Species & Dataset

Experiment

Foliar Ozone Injury

  • Oryza sativa

  • Common name: Asian rice

  • Family: Poaceae

  • Cultivar: cv. Nipponbare; O. sativa L. japonica-type

  • Tissue: Third and fourth leaves of 2-week old rice plant

  • Ozone concentration: ​ 0.2 ppm

  • Ozone exposure: 24 hours

  • Sampling time: ​ 0, 6, 12 and 24 hrs after ozone treatment

  • Platform: DNA Microarray

  • Year of study: 2008

  • Location: Japan

Injury Rice.jpeg

Title: Integrated Transcriptomics, Proteomics, and Metabolomics analyses to survey ozone responses in the leaves of rice seedling

 

Summary: Ozone (O3), a serious air pollutant, is known to significantly reduce photosynthesis, growth, and yield and to cause foliar injury and senescence. Here, integrated transcriptomics, proteomics, and metabolomics approaches were applied to investigate the molecular responses of O3 in the leaves of 2-week-old rice (cv. Nipponbare) seedlings exposed to 0.2 ppm O3 for a period of 24 h. On the basis of the morphological alteration of O3-exposed rice leaves, transcript profiling of rice genes was performed in leaves exposed for 1, 12, and 24 h using rice DNA microarray chip. A total of 1535 non redundant genes showed altered expression of more than 5-fold over the control, representing 8 main functional categories. Genes involved in information storage and processing (10%) and cellular processing and signaling categories (24%) were highly represented within1h of O3 treatment; transcriptional factor and signal transduction, respectively, were the main subcategories. Genes categorized into information storage and processing (17, 23%), cellular processing and signaling (20, 16%) and metabolism (18, 19%) were mainly regulated at 12 and 24 h; their main subcategories were ribosomal protein, posttranslational modification, and signal transduction and secondary metabolites biosynthesis, respectively. Two dimensional gel electrophoresis-based proteomics analyses in combination with tandem mass spectrometer identified 23 differentially expressed protein spots (21 non redundant proteins) in leaves exposed to O3 for 24 h compared to respective control.Identified proteins were found to be involved in cellular processing and signaling (32%), photosynthesis (19%), and defense (14%). Capillary electrophoresis-mass spectrometry-based metabolomic profiling revealed accumulation of amino acids, gamma-aminobutyric acid, and glutathione in O3 exposed leaves until 24 h over control. This systematic survey showed that O3 triggers a chain reaction of altered gene, protein and metabolite expressions involved in multiple cellular processes in rice.

Reference: Cho, K., Shibato, J., Agrawal, G.K., Jung, Y.H., Kubo, A., Jwa, N.S., Tamogami, S., Satoh, K., Kikuchi, S., Higashi, T. and Kimura, S., 2008. Integrated transcriptomics, proteomics, and metabolomics analyses to survey ozone responses in the leaves of rice seedling. Journal of proteome research, 7(7), pp.2980-2998.

