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5. PHYTOCHROME AND PHOTOMORPHOGENESIS
A blue protein pigment with a molecular mass of about 125 kDa.
Mediates photomorphogenesis responses to red (660 nm) and far-red (730 nm) light.

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12. PHYTOCHROME CAN INTERCONVERT BETWEEN Pr AND Pfr FORMS
Red light
Pr Pfr
Far-red light

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14. PHOTOSTATIONARY STATE - Red Light
When Pr molecules absorb red light, most are converted to Pfr.
Since Pfr molecules can also absorb red light (see absorption spectrum), some of the Pfr molecules are converted back to Pr.
Thus after saturating irradiation with red light, only about 85% conversion of Pr to Pfr occurs.

15. PHOTOSTATIONARY STATE - Far-red light
When Pfr molecules are exposed to far-red light, nearly all the molecules are converted to the Pr form.
Since Pr molecules absorb almost no far-red light, there is almost no back reaction from Pr to Pfr.
Thus, after saturating far-red light there is about 97% conversion of Pfr to Pr.

16. Pfr is the Physiologically Active Form of Phytochrome (Is phytochrome response due to build-up of Pfr or tp the loss of Pr?)
In general, the magnitude of the physiological response to red light is proportional to the amount of Pfr produced.
In some cases the magnitude of the response is proportional to the ration of Pfr to pr, or of Pfr to Ptot.
Phytochrome deficient (hy) Arabidopsis mutants have long hypocotyls in both darkness and white light. If the red light response were due to a lack of Pr, we would expect the opposite to be true, i.e. the hypocotyls would be short in both darkness and white light.

17. PHYTOCHROME IS A DIMER COMPOSED OF TWO POLYPEPTIDES
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18. Synthesized in plastids
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19. Two Types of Phytochrome Have Been identified
Type I
a) About 9X more abundant in dark-grown tissues.
b) The Pfr form is rapidly degraded.
c) The Pfr form feed-back inhibits its own synthesis.
Type II
a) Present in in equal amounts with Type I phytochrome in light-grown tissues.
b) The Pfr form is not degraded.
c) Synthesis of Type II phytochrome is not feed-back inhibited by Pfr.

20. Phytochrome is Encoded By a Multigene Family
1. Arabidopsis has five structurally related phytochrome genes: PHYA, PHYB, PHYC, PHYD, and PHYE.
2. PHYA is the only Type I phytochrome
3. PHYB - PHYE are all Type II phytochromes.

21. Types I and II Phytochromes are Regulated Differently
Red
1. PHYA mRNA Pr Pfr Response
Far-red
Ubiquitin + ATP
Degradation
Degradation
Red
2. PHYB-E mRNA Pr Pfr Response
Far-red

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23. PHYTOCHROME RESPONSES VARY IN LAG TIME
LAG TIME - THE TIME BETWEEN THE STIMULUS AND THE OBSERVED RESPONSE
A. PHYTOCHROME RESPONSES MAY BE RAPID (A FEW MINUTES) OR LONG TERM (SEVERAL WEEKS).

24. PHYTOCHROME RESPONSES VARY IN THE AMOUNT OF LIGHT REQURIED
A. FLUENCE - TOTAL NUMBER OF PHOTONS IMPINGING ON A UNIT SURFACE AREA (micromoles/m2)
VLFR - VERY LOW FLUENCE RESPONSE
LFR - LOW FLUENCE RESPONSE
B. IRRADIANCE - FLUENCE RATE; NUMBER OF PHOTONS IMPINGING ON UNIT SURFACE AREA PER UNIT TIME (micromoles/m2/s)
1. HIR - HIGH IRRADIANCE RESPONSE

25. PHYTOCHROME RESPONSES VARY IN THEIR RECIPROCITY
LAW OF RECIPROCITY -
FLUENCE = FLUENCE RATE X TIME
(micromoles/m2) = (micromoles/m2/sec) X (sec)
B. According to the Law of Reciprocity, treating plants with a brief duration of high fluence rate (bright) light will five the same response as treating them with a long duration of low fluence rate (dim) light.
C. Reciprocity applies to most photochemical reactions, like the exposure of film.

