Download Interpretation of Arabidopsis Thaliana and T

Comparison of biological pathways
in zinc decificent Arabidopsis
thaliana to zinc excess Thlaspi
caerulescens
BioInformatics Lab
Tuesday, April 13, 2010
Kristoffer Chin
Salomon Garcia
Michael Piña
Outline
• Introduction
– Van der Mortal paper was used to find the differences in gene
between normal zinc accumulators and hyperaccumulators
– Results from paper yield to many differences in gene expression
from the conditions set
– Comparison of extreme conditions in order to find specific
differences form the 2,272 genes observed
• Materials and methods
– GeneMAPP and MAPPfinder used to visualize the genes that
were found in the deficient A. thaliana and excess T.
caerulescens
• Results
• Discussion
• References
Micronutrients are essential for plant
species in growth, protection, and etc.
• Microcuntrients play a role with the growth
and duration of plant life
• Zinc has been one of the most importaant
nutrients in plant growth
– Too much zinc can be toxic to plants
– Too little zinc can inhibit optimal growth fo
plants
• Zinc homeostasis is important to plant life
Van de Mortal’s paper uses A. thaliana and
T. caerulescens to better understand
hyperaccumulators
• T. caerulescens is a plant similar to A. thaliana
but is a known to be a zinc hyperaccumulator
• These two plants were used as subjects due to
their similarity
• Both plants were grown in 3 conditions,
Deficient, sufficient, and excess zinc, and then
had their genes analyzed
• DNA Microarray analysis showed an altered
expression of many genes in both plants,
specifically Zinc transport proteins and lignin
biosynthesis
A. thaliana and T. caerulescens share
88.5% DNA identity in coding regions
schaechter.asmblog.org
A. thaliana
T. caerulescens
608 genes were identified in A. thaliana and
organized into clusters
Cluster I
Cluster II
Cluster III
Cluster IV
# of genes
found
98 genes
128 genes
347 genes
35 genes
Condition
found in
Sufficient and
excess
Excess
Deficient
Deficient and
Sufficient
Functions
•stress
response
•Metabolism
•Heat schock
proteins
•15 with
unkown
function
•20 not
annotated
•Iron
homeostasis
•Metal
transporters
•Stress
response
•Metabolism
•Transcription
factors
•Metal
homeostasis
•Metal
transporter
•Protein
stability
•Signal
transduction
•Transcription
regulation
•Metabolism
•164 genes
unknown
•Secondary
metabolism
•Biotic stress
response
•Transcription
•5 genes with
unkown
function
350 genes were identified in T. caerulescens
and organized into 6 clusters
Cluster I
Cluster II
Cluster III
Cluster IV
# of genes
found
98 genes
128 genes
347 genes
35 genes
Condition
found in
Sufficient and
excess
Excess
Deficient
Deficient and
Sufficient
Functions
•stress
response
•Metabolism
•Heat schock
proteins
•15 with
unkown
function
•20 not
annotated
•Iron
homeostasis
•Metal
transporters
•Stress
response
•Metabolism
•Transcription
factors
•Metal
homeostasis
•Metal
transporter
•Protein
stability
•Signal
transduction
•Transcription
regulation
•Metabolism
•164 genes
unknown
•Secondary
metabolism
•Biotic stress
response
•Transcription
•5 genes with
unkown
function
An overall 2,272 genes were found to be
highly expressed between the two plants
A. thaliana
T. caerulescens
• 420 genes not expressed
in root
• Little variation in
expression among
conditions
• Less expression in PDF
genes
• Less lignin biosynthesis
genes
• Less cellular process
• Less transport process
• Less stress response
• Less transcription
• 420 genes expressed in
root
• High variation variation in
expression among
conditions
• More expression in PDF
genes
• More lignin biosynthesis
genes
• More cellular process
• More transport process
• More stress response
• More transcription
Comparison of extreme conditions
yields to significant gene differences
• Of the different combination, deficient A. thaliana
and excess T. caerulescens were chosen
• Extreme conditions chosen because it would
show the most altered expression of genes
• Genes that are expected to be found would deal
with zinc transporters, homeostasis, and lignin
biosynthesis
• Each gene has its own function which ultimately
helps the plant in deficient and sufficient
Genes labeled in Excel and data was
normalized to calculate in GenMAPP
• van de Mortel’s data set was labeled in a
different way and had to be altered in
order to understand the significance
• The data on excel was then normalized in
order to fit the GenMAPP protocol
• GenMAPP is used to visualize gene
expression
– Helps to group genes together and find its
functional expression for the subject
MAPPfinder finds the relativity of genes
that were increased or decreased in
extreme conditions
• GeneMAPP grouping was inserted in MAPP
finder in order to produce a tree that helps
visualize the genes
– Even though genes were found in the extreme
conditions, they can be related to one another
through DNA similarities
• MAPPfinder results were then placed in MS
Excel in order to filter out the amount of genes
found
– Numbers changed – Greater than 3, Less than 100
– Z score – Greater than 2
– PermuteP – Less than 0.05
Terpenoid metabolic processes are
upregulated
• Other branched processes of terpenoid
metabolic processes are also upregulated
– Isoprenoid metabolic process
• In plants, terpenoids are sometimes added to
proteins to increase attachment to cell
membranes
• Protein binding and import also show
upregulation, suggesting the plant is trying to
pump out as much zinc as possible using
membrane proteins
Chromosome and chromatin
processes are downregulated
• Excess zinc may be interfering with
regulation of genetic material
– Can lead to plant death
• Lipid catabolic process also
downregulated
– Terpenoids are lipids
– Plant may be preserving lipids to convert
them in to terpenoids
Lignin biosynthesis processes
were not found in our results
• We chose to do a comparison of deficient
zinc in A. thaliana and excess zinc in T.
caerulescens
• Paper found differences in lignin
biosynthesis among T. caerulescens with
deficient zinc
Areas for future study
• Create a new database for A. thaliana with
the most up to date information
• Create a MAPP file with GenMAPP in
order to visualize grouping of genes
References
• van de Mortel JE, Almar Villanueva L, Schat H,
Kwekkeboom J, Coughlan S, Moerland PD, Ver Loren
van Themaat E, Koornneef M, and Aarts MG. Large
expression differences in genes for iron and zinc
homeostasis, stress response, and lignin biosynthesis
distinguish roots of Arabidopsis thaliana and the related
metal hyperaccumulator Thlaspi caerulescens. Plant
Physiol 2006 Nov; 142(3) 1127-47.