1. Stress responses/stress avoidance
Plan C
We will pick a problem in plant biology and see where it takes us.
Plant products
Climate/CO2 change
Stress responses/stress avoidance

2. Plants & products chosen
Capsaicin
Capsicum sp.
Glucosinolates
Radishes (Raphanus sativus)
Mustard (Brassica juncea)
Alliin -> Allicin
Garlic (Allium sativum)

3. Other candidates
Propanethial-S-oxide
Onions (Allium cepa)
Portulacanones
Purslane (Portulaca oleracea)
Allyl isothiocyanate
Horseradish (Armoracia rusticana)
Wasabi (Eutrema japonicum)
eugenol (and others)
Basil (Ocimum basilicum)

4. Stresses Chosen
Climate change
Temperature
Increased pCO2
Drought pH
Nutrient deprivation
Metal toxicity (a result of low pH)
Predation
Shaking

5. Next Friday
Present a plant stressor, what is known about it, and why it might affect plant 2˚ compounds in an ~ 10 minute presentation.
Alternative: present another good plant/stressor response to study and why we should choose it over the ones already chosen.

6. Nutrient transport in roots
Move from soil to endodermis in apoplast
Move from endodermis to xylem in symplast

7. Nutrient uptake
Taken into endodermis by H+ symporters, channels, pumps

8. Nutrient transport in roots
Move from endodermis to xylem in symplast
Transported into xylem by
H+ antiporters, channels,
pumps

9. Transport to shoot
Nutrients move up
plant in xylem sap

10. Nutrient transport in leaves
Xylem sap moves through apoplast
Leaf cells take up what
they want

11. Nutrient assimilation
Assimilating N and S is very expensive!
Reducing NO3- to NH4+ costs 8 e- (1 NADPH + 6 Fd)
Assimilating NH4+ into amino acids also costs ATP + e-
Nitrogen fixation costs 16 ATP + 8 e-
SO42- reduction to S2- costs 8 e- + 2ATP
S2- assimilation into Cysteine costs 2 more e-
Most explosives are based on N or S!

12. Nutrient assimilation
Most explosives are based on N or S!
Most nutrient assimilation occurs in source leaves!

13. N cycle
Must convert N2 to a form that can be assimilated
N2 -> NO3- occurs in atmosphere: lightning (8%) & Photochemistry (2%) of annual total fixed
Remaining 90% comes from biological fixation to NH4+

14. N cycle
Soil bacteria denitrify NO3- & NH4+ back to N2
Plants must act fast!
Take up NO3- & NH4+ but generally prefer NO3-
Main form available due to bacteria

15. N assimilation by non-N fixers
Nitrate reductase in cytoplasm reduces
NO3- to NO2-
NO3- + NADPH = NO2- + NADP+
large enzyme with FAD & Mo cofactors

16. N assimilation by non-N fixers
Nitrate reductase in cytoplasm reduces
NO3- to NO2-
NO3- + NADPH = NO2- + NADP+
large enzyme with FAD & Mo cofactors
NO2- is imported to plastids & reduced
to NH4+ by nitrite reductase

17. N assimilation by non-N fixers
NO2- is imported to plastids & reduced
to NH4+ by nitrite reductase
NO Fdred + 8 H+ = NH Fdox + 2 H2O
0.2% of NO2- is released as N2O : another reason rape & corn biofuels increase global warming

18. N assimilation by non-N fixers
NO2- is imported to plastids & reduced
to NH4+ by nitrite reductase
NO Fdred + 8 H+ = NH Fdox + 2 H2O
0.2% of NO2- is released as N2O : another reason rape & corn biofuels increase global warming
Regulated at NO3- reductase; always << NO2- reductase
NO2- is toxic!

