Summary

MOB-30806 | Regulation of Plant Development Summary [WUR]

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Course
MOB-30806 | Regulation of Plant Development (MOB30806)

Institution
Wageningen University (WUR)

Book
Essential Cell Biology

Summary of the course Regulation of Plant Development [MOB-30806], a master course given at the Wageningen University. The summary consists of all theory given in the lectures, filled with additional notes and theory as the course only consisted of lectures.

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Uploaded on July 23, 2020
Number of pages 28
Written in 2019/2020
Type Summary

plant
structure
regulation
processes
physiology
genes
cells
mob 30806
wur
wageningen university
regulation of plant development

Book Title:Essential Cell Biology

Author(s):Bruce Alberts, Karen Hopkins

Edition:Unknown
ISBN:9780393680393
Edition:Unknown

Institution
Wageningen University (WUR)
Education
Biologie / Plantenwetenschappen / Plant Sciences
Course
MOB-30806 | Regulation of Plant Development (MOB30806)

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Regulation of Plant Development
To become a multicellular organism, a unicellular organism needs:
- Genes to glue single cells together to form a multicellular organism
- Genes to communicate between cells

A gene function can evolve via:
- Large scale gene amplifications and diversifications
- Minor rewiring of existing circuits (small changes)

This can be studies by comparative genomics. New genes have been evolved due to stress conditions. Genome
was duplicated instead of transferred to new generations. The duplicated genome could be modified to have a
new function. Contentious selection from the environment results in mutation in optimal conditions. Another
way is mutant analysis and also temporal and spatial gene expression analysis.

There are three functioning gene ways:
• Non-functionalization: one of the two copies remains original while the second copy
becomes disfunctionalized (pseudogene)
• Neo-functionalization: both copies (or one) acquire new functions which are no longer exactly
original
• Sub-functionalization: the function of the original gene copy is now fulfilled by two copies,
and none of them functions like the original copy.

Regulatory proteins are similar in plants and animals but have diverged differently. Two types of signals:
- Intrinsic; hormones, metabolites, mechanical forces
- External; light, temperature, predators, symbionts.

Signals are recognized by receptors, located on the inside of the cell wall. Mostly a chitin motif. Signal sensed
by phosphorylation. Animals mostly have peptide signals, plants not. Transcription factors (TF) have a same
molecular function but a different structure which makes them able to recognize different DNA structures. The
inside of a receptor (kinase domain) is always the same, the outside consists of different domains. As the plant
cell wall is rigid, plants don’t have cell migration and movement and folding of sheets of cells. Plant form is
shaped via:
1. Different rates of cell division
2. Division in different planes
a. Periclinal (vertical)
b. Anticlinal (horizontal)
3. Directed enlargement of cells

What are the mechanisms that control development stategies in plants and are the same in animals?
- Asymmetric cell division
- Response to positional signals
- Lateral inhibition
- Changes in gene expression in response to external signals

Use models to study (Arabidopsis; dicots) (Rice; monocots). Transformation can be via floral dip or T-DNA
insertion. A fate map is a representation of the developmental history of each cell in the body of an adult
organism. A fate map is supported by data of mutants. Thus, a fate map traces the products of each mitosis
from the single-cell zygote to the multi-cellular adult. Easy to obtain from Arabidopsis roots because;
- Transparent tissue
- Highly traceable system
- Detailed root map
o Radial axis: concentric rings of tissue layers
o Longitudinal axis: morphologically distinguishable developmental zones
- Transcriptome characteristics of all root cells.

,Mechanisms are regulated by hormones, mutants used to study signalling cascades and synthesise mechanism.
Receptors can be present in cell wall/membrane and cytoplasmic/nucleus. Auxin, JA and GA action in nucleus,
ABA BR and ethylene in cell. Ethylene also in ER.
Proteins can be degraded via an SCF mediated way. The function of the SCF complex is to degrade
proteins by catalysing the ubiquitination of proteins destined for proteosomal degradation. S means
for Skp, C means Cullin and F means F-box. They consist an complex of proteins that function as
ubiquitin ligase complex. They tag proteins for degradation by the 26S proteasome. The specifity is in
recognition proteins. Depending on present F-box, a protein bound that is then degraded by a 26S
proteasome.
• Skp= binding protein, forms
part of the horseshoe-shaped
complex, along with cullin (cul1).
Skp is essential in the recognition
and binding of the F-Box
• Cullin (cul1)= forms the
major structure scaffold of the SCF complex, linking the skp1 domain with the rbx1 domain.
• Rbx1= contains a small zinc-binding domain called RING finger, to which E2-ubiquitin
conjugate binds. This allows transfer of the ubiquitin to a lysine residue on the target protein.

