Plant biofuel related Novel biofuel Novel ways to

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 • C 4 rice Plant biotechnology related • Plantibodies • Other useful products made in plants • Bioremediation • Heavy metals • Pesticides

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

Light regulation of growth Plants sense 1. Light quantity 2. Light quality (colors) 3. Light duration 4. Direction it comes from Have photoreceptors that sense specific wavelengths

Blue Light Responses Circadian Rhythms Solar tracking Phototropism Inhibiting stem elongation Chloroplast movement Stomatal opening Gene expression Flowering in Arabidopsis

Blue Light Responses vary in their fluence requirements & lag time Stomatal opening is reversible by green light; others aren’t Multiple blue receptors with different functions!

Blue Light Responses vary in their fluence requirements & lag time Stomatal opening is reversible by green light; others aren’t Multiple blue receptors with different functions! Identified by mutants, then clone the gene and identify the protein

Blue Light Responses Cryptochromes repress hypocotyl elongation Stimulate flowering Set the circadian clock (in humans, too!) Stimulate anthocyanin synthesis

Blue Light Responses Cryptochromes repress hypocotyl elongation Stimulate flowering Set the circadian clock (in humans, too!) Stimulate anthocyanin synthesis 3 CRY genes

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 COP 1 & has nuclear localization signals CRY 1 & CRY 2 kinase proteins after absorbing blue

Blue Light Responses 3 CRY genes CRY 1 & CRY 2 kinase proteins after absorbing blue CRY 3 repairs mt & cp DNA!

Blue Light Responses 3 CRY genes 1. CRY 1 regulates blue effects on growth: light-stable • Triggers rapid changes in PM potential & growth

Blue Light Responses 3 CRY genes 1. CRY 1 regulates blue effects on growth: light-stable • Triggers rapid changes in PM potential & growth • Opens anion channels in PM

Blue Light Responses 3 CRY genes 1. CRY 1 regulates blue effects on growth: light-stable • Triggers rapid changes in PM potential & growth • Opens anion channels in PM • Stimulates anthocyanin synthesis

Blue Light Responses 3 CRY genes 1. CRY 1 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

Blue Light Responses 3 CRY genes 1. CRY 1 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 & COP 1 to regulate photomorphogenesis, probably by kinasing substrates

Blue Light Responses 3 CRY genes 1. CRY 1 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 & COP 1 to regulate photomorphogenesis, probably by kinasing substrates 2. CRY 2 controls flowering

Blue Light Responses 3 CRY genes 1. CRY 1 regulates blue effects on growth: light-stable 2. CRY 2 controls flowering: little effect on other processes • Light-labile

Blue Light Responses 3 CRY genes 1. CRY 1 regulates blue effects on growth: light-stable 2. CRY 2 controls flowering: little effect on other processes • Light-labile 3. CRY 3 enters cp & mito, where binds & repairs DNA!

Blue Light Responses 3 CRY genes 1. CRY 1 regulates blue effects on growth 2. CRY 2 controls flowering: little effect on other processes 3. CRY 3 enters cp & mito, where binds & repairs DNA! Cryptochromes are not involved in phototropism or stomatal opening!

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

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

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

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

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 LOV 1 (light-O 2 -voltage) and LOV 2 repeats

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 LOV 1 (light-O 2 -voltage) and LOV 2 repeats LOV 1 & LOV 2 bind Flavin. Mono. Nucleotide cofactors

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 LOV 1 (light-O 2 -voltage) and LOV 2 repeats LOV 1 & LOV 2 bind Flavin. Mono. Nucleotide cofactors After absorbing blue rapidly autophosphorylate & kinase other proteins

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

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

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

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 PHOT 2 mediates HIR

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

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

Phototropins 2 nd result = stomatal opening via stimulation of guard cell PM proton pump Also requires photosynthesis by guard cells & signaling from xanthophylls npq mutants don’t make zeaxanthin & lack specific blue response

Phototropins 2 nd result = stomatal opening via stimulation of guard cell PM proton pump Also requires photosynthesis by guard cells & signaling from xanthophylls npq mutants don’t make zeaxanthin & lack specific blue response Basic idea: open when pump in K+

