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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.


Enzyme profiles descriptive statistics. Boxplot of enzyme BLUP value profiles of the core subset of the IBM population. Enzymes are sorted in ascending order along the x-axis according to the estimated variance.
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Figure 2: Enzyme profiles descriptive statistics. Boxplot of enzyme BLUP value profiles of the core subset of the IBM population. Enzymes are sorted in ascending order along the x-axis according to the estimated variance.

Mentions: The understanding of C-N metabolism and its underlying genetic regulation of C4 plants is a key aspect for the amelioration of crop plants toward higher yields (Zhang et al., 2015). In the current study we made use of the maize IBM subset collection to measure the relative content of metabolites and enzymes associated with C-N metabolism in the leaf. In total, we unequivocally identified and measured 43 metabolites of central metabolism and 13 enzymes related to it. First, we standardized and normalized all enzymes and metabolites (for details see Materials and Methods: data processing and statistics) and then calculated the corresponding averages and variances, illustrated as boxplots (Figures 1, 2, respectively). Metabolite variance ranged from ~9.450e+03 to ~3.746e+09. On the lower extreme of the variance spectra were fructose-6-phosphate, glucose-6-phosphate, glycerate-3-phosphate, and glycerol-3-phosphate (Figure 1). By contrast, amino acids, including pyroglutamate, glycine, glutamate, and aspartate, showed the highest variance within the population.


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)

Enzyme profiles descriptive statistics. Boxplot of enzyme BLUP value profiles of the core subset of the IBM population. Enzymes are sorted in ascending order along the x-axis according to the estimated variance.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: Enzyme profiles descriptive statistics. Boxplot of enzyme BLUP value profiles of the core subset of the IBM population. Enzymes are sorted in ascending order along the x-axis according to the estimated variance.
Mentions: The understanding of C-N metabolism and its underlying genetic regulation of C4 plants is a key aspect for the amelioration of crop plants toward higher yields (Zhang et al., 2015). In the current study we made use of the maize IBM subset collection to measure the relative content of metabolites and enzymes associated with C-N metabolism in the leaf. In total, we unequivocally identified and measured 43 metabolites of central metabolism and 13 enzymes related to it. First, we standardized and normalized all enzymes and metabolites (for details see Materials and Methods: data processing and statistics) and then calculated the corresponding averages and variances, illustrated as boxplots (Figures 1, 2, respectively). Metabolite variance ranged from ~9.450e+03 to ~3.746e+09. On the lower extreme of the variance spectra were fructose-6-phosphate, glucose-6-phosphate, glycerate-3-phosphate, and glycerol-3-phosphate (Figure 1). By contrast, amino acids, including pyroglutamate, glycine, glutamate, and aspartate, showed the highest variance within the population.

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.