Plant biofuel related

1

• Plant biofuel related
• Novel biofuel
• Novel ways to enhance biofuel production
• Biophotovoltaics
• Photosynthesis related
• Enhancing light harvesting
• Enhancing carbon capture
• Carboxysomes in higher plants
• Carbonic anhydrase
• C4 rice
• Plant biotechnology related
• Plantibodies
• Other useful products made in plants
• Bioremediation
• Heavy metals
• Pesticides

2

• Agriculture related
• Improving nutritional value by GMO or
  wide-breeding
• Vitamins
• Essential amino acids
• Iron
• Other nutrients
• Reducing fertilizer needs
• Selecting for water-use efficiency
• Selecting for efficiency of other nutrients
• Moving N-fixation to other species
• Improving mycorrhizae
• GMO for weed and pest control
• Round-up resistance
• BT toxin
• Treating viruses, viroids, etc by GMO

3

• Light regulation of growth
• Plants sense
• Light quantity
• Light quality (colors)
• Light duration
• Direction it comes from
• Have photoreceptors
• that sense specific
• wavelengths

4
Blue Light Responses Circadian Rhythms Solar
tracking Phototropism Inhibiting stem
elongation Chloroplast movement Stomatal
opening Gene expression Flowering in Arabidopsis
5
Blue Light Responses Responses vary in their
fluence requirements lag time Stomatal opening
is reversible by green light others
arent Multiple blue receptors with different
functions!
6
Blue Light Responses Responses vary in their
fluence requirements lag time Stomatal opening
is reversible by green light others
arent Multiple blue receptors with different
functions! Identified by mutants, then clone the
gene and identify the protein
7
Blue Light Responses Cryptochromes repress
hypocotyl elongation Stimulate flowering Set the
circadian clock (in humans, too!) Stimulate
anthocyanin synthesis
8
Blue Light Responses Cryptochromes repress
hypocotyl elongation Stimulate flowering Set the
circadian clock (in humans, too!) Stimulate
anthocyanin synthesis 3 CRY genes
9
Blue Light Responses 3 CRY genes All have same
basic structure Photolyase-like domain binds FAD
and a pterin (MTHF) that absorbs blue transfers
energy to FAD in photolyase (an enzyme that uses
light energy to repair pyr dimers) DAS binds COP1
has nuclear localization signals CRY1 CRY2
kinase proteins after absorbing blue
10
Blue Light Responses 3 CRY genes CRY1 CRY2
kinase proteins after absorbing blue CRY3 repairs
mt cp DNA!
11

• Blue Light Responses
• 3 CRY genes
• CRY1 regulates blue effects on growth
  light-stable
• Triggers rapid changes in PM potential growth

12

• Blue Light Responses
• 3 CRY genes
• CRY1 regulates blue effects on growth
  light-stable
• Triggers rapid changes in PM potential growth
• Opens anion channels in PM

13

• Blue Light Responses
• 3 CRY genes
• CRY1 regulates blue effects on growth
  light-stable
• Triggers rapid changes in PM potential growth
• Opens anion channels in PM
• Stimulates anthocyanin synthesis

14

• Blue Light Responses
• 3 CRY genes
• CRY1 regulates blue effects on growth
  light-stable
• Triggers rapid changes in PM potential growth
• Opens anion channels in PM
• Stimulates anthocyanin synthesis
• Entrains the circadian clock

15

• Blue Light Responses
• 3 CRY genes
• CRY1 regulates blue effects on growth
  light-stable
• Triggers rapid changes in PM potential growth
• Opens anion channels in PM
• Stimulates anthocyanin synthesis
• Entrains the circadian clock
• Also accumulates in nucleus interacts with PHY
  COP1 to regulate photomorphogenesis, probably
  by kinasing substrates

16

• Blue Light Responses
• 3 CRY genes
• CRY1 regulates blue effects on growth
  light-stable
• Triggers rapid changes in PM potential growth
• Opens anion channels in PM
• Stimulates anthocyanin synthesis
• Entrains the circadian clock
• Also accumulates in nucleus interacts with PHY
  COP1 to regulate photomorphogenesis, probably
  by kinasing substrates
• 2. CRY2 controls flowering

17

• Blue Light Responses
• 3 CRY genes
• CRY1 regulates blue effects on growth
  light-stable
• 2. CRY2 controls flowering little effect on
  other processes
• Light-labile

18

• Blue Light Responses
• 3 CRY genes
• CRY1 regulates blue effects on growth
  light-stable
• 2. CRY2 controls flowering little effect on
  other processes
• Light-labile
• 3. CRY3 enters cp mito, where binds repairs
  DNA!

