Transcriptome Analysis Identifies
Candidate Genes in Response to Biotic
and Abiotic Stresses in Arabidopsis
Dr. Synan AbuQamar
Plants are exposed to various environmental stresses
Fungi (i.e. Botrytis cinerea)
Osmotic
Heat
Nematodes
Salinity
bacteria
Drought
Insects
Cold
Animal
Oxidative
viruses
Abiotic Stresses
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Biotic Stresses
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Botrytis cinerea is a major disease problem
* Botrytis is a necrotrophic pathogen
- A broad host range
- Grey mold under diverse conditions
- Significant yield losses
* Disease management-Fungicide application
tomato
* No G-F-G Interaction
* JA/ET- & ABA-mediated
necrotroph
strawberry
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grape
3
Plant Defense Mechanisms
Passive
Active
(induced when the plant is
challenged by a pathogen)
Physical
cuticle, cell wall
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Chemical
phenolics, alkaloids
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Research Scheme – Reverse Genetics
Arabidopsis
Stress - B. cinerea
Microarray chip
?
Function
Data analysis
Microarray hybridization
5
Previous work on Arabidopsis and tomato
The Plant Cell, Vol. 18, 257–273, January 2006, www.plantcell.org ª 2005 American Society of Plant Biologists
The Membrane-Anchored BOTRYTIS-INDUCED KINASE1
Plays Distinct Roles in Arabidopsis Resistance to Necrotrophic
and Biotrophic Pathogens
W
Paola Veronese,a Hirofumi Nakagami,b Burton Bluhm,a Synan AbuQamar,a Xi Chen,c John Salmeron,c
Robert A. Dietrich,c Heribert Hirt,b and Tesfaye Mengistea,1
The Plant Cell, Vol. 15, 2551–2565, November 2003, www.plantcell.org © 2003 American Society of Plant Biologists
The BOTRYTIS SUSCEPTIBLE1 Gene Encodes an R2R3MYB
Transcription Factor Protein That Is Required for Biotic and
Abiotic Stress Responses in Arabidopsis
Tesfaye Mengiste,a,1 Xi Chen,b John Salmeron,b and Robert Dietrichb
The Plant Cell, Vol. 20: 1964–1983, July 2008, www.plantcell.org ã 2008 American Society of Plant Biologists
Tomato Protein Kinase 1b Mediates Signaling of Plant
Responses to Necrotrophic Fungi and Insect Herbivory
W
Synan AbuQamar, Mao-Feng Chai, Hongli Luo, Fengming Song,1 and Tesfaye Mengiste2
The Plant Journal
(2009) 58, 347–360
doi: 10.1111/j.1365-313X.2008.03783.x
Crosstalk between biotic and abiotic stress responses
in tomato is mediated by the AIM1 transcription factor
Synan AbuQamar1, Hongli Luo1, Kristin Laluk1, Michael V. Mickelbart2 and Tesfaye Mengiste1,*
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Previous work on Arabidopsis and tomato
M OL E CUL A R P LA N T PA THOL OGY (20 1 3) 14(8) , 813 –827
D O I : 1 0 . 1 1 1 1 / m p p. 1 2 0 4 9
A mutation in the expansin-like A2 gene enhances resistance to
necrotrophic fungi and hypersensitivity to abiotic stress in
Arabidopsis thaliana
SYNAN ABUQAMAR*, SUAD AJEB, ARJUN SHAM, MOHAMED RIZQ ENAN AND RABAH IRATNI
Department of Biology, College of Science, United Arab Emirates University, PO Box 15551, Al-Ain, United Arab Emirates
Plant Biochemistry & Physiology
Editorial
AbuQamar, J Plant Biochem Physiol 2014, 2:1
http://dx.doi.org/10.4172/2329-9029.1000e118
Open Access
Expansins: Cell Wall Remodeling Proteins with a Potential Function in
Plant Defense
Synan AbuQamar*
Department of Biology, College of Science, United Arab Emirates University, UAE
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Transcriptome Analysis Reveals Genes Commonly
Induced by Botrytis cinerea Infection and Major
Abiotic Stresses in Arabidopsis
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Highly conserved expression status of genes common to
B. cinerea and abiotic stress responses
Upregulated
Heat
Osmotic
stress
B. cinerea
Salinity
Downregulated
Heat
B. cinerea
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Osmotic
stress
Salinity
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Comparisons of gene expression in Arabidopsis plants under biotic
and abiotic stress conditions.