19. N assimilation by non-N fixers
Regulated at NO3- reductase; always << NO2- reductase
NO2- is toxic!
NR induced by light & nitrate

20. N assimilation by non-N fixers
Regulated at NO3- reductase; always << NO2- reductase
NO2- is toxic!
NR induced by light & nitrate
Regulated by kinase in dark, dephosphorylation in day

21. NH4 assimilation
GS -> GOGAT
Glutamate + NH4+ + ATP <=> Glutamine + ADP +Pi

22. GS -> GOGAT
Glutamate + NH4+ + ATP <=> Glutamine + ADP +Pi
Glutamine + a-ketoglutarate + NADH/2 Fdred <=>
2 Glutamate + NAD+/ 2 Fdox

23. GS -> GOGAT
Glutamate + NH4+ + ATP <=> Glutamine + ADP +Pi
Glutamine + a-ketoglutarate + NADH/2 Fdred <=>
2 Glutamate + NAD+/ 2 Fdox
3. Fd GOGAT lives in source cp

24. GS -> GOGAT
Fd GOGAT lives in source cp
NADH GOGAT lives in sinks

25. GS -> GOGAT
Glutamate + NH4+ + ATP <=> Glutamine + ADP +Pi
Glutamine + a-ketoglutarate + NADH/2 Fdred <=>
2 Glutamate + NAD+/ 2 Fdox
3. Use glutamate to make other a.a. by transamination

26. GS -> GOGAT
3. Use glutamate to make other a.a. by transamination
Glutamate, aspartate & alanine can be converted to the other a.a.

27. N assimilation by N fixers
Exclusively performed by prokaryotes
Dramatically improve the growth of many plants

28. N assimilation by N fixers
Exclusively done by prokaryotes
Most are free-living in soil or water

29. N assimilation by N fixers
Exclusively done by prokaryotes
Most are free-living in soil or water
Some form symbioses with plants

30. N assimilation by N fixers
Exclusively done by prokaryotes
Most are free-living in soil or water
Some form symbioses with plants
Legumes are best-known, but
many others including mosses,
ferns, lichens

31. N assimilation by N fixers
Exclusively done by prokaryotes
Most are free-living in soil or water
Some form symbioses with plants
Legumes are best-known, but
many others including mosses,
ferns, lichens
Also have associations where
N-fixers form films on leaves or
roots and are fed by plant

32. N assimilation by N fixers
Exclusively done by prokaryotes
Also have associations where
N-fixers form films on leaves or
roots and are fed by plant
All must form O2-free
environment for nitrogenase

33. N assimilation by N fixers
All must form O2-free
environment for nitrogenase
O2 binds & inactivates e-transfer
sites

34. N assimilation by N fixers
O2 binds & inactivates e-transfer
sites
Heterocysts lack PSII, have
other mechs to lower pO2

35. N assimilation by N fixers
Heterocysts lack PSII, have
other mechs to lower O2
Nodules have special
structure + leghemoglobin
to protect from O2

36. Nodule formation
Nodules have special structure + leghemoglobin to protect from O2
Bacteria induce the plant to form nodules

37. Nodule formation
Bacteria induce the plant to form nodules
Root hairs secrete chemicals that attract N-fixers

38. Nodule formation
Bacteria induce the plant to form nodules
Root hairs secrete chemicals that attract N-fixers
Bacteria secrete Nod factors that induce root hair coiling
Nod factors determine species-specificity

39. Nodule formation
Root hairs secrete chemicals that attract N-fixers
Bacteria secrete Nod factors that induce root hair coiling
Nod factors determine species-specificity
Nod factors induce degradation of root cell wall

40. Nodule formation
Nod factors induce degradation of root cell wall
Plant forms "infection thread"= internal protusion of plasma membrane that grows into cell
When reaches end of cell bacteria are released into apoplast and repeat the process on inner cells

41. Nodule formation
When reaches end of cell bacteria are released into apoplast and repeat the process on inner cells
Cortical cells near xylem form a nodule primordium

42. Nodule formation
When reaches end of cell bacteria are released into apoplast and repeat the process on inner cells
Cortical cells near xylem form a nodule primordium
When bacteria reach these cells the infection thread breaks off, forming vesicles with bacteria inside

43. Nodule formation
When bacteria reach these cells the infection thread breaks off, forming vesicles with bacteria inside
Vesicles fuse, form the peribacteroid membrane and bacteria differentiate into bacteroids.

