Figure 1.
The interaction between two enzymes in genome-scale enzyme correlation network models.
The reactions between metabolites were used to determine the interactions among enzymes. If enzyme 1 is catalyzed to produce substrates A and B, which are then used by enzyme 2 (substrate A or B produce C), the interaction was defined as enzyme 1 and enzymes 2.
Figure 2.
Schematic of “guilt by association” computational pipeline.
Metabolome of the pollen (tube) of lily (Lilium longiflorum), the significant DEGs of the Arabidopsis pollen tube and the DEGs of Arabidopsis and of maize stigmas were identified in the platform of Oracle Database and SQL (Structured Query Language). Then, metabolome of the pollen (tube) of lily, the significant DEGs that encoded enzymes of Arabidopsis and of maize were mapped to the GECN model and the protein–protein interactome network of Arabidopsis, and a sub-interaction network was constructed by the Cytoscape software. Furthermore, community analyses (NetworkAnalyzer) were used to investigate the characteristics of the systemic structure of the sub-interaction network, and to analyze transcriptional levels of genes encoding co-expressed enzymes in the consecutive steps for metabolic routes in the biological process.
Figure 3.
(a) Full GECN model of maize silk. SIF Cytoscape formation in Data S2. (b)Sub-interaction network of maize silk. .xlse file in Data S5. (c) Full GECN model of Arabidopsis. SIF Cytoscape formation in Data S1. (d) Sub-interaction network of Arabidopsis pistil. .xlse file in Data S5. (e) Distribution of enzymes in maize and Arabidopsis pistil. .xlse file in Data S3. (f) Overlap structure of GECN models of maize and Arabidopsis. .xlse file in Data S3 . (g) Distribution of enzymes of Arabidopsis pollen tube in response to pollination. .xlse file in Data S3 and Data S5. Connected pairs of nodes analyzed by NetworkAnalyzer were marked by red. Graph was generated with the Cytoscape software [75].
Figure 4.
Co-expressed enzymes and consecutive steps for superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle in lily pollen tube in vitro.
(1) –(9) present the enzymes and substrates that catalyze consecutive steps, constructing a metabolic route. These findings support the idea that pollen germination and tube growth are high-energy-consuming processes. EC numbers of enzyme were marked by red, enzymes were marked by pink, metabolic product were marked by blue.
Figure 5.
Consecutive steps of ethanol degradation II of Arabidopsis pollen tube in response to pollination.
(1)–(3) present the significant DEGs that encoded the enzymes, enzymes and substrates that catalyze consecutive steps, thereby constructing a metabolic route for ethanol degradation II of the Arabidopsis pollen tube in response to pollination. EC numbers of enzyme were marked by red, enzymes were marked by pink, metabolic product were marked by blue, significant DEGs encoded enzymes were marked by black.
Figure 6.
Consecutive steps of TCA cycle variation of Arabidopsis pollen tube in response to pollination.
(1)–(4) present the significant DEGs that encoded the enzymes, enzymes and substrates that catalyze consecutive steps, thereby constructing a metabolic route for TCA cycle variation of the Arabidopsis pollen tube in response to pollination. EC numbers of enzyme were marked by red, enzymes were marked by pink, metabolic product were marked by blue, significant DEGs encoded enzymes were marked by black.
Figure 7.
Consecutive steps of glycolysis IV pathways in Arabidopsis and maize stigmas.
(1)–(7) present the significant DEGs that encoded the enzymes, enzymes and substrates that catalyze consecutive steps, thereby constructing a metabolic route for glycolysis IV (plant cytosol) that produce high-energy nutrients (ethanol) in Arabidopsis and maize stigmas during pollination. EC numbers of enzyme were marked by red, enzymes were marked by pink, metabolic product were marked by blue, significant DEGs encoded enzymes were marked by black.
Figure 8.
Consecutive steps of kaempferol biosynthesis pathways in Arabidopsis and maize stigmas.
(1)–(7) present the significant DEGs that encoded the enzymes, enzymes and substrates that catalyze consecutive steps, thereby constructing a metabolic route for kaempferol biosynthesis from L-phenylalanine in Arabidopsis and maize stigmas. EC numbers of enzyme were marked by red, enzymes were marked by pink, metabolic product were marked by blue, significant DEGs encoded enzymes were marked by black.
Figure 9.
Cooperating of kaempferol and dTDP-alpha-L-rhamnose biosynthesis.
(1)–(4) present the significant DEGs that encoded the enzymes, enzymes and substrates that catalyze consecutive steps, thereby constructing a metabolic route that the cooperation between kaempferol and dTDP-alpha-L-rhamnose may be involved in the regulation of cell walls in the stigmatic secretory zone and the TT. EC numbers of enzyme were marked by red, enzymes were marked by pink, metabolic product were marked by blue, significant DEGs encoded enzymes were marked by black.
Figure 10.
Consecutive enzymes and metabolic routes required for the synthesis of PA in maize and Arabidopsis.
(1)–(9) present the significant DEGs that encoded the enzymes, enzymes and substrates that catalyze consecutive steps, thereby constructing a metabolic route of production of PA in Arabidopsis and maize stigmas. EC numbers of enzyme were marked by red, enzymes were marked by pink, metabolic product were marked by blue, significant DEGs encoded enzymes were marked by black.
Figure 11.
Consecutive steps of glutamate degradation IV pathways in Arabidopsis and maize stigmas.
(1)–(3) present the significant DEGs that encoded the enzymes, enzymes and substrates that catalyze consecutive steps, thereby constructing a metabolic route for glutamate degradation IV in Arabidopsis and maize stigmas. EC numbers of enzyme were marked by red, enzymes were marked by pink, metabolic product were marked by blue, significant DEGs encoded enzymes were marked by black.
Figure 12.
Schematic representation of the inferred pattern of pollen tube-stigma ethanol coupling when pollen tube elongation in the TT of the pistil.
(i) Pollen germination and tube growth are high-energy-consuming processes. (ii) When the pollen tube elongates in the TT of the pistil, pollen tube elongation triggers the mobilization of energy from glycolysis in TT cells of the pistil, which are activated to convert sugars into pyruvate. (iii) Pyruvates are further metabolized to high-energy nutrients (alcohol/ethanol), which are secreted as energy-rich metabolites (ethanol) that can then be taken up by the pollen tube.(iv) High-energy nutrients (alcohol/ethanol) are further metabolized to acetyl-CoA by ethanol degradation II in the pollen tube.(v) Acetyl-CoA is incorporated into the pollen tube's TCA cycle variation, leading to enhanced ATP production for facilitating pollen tube growth.