MADSbox gene family

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MADS-box gene family

• with bioinformatics tools
• Bixia Xiang
• Fw 5510
• Instructor Dr. C. P. Joshi

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Whats MADS-box genes?

• In order to understand Mads box gene we must go
  through the flower process first.

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Flowering is a massively complex process
So only a brief outline can be provided here-)
The floral meristem under goes a series of
developmental changes that eventually give rise
to the four basic structures of the flower ---
sepals, petals, stamens and carpels. If you move
from the base of the flower upwards and inwards
you will encounter the four organs
in the same order in which they are developed.
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A model was developed that attempts to explain
the interactions of the different genes that
control floral organ identity

• All the genes are classified as expressing one of
  three activities, A, B, or C
• The A gene activities control the development of
  the sepal and petal
• The B gene activities control petal and stamen
  development
• The C gene activities control stamen and carpel
  development

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The study of the genes which control floral
development provides a valuable insight to power
of Mendelian or classic
genetics. Through the careful study of mutants
at the phenotypic level,
predictions could be made regarding the
molecular expression of the genes.
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Phenotypic Effects of Mutations in A, B or C
Function Floral Identity Genes
Mutation Whorl 1 Whorl 2
Whorl 3 Whorl 4 Wild Type
Sepal Petal Stamen
Carpel A Function Carpel
Stamen Stamen Carpel B
Function Sepal Sepal
Carpel Carpel C Function
Sepal Petal Petal
New Flower
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A function genes
Image shows the APETALA2 mutant.
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B function genes
Image shows the APETALA3 mutant
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Image shows the AGAMOUS mutant.
C gene functions are defined by the gene AGAMOUS.
Mutants of this gene have the third whorl stamen
replaced by a petal, and the fourth whorl
develops into a new flower with the
sepal-petal-petal pattern.
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• The image show the phenotype of the APETALA1
  mutant.

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• The image above shows the phenotype of the
• APETALA1 CAULIFLOWER double mutant.

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How is this conclusion regarding the function of
the gene reached? If we believe that a gene
defines a phenotype, when that gene is not
functioning normally, that is when the gene is
mutated, its phenotype is not expressed. When
we are considering genes involved in development,
then the developmental stage that is altered is
controlled at least partially by the gene that is
mutated
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Finally what would be expected with an A, B and C
function triple mutant?
This mutant would have no genes functioning that
determine normal floral organ development. As
expected, the triple mutants lack any floral
organs, and the flower essentially consists of
leaves developing from each of the whorls.
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Where the database from?
Hundreds of molecular scientist have done or are
doing gene cloning work on flowering and flower
Organ Genes and submit the sequence data to
GENEBANK for communication and further study
Cloning Methods and Basic Structure of genes
Involved in Flowering Gene
Cloning Method
Sequence Structure
LEAFY flo probe
Unique
APETALA1 MADS-Box Cloning
MADS-box
CAULIFLOWER APETALA1 probe
MADS-box AGAMOUS
T-DNA Tagging
MADS-box APETALA3
DEFICIENS A probe MADS-box
PISTILLATA GLOBOSA
probe MADS-box
APETALA2 T-DNA Tagging
Unique
The above table clearly demonstrates that
MADS-box genes play a central role in the
development of flowers in plants
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The MADS box is a highly conserved sequence motif
found in a family of transcription factors. The
conserved domain was recognized after the first
four members of the family, which were
Definition of the MADS box

• M CM1, a gene from budding yeast (Saccharomyces
  cerviseae) involved in mating type switch.
• A gamous, a gene from Arabidopsis thaliana
  involved in floral development.
• D eficiens, a gene from Antirrhinum majus, also
  involved in floral development.
• S RF, the Serum Response Factor, a human gene

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The name MADS was constructed form the
"initials" of these four "founders".

• M CM1, a gene from budding yeast (Saccharomyces
  cerviseae) involved in mating type switch.
• A gamous, a gene from Arabidopsis thaliana
  involved in floral development.
• D eficiens, a gene from Antirrhinum majus, also
  involved in floral development.
• S RF, the Serum Response Factor, a human gene

MADS
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MADS-domain proteins known to date have
additional domains attached to the C-terminus of
the MADS-domain, and some also have N-terminal
extensions. According to this overall structure,
MADS-domain proteins can be subdivided into three
different types which shown in the following
sketch.
0 100
200 300
400 -------------------
-----------------------------------------------
---------- ------------------
-------------------------- - MCM1
MADS SAM
-------------------------
---------------------
-----------------------------------------------
---------------------- MEF2B MADS
MEF2

-----------------------------------------------
----------------------
------------------------------------------- D
EF MADS I K
C
-------------------------------------------
ltMADS gt
domain lt------
MIK domain -------gt
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The figure from Dr. Martin Yanofsky summarizes
the general structure of MADS-box genes.
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Why was it so interesting to work with MADs-box
gene family
Can you imagine how important of the floral
development process?
Formation of a flower's reproductive organs --
the plant parts that provide most of the world's
food (fruit/seed production)-- the new results
will be of particular interest to agricultural
scientists. The potential to control
petal-formation will be of interest to
horticultural researchers, in an industry always
looking for more petals. The research is also
likely to lead to applications in biotechnology
manipulation of flowering genes to create sterile
trees (trees that don't shed pollen) would ensure
environmental safety before the commercialization
of genetically engineered trees.