44. Nodule formation
Vesicles fuse, form the peribacteroid membrane and bacteria differentiate into bacteroids.
Plant cells differentiate into nodules

45. Nodule formation
Vesicles fuse, form the peribacteroid membrane and bacteria differentiate into bacteroids.
Plant cells differentiate into nodules: have layer of cells to exclude O2 & vasculature
to exchange nutrients

46. Nodule formation
Plant cells differentiate into nodules: have layer of cells to exclude O2 & vasculature to exchange nutrients
Complex process that is difficult to engineer: 21 non-legume plant genera have N-fixers

47. N2 + 8H+ + 8e− + 16 ATP → 2NH3 + H2 + 16ADP + 16 Pi
Nitrogen fixation
N2 + 8H+ + 8e− + 16 ATP → 2NH3 + H2 + 16ADP + 16 Pi
Catalysed by nitrogenase, a very complex enzyme!

48. N2 + 8H+ + 8e− + 16 ATP → 2NH3 + H2 + 16ADP + 16 Pi
Nitrogen fixation
N2 + 8H+ + 8e− + 16 ATP → 2NH3 + H2 + 16ADP + 16 Pi
Catalysed by nitrogenase, a very complex enzyme!
Also catalyzes many other reactions
Usually assayed by acetylene reduction

49. N2 + 8H+ + 8e− + 16 ATP → 2NH3 + H2 + 16ADP + 16 Pi
Nitrogen fixation
N2 + 8H+ + 8e− + 16 ATP → 2NH3 + H2 + 16ADP + 16 Pi
Usually assayed by acetylene reduction
Sequentially adds 2 H per cycle until reach NH3

50. Nitrogen fixation
Sequentially adds 2 H per cycle until
reach NH3
May then be exported to cytosol &
assimilated by GS/GOGAT or assimilated
inside bacteroid

51. Nitrogen fixation
Sequentially adds 2 H per cycle until
reach NH3
May then be exported to cytosol &
assimilated by GS/GOGAT or assimilated
inside bacteroid
Are then converted to amides or ureides
& exported to rest of plant in the xylem!

52. S assimilation
SO42- comes from weathering or from rain: now an important source!
Main cause of rain acid!

53. S assimilation
S is used in cysteine & methionine

54. S assimilation
S is used in cysteine & methionine
Also used in CoA, S-adenosylmethionine

55. S assimilation
S is used in cysteine & methionine
Also used in CoA, S-adenosylmethionine
Also used in sulphoquinovosyl-diacylglycerol

56. S assimilation
S is used in cysteine & methionine
Also used in CoA, S-adenosylmethionine
Also used in sulphoquinovosyl-diacylglycerol
And in many storage compounds: eg allicin (garlic)

57. S assimilation
SO42- comes from weathering or from rain: now an important source! Main thing that makes rain acid!
Some bacteria use SO42- as e- acceptor -> H2S

58. S assimilation
SO42- comes from weathering or from rain: now an important source! Main thing that makes rain acid!
Some bacteria use SO42- as e- acceptor -> H2S
Some photosynthetic bacteria use reduced S as e- donor!

59. S assimilation
SO42- comes from weathering or from rain: now an important source! Main thing that makes rain acid!
Some bacteria use SO42- as e- acceptor -> H2S
Some photosynthetic bacteria use reduced S as e- donor!
Now that acid rain has declined in N. Europe Brassica & wheat need S in many places

60. S assimilation
SO4 2- is taken up by roots &
transported to leaves in xylem
Most is reduced in cp

61. S assimilation
SO4 2- is taken up by roots &
transported to leaves in xylem
Most is reduced in cp
1. add SO4 2- to ATP -> APS

62. S assimilation
add SO4 2- to ATP -> APS
Transfer S to Glutathione -> S-sulfoglutathione

63. S assimilation
add SO4 2- to ATP -> APS
Transfer S to Glutathione -> S-sulfoglutathione
S-sulfoglutathione + GSH -> SO32- + GSSG

64. S assimilation
add SO4 2- to ATP -> APS
Transfer S to Glutathione -> S-sulfoglutathione
S-sulfoglutathione + GSH -> SO32- + GSSG
Sulfite + 6 Fd -> Sulfide

65. S assimilation
add SO4 2- to ATP -> APS
Transfer S to Glutathione -> S-sulfoglutathione
S-sulfoglutathione + GSH -> SO32- + GSSG
Sulfite + 6 Fd -> Sulfide
Sulfide + O-acetylserine -> cysteine + acetate
O-acetylserine was made from serine + acetyl-CoA

