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Correlation-Based Network Analysis of Metabolite and Enzyme Profiles Reveals a Role of Citrate Biosynthesis in Modulating N and C Metabolism in Zea mays.

Toubiana D, Xue W, Zhang N, Kremling K, Gur A, Pilosof S, Gibon Y, Stitt M, Buckler ES, Fernie AR, Fait A - Front Plant Sci (2016)

Bottom Line: The overall higher CV values for metabolites as compared to the tested enzymes are indicative for their greater phenotypic plasticity.H(2) tests revealed galactinol (1) and asparagine (0.91) as the highest scorers among metabolites and nitrate reductase (0.73), NAD-glutamate dehydrogenase (0.52), and phosphoglucomutase (0.51) among enzymes.The latter displayed the strongest node-betweenness value (185.25) of all nodes highlighting its fundamental structural role in the connectivity of the network by linking between different communities and to the also strongly connected enzyme aldolase.

View Article: PubMed Central - PubMed

Affiliation: Institute of Dryland Biotechnology and Agriculture, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev Midreshet Ben-Gurion, Israel.

ABSTRACT
To investigate the natural variability of leaf metabolism and enzymatic activity in a maize inbred population, statistical and network analyses were employed on metabolite and enzyme profiles. The test of coefficient of variation showed that sugars and amino acids displayed opposite trends in their variance within the population, consistently with their related enzymes. The overall higher CV values for metabolites as compared to the tested enzymes are indicative for their greater phenotypic plasticity. H(2) tests revealed galactinol (1) and asparagine (0.91) as the highest scorers among metabolites and nitrate reductase (0.73), NAD-glutamate dehydrogenase (0.52), and phosphoglucomutase (0.51) among enzymes. The overall low H(2) scores for metabolites and enzymes are suggestive for a great environmental impact or gene-environment interaction. Correlation-based network generation followed by community detection analysis, partitioned the network into three main communities and one dyad, (i) reflecting the different levels of phenotypic plasticity of the two molecular classes as observed for the CV values and (ii) highlighting the concerted changes between classes of chemically related metabolites. Community 1 is composed mainly of enzymes and specialized metabolites, community 2' is enriched in N-containing compounds and phosphorylated-intermediates. The third community contains mainly organic acids and sugars. Cross-community linkages are supported by aspartate, by the photorespiration amino acids glycine and serine, by the metabolically related GABA and putrescine, and by citrate. The latter displayed the strongest node-betweenness value (185.25) of all nodes highlighting its fundamental structural role in the connectivity of the network by linking between different communities and to the also strongly connected enzyme aldolase.

No MeSH data available.


Metabolic pathway schematic overview. Schematic overview of metabolic pathways highlighting the TCA cycle in respect to glutamate, putrescine and GABA synthesis. Metabolites and enzymes are color-coded in accordance to compound classes and enzymes in the network (Figure 3, (Supplementary Figure 1). Adobe Illustrators was used to generate graphical output.
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Figure 5: Metabolic pathway schematic overview. Schematic overview of metabolic pathways highlighting the TCA cycle in respect to glutamate, putrescine and GABA synthesis. Metabolites and enzymes are color-coded in accordance to compound classes and enzymes in the network (Figure 3, (Supplementary Figure 1). Adobe Illustrators was used to generate graphical output.

Mentions: Last, the polyamine putrescine significantly correlated with the amino acid GABA. Both metabolites showed an interesting link with NAD isocitrate dehydrogenase, which could indicate a coordination of 2-oxo-glutarate biosynthesis with its integration within the GABA shunt both as a precursor of glutamate (via GDH) and as an amino acceptor (via GABA transaminase) (Figure 5). The pathway from putrescine to GABA is known (Ditomaso et al., 1992; Fait et al., 2008) and reference therein): putrescine can be converted via a two step oxidation into GABA (Figure 5). Though the pathway has been defined, only few other studies identified robust links between these two metabolites (Flores and Filner, 1985) and under stress (Shelp et al., 2012).