In what manner are SCFs required for auxin, jasmonate and gibberellin signalling?
The response is dependent on the intracellular concentration of the hormone. For auxin (a); if there is a low
concentration of auxin, then ARF does not interact with AuxIAA. AuxIAA is an influx carrier. But in a high
concertation of auxin, AuxIAA can be recognized and formed into a different shape. This shape can be
recognized by the 26S proteasome, auxin can be degredaded and the ARF can be transcribed which leads to a
positive response. The target protein is specific per type of hormone.
For JA, MYC2 is normally bound to JAZ (co-receptor). Under high JA concentrations, JA can bind to a JAR protein
which can cause JAZ to be recognized by COI1. This leads to degradation of JA and a jasmonate response as
MYC2 is now free.
For GA, DELLA Is the repressor that is bound to PIF3/4 under low GA concentrations. Differently is that not
DELLA gets recognized under high GA concentrations, but a co-receptor named GID1. This undergoes a
→ →
formational change that can then bind and activate DELLA polyubiquitination of DELLA GA response.
All responses are down-regulated due to high hormone concentrations. The core of such protein complex is
always the same:
CUL1: major structural scaffold.
RBX1: contains small zinc-binding domain called RING finger, to which E2-ubiquitin conjugate binds.
ASK1: is essential in the recognition and binding of the F-box within the F-box protein. F-box gives the specifity
of the reaction. TIR1, COI1, SLY1; f-box containing proteins and hormone receptors.

Why there are many responses of just one hormone?
One hormone can give many responses because there are many different F-Box families, recognition proteins
and transcription factors that can all act on the same type of hormone. One of them is the transcription factor

named ARF (= auxin-response factor), bound
by suppressor (Aux/IAA). TIR can bind with
transcriptional repressors (Aux/IAA) to
degrade it. Genes are off. If auxin comes in,
auxin binds with TIR receptor. Aux/IAA gets
degraded, gene can be transcribed.

, There are many ARFs present, and different groups of them are
essential in early embryo developmental stages. As they are TFs, they
end up in the nucleus and can thus be stained with GFP. Therefore, ARF-
GFP fusions can be seen in the nucleus and different groups seem to
function in different places of the nucleus. `

How can we then see the auxin signalling pathway to visualize auxin
in action?
The ARF transcription factor elements can be hooked up in a reporter
gene, by taking a part of an element and construct it multiple times
after each, and so that it becomes a sensitive auxin detection marker.
Now it can be expresses simultaneously with ARF and then you see a
fluorescence. However, this is not still quantitative. Therefore, DR5
system is an alternative with two affinities, one with GFP (DR5) and
one with modified (DR5v2). So, by combining these two genes into one
cassette, you can now detect low concentrations of auxin as the DR5 is
more sensitive and thus can sense low auxin concentrations.

What all AUX/IAA proteins have in common is that they have a DII motif, that is
recognized by the F-box protein. So, the DII motif determines if degradation can
happen. Hooking this up to Venus can result in a quantitative detection based
on affinity. So, depending on the higher concentration, there will be more
affinity of auxin to DII-Venus. The absence of the Venus marker says that there
is lots of auxin. So, a mutated DII version is no longer degraded in an auxin
mediated manner.

How does auxin get internalized into cells?
Passive (diffusion) or active (in- efflux carriers). Local biosynthesis. Transport of auxin
is easily as it can penetrate through cell walls. Auxin influx carrier (AUX1) facilitates
auxin uptake for active transport. But differences in pH regulate transport of IAA
inside the cell. Inside cell, cytoplasm pH is 7 and outside it is 5.5 so auxin gets
protonated when inside the cell. Basic pH of cytoplasm, traps IAA as auxin gets
deprotonated. Then, IAA- can only leave cell via active efflux by carries (PINs).
Asymmetric distribution of efflux carries within each cell, promotes unidirectional
(polar) auxin transport from cell to cell. ABC transporters of the PGP family mediate
additional efflux and influx. Diffuse is slow process of transport. Carriers are polar
distributed. Influx carrier is at top of the cell and efflux carrier at bottom of the cell.
Auxin therefore is downstream transported. Gene duplication with slight modification
results in different PIN genes, with specific localizations and expression patterns.
Localization changes transport direction. Due to different transport directions, there
are always high concentrations of auxin at the tip of the root to promote growth.
Depending on which PIN is mutated, different auxin distributions occur and different
phenotypes. Localization of PIN and AUX cause a gradient and flow of auxin. How is
this figured out, via mutants. There are 4 AUX and 7 PINs in Arabidopsis. By slight
mutations in the proteins can the phenotype be
determined. The localization is
specific and also the expression
pattern.

What determines correct
localization?
A central role for the kinase PINOID
(PID) in phosphorylation. Depending
on which PINs get phosphorylated, a basal-to-apical shift can

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