http://www.timesleader.com/stories/Report-Warming-bringing-big-changes-to-forests,2602821.Arabidopsis2.Fast plant3. Sorghum4. Brachypodium distachyon5. Amaranthus (C4 dicot)6. Quinoa7. Kalanchoe8. Venus fly traps9. C3 vs C4 Atriplex10. C3 vs C4 Flaveria11. C3 vs C4 Panicum12. P. oleracea C4-CAM 13. P. afra C3-CAM 14. M. crystallinum C3-CAM

Transition to FloweringAdults are competent to flower, but need correct signalsVery complex process!Can be affected by:• Daylength• T (esp Cold)• Water stress• Nutrition• Hormones• Age

Light regulation of Plant DevelopmentLight regulation of Plant Development•GerminationGermination•MorphogenesisMorphogenesis•Sun/shade & shade avoidanceSun/shade & shade avoidance•FloweringFlowering•SenescenceSenescence

Light regulation of growthPlants sense1. Light quantity2. Light quality (colors)3. Light duration4. Direction it comes from

PhytochromeDarwin showed blue works best for phototropismRed light (666 nm) promotes germinationFar red light (>700 nm) blocks germinationAfter alternate R/FR color of final flash decides outcomeSeeds don't want to germinate in the shade!

Pigment is photoreversible

PhytochromeRed light (666 nm) promotes germinationFar red light (730 nm) blocks germinationAfter alternate R/FR color of final flash decides outcomePigment is photoreversible! -> helped purify it!Looked for pigment that absorbs first at 666 nm, then 730

PhytochromeRed light (666 nm) promotes germinationFar red light (730 nm) blocks germinationAfter alternate R/FR color of final flash decides outcomePigment is photoreversible! -> helped purify it!Looked for pigment that absorbs first at 666 nm, then 730

PhytochromeRed light (666 nm) promotes germinationFar red light (730 nm) blocks germinationAfter alternate R/FR color of final flash decides outcomePigment is photoreversible! -> helped purify it!Looked for pigment that absorbs first at 666 nm, then 730Made as inactive cytoplasmic Pr that absorbs at 666 nm

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

PhytochromeMade 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

PhytochromeMade 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 lightAlso slowly reverts in dark

PhytochromeMade 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 lightAlso slowly reverts in dark: how plants sense night length

Types of Phytochrome ResponsesTwo categories based on speed1. Rapid biochemical events2. Morphological changes

Types of Phytochrome ResponsesTwo categories based on speed1. Rapid biochemical events2. Morphological changes Lag time also varies from minutes to weeks

Types of Phytochrome ResponsesTwo categories based on speed1. Rapid biochemical events2. Morphological changes Lag time also varies from minutes to weeks: numbers of

steps after Pfr vary

Types of Phytochrome ResponsesLag 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

Types of Phytochrome ResponsesLag 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 jobConclusions: phytochrome acts on many processes in

many ways

Types of Phytochrome ResponsesTwo categories based on speed3 classes based on fluence (amount of light needed)1. VLF:induced by 0.1 nmol/m-2 , saturate @ 50nmol/m-2

Types of Phytochrome ResponsesTwo categories based on speed3 classes based on fluence (amount of light needed)1. VLF:induced by 0.1 nmol/m-2 , saturate @ 50nmol/m-2

• Changes 0.02% of Pr to Pfr

Types of Phytochrome Responses3 classes based on fluence (amount of light needed)1. VLF:induced by 0.1 nmol/m-2 , saturate @ 50nmol/m-2

• Changes 0.02% of Pr to Pfr• Are not FR-reversible!

Types of Phytochrome Responses3 classes based on fluence (amount of light needed)1. VLF:induced by 0.1 nmol/m-2 , saturate @ 50nmol/m-2

• Changes 0.02% of Pr to Pfr• Are not FR-reversible! But action spectrum same as Pr

Types of Phytochrome Responses3 classes based on fluence (amount of light needed)1. VLF:induced by 0.1 nmol/m-2 , saturate @ 50nmol/m-2

• Changes 0.02% of Pr to Pfr• Are not FR-reversible! But action spectrum same as Pr• Induced by FR!