Up-regulated Down-regulated
Table 1. Regulation of B. cinerea-regulated genes by different stimuli.
Co-upregulated genes
Co-downregulated genes
Treatment
No of genes Percentagea No of genes Percentage
Coldb
373
24.9
377
33.1
Droughtb
92
6.1
77
6.8
b
Oxidative stress
176
11.7
63
5.5
Heat
37
2.5
87
7.6
Salinity
284
19.0
215
18.9
Osmotic stress
618
41.2
546
47.8
All stresses
3
0.2
12
1.1
Shown are percentages of BUGs and BDGs (at least twofold) that were also
at least twofold increased or decreased by the abiotic stress listed above.
a
Percentage = No of up- or down-regulated genes of the abiotic stress/No of
BUGs (1498 genes) or BDGs (1138 genes). BUGs and BDGs were obtained
from [20].
b
Results were obtained from [20].
1
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Changes in expression of up- or down-regulated genes during
B. cinerea and abiotic stress treatments in Arabidopsis plants
Gene ID
Gene family
Probe set
B. cinerea
Abiotic stress
Cold
Drought
Oxidative
stress
At1g73480
Hydrolase
245734
2.37
15.39
2.07
2.33
At4g34980
Subtilisin-like serine protease 2 (SLP2)
253218
2.09
3.02
2.96
2.64
At4g23600
Coronatine induced 1 (CORI3)/Jasmonic acid
responsive 2 (JR2)
254232
24.81
5.84
3.90
2.01
At2g33380
Responsive to desiccation 20 (RD20)
255795
5.15
13.81
5.24
3.30
At3g05030
Sodium proton exchanger 2 (NHX2)
259081
2.63
2.21
2.56
2.11
At1g72380
Unknown
260450
2.24
2.05
2.11
2.02
At2g39420
Esterase/lipase/thioesterase
266977
3.72
2.05
3.23
2.12
At2g39250
Schnarchzapfen (SNZ)
267010
2.41
4.98
2.02
2.37
At2g41870
Remorin
267538
2.54
3.35
3.20
2.45
At5g64570
Beta-xylosidase 4 (BXL4/XYL4)
247266
22.35
217.18
23.23
22.08
At5g57560
Touch 4 (TCH4)
247925
22.63
26.42
27.02
23.73
At5g49450
Basic leucine-zipper 1 (BZIP1)
248606
22.94
211.97
22.80
22.73
At5g48430
Aspartic-type endopeptidase/pepsin
248703
22.08
22.96
22.12
23.56
At5g41080
Glycerophosphoryl diester phosphodiesterase
(GDPD2)
249337
22.19
214.76
25.96
25.14
At5g24030
SLAC1 homolog 3 (SLAH3)
249765
22.65
24.89
22.86
22.03
At5g19120
Aspartic-type endopeptidase/pepsin
249923
22.08
220.05
23.17
22.46
At3g59900
Unknown
251436
22.88
22.59
26.24
22.89
At3g50560
Short-chain dehydrogenase/reductase (SDR)
252167
25.21
24.99
22.52
22.58
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Identification of differentially expressed genes in response to
Table 2. Changes in expression of up-/down-regulated genes encoding putative proteins during
B.andcinerea
B. cinerea infection and heat, salinity,
osmotic stress treatments in wild-type Arabidopsis
plants.
