are due to changes in ion fluxes

51. Phytochrome
Pfr is a protein kinase: acts by kinasing key proteins
some stays in cytoplasm & activates ion pumps
Rapid responses are due to changes in ion fluxes
Increase growth by activating PM H+ pump

52. Phytochrome
Pfr is a protein kinase: acts by kinasing key proteins
some stay in cytoplasm & activate ion pumps
Rapid responses are due to changes in ion fluxes
most enter nucleus and kinase transcription factors

53. Phytochrome
some stay in cytoplasm & activate ion pumps
Rapid responses are due to changes in ion fluxes
most enter nucleus and kinase transcription factors
Slow responses are due to changes in gene expression

54. Phytochrome
most enter nucleus and kinase transcription factors
Slow responses are due to changes in gene expression
Many targets of PHY are transcription factors, eg PIF3

55. Phytochrome
most enter nucleus and kinase transcription factors
Slow responses are due to changes in gene expression
Many targets of PHY are transcription factors, eg PIF3
Activate cascades of genes for photomorphogenesis

56. Phytochrome
Slow responses are due to changes in gene expression
Many targets of PHY are transcription factors, eg PIF3
Activate cascades of genes for light responses
Some overlap, and some are unique to each phy

57. Phytochrome
Slow responses are due to changes in gene expression
Many targets of PHY are transcription factors, eg PIF3
Activate cascades of genes for light responses
Some overlap, and some are unique to each phy
20% of genes are light-regulated

58. Phytochrome
20% of genes are light-regulated
Protein degradation is important for light regulation

59. Phytochrome
20% of genes are light-regulated
Protein degradation is important for light regulation
Cop mutants can’t degrade specific proteins

60. Phytochrome
Protein degradation is important for light regulation
Cop mutants can’t degrade specific proteins
COP1/SPA targets specific transcription factors for degradation

61. Phytochrome
Protein degradation is important for light regulation
Cop mutants can’t degrade specific proteins
COP1/SPA targets specific
TF for degradation
DDA1/DET1/COP10 target
other proteins for degradation

62. Phytochrome
Protein degradation is important for light regulation
Cop mutants can’t degrade specific proteins
COP1/SPA targets specific
TF for degradation
DDA1/DET1/COP10 target
other proteins for degradation
Other COPs form part of
COP9 signalosome

63. Phytochrome
Protein degradation is important for light regulation
Cop mutants can’t degrade specific proteins
COP1/SPA targets specific TF for degradation
DDA1/DET1/COP10 target other proteins
Other COPs form part of COP9 signalosome
W/O COPs these TF act in dark

64. Phytochrome
COPs target specific TF for degradation
W/O COPs they act in dark
In light COP1 is exported to cytoplasm so TF can act
Tags PHYA by itself on the way out!

65. Other Phytochrome Responses
In shade avoidance FR stimulates IAA synthesis from trp!
Occurs in < 1 hour

66. Other Phytochrome Responses
In shade avoidance FR stimulates IAA synthesis from trp!
Occurs in < 1 hour
Also occurs in response to endogenous ethylene!

67. Other Phytochrome Responses
Flowering under short days is controlled via protein deg
COP & CUL4 mutants flower early

68. Other Phytochrome Responses
Flowering under short days is controlled via protein deg
COP & CUL4 mutants flower early
Accumulate FT (Flowering locus T) mRNA early
FT mRNA abundance shows strong circadian rhythm

69. Other Phytochrome Responses
Circadian rhythms
Many plant responses, some developmental, some physiological, show circadian rhythms

70. Circadian rhythms
Many plant responses, some developmental, some physiological, show circadian rhythms
Leaves move due to circadian ion fluxes in/out of dorsal & ventral motor cells

71. Circadian rhythms
Many plant responses show circadian rhythms
Once entrained, continue in constant dark

72. Circadian rhythms
Many plant responses show circadian rhythms
Once entrained, continue in constant dark, or light

73. Circadian rhythms
Many plant responses show circadian rhythms
Once entrained, continue in constant dark, or light!
Gives plant headstart on photosynthesis, other processes that need gene expression

74. Circadian rhythms
Many plant responses show circadian rhythms
Once entrained, continue in constant dark, or light!
Gives plant headstart on photosynthesis, other processes that need gene expression
eg elongation at night!

75. Circadian rhythms
Gives plant headstart on photosynthesis, other processes that need gene expression
eg elongate at night!
Endogenous oscillator is temperature-compensated, so runs at same speed at all times

76. Circadian rhythms
Endogenous oscillator is temperature-compensated, so runs at same speed at all times
Is a negative feedback loop of transcription-translation
Light & TOC1 activate LHY & CCA1 at dawn

77. Circadian rhythms
Light & TOC1 activate LHY & CCA1 at dawn
LHY & CCA1 repress TOC1 in day, so they decline too

78. Circadian rhythms
Light & TOC1 activate LHY & CCA1 at dawn
LHY & CCA1 repress TOC1 in day, so they decline too
At night TOC1 is activated (not enough LHY & CCA1)

79. Circadian rhythms
Light & TOC1 activate LHY & CCA1 at dawn
LHY & CCA1 repress TOC1 in day, so they decline too
At night TOC1 is activated (not enough LHY & CCA1)
Phytochrome entrains the clock

80. Circadian rhythms
Light & TOC1 activate LHY & CCA1 at dawn
LHY & CCA1 repress TOC1 in day, so they decline too
At night TOC1 is activated (not enough LHY & CCA1)
Phytochrome entrains the clock So does blue light