Desiccation tolerance in Arabidopsis seeds: ‘omics’ data integration challenge

Description

One of the biggest challenges life encountered during its evolution and complexification was moving from sea to land. During this transition, living organisms faced new conditions such as air dryness, more intense radiation exposure and steeper fluctuating temperatures as compared to the underwater environments. Consequently, to deal with air dryness life randomly evolved a new biological program known as desiccation tolerance (DT) (Gaff & Oliver, 2013).

DT is the ability of certain organisms to deal with extreme water loss to levels below 0.1g H2O per gram dry weight and subsequent re-hydration without accumulation of lethal damage. Because of its importance in bridging periods of adverse conditions, DT remains a common trait which can be found in a broad range of organisms. DT can be found in bacteria, algae, mosses, ferns, higher plants, fungi, tardigrades, nematodes and in their spores, pollen and cystic forms, but is especially a very common trait in seeds (Potts, 1994; Challabathula & Bartels, 2013).

To express DT these organisms have to successfully employ a series of complex responses in the transcriptome, proteome and metabolome levels. These modification will lead to the perception and transduction of stress or developmental signals, the alteration of the composition of cell walls, organs and organelles, the accumulation of protective macromolecules, the induction of a repair system, and the removal of reactive oxygen species (ROS) (Moore et al., 2009; Bewley et al., 2013).

Recently we developed a method to re-induce desiccation tolerance in germinated, desiccation sensitive (DS), Arabidopsis thaliana (thale cress) seeds to facilitate the investigation of the molecular basis of DT (Maia et al., 2011). We demonstrated that DT can be fully rescued in germinated Arabidopsis seeds by the application of an osmotic treatment before drying (Maia et al., 2011). Furthermore, with the aid of some abscisic acid (ABA) insensitive and ABA-deficient mutants we have shown that ABA is necessary for the re-establishment of DT (Maia et al., 2014). We also revealed that ABA alone is sufficient to rescue DT in Col-0 and aba2-1 seeds and that aba2-1 seeds treated only with PEG failed to fully re-establish DT. Based on these results we defined an experimental design to further explore DT related mechanisms and to investigate the differences between osmotic- and ABA-induced DT (Figure 1).

With the aid of this experimental system we have generated DT related datasets for the transcriptome, metabolome and proteome. Despite our efforts to analyse these three datasets in detail, we were not able to exploit their full potential yet. Comparing such datasets with the available information is a challenge and will require new tools for data analysis, interpretation and visualization. Thus, our goal in this project is to integrate the three datasets to get better insight in the mechanisms controlling DT and to narrow down the selection of candidate genes for further gene function studies. To visualize the data and get insights from it, strategies like advanced co-expression network analysis and networks overlaying will have to be employed. This work will be developed in collaboration with the Biometrics Department and we hope that this joint effort will lead to new ideas on how to deal with and integrate big datasets that comprise biological information in different levels of complexity.

Aim of the MSc project

During the MSc thesis you take part in on the project integrating the three datasets as described above.

Key words

Desiccation tolerance, selection of candidate genes, co-expression network analysis

References

Bewley JD, Bradford K, Hilhorst H, Nonogaki H. 2013. Seeds: Physiology of Development, Germination and Dormancy: New York, US: Springer.

Challabathula D, Bartels D. 2013. Desiccation tolerance in resurrection plants: new insights from transcriptome, proteome and metabolome analysis. Frontiers in Plant Science 4.

Gaff DF, Oliver M. 2013. The evolution of desiccation tolerance in angiosperm plants: a rare yet common phenomenon. Functional Plant Biology 40(4): 315-328.

Maia J, Dekkers BJW, Provart NJ, Ligterink W, Hilhorst HWM. 2011. The re-establishment of desiccation tolerance in germinated Arabidopsis thaliana seeds and its associated transcriptome. PLoS ONE 6(12).

Maia J, Dekkers BJW, Dolle JM, Ligterink W, Hilhorst HWM. 2014. Abscisic acid (ABA) sensitivity regulates desiccation tolerance in germinated Arabidop­sis seeds. New Phytologist DOI: 10.1111/nph.12785.

Moore JP, Le NT, Brandt WF, Driouich A, Farrant JM. 2009. Towards a systems-based understanding of plant desiccation tolerance. Trends Plant Sci 14(2): 110-117.

Potts M. 1994. Desiccation tolerance of prokaryotes. Microbiological Reviews 58(4): 755-805.