Gene
locus
At5g22860
At5g06190
At4g13800
At4g12910
At2g33380
At3g14067
At3g03310
At3g05030
At1g70900
At2g42540
At2g06890
At2g46240
At2g39250
At5g25190
At5g49450
At5g48430
At5g41080
At5g39580
At5g19120
At5g05440
At3g50560
At3g50060
At3g46280
At4g21870
06/10/2015 At4g12470
Gene family
Probe
set
B.cinereaa,b
serine carboxypeptidase S28
Unknown
permease-related
SCPL20
RD20
subtilase
LCAT3
NHX2
Unknown
COR15A
transposable element gene
BAG6
SNZ
ESE3
BZIP1
aspartyl protease/Pepsin A30
GDPD2
Peroxidase
aspartyl protease/Pepsin A20
PYL5/RCAR8
SDR
MYB77
protein kinase-related
HSP26.5-P
protease inhibitor (AZI1)
249860
250722
254683
254791
255795
256997
259057
259081
262313
263497
266214
266590
267010
246932
248606
248703
249337
249459
249923
250777
252167
252193
252511
254384
254818
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6.511
2.241
2.487
3.236
5.153
2.271
2.88
2.627
2.10
7.40
2.43
2.631
2.413
-2.18
-2.94
-2.08
-2.19
-6.16
-2.08
-2.24
-5.21
-3.01
-10.92
-2.18
-4.07
Abiotic stressa
Osmotic
Heat
Salinity
stress
2.222
3.116
12.929
2.133
3.335
3.757
2.425
3.214
12.075
2.070
2.909
2.735
2.360
5.936
26.651
2.166
2.684
6.830
2.38
5.18
17.57
3.144
3.396
4.889
2.01
2.83
4.92
2.88
88.16
102.16
2.40
2.18
2.44
2.023
56.992
3.703
2.432
4.054
11.476
-3.85
-8.93
-5.73
-5.76
-2.47
-8.42
-2.28
-4.65
-3.80
-11.50
-3.33
-8.52
-9.85
-7.38
-11.29
-5.61
-14.62
-27.66
-8.22
-15.34
-11.26
-2.15
-6.98
-5.91
-4.63
-5.27
-2.43
-15.38
-5.26
-25.77
-3.06
-9.16
-7.77
-13.71
-14.99
-14.45
12
Validation of expression profiles of common genes to B.
cinerea infection
At2g20670
At2g20670
At2g17880
DJC24
At1g15550
GA4/GA3ox1
At1g21910
DREB26
At4g08950
EXO
At2g39420
At2g39420
At2g33380
RD20
At4g23600
CORI3
At1g73480
At1g73480
-7
-7
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-5
-5
-3
-3
1
3
-1
-1 1
3
Fold Change
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5
7
7
9
9
11
11
13
13
RD20 gene contributes to the plant resistance to biotic and
abiotic stresses
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α-linolenic acid
LOX
AOS
ROS
AOC
PPA1
OPDA
OPR3
OPCs
β-oxidation
JA
Electrophile
Effect
JA-Ile
COI1
COI1
COI1
PHO1;H10
JR3
HPL
VSP2
MRP
TGA
Gene expression and Response
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Enzymatic pathway
Nonenzymatic pathway
Botrytis
Regulation of cyclopentenone-induced genes during B. cinerea
infection and abiotic stress
Array Element
Gene Locus
Description
Normalized Fold Inductiona
PPA1b
OPDAb
TGACGb
B. cinereac
Abiotic
stressd
OBUGs
249417_at
At5g39670
Calcium-binding EF-hand family
protein
N
2.8
2.2
250781_at
At5g05410
Dehydration-responsive element- N
binding (DREB2A)
4.4
3.4
C,Ox
256576_at
At3g28210
Zinc-finger protein (PMZ)
N
17.4
7.9
C,Ox
247655_at
At5g59820
Zinc-finger protein (ZAT12/
RHL41)
N
3.5
3.6
C,Ox
264968_at
At1g67360
Rubber elongation factor (REF)
N
2.0
3.5
C
251336_at
At3g61190
BON1-associated protein 1
(BAP1)
N
2.5
2.6
