Plant-environment interaction 1:
How do plants respond to light?
Lecture 1: The phytochrome pathways
• Photomorphogenesis -- The light-induced developmental and
morphological changes. So light not only serves as energy
source for photosynthesis but also as a signal for growth and
development. How does plants respond to light signal?
2. Molecular changes during photomorphogenesis
From signal (light) to responses at the molecular level
Light-induced gene expression—the “greening” process as a model.
Etiolated plants---exposed to light---genes that are activated (related to
the greening process---building the chloroplasts for
3. Plants have different receptors to detect various spectra of light
Red light receptors and blue light receptors are best defined. The
receptors are the beginning step in light signaling pathways.
4. The phytochrome pathway
1) The function of red light in development: seed germination,
greening (chloroplast development), regulation of internode
elongation, flowering time, bud dormancy etc…
2) The red light receptors—phytochrome family—have two
reversible light absorbing forms---Pr for red light-absorbing form
and Pfr for far red absorbing form. The Pfr is the biologically
active form.
Red/far red switch in seed germination
3) In arabidopsis there
are at least 5 different
isoforms of phytochrome
PhyA,B,C,D,E. Each of
them is a peptide of about
120 kDa. The native form
is a dimer of about 250
kDa with chromophore
group called
phytochromobilin. PhyAE function differently but
with some overlap. PhyA
and PhyB are better
Upon red/far red switch,
the protein and the
chromophore both change
4) The phytochrome domains
The chromophore-binding domain and the signaling domain:
PEST is for photo-degradation
5) The mechanism of signaling: from phytochrome to gene
expression in the nucleus
a) Where is phytochrome? From cytosol to nucleus!
Much phyA/B protein
Are found in the cytosol in
the dark but light induce
nuclear localization of the
Phy proteins, suggesting
that downstream events
may occur in the nucleus
But things are more
complicated—studies show
that both cytosolic and
nuclear pathways exist
b) The pathways:
PhyB directly interacts
with the transcriptional
The yeast two hybrid system:
A powerful tool to find the
partner proteins—as
most proteins function by
interacting with other
proteins, finding partner
proteins is critical for
identifying functions of a
protein in the cell.
Your protein of interest is
used as a “bait” to fish
out the “prey” in a cDNA
A partner protein is identified for PhyB called PIF3 (PhyBInteracting Factor #3).
Red light causes
PhyB to move into
nucleus and
interact with PIF3,
a transcription
factor that
activates the genes
encoding other
factors for
activation of
ii) The phyA serves as a protein kinase and phosphorylates
substrates in the cytoplasm
The bacterial phytochrome is a histidine kinase:
iii) The G protein pathway?
phyA mutant rescue by microinjection of G protein pathway
components (GTP) and calcium-CaM, and cGMP.
iv) What is going on in the nucleus?
Protein degradation is a key regulatory process.
Identification of a E3 ligase (called COP1) as a negative
regulator in the light signaling pathway—mutant causes
constitutive photomorphogenesis---the gene encodes a
ubiquitin pathway ligase for degrading transcription factors
required for light-induced genes expression.
v) Other photoreceptors modulate phytochrome pathway