Types of Phytochrome Responses3 classes based on fluence (amount of light needed)1. VLF:induced by 0.1 nmol/m-2 , saturate @ 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

Types of Phytochrome Responses3 classes based on fluence (amount of light needed)1. VLF:induced by 0.1 nmol/m-2 , saturate @ 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 secExamples: Cab gene induction, oat coleoptile growth

Types of Phytochrome Responses3 classes based on fluence (amount of light needed)1. VLF:induced by 0.1 nmol/m-2 , saturate @ 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 secExamples: Cab gene induction, oat coleoptile growth2. LF: induced by 1 µmol/m-2, saturate @ 1000 µmol/m-2

Types of Phytochrome Responses3 classes based on fluence (amount of light needed)1. 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

Are FR-reversible!

Types of Phytochrome Responses3 classes based on fluence (amount of light needed)1. 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

Are FR-reversible! Need > 3% Pfr

Types of Phytochrome Responses3 classes based on fluence (amount of light needed)1. 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

Are FR-reversible! Need > 3% PfrObey law of reciprocity

Types of Phytochrome Responses3 classes based on fluence (amount of light needed)1. 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

Are FR-reversible! Need > 3% PfrObey law of reciprocityExamples : Lettuce seedgermination, mustardphotomorphogenesis, inhibits flowering in SDP

Types of Phytochrome Responses3 classes based on fluence (amount of light needed)1. 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

Are FR-reversible! Need > 3% PfrObey law of reciprocityExamples : Lettuce seedGermination, mustardphotomorphogenesis, inhibits flowering in SDP3. HIR: require prolonged exposure to higher fluence

Types of Phytochrome Responses3 classes based on fluence (amount of light needed)1. 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 fluenceEffect is proportional to Fluence

Types of Phytochrome Responses3 classes based on fluence (amount of light needed)1. 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 fluenceEffect is proportional to FluenceDisobey law of reciprocityAre not FR-reversible!

Types of Phytochrome Responses3 classes based on fluence (amount of light needed)1. 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 fluenceEffect is proportional to fluenceDisobey law of reciprocityAre not FR-reversible!Some are induced by FR!

Types of Phytochrome Responses3 classes based on fluence (amount of light needed)1. 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 fluenceEffect is proportional to fluenceDisobey law of reciprocityAre not FR-reversible!Some are induced by FR!Examples: inhibition of hypocotyl elongation in many seedlings, anthocyanin synthesis

Types of Phytochrome Responses3 classes based on fluence (amount of light needed)1. 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 fluenceEffect is proportional to fluenceDisobey law of reciprocityAre not FR-reversible!Some are induced by FR!Examples: inhibition of hypocotyl elongation in many seedlings, anthocyanin synthesisDifferent responses = Different phytochromes

Types of Phytochrome Responses3 classes based on fluence (amount of light needed)1. 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 fluenceDifferent responses = Different phytochromes:3 in rice, 5 in Arabidopsis

Types of Phytochrome ResponsesDifferent responses = Different phytochromes:3 in rice, 5 in Arabidopsis1. PHYA mediates VLF and HIR due to FR

Types of Phytochrome ResponsesDifferent responses = Different phytochromes:3 in rice, 5 in Arabidopsis1. PHYA mediates VLF and HIR due to FR• Very labile in light

Types of Phytochrome ResponsesDifferent responses = Different phytochromes:3 in rice, 5 in Arabidopsis1. PHYA mediates VLF and HIR due to FR• Very labile in light2. PHYB mediates LF and HIR due to R• Stable in light

Types of Phytochrome Responses1. PHYA mediates VLF and HIR due to FR• Very labile in light2. PHYB mediates LF and HIR due to R• Stable in light3. Roles of PHYs C, D & E not so clearPHYA & PHYB are often antagonistic.