Gene Id
1hr
12hr-1
24hr-2
Annotation
AK110551
11.41
NA
NA
Unknown expressed protein
AK110584
NA
0.05
0.14
Arabidopsis thaliana AT4g32480/F8B4_180 mRNA, complete cds.|PLN
AK110725
NA
50.60
32.25
Arabidopsis thaliana unknown protein (At3g22060) mRNA, complete cds.|PLN
AK110901
NA
5.22
NA
Unknown expressed protein
AK111011
10.20
9.80
17.00
Unknown expressed protein
AK111022
5.26
NA
NA
Unknown expressed protein
AK111059
41.13
NA
NA
Unknown expressed protein
AK111091
NA
20.68
6.07
Unknown expressed protein
AK111094
11.30
6.31
NA
Unknown expressed protein
AK111117
12.55
NA
NA
Unknown expressed protein
AK111144
NA
6.12
NA
Unknown expressed protein
AK111266
36.69
8.21
NA
Unknown expressed protein
AK111314
NA
0.12
NA
Unknown expressed protein
AK111335
6.57
NA
NA
Unknown expressed protein
AK111686
NA
5.88
NA
Unknown expressed protein
AK111876
NA
9.91
6.35
Arabidopsis thaliana unknown protein (At1g08470) mRNA, complete cds.|PLN
AK111957
NA
5.57
NA
Arabidopsis thaliana clone 26264 mRNA, complete sequence.|PLN
AK111961
NA
7.37
NA
Unknown expressed protein
AK112034
NA
9.55
6.69
Arabidopsis thaliana unknown protein (At4g02450/T14P8_5) mRNA, complete cds.|PLN
AK107176
14.45
NA
NA
Unknown expressed protein
AK107273
NA
22.67
6.96
Arabidopsis thaliana unknown protein (At1g18480/F15H18_1) mRNA, complete cds.|PLN
AK107476
21.52
18.81
8.74
Unknown expressed protein
AK107507
NA
14.93
7.87
Unknown expressed protein
AK107574
NA
8.14
NA
Unknown expressed protein
AK107576
NA
11.96
NA
Unknown expressed protein
AK107732
12.14
41.57
22.96
Unknown expressed protein
AK107734
NA
9.93
7.46
Unknown expressed protein
AK107784
NA
7.18
6.23
Arabidopsis thaliana Unknown protein (At1g65030) mRNA, complete cds.|PLN
AK107842
5.05
NA
NA
Unknown expressed protein
AK107853
NA
8.91
8.28
Unknown expressed protein
AK107893
NA
40.13
26.18
Unknown expressed protein
AK107899
NA
NA
5.90
Unknown expressed protein
AK107906
NA
5.17
NA
A. thaliana clone 25159 mRNA; Eukaryotic protein of unknown function DUF842 family protein
AK107937
23.73
5.00
NA
Unknown expressed protein
AK107938
8.86
22.57
7.73
Unknown expressed protein
AK107964
5.08
NA
NA
Arabidopsis thaliana At1g76250 mRNA for unknown protein, complete cds,
AK107983
16.36
14.23
6.58
Unknown expressed protein
AK107989
83.67
NA
NA
Unknown expressed protein
AK108001
38.36
NA
NA
Unknown expressed protein
AK108002
13.92
6.06
NA
Unknown expressed protein
AK108109
9.58
9.17
5.06
Unknown expressed protein
AK108186
NA
NA
5.40
Arabidopsis thaliana unknown protein (At5g42500) mRNA, complete cds.|PLN
AK108198
NA
5.31
NA
Unknown expressed protein
AK108239
5.50
NA
NA
Unknown expressed protein
AK108264
NA
6.12
NA
Unknown expressed protein
AK108297
8.52
13.55
6.77
Unknown expressed protein
AK108349
NA
0.14
NA
Unknown expressed protein
AK108389
NA
14.26
12.23
A. thaliana clone C103116 (D) unknown protein (At4g11070) mRNA, complete cds.|PLN
AK108491
NA
8.24
6.38
Arabidopsis thaliana clone 106078 mRNA, complete sequence.|PLN
AK108536
17.03
NA
NA
Unknown expressed protein
AK108549
9.80
9.65
5.41
Unknown expressed protein
AK108716
NA
21.52
14.21
Arabidopsis thaliana unknown protein (At1g13510) mRNA, complete cds.|PLN
AK108734
NA
NA
0.16
A. thaliana At2g27770 mRNA for unknown protein, complete cds, clone: RAFL16-75-C06.|PLN
AK108889
NA
NA
5.05
Arabidopsis thaliana unknown protein (At5g04830) mRNA, complete cds.|PLN
AK109087
14.81
NA
NA
Unknown expressed protein
AK109098
NA
5.36
NA
Unknown expressed protein
AK109213
0.17
0.19
0.16
Unknown expressed protein
AK109216