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These findings will help researchers understand
the diversity of growth and blooming seen in
different species of plants. The cloning of the
floral commitment and organ genes next permitted
the study of the expression of these genes in the
tissues and cells giving rise to the
flowers The evolutionary origin of flowering
plants has long been contentious. The large
morphological gap between flowering plants and
their potential gymnosperm relatives makes
homology difficult to assess, the recent
discovery of homeotic genes that specify flowers
and flower organs raises the possibility of a new
class of evidence bearing on flower origins
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Search results with NCBI
User Query mads_box
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Query words is critical
NOTE search time is 25th March, 2001
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(No Transcript)
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Mads_box AND Pinus 27
Species gene num Pinus
radiata 14 Monterey pine
9 Canadian red pine 1 Pinus
resinosa 2 total
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zea mays 1
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Any research clues?
For bioinformatics scientist
set up the database with more uniform criteria
For data mining scientist
try more entry words to make sure your data is
right and updated
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Research with GCG programs
Create the Mads_box AND Pinus list file
GCG program Fetch and Pico
Importing those sequences to seqlab
Analysis data by runing programs PileUp, Pretty,
MEME, Distance, PaupDisplay, PAUPsearch, motif,
Output for further analysis
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Pinus radiata Monterey pine Pinus radiata
Pinus radiata Monterey pine Pinus radiata
Monterey pine Pinus radiata Monterey
pine Pinus radiata Monterey pine Pinus radiata
Monterey pine Pinus radiata Monterey pine Pinus
radiata Pinus radiata Monterey pine Pinus
radiata Monterey pine Pinus radiata Canadian
red pine Pinus radiata Pinus radiata
Pinus resinosa
Pinus resinosa
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PAUPsearch reconstructs phylogenetic trees
using maximum parsimony criteria
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PAUPsearch tree Demonstrate A paralogous
duplication of mads-box predated the divergence
of pinus. MAD-box is not always single copy in
species but has persisted as paralogs for a long
interval.
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MADS-box genes in the evolution of vascular plants
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The topology of the tree is controversial that
Genetales are more closely related to conifers
than to angiosperms could be concluded from some
of our studies on MADS-box genes in these taxa
(Winter et al. unpublis hed data), but is in
contrast to textbook interpretations of
morphological data.
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The MADS box is a conserved sequence motif of 168
bp that occurs in several eucaryotic
transcription factors..
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Protein characteristics analysis isoelectric,
helicalwheel, hthscan, coilscan, motifs, pepdat
a, pepplot, peptidemap, peptidesort, peptidestruc
ture
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People and groups researching on MADS box genes
The Division of Gene Expression an Regulation at
the National Institute for Basic Biology in Japan
studies development and morphogenesis of flowers
using Arabidopsis thaliana. Victor Albert
in the New York Botanical Garden studies MADS-box
genes in Asteraceae. Gynheung An in the
Department of Life Sciences Pohang University of
Science and Technology studies MADS-box genes in
rice (Oryza sativa) Jo Ann Banks in the
Department of Botany and Plant Pathology, Purdue
University is interested in MADS-box genes in the
fern Ceratopteris richardii. Peter Engström in
the Department of Physiological Botany, Uppsala
University, studies MADS-box genes in Norway
spruce (Picea abies) and in a lycopod
(Lycopodium annotinum) Michael Frohlich and
Susan Fuerstenberg at the University of Michigan
Herbarium are interested in the evolution of
MADS-box genes and of flowers. Vivian
Irish in the Department of Biology at the Yale
University is especially interested in floral
homeotic genes of the B-type. Hong Ma in
the Cold Spring Harbor Laboratory studies
MADS-box genes in Arabidopsis. The Krizek
lab is interested in understanding the
developmental processes that are involved in
patterning a flower and uses Arabidopsis as a
model system. Bill Martin and Jens Pahnke in
the Institut für Genetik, Technische Universitaet
Braunschweig, work on MADS-box genes in the fern
Ceratopteris richardii (in cooperation with
Theissen group).
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The Meyerowitz lab studies several plant
processes, using Arabidopsis thaliana as a model
system. M. Enrico Pë in the Dept. of
Genetics and Microbiology, works on MADS-box
genes in rice, maize and sorghum. Michael
D. Purugganan at the NCSU genetics department
investigates the molecular evolution of flower
development. The Richmond lab at the ETHZ
in Switzerland specializes in X ray
crystallography and has resolved the structure of
serum response factor core bound to DNA
Robert J. Schmidt at the University of
California - San Diego works on MADS-box genes in
maize (Zea mays) Bob Teasdale and Aidyn
Mouradov at ForBio Ltd work on MADS-box genes in
the pine Pinus radiata. The Theißen group at the
Max-Planck-Institut für Züchtungsforschung in
Cologne, Germany works on MADS box genes in Zea
mays and in ferns like Ceratopteris and
Ophioglossum. The Transcription Laboratory at
the Imperial Cancer Research Fund (Treisman
group) Detlef Weigel at the Salk Institute for
Biological Studies works on LEAFY, a gene which
controls flower formation in Arabidopsis
thaliana. The Yanofsky lab at the University of
California, San Diego, USA. The Yanofsky group is
working on MADS box genes in Arabidopsis
thaliana. The Research Programme in Plant
Biotechnology, part of the Institute of
Biotechnology at the University of Helsinki,
studies regulation of flower development in
gerbera. Gerco Angenent at Plant Research
International (former CPRO) in Wageningen studies
MADS box genes in Petunia and Arabidopsis.
... and many others ...
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-)
Thanks
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Questions ?
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Questio
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The Concepts of Orthology and Paralogy