C
265499_at
At2g15480
UDP-glucose transferase
(UGT73B5)
N
6.7
3.1
Ox
252515_at
At3g46230
Heat-shock protein 17.4
(HSP17.4)
N
12.4
3.3
Ox
254890_at
At4g11600
Glutathione peroxidase 6 (GPX6) N
3.2
5.2
C
249719_at
At5g35735
Auxin-induced protein
N
3.4
12.3
C,Ox
264929_at
At1g60730
Aldo/keto reductase (NADP activ- N
ity)
4.6
5.4
Ox
262517_at
At1g17180
GSTU25
17
N
10.8
Ox
266267_at
At2g29460
GSTU4/GST22
3.7
N
9.3
Ox
266752_at
At2g47000
Multidrug-resistant ABC transpor- 8.7
ter (MDR4)
N
6.6
Ox
256221_at
At1g56300
DNAJ heat shock
N
26.7
C
252984_at
At4g37990
Cinnamyl-alcohol dehydrogenase 15
(CADB2)/Elicitor activated gene
(ELI3-2)
N
75.2
Ox
At3g12110
ACT11
23.6
N
24.2
C
22.6
Ox
18.3
Ox
PBUGs
3.5
PBDGs
256275_at
OBUGs and PBUGs
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261763_at
At1g15520
ABC transporter (PDR12)
24.5
18.7
258277_at
At3g26830
Phytoalexin deficient 3 (PAD3)
9.6
7.9
249942_at
At5g22300
Nitrilase 4 (NIT4)
9.3
6.6
P
4.1
266995_at
At2g34500
Cytochrome P450 family
(CYP710A1)
5.8
3.8
P
9.3
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Ox
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Expression of OBUGs/PBUGs and abiotic stress-regulated
genes to B. cinerea infection.
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Conclusion
• We showed a complex network of biological systems that control
plant/environment interactions
gene function/dynamic relationships
at the molecular levels.
• Many genes were identified
general markers of common responses
to biotic and abiotic stresses (in some cases as responses mediated by
oxylipin cyclopentenones),
• Identification of common regulators of plant responses to environmental
constraints
genetic engineering and breeding programs to develop
broad-spectrum stress-tolerant crops,
• Future research
dissect specific functions of stress-involved
components; and to map all implicated elements in stress signal
transduction pathways.
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RESEARCH ARTICLE
Transcriptome Analysis Reveals Genes
Commonly Induced by Botrytis cinerea
Infection, Cold, Drought and Oxidative
Stresses in Arabidopsis
Arjun Sham1., Ahmed Al-Azzawi1., Salma Al-Ameri1, Bassam Al-Mahmoud1,
Falah Awwad2, Ahmed Al-Rawashdeh3, Rabah Iratni1, Synan AbuQamar1*
RESEARCH ARTICLE
Identification of Arabidopsis Candidate
Genes in Response to Biotic and Abiotic
Stresses Using Comparative Microarrays
Arjun Sham1, Khaled Moustafa 2, Salma Al-Ameri1, Ahmed Al-Azzawi1,
Rabah Iratni1, Synan AbuQamar1*
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Acknowledgments
•
•
•
•
•
•
•
Mr. Arjun Sham
Ms. Salma Al-Ameri
Mr. Ahmed Al-Azzawi
Mr. Noushad Karuvantevida
Dr. Rabah Iratni
Dr. Falah Awwad
Dr. Ahmed Al-Rawashdeh
• Prof. Elizabeth Blee/Laboratoire
des Phytooxylipines - France
Financial Support
Khalifa Center for
Genetic Engineering &
Biotechnology
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