5.49
36.50
26.42
Unknown expressed protein
AK109217
NA
0.19
NA
Unknown expressed protein
AK109228
25.14
NA
NA
Unknown expressed protein
AK109248
NA
11.84
5.72
Unknown expressed protein
AK109331
NA
5.07
NA
Unknown expressed protein
AK109337
0.17
NA
NA
Arabidopsis thaliana At5g05480/MOP10_2 mRNA, complete cds.|PLN
AK109364
NA
NA
5.78
Unknown expressed protein
AK109495
NA
0.20
NA
Unknown expressed protein
AK109525
NA
0.13
NA
Arabidopsis thaliana unknown protein (not annotated) mRNA, complete cds.|PLN
AK109659
7.29
42.94
25.68
Arabidopsis thaliana unknown protein (At1g80110) mRNA, complete cds.|PLN
AK109664
13.36
13.72
14.79
Arabidopsis thaliana unknown protein (At4g13010) mRNA, complete cds.|PLN
AK109672
NA
0.04
0.07
Unknown expressed protein
AK102548
NA
13.48
NA
Unknown expressed protein
AK102682
11.75
NA
NA
Unknown expressed protein
AK102872
NA
5.53
NA
Arabidopsis thaliana unknown protein mRNA, complete cds.|PLN
AK102921
NA
7.89
8.10
Rattus norvegicus pEachy mRNA, complete cds.|ROD
AK103002
5.69
NA
NA
Unknown expressed protein
AK103013
16.74
12.53
NA
Unknown expressed protein
AK103060
7.73
NA
NA
Unknown expressed protein
AK103305
6.58
NA
NA
Unknown expressed protein
AK103409
8.56
NA
NA
Arabidopsis thaliana Unknown protein (At3g10300; F14P13.10) mRNA, complete cds.|PLN
AK103474
NA
8.71
5.04
Arabidopsis thaliana unknown protein (At3g22280) mRNA, complete cds.|PLN
AK103542
NA
NA
7.08
Unknown expressed protein
AK103579
NA
8.15
NA
Oryza sativa Rtac1 (rtac1) mRNA, complete cds.|PLN
AK103603
NA
26.79
16.85
Unknown expressed protein
AK103897
NA
8.61
6.46
Arabidopsis thaliana unknown protein (At2g37340) mRNA, complete cds.|PLN
AK104054
NA
0.16
NA
Arabidopsis thaliana putative protein (At3g55760) mRNA, complete cds.|PLN
AK104688
NA
6.83
NA
A. thaliana unknown protein (At5g25754) mRNA, complete cds.|PLN
AK104991
25.16
NA
NA
Unknown expressed protein
AK105108
NA
6.64
NA
Arabidopsis thaliana clone U09348 unknown protein (At1g21250) mRNA, complete cds.|PLN
AK105175
10.80
20.18
8.99
Unknown expressed protein
AK105199
NA
6.00
6.74
Arabidopsis thaliana unknown protein (At3g47833) mRNA, complete cds.|PLN
AK105221
NA
6.80
9.01
Unknown expressed protein
AK105235
NA
7.93
NA
Arabidopsis thaliana unknown protein (At2g32560) mRNA, complete cds.|PLN
AK105248
NA
0.17
NA
Pharbitis nil PnC401 mRNA for leaf protein
AK105306
5.30
NA
NA
Arabidopsis thaliana AT4g05150/C17L7_70 mRNA, complete cds.|PLN
AK105331
132.84
5.62
NA
Arabidopsis thaliana At5g12010/F14F18_180 mRNA, complete cds.|PLN
AK105373
0.13
0.17
0.18
Unknown expressed protein
AK105387
NA
NA
19.68
Unknown expressed protein
AK105396
7.05
NA
NA
Unknown expressed protein
AK105511
16.14
6.80
NA
Unknown expressed protein
AK105691
5.57
NA
NA
Arabidopsis thaliana At4g28990 mRNA for unknown protein, complete cds
AK105719
NA
6.18
NA
Arabidopsis thaliana unknown protein (At4g36860) mRNA, complete cds.|PLN
AK105763
NA
5.57
7.00
Arabidopsis thaliana unknown protein (At5g64550) mRNA, complete cds.|PLN
AK105813
NA
0.20
NA
Unknown expressed protein
AK105866
NA
18.26
20.75
Unknown expressed protein
AK105937
NA
0.18
NA
Unknown expressed protein
AK105952
NA
0.18
0.12
Arabidopsis thaliana unknown protein (At1g25510) mRNA, complete cds.|PLN
AK106003
6.10
NA
NA
Arabidopsis thaliana At2g39720/T5I7.2 mRNA, complete cds.|PLN
AK106007
NA
8.94
6.89
Arabidopsis thaliana AT3g15000/K15M2_14 mRNA, complete cds.|PLN
AK106067
NA
0.19
NA
Arabidopsis thaliana AT4g03420/F9H3_4 mRNA, complete cds.|PLN
AK106155
NA
8.05
5.79