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32. ECOLOGICAAL FUNCTIONS OF PHYTOCHROME: SHADE AVOIDANCE
PHYTOCHROME HELPS PLANTS TO ADAPT TO CHANGING LIGHT CONDITIONS BY SENSING THE RATIO OF RED AND FAR-RED LIGHT

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34. ECOLOGICAAL FUNCTIONS OF PHYTOCHROME: SHADE AVOIDANCE
PHYTOCHROME HELPS PLANTS TO AVOID SHADING BY OTHER PLANTS BY SENSING THE RATIO Pfr/Ptotal
A GREATER PROPORTION OF FAR-RED LIGHT CONVERTS MORE Pfr TO Pr, AND THE Pfr/Ptotal RATIO DECREASES.
ONLY “SUN PLANTS’ EXHIBIT SHADE AVOIDANCE.
“SHADE PLANTS” ARE ADAPTED TO SHADING, AND THEREFORE DO NOT EXHIBIT SHADE AVOIDANCE.

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36. PHYTOCHROME REGULATES CIRCADIAN RHYTHMS
CIRCADIAN RHYTHM = APPROXIMATELY A DAY
PERIOD = TIME BETWEEN SUCCESSIVE PEAKS OR TROUGHS IN A CYCLE
ENDOGENOUS RHYTHM = UNAFFECTED BY EXTERNAL STIMULI; REGULATED BY INTERNAL FACTORS
OSCILLATOR = BIOLOGICAL CLOCK MECHANISM
TEMPERATURE COMPENSATION = RHYTHM UNAFFECTED BY TEMPERATURE
ENTRAINMENT = ABILITY OF A STIMULUS (TYPICALLY LIGHT) TO RESET OR SYNCHRONIZE THE RHYTHM.

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39. THE CIRCADIAN OSCILLATOR INVOLVES A TRANSCRIPTIONAL NEGATIVE FEEDBACK LOOP
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40. DIFFERENT PHYTOCHROMES HAVE DIFFERENT ECOLOGICAL FUNCTIONS
PHYTOCHROME B MEDIATES THE RESPONSE TO CONTINUOUS RED OR WHITE LIGHT
PHYTOCHROME A IS REQUIRED FOR THE RESPONSE TO CONTINUOUS FAR-RED LIGHT
PHYA AND PHYB CAN HAVE MUTUALLY ANTAGONISTIC EFFECTS

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44. PHYTOCHROME REGULATES GENE EXPRESSION
THE STIMULATION AND REPRESSION OF GENE TRANSCRIPTION BY LIGHT CAN BE VERY RAPID (~5 MINUTES).
THESE RAPID CHANGES INVOLVE DIRECT ACTIVATION OF TRANSCRIPTION FACTORS BY ONE OR MORE SIGNAL TRANSDUCTION PATHWAYS.
SOME OF THE EARLY GENE PRODUCTS ARE TRANSCRIPTION FACTORS WHICH ACTIVATE THE EXPRESSION OF OTHER GENES.
EXPRESSION OF THE EARLY GENES, CALLED PRIMARY RESPONSE GENES, IS INDEPENDENT OF PROTEIN SYNTHESIS AND INVOLVES ACTIVATION OF PRE-EXISTING TRANSCRIPTION FACTOR PROTEINS

45. Secondary response gene Primary response gene
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46. PHYTOCHROME MOVES INTO THE NUCLEUS
phyA-GFP, continuous FR light
phyB-GFP, continuous white light
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48. Phytochrome is a Serine/Threonine Protein Kinase
Cyanobacterial phytochrome is part of a two-component system signal transduction pathway
Cyanobacterial phytochrome is a histidine kinase
Eukaryotic phytochrome is a serine/threonine kinase.

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