Plant biofuel related Novel biofuel Novel ways to enhance biofuel production Biophotovoltaics

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

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

5. 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

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

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

8. 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

9. 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

10. 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

11. 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"

12. Phytochrome Pr has cis-chromophore

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

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

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

16. 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

17. 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

18. 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

19. 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

20. 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

21. 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

22. 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

23. 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

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

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

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

27. 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

28. 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

29. 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

30. 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!

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

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

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

34. 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

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

36. 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

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

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

39. 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

40. 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!

41. 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

42. 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

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

44. 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)

45. 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

46. 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

47. Blue Light Responses • Circadian Rhythms

48. Blue Light Responses • Circadian Rhythms • Solar tracking

49. Blue Light Responses Circadian Rhythms Solar tracking Phototropism

50. Blue Light Responses • Circadian Rhythms • Solar tracking • Phototropism • Inhibiting stem elongation