Basic overview of some key genes in plant development.

1. Sandeep Yadav
2011BS19D
CCSHAU, Hisar
Plant development defects

2. PLANT DEVELOPMENT
• Plant organ development is important for adaptation to a
changing environment.
• In developmental plant biology, the model organism for
genetic analysis is Arabidopsis thaliana.
• Like Drosophila, Arabidopsis can be subjected to mutagens
to generate mutations that alter developmental processes.
• The small genome size of this organism makes it relatively
easy to map these mutant alleles and eventually clone the
relevant genes.

3. Developmental steps in the formation of a
plant embryo
(a) The two-cell stage consists of the apical cell and basal cell.
(b) The eight-cell stage consists of a proembryo and a suspensor. The suspensor gives rise to
extraembryonic tissue, which is needed for seed formation.
(c) At this stage of embryonic development, the three main regions of the embryo (i.e., apical,
central, and basal) have been determined.
(d) At the heart stage, all of the plant tissues have begun to form. Note that the shoot meristem is
located between the future cotyledons, and the root meristem
is on the opposite side.
(e) A seedling.

4. Organization of a shoot meristem
• The organization of a shoot meristem is
controlled by the WUS and CLV3 genes,
which are abbreviations for Wuschel and
clavata, respectively.
• The WUS gene is expressed in the
organizing center and induces the cells in
the central zone to become
undifferentiated stem cells.
• The red arrow indicates that the WUS
protein induces these stem cells to turn
on the CLV3 gene, which encodes a
secreted protein that binds to receptors in
the cells of the peripheral zone.
• The cells in the peripheral zone are
allowed to grow and differentiate into
lateral structures such as leaves.

5. • In the seedling, three main regions are observed: apical,
central and basal region.
• By analysing mutants that disrupt the developmental
process, researchers have discovered that these three
regions express different sets of genes.
• Plant biologists have identified a category of genes, known
as apical-basal-patterning genes, that are important in the
early stages of development.

6. • Defects in apical-basal-patterning genes cause dramatic effects in each
of the three main regions.
• For example, the Gurke gene is necessary for apical development.
When it is defective, the embryo lacks apical structures.
• Currently, a great amount of effort is directed toward the identification
of genes that govern pattern formation in the three regions of
Arabidopsis and other plants.

7. Examples of Arabidopsis Apical-Basal-Patterning Genes That Affect the
Development of the Apical, Central, or Basal Region

10. Plant Homeotic Genes Control
Flower Development
• Many homeotic mutations affecting flower development have been identified in
Arabidopsis and also in the snapdragon (Antirrhinum majus).
• The homeotic mutants undergone transformations of particular whorls.
(a) A normal flower. It is composed of four concentric whorls of structures: sepals, petals, stamens, and carpel.
(b) A homeotic mutant in which the sepals have been transformed into carpels and the petals have been
transformed into stamens.
(c) A triple mutant in which all of the whorls have been changed into leaves.

11. ABC model for flower development
• By analysing the effects of many different homeotic mutations in
Arabidopsis, Elliot Meyerowitz and colleagues proposed the ABC
model for flower development.
• In this model, three classes of genes, called A, B, and C, govern the
formation of sepals, petals, stamens, and carpels.
• More recently, a fourth category of genes called the Sepallata genes
(SEP genes) have been found to be required for this process.

12. ABC model for flower development
• Gene A products are made in the outermost whorl (whorl 1),
promoting sepal formation.
• In whorl 2, gene A, gene B, and SEP gene products are made, which
promotes petal formation.
• The expression of gene B, gene C, and SEP genes in whorl 3 causes
stamens to be made.
• Finally, in whorl 4, gene C and SEP genes promote carpel formation.

13. Molecular explanation for how the homeotic mutants in the A, B, C, or SEP
genes cause their phenotypic effects
• In the original ABC model, it was proposed that genes A and C
repress each other’s expression, and gene B functions
independently.
• In a mutant defective in gene A expression, gene C is also be
expressed in whorls 1 and 2. This produces a carpel-stamen-
stamen-carpel arrangement.
• When gene B is defective, a flower cannot make petals or
stamens. Therefore, a gene B defect yields a flower with a
sepal-sepal-carpel-carpel arrangement.
• When gene C is defective, gene A is expressed in all four
whorls. This results in a sepal-petal-petal-sepal pattern.
• If the expression of SEP genes is defective, the flower consists
entirely of sepals, which is the origin of the gene’s name.