Correlation-Based Network Analysis of Metabolite and Enzyme Profiles Reveals a Role of Citrate Biosynthesis in Modulating N and C Metabolism in Zea mays.

Toubiana D, Xue W, Zhang N, Kremling K, Gur A, Pilosof S, Gibon Y, Stitt M, Buckler ES, Fernie AR, Fait A - Front Plant Sci (2016)

Metabolic pathway schematic overview. Schematic overview of metabolic pathways highlighting the TCA cycle in respect to glutamate, putrescine and GABA synthesis. Metabolites and enzymes are color-coded in accordance to compound classes and enzymes in the network (Figure 3, (Supplementary Figure 1). Adobe Illustrators was used to generate graphical output.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4940414&req=5

Figure 5: Metabolic pathway schematic overview. Schematic overview of metabolic pathways highlighting the TCA cycle in respect to glutamate, putrescine and GABA synthesis. Metabolites and enzymes are color-coded in accordance to compound classes and enzymes in the network (Figure 3, (Supplementary Figure 1). Adobe Illustrators was used to generate graphical output.
Mentions: Last, the polyamine putrescine significantly correlated with the amino acid GABA. Both metabolites showed an interesting link with NAD isocitrate dehydrogenase, which could indicate a coordination of 2-oxo-glutarate biosynthesis with its integration within the GABA shunt both as a precursor of glutamate (via GDH) and as an amino acceptor (via GABA transaminase) (Figure 5). The pathway from putrescine to GABA is known (Ditomaso et al., 1992; Fait et al., 2008) and reference therein): putrescine can be converted via a two step oxidation into GABA (Figure 5). Though the pathway has been defined, only few other studies identified robust links between these two metabolites (Flores and Filner, 1985) and under stress (Shelp et al., 2012).

Bottom Line: The overall higher CV values for metabolites as compared to the tested enzymes are indicative for their greater phenotypic plasticity.H(2) tests revealed galactinol (1) and asparagine (0.91) as the highest scorers among metabolites and nitrate reductase (0.73), NAD-glutamate dehydrogenase (0.52), and phosphoglucomutase (0.51) among enzymes.The latter displayed the strongest node-betweenness value (185.25) of all nodes highlighting its fundamental structural role in the connectivity of the network by linking between different communities and to the also strongly connected enzyme aldolase.

View Article: PubMed Central - PubMed

Affiliation: Institute of Dryland Biotechnology and Agriculture, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev Midreshet Ben-Gurion, Israel.

ABSTRACT
To investigate the natural variability of leaf metabolism and enzymatic activity in a maize inbred population, statistical and network analyses were employed on metabolite and enzyme profiles. The test of coefficient of variation showed that sugars and amino acids displayed opposite trends in their variance within the population, consistently with their related enzymes. The overall higher CV values for metabolites as compared to the tested enzymes are indicative for their greater phenotypic plasticity. H(2) tests revealed galactinol (1) and asparagine (0.91) as the highest scorers among metabolites and nitrate reductase (0.73), NAD-glutamate dehydrogenase (0.52), and phosphoglucomutase (0.51) among enzymes. The overall low H(2) scores for metabolites and enzymes are suggestive for a great environmental impact or gene-environment interaction. Correlation-based network generation followed by community detection analysis, partitioned the network into three main communities and one dyad, (i) reflecting the different levels of phenotypic plasticity of the two molecular classes as observed for the CV values and (ii) highlighting the concerted changes between classes of chemically related metabolites. Community 1 is composed mainly of enzymes and specialized metabolites, community 2' is enriched in N-containing compounds and phosphorylated-intermediates. The third community contains mainly organic acids and sugars. Cross-community linkages are supported by aspartate, by the photorespiration amino acids glycine and serine, by the metabolically related GABA and putrescine, and by citrate. The latter displayed the strongest node-betweenness value (185.25) of all nodes highlighting its fundamental structural role in the connectivity of the network by linking between different communities and to the also strongly connected enzyme aldolase.

No MeSH data available.