Metabolomics integrated with transcriptomics: assessing systems response to sulfur‐deficiency stress

Sulfur-containing amino acids, cysteine and methionine synthesized in plants are essential for human and animal nutrition. That is why understanding of how inorganic sulfur is taken up by plants and built into the organic molecules in the process of sulfur assimilation is important. As complex biological systems, plants subsist as integrated molecular, organelle, cell, tissue and organ entities, being in permanent synergistic coordination. The process of sulfur uptake and assimilation is an integral part of this dense network of influences, its reconstruction may help in manipulating the bioproduction of organic sulfur-containing compounds. New high-throughput technologies allow the systems' view on the coordination of complex processes in living organisms. Among them, transcriptomics and metabolomics studies were applied to Arabidopsis plants subjected to sulfur-deficiency stress. From the integrated analysis of the obtained data, the mosaic picture of distinct sulfur stress response events and processes are starting to be assembled into the whole systems' network of sulfur assimilation. At the time trajectory of sulfur stress response, two system states can be distinguished. The first state of short-term responses is characterized by the development of enhanced lateral roots exploring the space in search for the lacking nutrient. When this physiological reaction cannot be accomplished by bringing the system back to the initial state of sulfur sufficiency, a new program is toggled aiming at saving the organismal resources for vital seed production. Here, we describe the biological reasoning in these two system states and the process of state transition between them.