14. Flower formation comes from modifications of the leaf
• Leaf structure is the default pathway and that the A, B,
C and SEP genes cause development to deviate from a
leaf structure in order to make something else.
• In this regard, the sepals, petals, stamens, and carpels
can be viewed as modified leaves.

15. Arabidopsis homeotic genes
• Arabidopsis has two types of gene A (apetala1 and
apetala2), two types of gene B (apetala3 and pistillata),
one type of gene C (agamous), and three SEP genes
(SEP1, SEP2, and SEP3).
• All of these plant homeotic genes encode transcription
factor proteins that contain a DNA-binding domain and
a dimerization domain.
• However, the Arabidopsis homeotic genes do not
contain a sequence similar to the homeobox found in
animal homeotic genes.

16. Research papers
• In this study, 66 candidate rice miRNAs out of 1,650 small RNA
sequences (19 to approximately 25 nt), and they could be further
grouped into 21 families, 12 of which are newly identified and
three of which, OsmiR528, OsmiR529, and OsmiR530, have been
confirmed by northern blot.
• To study the function of rice DCL proteins (OsDCLs) in the
biogenesis of miRNAs and siRNAs, they searched genome
databases and identified four OsDCLs.
• An RNA interference approach was applied to knock down two
OsDCLs, OsDCL1 and OsDCL4, respectively.
• Strong loss of function of OsDCL1IR transformants that expressed
inverted repeats of OsDCL1 resulted in developmental arrest at
the seedling stage, and weak loss of function of OsDCL1IR
transformants caused pleiotropic developmental defects.

17. OsDCL1 Is Required for Rice Developm ent
• Strong loss of function of OsDCL1IR
transformants showed overall shoot and
root abnormalities such as severe dwarfism
and dark green color.
• These plants often produced rolled leaves
and malformed shoots.
• A) Root elongation was also greatly reduced
in OsDCL1IR transformants.
• B) These plants showed developmental
arrest during rooting or at the young
seedling stage and eventually died either on
sterile medium or in soil.
• C) They also have fewer adventitious roots.

18. OsDCL1 Is Required for Rice Developm ent
• D) & E) The adventitious
roots of weak loss of
function of OsDCL1IR
transformants were short
and radically swollen when
grown on sterile medium.
• F) & G) Ectopically
developed chloroplasts
were found in OsDCL1IR
transformants roots;
however, the cell number
and overall cellular
organization of OsDCL1IR
transformants roots did not
change.

19. • Genetic and physiological studies have revealed that plant hormones
play key roles in lateral root formation.
• In this study, they show that MIZU-KUSSEI1 (MIZ1), which was
identified originally as a regulator of hydrotropism, functions as a
novel regulator of hormonally mediated lateral root development.
• Overexpression of MIZ1(MIZ1OE) in roots resulted in a reduced
number of lateral roots being formed; however, this defect could be
recovered with the application of auxin.

20. • Indole-3-acetic acid quantification analyses showed that free
indole-3-acetic acid levels decreased in MIZ1OE roots, which
indicates that alteration of auxin level is critical for the
inhibition of lateral root formation in MIZ1OE plants.
• In addition, MIZ1negatively regulates cytokinin sensitivity on
root development.
• Application of cytokinin strongly induced the localization of
MIZ1-green fluorescent protein to lateral root primordia,
which suggests that the inhibition of lateral root
development by MIZ1 occurs downstream of cytokinin
signaling.
• These results suggest that MIZ1 plays a role in lateral root
development by maintaining auxin levels and that its function
requires GNOM activity.

21. • Examination of cell wall polysaccharide preparations from RGP1 and
RGP2 knockout mutants showed a significant reduction in total L -Ara
content (12–31%) compared with wild-type plants.
• Concomitant downregulation of Reversibly Glycosylated Proteins
(RGP1 and RGP2) expression results in plants almost completely
deficient in cell wall–derived L -Ara and exhibiting severe
developmental defects.

22. Quantitative RT-PCR Analysis of RGP
Expression at Different Developmental Stages
• RGP1, RGP2, and RGP5 transcripts were detected in all
examined tissues, with highest amounts in flowers,
seedlings, and developing siliques.

23. RGPpro: RGP-YFP Expression Pattern

24. • N 6-methyladenosine (m6A) mRNA methylase is essential
during Arabidopsis thaliana embryonic development .
• A 90% reduction in m6A levels during later growth stages
gives rise to plants with altered growth patterns and reduced
apical dominance.
• The flowers of these plants commonly show defects in their
floral organ number, size, and identity.
• The global analysis of gene expression from reduced m6A
plants show that a significant number of down-regulated
genes are involved in transport, or targeted transport, and
most of the up-regulated genes are involved in stress and
stimulus response processes.