19

• Blue Light Responses
• 3 CRY genes
• CRY1 regulates blue effects on growth
• 2. CRY2 controls flowering little effect on
  other processes
• CRY3 enters cp mito, where binds repairs DNA!
• Cryptochromes are not
• involved in phototropism or
• stomatal opening!

20

• Blue Light Responses
• Cryptochromes are not involved in phototropism or
• stomatal opening!
• Phototropins are!

21

• Blue Light Responses
• Phototropins are involved in phototropism
  stomatal opening!
• Many names (nph, phot, rpt) since found by
  several different mutant screens

22

• Phototropins
• Many names (nph, phot, rpt) since found by
  several different mutant screens
• Mediate blue light-induced growth enhancements

23

• Phototropins
• Many names (nph, phot, rpt) since found by
  several different mutant screens
• Mediate blue light-induced growth enhancement
  blue light-dependent activation of the plasma
  membrane H-ATPase in guard cells

24

• Phototropins
• Many names (nph, phot, rpt) since found by
  several different mutant screens
• Mediate blue light-induced growth enhancement
  blue light-dependent activation of the plasma
  membrane H-ATPase in guard cells
• Contain light-activated serine-threonine kinase
  domain and LOV1 (light-O2-voltage) and LOV2
  repeats

25

• Phototropins
• Many names (nph, phot, rpt) since found by
  several different mutant screens
• Mediate blue light-induced growth enhancement
  blue light-dependent activation of the plasma
  membrane H-ATPase in guard cells
• Contain light-activated serine-threonine kinase
  domain and LOV1 (light-O2-voltage) and LOV2
  repeats
• LOV1 LOV2 bind FlavinMonoNucleotide cofactors

26

• Phototropins
• Many names (nph, phot, rpt) since found by
  several different mutant screens
• Mediate blue light-induced growth enhancement
  blue light-dependent activation of the plasma
  membrane H-ATPase in guard cells
• Contain light-activated serine-threonine kinase
  domain and LOV1 (light-O2-voltage) and LOV2
  repeats
• LOV1 LOV2 bind FlavinMonoNucleotide cofactors
• After absorbing blue rapidly autophosphorylate
  kinase other proteins

27

• Phototropins
• After absorbing blue rapidly autophosphorylate
  kinase other proteins
• 1 result phototropism
• due to uneven auxin
• transport

28

• Phototropins
• After absorbing blue rapidly autophosphorylate
  kinase other proteins
• 1 result phototropism
• due to uneven auxin
• transport
• Send more to side away
• from light!

29

• Phototropins
• After absorbing blue rapidly autophosphorylate
  kinase other proteins
• 1 result phototropism
• due to uneven auxin
• transport
• Send more to side away
• from light!
• Phot 1 mediates LF

30

• Phototropins
• After absorbing blue rapidly autophosphorylate
  kinase other proteins
• 1 result phototropism
• due to uneven auxin
• transport
• Send more to side away
• from light!
• PHOT 1 mediates LF
• PHOT2 mediates HIR

31

• Phototropins
• 2nd result stomatal opening via stimulation of
  guard cell PM proton pump
• Also requires photosynthesis by guard cells!

32

• Phototropins
• 2nd result stomatal opening via stimulation of
  guard cell PM proton pump
• Also requires photosynthesis by guard cells
  signaling from xanthophylls

33

• Phototropins
• 2nd result stomatal opening via stimulation of
  guard cell PM proton pump
• Also requires photosynthesis by guard cells
  signaling from xanthophylls
• npq mutants dont
• make zeaxanthin
• lack specific blue
• response

34

• Phototropins
• 2nd result stomatal opening via stimulation of
  guard cell PM proton pump
• Also requires photosynthesis by guard cells
  signaling from xanthophylls
• npq mutants dont
• make zeaxanthin
• lack specific blue
• response
• Basic idea open when pump in K

35

• Phototropins
• 2nd result stomatal opening via stimulation of
  guard cell PM proton pump
• Also requires photosynthesis by guard cells
  signaling from xanthophylls
• npq mutants dont
• make zeaxanthin
• lack specific blue
• response
• Basic idea open when pump in K
• Close when pump out K

36

• Phototropins
• Basic idea open when pump in K
• Close when pump out K
• Control is hideously complicated!