Arabidopsis thaliana Unknown protein (At1g47420) mRNA, complete cds.|PLN
AK106226
NA
7.26
6.92
Unknown expressed protein
AK106333
20.22
16.13
8.94
Unknown expressed protein
AK106356
NA
24.68
10.62
Arabidopsis thaliana unknown protein (At1g13510) mRNA, complete cds.|PLN
AK106379
10.91
NA
NA
Unknown expressed protein
AK106415
5.47
NA
NA
Arabidopsis thaliana At1g59710/T30E16_31 mRNA, complete cds.|PLN
AK106553
NA
5.34
NA
Arabidopsis thaliana Unknown protein mRNA, complete cds.|PLN
AK106757
0.18
0.02
0.03
Arabidopsis thaliana unknown protein (At2g31560) mRNA, complete cds.|PLN
AK107053
NA
7.86
NA
Unknown expressed protein
AK107136
NA
8.81
6.12
A. thaliana At5g06570 mRNA for unknown protein, complete cds, clone: RAFL19-81-P07.|PLN
AK107137
NA
6.05
NA
Arabidopsis thaliana unknown protein (At3g17510) mRNA, complete cds.|PLN
AK072854
9.44
6.53
NA
Arabidopsis thaliana unknown protein mRNA, complete cds.|PLN
AK072916
NA
0.18
NA
Arabidopsis thaliana unknown protein (At5g53470) mRNA, complete cds.|PLN
AK072982
9.62
NA
NA
Unknown expressed protein
AK073116
NA
5.30
NA
Unknown expressed protein
AK073300
NA
0.11
NA
Arabidopsis thaliana clone 1230 mRNA, complete sequence.|PLN
AK073397
NA
7.14
5.81
Unknown expressed protein
AK073475
15.03
NA
NA
Arabidopsis thaliana putative protein (At4g20400) mRNA, complete cds.|PLN
AK073492
NA
0.10
NA
Arabidopsis thaliana At2g23390/F26B6.4 mRNA, complete cds.|PLN
AK073580
6.01
NA
NA
Arabidopsis thaliana clone U20002 unknown protein (At5g03540) mRNA, complete cds.|PLN
AK073631
NA
8.27
6.25
Arabidopsis thaliana unknown protein (At1g70810) mRNA, complete cds.|PLN
AK073645
NA
5.30
6.66
Arabidopsis thaliana unknown protein (At5g64670) mRNA, complete cds.|PLN
AK073689
NA
NA
0.18
Arabidopsis thaliana unknown protein (At2g26770) mRNA, complete cds.|PLN
AK073716
NA
7.16
NA
Unknown expressed protein
AK073831
NA
0.12
NA
Unknown expressed protein
AK073913
8.34
NA
NA
Unknown expressed protein
AK099155
NA
16.33
8.46
Unknown expressed protein
AK099411
NA
0.15
0.20
Unknown expressed protein
AK099418
NA
5.04
NA
Arabidopsis thaliana unknown protein (At5g15550) mRNA, complete cds.|PLN
AK099421
NA
0.11
NA
Arabidopsis thaliana AT3g29240/MXO21_9 mRNA, complete cds.|PLN
AK099435
NA
5.11
NA
A. thaliana At1g31710 mRNA for unknown protein, complete cds, clone: RAFL16-73-D01.|PLN
AK099449
NA
NA
7.33
A. thaliana At3g02220 mRNA for unknown protein, complete cds, clone: RAFL21-38-C15.|PLN
AK099466
NA
6.11
8.98
Unknown expressed protein
AK099530
NA
15.64
7.16
Arabidopsis thaliana AT4g27310/M4I22_120 mRNA, complete cds.|PLN
AK099560
NA
0.09
NA
Arabidopsis thaliana unknown protein mRNA, complete cds.|PLN
AK099569
NA
10.83
NA
Arabidopsis thaliana unknown protein (At4g04330) mRNA, complete cds.|PLN
AK099586
NA
0.07
0.17
Arabidopsis thaliana unknown protein (At1g42550) mRNA, complete cds.|PLN
AK099618
NA
10.67
6.29
Unknown expressed protein
AK099629
NA
6.94
NA
Arabidopsis thaliana unknown protein (At3g10500) mRNA, complete cds.|PLN
AK099828
6.51
NA
NA
Unknown expressed protein
AK099916
8.16
NA
NA
Arabidopsis thaliana At2g43320/T1O24.6 mRNA, complete cds.|PLN
AK099934
NA
6.11
NA
Arabidopsis thaliana At2g31040/T16B12.15 mRNA, complete cds.|PLN
AK099949
NA
0.10
NA
Arabidopsis thaliana putative protein (At5g02540) mRNA, complete cds.|PLN
AK099963
NA
34.92
NA
Arabidopsis thaliana unknown protein (At4g37300) mRNA, complete cds.|PLN
AK099966
NA
0.15
NA
Arabidopsis thaliana unknown protein (At1g52510) mRNA, complete cds.|PLN
AK100058
8.28
10.79
7.75
Unknown expressed protein
AK100100
7.17
NA
NA
