Abstract
Elucidating the dynamics of molecular processes in living organisms in response to external perturbations is a central goal in modern systems biology. We investigated the dynamics of protein phosphorylation events in Arabidopsis thaliana exposed to changing nutrient conditions. Phosphopeptide expression levels were detected at five consecutive time points over a time interval of 30 min after nutrient resupply following prior starvation. The three tested inorganic, ionic nutrients NH+4, NO−3, PO3−4 elicited similar phosphosignaling responses that were distinguishable from those invoked by the sugars mannitol, sucrose. When embedded in the protein–protein interaction network of Arabidopsis thaliana, phosphoproteins were found to exhibit a higher degree compared to average proteins. Based on the time-series data, we reconstructed a network of regulatory interactions mediated by phosphorylation. The performance of different network inference methods was evaluated by the observed likelihood of physical interactions within and across different subcellular compartments and based on gene ontology semantic similarity. The dynamic phosphorylation network was then reconstructed using a Pearson correlation method with added directionality based on partial variance differences. The topology of the inferred integrated network corresponds to an information dissemination architecture, in which the phosphorylation signal is passed on to an increasing number of phosphoproteins stratified into an initiation, processing, and effector layer. Specific phosphorylation peptide motifs associated with the distinct layers were identified indicating the action of layer-specific kinases. Despite the limited temporal resolution, combined with information on subcellular location, the available time-series data proved useful for reconstructing the dynamics of the molecular signaling cascade in response to nutrient stress conditions in the plant Arabidopsis thaliana.
Highlights
Intra-cellular communication and information processing is performed by complex, dynamic, and context-specific molecular signaling networks (Terfve and Saez-Rodriguez, 2012)
We investigated the dynamics of protein phosphorylation events in Arabidopsis thaliana exposed to changing nutrient conditions
Time course studies of phosphorylation events are of high value in the context of signaling as they allow to reveal the dynamics and the cause-effect relationships between all molecular components involved in the signal transduction process (Blagoev et al, 2004; Olsen et al, 2006; Niittylä et al, 2007; Engelsberger and Schulze, 2012)
Summary
Intra-cellular communication and information processing is performed by complex, dynamic, and context-specific molecular signaling networks (Terfve and Saez-Rodriguez, 2012). Time course studies of phosphorylation events are of high value in the context of signaling as they allow to reveal the dynamics and the cause-effect relationships between all molecular components involved in the signal transduction process (Blagoev et al, 2004; Olsen et al, 2006; Niittylä et al, 2007; Engelsberger and Schulze, 2012). Besides advances on the instrumentation side, computational methods have been devised to interrogate the resulting data sets Both descriptive as well as predictive computational methods have been developed [For review, see Janes and Yaffe (2006)]. Predictive approaches employ input/output regression based methods
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