Simplified model structure of the primary metabolism according to metabolic clusters.

<p>The model was derived by interconnecting the metabolic clusters by functions of interconversion (<i>f_i</i>). Clusters are named according to the description in the main text (<i>Results)</i> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092299#pone.0092299.s002" target="_blank">Table S1</a>.</p

Relative changes of metabolic clusters under light and extended night conditions.

<p>Bars indicate the ratios of metabolic clusters from Col-0 under extended night and light conditions. Clusters are named according to the description in the main text (<i>Results)</i> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092299#pone.0092299.s002" target="_blank">Table S1</a>.</p

Relative activity of the pyruvate dehydrogenase complex in Col-0 under conditions of light and extended night.

<p>Enzyme activity is given in arbitrary units which are normalised to gram fresh weight. The blue bar shows relative activity under normal light condition, the red bar shows activity under condition of extended darkness. The difference of relative activity is significant (p<0.05) and bars represent means ± SD (n  = 5).</p

Development of a superpathway model for primary leaf metabolism.

<p>The model structure was derived from stoichiometric and biochemical information provided by genome-scale metabolic networks and databases. The model is provided in SBML format in the supplements (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092299#pone.0092299.s003" target="_blank">Model S1</a>).</p

Differential Jacobian of Col-0 under conditions of light and extended night.

<p>Bars represent the log₂-ratio of the entries in the Jacobian matrices of Col-0 under conditions of light (L) and extended night (EN), which were derived from covariance data of metabolomics data sets. Blue colour indicates a ratio >1, i.e. the Jacobian entry of the samples of extended night was higher than under normal light. White colour indicates a ratio <1, i.e. the Jacobian entry of the samples of extended night was lower than under normal light. All entries represent median values of 10³ calculations normalised to the square of interquartile distance. (<b>A</b>) and characterize the entries of the Jacobian matrix and refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092299#pone.0092299.e001" target="_blank">equation 1</a>. (<b>B</b>) shows the diagonal entries of the Jacobian matrix belonging to the metabolites described on the horizontal axis.</p

Contribution of metabolite interconversion functions to the best numerical solution of the simplified metabolic network model.

<p>Numbers of metabolite interconversion functions are indicated on x- and y-axis. The colour bar indicates the relative decrease of the cost function value, i.e. improvement of solution, when a function or a combination of functions was varied during the optimization process. All cost function values were normalised to the best of all optimization runs (100%). Functions were optimized for the simulation of the metabolic homeostasis of Col-0 under extended darkness.</p

Integration of the changes in the metabolites associated with selected metabolic pathways in the upper non-inoculated leaves from the PVY^N-inoculated and PVY^NTN-inoculated plants, relative to the mock-inoculated plants.

<p>The metabolites identified from the primary and secondary metabolism and from redox reactions are shown. Each coloured square represents the log2 ratios of the concentration (red, high; green, low) at 3 and 6 dpi in the upper non-inoculated leaves of the PVY^N-inoculated (N:m) and PVY^NTM-inoculated (NTN:m) plants, relative to the mock-inoculated plants (as indicated). MapMan BINs linked to primary metabolism: 2.1.1 major CHO metabolism, sucrose synthesis; 2.2.1 major CHO metabolism, sucrose degradation; 2.2.2 major CHO metabolism, starch degradation. MapMan BINs linked to the GABA shunt: 13.1.1.1 amino-acid metabolism, GABA synthesis; 8.1. TCA; 22. polyamine metabolism; 12.2.1002 N-metabolism, ammonia. MapMan BINs linked to secondary metabolism: 16.2.1 secondary metabolism, phenylpropanoids biosynthesis; 13.1. amino-acid synthesis.</p

Overview of the response of individual leaf sample and changes of metabolites in inoculated leaves.

<p>Mock-inoculated (S, 1 to 6), PVY^N-inoculated (N, 1 to 6), and PVY^NTN-inoculated (NTN, 1 to 6) leaves, collected at 1, 3 and 6 dpi, are shown. Distance matrix (A) shows more similar responses between samples collected at 1 dpi and at 6 dpi, while less uniform response is observed in samples collected at 3 dpi. Hierarchical clustering (B) was done on a set of identified metabolites to which metabolite ontology (metabolic pathway) was assigned. Clusters of metabolites linked to amino-acid synthesis and those linked to secondary metabolism and cell wall clustered together.</p

Integration of the changes in the metabolites and transcripts associated with selected metabolic pathways in the PVY^N-inoculated and PVY^NTN-inoculated leaves, relative to the mock-inoculated leaves.

<p>The metabolites identified and the genes analysed from the primary and secondary metabolism and from redox reactions are shown. Each coloured square represents the log2 ratios of the expression or abundance (red, high; green, low) at 1, 3 and 6 dpi in the PVY^N-inoculated (N:m) and PVY^NTN-inoculated (NTN:m) leaves, relative to the mock-inoculated leaves (as indicated). MapMan BINs linked to primary metabolism: 2.1.1 major CHO metabolism, sucrose synthesis; 2.2.1 major CHO metabolism, sucrose degradation; 2.2.2 major CHO metabolism, starch degradation. MapMan BINs linked to the GABA shunt: 13.1.1.1 amino-acid metabolism, GABA synthesis; 8.1. TCA; 22. polyamine metabolism; 12.2.1002 N-metabolism, ammonia. MapMan BINs linked to secondary metabolism: 16.2.1 secondary metabolism, phenylpropanoids biosynthesis; 13.1. amino-acid synthesis.</p