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

PhytochromePr has cis-chromophore

PhytochromePr has cis-chromophore

Red converts it to trans = active shape

PhytochromePr has cis-chromophore

Red converts it to trans = active shapeFar-red reverts it to cis

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

PhytochromePfr 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

PhytochromePfr 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

PhytochromePfr 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

PhytochromePfr is a protein kinase: acts by kinasing key proteins• most enter nucleus and kinase transcription factors• Lack NLS, nuclear import requires FHY1 and FHL

PhytochromePfr is a protein kinase: acts by kinasing key proteins• most enter nucleus and kinase transcription factors• Lack NLS, nuclear import requires FHY1 and FHL• Slow responses are due to changes in gene expression

Phytochromemost enter nucleus and kinase transcription factors• Slow responses are due to changes in gene expression• Many targets of PHY are transcription factors, eg PIF3

Phytochromemost 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 photomorphogenesis• 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 are defective in specific types of protein

degradation

Phytochrome• Protein degradation is important for light regulation• Cop mutants are defective in specific types of protein

degradation• COP1 helps target transcription factors for degradation

Phytochrome• Protein degradation is important for light regulation• Cop mutants are defective in specific types of protein

degradation• COP1 helps target transcription factors for degradation• W/O COP1 they act in dark

Phytochrome• Protein degradation is important for light regulation• Cop mutants are defective in specific types of protein

degradation• COP1 helps target transcription factors for degradation• W/O COP1 they act in dark• In light COP1 is exported to cytoplasm so TF can act

Phytochrome• Protein degradation is important for light regulation• Cop mutants are defective in specific types of protein

degradation• COP1 helps target transcription factors for degradation• W/O COP1 they act in dark• In light COP1 is exported to cytoplasm so TF can act• Other COPs arepart of proteindeg apparatus(signalosome)

Other Phytochrome ResponsesCircadian rhythms• Many plant responses show circadian rhythms

Circadian rhythmsMany plant responses show circadian rhythmsLeaves move due to circadian ion fluxes in/out of dorsal &

ventral motor cells

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

Circadian rhythmsMany plant responses show circadian rhythms• Once entrained, continue in constant dark or light!

Circadian rhythmsMany plant responses show circadian rhythms• Once entrained, continue in constant dark or light!• Give plant headstart on photosynthesis, other processes

that need gene expression

Circadian rhythmsMany plant responses show circadian rhythms• Once entrained, continue in constant dark or light!• Give plant headstart on photosynthesis, other processes

that need gene expression• Or elongate at night!

Circadian rhythmsGive plant headstart on photosynthesis, other processes

that need gene expression• Or elongate at night!• Endogenous oscillator is temperature-compensated, so

runs at same speed at all times

Circadian rhythmsEndogenous oscillator is temperature-compensated, so

runs at same speed at all times• Is a negative feedback loop of transcription-translation

Circadian rhythmsIs a negative feedback loop of transcription-translation• Light & TOC1 activate LHY & CCA1 at dawn

Circadian rhythmsLight & TOC1 activate LHY & CCA1 at dawnLHY & CCA1 repress TOC1 in day, so they decline too

Circadian rhythmsLight & TOC1 activate LHY & CCA1 at dawnLHY & CCA1 repress TOC1 in day, so they decline tooAt night TOC1 is activated (not enough LHY & CCA1)

Circadian rhythmsLight & TOC1 activate LHY & CCA1 at dawnLHY & CCA1 repress TOC1 in day, so they decline tooAt night TOC1 is activated (not enough LHY & CCA1)Phytochrome entrains the clock

Circadian rhythmsLight & TOC1 activate LHY & CCA1 at dawnLHY & CCA1 repress TOC1 in day, so they decline tooAt night TOC1 is activated (not enough LHY & CCA1)Full story is far more complicated!

Circadian rhythmsLight & TOC1 activate LHY & CCA1 at dawnLHY & CCA1 repress TOC1 in day, so they decline tooAt night TOC1 is activated (not enough LHY & CCA1)Phytochrome entrains the clock So does blue light