This study is partially supported by the National Research Fund Luxembourg (FNR) in the AFR grant scheme
Symposium Systems Biology for Food, Feed, and Health 24th June 2014 Wageningen, The Netherlands.
A systems biology approach to unravel the effects of cadmium exposure on Arabidopsis thaliana. S. Bohler1, A. Bohler2,3, J. Deckers1, J. Vangronsveld1, J.-P. Noben4, C. Evelo2,3,J. Renaut5, A. Cuypers1 1Centre 2Department
4Biomedical
for Environmental Sciences, Hasselt University, Belgium.
of Bioinformatics-BIGCAT, Maastricht University, The Netherlands.
3Netherlands
5Centre
Consortium of Systems Biology, The Netherlands.
Institute, Hasselt University, Belgium.
de Recherche Public - Gabriel Lippmann, Department of Environment and Agrobiotechnologies, Luxembourg.
[email protected]
INTRODUCTION Cadmium (Cd) is a biologically non-essential, toxic, metallic trace element. It is a pollutant which mostly accumulates in soils due to mining, metal industry, waste incineration, and the application of phosphate fertilizers. In plants, Cd leads to decreased yield and, eventually, death. Furthermore, Cd enters the food chain through plants to reach food and feed, in which it has detrimental effects for animal and human health. Cleansing of contaminated soils by phytoremediation has been proposed, but due to the negative effects of Cd in plants, such as the induction of oxidative stress, it is necessary to have a thorough understanding of the underlying molecular responses of plants to Cd exposure.
MATERIALS AND METHODS • Arabidopsis
thaliana
(Columbia)
plants
Fig. 1: Cadmium (Source: Wikipedia)
VISIBLE SYMPTOMS were
grown
in
a
hydroponics
system
(Hoogland). After 19 days of growth 5 µM CdSO4 was added to the nutrient solution of treated plants. Control and treated Arabidopsis rosettes of were harvested after 0, 24 h and 72 h of treatment (Fig. 2). • Proteins
were
extracted
using
TCA/acetone
and
separated
by
different
gel
electrophoresis (DiGE). Genes of interest were selected according to the proteomics results and transcript abundance was measured by qPCR (Fig. 3). • Proteomics and transcriptomics data was integratively visualized on the Arabidopsis
Fig. 2: After only 72 hours of treatment clear signs of stress were visible in the form of
Primary Plant Metabolism pathway drawn using PathViso and shared on WikiPathways
necroses on leaves.
(WP2499) (Fig. 4).
REPRESENTATION OF OMICS DATA p-value < 0,001 p-value < 0,01 p-value < 0,05
Gene expression 72 h p-value Gene expression 72 h fold change Gene expression 24 h p-value Gene expression 24 h fold change Protein abundance p-value Protein abundance 72 h fold change Protein abundance 24 h fold change
rule not met fold change > 1,5 fold change < -1,5 rule not met
337
Fig. 2: 2DE
407 333
589 618
gel image of
1222
1258
the internal
1308
1268
550
524
596 523
816 597
1092
600 1276
1279
826 1403
1163
1247 1481
1346 1468
standard
1520
1484
1434 1599
1706
1695 1700
showing
1760
1827
1839
1931 1982
2165
2210 2345
identified
2398 2295 2461
differentially
2479
2438
2683 2571
abundant
2742
2807
proteins.
2828
DISCUSSION • Differentially abundant proteins were mostly involved in primary
carbon
metabolism,
photosynthesis,
and
glutathione based detoxification. • Transcriptomics data was mostly confirmatory of the Proteomics results. • Many
of
the
proteins
of
interest
use
NAD/NADH
or
NADP/NADPH as a cofactor. NADH and NADPH are the most important carriers of reducing power and of utter importance during oxidative stress. Furthermore this is an indication of the importance of redox regulation. Fig. 4: Proteomics and transcriptomics data visualized on the Arabidopsis Primary Plant Metabolism pathway (WP2499).