Phototropins 2 nd result = stomatal opening via stimulation of guard cell PM proton pump Also requires photosynthesis by guard cells & signaling from xanthophylls npq mutants don’t make zeaxanthin & lack specific blue response Basic idea: open when pump in K+ Close when pump out K+

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

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

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

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

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

Phototropins Mainly controlled by blue light, but red also plays role Light intensity is also important due to effect on [photosynthate] in guard cells PHOT 1 &2 also help

Phototropins Mainly controlled by blue light, but red also plays role Light intensity is also important due to effect on [photosynthate] in guard cells PHOT 1 &2 also help Main GC blue receptor is zeaxanthin!

Phototropins Mainly controlled by blue light, but red also plays role Light intensity is also important due to effect on [photosynthate] in guard cells PHOT 1 &2 also help Main GC blue receptor is zeaxanthin! Reason for green reversal

Phototropins Mainly controlled by blue light, but red also plays role Light intensity is also important due to effect on [photosynthate] in guard cells PHOT 1 &2 also help Main GC blue receptor is zeaxanthin! Reason for green reversal water stress overrides light!

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

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

UV-B perception Plants also use UV-B to control development Absorbed by UVR 8: goes from inactive dimer to active monomer

UV-B perception Plants also use UV-B to control development Absorbed by UVR 8: goes from inactive dimer to active monomer +ve regulators = COP 1 & HY 5

UV-B perception Plants also use UV-B to control development Absorbed by UVR 8: goes from inactive dimer to active monomer +ve regulators = COP 1 & HY 5 -ve regulators = RUP 1 & RUP 2

Growth regulators 1. Auxins 2. Cytokinins 3. Gibberellins 4. Abscisic acid 5. Ethylene 6. Brassinosteroids All are small organics: made in one part, affect another part

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!

Auxin First studied by Darwins! Showed that a "transmissible influence" made at tips caused bending lower down

Auxin First studied by Darwins! Showed that a "transmissible influence" made at tips caused bending lower down No tip, no curve!

Auxin First studied by Darwins! Showed that a "transmissible influence" made at tips caused bending lower down No tip, no curve! 1913: Boysen-Jensen showed that diffused through agar blocks but not through mica

Auxin 1913: Boysen-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

Auxin 1913: Boysen-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

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

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

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]

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

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 4 -CI-IAA IBA PA

Auxin IAA is the main auxin in vivo. Many synthetic auxins have been identified IAA

Auxin IAA is the main auxin in vivo. Many synthetic auxins have been identified No obvious structural similarity, yet all work!

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

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

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 1: 1 2, 4 -D and 2, 4, 5 -T

Auxin weed killers! Agent orange was 1: 1 2, 4 -D and 2, 4, 5 -T was contaminated with dioxin, a carcinogen IAA

Auxin weed killers! Agent orange was 1: 1 2, 4 -D and 2, 4, 5 -T was contaminated with dioxin, a carcinogen 2, 4 -D is still widely used: selectively kills dicots IAA

Auxin IAA 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.

Auxin >90%of IAA is conjugated to sugars in vivo!

Auxin >90%of IAA is conjugated to sugars in vivo! Inactive, but readily activated!

Auxin >90%of IAA is conjugated to sugars in vivo! Inactive, but readily activated! Best way to measure [auxin] is bioassay!

Auxin >90%of IAA is conjugated to sugars in vivo! Inactive, but readily activated! Best way to measure [auxin] is bioassay! Critical concentration varies between tissues

Auxin >90%of 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!

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!

Auxin Synthesis Made in leaves & transported to roots so [IAA] decreases going down the plant Most is made from trp

Auxin Synthesis Most is made from trp Also made by trp-independent pathway: exits before trp

Auxin Synthesis Most is made from trp Also made by trp-independent pathway: exits before trp Path used varies between tissues

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

Auxin Levels No way to run out of IAA! [IAA] depends on metabolism

Auxin Levels No way to run out of IAA! [IAA] depends on metabolism Most cells are IAA sinks!

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

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

Auxin Transport IAA transport therefore affects growth & development is polar and basipetal: New roots form at base of stem even if stored upside-down

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