Arabidopsis thaliana At1g74800/F25A4_38 mRNA, complete cds.|PLN
AK100281
NA
0.13
NA
Unknown expressed protein
AK100305
NA
7.65
NA
A. thaliana At3g18170 mRNA: Protein of unknown function DUF563 family protein
AK100347
9.22
11.81
NA
Arabidopsis thaliana Unknown protein (At3g27390) mRNA, complete cds.|PLN
AK100715
NA
6.96
NA
Unknown expressed protein
AK100921
NA
5.20
NA
Arabidopsis thaliana unknown protein (At3g45090) mRNA, complete cds.|PLN
AK101050
NA
5.20
NA
Arabidopsis thaliana unknown protein mRNA, complete cds.|PLN
AK101106
5.29
11.67
6.71
A. thaliana At3g25070 mRNA for unknown protein, complete cds, clone: RAFL17-11-N11.|PLN
AK101110
NA
8.00
NA
Arabidopsis thaliana unknown protein (At2g36430) mRNA, complete cds.|PLN
AK101217
NA
0.14
NA
Unknown expressed protein
AK101258
14.73
11.92
5.10
Arabidopsis thaliana Unknown protein (At1g53590; T3F20.10) mRNA, complete cds.|PLN
AK101444
NA
7.90
NA
A. thaliana clone 13580 mRNA: Protein of unknown function DUF788 family protein
AK102207
NA
5.78
NA
A. thaliana AT4g15470/dl3775w mRNA; Protein of unknown function UPF0005 family protein
AK102303
NA
10.94
8.04
Arabidopsis thaliana unknown protein (At1g32230) mRNA, complete cds.|PLN
AK102507
NA
0.13
0.18
Arabidopsis thaliana unknown protein (At1g79910) mRNA, complete cds.|PLN
AK069702
NA
53.15
26.37
Arabidopsis thaliana clone 4043 mRNA, complete sequence.|PLN
AK069730
5.32
NA
NA
Unknown expressed protein
AK069792
12.01
NA
NA
Arabidopsis thaliana unknown protein (At5g52450) mRNA, complete cds.|PLN
AK069802
9.38
6.08
NA
Arabidopsis thaliana unknown protein (At1g73810) mRNA, complete cds.|PLN
AK069808
NA
7.79
NA
Arabidopsis thaliana AT3g27210/K17E12_3 mRNA, complete cds.|PLN
AK069851
0.13
NA
NA
Arabidopsis thaliana unknown protein (At5g56860; MPI10.2) mRNA, complete cds.|PLN
AK069864
6.18
NA
NA
Arabidopsis thaliana unknown protein (At1g33420) mRNA, complete cds.|PLN
AK070071
NA
12.13
6.98
Arabidopsis thaliana clone U10771 unknown protein (At3g62370) mRNA, complete cds.|PLN
AK070265
NA
6.31
NA
Arabidopsis thaliana clone 39286 mRNA, complete sequence.|PLN
AK070285
13.35
14.45
6.87
S.stapfianus pSD.13 mRNA.|PLN
AK070459
NA
9.08
NA
Unknown expressed protein
AK070474
NA
0.15
NA
Arabidopsis thaliana unknown protein (At3g26090) mRNA, complete cds.|PLN
AK070515
NA
0.15
NA
Arabidopsis thaliana clone 40589 mRNA, complete sequence.|PLN
AK070606
14.06
8.70
NA
Arabidopsis thaliana unknown protein (At1g26810) mRNA, complete cds.|PLN
AK070649
32.08
12.92
5.90
Unknown expressed protein
AK070652
11.55
9.22
NA
Arabidopsis thaliana unknown protein (At1g70090) mRNA, complete cds.|PLN
AK070704
NA
5.94
NA
Arabidopsis thaliana unknown protein (At5g54580) mRNA, complete cds.|PLN
AK070706
13.15
26.75
8.73
Unknown expressed protein
AK070731
NA
8.67
7.60
Arabidopsis thaliana unknown protein (At3g28580) mRNA, complete cds.|PLN
AK070832
0.17
0.07
0.14
Unknown expressed protein
AK070844
37.76
NA
NA
Arabidopsis thaliana clone U18725 putative nodulin protein (At1g21890) mRNA, complete cds.|PLN
AK070897
NA
6.27
NA
Arabidopsis thaliana unknown protein (F28J15.12) mRNA, complete cds.|PLN
AK070959
14.78
NA
NA
Arabidopsis thaliana clone 20442 mRNA, complete sequence.|PLN
AK070966
NA
11.07
NA
A. thaliana At2g38300 mRNA for unknown protein, complete cds, clone: RAFL17-35-G17.|PLN
AK071106
NA
NA
8.63
Unknown expressed protein
AK071110
NA
6.81
NA
Homo sapiens mRNA for ETEA;
AK071155
NA
29.31
8.56
Unknown expressed protein
AK071250
NA
0.17
NA
Arabidopsis thaliana clone 21882 mRNA, complete sequence.|PLN