Download T. caerulescens

Comparison of biological pathways in
zinc deficient 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
– GenMAPP and MAPPFinder
– Processes for Criterion 0
– Processes for Criterion 1
•
Discussion
– Terpenoid metabolic processes upregulated
– Chromatin processes downregulated
•
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 were 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
Results from GenMAPP and MAPPFinder
• 1778 errors were found in the genes
– “Gene not found in TAIR or any related system”
• The total amount of genes found in Criterion 0
were 303 distinct genes
• The total amount of genes found in Criterion 1
were 597 distinct genes
Top processes for criterion 0
• terpenoid metabolic process
• cell surface receptor linked signal
transduction
• anchored to plasma membrane
• response to starvation
• intrinsic to plasma membrane
• isoprenoid metabolic process
• serine family amino acid
metabolic process
•
•
•
•
•
•
•
•
response to nutrient levels
response to salicylic acid stimulus
response to extracellular stimulus
protein binding
protein import
mRNA processing
response to jasmonic acid stimulus
methyltransferase activity
Top processes for criterion 1
•
•
•
•
•
•
•
•
extracellular region
lipid catabolic process
chromatin modification
establishment or maintenance of
chromatin architecture
glutamine family amino acid
metabolic process
covalent chromatin modification
pyridoxal phosphate binding
nucleosome
•
•
•
•
•
•
•
regulation of gene expression,
epigenetic
regulation of gene expression
hydrolase activity, acting on ester
bonds
chromosome organization
regulation of macromolecule
metabolic process
jasmonic acid mediated signaling
pathway
two-component response regulator
activity
Terpenoid metabolic processes are upregulated
• Terpenoids are a broad group of chemicals
• 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 instead of breaking them down
Lignin biosynthesis processes were not
seen in our results
• This does not necessarily mean the paper was
wrong
– 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.
• http://www.cyberlipid.org/simple/simp0004.ht
• A special thanks to Dr. Dahlquist for her guidance throughout
this project