37

• Phototropins
• Basic idea open when pump in K
• Close when pump out K
• Control is hideously complicated!
• Mainly controlled by blue light

38

• Phototropins
• Basic idea open when pump in K
• Close when pump out K
• Control is hideously complicated!
• Mainly controlled by blue light, but red also
  plays role

39

• Phototropins
• Basic idea open when pump in K
• Close when pump out K
• Control is hideously complicated!
• Mainly controlled by blue light,
• but red also plays role
• Light intensity is also important

40

• Phototropins
• Mainly controlled by blue light, but red also
  plays role
• Light intensity is also important due to effect
  on
• photosynthate in guard cells

41

• Phototropins
• Mainly controlled by blue light, but red also
  plays role
• Light intensity is also important due to effect
  on
• photosynthate in guard cells
• PHOT1 2 also help

42

• Phototropins
• Mainly controlled by blue light, but red also
  plays role
• Light intensity is also important due to effect
  on
• photosynthate in guard cells
• PHOT1 2 also help
• Main GC blue
• receptor is zeaxanthin!

43

• Phototropins
• Mainly controlled by blue light, but red also
  plays role
• Light intensity is also important due to effect
  on
• photosynthate in guard cells
• PHOT1 2 also help
• Main GC blue
• receptor is zeaxanthin!
• Reason for green reversal

44

• Phototropins
• Mainly controlled by blue light, but red also
  plays role
• Light intensity is also important due to effect
  on
• photosynthate in guard cells
• PHOT1 2 also help
• Main GC blue
• receptor is zeaxanthin!
• Reason for green reversal
• water stress overrides light!

45

• Phototropins
• water stress overrides light roots make Abscisic
  Acid closes stomates blocks opening regardless
  of other signals!

46

• UV-B perception
• Plants also use UV-B to control development

47

• UV-B perception
• Plants also use UV-B to
• control development

48

• UV-B perception
• Plants also use UV-B to
• control development

49

• UV-B perception
• Plants also use UV-B to control development
• Absorbed by UVR8 goes from inactive dimer to
  active monomer

50

• UV-B perception
• Plants also use UV-B to control development
• Absorbed by UVR8 goes from inactive dimer to
  active monomer
• ve regulators COP1 HY5

51

• UV-B perception
• Plants also use UV-B to control development
• Absorbed by UVR8 goes from inactive dimer to
  active monomer
• ve regulators COP1 HY5
• -ve regulators
• RUP1 RUP2

52

• Growth regulators
• Auxins
• Cytokinins
• Gibberellins
• Abscisic acid
• Ethylene
• Brassinosteroids
• All are small
• organics made in
• one part, affect
• another part

53

• Growth regulators
• All are small organics made in one part, affect
  another part
• Treating a plant tissue with a hormone is like
  putting a dime in a vending machine. It depends
  on the machine, not the dime!

54
Auxin First studied by Darwins! Showed that a
"transmissible influence" made at tips caused
bending lower down
55
Auxin First studied by Darwins! Showed that a
"transmissible influence" made at tips caused
bending lower down No tip, no curve!
56
Auxin First studied by Darwins! Showed that a
"transmissible influence" made at tips caused
bending lower down No tip, no curve! 1913Boysen-J
ensen showed that diffused through agar blocks
but not through mica
57
Auxin 1913Boysen-Jensen showed that diffused
through agar blocks but not through mica 1919
Paal showed that if tip was replaced
asymmetrically, plant grew asymmetrically even in
dark
58
Auxin 1913Boysen-Jensen showed that diffused
through agar blocks but not through mica 1919
Paal showed that if tip was replaced
asymmetrically, plant grew asymmetrically even in
dark Uneven amounts of "transmissible influence"
makes bend
59
Auxin 1919 Paal showed that if tip was replaced
asymmetrically, plant grew asymmetrically even in
dark Uneven amounts of "transmissible influence"
makes bend 1926 Went showed that a chemical that
diffused from tips into blocks caused growth
60
Auxin 1919 Paal showed that if tip was replaced
asymmetrically, plant grew asymmetrically even in
dark Uneven amounts of "transmissible influence"
makes bend 1926 Went showed that a chemical that
diffused from tips into blocks caused growth If
placed asymmetrically get bending due to
asymmetrical growth
61
Auxin 1919 Paal showed that if tip was replaced
asymmetrically, plant grew asymmetrically even in
dark Uneven amounts of "transmissible influence"
makes bend 1926 Went showed that a chemical that
diffused from tips into blocks caused growth If
placed asymmetrically get bending due to
asymmetrical growth Amount of bending depends on
auxin
62
Auxin 1919 Paal showed that if tip was replaced
asymmetrically, plant grew asymmetrically even in
dark Uneven amounts of "transmissible influence"
makes bend 1926 Went showed that a chemical that
diffused from tips into blocks caused growth If
placed asymmetrically get bending due to
asymmetrical growth Amount of bending depends on
auxin 1934 Indole-3-Acetic acid (IAA) from the
urine of pregnant women was shown to cause
bending
63
Auxin 1934 Indole-3-Acetic acid (IAA) from the
urine of pregnant women was shown to cause
bending IAA is the main auxin in vivo. Others
include Indole-3-butyric acid (IBA),
4-Chloroindole-3-acetic acid and phenylacetic
acid (PA)
IAA
IBA
PA
4-CI-IAA
64
Auxin IAA is the main auxin in vivo. Many
synthetic auxins have been identified
IAA
65
Auxin IAA is the main auxin in vivo. Many
synthetic auxins have been identified No obvious
structural similarity, yet all work!
IAA
66
Auxin IAA is the main auxin in vivo. Many
synthetic auxins have been identified No obvious
structural similarity, yet all work! Widely used
in agriculture
IAA
67