25. N6-methyladenosine (m6A) base modification
• An analysis of m6A distribution in fragmented mRNA suggests that the
m6A is predominantly positioned toward the 3’ end of transcripts in a
region 100–150 bp before the poly(A) tail.
• N 6-methyladenosine (m6A) is a ubiquitous base modification found
internally in the mRNA of most Eukaryotes.
• Levels of methylation equivalent to at least 50% of transcripts carrying m6A
are common.
• Ribonuclease fragmentation and labeling studies on mRNA show m6A to be
present only at the central A within the sequence context GAC and AAC,
with a 75% preference for GAC, and this consensus appears to be
conserved amongst plants, yeast and mammals
Bodi et al., 2010

26. Developmental defects due to reduced m6A
levels
• Plants with reduced levels
of m6A are more
compact, have leaf
crinkling, shorter
inflorescence, and
reduced apical
dominance

27. Developmental defects due to reduced m6A
levels
• i,ii) Floral defects
are common in the
reduced m6A
plants. Some
stamens show
partial conversion
to petals.
• iii) sepals and petals
removed for clarity
and organ order is
also sometimes
affected

28. Importance of N6-methyladenosine
• It was shown that the primary function of the human
fat mass and obesity associated protein (FTO ) is to
remove the methyl groups from N6 methylated
adenosines in mRNA.
• Overexpression of FTO (implying reduced
methylation) is associated with obesity, diabetes, and
risk of Alzheimer’s.
• Thus there is an intriguing link between nutrition and
mRNA methylation in both yeast and mammals.
Jia et al., 2011

29. • ABC1 (activity of bc1 complex) is a newly
discovered atypical kinase in plants.
• Here, it was reported that an ABC1 protein
kinase-encoded gene, AtACDO1 (ABC1-like
kinase related to chlorophyll degradation
and oxidative stress), located in
chloroplasts, was up-regulated by methyl
viologen (MV) treatment.
• AtACDO1 RNAi (RNA interference) plants
showed developmental defects, including
yellow-green leaves and reduced contents
of carotenoids and chlorophyll; the
chlorophyll reduction was associated with a
change in the numbers of chlorophyll-
binding proteins of the photosynthetic
complexes.

30. • Chlorophyllide (Chlide) a the first product of chlorophyll
degradation, and pheophorbide a, a subsequent
intermediate of Chlide a degradation, were increased
inAtACDO1 RNAi plants.
• The AtACDO1 RNAi plants had lower transcript levels of
the oxidative stress response genes FSD1, CSD1, CAT1, and
UTG71C1 after MV treatment compared with wild-type or
35S::AtACDO1 plants.
• Results suggest that the chloroplast AtACDO1 protein
plays important roles in mediating chlorophyll
degradation and maintaining the number of chlorophyll-
binding photosynthetic thylakoid membranes, as well as
in the photooxidative stress response.

31. • Ethanolamine is important for synthesis of choline,
phosphatidylethanolamine (PE) and phosphatidylcholine (PC) in
plants. The latter two phospholipids are the major phospholipids
in eukaryotic membranes.
• In plants, ethanolamine is mainly synthesized directly from serine
by serine decarboxylase.
• Arabidopsis mutant defective in serine decarboxylase, named
atsdc-1 (Arabidopsis thaliana serine decarboxylase-1) were studied
in this study.

32. Results
• The atsdc-1 mutants showed
necrotic lesions in leaves, multiple
inflorescences, sterility in flower,
and early flowering in short day
conditions.
• These defects were rescued by
ethanolamine application to atsdc-
1, suggesting the roles of
ethanolamine as well as serine
decarboxylase in plant
development.
• In addition, molecular analysis of
serine decarboxylase suggests that
Arabidopsis serine decarboxylase is
cytosol-localized and expressed in all
tissue.

33. • Plants contain an extensive family of PsbP-related proteins termed
PsbP-like (PPL) and PsbP domain (PPD) proteins, which are localized
to the thylakoid lumen.
• The functions of the photosynthetic electron transfer reactions are
largely unaltered in the ppd5 mutants, except for a modest though
significant decrease in NADPH dehydrogenase (NDH) activity.
• Relative to the wild-type Col-0 plants, the ppd5 mutants exhibit both
increased lateral root branching and defects associated with axillary
bud formation.