66. S assimilation
Most cysteine is converted to
glutathione or methionine

67. S assimilation
Most cysteine is converted to
glutathione or methionine
Glutathione is main form
exported

68. S assimilation
Most cysteine is converted to
glutathione or methionine
Glutathione is main form
exported
Also used to make many other
S-compounds

69. S assimilation
Most cysteine is converted to
glutathione or methionine
Glutathione is main form
exported
Also used to make many other
S-compounds
Methionine also has many uses
besides protein synthesis

70. S assimilation
Most cysteine is converted to glutathione or methionine
Cys + homoserine -> cystathione

71. S assimilation
Most cysteine is converted to glutathione or methionine
Cys + homoserine -> cystathione
Cystathione -> homocysteine + Pyruvate + NH4+

72. S assimilation
Most cysteine is converted to glutathione or methionine
Cys + homoserine -> cystathione
Cystathione -> homocysteine + Pyruvate + NH4+
Homocysteine + CH2=THF -> Met + THF
80% of met is converted to S-adenosylmethionine & used for biosyntheses

73. S assimilation
Most cysteine is converted to glutathione or methionine
Glutathione is made enzymatically!
Glutamate + Cysteine -> g-glutamyl cysteine

74. S assimilation
Glutathione (GluCysGly) is made enzymatically!
Glutamate + Cysteine -> g-glutamyl cysteine
g-glutamyl cysteine + glycine -> glutathionine

75. S assimilation
Glutathione (GluCysGly) is made enzymatically!
Glutamate + Cysteine -> g-glutamyl cysteine
g-glutamyl cysteine + glycine -> glutathionine
Glutathione is precursor for many chems, eg phytochelatins

76. S assimilation
Glutathione (GluCysGly) is made enzymatically!
Glutamate + Cysteine -> g-glutamyl cysteine
g-glutamyl cysteine + glycine -> glutathionine
Glutathione is precursor for many chemicals, eg phytochelatins
SAM & glutathione are also precursors for many cell wall components

77. Secondary Metabolites
1˚ metabolites are essential for growth & development
therefore present in all plants
2˚ metabolites “not” required for growth & development
therefore not present in all plants

78. 1˚ metabolites are essential for growth & development
Natural Products
1˚ metabolites are essential for growth & development
therefore present in all plants
2˚ metabolites “not” required for growth & development
therefore not present in all plants
Often only found
in one or a few spp.
capsaicin
Nepetalactone, menthol
Nepetalactone Menthol

79. Natural Products
1˚ metabolites are essential for growth & development
therefore present in all plants
2˚ metabolites “not” required for growth & development
therefore not present in all plants
Often only found
in one or a few spp.
Derived from 1˚
metabs

80. Natural Products
2˚ metabolites “not” required for growth & development
therefore not present in all plants
Often only found in one or a few spp.
Derived from 1˚ metabs,
can be hard to draw line

81. Natural Products
2˚ metabolites “not” required for growth & development
therefore not present in all plants
Often only found in one or a few spp.
Derived from 1˚ metabs, can be hard to draw line

82. Natural Products
2˚ metabolites not present in all plants
Often only found in one or a few spp.
Derived from 1˚ metabs, can be hard to draw line
Can be up to 3% of dry weight: very expensive to the the plant!

83. >100,000 types; tremendous variety of functions Defense Herbivores
Natural Products
>100,000 types; tremendous variety of functions
Defense
Herbivores
nicotine

84. >100,000 types; tremendous variety of functions Defense Herbivores
Natural Products
>100,000 types; tremendous variety of functions
Defense
Herbivores
Pathogens
Resveratrol
Brassilexin = antifungal
Berberine = antibacterial

85. >100,000 types; tremendous variety of functions Defense Herbivores
Natural Products
>100,000 types; tremendous variety of functions
Defense
Herbivores
Pathogens
Other plants
leptospermone
leptospermone

86. >100,000 types; tremendous variety of functions Defense Attractant
Natural Products
>100,000 types; tremendous variety of functions
Defense
Attractant
Pollinators
Odors
Colors
Limalool smells nice
Cyanidin colors blueberries, grapes, etc