• Auxin
• IAA is the main auxin in vivo.
• Many synthetic auxins have been identified
• No obvious structural similarity, yet all work!
• Widely used in agriculture
• to promote growth (flowering, cuttings)

IAA
68

• Auxin
• IAA is the main auxin in vivo.
• Many synthetic auxins have been identified
• No obvious structural similarity, yet all work!
• Widely used in agriculture
• to promote growth (flowering, cuttings)
• as weed killers!
• Agent orange was 11
• 2,4-D and 2,4,5-T

IAA
69

• Auxin
• weed killers!
• Agent orange was 11
• 2,4-D and 2,4,5-T
• 2,4,5-T was contaminated
• with dioxin, a carcinogen

IAA
70

• Auxin
• weed killers!
• Agent orange was 11
• 2,4-D and 2,4,5-T
• 2,4,5-T was contaminated
• with dioxin, a carcinogen
• 2,4-D is still widely used
• selectively kills dicots

IAA
71

• Auxin
• weed killers!
• 2,4-D is still widely used selectively kills
  dicots
• Controls weeds in monocot crops
• (corn, rice, wheat)
• Mech unclear may cause excess ethylene
• or ABA production.

IAA
72

• Auxin
• weed killers!
• 2,4-D is still widely used selectively kills
  dicots
• Controls weeds in monocot crops
• (corn, rice, wheat)
• Mech unclear may cause excess ethylene
• or ABA production.

IAA
73
Auxin gt90of IAA is conjugated to sugars in vivo!
74
Auxin gt90of IAA is conjugated to sugars in
vivo! Inactive, but readily activated!
75
Auxin gt90of IAA is conjugated to sugars in
vivo! Inactive, but readily activated! Best way
to measure auxin is bioassay!
76
Auxin gt90of IAA is conjugated to sugars in
vivo! Inactive, but readily activated! Best way
to measure auxin is bioassay! Critical
concentration varies between tissues
77
Auxin gt90of IAA is conjugated to sugars in
vivo! Inactive, but readily activated! Best way
to measure auxin is bioassay! Critical
concentration varies between tissues Roots are
much more sensitive than leaves!
78
Auxin Critical concentration varies between
tissues Roots are much more sensitive than
leaves! Made in leaves transported to roots so
IAA decreases going down the plant Most cells
are IAA sinks!
79
Auxin Synthesis Made in leaves transported to
roots so IAA decreases going down the
plant Most is made from trp
80
Auxin Synthesis Most is made from trp Also made
by trp-independent pathway exits before trp
81
Auxin Synthesis Most is made from trp Also made
by trp-independent pathway exits before trp Path
used varies between tissues
82
Auxin Synthesis Most is made from trp Also made
by trp-independent pathway exits before trp Path
used varies between tissues No way to run out of
IAA
83
Auxin Levels No way to run out of IAA! IAA
depends on metabolism
84
Auxin Levels No way to run out of IAA! IAA
depends on metabolism Most cells are IAA sinks!
85
Auxin Levels No way to run out of IAA! IAA
depends on metabolism Most cells are IAA sinks!
IAA is made at shoot apex transported down
basipetal
86
Auxin Levels No way to run out of IAA! IAA
depends on metabolism Most cells are IAA sinks!
IAA is made at shoot apex transported down
basipetal IAA transport therefore affects growth
development
87
Auxin Transport IAA transport therefore affects
growth development is polar and basipetal New
roots form at base of stem even if stored
upside-down
88
Auxin Transport IAA transport therefore affects
development is polar and basipetal. New roots
form at base of stem even if stored
upside-down. Stem sections only move IAA
basipetally