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

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 Plant Development Plants use light as food and information Use information to control development

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

Light regulation of growth 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

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

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

Types of Phytochrome Responses 3 classes based on fluence (amount of light needed) VLF:induced by 0.1 nmol/m-2 , saturate @ 50nmol/m-2 2. LF: induced by 1 µmol/m-2, saturate @ 1000 µmol/m-2 3. HIR: require prolonged exposure to higher fluence Effect is proportional to Fluence

Types of Phytochrome Responses 3 classes based on fluence (amount of light needed) VLF:induced by 0.1 nmol/m-2 , saturate @ 50nmol/m-2 2. LF: induced by 1 µmol/m-2, saturate @ 1000 µmol/m-2 3. HIR: require prolonged exposure to higher fluence Different responses = Different phytochromes: 3 in rice, 5 in Arabidopsis

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

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"

Phytochrome Pr has cis-chromophore

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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!

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

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

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

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

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

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

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

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

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

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!

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

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

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

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)

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

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

Blue Light Responses Circadian Rhythms

Blue Light Responses Circadian Rhythms Solar tracking

Blue Light Responses Circadian Rhythms Solar tracking Phototropism

Blue Light Responses Circadian Rhythms Solar tracking Phototropism Inhibiting stem elongation

Blue Light Responses Circadian Rhythms Solar tracking Phototropism Inhibiting stem elongation Chloroplast movement

Blue Light Responses Circadian Rhythms Solar tracking Phototropism Inhibiting stem elongation Chloroplast movement Stomatal opening

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

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

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

Blue Light Responses Circadian Rhythms Solar tracking Phototropism Inhibiting stem elongation Chloroplast movement Stomatal opening Gene expression Flowering in Arabidopsis Responses vary in their fluence requirements & lag times

Blue Light Responses Responses vary in their fluence requirements & lag time Stomatal opening is reversible by green light; others aren’t

Blue Light Responses 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 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

Blue Light Responses 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 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 Cryptochromes repress hypocotyl elongation

Blue Light Responses Cryptochromes repress hypocotyl elongation Stimulate flowering

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

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)

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

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

Blue Light Responses 3 CRY genes CRY1 & CRY2 kinase proteins after absorbing blue CRY3 repairs mt & cp DNA!

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

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

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

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

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

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

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

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!

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!

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 LOV1 (light-O2-voltage) and LOV2 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 LOV1 (light-O2-voltage) and LOV2 repeats LOV1 & LOV2 bind FlavinMonoNucleotide 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 LOV1 (light-O2-voltage) and LOV2 repeats LOV1 & LOV2 bind FlavinMonoNucleotide 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 PHOT2 mediates HIR

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

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

Phototropins 2nd 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 2nd 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 2nd 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 PHOT1 &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 PHOT1 &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 PHOT1 &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 PHOT1 &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!