87. Natural Products
>100,000 types; tremendous variety of functions
Defense
Attractant
Pollinators
Symbionts

88. Natural Products
>100,000 types; tremendous variety of functions
Defense
Attractant
Pollinators
Symbionts
Seed dispersers Methyl anthranilate(strawberries)
Pentyl butyrate (pears, apricots)

89. Natural Products
>100,000 types; tremendous variety of functions
Defense
Attractant
Pollinators
Symbionts
Seed dispersers
“protectors” (tritrophic interactions)

90. Natural Products
>100,000 types; tremendous variety of functions
Defense
Attractant
Protecting from UV

91. Natural Products
>100,000 types; tremendous variety of functions
Defense
Attractant
Protecting from UV
metal uptake and transport

92. Natural Products
>100,000 types; tremendous variety of functions
Defense
Attractant
Protecting from UV
metal uptake and transport
Hardening cell walls

93. Natural Products
>100,000 types; tremendous variety of functions
Some are made constitutively

94. Natural Products
>100,000 types; tremendous variety of functions
Some are made constitutively
Others are induced, especially defense compounds

95. Natural Products
>100,000 types; tremendous variety of functions
Some are made constitutively, others are induced
Made in many cellular locations
Cytoplasm: most hydrophilics

96. Natural Products
>100,000 types; tremendous variety of functions
Some are made constitutively, others are induced
Made in many cellular locations
Cytoplasm: most hydrophilics
Chloroplasts: terpenoids and some alkaloids

97. Natural Products
>100,000 types; tremendous variety of functions
Some are made constitutively, others are induced
Made in many cellular locations
Cytoplasm: most hydrophilics
Chloroplasts: terpenoids and some alkaloids
Mitochondria: some alkaloids and some amines

98. Natural Products
>100,000 types; tremendous variety of functions
Some are made constitutively, others are induced
Made in many cellular locations
Cytoplasm: most hydrophilics
Chloroplasts: terpenoids and
some alkaloids
Mitochondria: some alkaloids
and some amines
Peroxisomes: some terpenoids,
convert glucosinolates to active
form upon pathogen attack

99. Natural Products
>100,000 types; tremendous variety of functions
Some are made constitutively, others are induced
Made in many cellular locations
Cytoplasm: most hydrophilics
Chloroplasts: terpenoids and some alkaloids
Mitochondria: some alkaloids and some amines
Peroxisomes: some terpenoids, convert glucosinolates to active form upon pathogen attack
Endoplasmic reticulum: fatty acid derivatives, other nonpolars

100. Natural Products
>100,000 types; tremendous variety of functions
Made in many cellular locations
Made in many cell types
Some in all

101. Natural Products
>100,000 types; tremendous variety of functions
Made in many cellular locations
Made in many cell types
Some in all
Others in specialized cells or tissues

102. Natural Products
>100,000 types; tremendous variety of functions
Made in many cellular locations
Made in many cell types
Some in all
Others in specialized cells or tissues
Some are transported in xylem or phloem from site of synthesis to where they are stored

103. Natural Products
>100,000 types; tremendous variety of functions
Made in many cellular locations
Made in many cell types
Many are stored in vacuole

104. Natural Products
>100,000 types; tremendous variety of functions
Made in many cellular locations
Made in many cell types
Many are stored in vacuole
Others in plastids or ER

105. Natural Products
>100,000 types; tremendous variety of functions
Made in many cellular locations
Made in many cell types
Some are stored in special cell types, eg trichomes

106. >100,000 types; tremendous variety of functions
Natural Products
>100,000 types; tremendous variety of functions
Made in many cellular locations
Made in many cell types
Some are stored in special cell types
Others in special cavities or ducts
Left = lemon secretory cavity
Right = pine resin duct
Secretory cavity in lemon Pine resin duct

107. >100,000 types; tremendous variety of functions
Natural Products
>100,000 types; tremendous variety of functions
Made in many cellular locations
Made in many cell types
Some are stored in special cell types
Others in special cavities or ducts
Others in flowers, leaves or fruits
Left = lemon secretory cavity
Right = pine resin duct

108. Natural Products
>100,000 types; 3 main groups
Terpenoids
Alkaloids
Phenolics